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WO2020146779A1 - mTORC1 INHIBITORS FOR ACTIVATING AUTOPHAGY - Google Patents

mTORC1 INHIBITORS FOR ACTIVATING AUTOPHAGY Download PDF

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Publication number
WO2020146779A1
WO2020146779A1 PCT/US2020/013158 US2020013158W WO2020146779A1 WO 2020146779 A1 WO2020146779 A1 WO 2020146779A1 US 2020013158 W US2020013158 W US 2020013158W WO 2020146779 A1 WO2020146779 A1 WO 2020146779A1
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Prior art keywords
substituted
unsubstituted
och
membered
independently
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PCT/US2020/013158
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French (fr)
Inventor
Daniel K. Nomura
Roberto ZONCU
Yik Sham Clive CHUNG
Hijai SHIN
Stephen CANHAM
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The Regents Of The University Of California
Novartis Ag
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Publication of WO2020146779A1 publication Critical patent/WO2020146779A1/en

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
    • A61K31/415—1,2-Diazoles
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D231/00—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings
    • C07D231/02—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings
    • C07D231/10—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members
    • C07D231/14—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D231/00—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings
    • C07D231/02—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings
    • C07D231/10—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members
    • C07D231/14—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C07D231/16—Halogen atoms or nitro radicals

Definitions

  • Autophagy is central to the maintenance of organismal homeostasis in both physiological and pathological situations. It is an essential, conserved lysosomal degradation pathway that controls the quality of the cytoplasm by eliminating aggregated proteins and damaged organelles. Accordingly, alterations in autophagy have been linked to a wide range of diseases and conditions, including aging, cancer, metabolic disorders, and
  • Ring A is a phenyl or 5 to 6 membered heteroaryl.
  • Ring B is a phenyl or 5 to 6 membered heteroaryl.
  • L 1 is independently a bond, -S(O) 2 -, -N(R 5 )-, -O-, -S-, -C(O)-, -C(O)N(R 5 )-, -N(R 5 )C(O)-, -N(R 5 )C(O)NH-, -NHC(O)N(R 5 )-, -C(O)O-, -OC(O)-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or
  • R 5 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC
  • heterocycloalkyl substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent -L 1 -R 1 substituents may optionally be joined to form a substituted or
  • E is an electrophilic moiety.
  • R 2 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2 Cl,
  • R 3 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2 Cl,
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3
  • R 4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R 3 and R 4 are independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -
  • R 1A , R 1B , R 1C , and R 1D are independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 ,
  • R 1A , R 1B , R 1C , and R 1D are independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3
  • X 1 is independently–F, -Cl, -Br, or–I.
  • n1 is independently an integer from 0 to 4.
  • m1 and v1 are independently 1 or 2.
  • z1 is independently an integer from 0 to 5.
  • z3 is independently an integer from 0 to 2.
  • z4 is independently an integer from 0 to 5.
  • a pharmaceutical composition including a compound described herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
  • a method for treating cancer in a subject in need thereof including administering to the subject in need thereof a therapeutically effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method for treating a neurodegenerative disease the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method for treating a metabolic disease the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method for treating aging including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of mTORC1 in a subject in need thereof the method including administering to the subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of mTORC1 in a cell the method including contacting a Vacuolar H + -ATPase in the cell with a compound as described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of a Vacuolar H + - ATPase including contacting the Vacuolar H + -ATPase with a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of a Vacuolar H + - ATPase protein complex the method including contacting a ATP6V1A in the Vacuolar H + - ATPase protein complex with a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of mTORC1 in a cell including contacting a ATP6V1A in the cell with a compound as described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of an ATP6V1A the method including contacting the ATP6V1A with a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method for increasing autophagy in a subject in need thereof the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • Vacuolar H + -ATPase protein complex covalently bonded to a compound described herein, or a pharmaceutically acceptable salt thereof, which may be referred to herein as a Vacuolar H + -ATPase protein complex-compound complex.
  • a ATP6V1A protein covalently bonded to a compound described herein, or a pharmaceutically acceptable salt thereof, which may be referred to herein as a ATP6V1A protein-compound complex.
  • FIGS.1A-1F Covalent ligand screen for autophagy activators.
  • FIG.1A A covalent ligand screen in MEF cells. MEF cells expressing a fluorescent probe GFP-LC3- RFP-LC3DG to measure autophagic flux 32, were treated with vehicle DMSO or a covalent ligand (50 mM) for 24 h and GFP/RFP ratios were analyzed.
  • the covalent ligand or vehicle is: Torin 1, TRH 1-194, Rapamycin, EN6, KEA 1-37, DKM 3-16, DKM 2- 37, DKM 2-98, TRH 1-170, DKM 3-30, TRH 1-168, TRH 1-60, EN2, KEA 1-69, KEA 1- 100, TRH 1-57, DKM 3-3, KEA 1-46, TRH 1-179, TRH 1-58, TRH 1-140, TRH 1-152, EN59, EN53, KEA1-31, TRH 1-78, EN84, TRH 1-20, DKM 3-12, KEA 1-98, KEA 1-40, EN51, TRH 1-12, TRH 1-27, DKM 2-47, DKM 3-36, DKM 3-9, EN8, EN71, DKM 3-7, TRH 1-156, TRH 1-65, DKM 2-85, DKM 2-116, DKM 2-43, KEA 1-91, TRH 1-54, DKM 2- 71, EN62, TRH 1-59, EN54, KE
  • FIG.1B Compounds that showed significantly (p ⁇ 0.05 compared to vehicle-treated controls) lower GFP/RFP ratios in MEF cells were screened in HEK293A cells expressing the same fluorescent autophagic flux probe.
  • the covalent ligand or vehicle is: Torin1, EN6, DKM 3-16, Rapamycin, EN2, DKM 3-30, DKM 3-70, DKM 2-84, KEA 1-46, TRH 1-168, EN14, KEA 1-100, DKM 2-72, KEA 1-80, KEA 1-36, KEA 1-75, TRH 1-170, DKM 2-102, DKM 2-95, EN30, TRH 1-170, TRH 1-60, TRH 1-140, EN28, KEA 1-37, KEA 1-79, TRH 1-194, DMSO, DKM 3-3, DKM 2-89, KEA 1-69, DKM 2-37, TRH 1-50, DKM 2-98, and TRH 1- 155.
  • FIG.1C Structure of cysteine-reactive covalent ligand hit EN6 that shows autophagy activating in both MEF and HEK293A cells.
  • FIG.1D Dose-response of EN6 in HEK293A cells expressing the fluorescent autophagic flux probe.
  • FIG.1E LC3B levels in HEK293A cells treated with EN6 (50 mM).
  • FIG.1F LC3B puncta in HEK293 cells treated with vehicle DMSO, EN6 (50 mM), or Torin1 (0.25 mM).
  • FIGS.2A-2C Chemoproteomic profiling to identify targets of EN6.
  • FIG.2A Schematic of isoTOP-ABPP in which cells were pre-treated with DMSO or EN6 (50 mM, 4 h in situ) prior to labeling of proteomes in vitro with IA-alkyne (100 mM, 1 h), followed by appendage of isotopically light (for DMSO-treated) or heavy (for EN6-treated) TEV protease cleavable biotin-azide tags by copper-catalyzed azide-alkyne cycloaddition (CuAAC).
  • CuAAC copper-catalyzed azide-alkyne cycloaddition
  • FIG.2B isoTOP-ABPP analysis of EN6 (50 mM) in MEF cells in situ analyzed as described in FIG.2A.
  • FIG.2C Gel-based ABPP analysis of EN6 interactions with recombinant ATP6V1A.
  • FIGS.3A-3E EN6 inhibits mTORC1 signaling and lysosomal recruitment.
  • FIG. 3A mTORC1 signaling with EN6 treatment in HEK293A cells.
  • FIG.3B AKT signaling in HEK293 cells treated with vehicle DMSO, rapamycin (0.1 mM), Torin1 (0.25 mM), or EN6 (25 mM) for 4 h. AKT signaling was assessed by Western blotting.
  • FIG.3C ATP6V1A knockdown by short hairpin (shRNA) assessed by Western blotting.
  • FIG.3D LC3B levels and mTORC1 signaling in Hela cells treated with EN6.
  • FIG.4B Localization of TFEB- GFP in Hela cells treated with vehicle DMSO or EN6 (25 mM, 4 h). Cells were stained with Hoechst 33342 and GFP-TFEB were imaged by microscopy.
  • FIG. 4D Lysosomal acidification of HEK293A cells treated with vehicle DMSO, bafilomycin A1 (0.2 mM), EN6 (50 mM), or with co-treatment of EN6 and bafilomycin A1 for 4 h, readout by LysoSensor DND-160.
  • FIG.4E Quantification of lysosomal acidification from experiment described in FIG.4D. Statistical significance calculated with unpaired two- tailed Student’s t-tests. Significance in FIG.4B and FIG.4C expressed as *p ⁇ 0.05 compared to vehicle-treated controls or 0 h EN6-treated controls, respectively. Significance in FIG.4E is expressed as *p ⁇ 0.05 compared to the vehicle-treated group, #p ⁇ 0.05 compared to EN6- treated group. [0042] FIGS.5A-5B. EN6 improves clearance of TDP-43 aggregates in cells. Effect of EN6 and bafilomycin treatment on TDP-43 aggregate clearance.
  • U2OS cells expressing an IPTG-inducible GFP-TDP-43 were co-treated with vehicle DMSO, IPTG (50 mM), IPTG and EN6 (25 mM), or IPTG, EN6, and bafilomycin (0.2 mM) for 7 h.
  • Cells were stained with Hoechst 33342 and GFP-TDP-43 puncta were imaged by microscopy in FIG.5A.
  • FIGS.6A-6C EN6 inhibits mTORC1 signaling in mice.
  • C57BL/6 male mice were treated intraperitoneally with vehicle (18:1:1 saline:ethanol:PEG40), rapamycin (10 mg/kg) or EN6 (50 mg/kg) for 4 h.
  • mTORC1 signaling and LC3B levels were measured by Western blotting and quantified by densitometry.
  • FIG.7 Scheme of v-ATPase/mTORC1 regulation of autophagy and action of EN6.
  • alkyl by itself or as part of another substituent, means, unless otherwise stated, a straight (i.e., unbranched) or branched carbon chain (or carbon), or combination thereof, which may be fully saturated, mono- or polyunsaturated and can include mono-, di-, and multivalent radicals.
  • the alkyl may include a designated number of carbons (e.g., C 1 -C 10 means one to ten carbons).
  • Alkyl is an uncyclized chain.
  • saturated hydrocarbon radicals include, but are not limited to, groups such as methyl, ethyl, n-propyl, isopropyl, n- butyl, t-butyl, isobutyl, sec-butyl, methyl, homologs and isomers of, for example, n-pentyl, n- hexyl, n-heptyl, n-octyl, and the like.
  • An unsaturated alkyl group is one having one or more double bonds or triple bonds.
  • Examples of unsaturated alkyl groups include, but are not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(1,4- pentadienyl), ethynyl, 1- and 3-propynyl, 3-butynyl, and the higher homologs and isomers.
  • An alkoxy is an alkyl attached to the remainder of the molecule via an oxygen linker (-O-).
  • An alkyl moiety may be an alkenyl moiety.
  • An alkyl moiety may be an alkynyl moiety.
  • An alkyl moiety may be fully saturated.
  • alkenyl may include more than one double bond and/or one or more triple bonds in addition to the one or more double bonds.
  • An alkynyl may include more than one triple bond and/or one or more double bonds in addition to the one or more triple bonds.
  • alkylene by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkyl, as exemplified, but not limited by, -CH 2 CH 2 CH 2 CH 2 -.
  • an alkyl (or alkylene) group will have from 1 to 24 carbon atoms, with those groups having 10 or fewer carbon atoms being preferred herein.
  • A“lower alkyl” or“lower alkylene” is a shorter chain alkyl or alkylene group, generally having eight or fewer carbon atoms.
  • the term“alkenylene,” by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkene.
  • the term“heteroalkyl,” by itself or in combination with another term, means, unless otherwise stated, a stable straight or branched chain, or combinations thereof, including at least one carbon atom and at least one heteroatom (e.g., O, N, P, Si, and S), and wherein the nitrogen and sulfur atoms may optionally be oxidized, and the nitrogen heteroatom may optionally be quaternized.
  • heteroatom(s) may be placed at any interior position of the heteroalkyl group or at the position at which the alkyl group is attached to the remainder of the molecule.
  • Heteroalkyl is an uncyclized chain. Examples include, but are not limited to: -CH 2 -CH 2 -O-CH 3 , -CH 2 -CH 2 -NH-CH 3 ,
  • a heteroalkyl moiety may include one heteroatom (e.g., O, N, S, Si, or P).
  • a heteroalkyl moiety may include two optionally different heteroatoms (e.g., O, N, S, Si, or P).
  • a heteroalkyl moiety may include three optionally different heteroatoms (e.g., O, N, S, Si, or P).
  • a heteroalkyl moiety may include four optionally different heteroatoms (e.g., O, N, S, Si, or P).
  • a heteroalkyl moiety may include five optionally different heteroatoms (e.g., O, N, S, Si, or P).
  • a heteroalkyl moiety may include up to 8 optionally different heteroatoms (e.g., O, N, S, Si, or P).
  • the term “heteroalkenyl,” by itself or in combination with another term, means, unless otherwise stated, a heteroalkyl including at least one double bond.
  • a heteroalkenyl may optionally include more than one double bond and/or one or more triple bonds in additional to the one or more double bonds.
  • the term“heteroalkynyl,” by itself or in combination with another term means, unless otherwise stated, a heteroalkyl including at least one triple bond.
  • heteroalkynyl may optionally include more than one triple bond and/or one or more double bonds in additional to the one or more triple bonds.
  • a heteroalkyl (or heteroalkylene) group will have from 2 to 24 atoms including at least one carbon atom and at least one heteroatom (e.g., O, N, P, Si, and S), with those groups having 10 or fewer atoms being preferred herein.
  • heteroalkylene by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from heteroalkyl, as exemplified, but not limited by, -CH 2 -CH 2 -S-CH 2 -CH 2 - and -CH 2 -S-CH 2 -CH 2 -NH-CH 2 -.
  • heteroalkylene groups heteroatoms can also occupy either or both of the chain termini (e.g., alkyleneoxy, alkylenedioxy, alkyleneamino, alkylenediamino, and the like). Still further, for alkylene and heteroalkylene linking groups, no orientation of the linking group is implied by the direction in which the formula of the linking group is written. For example, the formula -C(O) 2 R'- represents both -C(O) 2 R'- and -R'C(O) 2 -.
  • heteroalkyl groups include those groups that are attached to the remainder of the molecule through a heteroatom, such as -C(O)R', -C(O)NR', -NR'R'', -OR', -SR', and/or -SO 2 R'.
  • heteroalkyl is recited, followed by recitations of specific heteroalkyl groups, such as - NR'R'' or the like, it will be understood that the terms heteroalkyl and -NR'R'' are not redundant or mutually exclusive. Rather, the specific heteroalkyl groups are recited to add clarity.
  • heteroalkyl should not be interpreted herein as excluding specific heteroalkyl groups, such as -NR'R'' or the like.
  • cycloalkyl examples include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl, and the like.
  • heterocycloalkyl examples include, but are not limited to, 1- (1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 4-morpholinyl, 3- morpholinyl, tetrahydrofuran-2-yl, tetrahydrofuran-3-yl, tetrahydrothien-2-yl,
  • a cycloalkyl (or cycloalkylene) group will have from 3 to 8 carbon atoms.
  • a cycloalkyl (or cycloalkylene) group will have from 3 to 8 carbon atoms.
  • heterocycloalkyl (or heterocycloalkylene) group will have from 3 to 8 atoms including at least one carbon atom and at least one heteroatom (e.g., O, N, P, Si, and S).
  • heteroatom e.g., O, N, P, Si, and S.
  • halo(C 1 -C 4 )alkyl includes, but is not limited to, fluoromethyl, difluoromethyl, trifluoromethyl, 2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the like.
  • acyl means, unless otherwise stated, -C(O)R where R is a substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • aryl means, unless otherwise stated, a polyunsaturated, aromatic, hydrocarbon substituent, which can be a single ring or multiple rings (preferably from 1 to 3 rings) that are fused together (i.e., a fused ring aryl) or linked covalently.
  • a fused ring aryl refers to multiple rings fused together wherein at least one of the fused rings is an aryl ring.
  • heteroaryl refers to aryl groups (or rings) that contain at least one heteroatom such as N, O, or S, wherein the nitrogen and sulfur atoms are optionally oxidized, and the nitrogen atom(s) are optionally quaternized.
  • heteroaryl includes fused ring heteroaryl groups (i.e., multiple rings fused together wherein at least one of the fused rings is a heteroaromatic ring).
  • a 5,6-fused ring heteroarylene refers to two rings fused together, wherein one ring has 5 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring.
  • a 6,6-fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring.
  • a 6,5-fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 5 members, and wherein at least one ring is a heteroaryl ring.
  • a heteroaryl group can be attached to the remainder of the molecule through a carbon or heteroatom.
  • Non-limiting examples of aryl and heteroaryl groups include phenyl, naphthyl, pyrrolyl, pyrazolyl, pyridazinyl, triazinyl, pyrimidinyl, imidazolyl, pyrazinyl, purinyl, oxazolyl, isoxazolyl, thiazolyl, furyl, thienyl, pyridyl, pyrimidyl, benzothiazolyl, benzoxazoyl benzimidazolyl, benzofuran,
  • Substituents for each of the above noted aryl and heteroaryl ring systems are selected from the group of acceptable substituents described below.
  • An“arylene” and a“heteroarylene,” alone or as part of another substituent mean a divalent radical derived from an aryl and heteroaryl, respectively.
  • a heteroaryl group substituent may be -O- bonded to a ring heteroatom nitrogen.
  • an aryl (or arylene) group will have from 6 to 10 carbon atoms.
  • a heteroaryl (or heteroarylene) group will have from 5 to 10 atoms including at least one carbon atom and at least one heteroatom (e.g., O, N, P, Si, and S).
  • Spirocyclic rings are two or more rings wherein adjacent rings are attached through a single atom.
  • the individual rings within spirocyclic rings may be identical or different.
  • Individual rings in spirocyclic rings may be substituted or unsubstituted and may have different substituents from other individual rings within a set of spirocyclic rings.
  • Possible substituents for individual rings within spirocyclic rings are the possible substituents for the same ring when not part of spirocyclic rings (e.g., substituents for cycloalkyl or
  • Spirocylic rings may be substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heterocycloalkylene and individual rings within a spirocyclic ring group may be any of the immediately previous list, including having all rings of one type (e.g., all rings being substituted heterocycloalkylene wherein each ring may be the same or different substituted heterocycloalkylene).
  • heterocyclic spirocyclic rings means a spirocyclic rings wherein at least one ring is a heterocyclic ring and wherein each ring may be a different ring.
  • substituted spirocyclic rings means that at least one ring is substituted and each substituent may optionally be different.
  • alkylarylene as an arylene moiety covalently bonded to an alkylene moiety (also referred to herein as an alkylene linker).
  • the alkylarylene group has the formula: [0060]
  • An alkylarylene moiety may be substituted (e.g., with a substituent group) on the alkylene moiety or the arylene linker (e.g., at carbons 2, 3, 4, or 6) with halogen, oxo, -N 3 , -CF 3 , -CCl 3 , -CBr 3 , -CI 3 , -CN, -CHO, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 2 CH 3 , -SO 3 H, -OSO 3 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , substituted or
  • heterocycloalkyl “aryl,” and“heteroaryl”) includes both substituted and unsubstituted forms of the indicated radical. Preferred substituents for each type of radical are provided below.
  • R, R', R'', R'', and R''' each preferably independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl (e.g., aryl substituted with 1-3 halogens), substituted or unsubstituted heteroaryl, substituted or unsubstituted alkyl, alkoxy, or thioalkoxy groups, or arylalkyl groups.
  • aryl e.g., aryl substituted with 1-3 halogens
  • substituted or unsubstituted heteroaryl substituted or unsubstituted alkyl, alkoxy, or thioalkoxy groups, or arylalkyl groups.
  • each of the R groups is independently selected as are each R', R'', R''', and R''' group when more than one of these groups is present.
  • R' and R'' are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 4-, 5-, 6-, or 7- membered ring.
  • -NR'R'' includes, but is not limited to, 1-pyrrolidinyl and 4- morpholinyl.
  • alkyl is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (e.g., -CF 3 and -CH 2 CF 3 ) and acyl (e.g., -C(O)CH 3 , -C(O)CF 3 , -C(O)CH 2 OCH 3 , and the like).
  • haloalkyl e.g., -CF 3 and -CH 2 CF 3
  • acyl e.g., -C(O)CH 3 , -C(O)CF 3 , -C(O)CH 2 OCH 3 , and the like.
  • R', R'', R'', and R''' are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.
  • each of the R groups is independently selected as are each R', R'', R'', and R''' groups when more than one of these groups is present.
  • Substituents for rings e.g., cycloalkyl, heterocycloalkyl, aryl, heteroaryl, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene
  • substituents on the ring may be depicted as substituents on the ring rather than on a specific atom of a ring (commonly referred to as a floating substituent).
  • the substituent may be attached to any of the ring atoms (obeying the rules of chemical valency) and in the case of fused rings or spirocyclic rings, a substituent depicted as associated with one member of the fused rings or spirocyclic rings (a floating substituent on a single ring), may be a substituent on any of the fused rings or spirocyclic rings (a floating substituent on multiple rings).
  • the multiple substituents may be on the same atom, same ring, different atoms, different fused rings, different spirocyclic rings, and each substituent may optionally be different.
  • a point of attachment of a ring to the remainder of a molecule is not limited to a single atom (a floating substituent)
  • the attachment point may be any atom of the ring and in the case of a fused ring or spirocyclic ring, any atom of any of the fused rings or spirocyclic rings while obeying the rules of chemical valency.
  • a ring, fused rings, or spirocyclic rings contain one or more ring heteroatoms and the ring, fused rings, or spirocyclic rings are shown with one more floating substituents (including, but not limited to, points of attachment to the remainder of the molecule), the floating substituents may be bonded to the heteroatoms.
  • the ring heteroatoms are shown bound to one or more hydrogens (e.g., a ring nitrogen with two bonds to ring atoms and a third bond to a hydrogen) in the structure or formula with the floating substituent, when the heteroatom is bonded to the floating substituent, the substituent will be understood to replace the hydrogen, while obeying the rules of chemical valency.
  • Two or more substituents may optionally be joined to form aryl, heteroaryl, cycloalkyl, or heterocycloalkyl groups.
  • Such so-called ring-forming substituents are typically, though not necessarily, found attached to a cyclic base structure.
  • the ring-forming substituents are attached to adjacent members of the base structure.
  • two ring-forming substituents attached to adjacent members of a cyclic base structure create a fused ring structure.
  • the ring-forming substituents are attached to a single member of the base structure.
  • two ring- forming substituents attached to a single member of a cyclic base structure create a spirocyclic structure.
  • the ring-forming substituents are attached to non-adjacent members of the base structure.
  • Two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally form a ring of the formula -T-C(O)-(CRR') q -U-, wherein T and U are
  • q is an integer of from 0 to 3.
  • two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -A-(CH 2 )r-B-, wherein A and B are independently -CRR'-, -O-, -NR-, -S-, -S(O) -, -S(O) 2 -, -S(O) 2 NR'-, or a single bond, and r is an integer of from 1 to 4.
  • One of the single bonds of the new ring so formed may optionally be replaced with a double bond.
  • two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -(CRR') s -X'- (C''R''R'') d -, where s and d are independently integers of from 0 to 3, and X' is -O-, -NR'-, -S-, -S(O)-, -S(O) 2 -, or -S(O) 2 NR'-.
  • R, R', R'', and R''' are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.
  • the terms“heteroatom” or“ring heteroatom” are meant to include oxygen (O), nitrogen (N), sulfur (S), phosphorus (P), and silicon (Si).
  • A“substituent group,” as used herein, means a group selected from the following moieties: (A) oxo, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 ,
  • unsubstituted alkyl e.g., C 1 -C 8 alkyl, C 1 -C 6 alkyl, or C 1 -C 4 alkyl
  • unsubstituted heteroalkyl e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl
  • unsubstituted cycloalkyl e.g., C 3 -C 8 cycloalkyl, C 3 -C 6 cycloalkyl, or C 5 -C 6 cycloalkyl
  • unsubstituted heterocycloalkyl e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl
  • unsubstituted aryl e.g., C 6 - C 10 aryl, C 10 aryl, or phenyl
  • heteroalkyl cycloalkyl (e.g., C 3 -C 8 cycloalkyl, C 3 -C 6 cycloalkyl, or C 5 -C 6 cycloalkyl), heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), aryl (e.g., C 6 -C 10 aryl, C 10 aryl, or phenyl), heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), substituted with at least one substituent selected from: (i) oxo, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CHCl 2 , -CHBr 2 , -CHF 2 , -
  • A“size-limited substituent” or“ size-limited substituent group,” as used herein, means a group selected from all of the substituents described above for a“substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted C 1 -C 20 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C 8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 -C 10 aryl, and each substituted or unsubstituted heteroary
  • A“lower substituent” or“ lower substituent group,” as used herein, means a group selected from all of the substituents described above for a“substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted C 1 -C 8 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 - C 7 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 -C 10 aryl, and each substituted or unsubstituted heteroaryl is a group selected
  • heterocycloalkyl substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene described in the compounds herein are substituted with at least one substituent group. In other embodiments, at least one or all of these groups are substituted with at least one size-limited substituent group. In other embodiments, at least one or all of these groups are substituted with at least one lower substituent group.
  • each substituted or unsubstituted alkyl may be a substituted or unsubstituted C 1 -C 20 alkyl
  • each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl
  • each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C 8 cycloalkyl
  • each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered
  • each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 - C 10 aryl
  • each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 10 membered heteroaryl.
  • each substituted or unsubstituted alkylene is a substituted or unsubstituted C 1 -C 20 alkylene
  • each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 20 membered
  • heteroalkylene each substituted or unsubstituted cycloalkylene is a substituted or
  • each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 8 membered heterocycloalkylene
  • each substituted or unsubstituted arylene is a substituted or unsubstituted C 6 -C 10 arylene
  • each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 10 membered
  • each substituted or unsubstituted alkyl is a substituted or unsubstituted C 1 -C 8 alkyl
  • each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl
  • each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C 7 cycloalkyl
  • each substituted or unsubstituted or unsubstituted alkyl is a substituted or unsubstituted C 1 -C 8 alkyl
  • each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl
  • each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C 7 cycloalkyl
  • heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl
  • each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 -C 10 aryl
  • each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 9 membered heteroaryl.
  • each substituted or unsubstituted alkylene is a substituted or unsubstituted C 1 -C 8 alkylene
  • each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 8 membered heteroalkylene
  • unsubstituted cycloalkylene is a substituted or unsubstituted C 3 -C 7 cycloalkylene
  • each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 7 membered heterocycloalkylene
  • each substituted or unsubstituted arylene is a substituted or unsubstituted C 6 -C 10 arylene
  • each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 9 membered heteroarylene.
  • the compound is a chemical species set forth in the Examples section, figures, or tables below.
  • a substituted or unsubstituted moiety e.g., substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, and/or substituted or unsubstituted heteroarylene) is unsubstituted (e.g., is an unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted
  • a substituted or unsubstituted moiety e.g., substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted
  • cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, and/or substituted or unsubstituted heteroarylene is substituted (e.g., is a substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene, respectively).
  • a substituted moiety e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene
  • is substituted with at least one substituent group wherein if the substituted moiety is substituted with a plurality of substituent groups, each substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of substituent groups, each substituent group is different.
  • a substituted moiety e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene
  • is substituted with at least one size-limited substituent group wherein if the substituted moiety is substituted with a plurality of size-limited substituent groups, each size-limited substituent group may optionally be different.
  • each size-limited substituent group is different.
  • a substituted moiety e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene
  • each lower substituent group is different.
  • a substituted moiety e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene
  • each substituent group, size-limited substituent group, and/or lower substituent group is different.
  • each R substituent or L linker that is described as being“substituted” without reference as to the identity of any chemical moiety that composes the“substituted” group also referred to herein as an“open substitution” on an R substituent or L linker or an“openly substituted” R substituent or L linker
  • the recited R substituent or L linker may, in embodiments, be substituted with one or more first substituent groups as defined below.
  • the first substituent group is denoted with a corresponding first decimal point numbering system such that, for example, R 1 may be substituted with one or more first substituent groups denoted by R 1.1 , R 2 may be substituted with one or more first substituent groups denoted by R 2.1 , R 3 may be substituted with one or more first substituent groups denoted by R 3.1 , R 4 may be substituted with one or more first substituent groups denoted by R 4.1 , R 5 may be substituted with one or more first substituent groups denoted by R 5.1 , and the like up to or exceeding an R 100 that may be substituted with one or more first substituent groups denoted by R 100.1 .
  • R 1A may be substituted with one or more first substituent groups denoted by R 1A.1
  • R 2A may be substituted with one or more first substituent groups denoted by R 2A.1
  • R 3A may be substituted with one or more first substituent groups denoted by R 3A.1
  • R 4A may be substituted with one or more first substituent groups denoted by R 4A.1
  • R 5A may be substituted with one or more first substituent groups denoted by R 5A.1 and the like up to or exceeding an R 100A may be substituted with one or more first substituent groups denoted by R 100A.1 .
  • L 1 may be substituted with one or more first substituent groups denoted by R L1.1
  • L 2 may be substituted with one or more first substituent groups denoted by R L2.1
  • L 3 may be substituted with one or more first substituent groups denoted by R L3.1
  • L 4 may be substituted with one or more first substituent groups denoted by R L4.1
  • L 5 may be substituted with one or more first substituent groups denoted by R L5.1 and the like up to or exceeding an L 100 which may be substituted with one or more first substituent groups denoted by R L100.1 .
  • each numbered R group or L group may be substituted with one or more first substituent groups denoted by R L1.1
  • L 2 may be substituted with one or more first substituent groups denoted by R L2.1
  • L 3 may be substituted with one or more first substituent groups denoted by R L3.1
  • L 4 may be substituted with one or more first substituent groups denoted by R L4.1
  • L 5 may be substituted with one
  • R WW or L WW wherein“WW” represents the stated superscript number of the subject R group or L group may be substituted with one or more first substituent groups referred to herein generally as R WW.1 or R LWW.1 , respectively.
  • each first substituent group (e.g., R 1.1 , R 2.1 , R 3.1 , R 4.1 , R 5.1 ... R 100.1 ; R 1A.1 , R 2A.1 , R 3A.1 , R 4A.1 , R 5A.1 ... R 100A.1 ; R L1.1 , R L2.1 , R L3.1 , R L4.1 , R L5.1 ... R L100.1 ) may be further substituted with one or more second substituent groups (e.g., R 1.2 , R 2.2 , R 3.2 , R 4.2 , R 5.2 ... R 100.2 ; R 1A.2 , R 2A.2 , R 3A.2 , R 4A.2 , R 5A.2 ... R 100A.2 ; R L1.2 , R L2.2 , R L3.2 , R L4.2 , R L5.2 ... R L100.2 , respectively).
  • each first substituent group which may alternatively be represented herein as R WW.1 as described above, may be further substituted with one or more second substituent groups, which may alternatively be represented herein as R WW.2 .
  • each second substituent group e.g., R 1.2 , R 2.2 , R 3.2 , R 4.2 , R 5.2 ... R 100.2 ; R 1A.2 , R 2A.2 , R 3A.2 , R 4A.2 , R 5A.2 ... R 100A.2 ; R L1.2 , R L2.2 , R L3.2 , R L4.2 , R L5.2 ... R L100.2
  • may be further substituted with one or more third substituent groups e.g., R 1.3 , R 2.3 , R 3.3 , R 4.3 , R 5.3 ... R 100.3 ; R 1A.3 , R 2A.3 , R 3A.3 , R 4A.3 , R 5A.
  • each second substituent group which may alternatively be represented herein as R WW.2 as described above, may be further substituted with one or more third substituent groups, which may alternatively be represented herein as R WW.3 .
  • Each of the first substituent groups may be optionally different.
  • Each of the second substituent groups may be optionally different.
  • Each of the third substituent groups may be optionally different.
  • R WW represents a substituent recited in a claim or chemical formula description herein which is openly substituted.“WW” represents the stated superscript number of the subject R group (1, 2, 3, 1A, 2A, 3A, 1B, 2B, 3B, etc.).
  • L WW is a linker recited in a claim or chemical formula description herein which is openly substituted.
  • “WW” represents the stated superscript number of the subject L group (1, 2, 3, 1A, 2A, 3A, 1B, 2B, 3B, etc.).
  • each R WW may be unsubstituted or independently substituted with one or more first substituent groups, referred to herein as R WW.1 ; each first substituent group, R WW.1 , may be unsubstituted or independently substituted with one or more second substituent groups, referred to herein as R WW.2 ; and each second substituent group may be unsubstituted or independently substituted with one or more third substituent groups, referred to herein as R WW.3 .
  • each L WW linker may be unsubstituted or independently substituted with one or more first substituent groups, referred to herein as R LWW.1 ; each first substituent group, R LWW.1 , may be unsubstituted or
  • each second substituent group may be unsubstituted or independently substituted with one or more third substituent groups, referred to herein as R LWW.3 .
  • Each first substituent group is optionally different.
  • Each second substituent group is optionally different.
  • Each third substituent group is optionally different.
  • R WW is phenyl
  • the said phenyl group is optionally substituted by one or more R WW.1 groups as defined herein below, e.g., when R WW.1 is R WW.2 -substituted alkyl, examples of groups so formed include but are not limited to itself optionally substituted by 1 or more R WW.2 , which R WW.2 is optionally substituted by one or more R WW.3 .
  • R WW.1 is alkyl
  • groups that could be formed include but are not limited to:
  • R WW.1 is independently oxo, halogen, -CX WW.1 3, -CHX WW.1 2, -CH 2 X WW.1 ,
  • R WW.2 -substituted or unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • R WW.2 -substituted or unsubstituted heteroalkyl e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered
  • R WW.2 -substituted or unsubstituted cycloalkyl e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 - C 6
  • R WW.2 -substituted or unsubstituted heterocycloalkyl e.g., 3
  • R WW.2 is independently oxo, halogen, -CX WW.2 3, -CHX WW.2 2, -CH 2 X WW.2 ,
  • R WW.3 -substituted or unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • R WW.3 -substituted or unsubstituted heteroalkyl e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered
  • R WW.3 -substituted or unsubstituted cycloalkyl e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 - C 6
  • R WW.3 -substituted or unsubstituted heterocycloalkyl e.g.,
  • R WW.3 is independently oxo, halogen, -CX WW.3 3 , -CHX WW.3 2 , -CH 2 X WW.3 ,
  • unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • unsubstituted heteroalkyl e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered
  • unsubstituted cycloalkyl e.g., C 3 -C 8 , C3- C 6 , C 4 -C 6 , or C 5 -C 6
  • unsubstituted heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered
  • unsubstituted aryl e.g.,
  • X WW.3 is independently–F, -Cl, -Br, or–I.
  • the openly substituted ring may be independently substituted with one or more first substituent groups, referred to herein as R WW.1 ; each first substituent group, R WW.1 , may be unsubstituted or independently substituted with one or more second substituent groups, referred to herein as R WW.2 ; and each second substituent group, R WW.2 , may be unsubstituted or independently substituted with one or more third substituent groups, referred to herein as R WW.3 ; and each third substituent group, R WW.3 , is unsubstituted.
  • Each first substituent group is optionally different.
  • Each second substituent group is optionally different.
  • Each third substituent group is optionally different.
  • the“WW” symbol in the R WW.1 , R WW.2 and R WW.3 refers to the designated number of one of the two different R WW substituents.
  • R WW.1 is R 100A.1
  • R WW.2 is R 100A.2
  • R WW.3 is R 100A.3 .
  • R WW.1 is R 100B.1
  • R WW.2 is R 100B.2
  • R WW.3 is R 100B.3 .
  • R WW.1 , R WW.2 and R WW.3 in this paragraph are as defined in the preceding paragraphs.
  • R LWW.1 is independently oxo, halogen, -CX LWW.1 3 ,
  • X LWW.1 is independently–F, -Cl, -Br, or–I.
  • R LWW.3 -substituted or unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • R LWW.3 -substituted or unsubstituted heteroalkyl e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered
  • R WW.3 -substituted or unsubstituted cycloalkyl e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 - C 6
  • R LWW.3 -substituted or unsubstituted heterocycloalkyl e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 - C
  • R LWW.2 is independently oxo, halogen, -CX LWW.2 3,
  • X LWW.2 is independently–F, -Cl, -Br, or–I.
  • unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • unsubstituted heteroalkyl e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered
  • unsubstituted cycloalkyl e.g., C 3 -C 8 , C 3 - C 6 , C4-C 6 , or C 5 -C 6
  • unsubstituted heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered
  • unsubstituted aryl e.g.,
  • X LWW.3 is independently–F, -Cl, -Br, or–I.
  • R WW substituent any R group recited in a claim or chemical formula description set forth herein (R WW substituent) is not specifically defined in this disclosure, then that R group (R WW group) is hereby defined as independently oxo, halogen, -CX WW 3, -CHX WW 2,
  • X WW is independently–F, -Cl, -Br, or–I.
  • “WW” represents the stated superscript number of the subject R group (e.g., 1, 2, 3, 1A, 2A, 3A, 1B, 2B, 3B, etc.).
  • R WW.1 , R WW.2 , and R WW.3 are as defined above.
  • L group L WW group is herein defined as independently a bond,–O-, -NH-, -C(O)-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, -C(O)O-, -OC(O)-, -S-, -SO 2 NH-, R LWW.1 -substituted or unsubstituted alkylene (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ), R LWW.1 -substituted or unsubstituted heteroalkylene (e.g., 2 to
  • R LWW.1 represents the stated superscript number of the subject L group (1, 2, 3, 1A, 2A, 3A, 1B, 2B, 3B, etc.).
  • R LWW.1 as well as R LWW.2 and R LWW.3 are as defined above.
  • Certain compounds of the present disclosure possess asymmetric carbon atoms (optical or chiral centers) or double bonds; the enantiomers, racemates, diastereomers, tautomers, geometric isomers, stereoisometric forms that may be defined, in terms of absolute stereochemistry, as (R)-or (S)- or, as (D)- or (L)- for amino acids, and individual isomers are encompassed within the scope of the present disclosure.
  • the compounds of the present disclosure do not include those that are known in art to be too unstable to synthesize and/or isolate.
  • the present disclosure is meant to include compounds in racemic and optically pure forms.
  • Optically active (R)- and (S)-, or (D)- and (L)-isomers may be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques.
  • the compounds described herein contain olefinic bonds or other centers of geometric asymmetry, and unless specified otherwise, it is intended that the compounds include both E and Z geometric isomers.
  • the term“isomers” refers to compounds having the same number and kind of atoms, and hence the same molecular weight, but differing in respect to the structural arrangement or configuration of the atoms.
  • the term“tautomer,” as used herein, refers to one of two or more structural isomers which exist in equilibrium and which are readily converted from one isomeric form to another.
  • certain compounds of this disclosure may exist in tautomeric forms, all such tautomeric forms of the compounds being within the scope of the disclosure.
  • structures depicted herein are also meant to include all stereochemical forms of the structure; i.e., the R and S configurations for each asymmetric center. Therefore, single stereochemical isomers as well as enantiomeric and diastereomeric mixtures of the present compounds are within the scope of the disclosure.
  • structures depicted herein are also meant to include compounds which differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of a hydrogen by a deuterium or tritium, or the replacement of a carbon by 13 C- or 14 C-enriched carbon are within the scope of this disclosure.
  • the compounds of the present disclosure may also contain unnatural proportions of atomic isotopes at one or more of the atoms that constitute such compounds.
  • the compounds may be radiolabeled with radioactive isotopes, such as for example tritium ( 3 H), iodine-125 ( 125 I), or carbon-14 ( 14 C). All isotopic variations of the compounds of the present disclosure, whether radioactive or not, are encompassed within the scope of the present disclosure.
  • radioactive isotopes such as for example tritium ( 3 H), iodine-125 ( 125 I), or carbon-14 ( 14 C). All isotopic variations of the compounds of the present disclosure, whether radioactive or not, are encompassed within the scope of the present disclosure.
  • bioconjugate and“bioconjugate linker” refer to the resulting association between atoms or molecules of bioconjugate reactive groups or bioconjugate reactive moieties. The association can be direct or indirect.
  • a conjugate between a first bioconjugate reactive group (e.g.,–NH 2 ,–COOH,–N- hydroxysuccinimide, or–maleimide) and a second bioconjugate reactive group (e.g., sulfhydryl, sulfur-containing amino acid, amine, amine sidechain containing amino acid, or carboxylate) provided herein can be direct, e.g., by covalent bond or linker (e.g., a first linker of second linker), or indirect, e.g., by non-covalent bond (e.g., electrostatic interactions (e.g., ionic bond, hydrogen bond, halogen bond), van der Waals interactions (e.g., dipole-dipole, dipole-induced dipole, London dispersion), ring stacking (pi effects), hydrophobic interactions and the like).
  • a first bioconjugate reactive group e.g.,–NH 2 ,–COOH,–N- hydroxysuccinimi
  • bioconjugates or bioconjugate linkers are formed using bioconjugate chemistry (i.e., the association of two bioconjugate reactive groups) including, but are not limited to nucleophilic substitutions (e.g., reactions of amines and alcohols with acyl halides, active esters), electrophilic substitutions (e.g., enamine reactions) and additions to carbon-carbon and carbon-heteroatom multiple bonds (e.g., Michael reaction, Diels-Alder addition).
  • bioconjugate chemistry i.e., the association of two bioconjugate reactive groups
  • nucleophilic substitutions e.g., reactions of amines and alcohols with acyl halides, active esters
  • electrophilic substitutions e.g., enamine reactions
  • additions to carbon-carbon and carbon-heteroatom multiple bonds e.g., Michael reaction, Diels-Alder addition.
  • the first bioconjugate reactive group e.g., maleimide moiety
  • the second bioconjugate reactive group e.g., a sulfhydryl
  • the first bioconjugate reactive group (e.g., haloacetyl moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl).
  • the first bioconjugate reactive group (e.g., pyridyl moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl).
  • the first bioconjugate reactive group e.g.,–N- hydroxysuccinimide moiety
  • is covalently attached to the second bioconjugate reactive group (e.g., an amine).
  • the first bioconjugate reactive group (e.g., maleimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl).
  • the first bioconjugate reactive group (e.g.,–sulfo–N-hydroxysuccinimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., an amine).
  • bioconjugate reactive moieties used for bioconjugate chemistries herein include, for example: (a) carboxyl groups and various derivatives thereof including, but not limited to, N- hydroxysuccinimide esters, N-hydroxybenztriazole esters, acid halides, acyl imidazoles, thioesters, p-nitrophenyl esters, alkyl, alkenyl, alkynyl and aromatic esters; (b) hydroxyl groups which can be converted to esters, ethers, aldehydes, etc.; (c) haloalkyl groups wherein the halide can be later displaced with a nucleophilic group such as, for example, an amine, a carboxylate anion, thiol anion, carbanion, or an alkoxide ion, thereby resulting in the covalent attachment of a new group at the site of the halogen atom; (d) dienophile groups which are capable of participating in
  • bioconjugate reactive groups can be chosen such that they do not participate in, or interfere with, the chemical stability of the conjugate described herein.
  • a reactive functional group can be protected from participating in the crosslinking reaction by the presence of a protecting group.
  • the bioconjugate comprises a molecular entity derived from the reaction of an unsaturated bond, such as a maleimide, and a sulfhydryl group.
  • Analog “Analog,”“analogue,” or“derivative” is used in accordance with its plain ordinary meaning within Chemistry and Biology and refers to a chemical compound that is structurally similar to another compound (i.e., a so-called“reference” compound) but differs in composition, e.g., in the replacement of one atom by an atom of a different element, or in the presence of a particular functional group, or the replacement of one functional group by another functional group, or the absolute stereochemistry of one or more chiral centers of the reference compound. Accordingly, an analog is a compound that is similar or comparable in function and appearance but not in structure or origin to a reference compound.
  • the terms“a” or“an,” as used in herein means one or more.
  • substituted with a[n] means the specified group may be substituted with one or more of any or all of the named substituents.
  • a group such as an alkyl or heteroaryl group, is“substituted with an unsubstituted C 1 -C 20 alkyl, or unsubstituted 2 to 20 membered heteroalkyl,” the group may contain one or more unsubstituted C 1 -C 20 alkyls, and/or one or more unsubstituted 2 to 20 membered heteroalkyls.
  • R-substituted where a moiety is substituted with an R substituent, the group may be referred to as“R-substituted.” Where a moiety is R-substituted, the moiety is substituted with at least one R substituent and each R substituent is optionally different. Where a particular R group is present in the description of a chemical genus (such as Formula (I)), a Roman alphabetic symbol may be used to distinguish each appearance of that particular R group. For example, where multiple R 13 substituents are present, each R 13 substituent may be distinguished as R 13A , R 13B , R 13C , R 13D , etc., wherein each of R 13A , R 13B , R 13C , R 13D , etc.
  • salts are meant to include salts of the active compounds that are prepared with relatively nontoxic acids or bases, depending on the particular substituents found on the compounds described herein.
  • base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent.
  • pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt.
  • acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent.
  • pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic,
  • salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, for example, Berge et al.,“Pharmaceutical Salts”, Journal of Pharmaceutical Science, 1977, 66, 1-19).
  • Certain specific compounds of the present disclosure contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts.
  • the compounds of the present disclosure may exist as salts, such as with pharmaceutically acceptable acids.
  • the present disclosure includes such salts.
  • Non-limiting examples of such salts include hydrochlorides, hydrobromides, phosphates, sulfates, methanesulfonates, nitrates, maleates, acetates, citrates, fumarates, proprionates, tartrates (e.g., (+)-tartrates, (-)-tartrates, or mixtures thereof including racemic mixtures), succinates, benzoates, and salts with amino acids such as glutamic acid, and quaternary ammonium salts (e.g., methyl iodide, ethyl iodide, and the like). These salts may be prepared by methods known to those skilled in the art.
  • the neutral forms of the compounds are preferably regenerated by contacting the salt with a base or acid and isolating the parent compound in the conventional manner.
  • the parent form of the compound may differ from the various salt forms in certain physical properties, such as solubility in polar solvents.
  • the present disclosure provides compounds, which are in a prodrug form.
  • Prodrugs of the compounds described herein are those compounds that readily undergo chemical changes under physiological conditions to provide the compounds of the present disclosure.
  • Prodrugs of the compounds described herein may be converted in vivo after administration.
  • prodrugs can be converted to the compounds of the present disclosure by chemical or biochemical methods in an ex vivo environment, such as, for example, when contacted with a suitable enzyme or chemical reagent.
  • Certain compounds of the present disclosure can exist in unsolvated forms as well as solvated forms, including hydrated forms. In general, the solvated forms are equivalent to unsolvated forms and are encompassed within the scope of the present disclosure. Certain compounds of the present disclosure may exist in multiple crystalline or amorphous forms. In general, all physical forms are equivalent for the uses contemplated by the present disclosure and are intended to be within the scope of the present disclosure.
  • a polypeptide, or a cell is“recombinant” when it is artificial or engineered, or derived from or contains an artificial or engineered protein or nucleic acid (e.g., non-natural or not wild type).
  • a polynucleotide that is inserted into a vector or any other heterologous location, e.g., in a genome of a recombinant organism, such that it is not associated with nucleotide sequences that normally flank the polynucleotide as it is found in nature is a recombinant polynucleotide.
  • a protein expressed in vitro or in vivo from a recombinant polynucleotide is an example of a recombinant polypeptide.
  • a polynucleotide sequence that does not appear in nature, for example a variant of a naturally occurring gene is recombinant.
  • the term“about” means a range of values including the specified value, which a person of ordinary skill in the art would consider reasonably similar to the specified value. In embodiments, about means within a standard deviation using
  • compositions described herein are administered at the same time, just prior to, or just after the administration of one or more additional therapies.
  • the compounds of the invention can be administered alone or can be coadministered to the patient.
  • Co-administration is meant to include simultaneous or sequential administration of the compounds individually or in combination (more than one compound).
  • the preparations can also be combined, when desired, with other active substances (e.g., to reduce metabolic degradation).
  • compositions of the present invention can be delivered transdermally, by a topical route, or formulated as applicator sticks, solutions, suspensions, emulsions, gels, creams, ointments, pastes, jellies, paints, powders, and aerosols.
  • A“cell” as used herein refers to a cell carrying out metabolic or other function sufficient to preserve or replicate its genomic DNA.
  • a cell can be identified by well-known methods in the art including, for example, presence of an intact membrane, staining by a particular dye, ability to produce progeny or, in the case of a gamete, ability to combine with a second gamete to produce a viable offspring.
  • Cells may include prokaryotic and eukaroytic cells.
  • Prokaryotic cells include but are not limited to bacteria.
  • Eukaryotic cells include but are not limited to yeast cells and cells derived from plants and animals, for example mammalian, insect (e.g., spodoptera) and human cells. Cells may be useful when they are naturally nonadherent or have been treated not to adhere to surfaces, for example by trypsinization.
  • the terms“treating” or“treatment” refers to any indicia of success in the treatment or amelioration of an injury, disease, pathology or condition, including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the injury, pathology or condition more tolerable to the patient; slowing in the rate of
  • treating cancer includes slowing the rate of growth or spread of cancer cells, reducing metastasis, or reducing the growth of metastatic tumors.
  • the term“treating” and conjugations thereof, include prevention of an injury, pathology, condition, or disease.
  • treating is preventing.
  • treating does not include preventing.
  • the treating or treatment is no prophylactic treatment.
  • An“effective amount” is an amount sufficient for a compound to accomplish a stated purpose relative to the absence of the compound (e.g., achieve the effect for which it is administered, treat a disease, reduce enzyme activity, increase enzyme activity, reduce signaling pathway, reduce one or more symptoms of a disease or condition (e.g., reduce signaling pathway stimulated by an autophagy adapter protein, reduce the signaling pathway activity of an autophagy protein).
  • An example of an“effective amount” is an amount sufficient to contribute to the treatment, prevention, or reduction of a symptom or symptoms of a disease, which could also be referred to as a“therapeutically effective amount” when referred to in this context.
  • A“reduction” of a symptom or symptoms means decreasing of the severity or frequency of the symptom(s), or elimination of the symptom(s).
  • A“prophylactically effective amount” of a drug is an amount of a drug that, when administered to a subject, will have the intended prophylactic effect, e.g., preventing or delaying the onset (or reoccurrence) of an injury, disease, pathology or condition, or reducing the likelihood of the onset (or reoccurrence) of an injury, disease, pathology, or condition, or their symptoms.
  • the full prophylactic effect does not necessarily occur by administration of one dose, and may occur only after administration of a series of doses.
  • a prophylactically effective amount may be administered in one or more administrations.
  • An“activity decreasing amount,” as used herein, refers to an amount of antagonist required to decrease the activity of an enzyme relative to the absence of the antagonist.
  • A“function disrupting amount,” as used herein, refers to the amount of antagonist required to disrupt the function of an enzyme or protein relative to the absence of the antagonist. The exact amounts will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman,
  • Control or“control experiment” is used in accordance with its plain ordinary meaning and refers to an experiment in which the subjects or reagents of the experiment are treated as in a parallel experiment except for omission of a procedure, reagent, or variable of the experiment. In some instances, the control is used as a standard of comparison in evaluating experimental effects.
  • a control is the measurement of the activity (e.g., signaling pathway) of a protein in the absence of a compound as described herein (including embodiments, examples, figures, or Tables).
  • Contacting is used in accordance with its plain ordinary meaning and refers to the process of allowing at least two distinct species (e.g., chemical compounds including biomolecules, or cells) to become sufficiently proximal to react, interact or physically touch. It should be appreciated; however, the resulting reaction product can be produced directly from a reaction between the added reagents or from an intermediate from one or more of the added reagents which can be produced in the reaction mixture.
  • the term“contacting” may include allowing two species to react, interact, or physically touch, wherein the two species may be a compound as described herein and a cellular component (e.g., protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, virus, lipid droplet, vesicle, small molecule, protein complex, protein aggregate, or macromolecule).
  • a cellular component e.g., protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, virus, lipid droplet, vesicle, small molecule, protein complex, protein aggregate, or macromolecule.
  • contacting includes allowing a compound described herein to interact with a cellular component (e.g., protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, virus, lipid droplet, organelle, cellular compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or macromolecule) that is involved in a signaling pathway.
  • a cellular component e.g., protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, virus, lipid droplet, organelle, cellular compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or macromolecule
  • the term“inhibition,”“inhibit,”“inhibiting” and the like in reference to a cellular component-inhibitor interaction means negatively affecting (e.g., decreasing) the activity or function of the cellular component (e.g., decreasing the signaling pathway stimulated by a cellular component (e.g., protein, ion, lipid, virus, lipid droplet, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or
  • a cellular component e.g., protein, ion, lipid, virus, lipid droplet, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or
  • inhibition refers to reduction of a disease or symptoms of disease. In some embodiments, inhibition refers to a reduction in the activity of a signal transduction pathway or signaling pathway (e.g., reduction of a pathway involving the cellular component).
  • inhibition includes, at least in part, partially or totally blocking stimulation, decreasing, preventing, or delaying activation, or inactivating, desensitizing, or down-regulating the signaling pathway or enzymatic activity or the amount of a cellular component.
  • modulator refers to a composition that increases or decreases the level of a target molecule or the function of a target molecule or the physical state of the target of the molecule (e.g., a target may be a cellular component (e.g., protein, ion, lipid, virus, lipid droplet, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular
  • a target may be a cellular component (e.g., protein, ion, lipid, virus, lipid droplet, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular
  • “modulate” is used in accordance with its plain ordinary meaning and refers to the act of changing or varying one or more properties.“Modulation” refers to the process of changing or varying one or more properties. For example, as applied to the effects of a modulator on a target protein, to modulate means to change by increasing or decreasing a property or function of the target molecule or the amount of the target molecule.
  • “Patient” or“subject in need thereof” refers to a living organism suffering from or prone to a disease or condition that can be treated by administration of a pharmaceutical composition as provided herein.
  • Non-limiting examples include humans, other mammals, bovines, rats, mice, dogs, monkeys, goat, sheep, cows, deer, and other non-mammalian animals.
  • a patient is human.
  • Disease” or“condition” refer to a state of being or health status of a patient or subject capable of being treated with the compounds or methods provided herein.
  • the disease is a disease related to (e.g., caused by) a cellular component (e.g., protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or macromolecule).
  • a cellular component e.g., protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or macromolecule.
  • cancer refers to all types of cancer, neoplasm or malignant tumors found in mammals (e.g., humans), including leukemia, lymphoma, carcinomas and sarcomas.
  • Exemplary cancers that may be treated with a compound or method provided herein include cancer of the thyroid, endocrine system, brain, breast, cervix, colon, head & neck, liver, kidney, lung, non-small cell lung, melanoma, mesothelioma, ovary, sarcoma, stomach, uterus, Medulloblastoma, colorectal cancer, pancreatic cancer. Additional examples include, Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer,
  • rhabdomyosarcoma primary thrombocytosis, primary macroglobulinemia, primary brain tumors, cancer, malignant pancreatic insulanoma, malignant carcinoid, urinary bladder cancer, premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer,
  • neuroblastoma esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, endometrial cancer, adrenal cortical cancer, neoplasms of the endocrine or exocrine pancreas, medullary thyroid cancer, medullary thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid cancer, hepatocellular carcinoma, or prostate cancer.
  • leukemia refers broadly to progressive, malignant diseases of the blood- forming organs and is generally characterized by a distorted proliferation and development of leukocytes and their precursors in the blood and bone marrow.
  • Leukemia is generally clinically classified on the basis of (1) the duration and character of the disease-acute or chronic; (2) the type of cell involved; myeloid (myelogenous), lymphoid (lymphogenous), or monocytic; and (3) the increase or non-increase in the number abnormal cells in the blood- leukemic or aleukemic (subleukemic).
  • Exemplary leukemias that may be treated with a compound or method provided herein include, for example, acute nonlymphocytic leukemia, chronic lymphocytic leukemia, acute granulocytic leukemia, chronic granulocytic leukemia, acute promyelocytic leukemia, adult T-cell leukemia, aleukemic leukemia, a leukocythemic leukemia, basophylic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross’ leukemia, hairy-cell leukemia, hemoblastic leukemia, hemocytoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenous leukemia,
  • lymphoma refers to a group of cancers affecting hematopoietic and lymphoid tissues. It begins in lymphocytes, the blood cells that are found primarily in lymph nodes, spleen, thymus, and bone marrow. Two main types of lymphoma are non-Hodgkin lymphoma and Hodgkin’s disease. Hodgkin’s disease represents approximately 15% of all diagnosed lymphomas. This is a cancer associated with Reed- Sternberg malignant B lymphocytes. Non-Hodgkin’s lymphomas (NHL) can be classified based on the rate at which cancer grows and the type of cells involved.
  • B-cell lymphomas that may be treated with a compound or method provided herein include, but are not limited to, small lymphocytic lymphoma, Mantle cell lymphoma, follicular lymphoma, marginal zone lymphoma, extranodal (MALT) lymphoma, nodal (monocytoid B-cell) lymphoma, splenic lymphoma, diffuse large cell B-lymphoma, Burkitt’s lymphoma, lymphoblastic lymphoma,
  • T- cell lymphomas that may be treated with a compound or method provided herein include, but are not limited to, cunateous T-cell lymphoma, peripheral T-cell lymphoma, anaplastic large cell lymphoma, mycosis fungoides, and precursor T-lymphoblastic lymphoma.
  • the term“sarcoma” generally refers to a tumor which is made up of a substance like the embryonic connective tissue and is generally composed of closely packed cells embedded in a fibrillar or homogeneous substance.
  • Sarcomas that may be treated with a compound or method provided herein include a chondrosarcoma, fibrosarcoma,
  • lymphosarcoma melanosarcoma, myxosarcoma, osteosarcoma, Abemethy's sarcoma, adipose sarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, chorio carcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, immunoblastic sarcoma of B cells, lymphoma,
  • immunoblastic sarcoma of T-cells Jensen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukosarcoma, malignant mesenchymoma sarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma, serocystic sarcoma, synovial sarcoma, or telangiectaltic sarcoma.
  • the term“melanoma” is taken to mean a tumor arising from the melanocytic system of the skin and other organs.
  • Melanomas that may be treated with a compound or method provided herein include, for example, acral-lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Cloudman's melanoma, S91 melanoma, Harding-Passey melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungal melanoma, or superficial spreading melanoma.
  • the term“carcinoma” refers to a malignant new growth made up of epithelial cells tending to infiltrate the surrounding tissues and give rise to metastases.
  • carcinomas that may be treated with a compound or method provided herein include, for example, medullary thyroid carcinoma, familial medullary thyroid carcinoma, acinar carcinoma, acinous carcinoma, adenocystic carcinoma, adenoid cystic carcinoma, carcinoma adenomatosum, carcinoma of adrenal cortex, alveolar carcinoma, alveolar cell carcinoma, basal cell carcinoma, carcinoma basocellulare, basaloid carcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma, bronchogenic carcinoma, cerebriform carcinoma, cholangiocellular carcinoma, chorionic carcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform carcinoma, carcinoma en cuirasse, carcinoma cutaneum, cylindrical carcinoma, cylindrical cell carcinoma, duct carcinoma, carcinoma durum, embryonal carcinoma, encephaloid carcinoma, epiermoid carcinoma, carcinoma epitheliale adenoides, exophytic carcinoma, carcinoma ex ulcere, carcinoma fibrosum, gelatiniforni carcinoma, gelatinous carcinoma
  • autoimmune disease refers to a disease or condition in which a subject’s immune system has an aberrant immune response against a substance that does not normally elicit an immune response in a healthy subject.
  • autoimmune diseases include Acute Disseminated Encephalomyelitis (ADEM), Acute necrotizing hemorrhagic leukoencephalitis, Addison’s disease, Agammaglobulinemia, Alopecia areata, Amyloidosis, Ankylosing spondylitis, Anti-GBM/Anti-TBM nephritis, Antiphospholipid syndrome (APS), Autoimmune angioedema, Autoimmune aplastic anemia, Autoimmune dysautonomia, Autoimmune hepatitis, Autoimmune hyperlipidemia, Autoimmune immunodeficiency, Autoimmune inner ear disease (AIED), Autoimmune myo
  • Acute Disseminated Encephalomyelitis Acute necrotizing hemorrhagic le
  • cryoglobulinemia Demyelinating neuropathies, Dermatitis herpetiformis, Dermatomyositis, Devic’s disease (neuromyelitis optica), Discoid lupus, Dressler’s syndrome, Endometriosis, Eosinophilic esophagitis, Eosinophilic fasciitis, Erythema nodosum, Experimental allergic encephalomyelitis, Evans syndrome, Fibromyalgia, Fibrosing alveolitis, Giant cell arteritis (temporal arteritis), Giant cell myocarditis, Glomerulonephritis, Goodpasture’s syndrome, Granulomatosis with Polyangiitis (GPA) (formerly called Wegener’s Granulomatosis), Graves’ disease, Guillain-Barre syndrome, Hashimoto’s encephalitis, Hashimoto’s thyroiditis, Hemolytic anemia, Henoch-Schonlein purpura, Herpes
  • Idiopathic thrombocytopenic purpura Idiopathic thrombocytopenic purpura (ITP), IgA nephropathy, IgG4-related sclerosing disease, Immunoregulatory lipoproteins, Inclusion body myositis, Interstitial cystitis, Juvenile arthritis, Juvenile diabetes (Type 1 diabetes), Juvenile myositis, Kawasaki syndrome, Lambert-Eaton syndrome, Leukocytoclastic vasculitis, Lichen planus, Lichen sclerosus, Ligneous conjunctivitis, Linear IgA disease (LAD), Lupus (SLE), Lyme disease, chronic, Meniere’s disease, Microscopic polyangiitis, Mixed connective tissue disease (MCTD), Mooren’s ulcer, Mucha-Habermann disease, Multiple sclerosis, Myasthenia gravis, Myositis, Narcolepsy, Neuromyelitis optica (Devic’s), Neutropenia, Ocular cica
  • Polyarteritis nodosa Type I, II, & III autoimmune polyglandular syndromes, Polymyalgia rheumatica, Polymyositis, Postmyocardial infarction syndrome, Postpericardiotomy syndrome, Progesterone dermatitis, Primary biliary cirrhosis, Primary sclerosing cholangitis, Psoriasis, Psoriatic arthritis, Idiopathic pulmonary fibrosis, Pyoderma gangrenosum, Pure red cell aplasia, Raynauds phenomenon, Reactive Arthritis, Reflex sympathetic dystrophy, Reiter’s syndrome, Relapsing polychondritis, Restless legs syndrome, Retroperitoneal fibrosis, Rheumatic fever, Rheumatoid arthritis, Sarcoidosis, Schmidt syndrome, Scleritis, Scleroderma, Sjogren’s syndrome, Sperm & testicular autoimmunity, Stiff person syndrome, Subacute bacterial
  • Takayasu’s arteritis Temporal arteritis/Giant cell arteritis, Thrombocytopenic purpura (TTP), Tolosa-Hunt syndrome, Transverse myelitis, Type 1 diabetes, Ulcerative colitis,
  • UCTD Undifferentiated connective tissue disease
  • Uveitis a disease or condition in which the function of a subject’s nervous system becomes impaired.
  • Vasculitis a disease or condition in which the function of a subject’s nervous system becomes impaired.
  • GPA Polyangiitis
  • neurodegenerative diseases that may be treated with a compound, pharmaceutical composition, or method described herein include Alexander's disease, Alper's disease, Alzheimer's disease, Amyotrophic lateral sclerosis, Ataxia telangiectasia, Batten disease (also known as Spielmeyer-Vogt-Sjogren-Batten disease), Bovine spongiform encephalopathy (BSE), Canavan disease, Cockayne syndrome, Corticobasal degeneration, Creutzfeldt-Jakob disease, frontotemporal dementia, Gerstmann-St syndromesler-Scheinker syndrome, Huntington's disease, HIV-associated dementia, Kennedy's disease, Krabbe's disease, kuru, Lewy body dementia, Machado-Joseph disease (Spinocerebellar ataxia type 3), Multiple sclerosis, Multiple System Atrophy, Narcolepsy, Neuroborreliosis, Parkinson's disease, Pelizaeus- Merzbacher Disease, Pick’s disease,
  • metabolic disease refers to a disease or condition in which a subject’s metabolism or metabolic system (e.g., function of storing or utilizing energy) becomes impaired.
  • metabolic diseases include diabetes (e.g., type I or type II), obesity, metabolic syndrome, or a mitochondrial disease (e.g., dysfunction of mitochondria or aberrant mitochondrial function).
  • the term“cellular component associated disease” e.g., the cellular component may be a protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, virus, vesicle, small molecule, protein complex, protein aggregate, or macromolecule; the disease may be a neurodegenerative disease, cancer, a metabolic disease, authoimmune disease, inflammatory disease, or infectious disease) (also referred to herein as“cellular component related disease”) refers to a disease caused by the celllular component.
  • Other diseases that are associated with aberrant activity or level of the cellular component are well known in the art and determining such diseases are within the skill of a person of skill in the art.
  • “Pharmaceutically acceptable excipient” and“pharmaceutically acceptable carrier” refer to a substance that aids the administration of an active agent to and absorption by a subject and can be included in the compositions of the present invention without causing a significant adverse toxicological effect on the patient.
  • “pharmaceutically acceptable excipient” and“pharmaceutically acceptable carrier” refer to a substance that aids the administration of an active agent to and absorption by a subject and can be included in the compositions of the present invention without causing a significant adverse toxicological effect on the patient.
  • pharmaceutically acceptable excipients include water, NaCl, normal saline solutions, lactated Ringer’s, normal sucrose, normal glucose, binders, fillers, disintegrants, lubricants, coatings, sweeteners, flavors, salt solutions (such as Ringer's solution), alcohols, oils, gelatins, carbohydrates such as lactose, amylose or starch, fatty acid esters, hydroxymethycellulose, polyvinyl pyrrolidine, and colors, and the like.
  • preparations can be sterilized and, if desired, mixed with auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, and/or aromatic substances and the like that do not deleteriously react with the compounds of the invention.
  • auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, and/or aromatic substances and the like that do not deleteriously react with the compounds of the invention.
  • auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, and/or aromatic substances and the like that do not deleteriously react with the compounds of the invention.
  • auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents,
  • administering means oral administration, administration as a suppository, topical contact, intravenous, intraperitoneal, intramuscular, intralesional, intrathecal, intranasal or subcutaneous administration, or the implantation of a slow-release device, e.g., a mini-osmotic pump, to a subject.
  • Administration is by any route, including parenteral and transmucosal (e.g., buccal, sublingual, palatal, gingival, nasal, vaginal, rectal, or transdermal).
  • Parenteral administration includes, e.g., intravenous, intramuscular, intra- arteriole, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial.
  • Other modes of delivery include, but are not limited to, the use of liposomal formulations, intravenous infusion, transdermal patches, etc.
  • co-administer it is meant that a composition described herein is administered at the same time, just prior to, or just after the administration of one or more additional therapies, for example cancer therapies such as chemotherapy, hormonal therapy, radiotherapy, or immunotherapy.
  • the compounds of the invention can be administered alone or can be coadministered to the patient.
  • Coadministration is meant to include simultaneous or sequential administration of the compounds individually or in combination (more than one compound).
  • compositions of the present invention can be delivered by transdermally, by a topical route, formulated as applicator sticks, solutions, suspensions, emulsions, gels, creams, ointments, pastes, jellies, paints, powders, and aerosols.
  • the compounds described herein can be used in combination with one another, with other active agents known to be useful in treating a disease associated with cells expressing a disease associated cellular component, or with adjunctive agents that may not be effective alone, but may contribute to the efficacy of the active agent.
  • co-administration includes administering one active agent within 0.5, 1, 2, 4, 6, 8, 10, 12, 16, 20, or 24 hours of a second active agent.
  • Co- administration includes administering two active agents simultaneously, approximately simultaneously (e.g., within about 1, 5, 10, 15, 20, or 30 minutes of each other), or sequentially in any order.
  • co-administration can be accomplished by co-formulation, i.e., preparing a single pharmaceutical composition including both active agents.
  • the active agents can be formulated separately.
  • the active and/or adjunctive agents may be linked or conjugated to one another.
  • the compounds described herein can be co-administered with conventional chemotherapeutic agents including alkylating agents (e.g.,
  • cyclophosphamide ifosfamide, chlorambucil, busulfan, melphalan, mechlorethamine, uramustine, thiotepa, nitrosoureas, etc.
  • anti-metabolites e.g., 5-fluorouracil, azathioprine, methotrexate, leucovorin, capecitabine, cytarabine, floxuridine, fludarabine, gemcitabine, pemetrexed, raltitrexed, etc.
  • plant alkaloids e.g., vincristine, vinblastine, vinorelbine, vindesine, podophyllotoxin, paclitaxel, docetaxel, etc.
  • topoisomerase inhibitors e.g., irinotecan, topotecan, amsacrine, etoposide (VP16), etoposide phosphate, teniposide, etc.
  • the compounds described herein can also be co-administered with conventional hormonal therapeutic agents including, but not limited to, steroids (e.g., dexamethasone), finasteride, aromatase inhibitors, tamoxifen, and gonadotropin-releasing hormone agonists (GnRH) such as goserelin.
  • steroids e.g., dexamethasone
  • finasteride e.g., aromatase inhibitors
  • tamoxifen e.g., tamoxifen
  • GnRH gonadotropin-releasing hormone agonists
  • the compounds described herein can be co-administered with conventional immunotherapeutic agents including, but not limited to, immunostimulants (e.g., Bacillus Calmette-Guérin (BCG), levamisole, interleukin-2, alpha-interferon, etc.), monoclonal antibodies (e.g., anti-CD20, anti-HER2, anti-CD52, anti-HLA-DR, and anti- VEGF monoclonal antibodies), immunotoxins (e.g., anti-CD33 monoclonal antibody- calicheamicin conjugate, anti-CD22 monoclonal antibody-pseudomonas exotoxin conjugate, etc.), and radioimmunotherapy (e.g., anti-CD20 monoclonal antibody conjugated to 111 In, 90 Y, or 131 I, etc.).
  • immunostimulants e.g., Bacillus Calmette-Guérin (BCG), levamisole, interleukin-2, alpha-interfer
  • the compounds described herein can be co-administered with conventional radiotherapeutic agents including, but not limited to, radionuclides such as 47 Sc, 64 Cu, 67 Cu, 89 Sr, 86 Y, 87 Y, 90 Y, 105 Rh, 111 Ag, 111 In, 117m Sn, 149 Pm, 153 Sm, 166 Ho, 177 Lu, 186 Re, 188 Re, 211 At, and 212 Bi, optionally conjugated to antibodies directed against tumor antigens.
  • radionuclides such as 47 Sc, 64 Cu, 67 Cu, 89 Sr, 86 Y, 87 Y, 90 Y, 105 Rh, 111 Ag, 111 In, 117m Sn, 149 Pm, 153 Sm, 166 Ho, 177 Lu, 186 Re, 188 Re, 211 At, and 212 Bi, optionally conjugated to antibodies directed against tumor antigens.
  • compound utilized in the pharmaceutical compositions of the present invention may be administered at the initial dosage of
  • a daily dose range of about 0.01 mg/kg to about 500 mg/kg, or about 0.1 mg/kg to about 200 mg/kg, or about 1 mg/kg to about 100 mg/kg, or about 10 mg/kg to about 50 mg/kg, can be used.
  • the dosages may be varied depending upon the requirements of the patient, the severity of the condition being treated, and the compound or drug being employed. For example, dosages can be empirically determined considering the type and stage of cancer diagnosed in a particular patient.
  • the dose administered to a patient, in the context of the present invention, should be sufficient to affect a beneficial therapeutic response in the patient over time.
  • the size of the dose will also be determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of a compound in a particular patient.
  • the proper dosage for a particular situation is within the skill of the practitioner. Generally, treatment is initiated with smaller dosages which are less than the optimum dose of the compound. Thereafter, the dosage is increased by small increments until the optimum effect under circumstances is reached. For convenience, the total daily dosage may be divided and administered in portions during the day, if desired.
  • the compounds described herein can be used in combination with one another, with other active agents known to be useful in treating cancer or with adjunctive agents that may not be effective alone, but may contribute to the efficacy of the active agent.
  • the term“associated” or“associated with” in the context of a substance or substance activity or function associated with a disease means that the disease (e.g., neurodegenerative disease, cancer) is caused by (in whole or in part), or a symptom of the disease is caused by (in whole or in part) the substance or substance activity or function or the disease or a symptom of the disease may be treated by modulating (e.g., inhibiting or activating) the substance (e.g., cellular component).
  • a neurodegenerative disease associated with a protein aggregate may be a neurodegenerative disease that results (entirely or partially) from aberrant protein aggregation or a neurodegenerative disease wherein a particular symptom of the disease is caused (entirely or partially) by aberrant protein aggregation.
  • a neurodegenerative disease associated with aberrant protein aggregation or a protein aggregate associated neurodegenerative disease may be treated with a protein aggregate modulator or protein aggregate targeted autophagy degrader, in the instance where increased protein aggregation causes the neurodegenerative disease.
  • aberrant refers to different from normal. When used to describe enzymatic activity, aberrant refers to activity that is greater or less than a normal control or the average of normal non-diseased control samples. Aberrant activity may refer to an amount of activity that results in a disease, wherein returning the aberrant activity to a normal or non-disease-associated amount (e.g., by administering a compound or using a method as described herein), results in reduction of the disease or one or more disease symptoms.
  • Anti-cancer agent is used in accordance with its plain ordinary meaning and refers to a composition (e.g., compound, drug, antagonist, inhibitor, modulator) having
  • an anti-cancer agent is a chemotherapeutic.
  • an anti- cancer agent is an agent identified herein having utility in methods of treating cancer.
  • an anti-cancer agent is an agent approved by the FDA or similar regulatory agency of a country other than the USA, for treating cancer.
  • an anti-cancer agent is an inhibitor of K-Ras, RAF, MEK, Erk, PI3K, Akt, RTK, or mTOR.
  • an anti-cancer agent is an MDM2 inhibitor or a genotoxic anti-cancer agent.
  • an anti-cancer agent is nutlin-1, nutlin-2, nutlin-3, nutlin-3a, nutlin-3b, YH239-EE, MI-219, MI-773, MI-77301, MI-888, MX69, RG7112, RG7388, RITA, idasanutlin, DS-3032b, or AMG232.
  • an anti-cancer agent is an alkylating agent, intercalating agent, or DNA replication inhibitor.
  • anti-cancer agents include, but are not limited to, MEK (e.g., MEK1, MEK2, or MEK1 and MEK2) inhibitors (e.g., XL518, CI-1040, PD035901, selumetinib/ AZD6244, GSK1120212/ trametinib, GDC- 0973, ARRY-162, ARRY-300, AZD8330, PD0325901, U0126, PD98059, TAK-733, PD318088, AS703026, BAY 869766), alkylating agents (e.g., cyclophosphamide, ifosfamide, chlorambucil, busulfan, melphalan, mechlorethamine, uramustine, thiotepa, nitrosoureas, nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, meiphalan),
  • LY294002 Syk inhibitors, mTOR inhibitors, antibodies (e.g., rituxan), gossyphol, genasense, polyphenol E, Chlorofusin, all trans-retinoic acid (ATRA), bryostatin, tumor necrosis factor- related apoptosis-inducing ligand (TRAIL), 5-aza-2'-deoxycytidine, all trans retinoic acid, doxorubicin, vincristine, etoposide, gemcitabine, imatinib (Gleevec.RTM.), geldanamycin, 17-N-Allylamino-17-Demethoxygeldanamycin (17-AAG), flavopiridol, LY294002, bortezomib, trastuzumab, BAY 11-7082, PKC412, PD184352, 20-epi-1, 25
  • ATRA trans-retinoic acid
  • TRAIL tumor necrosis factor-
  • amifostine aminolevulinic acid
  • amrubicin amsacrine
  • anagrelide anastrozole
  • antineoplaston antisense oligonucleotides; aphidicolin glycinate; apoptosis gene modulators; apoptosis regulators; apurinic acid; ara-CDP-DL-PTBA; arginine deaminase; asulacrine; atamestane; atrimustine; axinastatin 1; axinastatin 2; axinastatin 3; azasetron; azatoxin;
  • azatyrosine baccatin III derivatives; balanol; batimastat; BCR/ABL antagonists;
  • benzochlorins benzoylstaurosporine; beta lactam derivatives; beta-alethine; betaclamycin B; betulinic acid; bFGF inhibitor; bicalutamide; bisantrene; bisaziridinylspermine; bisnafide; bistratene A; bizelesin; breflate; bropirimine; budotitane; buthionine sulfoximine;
  • calcipotriol calphostin C; camptothecin derivatives; canarypox IL-2; capecitabine;
  • carboxamide-amino-triazole carboxyamidotriazole; CaRest M3; CARN 700; cartilage derived inhibitor; carzelesin; casein kinase inhibitors (ICOS); castanospermine; cecropin B; cetrorelix; chlorins; chloroquinoxaline sulfonamide; cicaprost; cis-porphyrin; cladribine; clomifene analogues; clotrimazole; collismycin A; collismycin B; combretastatin A4;
  • combretastatin analogue conagenin; crambescidin 816; crisnatol; cryptophycin 8;
  • cryptophycin A derivatives curacin A; cyclopentanthraquinones; cycloplatam; cypemycin; cytarabine ocfosfate; cytolytic factor; cytostatin; dacliximab; decitabine; dehydrodidemnin B; deslorelin; dexamethasone; dexifosfamide; dexrazoxane; dexverapamil; diaziquone;
  • didemnin B didemnin B; didox; diethylnorspermine; dihydro-5-azacytidine; 9-dioxamycin; diphenyl spiromustine; docosanol; dolasetron; doxifluridine; droloxifene; dronabinol; duocarmycin SA; ebselen; ecomustine; edelfosine; edrecolomab; eflornithine; elemene; emitefur;
  • epirubicin epristeride
  • estramustine analogue epristeride
  • estrogen agonists epristeride
  • estrogen antagonists epristeride
  • estramustine analogue epristeride
  • estrogen agonists epristeride
  • estrogen antagonists epristeride
  • etanidazole etoposide phosphate; exemestane; fadrozole; trasrabine; fenretinide; filgrastim; finasteride; flavopiridol; flezelastine; fluasterone; fludarabine; fluorodaunorunicin
  • hydrochloride forfenimex; formestane; fostriecin; fotemustine; gadolinium texaphyrin;
  • leuprolide+estrogen+progesterone leuprorelin; levamisole; liarozole; linear polyamine analogue; lipophilic disaccharide peptide; lipophilic platinum compounds; lissoclinamide 7; lobaplatin; lombricine; lometrexol; lonidamine; losoxantrone; lovastatin; loxoribine;
  • marimastat masoprocol; maspin; matrilysin inhibitors; matrix metalloproteinase inhibitors; menogaril; merbarone; meterelin; methioninase; metoclopramide; MIF inhibitor;
  • mifepristone miltefosine; mirimostim; mismatched double stranded RNA; mitoguazone; mitolactol; mitomycin analogues; mitonafide; mitotoxin fibroblast growth factor-saporin; mitoxantrone; mofarotene; molgramostim; monoclonal antibody, human chorionic gonadotrophin; monophosphoryl lipid A+myobacterium cell wall sk; mopidamol; multiple drug resistance gene inhibitor; multiple tumor suppressor 1-based therapy; mustard anticancer agent; mycaperoxide B; mycobacterial cell wall extract; myriaporone; N-acetyldinaline; N- substituted benzamides; nafarelin; nagrestip; naloxone+pentazocine; napavin; naphterpin; nartograstim; nedaplatin; nemorubicin; neridronic acid; neutral end
  • octreotide okicenone; oligonucleotides; onapristone; ondansetron; ondansetron; oracin; oral cytokine inducer; ormaplatin; osaterone; oxaliplatin; oxaunomycin; palauamine;
  • palmitoylrhizoxin pamidronic acid; panaxytriol; panomifene; parabactin; pazelliptine;
  • pegaspargase peldesine; pentosan polysulfate sodium; pentostatin; pentrozole; perflubron; perfosfamide; perillyl alcohol; phenazinomycin; phenylacetate; phosphatase inhibitors; picibanil; pilocarpine hydrochloride; pirarubicin; piritrexim; placetin A; placetin B;
  • plasminogen activator inhibitor platinum complex; platinum compounds; platinum-triamine complex; porfimer sodium; porfiromycin; prednisone; propyl bis-acridone; prostaglandin J2; proteasome inhibitors; protein A-based immune modulator; protein kinase C inhibitor;
  • protein kinase C inhibitors microalgal; protein tyrosine phosphatase inhibitors; purine nucleoside phosphorylase inhibitors; purpurins; pyrazoloacridine; pyridoxylated hemoglobin polyoxyethylerie conjugate; raf antagonists; raltitrexed; ramosetron; ras farnesyl protein transferase inhibitors; ras inhibitors; ras-GAP inhibitor; retelliptine demethylated; rhenium Re 186 etidronate; rhizoxin; ribozymes; RII retinamide; rogletimide; rohitukine; romurtide; roquinimex; rubiginone B1; ruboxyl; safingol; saintopin; SarCNU; sarcophytol A;
  • oligonucleotides oligonucleotides; signal transduction inhibitors; signal transduction modulators; single chain antigen-binding protein; sizofuran; sobuzoxane; sodium borocaptate; sodium phenylacetate; solverol; somatomedin binding protein; sonermin; sparfosic acid; spicamycin D;
  • spiromustine splenopentin
  • spongistatin 1 squalamine
  • stem cell inhibitor stem-cell division inhibitors
  • stipiamide stem-cell division inhibitors
  • stromelysin inhibitors sulfinosine
  • superactive vasoactive intestinal peptide antagonist suradista; suramin; swainsonine; synthetic glycosaminoglycans;
  • tallimustine tallimustine; tamoxifen methiodide; tauromustine; tazarotene; tecogalan sodium; tegafur; tellurapyrylium; telomerase inhibitors; temoporfin; temozolomide; teniposide;
  • thrombopoietin mimetic thymalfasin; thymopoietin receptor agonist; thymotrinan; thyroid stimulating hormone; tin ethyl etiopurpurin; tirapazamine; titanocene bichloride; topsentin; toremifene; totipotent stem cell factor; translation inhibitors; tretinoin; triacetyluridine;
  • triciribine trimetrexate; triptorelin; tropisetron; turosteride; tyrosine kinase inhibitors;
  • tyrphostins UBC inhibitors; ubenimex; urogenital sinus-derived growth inhibitory factor; urokinase receptor antagonists; vapreotide; variolin B; vector system, erythrocyte gene therapy; velaresol; veramine; verdins; verteporfin; vinorelbine; vinxaltine; vitaxin; vorozole; zanoterone; zeniplatin; zilascorb; zinostatin stimalamer, Adriamycin, Dactinomycin, Bleomycin, Vinblastine, Cisplatin, acivicin; aclarubicin; acodazole hydrochloride; acronine; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine;
  • azotomycin batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan;
  • cactinomycin calusterone; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; carzelesin; cedefingol; chlorambucil; cirolemycin; cladribine; crisnatol mesylate; cyclophosphamide; cytarabine; dacarbazine; daunorubicin hydrochloride;
  • decitabine dexormaplatin; dezaguanine; dezaguanine mesylate; diaziquone; doxorubicin; doxorubicin hydrochloride; droloxifene; droloxifene citrate; dromostanolone propionate; duazomycin; edatrexate; eflornithine hydrochloride; elsamitrucin; enloplatin; enpromate; epipropidine; epirubicin hydrochloride; erbulozole; esorubicin hydrochloride; estramustine; estramustine phosphate sodium; etanidazole; etoposide; etoposide phosphate; etoprine; fadrozole hydrochloride; camrabine; fenretinide; floxuridine; fludarabine phosphate;
  • melphalan menogaril; mercaptopurine; methotrexate; methotrexate sodium; metoprine; meturedepa; mitindomide; mitocarcin; mitocromin; mitogillin; mitomalcin; mitomycin; mitosper; mitotane; mitoxantrone hydrochloride; mycophenolic acid; nocodazoie;
  • Taxotere.TM compounds comprising the taxane skeleton, Erbulozole (i.e., R- 55104), Dolastatin 10 (i.e., DLS-10 and NSC-376128), Mivobulin isethionate (i.e., as CI- 980), Vincristine, NSC-639829, Discodermolide (i.e., as NVP-XX-A-296), ABT-751 (Abbott, i.e., E-7010), Altorhyrtins (e.g., Altorhyrtin A and Altorhyrtin C), Spongistatins (e.g., Spongistatin 1, Spongistatin 2, Spongistatin 3, Spongistatin 4, Spongistatin 5,
  • Altorhyrtins e.g., Altorhyrtin A and Altorhyrtin C
  • Spongistatins e.g., Spongist
  • Epothilones e.g., Epothilone A, Epothilone B, Epothilone C (i.e., desoxyepothilone A or dEpoA), Epothilone D (i.e., KOS-862, dEpoB, and desoxyepothilone B), Epothilone E, Epothilone F, Epothilone B N-oxide, Epothilone A N- oxide, 16-aza-epothilone B, 21-aminoepothilone B (i.e., BMS-310705), 21- hydroxyepothilone D (i.e., Desoxyepothilone F and dEpoF), 26-fluoroepothilones (e.g., Epothilone A, Epothilone B, Epothilone C (i.e., desoxyepothilone A or dEpoA), Epothilone D
  • WS- 9885B GS-164 (Takeda), GS-198 (Takeda), KAR-2 (Hungarian Academy of Sciences), BSF-223651 (BASF, i.e., ILX-651 and LU-223651), SAH-49960 (Lilly/Novartis), SDZ- 268970 (Lilly/Novartis), AM-97 (Armad/Kyowa Hakko), AM-132 (Armad), AM-138 (Armad/Kyowa Hakko), IDN-5005 (Indena), Cryptophycin 52 (i.e., LY-355703), AC-7739 (Ajinomoto, i.e., AVE-8063A and CS-39.HCl), AC-7700 (Ajinomoto, i.e., AVE-8062, AVE- 8062A, CS-39-L-Ser.HCl, and RPR-258062A), Vitilevuamide, Tubulysin
  • steroids e.g., dexamethasone
  • finasteride aromatase inhibitors
  • GnRH gonadotropin-releasing hormone agonists
  • adrenocorticosteroids e.g., prednisone
  • progestins e.g., hydroxyprogesterone caproate, megestrol acetate, medroxyprogesterone acetate
  • estrogens e.g., diethlystilbestrol, ethinyl estradiol
  • antiestrogen e.g., tamoxifen
  • androgens e.g., testosterone propionate, fluoxymesterone
  • antiandrogen e.g., flutamide
  • immunostimulants e.g., testosterone propionate, fluoxymesterone
  • antiandrogen e.g., flutamide
  • a moiety of an anti-cancer agent is a monovalent anti-cancer agent (e.g., a monovalent form of an agent listed above).
  • “Chemotherapeutic” or“chemotherapeutic agent” is used in accordance with its plain ordinary meaning and refers to a chemical composition or compound having antineoplastic properties or the ability to inhibit the growth or proliferation of cells.
  • the term“electrophilic” as used herein refers to a chemical group that is capable of accepting electron density.
  • an“electrophilic substituent,”“electrophilic chemical moiety,” or“electrophic moiety” refers to an electron-poor chemical group, substitutent, or moiety (monovalent chemical group), which may react with an electron-donating group, such as a nucleophile, by accepting an electron pair or electron density to form a bond.
  • the electrophilic substituent of the compound is capable of reacting with a cysteine residue.
  • the electrophilic substituent is capable of forming a covalent bond with a cysteine residue (e.g., ATP6V1A) and may be referred to as a“covalent cysteine modifier moiety” or“covalent cysteine modifier substituent.”
  • the covalent bond formed between the electrophilic substituent and the sulfhydryl group of the cysteine may be a reversible or irreversible bond.
  • the electrophilic substituent of the compound is capable of reacting with a lysine residue.
  • the electrophilic substituent of the compound is capable of reacting with a serine residue.
  • the electrophilic substituent of the compound is capable of reacting with a methionine residue.
  • “Nucleophilic” as used herein refers to a chemical group that is capable of donating electron density.
  • An amino acid residue in a protein “corresponds” to a given residue when it occupies the same essential structural position within the protein as the given residue.
  • a selected residue in a selected protein corresponds to C277 of human Vacuolar H + - ATPase protein when the selected residue occupies the same essential spatial or other structural relationship as C277 in human Vacuolar H + -ATPase protein.
  • a selected protein is aligned for maximum homology with the human Vacuolar H + -ATPase protein
  • the position in the aligned selected protein aligning with C277 is said to correspond to C277.
  • a three dimensional structural alignment can also be used, e.g., where the structure of the selected protein is aligned for maximum correspondence with the human Vacuolar H + -ATPase protein and the overall structures compared.
  • an amino acid that occupies the same essential position as C277 in the structural model is said to correspond to the C277 residue.
  • An amino acid residue in a protein“corresponds” to a given residue when it occupies the same essential structural position within the protein as the given residue.
  • a selected residue in a selected protein corresponds to C277 of human ATP6V1A protein when the selected residue occupies the same essential spatial or other structural relationship as C277 in human ATP6V1A protein.
  • the position in the aligned selected protein aligning with C277 is said to correspond to C277.
  • a three dimensional structural alignment can also be used, e.g., where the structure of the selected protein is aligned for maximum correspondence with the human ATP6V1A protein and the overall structures compared.
  • nucleic acid or protein when applied to a nucleic acid or protein, denotes that the nucleic acid or protein is essentially free of other cellular components with which it is associated in the natural state. It can be, for example, in a homogeneous state and may be in either a dry or aqueous solution. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein that is the predominant species present in a preparation is substantially purified.
  • amino acid refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.
  • Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, g- carboxyglutamate, and O-phosphoserine.
  • Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
  • Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
  • non-naturally occurring amino acid and“unnatural amino acid” refer to amino acid analogs, synthetic amino acids, and amino acid mimetics which are not found in nature.
  • Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
  • polypeptide “peptide,” and“protein” are used interchangeably herein to refer to a polymer of amino acid residues, wherein the polymer may in embodiments be conjugated to a moiety that does not consist of amino acids.
  • Percentage of sequence identity is determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences.
  • the percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.
  • nucleic acids or polypeptide sequences refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI web site http://www.ncbi.nlm.nih.gov/BLAST/ or the like).
  • sequences are then said to be“substantially identical.”
  • This definition also refers to, or may be applied to, the compliment of a test sequence.
  • the definition also includes sequences that have deletions and/or additions, as well as those that have substitutions.
  • the preferred algorithms can account for gaps and the like.
  • identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length.
  • Percentage of sequence identity is determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.
  • amino acid or nucleotide base“position” is denoted by a number that sequentially identifies each amino acid (or nucleotide base) in the reference sequence based on its position relative to the N-terminus (or 5'-end). Due to deletions, insertions, truncations, fusions, and the like that must be taken into account when determining an optimal alignment, in general the amino acid residue number in a test sequence determined by simply counting from the N-terminus will not necessarily be the same as the number of its corresponding position in the reference sequence. For example, in a case where a variant has a deletion relative to an aligned reference sequence, there will be no amino acid in the variant that corresponds to a position in the reference sequence at the site of deletion.
  • protein complex is used in accordance with its plain ordinary meaning and refers to a protein which is associated with an additional substance (e.g., another protein, protein subunit, or a compound). Protein complexes typically have defined quaternary structure. The association between the protein and the additional substance may be a covalent bond. In embodiments, the association between the protein and the additional substance (e.g., compound) is via non-covalent interactions. In embodiments, a protein complex refers to a group of two or more polypeptide chains. Proteins in a protein complex are linked by non-covalent protein–protein interactions. A non-limiting example of a protein complex is the proteasome.
  • protein aggregate is used in accordance with its plain ordinary meaning and refers to an abberrant collection or accumulation of proteins (e.g., misfolded proteins). Protein aggregates are often associated with diseases (e.g., amyloidosis). Typically, when a protien misfolds as a result of a change in the amino acid sequence or a change in the native environment which disrupts normal non-covalent interactions, and the misfolded protein is not corrected or degraded, the unfolded/misfolded protein may aggregate. There are three main types of protein aggregates that may form: amorphous aggregates, oligomers, and amyloid fibrils. In embodiments, protein aggregates are termed aggresomes. In
  • the protein aggregate is TDP43, HTT, APP, SNCA, or MAPT.
  • the protein aggregate includes the protein Beta amyloid, Amyloid precursor protein, IAPP (Amylin), Alpha-synuclein, PrPSc, PrPSc, Huntingtin, Calcitonin, Atrial natriuretic factor, Apolipoprotein AI, Serum amyloid A, Medin, Prolactin, Transthyretin, Lysozyme, Beta-2 microglobulin, Gelsolin, Keratoepithelin, Beta amyloid, Cystatin, Immunoglobulin light chain AL, TDP43, or S-IBM.
  • the term“vesicle” is used in accordance with its plain ordinary meaning and refers to a small membrane enclosed compartment within a cell.
  • Vesicles are typically involved in transport, buoyancy control, or enzyme storage within a cell. Some vesicles, for example a lysosome, may include enzymes, proteins, polysaccharides, lipids, nucleic acids, or organelles within the compartment. Vesicles are typically formed within cells as a result of exocytosis or phagocytosis, however some vesicles are formed at the Golgi complex and transported to the cell membrane. Vesicles may be unilamellar or multilamellar.
  • V-ATPase refers to an enzyme that acidifies a wide array of intracellular organelles (e.g., lysosomes) and pump protons across the plasma membranes of cells.
  • V-ATPases including ATP6V1A as a component, couple the energy of ATP hydrolysis to proton transport across intracellular and plasma membranes of eukaryotic cells.
  • ATP6V1A refers to a gene that encodes a component of vacuolar ATPase (v-ATPase), which is an enzyme that mediates amino acid-dependent recruitment of mTORC1 to the lysosome.
  • ATP6V1A refers to UniProt P38606-1.
  • ATP6V1A refers to human ATP6V1A.
  • ATP6V1A refers to Entrez 523.
  • ATP6V1A refers to RefSeq NM_001690.3.
  • ATP6V1A refers to RefSeq NP_001681.2.
  • ATP6V1A has the sequence:
  • mTOR may refer to the nucleotide sequence or protein sequence of human mTOR (e.g., Entrez 2475, Uniprot P42345, RefSeq NM_004958, or RefSeq NP_004949).
  • the term“mTOR” includes both the wild-type form of the nucleotide sequences or proteins as well as any mutants thereof.
  • “mTOR” is wild-type mTOR.
  • “mTOR” is one or more mutant forms.
  • mTOR refers to a nucleotide sequence or protein of a mutant mTOR wherein the Y numbered amino acid of mTOR that normally has an X amino acid in the wildtype, instead has a Z amino acid in the mutant.
  • an mTOR is the human mTOR.
  • the mTOR has the following amino acid sequence:
  • mTORC1 refers to the protein complex including mTOR and Raptor (regulatory-associated protein of mTOR). mTORC1 may also include MLST8 (mammalian lethal with SEC13 protein 8), PRAS40, and/or DEPTOR. mTORC1 may function as a nutrient/energy/redox sensor and regulator of protein synthesis.
  • the term“mTORC1 pathway” or“mTORC1 signal transduction pathway” refers to a cellular pathway including mTORC1. An mTORC1 pathway includes the pathway components upstream and downstream from mTORC1. An mTORC1 pathway is a signaling pathway that is modulated by modulation of mTORC1 activity.
  • an mTORC1 pathway is a signaling pathway that is modulated by modulation of mTORC1 activity but not by modulation of mTORC2 activity. In embodiments, an mTORC1 pathway is a signaling pathway that is modulated to a greater extent by modulation of mTORC1 activity than by modulation of mTORC2 activity.
  • the term“mTORC2” refers to the protein complex including mTOR and RICTOR (rapamycin-insensitive companion of mTOR). mTORC2 may also include GbL, mSIN1 (mammalian stress-activated protein kinase interacting protein 1), Protor 1/2, DEPTOR, TTI1, and/or TEL2.
  • mTORC2 may regulate cellular metabolism and the cytoskeleton.
  • the term“mTORC2 pathway” or“mTORC2 signal transduction pathway” refers to a cellular pathway including mTORC2.
  • An mTORC2 pathway includes the pathway components upstream and downstream from mTORC2.
  • An mTORC2 pathway is a signaling pathway that is modulated by modulation of mTORC2 activity.
  • an mTORC2 pathway is a signaling pathway that is modulated by modulation of mTORC2 activity but not by modulation of mTORC1 activity.
  • an mTORC2 pathway is a signaling pathway that is modulated to a greater extent by modulation of mTORC2 activity than by modulation of mTORC1 activity.
  • the term“Sequestosome-1” or“SQSTM1” or“p62/SQSTM1” or“ubiquitin- binding protein p62” or“p62” refers to an autophagosome cargo protein (including homologs, isoforms, and functional fragments thereof) that targets other proteins that bind to it for selective autophagy. p62 harbors active nuclear import and export signals and shuttles between the nucleus and cytoplasm.
  • the term“p62” refers to the nucleotide sequences or proteins of human p62.
  • the term“p62” includes both the wild-type form of the nucleotide sequences or proteins as well as any mutants thereof. In some embodiments,“p62” is wild- type p62.
  • “p62” is one or more mutant forms.
  • the term“p62” XYZ refers to a nucleotide sequence or protein of a mutant p62 wherein the Y numbered amino acid of p62 that has an X amino acid in the wildtype instead has a Z amino acid in the mutant.
  • p62 is a functional fragment thereof.
  • p62 refers to UniProt C9J6J8, having the sequence: MASLTVKAYLLGKEDAAREIRRFSFCCSPEPEAEAEAAAGPGPCERLLSRVAALFPAL RPGGFQAHYRGGGFR (SEQ ID NO:3).
  • p62 refers to Entrez 8878.
  • p62 refers to RefSeq NM_001142298.1, RefSeq NM_001142299.1, RefSeq NM_003900.4, RefSeq
  • NP_001135770.1 RefSeq NP_001135771.1
  • RefSeq NP_003891.1 RefSeq NP_003891.1
  • p62 refers to UniProt Q13501, having the sequence:
  • LC3B refers to a central protein in the autophagy pathway, where it functions, for example, in autophagy substrate selection.
  • the term“LC3B” may refer to the nucleotide sequence or protein sequence of human LC3B.
  • LC3B is LC3BII.
  • LC3B is Entrez 81631, Uniprot Q9GZQ8, RefSeq NM_022818.4, or RefSeq NP_073729.1.
  • the LC3B has the following amino acid sequence:
  • the term“4EBP1” or“eukaryotic translation initiation factor 4E-binding protein 1” refers to a protein that interacts with eukaryotic translation initiation factor 4E, which is a component of the multisubunit complex that recruits 40S ribosomal subunits to the 5’ end of mRNAs.
  • the term“4EBP1” may refer to the nucleotide sequence or protein sequence of human 4EBP1. In embodiments, 4EBP1 is Entrez 1978, Uniprot Q13541, RefSeq
  • the 4EBP1 has the following amino acid sequence:
  • TFEB or“transcription factor EB” refers to a protein involved in lysosomal biogenesis.
  • the TFEB protein coordinates, for example, expression of lysosomal hydrolases, membrane proteins, and genes involved in autophagy.
  • the TFEB protein is encoded by the TFEB gene.
  • the term“TFEB” may refer to the nucleotide sequence or protein sequence of human TFEB.
  • TFEB is Entrez 7942, Uniprot P19484, RefSeq NM_001167827.2, RefSeq NM_001271943.1, RefSeq NM_001271944.1, RefSeq NM_001271945.1, RefSeq NM_007162.2, RefSeq NP_001161299.2, RefSeq
  • the TFEB has the following amino acid sequence:
  • TFE3 or“transcription factor E3” refers to a protein that activates expression of CD30L in T-cells.
  • the TFE3 protein is encoded by the TFE3 gene.
  • TFE3 may refer to the nucleotide sequence or protein sequence of human TFE3.
  • TFE3 is Entrez 7030, Uniprot P19532, RefSeq NM_001282142.1, RefSeq NM_006521.5, RefSeq NP_001269071.1, or RefSeq NP_006512.2.
  • the TFE3 has the following amino acid sequence:
  • autophagosome is used in accordance with its plain ordinary meaning and refers to a vesicle that contains a cellular component slated to be degraded by autophagy.
  • autophagosome formation is a multistep process that includes the biogenesis of the phagophore, followed by its elongation and closure.
  • more than 15 autophagy-related ATG proteins, as well as class III PI3 kinases, may be required to construct the autophagosome, including the transmembrane ATG protein ATG9, along with
  • Nucleic acid refers to nucleotides (e.g., deoxyribonucleotides or ribonucleotides) and polymers thereof in either single-, double- or multiple-stranded form, or complements thereof; or nucleosides (e.g., deoxyribonucleosides or ribonucleosides). In embodiments, “nucleic acid” does not include nucleosides.
  • the terms“polynucleotide,”“oligonucleotide,” “oligo,” or the like refer, in the usual and customary sense, to a linear sequence of
  • nucleotides are typically from about 5, 6, 7, 8, 9, 10, 12, 15, 25, 30, 40, 50 or more nucleotides in length, up to about 100 nucleotides in length.
  • Nucleic acids and polynucleotides are a polymers of any length, including longer lengths, e.g., 200, 300, 500, 1000, 2000, 3000, 5000, 7000, 10,000, etc. In certain embodiments the nucleic acids herein contain phosphodiester bonds.
  • nucleic acid analogs are included that may have alternate backbones, comprising, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O-methylphosphoroamidite linkages (see, Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press); and peptide nucleic acid backbones and linkages.
  • Other analog nucleic acids include those with positive backbones; non-ionic backbones, and non-ribose backbones, including those described in U.S. Patent Nos.5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580,
  • nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half-life of such molecules in physiological environments or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs can be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made.
  • nucleic acid is a monomer of the nucleic acid (e.g., a nucleotide).
  • nucleoside refers, in the usual and customary sense, to a glycosylamine including a nucleobase and a five-carbon sugar (ribose or deoxyribose).
  • nucleosides include, cytidine, uridine, adenosine, guanosine, thymidine and inosine. Nucleosides may be modified at the base and/or and the sugar.
  • nucleotide refers, in the usual and customary sense, to a single unit of a polynucleotide, i.e., a monomer. Nucleotides can be ribonucleotides, deoxyribonucleotides, or modified versions thereof. Examples of polynucleotides contemplated herein include single and double stranded DNA, single and double stranded RNA, and hybrid molecules having mixtures of single and double stranded DNA and RNA.
  • nucleic acid examples include any types of RNA, e.g., mRNA, siRNA, miRNA, and guide RNA and any types of DNA, genomic DNA, plasmid DNA, and minicircle DNA, and any fragments thereof.
  • the term“duplex” in the context of polynucleotides refers, in the usual and customary sense, to double strandedness.
  • Nucleic acids can be linear or branched.
  • nucleic acids can be a linear chain of nucleotides or the nucleic acids can be branched, e.g., such that the nucleic acids comprise one or more arms or branches of nucleotides.
  • nucleotide refers to a nucleoside-5’-polyphosphate compound, or a structural analog thereof, which can be incorporated (e.g., partially incorporated as a nucleoside-5’-monophosphate or derivative thereof) by a nucleic acid polymerase to extend a growing nucleic acid chain (such as a primer).
  • Nucleotides may comprise bases such as A, C, G, T, U, or analogues thereof, and may comprise 2, 3, 4, 5, 6, 7, 8, or more phosphates in the phosphate group.
  • Nucleotides may be modified at one or more of the base, sugar, or phosphate group.
  • a nucleotide may have a label or tag attached (a“labeled nucleotide” or “tagged nucleotide”).
  • the terms also encompass nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non- naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphodiester derivatives including, e.g.,
  • phosphoramidate, phosphorodiamidate, phosphorothioate also known as phosphothioate having double bonded sulfur replacing oxygen in the phosphate
  • phosphorodithioate also known as phosphothioate having double bonded sulfur replacing oxygen in the phosphate
  • phosphonocarboxylic acids also known as phosphothioate having double bonded sulfur replacing oxygen in the phosphate
  • phosphonocarboxylic acids also known as phosphothioate having double bonded sulfur replacing oxygen in the phosphate
  • phosphonocarboxylates also known as phosphothioate having double bonded sulfur replacing oxygen in the phosphate
  • phosphonoacetic acid also known as phosphonoformic acid
  • phosphonoformic acid methyl phosphonate
  • boron phosphonate or O-methylphosphoroamidite linkages
  • nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids.
  • Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half-life of such molecules in physiological environments or as probes on a biochip.
  • Mixtures of naturally occurring nucleic acids and analogs can be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made.
  • the internucleotide linkages in DNA are phosphodiester, phosphodiester derivatives, or a combination of both.
  • Nucleic acids can include nonspecific sequences.
  • nonspecific sequence refers to a nucleic acid sequence that contains a series of residues that are not designed to be complementary to or are only partially complementary to any other nucleic acid sequence.
  • a nonspecific nucleic acid sequence is a sequence of nucleic acid residues that does not function as an inhibitory nucleic acid when contacted with a cell or organism.
  • An“antisense nucleic acid” as referred to herein is a nucleic acid (e.g., DNA or RNA molecule) that is complementary to at least a portion of a specific target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) and is capable of reducing transcription of the target nucleic acid (e.g., mRNA from DNA), reducing the translation of the target nucleic acid (e.g., mRNA), altering transcript splicing (e.g., single stranded morpholino oligo), or interfering with the target nucleic acid (e.g., mRNA from DNA), reducing the translation of the target nucleic acid (e.g., mRNA), altering transcript splicing (e.g., single stranded morpholino oligo), or interfering with the target nucleic acid (e.g., mRNA from
  • antisense nucleic acids are generally between 15 and 25 bases in length.
  • antisense nucleic acids are capable of hybridizing to (e.g., selectively hybridizing to) a target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein).
  • the antisense nucleic acid hybridizes to the target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) in vitro. In embodiments, the antisense nucleic acid hybridizes to the target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) in a cell. In embodiments, the antisense nucleic acid hybridizes to the target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) in an organism.
  • the target nucleic acid e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein
  • the antisense nucleic acid hybridizes to the target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) under physiological conditions.
  • Antisense nucleic acids may comprise naturally occurring nucleotides or modified nucleotides such as, e.g., phosphorothioate, methylphosphonate, and -anomeric sugar- phosphate, backbonemodified nucleotides.
  • the antisense nucleic acids hybridize to the corresponding RNA (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) forming a double-stranded molecule.
  • the antisense nucleic acids interfere with the endogenous behavior of the RNA (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) and inhibit its function relative to the absence of the antisense nucleic acid.
  • the double-stranded molecule may be degraded via the RNAi pathway.
  • antisense methods to inhibit the in vitro translation of genes is well known in the art (Marcus-Sakura, Anal. Biochem., 172:289, (1988)). Further, antisense molecules which bind directly to the DNA may be used.
  • Antisense nucleic acids may be single or double stranded nucleic acids.
  • Non-limiting examples of antisense nucleic acids include siRNAs (including their derivatives or pre- cursors, such as nucleotide analogs), short hairpin RNAs (shRNA), micro RNAs (miRNA), saRNAs (small activating RNAs) and small nucleolar RNAs (snoRNA) or certain of their derivatives or pre-cursors.
  • siRNAs including their derivatives or pre- cursors, such as nucleotide analogs
  • shRNA short hairpin RNAs
  • miRNA micro RNAs
  • saRNAs small activating RNAs
  • small nucleolar RNAs small nucleolar RNAs
  • a complement may include a sequence of nucleotides that base pair with corresponding complementary nucleotides of a second nucleic acid sequence.
  • the nucleotides of a complement may partially or completely match the nucleotides of the second nucleic acid sequence. Where the nucleotides of the complement completely match each nucleotide of the second nucleic acid sequence, the complement forms base pairs with each nucleotide of the second nucleic acid sequence.
  • nucleotides of the complement partially match the nucleotides of the second nucleic acid sequence only some of the nucleotides of the complement form base pairs with nucleotides of the second nucleic acid sequence.
  • complementary sequences include coding and a non-coding sequences, wherein the non-coding sequence contains complementary nucleotides to the coding sequence and thus forms the complement of the coding sequence.
  • complementary sequences are sense and antisense sequences, wherein the sense sequence contains complementary nucleotides to the antisense sequence and thus forms the complement of the antisense sequence.
  • sequences may be partial, in which only some of the nucleic acids match according to base pairing, or complete, where all the nucleic acids match according to base pairing.
  • two sequences that are complementary to each other may have a specified percentage of nucleotides that are the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region).
  • the term“antibody” refers to a polypeptide encoded by an immunoglobulin gene or functional fragments thereof that specifically binds and recognizes an antigen.
  • the recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes.
  • Light chains are classified as either kappa or lambda.
  • Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.
  • An exemplary immunoglobulin (antibody) structural unit comprises a tetramer.
  • Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one“heavy” chain (about 50-70 kDa).
  • the N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition.
  • the terms“variable heavy chain,”“VH,” or“VH” refer to the variable region of an immunoglobulin heavy chain, including an Fv, scFv, dsFv, or Fab; while the terms“variable light chain,”“VL,” or“VL” refer to the variable region of an immunoglobulin light chain, including of an Fv, scFv, dsFv, or Fab.
  • antibody functional fragments include, but are not limited to, complete antibody molecules, antibody fragments, such as Fv, single chain Fv (scFv), complementarity determining regions (CDRs), VL (light chain variable region), VH (heavy chain variable region), Fab, F(ab)2' and any combination of those or any other functional portion of an immunoglobulin peptide capable of binding to target antigen (see, e.g., F UNDAMENTAL IMMUNOLOGY (Paul ed., 4th ed.2001).
  • various antibody fragments can be obtained by a variety of methods, for example, digestion of an intact antibody with an enzyme, such as pepsin; or de novo synthesis.
  • Antibody fragments are often synthesized de novo either chemically or by using recombinant DNA methodology.
  • the term antibody includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty et al., (1990) Nature 348:552).
  • the term“antibody” also includes bivalent or bispecific molecules, diabodies, triabodies, and tetrabodies. Bivalent and bispecific molecules are described in, e.g., Kostelny et al. (1992) J.
  • the term“irreversible covalent bond” is used in accordance with its plain ordinary meaning in the art and refers to the resulting association between atoms or molecules of (e.g., electrophilic chemical moiety and nucleophilic moiety) wherein the probability of dissociation is low.
  • the irreversible covalent bond does not easily dissociate under normal biological conditions.
  • the irreversible covalent bond is formed through a chemical reaction between two species (e.g., electrophilic chemical moiety and cysteine).
  • Ring A is a phenyl or 5 to 6 membered heteroaryl.
  • Ring B is a phenyl or 5 to 6 membered heteroaryl.
  • L 1 is independently a bond, -S(O) 2 -, -N(R 5 )-, -O-, -S-, -C(O)-, -C(O)N(R 5 )-, -N(R 5 )C(O)-, -N(R 5 )C(O)NH-, -NHC(O)N(R 5 )-, -C(O)O-, -OC(O)-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or
  • R 5 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC
  • heterocycloalkyl substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent -L 1 -R 1 substituents may optionally be joined to form a substituted or
  • E is an electrophilic moiety.
  • R 2 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2 Cl,
  • R 3 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2 Cl,
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3
  • R 4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R 1A , R 1B , R 1C , and R 1D are independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 ,
  • X 1 is independently–F, -Cl, -Br, or–I.
  • n1 is independently an integer from 0 to 4.
  • m1 and v1 are independently 1 or 2.
  • z1 is independently an integer from 0 to 5.
  • z3 is independently an integer from 0 to 2.
  • z4 is independently an integer from 0 to 5.
  • the compound has the formula:
  • L 1 , E, R 1 , z1, R 4 , and z4 are as described herein, including in embodiments.
  • the compound has the formula: L 1 , E, R 1 , and R 4 are as described herein, including in embodiments.
  • the compound has the formula:
  • L 1 , E, R 1 , and R 4 are as described herein, including in
  • the compound has the formula:
  • L 1 , E, R 1 , z1, R 3 , R 4 , and z4 are as described herein,
  • the compound has the formula:
  • L 1 , E, R 1 , z1, R 3 , R 4 , and z4 are as described
  • the compound has the formula:
  • L 1 , E, R 1 , R 3 , and R 4 are as described herein, including in embodiments.
  • the compound has the formula:
  • L 1 , E, R 1 , R 3 , and R 4 are as described herein,
  • the compound has the formula:
  • L 1 , E, R 1 , R 3 , and R 4 are as described herein, including in embodiments.
  • the compound has the formula: L 1 , E, R 1 , R 3 , and R 4 are as described herein, including in embodiments. [0219] In embodiments, the compound has the formula:
  • L 1 , E, R 1 , z1, R 2 , R 4 , and z4 are as described herein, including in embodiments.
  • R 2 is independently C 1 -C 6 alkyl.
  • R 2 is independently unsubstituted C 1 -C 4 alkyl. In embodiments, R 2 is independently unsubstituted methyl. In embodiments, R 2 is independently unsubstituted ethyl. In embodiments, R 2 is independently C 3 -C 6 cycloalkyl. [0220] In embodiments, the compound has the formula:
  • L 1 , E, R 1 , R 2 , and R 4 are as described herein, including in
  • R 2 is independently C 1 -C 6 alkyl. In embodiments, R 2 is independently unsubstituted C 1 -C 4 alkyl. In embodiments, R 2 is independently unsubstituted methyl. In embodiments, R 2 is independently unsubstituted ethyl. In embodiments, R 2 is independently C 3 -C 6 cycloalkyl. [0221] In embodiments, the compound has the formula: L 1 , E, R 1 , R 2 , and R 4 are as described herein, including in embodiments. In embodiments, R 2 is independently C 1 -C 6 alkyl. In embodiments, R 2 is independently unsubstituted C 1 -C 4 alkyl.
  • R 2 is independently unsubstituted methyl. In embodiments, R 2 is independently unsubstituted ethyl. In embodiments, R 2 is independently C 3 -C 6 cycloalkyl. [0222] In embodiments, the compound has the formula:
  • L 1 , E, R 1 , z1, R 2 , R 3 , R 4 , and z4 are as described herein,
  • R 2 is independently C 1 -C 6 alkyl.
  • R 2 is independently unsubstituted C 1 -C 4 alkyl. In embodiments, R 2 is independently unsubstituted methyl. In embodiments, R 2 is independently unsubstituted ethyl. In embodiments, R 2 is independently C 3 -C 6 cycloalkyl. [0223] In embodiments, the compound has the formula:
  • L 1 , E, R 1 , z1, R 2 , R 3 , R 4 , and z4 are as described herein, including in embodiments.
  • R 2 is independently C 1 -C 6 alkyl.
  • R 2 is independently unsubstituted C 1 -C 4 alkyl.
  • R 2 is independently unsubstituted methyl.
  • R 2 is independently unsubstituted ethyl.
  • R 2 is independently C 3 -C 6 cycloalkyl.
  • L 1 , E, R 1 , R 2 , R 3 , and R 4 are as described herein, including in embodiments.
  • R 2 is independently C 1 -C 6 alkyl.
  • R 2 is independently unsubstituted C 1 -C 4 alkyl.
  • R 2 is independently unsubstituted methyl.
  • R 2 is independently unsubstituted ethyl.
  • R 2 is independently C 3 -C 6 cycloalkyl.
  • L 1 , E, R 1 , R 2 , R 3 , and R 4 are as described herein, including in embodiments.
  • R 2 is independently C 1 -C 6 alkyl.
  • R 2 is independently unsubstituted C 1 -C 4 alkyl.
  • R 2 is independently unsubstituted methyl.
  • R 2 is independently unsubstituted ethyl.
  • R 2 is independently C 3 -C 6 cycloalkyl.
  • L 1 , E, R 1 , R 2 , R 3 , and R 4 are as described
  • R 2 is independently C 1 -C 6 alkyl. In embodiments, R 2 is independently unsubstituted C 1 -C 4 alkyl. In embodiments, R 2 is independently unsubstituted methyl. In embodiments, R 2 is independently unsubstituted ethyl. In embodiments, R 2 is independently C 3 -C 6 cycloalkyl. [0227] In embodiments, the compound has the formula:
  • L 1 , E, R 1 , R 2 , R 3 , and R 4 are as described herein, including in embodiments.
  • R 2 is independently C 1 -C 6 alkyl.
  • R 2 is independently unsubstituted C 1 -C 4 alkyl.
  • R 2 is independently unsubstituted methyl.
  • R 2 is independently unsubstituted ethyl.
  • R 2 is independently C 3 -C 6 cycloalkyl.
  • L 1 is independently a bond, -S(O) 2 -, -N(R 5 )-, -O-, -S-, -C(O)-, -C(O)N(R 5 )-, -N(R 5 )C(O)-, -N(R 5 )C(O)NH-, -NHC(O)N(R 5 )-, -C(O)O-, -OC(O)-, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkylene (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkylene (e.g.,
  • heteroalkylene substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene
  • the substituted L 1 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • L 1 when L 1 is substituted, it is substituted with at least one substituent group. In embodiments, when L 1 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when L 1 is substituted, it is substituted with at least one lower substituent group. [0230] In embodiments, L 1 is independently a bond, -S(O) 2 -, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene.
  • L 1 is independently -S(O) 2 -, -NH-, or substituted or unsubstituted 5 to 6 membered heterocycloalkylene.
  • L 1 is independently -S(O) 2 -, -NH-, unsubstituted pyrrolidinylene, unsubstituted piperidinylene, or unsubstituted piperazinylene.
  • L 1 is independently -NH-.
  • L 1 is independently -N(R 5 )-, and R 5 is as described herein, including in embodiments.
  • L 1 is independently -N(R 5 )-, and R 5 is independently hydrogen or unsubstituted alkyl. In embodiments, L 1 is independently -N(R 5 )-, and R 5 is independently hydrogen or substituted or unsubstituted alkyl. In embodiments, L 1 is independently -N(R 5 )-, and R 5 is independently hydrogen or
  • L 1 is independently -N(R 5 )-, and R 5 is independently hydrogen or unsubstituted C 1 -C 4 alkyl. In embodiments, L 1 is independently -N(R 5 )-, and R 5 is independently hydrogen or unsubstituted methyl.
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2
  • a substituted R 1 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 1 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 1 is substituted, it is substituted with at least one substituent group.
  • R 1 when R 1 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 1 is substituted, it is substituted with at least one lower substituent group.
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O
  • two adjacent R 1 substituents are joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • two adjacent R 1 substituents are joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 -C 6 ), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C 6 -C 10 or phenyl), or substituted (e.
  • substituted e.
  • a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by joining two adjacent R 1 substituents is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R 1 substituents when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R 1 substituents is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R 1 substituents is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted cycloalkyl, substituted
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC
  • R 1 is independently halogen. In embodiments, R 1 is independently –F. In embodiments, R 1 is independently–Cl. In embodiments, R 1 is independently–Br. In embodiments, R 1 is independently–I. [0243] In embodiments, R 1 is independently halogen. [0244] In embodiments, R 1 is -F.
  • R 1 is independently halogen, -CX 1 3 , -CHX 1 2 , -CH 2 X 1 , -OCX 1 3 , -OCH 2 X 1 , -OCHX 1 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, substituted or unsubstituted C 1 -C 6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C 3 -C 8 cycloalkyl, substituted
  • R 1 is independently halogen, -CF 3 , -CHF 2 , -CH 2 F, -OH, -SH, -OCF 3 , -OCHF 2 , -OCH 2 F, -CH 3 , -CH 2 CH 3 , -OCH 3 , -OCH 2 CH 3 , -SCH 3 , or -SCH 2 CH 3 .
  • R 1 is substituted or unsubstituted C 1 -C 6 alkyl.
  • R 1 is substituted or unsubstituted 2 to 6 membered heteroalkyl.
  • R 1 is substituted or unsubstituted C 3 -C 8 cycloalkyl.
  • R 1 is substituted or unsubstituted 3 to 8 membered heterocycloalkyl. In embodiments, R 1 is substituted or unsubstituted phenyl. In embodiments, R 1 is substituted or unsubstituted 5 to 6 membered heteroaryl. In embodiments, R 1 is independently halogen. In embodiments, R 1 is independently -CX 1 3 . In embodiments, R 1 is independently -CHX 1 2 . In embodiments, R 1 is independently -CH 2 X 1 . In embodiments, R 1 is independently -OCX 1 3. In embodiments, R 1 is independently -OCH 2 X 1 . In embodiments, R 1 is independently
  • R 1 is independently -OCHX 1 2 .
  • R 1 is independently -OCH 2 X 1 .
  • R 1 is independently -CN.
  • R 1 is independently -SOn1R 1D .
  • R 1 is independently -SOv1NR 1A R 1B .
  • R 1 is independently -NHC(O)NR 1A R 1B .
  • R 1 is independently -N(O) m1 .
  • R 1 is independently -NR 1A R 1B .
  • R 1 is independently -C(O)R 1C .
  • R 1 is independently -C(O)OR 1C .
  • R 1 is independently -C(O)NR 1A R 1B . In embodiments, R 1 is independently -OR 1D . In embodiments, R 1 is independently -NR 1A SO 2 R 1D . In embodiments, R 1 is independently -NR 1A C(O)R 1C . In embodiments, R 1 is independently -NR 1A C(O)OR 1C . In embodiments, R 1 is independently -NR 1A OR 1C . In embodiments, R 1 is independently -OH. In embodiments, R 1 is independently -NH 2 . In embodiments, R 1 is independently -COOH. In embodiments, R 1 is independently -CONH 2 . In embodiments, R 1 is independently -NO 2 .
  • R 1 is independently -SH. In embodiments, R 1 is independently -CF 3 . In embodiments, R 1 is independently -CHF 2 . In embodiments, R 1 is independently -CH 2 F. In embodiments, R 1 is independently -OCF 3 . In embodiments, R 1 is independently -OCH 2 F. In embodiments, R 1 is independently -OCHF 2 . In embodiments, R 1 is independently–OCH 3 . In embodiments, R 1 is independently–OCH 2 CH 3 . In embodiments, R 1 is independently –OCH 2 CH 2 CH 3 . In embodiments, R 1 is independently–OCH(CH 3 ) 2 . In embodiments, R 1 is independently–OC(CH 3 ) 3 .
  • R 1 is independently–SCH 3 . In embodiments, R 1 is independently–SCH 2 CH 3 . In embodiments, R 1 is independently–SCH 2 CH 2 CH 3 . In embodiments, R 1 is independently–SCH(CH 3 ) 2 . In embodiments, R 1 is independently –SC(CH 3 ) 3 . In embodiments, R 1 is independently–CH 3 . In embodiments, R 1 is
  • R 1 is independently–CH 2 CH 2 CH 3 .
  • R 1 is independently–CH 2 CH 2 CH 3 .
  • R 1 is independently–CH(CH 3 ) 2 . In embodiments, R 1 is independently –C(CH 3 )3. In embodiments, R 1 is independently–F. In embodiments, R 1 is independently –Cl. In embodiments, R 1 is independently–Br. In embodiments, R 1 is independently–I. In embodiments, R 1 is independently unsubstituted methyl. In embodiments, R 1 is
  • R 1 independently unsubstituted ethyl. In embodiments, R 1 is independently unsubstituted propyl. In embodiments, R 1 is independently unsubstituted n-propyl. In embodiments, R 1 is independently unsubstituted isopropyl. In embodiments, R 1 is independently unsubstituted butyl. In embodiments, R 1 is independently unsubstituted n-butyl. In embodiments, R 1 is independently unsubstituted isobutyl. In embodiments, R 1 is independently unsubstituted tert-butyl. In embodiments, R 1 is independently unsubstituted pentyl.
  • two adjacent -L 1 -R 1 substituents are joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 -C 6 ), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C 6 -C 10 or phenyl),
  • substituted e.
  • a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by joining two adjacent -L 1 -R 1 substituents is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent -L 1 -R 1 substituents is substituted, it is substituted with at least one substituent group.
  • a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent -L 1 -R 1 substituents when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent -L 1 -R 1 substituents is substituted, it is substituted with at least one size-limited substituent group.
  • a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent -L 1 -R 1 substituents when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent -L 1 -R 1 substituents is substituted, it is substituted with at least one lower substituent group.
  • two adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • two adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted cycloalkyl.
  • two adjacent -L 1 -R 1 substituents are joined to form a substituted or
  • two adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted aryl.
  • two adjacent R 1 substituents are joined to form a substituted or unsubstituted heteroaryl.
  • two adjacent R 1 substituents are joined to form a substituted or unsubstituted heteroaryl.
  • adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted C 3 -C 8 cycloalkyl. In embodiments, two adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted 3 to 8 membered heterocycloalkyl. In embodiments, two adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted C 6 -C 10 aryl. In embodiments, two adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted 5 to 10 membered heteroaryl.
  • two adjacent R 1 substituents are joined to form a substituted or unsubstituted C 3 -C 6 cycloalkyl.
  • two adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted 3 to 6 membered
  • heterocycloalkyl In embodiments, two adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted phenyl. In embodiments, two adjacent -L 1 -R 1 substituents are joined to form a substituted or unsubstituted 5 to 6 membered heteroaryl. It will be understood that when two adjacent L 1 substituents are a bond, two adjacent -L 1 -R 1 substituents that are joined are equivalent to two adjacent -R 1 substituents being joined and may be depicted as such in a formula.
  • R 1A , R 1B , R 1C , and R 1D are independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3
  • R 1A is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 ,
  • a substituted R 1A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 1A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 1A is substituted, it is substituted with at least one substituent group.
  • R 1A when R 1A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 1A is substituted, it is substituted with at least one lower substituent group.
  • R 1A is independently hydrogen. In embodiments, R 1A is independently -CX 1A 3 . In embodiments, R 1A is independently -CHX 1A 2 . In embodiments, R 1A is independently -CH 2 X 1A . In embodiments, R 1A is independently -CN. In
  • R 1A is independently -COOH. In embodiments, R 1A is independently
  • X 1A is independently–F, -Cl, -Br, or -I.
  • R 1A is independently substituted or unsubstituted alkyl (e.g., C1- C8, C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ).
  • R 1A is independently substituted alkyl (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ).
  • R 1A is independently unsubstituted alkyl (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ). In embodiments, R 1A is independently unsubstituted methyl. In embodiments, R 1A is independently unsubstituted ethyl. In embodiments, R 1A is independently unsubstituted propyl. In embodiments, R 1A is independently unsubstituted isopropyl. In embodiments, R 1A is independently unsubstituted tert-butyl.
  • R 1A is independently substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1A is independently substituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1A is independently unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1A is independently substituted or unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6 ). In embodiments, R 1A is independently substituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 -C 6 ). In embodiments, R 1A is independently unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6 ).
  • R 1A is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1A is independently substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1A is independently unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1A is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1A is independently substituted or
  • R 1A is independently substituted or unsubstituted aryl (e.g., C 6 -C 10 or phenyl). In embodiments, R 1A is independently substituted aryl (e.g., C 6 -C 10 or phenyl). In embodiments, R 1A is
  • R 1A is independently unsubstituted aryl (e.g., C 6 -C 10 or phenyl).
  • R 1A is
  • R 1A independently substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1A is independently substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1A is independently unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1B is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 ,
  • a substituted R 1B (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 1B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 1B is substituted, it is substituted with at least one substituent group.
  • R 1B when R 1B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 1B is substituted, it is substituted with at least one lower substituent group.
  • R 1B is independently hydrogen. In embodiments, R 1B is independently -CX 1B 3 . In embodiments, R 1B is independently -CHX 1B 2 . In embodiments, R 1B is independently -CH 2 X 1B . In embodiments, R 1B is independently -CN. In embodiments, R 1B is independently -COOH. In embodiments, R 1B is independently -CONH 2 .
  • X 1B is independently–F, -Cl, -Br, or -I.
  • R 1B is independently substituted or unsubstituted alkyl (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ). In embodiments, R 1B is independently substituted alkyl (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ). In embodiments, R 1B is independently unsubstituted alkyl (e.g., C 1 - C8, C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ). In embodiments, R 1B is independently unsubstituted methyl. In embodiments, R 1B is independently unsubstituted ethyl. In embodiments, R 1B is
  • R 1B independently unsubstituted propyl.
  • R 1B is independently unsubstituted isopropyl.
  • R 1B is independently unsubstituted tert-butyl.
  • R 1B is independently substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1B is independently substituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1B is independently unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1B is independently substituted or unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6 ).
  • R 1B is independently substituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 -C 6 ).
  • R 1B is independently unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6 ).
  • R 1B is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1B is independently substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1B is independently unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R 1B is
  • R 1B is independently substituted aryl (e.g., C 6 -C 10 or phenyl). In embodiments, R 1B is
  • R 1B is independently unsubstituted aryl (e.g., C 6 -C 10 or phenyl).
  • R 1B is independently substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1B is independently substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1B is independently unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • a substituted e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group
  • unsubstituted heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered.
  • R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form a substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • a substituted heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered.
  • substituents bonded to the same nitrogen atom may be joined to form an unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • an unsubstituted heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered.
  • a substituted heterocycloalkyl formed by joining R 1A and R 1B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • when a substituted heterocycloalkyl formed by joining R 1A and R 1B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group.
  • R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form a substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form a substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form an unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1A and R 1B may be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1A and R 1B may be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membere
  • substituents bonded to the same nitrogen atom may be joined to form a substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form an unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • a substituted heteroaryl formed by joining R 1A and R 1B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • when a substituted heteroaryl formed by joining R 1A and R 1B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group.
  • R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form a substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form a substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R 1A and R 1B substituents bonded to the same nitrogen atom may be joined to form an unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1C is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 ,
  • a substituted R 1C (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 1C is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 1C is substituted, it is substituted with at least one substituent group.
  • R 1C when R 1C is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 1C is substituted, it is substituted with at least one lower substituent group.
  • R 1C is independently hydrogen. In embodiments, R 1C is independently -CX 1C 3 . In embodiments, R 1C is independently -CHX 1C 2 . In embodiments, R 1C is independently -CH 2 X 1C . In embodiments, R 1C is independently -CN. In embodiments, R 1C is independently -COOH. In embodiments, R 1C is independently -CONH 2 .
  • X 1C is independently–F, -Cl, -Br, or -I.
  • R 1C is independently substituted or unsubstituted alkyl (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ). In embodiments, R 1C is independently substituted alkyl (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ). In embodiments, R 1C is independently unsubstituted alkyl (e.g., C1- C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ). In embodiments, R 1C is independently unsubstituted methyl. In embodiments, R 1C is independently unsubstituted ethyl. In embodiments, R 1C is
  • R 1C independently unsubstituted propyl.
  • R 1C is independently unsubstituted isopropyl.
  • R 1C is independently unsubstituted tert-butyl.
  • R 1C is independently substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1C is independently substituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1C is independently unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1C is independently substituted or unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 -C 6 ).
  • R 1C is independently substituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 -C 6 ).
  • R 1C is independently unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6 ).
  • R 1C is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1C is independently substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1C is independently unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R 1C is
  • R 1C is independently substituted or unsubstituted aryl (e.g., C 6 -C 10 or phenyl). In embodiments, R 1C is independently substituted aryl (e.g., C 6 -C 10 or phenyl). In embodiments, R 1C is
  • R 1C is independently unsubstituted aryl (e.g., C 6 -C 10 or phenyl).
  • R 1C is independently unsubstituted aryl (e.g., C 6 -C 10 or phenyl).
  • R 1C independently substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1C is independently substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1C is independently unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1D is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 ,
  • a substituted R 1D (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 1D is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 1D is substituted, it is substituted with at least one substituent group.
  • R 1D when R 1D is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 1D is substituted, it is substituted with at least one lower substituent group.
  • R 1D is independently hydrogen. In embodiments, R 1D is independently -CX 1D 3. In embodiments, R 1D is independently -CHX 1D 2. In embodiments, R 1D is independently -CH 2 X 1D . In embodiments, R 1D is independently -CN. In
  • R 1D is independently -COOH. In embodiments, R 1D is independently
  • X 1D is independently–F, -Cl, -Br, or -I.
  • R 1D is independently substituted or unsubstituted alkyl (e.g., C 1 - C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ).
  • R 1D is independently substituted alkyl (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ).
  • R 1D is independently unsubstituted alkyl (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ). In embodiments, R 1D is independently unsubstituted methyl. In embodiments, R 1D is independently unsubstituted ethyl. In embodiments, R 1D is independently unsubstituted propyl. In embodiments, R 1D is independently unsubstituted isopropyl. In embodiments, R 1D is independently unsubstituted tert-butyl.
  • R 1D is independently substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1D is independently substituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1D is independently unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered).
  • R 1D is independently substituted or unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 -C 6 ). In embodiments, R 1D is independently substituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 -C 6 ). In embodiments, R 1D is independently unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6 ).
  • R 1D is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1D is independently substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1D is independently unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1D is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • R 1D is independently substituted or
  • R 1D is independently substituted or unsubstituted aryl (e.g., C 6 -C 10 or phenyl). In embodiments, R 1D is independently substituted aryl (e.g., C 6 -C 10 or phenyl). In embodiments, R 1D is
  • R 1D is independently unsubstituted aryl (e.g., C 6 -C 10 or phenyl).
  • R 1D is independently unsubstituted aryl (e.g., C 6 -C 10 or phenyl).
  • R 1D independently substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1D is independently substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • R 1D is independently unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered
  • R 10 -substituted or unsubstituted aryl e.g., C 6 -C 10 or phenyl
  • R 10 -substituted or unsubstituted heteroaryl e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered.
  • X 1 is independently–F, -Cl, -Br, or–I.
  • R 1 is independently unsubstituted methyl.
  • R 1 is independently unsubstituted ethyl.
  • R 1 is independently R 10 -substituted 2 membered heteroalkyl.
  • R 1 is independently R 10 -substituted methoxy.
  • R 10 - substituted or unsubstituted cycloalkyl e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6
  • R 10 -substituted or unsubstituted heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered
  • R 10 -substituted or unsubstituted aryl e.g., C 6 -C 10 or phenyl
  • R 10 -substituted or unsubstituted heteroaryl e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered.
  • two adjacent–L 1 -R 1 substituents are joined to form an unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6 ), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C 6 -C 10 or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • unsubstituted cycloalkyl e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6
  • unsubstituted heterocycloalkyl e.g
  • two adjacent–L 1 -R 1 substituents are joined to form a R 10 -substituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6 ).
  • two adjacent–L 1 -R 1 substituents are joined to form a R 10 -substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • two adjacent–L 1 -R 1 substituents are joined to form a R 10 -substituted aryl (e.g., C 6 -C 10 or phenyl).
  • two adjacent–L 1 -R 1 substituents are joined to form a R 10 -substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • two adjacent–L 1 -R 1 substituents are joined to form an unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6 ).
  • two adjacent–L 1 -R 1 substituents are joined to form an unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered).
  • two adjacent–L 1 -R 1 substituents are joined to form an unsubstituted aryl (e.g., C 6 -C 10 or phenyl).
  • R 11 -substituted or unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • R 11 -substituted or unsubstituted heteroalkyl e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered
  • R 11 -substituted or unsubstituted cycloalkyl e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6
  • R 11 -substituted or unsubstituted heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered
  • R 12 -substituted or unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • R 12 -substituted or unsubstituted heteroalkyl e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered
  • R 12 -substituted or unsubstituted cycloalkyl e.g., C 3 -C 8 , C 3 -C 6 , C4-C 6 , or C 5 -C 6
  • R 12 -substituted or unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • R 12 unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), R 12 -substituted or unsubstituted aryl (e.g., C 6 -C 10 or phenyl), or R 12 -substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
  • X 11 is independently–F, -Cl, -Br, or–I.
  • R 11 is independently unsubstituted methyl.
  • R 11 is independently
  • unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • unsubstituted heteroalkyl e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered
  • unsubstituted cycloalkyl e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 - C 6
  • unsubstituted heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered
  • unsubstituted aryl e.g., C 6 -C 10 or phenyl
  • X 12 is independently–F, -Cl, -Br, or–I. In embodiments, R 12 is independently unsubstituted methyl. In embodiments, R 12 is independently unsubstituted ethyl.
  • n1 is 0. In embodiments, n1 is 1. In embodiments, n1 is 2. In embodiments, n1 is 3. In embodiments, n1 is 4. In embodiments, m1 is 1. In embodiments, m1 is 2. In embodiments, v1 is 1. In embodiments, v1 is 2. [0278] In embodiments, z1 is independently an integer from 0 to 4. In embodiments, z1 is 0. In embodiments, z1 is 1. In embodiments, z1 is 2.
  • R 2 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3
  • a substituted R 2 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 2 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 2 is substituted, it is substituted with at least one substituent group.
  • R 2 when R 2 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 2 is substituted, it is substituted with at least one lower substituent group.
  • R 2 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)
  • R 2 is independently hydrogen. In embodiments, R 2 is independently unsubstituted methyl. In embodiments, R 2 is independently unsubstituted ethyl. In embodiments, R 2 is independently unsubstituted propyl. In embodiments, R 2 is independently unsubstituted n-propyl. In embodiments, R 2 is independently unsubstituted isopropyl. In embodiments, R 2 is independently unsubstituted butyl. In embodiments, R 2 is independently unsubstituted n- butyl. In embodiments, R 2 is independently unsubstituted isobutyl. In embodiments, R 2 is independently unsubstituted tert-butyl.
  • R 2 is independently unsubstituted pentyl.
  • R 2 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3
  • R 2 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OC
  • R 2 is independently -CCl 3 .
  • R 2 is independently -CBr 3 .
  • R 2 is independently -CF 3 .
  • R 2 is independently -CI 3 .
  • R 2 is independently -CH 2 Cl.
  • R 2 is independently -CH 2 Br.
  • R 2 is independently -CH 2 F.
  • R 2 is independently -CH 2 I.
  • R 2 is independently -CHCl 2 .
  • R 2 is independently -CHBr 2 .
  • R 2 is independently -CHF 2 .
  • R 2 is independently -CHI 2 .
  • R 2 is independently unsubstituted C 1 -C 6 alkyl. In embodiments, R 2 is independently unsubstituted C 1 -C 4 alkyl. In embodiments, R 2 is independently unsubstituted methyl. In embodiments, R 2 is independently unsubstituted ethyl. In embodiments, R 2 is independently unsubstituted propyl. In embodiments, R 2 is independently unsubstituted n-propyl. In embodiments, R 2 is independently unsubstituted isopropyl. In embodiments, R 2 is independently unsubstituted butyl. In embodiments, R 2 is independently unsubstituted n-butyl.
  • R 2 is independently unsubstituted isobutyl. In embodiments, R 2 is independently unsubstituted tert-butyl. In embodiments, R 2 is independently unsubstituted pentyl. In embodiments, R 2 is independently unsubstituted hexyl. In embodiments, R 2 is independently unsubstituted C 3 -C 6 cycloalkyl.
  • R 3 and R 4 are independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -
  • R 3 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2
  • a substituted R 3 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 3 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 3 is substituted, it is substituted with at least one substituent group.
  • R 3 when R 3 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 3 is substituted, it is substituted with at least one lower substituent group.
  • R 3 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O
  • R 3 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2
  • R 3 is independently halogen. In embodiments, R 3 is independently –F. In embodiments, R 3 is independently–Cl. In embodiments, R 3 is independently–Br. In embodiments, R 3 is independently–I. In embodiments, R 3 is independently -CCl 3 . In embodiments, R 3 is independently -CBr 3 . In embodiments, R 3 is independently -CF 3 . In embodiments, R 3 is independently -CI 3 . In embodiments, R 3 is independently -CH 2 Cl. In embodiments, R 3 is independently -CH 2 Br. In embodiments, R 3 is independently -CH 2 F. In embodiments, R 3 is independently -CH 2 I.
  • R 3 is independently -CHCl 2 . In embodiments, R 3 is independently -CHBr 2 . In embodiments, R 3 is independently -CHF 2 . In embodiments, R 3 is independently -CHI 2 . In embodiments, R 3 is independently unsubstituted C 1 -C 4 alkyl. In embodiments, R 3 is independently unsubstituted methyl. In embodiments, R 3 is independently unsubstituted methyl. In embodiments, R 3 is independently unsubstituted ethyl. In embodiments, R 3 is independently unsubstituted propyl. In embodiments, R 3 is independently unsubstituted n-propyl.
  • R 3 is independently unsubstituted isopropyl. In embodiments, R 3 is independently unsubstituted butyl. In embodiments, R 3 is independently unsubstituted n-butyl. In embodiments, R 3 is independently unsubstituted isobutyl. In embodiments, R 3 is independently unsubstituted tert-butyl. [0291] In embodiments, z3 is 0. In embodiments, z3 is 1. In embodiments, z3 is 2.
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2
  • heterocycloalkyl e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered
  • substituted e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group
  • unsubstituted aryl e.g., C 6 -C 10 or phenyl
  • substituted e.g., substituted with at least one substituent group, size- limited substituent group, or lower substituent group
  • unsubstituted heteroaryl e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered.
  • a substituted R 4 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 4 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 4 is substituted, it is substituted with at least one substituent group.
  • R 4 when R 4 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 4 is substituted, it is substituted with at least one lower substituent group.
  • a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by joining two adjacent R 4 substituents is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R 4 substituents when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R 4 substituents is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R 4 substituents is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted cycloalkyl, substituted
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2
  • R 4 is independently halogen. In embodiments, R 4 is independently –F. In embodiments, R 4 is independently–Cl. In embodiments, R 4 is independently–Br. In embodiments, R 4 is independently–I. In embodiments, R 4 is independently–OH. In embodiments, R 4 is independently unsubstituted C 1 -C 4 alkyl. In embodiments, R 4 is independently unsubstituted methyl. In embodiments, R 4 is independently unsubstituted ethyl. In embodiments, R 4 is independently unsubstituted propyl. In embodiments, R 4 is independently unsubstituted n-propyl.
  • R 4 is independently unsubstituted isopropyl. In embodiments, R 4 is independently unsubstituted butyl. In embodiments, R 4 is independently unsubstituted n-butyl. In embodiments, R 4 is independently unsubstituted isobutyl. In embodiments, R 4 is independently unsubstituted tert-butyl. [0298] In embodiments, R 4 is independently halogen. [0299] In embodiments, R 4 is independently -F.
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OCH 2
  • z4 is independently an integer from 0 to 5. [0303] In embodiments, z4 is 0. In embodiments, z4 is 1. In embodiments, z4 is 2. In embodiments, z4 is 3. In embodiments, z4 is 4. In embodiments, z4 is 5.
  • R 5 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OC
  • a substituted R 5 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 5 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 5 is substituted, it is substituted with at least one substituent group.
  • R 5 when R 5 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 5 is substituted, it is substituted with at least one lower substituent group.
  • R 5 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)
  • R 5 is independently hydrogen. In embodiments, R 5 is independently unsubstituted methyl. In embodiments, R 5 is independently unsubstituted ethyl. In embodiments, R 5 is independently unsubstituted propyl. In embodiments, R 5 is independently unsubstituted n-propyl. In embodiments, R 5 is independently unsubstituted isopropyl. In embodiments, R 5 is independently unsubstituted butyl. In embodiments, R 5 is independently unsubstituted n- butyl. In embodiments, R 5 is independently unsubstituted isobutyl. In embodiments, R 5 is independently unsubstituted tert-butyl.
  • R 5 is independently unsubstituted pentyl.
  • R 5 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3
  • R 5 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 , -OC
  • E is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-phenyl
  • R 16 is independently hydrogen, halogen, -CX 16 3, -CHX 16 2, -CH 2 X 16 , -CN,
  • R 16A , R 16B , R 17A , R 17B , R 18A , R 18B , R 19A , and R 19B are independently hydrogen, -CX 3 , -CHX 2 , -CH 2 X, -CN, -OH, -COOH, -CONH 2 , substituted or unsubstituted alkyl (e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2 ), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C 3 -C 8 , C 3 -C 6 , C 4 -C 6 , or C 5 -C 6 ), substituted or unsubstituted al
  • X, X 16 , X 17 , X 18 and X 19 are independently–F, -Cl, -Br, or–I.
  • n16, n17, n18, and n19 are independently an integer from 0 to 4.
  • m16, m17, m18, m19, v16, v17, v18, and v19 are independently 1 or 2.
  • E is
  • E is a covalent cysteine modifier moiety.
  • E is In embodiments, E is . In
  • E is . In embodiments, E is . In embodiments, E is . In
  • E is . In embodiments, E is In
  • E is . In embodiments, E is In
  • E is . In embodiments, E is In embodiments, E is . In embodiments, E is In embodiments, E is . In embodiments, E is . In embodiments, E is . In embodiments, E is . In embodiments, E is R 16 ,
  • R 17 , R 18 , R 19 , and X 17 are as described herein. [0321] In embodiments, R 1 is independently
  • R 1 is independently .
  • R 16 , R 17 , R 18 , R 19 , and X 17 are as described herein. [0322] In embodiments, R 1 is independently
  • R 1 is independently a covalent cysteine modifier moiety.
  • R 1 is independently . In embodiments, R 1 is
  • R 1 is independently In
  • R 1 is independently . In embodiments, R 1 is independently . In embodiments, R 1 is independently . In embodiments, R 1 is independently . In embodiments, R 1 is independently . In
  • R 1 is independently . In embodiments, R 1 is independently . In embodiments, R 1 is independently . In embodiments, R 1 is independently . In embodiments, R 1 is independently . In
  • R 1 is independently . In embodiments, R 1 is independently . In embodiments, R 1 is independently . In embodiments, R 1 is independently . In embodiments, R 1 is
  • R 1 is independently .
  • R 1 is independently .
  • R 16 , R 17 , R 18 , R 19 , and X 17 are as described herein.
  • X may independently be–F.
  • X may independently be–Cl.
  • X may independently be–Br.
  • X may independently be–I.
  • X 16 may independently be–F.
  • X 16 may independently be–Cl.
  • X 16 may independently be–Br.
  • X 16 may independently be–I.
  • X 17 may
  • n16 may independently be 0. n16 may independently be 1. n16 may independently be 2. n16 may independently be 3. n16 may independently be 4. n17 may independently be 0. n17 may independently be 0. n17 may independently be 1. n17 may independently be 2. n17 may independently be 3. n17 may independently be 4. n18 may independently be 0.
  • n18 may independently be 1. n18 may independently be 2. n18 may independently be 3. n18 may independently be 4. n19 may independently be 0. n19 may independently be 1. n19 may independently be 2. n19 may independently be 3. n19 may independently be 4. [0327] v16 may independently be 1. v16 may independently be 2. v17 may independently be 1. v17 may independently be 2. v18 may independently be 1. v18 may independently be 2. v19 may independently be 1. v19 may independently be 2. [0328] m16 may independently be 1. m16 may independently be 2. m17 may each
  • R 16A , R 16B , R 17A , R 17B , R 18A , R 18B , R 19A , and R 19B are examples of substituents.
  • substituted e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group
  • unsubstituted alkyl e.g., C 1 -C 8 , C 1 -C 6 , C 1 -C 4 , or C 1 -C 2
  • substituted e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group
  • unsubstituted heteroalkyl e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered
  • substituted e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group
  • unsubstituted cycloalkyl e.
  • a substituted R 16A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 16A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 16A is substituted, it is substituted with at least one substituent group.
  • R 16A when R 16A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 16A is substituted, it is substituted with at least one lower substituent group.
  • a substituted R 16B e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl
  • R 16B is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 16B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • R 16B when R 16B is substituted, it is substituted with at least one substituent group. In embodiments, when R 16B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 16B is substituted, it is substituted with at least one lower substituent group.
  • a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 16A and R 16B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl or the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 16A and R 16B bonded to the same nitrogen when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 16A and R 16B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 16A and R 16B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 16A and R 16B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group.
  • a substituted R 17A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 17A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 17A is substituted, it is substituted with at least one substituent group.
  • R 17A when R 17A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 17A is substituted, it is substituted with at least one lower substituent group.
  • a substituted R 17B e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl
  • R 17B is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 17B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • R 17B when R 17B is substituted, it is substituted with at least one substituent group. In embodiments, when R 17B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 17B is substituted, it is substituted with at least one lower substituent group.
  • a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 17A and R 17B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl or the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 17A and R 17B bonded to the same nitrogen when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 17A and R 17B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 17A and R 17B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 17A and R 17B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group.
  • a substituted R 18A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 18A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 18A is substituted, it is substituted with at least one substituent group.
  • R 18A when R 18A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 18A is substituted, it is substituted with at least one lower substituent group.
  • a substituted R 18B e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl
  • R 18B is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 18B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • R 18B when R 18B is substituted, it is substituted with at least one substituent group. In embodiments, when R 18B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 18B is substituted, it is substituted with at least one lower substituent group.
  • a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 18A and R 18B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl or the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 18A and R 18B bonded to the same nitrogen when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 18A and R 18B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 18A and R 18B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 18A and R 18B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group.
  • a substituted R 19A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 19A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 19A is substituted, it is substituted with at least one substituent group.
  • R 19A when R 19A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 19A is substituted, it is substituted with at least one lower substituent group.
  • a substituted R 19B e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl
  • R 19B is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 19B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • R 19B when R 19B is substituted, it is substituted with at least one substituent group. In embodiments, when R 19B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 19B is substituted, it is substituted with at least one lower substituent group.
  • a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 19A and R 19B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl or the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different.
  • a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 19A and R 19B bonded to the same nitrogen when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 19A and R 19B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 19A and R 19B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R 19A and R 19B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group.
  • R 16 is independently hydrogen, halogen, -CX 16 3 , -CHX 16 2 , -CH 2 X 16 , -CN, -SO n16 R 16A , -SO v16 NR 16A R 16B , -NH NR 16A R 16B , -ONR 16A R 16B ,
  • a substituted R 16 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 16 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 16 is substituted, it is substituted with at least one substituent group.
  • R 16 when R 16 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 16 is substituted, it is substituted with at least one lower substituent group.
  • R 16 is independently hydrogen. In embodiments, R 16 is independently halogen. In embodiments, R 16 is independently–CN. In embodiments, R 16 is independently unsubstituted methyl. In embodiments, R 16 is independently unsubstituted ethyl. In embodiments, R 16 is independently unsubstituted propyl. In embodiments, R 16 is independently unsubstituted isopropyl. In embodiments, R 16 is independently unsubstituted butyl.
  • R 16 is independently unsubstituted tert-butyl. In embodiments, R 16 is independently–CH 2 Ph. In embodiments, R 16 is independently -F. In embodiments, R 16 is independently -Cl. In embodiments, R 16 is independently -Br. In embodiments, R 16 is independently -I. In embodiments, R 16 is independently unsubstituted methoxy. In embodiments, R 16 is independently unsubstituted ethoxy. In embodiments, R 16 is
  • R 16 is independently -CF 3 . In embodiments, R 16 is independently -CCl 3 . In embodiments, R 16 is independently -CX 16 3 . In embodiments, R 16 is independently -OH. In embodiments, R 16 is independently -NH 2 . In embodiments, R 16 is independently -COOH. In embodiments, R 16 is independently -CONH 2 . In embodiments, R 16 is independently -NO 2 . In embodiments, R 16 is independently -SH. In embodiments, R 16 is independently -SO 3 H. In embodiments, R 16 is independently -SO 4 H. In embodiments, R 16 is independently -SO 2 NH 2 . In embodiments, R 16 is independently -NH NH 2 . In embodiments, R 16 is independently -ONH 2 . In embodiments, R 16 is independently -NH C(O)NHNH 2 . In embodiments, R 16 is independently
  • R 16 is independently -NHSO 2 H. In embodiments, R 16 is independently -NHC(O)H. In embodiments, R 16 is independently -NHC(O)OH. In embodiments, R 16 is independently -NHOH. [0345] In embodiments, R 16A is independently hydrogen. In embodiments, R 16A is independently -CX3. In embodiments, R 16A is independently -CN. In embodiments, R 16A is independently -COOH. In embodiments, R 16A is independently -CONH 2 . In embodiments, R 16A is independently -CHX 2 . In embodiments, R 16A is independently -CH 2 X. In
  • R 16A is independently unsubstituted methyl. In embodiments, R 16A is independently unsubstituted ethyl. In embodiments, R 16A is independently unsubstituted propyl. In embodiments, R 16A is independently unsubstituted isopropyl. In embodiments, R 16A is independently unsubstituted butyl. In embodiments, R 16A is independently unsubstituted tert-butyl. [0346] In embodiments, R 16B is independently hydrogen. In embodiments, R 16B is independently -CX 3 . In embodiments, R 16B is independently -CN. In embodiments, R 16B is independently -COOH. In embodiments, R 16B is independently -CONH 2 . In embodiments, R 16B is independently -CHX2. In embodiments, R 16B is independently -CH 2 X. In
  • R 16B is independently unsubstituted methyl. In embodiments, R 16B is independently unsubstituted ethyl. In embodiments, R 16B is independently unsubstituted propyl. In embodiments, R 16B is independently unsubstituted isopropyl. In embodiments, R 16B is independently unsubstituted butyl. In embodiments, R 16B is independently unsubstituted tert-butyl.
  • R 17 is independently hydrogen, halogen, -CX 17 3, -CHX 17 2, -CH 2 X 17 , -CN, -SO n17 R 17A , -SO v17 NR 17A R 17B , -NH NR 17A R 17B , -ONR 17A R 17B ,
  • a substituted R 17 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 17 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 17 is substituted, it is substituted with at least one substituent group.
  • R 17 when R 17 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 17 is substituted, it is substituted with at least one lower substituent group.
  • R 17 is independently hydrogen. In embodiments, R 17 is independently halogen. In embodiments, R 17 is independently–CN. In embodiments, R 17 is independently unsubstituted methyl. In embodiments, R 17 is independently unsubstituted ethyl. In embodiments, R 17 is independently unsubstituted propyl. In embodiments, R 17 is independently unsubstituted isopropyl. In embodiments, R 17 is independently unsubstituted butyl.
  • R 17 is independently unsubstituted tert-butyl. In embodiments, R 17 is independently–CH 2 Ph. In embodiments, R 17 is independently -F. In embodiments, R 17 is independently -Cl. In embodiments, R 17 is independently -Br. In embodiments, R 17 is independently -I. In embodiments, R 17 is independently unsubstituted methoxy. In embodiments, R 17 is independently unsubstituted ethoxy. In embodiments, R 17 is
  • R 17 is independently -CF 3 . In embodiments, R 17 is independently -CCl 3 . In embodiments, R 17 is independently -CX 17 3 . In embodiments, R 17 is independently -OH. In embodiments, R 17 is independently -NH 2 . In embodiments, R 17 is independently -COOH. In embodiments, R 17 is independently -CONH 2 . In embodiments, R 17 is independently -NO 2 . In embodiments, R 17 is independently -SH. In embodiments, R 17 is independently -SO 3 H. In embodiments, R 17 is independently -SO 4 H. In embodiments, R 17 is independently -SO 2 NH 2 . In embodiments, R 17 is independently -NH NH 2 . In embodiments, R 17 is independently -ONH 2 . In embodiments, R 17 is independently -NH C(O)NHNH 2 . In embodiments, R 17 is independently
  • R 17 is independently -NHSO 2 H. In embodiments, R 17 is independently -NHC(O)H. In embodiments, R 17 is independently -NHC(O)OH. In embodiments, R 17 is independently -NHOH. [0350] In embodiments, R 17A is independently hydrogen. In embodiments, R 17A is independently -CX3. In embodiments, R 17A is independently -CN. In embodiments, R 17A is independently -COOH. In embodiments, R 17A is independently -CONH 2 . In embodiments, R 17A is independently -CHX 2 . In embodiments, R 17A is independently -CH 2 X. In
  • R 17A is independently unsubstituted methyl. In embodiments, R 17A is independently unsubstituted ethyl. In embodiments, R 17A is independently unsubstituted propyl. In embodiments, R 17A is independently unsubstituted isopropyl. In embodiments, R 17A is independently unsubstituted butyl. In embodiments, R 17A is independently unsubstituted tert-butyl. [0351] In embodiments, R 17B is independently hydrogen. In embodiments, R 17B is independently -CX 3 . In embodiments, R 17B is independently -CN. In embodiments, R 17B is independently -COOH. In embodiments, R 17B is independently -CONH 2 . In embodiments, R 17B is independently -CHX2. In embodiments, R 17B is independently -CH 2 X. In
  • R 17B is independently unsubstituted methyl. In embodiments, R 17B is independently unsubstituted ethyl. In embodiments, R 17B is independently unsubstituted propyl. In embodiments, R 17B is independently unsubstituted isopropyl. In embodiments, R 17B is independently unsubstituted butyl. In embodiments, R 17B is independently unsubstituted tert-butyl.
  • R 18 is independently hydrogen, halogen, -CX 18 3, -CHX 18 2, -CH 2 X 18 , -CN, -SO n18 R 18A , -SO v18 NR 18A R 18B , -NH NR 18A R 18B , -ONR 18A R 18B ,
  • a substituted R 18 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 18 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 18 is substituted, it is substituted with at least one substituent group.
  • R 18 when R 18 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 18 is substituted, it is substituted with at least one lower substituent group.
  • R 18 is independently hydrogen. In embodiments, R 18 is independently halogen. In embodiments, R 18 is independently–CN. In embodiments, R 18 is independently unsubstituted methyl. In embodiments, R 18 is independently unsubstituted ethyl. In embodiments, R 18 is independently unsubstituted propyl. In embodiments, R 18 is independently unsubstituted isopropyl. In embodiments, R 18 is independently unsubstituted butyl.
  • R 18 is independently unsubstituted tert-butyl. In embodiments, R 18 is independently–CH 2 Ph. In embodiments, R 18 is independently -F. In embodiments, R 18 is independently -Cl. In embodiments, R 18 is independently -Br. In embodiments, R 18 is independently -I. In embodiments, R 18 is independently unsubstituted methoxy. In embodiments, R 18 is independently unsubstituted ethoxy. In embodiments, R 18 is independently -CF 3 . In embodiments, R 18 is independently -CCl 3 . In embodiments, R 18 is independently -CX 18 3 . In embodiments, R 18 is independently -OH.
  • R 18 is independently -NH 2 . In embodiments, R 18 is independently -COOH. In embodiments, R 18 is independently -CONH 2 . In embodiments, R 18 is independently -NO 2 . In embodiments, R 18 is independently -SH. In embodiments, R 18 is independently -SO 3 H. In embodiments, R 18 is independently -SO 4 H. In embodiments, R 18 is independently -SO 2 NH 2 . In embodiments, R 18 is independently -NH NH 2 . In embodiments, R 18 is independently -ONH 2 . In embodiments, R 18 is independently -NH C(O)NHNH 2 . In embodiments, R 18 is independently
  • R 18 is independently -NHSO 2 H. In embodiments, R 18 is independently -NHC(O)H. In embodiments, R 18 is independently -NHC(O)OH. In embodiments, R 18 is independently -NHOH. [0355] In embodiments, R 18A is independently hydrogen. In embodiments, R 18A is independently -CX 3 . In embodiments, R 18A is independently -CN. In embodiments, R 18A is independently -COOH. In embodiments, R 18A is independently -CONH 2 . In embodiments, R 18A is independently -CHX 2 . In embodiments, R 18A is independently -CH 2 X. In
  • R 18A is independently unsubstituted methyl. In embodiments, R 18A is independently unsubstituted ethyl. In embodiments, R 18A is independently unsubstituted propyl. In embodiments, R 18A is independently unsubstituted isopropyl. In embodiments, R 18A is independently unsubstituted butyl. In embodiments, R 18A is independently unsubstituted tert-butyl. [0356] In embodiments, R 18B is independently hydrogen. In embodiments, R 18B is independently -CX 3 . In embodiments, R 18B is independently -CN. In embodiments, R 18B is independently -COOH. In embodiments, R 18B is independently -CONH 2 . In embodiments, R 18B is independently -CHX2. In embodiments, R 18B is independently -CH 2 X. In
  • R 18B is independently unsubstituted methyl. In embodiments, R 18B is independently unsubstituted ethyl. In embodiments, R 18B is independently unsubstituted propyl. In embodiments, R 18B is independently unsubstituted isopropyl. In embodiments, R 18B is independently unsubstituted butyl. In embodiments, R 18B is independently unsubstituted tert-butyl.
  • R 19 is independently hydrogen, halogen, -CX 19 3, -CHX 19 2, -CH 2 X 19 , -CN, -SOn19R 19A , -SOv19NR 19A R 19B , -NH NR 19A R 19B , -ONR 19A R 19B , -NHC(O)NHNR 19A R 19B , -NH C(O)NR 19A R 19B , -N(O)m19, -NR 19A R 19B , -C(O)R 19A ,
  • a substituted R 19 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R 19 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R 19 is substituted, it is substituted with at least one substituent group.
  • R 19 when R 19 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R 19 is substituted, it is substituted with at least one lower substituent group.
  • R 19 is independently hydrogen. In embodiments, R 19 is independently halogen. In embodiments, R 19 is independently–CN. In embodiments, R 19 is independently unsubstituted methyl. In embodiments, R 19 is independently unsubstituted ethyl. In embodiments, R 19 is independently unsubstituted propyl. In embodiments, R 19 is independently unsubstituted isopropyl. In embodiments, R 19 is independently unsubstituted butyl.
  • R 19 is independently unsubstituted tert-butyl. In embodiments, R 19 is independently–CH 2 Ph. In embodiments, R 19 is independently -F. In embodiments, R 19 is independently -Cl. In embodiments, R 19 is independently -Br. In embodiments, R 19 is independently -I. In embodiments, R 19 is independently unsubstituted methoxy. In embodiments, R 19 is independently unsubstituted ethoxy. In embodiments, R 19 is
  • R 19 is independently -CF 3 . In embodiments, R 19 is independently -CCl 3 . In embodiments, R 19 is independently -CX 19 3 . In embodiments, R 19 is independently -OH. In embodiments, R 19 is independently -NH 2 . In embodiments, R 19 is independently -COOH. In embodiments, R 19 is independently -CONH 2 . In embodiments, R 19 is independently -NO 2 . In embodiments, R 19 is independently -SH. In embodiments, R 19 is independently -SO 3 H. In embodiments, R 19 is independently -SO 4 H. In embodiments, R 19 is independently -SO 2 NH 2 . In embodiments, R 19 is independently -NH NH 2 . In embodiments, R 19 is independently -ONH 2 . In embodiments, R 19 is independently -NH C(O)NHNH 2 . In embodiments, R 19 is independently
  • R 19 is independently -NHSO 2 H. In embodiments, R 19 is independently -NHC(O)H. In embodiments, R 19 is independently -NHC(O)OH. In embodiments, R 19 is independently -NHOH. [0360] In embodiments, R 19A is independently hydrogen. In embodiments, R 19A is independently -CX 3 . In embodiments, R 19A is independently -CN. In embodiments, R 19A is independently -COOH. In embodiments, R 19A is independently -CONH 2 . In embodiments, R 19A is independently -CHX 2 . In embodiments, R 19A is independently -CH 2 X. In
  • R 19A is independently unsubstituted methyl. In embodiments, R 19A is independently unsubstituted ethyl. In embodiments, R 19A is independently unsubstituted propyl. In embodiments, R 19A is independently unsubstituted isopropyl. In embodiments, R 19A is independently unsubstituted butyl. In embodiments, R 19A is independently unsubstituted tert-butyl. [0361] In embodiments, R 19B is independently hydrogen. In embodiments, R 19B is independently -CX 3 . In embodiments, R 19B is independently -CN. In embodiments, R 19B is independently -COOH. In embodiments, R 19B is independently -CONH 2 . In embodiments, R 19B is independently -CHX 2 . In embodiments, R 19B is independently -CH 2 X. In
  • R 1.1 substituent group when an R 1.1 substituent group is substituted, the R 1.1 substituent group is substituted with one or more second substituent groups denoted by R 1.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 1.2 substituent group when an R 1.2 substituent group is substituted, the R 1.2 substituent group is substituted with one or more third substituent groups denoted by R 1.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1 , R 1.1 , R 1.2 , and R 1.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 1 , R 1.1 , R 1.2 , and R 1.3 , respectively.
  • R 1 substituents when two adjacent R 1 substituents are optionally joined to form a moiety that is substituted (e.g., a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R 1.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1.1 when an R 1.1 substituent group is substituted, the R 1.1 substituent group is substituted with one or more second substituent groups denoted by R 1.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 1.2 substituent group when an R 1.2 substituent group is substituted, the R 1.2 substituent group is substituted with one or more third substituent groups denoted by R 1.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1 , R 1.1 , R 1.2 , and R 1.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 1 , R 1.1 , R 1.2 , and R 1.3 , respectively.
  • R 1.2 substituent group when an R 1.2 substituent group is substituted, the R 1.2 substituent group is substituted with one or more third substituent groups denoted by R 1.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1.3 has values corresponding to the values of L WW , R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein L WW , R WW , R WW.1 , R WW.2 , and R WW.3 correspond to L 1 , R 1 , R 1.1 , R 1.2 , and R 1.3 , respectively.
  • R 1A when R 1A is substituted, R 1A is substituted with one or more first substituent groups denoted by R 1A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R 1A.1 substituent group is substituted, the R 1A.1 substituent group is substituted with one or more second substituent groups denoted by R 1A.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 1A.2 substituent group when an R 1A.2 substituent group is substituted, the R 1A.2 substituent group is substituted with one or more third substituent groups denoted by R 1A.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1A , R 1A.1 , R 1A.2 , and R 1A.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 1A , R 1A.1 , R 1A.2 , and R 1A.3 , respectively.
  • R 1B when R 1B is substituted, R 1B is substituted with one or more first substituent groups denoted by R 1B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R 1B.1 substituent group is substituted, the R 1B.1 substituent group is substituted with one or more second substituent groups denoted by R 1B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 1B.2 substituent group when an R 1B.2 substituent group is substituted, the R 1B.2 substituent group is substituted with one or more third substituent groups denoted by R 1B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1B , R 1B.1 , R 1B.2 , and R 1B.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 1B , R 1B.1 , R 1B.2 , and R 1B.3 , respectively.
  • R 1A and R 1B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 1A.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1A.1 when an R 1A.1 substituent group is substituted, the R 1A.1 substituent group is substituted with one or more second substituent groups denoted by R 1A.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 1A.2 substituent group when an R 1A.2 substituent group is substituted, the R 1A.2 substituent group is substituted with one or more third substituent groups denoted by R 1A.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1A , R 1A.1 , R 1A.2 , and R 1A.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 1A , R 1A.1 , R 1A.2 , and R 1A.3 , respectively.
  • R 1A and R 1B when R 1A and R 1B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 1B.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1B.1 when an R 1B.1 substituent group is substituted, the R 1B.1 substituent group is substituted with one or more second substituent groups denoted by R 1B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 1B.2 substituent group when an R 1B.2 substituent group is substituted, the R 1B.2 substituent group is substituted with one or more third substituent groups denoted by R 1B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1B , R 1B.1 , R 1B.2 , and R 1B.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 1B , R 1B.1 , R 1B.2 , and R 1B.3 , respectively.
  • R 1C when R 1C is substituted, R 1C is substituted with one or more first substituent groups denoted by R 1C.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R 1C.1 substituent group is substituted, the R 1C.1 substituent group is substituted with one or more second substituent groups denoted by R 1C.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 1C.2 substituent group when an R 1C.2 substituent group is substituted, the R 1C.2 substituent group is substituted with one or more third substituent groups denoted by R 1C.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1C , R 1C.1 , R 1C.2 , and R 1C.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 1C , R 1C.1 , R 1C.2 , and R 1C.3 , respectively.
  • R 1D when R 1D is substituted, R 1D is substituted with one or more first substituent groups denoted by R 1D.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1D.1 when an R 1D.1 substituent group is substituted, the R 1D.1 substituent group is substituted with one or more second substituent groups denoted by R 1D.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 1D.2 substituent group when an R 1D.2 substituent group is substituted, the R 1D.2 substituent group is substituted with one or more third substituent groups denoted by R 1D.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 1D , R 1D.1 , R 1D.2 , and R 1D.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 1D , R 1D.1 , R 1D.2 , and R 1D.3 , respectively.
  • R 2 when R 2 is substituted, R 2 is substituted with one or more first substituent groups denoted by R 2.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 2.1 substituent group when an R 2.1 substituent group is substituted, the R 2.1 substituent group is substituted with one or more second substituent groups denoted by R 2.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 2.2 substituent group when an R 2.2 substituent group is substituted, the R 2.2 substituent group is substituted with one or more third substituent groups denoted by R 2.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 2 , R 2.1 , R 2.2 , and R 2.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 2 , R 2.1 , R 2.2 , and R 2.3 , respectively.
  • R 3 when R 3 is substituted, R 3 is substituted with one or more first substituent groups denoted by R 3.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 3.1 substituent group when an R 3.1 substituent group is substituted, the R 3.1 substituent group is substituted with one or more second substituent groups denoted by R 3.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R 3.2 substituent group is substituted, the R 3.2 substituent group is substituted with one or more third substituent groups denoted by R 3.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 3 , R 3.1 , R 3.2 , and R 3.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 3 , R 3.1 , R 3.2 , and R 3.3 , respectively.
  • R 4 when R 4 is substituted, R 4 is substituted with one or more first substituent groups denoted by R 4.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 4.1 substituent group when an R 4.1 substituent group is substituted, the R 4.1 substituent group is substituted with one or more second substituent groups denoted by R 4.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 4.2 substituent group when an R 4.2 substituent group is substituted, the R 4.2 substituent group is substituted with one or more third substituent groups denoted by R 4.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 4 , R 4.1 , R 4.2 , and R 4.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 4 , R 4.1 , R 4.2 , and R 4.3 , respectively.
  • R 4 substituents when two adjacent R 4 substituents are optionally joined to form a moiety that is substituted (e.g., a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R 4.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 4.1 when an R 4.1 substituent group is substituted, the R 4.1 substituent group is substituted with one or more second substituent groups denoted by R 4.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 4.2 substituent group when an R 4.2 substituent group is substituted, the R 4.2 substituent group is substituted with one or more third substituent groups denoted by R 4.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 4 , R 4.1 , R 4.2 , and R 4.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 4 , R 4.1 , R 4.2 , and R 4.3 , respectively.
  • R 5 when R 5 is substituted, R 5 is substituted with one or more first substituent groups denoted by R 5.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 5.1 substituent group when an R 5.1 substituent group is substituted, the R 5.1 substituent group is substituted with one or more second substituent groups denoted by R 5.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 5.2 substituent group when an R 5.2 substituent group is substituted, the R 5.2 substituent group is substituted with one or more third substituent groups denoted by R 5.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 5 , R 5.1 , R 5.2 , and R 5.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 5 , R 5.1 , R 5.2 , and R 5.3 , respectively.
  • R 10 when R 10 is substituted, R 10 is substituted with one or more first substituent groups denoted by R 10.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 10.1 substituent group when an R 10.1 substituent group is substituted, the R 10.1 substituent group is substituted with one or more second substituent groups denoted by R 10.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 10.2 substituent group when an R 10.2 substituent group is substituted, the R 10.2 substituent group is substituted with one or more third substituent groups denoted by R 10.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 10 , R 10.1 , R 10.2 , and R 10.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 10 , R 10.1 , R 10.2 , and R 10.3 , respectively.
  • R 11 when R 11 is substituted, R 11 is substituted with one or more first substituent groups denoted by R 11.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 11.1 substituent group when an R 11.1 substituent group is substituted, the R 11.1 substituent group is substituted with one or more second substituent groups denoted by R 11.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 11.2 substituent group when an R 11.2 substituent group is substituted, the R 11.2 substituent group is substituted with one or more third substituent groups denoted by R 11.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 11 , R 11.1 , R 11.2 , and R 11.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 11 , R 11.1 , R 11.2 , and R 11.3 , respectively.
  • R 12 when R 12 is substituted, R 12 is substituted with one or more first substituent groups denoted by R 12.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 12.1 substituent group when an R 12.1 substituent group is substituted, the R 12.1 substituent group is substituted with one or more second substituent groups denoted by R 12.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R 12.2 substituent group is substituted, the R 12.2 substituent group is substituted with one or more third substituent groups denoted by R 12.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 12 , R 12.1 , R 12.2 , and R 12.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 12 , R 12.1 , R 12.2 , and R 12.3 , respectively.
  • R 16 when R 16 is substituted, R 16 is substituted with one or more first substituent groups denoted by R 16.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 16.1 substituent group when an R 16.1 substituent group is substituted, the R 16.1 substituent group is substituted with one or more second substituent groups denoted by R 16.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R 16.2 substituent group is substituted, the R 16.2 substituent group is substituted with one or more third substituent groups denoted by R 16.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 16 , R 16.1 , R 16.2 , and R 16.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 16 , R 16.1 , R 16.2 , and R 16.3 , respectively.
  • R 16A when R 16A is substituted, R 16A is substituted with one or more first substituent groups denoted by R 16A.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 16A.1 substituent group when an R 16A.1 substituent group is substituted, the R 16A.1 substituent group is substituted with one or more second substituent groups denoted by R 16A.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 16A.2 substituent group when an R 16A.2 substituent group is substituted, the R 16A.2 substituent group is substituted with one or more third substituent groups denoted by R 16A.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 16A , R 16A.1 , R 16A.2 , and R 16A.3 have values
  • R 16B when R 16B is substituted, R 16B is substituted with one or more first substituent groups denoted by R 16B.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 16B.1 substituent group when an R 16B.1 substituent group is substituted, the R 16B.1 substituent group is substituted with one or more second substituent groups denoted by R 16B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 16B.2 substituent group when an R 16B.2 substituent group is substituted, the R 16B.2 substituent group is substituted with one or more third substituent groups denoted by R 16B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 16B , R 16B.1 , R 16B.2 , and R 16B.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 16B , R 16B.1 , R 16B.2 , and R 16B.3 , respectively.
  • R 16A and R 16B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 16A.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 16A.1 when an R 16A.1 substituent group is substituted, the R 16A.1 substituent group is substituted with one or more second substituent groups denoted by R 16A.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 16A , R 16A.1 , R 16A.2 , and R 16A.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 16A , R 16A.1 , R 16A.2 , and R 16A.3 , respectively.
  • R 16A and R 16B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 16B.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 16B.1 when an R 16B.1 substituent group is substituted, the R 16B.1 substituent group is substituted with one or more second substituent groups denoted by R 16B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 16B.2 substituent group when an R 16B.2 substituent group is substituted, the R 16B.2 substituent group is substituted with one or more third substituent groups denoted by R 16B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 16B , R 16B.1 , R 16B.2 , and R 16B.3 have values
  • R 17 when R 17 is substituted, R 17 is substituted with one or more first substituent groups denoted by R 17.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • the R 17.1 substituent group when an R 17.1 substituent group is substituted, the R 17.1 substituent group is substituted with one or more second substituent groups denoted by R 17.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R 17.2 substituent group is substituted, the R 17.2 substituent group is substituted with one or more third substituent groups denoted by R 17.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 17 , R 17.1 , R 17.2 , and R 17.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 17 , R 17.1 , R 17.2 , and R 17.3 , respectively.
  • R 17A when R 17A is substituted, R 17A is substituted with one or more first substituent groups denoted by R 17A.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 17A , R 17A.1 , R 17A.2 , and R 17A.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 17A , R 17A.1 , R 17A.2 , and R 17A.3 , respectively.
  • R 17B when R 17B is substituted, R 17B is substituted with one or more first substituent groups denoted by R 17B.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 17B.1 substituent group when an R 17B.1 substituent group is substituted, the R 17B.1 substituent group is substituted with one or more second substituent groups denoted by R 17B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 17B.2 substituent group when an R 17B.2 substituent group is substituted, the R 17B.2 substituent group is substituted with one or more third substituent groups denoted by R 17B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 17B , R 17B.1 , R 17B.2 , and R 17B.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 17B , R 17B.1 , R 17B.2 , and R 17B.3 , respectively.
  • R 17A and R 17B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 17A.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 17A.1 when an R 17A.1 substituent group is substituted, the R 17A.1 substituent group is substituted with one or more second substituent groups denoted by R 17A.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 17A , R 17A.1 , R 17A.2 , and R 17A.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 17A , R 17A.1 , R 17A.2 , and R 17A.3 , respectively.
  • R 17A and R 17B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 17B.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 17B.1 when an R 17B.1 substituent group is substituted, the R 17B.1 substituent group is substituted with one or more second substituent groups denoted by R 17B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 17B.2 substituent group when an R 17B.2 substituent group is substituted, the R 17B.2 substituent group is substituted with one or more third substituent groups denoted by R 17B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 17B , R 17B.1 , R 17B.2 , and R 17B.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 17B , R 17B.1 , R 17B.2 , and R 17B.3 , respectively.
  • R 18 when R 18 is substituted, R 18 is substituted with one or more first substituent groups denoted by R 18.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 18.1 substituent group when an R 18.1 substituent group is substituted, the R 18.1 substituent group is substituted with one or more second substituent groups denoted by R 18.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R 18.2 substituent group is substituted, the R 18.2 substituent group is substituted with one or more third substituent groups denoted by R 18.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 18 , R 18.1 , R 18.2 , and R 18.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 18 , R 18.1 , R 18.2 , and R 18.3 , respectively.
  • R 18A when R 18A is substituted, R 18A is substituted with one or more first substituent groups denoted by R 18A.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 18A.1 substituent group when an R 18A.1 substituent group is substituted, the R 18A.1 substituent group is substituted with one or more second substituent groups denoted by R 18A.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 18A.2 substituent group when an R 18A.2 substituent group is substituted, the R 18A.2 substituent group is substituted with one or more third substituent groups denoted by R 18A.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 18A , R 18A.1 , R 18A.2 , and R 18A.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 18A , R 18A.1 , R 18A.2 , and R 18A.3 , respectively.
  • R 18B when R 18B is substituted, R 18B is substituted with one or more first substituent groups denoted by R 18B.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 18B.1 substituent group when an R 18B.1 substituent group is substituted, the R 18B.1 substituent group is substituted with one or more second substituent groups denoted by R 18B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 18B.2 substituent group when an R 18B.2 substituent group is substituted, the R 18B.2 substituent group is substituted with one or more third substituent groups denoted by R 18B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 18B , R 18B.1 , R 18B.2 , and R 18B.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 18B , R 18B.1 , R 18B.2 , and R 18B.3 , respectively.
  • R 18A and R 18B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 18A.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 18A.1 when an R 18A.1 substituent group is substituted, the R 18A.1 substituent group is substituted with one or more second substituent groups denoted by R 18A.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 18A , R 18A.1 , R 18A.2 , and R 18A.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 18A , R 18A.1 , R 18A.2 , and R 18A.3 , respectively.
  • R 18A and R 18B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 18B.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 18B.1 when an R 18B.1 substituent group is substituted, the R 18B.1 substituent group is substituted with one or more second substituent groups denoted by R 18B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 18B.2 substituent group when an R 18B.2 substituent group is substituted, the R 18B.2 substituent group is substituted with one or more third substituent groups denoted by R 18B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 18B , R 18B.1 , R 18B.2 , and R 18B.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 18B , R 18B.1 , R 18B.2 , and R 18B.3 , respectively.
  • R 19 when R 19 is substituted, R 19 is substituted with one or more first substituent groups denoted by R 19.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 19.1 substituent group when an R 19.1 substituent group is substituted, the R 19.1 substituent group is substituted with one or more second substituent groups denoted by R 19.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R 19.2 substituent group is substituted, the R 19.2 substituent group is substituted with one or more third substituent groups denoted by R 19.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 19 , R 19.1 , R 19.2 , and R 19.3 have values corresponding to the values of R WW , R WW.1 , R WW.2 , and R WW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 19 , R 19.1 , R 19.2 , and R 19.3 , respectively.
  • R 19A when R 19A is substituted, R 19A is substituted with one or more first substituent groups denoted by R 19A.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 19A.1 substituent group when an R 19A.1 substituent group is substituted, the R 19A.1 substituent group is substituted with one or more second substituent groups denoted by R 19A.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 19A.2 substituent group when an R 19A.2 substituent group is substituted, the R 19A.2 substituent group is substituted with one or more third substituent groups denoted by R 19A.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 19A , R 19A.1 , R 19A.2 , and R 19A.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 19A , R 19A.1 , R 19A.2 , and R 19A.3 , respectively.
  • R 19B when R 19B is substituted, R 19B is substituted with one or more first substituent groups denoted by R 19B.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 19B.1 substituent group when an R 19B.1 substituent group is substituted, the R 19B.1 substituent group is substituted with one or more second substituent groups denoted by R 19B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 19B.2 substituent group when an R 19B.2 substituent group is substituted, the R 19B.2 substituent group is substituted with one or more third substituent groups denoted by R 19B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 19B , R 19B.1 , R 19B.2 , and R 19B.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 19B , R 19B.1 , R 19B.2 , and R 19B.3 , respectively.
  • R 19A and R 19B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 19A.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 19A.1 when an R 19A.1 substituent group is substituted, the R 19A.1 substituent group is substituted with one or more second substituent groups denoted by R 19A.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 19A , R 19A.1 , R 19A.2 , and R 19A.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 19A , R 19A.1 , R 19A.2 , and R 19A.3 , respectively.
  • R 19A and R 19B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
  • the moiety is substituted with one or more first substituent groups denoted by R 19B.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 19B.1 when an R 19B.1 substituent group is substituted, the R 19B.1 substituent group is substituted with one or more second substituent groups denoted by R 19B.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R 19B.2 substituent group when an R 19B.2 substituent group is substituted, the R 19B.2 substituent group is substituted with one or more third substituent groups denoted by R 19B.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R 19B , R 19B.1 , R 19B.2 , and R 19B.3 have values
  • R WW , R WW.1 , R WW.2 , and R WW.3 correspond to R 19B , R 19B.1 , R 19B.2 , and R 19B.3 , respectively.
  • R L 1 when L 1 is substituted, L 1 is substituted with one or more first substituent groups denoted by R L1.1 as explained in the definitions section above in the description of“first substituent group(s)”.
  • R L1.1 substituent group when an R L1.1 substituent group is substituted, the R L1.1 substituent group is substituted with one or more second substituent groups denoted by R L1.2 as explained in the definitions section above in the description of “first substituent group(s)”.
  • R L1.2 substituent group when an R L1.2 substituent group is substituted, the R L1.2 substituent group is substituted with one or more third substituent groups denoted by R L1.3 as explained in the definitions section above in the description of“first substituent group(s)”.
  • L 1 , R L1.1 , R L1.2 , and R L1.3 have values corresponding to the values of L WW , R LWW.1 , R LWW.2 , and R LWW.3 , respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein L WW , R LWW.1 , R LWW.2 , and R LWW.3 are L 1 , R L1.1 , R L1.2 , and R L1.3 , respectively.
  • the compound is , wherein R 1 , R 2 , and R 4 are as described herein, including in embodiments. In embodiments, R 1 and R 4 are each independently halogen.
  • R 2 is independently C 1 -C 6 alkyl. In embodiments, R 2 is independently unsubstituted C 1 -C 4 alkyl. In embodiments, R 2 is independently unsubstituted methyl. In embodiments, R 2 is independently unsubstituted ethyl. In embodiments, R 2 is independently C 3 -C 6 cycloalkyl.
  • the compound is wherein R 2 is as described herein, including in embodiments.
  • R 2 is independently C 1 -C 6 alkyl.
  • R 2 is independently unsubstituted C 1 -C 4 alkyl.
  • R 2 is independently unsubstituted methyl.
  • R 2 is independently unsubstituted ethyl.
  • R 2 is independently C 3 -C 6 cycloalkyl.
  • the compound is wherein R 2 is as described herein, including in embodiments.
  • R 2 is independently C 1 -C 6 alkyl.
  • R 2 is independently unsubstituted C 1 -C 4 alkyl.
  • R 2 is independently unsubstituted methyl.
  • R 2 is independently unsubstituted ethyl.
  • R 2 is independently C 3 -C 6 cycloalkyl.
  • the compound is wherein R 2 is as described herein, including in embodiments.
  • R 2 is independently C 1 -C 6 alkyl.
  • R 2 is independently unsubstituted C 1 -C 4 alkyl.
  • R 2 is independently unsubstituted methyl.
  • R 2 is independently unsubstituted ethyl.
  • R 2 is independently C 3 -C 6 cycloalkyl.
  • the compound is wherein R 1 and R 4 are each independently halogen.
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is .
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoe)-2-aminoethyl
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is .
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • the compound is a compound described herein.
  • the compound, or a pharmaceutically acceptable salt thereof is the compound described herein.
  • the compound, or a pharmaceutically acceptable salt thereof is the pharmaceutically acceptable salt of a compound described herein.
  • the compound is not wherein R 1
  • R 4 are each independently halogen.
  • the compound is not
  • the compound is not
  • the compound is not
  • the compound is not .
  • the compound is not , wherein R 16 , R 17 , and R 18 are as defined herein.
  • R 1 is not–F.
  • R 4 is not–F.
  • R 1 is independently–F
  • R 4 is not–F.
  • R 1 is not–F.
  • a pharmaceutical composition including a compound described herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
  • a pharmaceutical composition including a compound described herein and a pharmaceutically acceptable excipient.
  • the pharmaceutical composition includes an effective amount of the compound.
  • the pharmaceutical composition includes a therapeutically effective amount of the compound.
  • the pharmaceutical composition includes a second agent (e.g., an anti-cancer agent).
  • the pharmaceutical composition includes a second agent in a therapeutically effective amount.
  • a method for treating cancer in a subject in need thereof including administering to the subject in need thereof a therapeutically effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method for treating cancer in a subject in need thereof the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof for use in a method of treating cancer including administering to a subject in need thereof a therapeutically effective amount of the compound, or a
  • the cancer is renal cell carcinoma, follicular lymphoma, glioblastoma, colorectal cancer, endometrial cancer, or lung cancer.
  • the cancer is renal cell carcinoma.
  • the cancer is follicular lymphoma.
  • the cancer is glioblastoma.
  • the cancer is colorectal cancer.
  • the cancer is endometrial cancer.
  • the cancer is lung cancer. In embodiments, the cancer is pancreatic cancer. In embodiments, the cancer is melanoma. In embodiments, the cancer is breast cancer. In embodiments, the cancer is acute myeloid leukemia. In embodiments, the cancer is endometrial cancer. In embodiments, the cancer is non-Hodgkin lymphoma. In
  • the cancer is mantle cell lymphoma.
  • the method includes immunomodulation.
  • the method includes cancer immunotherapy.
  • a method for treating a neurodegenerative disease the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method for treating a neurodegenerative disease the method including administering to a subject in need thereof an effective amount of a compound described herein.
  • the compound is included in a therapeutically effective amount.
  • the method is a method of treating nerve damage, the method including administering to a subject in need thereof an effective amount of a compound described herein.
  • the neurodegenerative disease is Huntington Disease. In embodiments, the neurodegenerative disease is Alzheimer Disease. In embodiments, the neurodegenerative disease is Parkinson’s Disease. In embodiments, the neurodegenerative disease is frontotemporal dementia. In embodiments, the method includes reducing protein aggregates (e.g., in the brain). In embodiments, the method includes reducing TDP-43 aggregates (e.g., in the brain). In embodiments, the neurodegenerative disease is amyotrophic lateral sclerosis. In embodiments, the neurodegenerative disease is chronic traumatic encephalopathy. In embodiments, the neurodegenerative disease is traumatic brain injury (e.g., concussion).
  • a compound described herein, or a pharmaceutically acceptable salt thereof for use in a method of treating a neurodegenerative disease including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • neurodegenerative disease the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • a method for treating a metabolic disease the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method for treating a metabolic disease the method including administering to a subject in need thereof an effective amount of a compound described herein.
  • the compound is included in a therapeutically effective amount.
  • the metabolic disease is diabetes.
  • the metabolic disease is type I diabetes.
  • the metabolic disease is type II diabetes.
  • the metabolic disease is obesity.
  • the metabolic disease is metabolic syndrome.
  • the metabolic disease is a mitochondrial disease (e.g., dysfunction of mitochondria or aberrant mitochondrial function).
  • a compound described herein, or a pharmaceutically acceptable salt thereof for use in a method of treating a metabolic disease including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for the treatment of a metabolic disease the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • a method for treating aging including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method for treating aging including administering to a subject in need thereof an effective amount of a compound described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof, for use in a method of treating aging including administering to a subject in need thereof a therapeutically effective amount of the compound, or a
  • a compound described herein, or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for the treatment of aging, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • a method of extending lifespan e.g., increased 1 day, increased 2 days, increased 3 days, increased 7 days, increased 1 month, increased 6 months, increased 12 months, increased 2 years, increased 5 years, etc.
  • the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method of extending lifespan e.g., increased 1 day, increased 2 days, increased 3 days, increased 7 days, increased 1 month, increased 6 months, increased 12 months, increased 2 years, increased 5 years, etc.
  • administering including administering to a subject in need thereof an effective amount of a compound described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof for use in a method of extending lifespan (e.g., increased 1 day, increased 2 days, increased 3 days, increased 7 days, increased 1 month, increased 6 months, increased 12 months, increased 2 years, increased 5 years, etc.) or inducing longevity, including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • lifespan e.g., increased 1 day, increased 2 days, increased 3 days, increased 7 days, increased 1 month, increased 6 months, increased 12 months, increased 2 years, increased 5 years, etc.
  • a compound described herein, or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for extending lifespan (e.g., increased 1 day, increased 2 days, increased 3 days, increased 7 days, increased 1 month, increased 6 months, increased 12 months, increased 2 years, increased 5 years, etc.) or inducing longevity, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of mTORC1 in a subject in need thereof the method including administering to the subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of mTORC1 in a subject in need thereof including administering to the subject in need thereof an effective amount of a compound described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of mTORC1 including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • a compound described herein, or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for reducing the level of activity of mTORC1, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of mTORC1 in a cell the method including contacting a Vacuolar H + -ATPase in the cell with a compound as described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of mTORC1 in a cell including contacting a Vacuolar H + -ATPase in the cell with a compound as described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of mTORC1 in a cell including contacting a Vacuolar H + -ATPase in the cell with the compound, or a
  • a compound described herein, or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for reducing the level of activity of mTORC1 in a cell, the use including contacting a Vacuolar H + -ATPase in the cell with the compound, or a pharmaceutically acceptable salt thereof.
  • the method includes dephosphorylation and/or nuclear
  • the method includes increasing the level of TFEB transcriptional targets in a cell or subject.
  • the method includes increasing the level of CTSA (e.g., RefSeq NM_000308.3 or RefSeq NP_000299.2), CTSB (e.g., RefSeq
  • CTSF e.g., RefSeq NM_003793.3 or RefSeq NP_003784.2
  • HEXB e.g., RefSeq NM_000521.4 or RefSeq NP_000512.2
  • CLN3 e.g., RefSeq NM_000086.2 or RefSeq NP_000077.1
  • CLCN7 e.g., RefSeq NM_001287.5 or RefSeq NP_001278.1
  • ATP6V0D1 e.g., RefSeq NM_004691.4 or RefSeq NP_004682.2
  • ATP6V0E1 e.g., RefSeq NM_003945.3 or RefSeq NP_003936.1
  • LAMP1 e.g., RefSeq NM_00556
  • the method includes increasing the level of TFE3 transcriptional targets in a cell or subject.
  • a method of reducing the level of activity of a Vacuolar H + - ATPase the method including contacting the Vacuolar H + -ATPase with a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of a Vacuolar H + - ATPase including contacting the Vacuolar H + -ATPase with a compound described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof for use in reducing the level of activity of a Vacuolar H + -ATPase including contacting contacting the Vacuolar H + -ATPase with the compound, or a pharmaceutically acceptable salt thereof.
  • a compound described herein, or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for reducing the level of activity of a Vacuolar H + -ATPase, the use including contacting the Vacuolar H + -ATPase with the compound, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of a Vacuolar H + - ATPase protein complex the method including contacting an ATP6V1A in the Vacuolar H + - ATPase protein complex with a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of a Vacuolar H + - ATPase protein complex including contacting an ATP6V1A in the Vacuolar H + - ATPase protein complex with a compound described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of a Vacuolar H + -ATPase protein complex including contacting contacting an ATP6V1A in the Vacuolar H + -ATPase protein complex with the compound, or a pharmaceutically acceptable salt thereof.
  • a compound described herein, or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for reducing the level of activity of a Vacuolar H + -ATPase protein complex, the use including contacting an ATP6V1A in the Vacuolar H + -ATPase protein complex with the compound, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of mTORC1 in a cell the method including contacting an ATP6V1A in the cell with a compound as described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of mTORC1 in a cell including contacting an ATP6V1A in the cell with a compound as described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of mTORC1 in a cell including contacting an ATP6V1A in the cell with the compound, or a pharmaceutically acceptable salt thereof.
  • a compound described herein, or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for reducing the level of activity of mTORC1 in a cell, the use including contacting an ATP6V1A in the cell with the compound, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of an ATP6V1A the method including contacting the ATP6V1A with a compound described herein, or a pharmaceutically acceptable salt thereof.
  • a method of reducing the level of activity of an ATP6V1A the method including contacting the ATP6V1A with a compound described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof for use in reducing the level of activity of an ATP6V1A including contacting the ATP6V1A with the compound, or a pharmaceutically acceptable salt thereof.
  • the method includes reducing the activity of mTORC1 more than reducing the activity of mTORC2 (e.g., at least 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9.2, 3, 4, 5, 6, 7, 8,910, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 100000, 1000000-fold more).
  • the method includes reducing the activity of mTORC1 more than reducing the activity of mTORC2 (e.g., about 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9.2, 3, 4, 5, 6, 7, 8,910, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 100000, 1000000-fold more).
  • the method includes reducing the activity of mTORC1 more than reducing the activity of mTORC2 (e.g., 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9.2, 3, 4, 5, 6, 7, 8,910, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 100000, 1000000-fold more).
  • the method includes reducing (e.g., reduced relative to a control) mTORC1 signaling by preventing mTORC1 localization to the lysosome.
  • the method includes modulating (e.g., preventing the formation) of the Ragulator complex. In embodiments, the method includes reducing (e.g., reduced relative to a control) mTORC1 signaling by causing an accumulation of Ragulator complex in the lysosome.
  • the method includes preventing the activation of the Ragulator complex. In embodiments, the method includes preventing the binding of mTORC1 to the Ragulator complex. In embodiments, the method includes preventing the formation of the Ragulator complex. [0482] In embodiments, the method includes inhibiting the activation of the Ragulator complex. In embodiments, the method includes inhibiting the binding of mTORC1 to the Ragulator complex. In embodiments, the method includes inhibiting the formation of the Ragulator complex. In embodiments, the method includes inhibiting the amino-acid-induced localization of mTORC1 to the lysosome. In embodiments, the method includes inhibiting the binding between the Vacuolar H + -ATPase protein complex and the Ragulator.
  • the method includes inhibiting the activity of Rag activity. In embodiments, the method includes inhibiting the GTPase activity of Rag. In embodiments, the method includes inhibiting the Rag GTPase-induced localization of mTORC1 to the lysosome. In embodiments, the method includes increased acidification of a lysosome. In embodiments, the method includes inhibiting the phosphorylation of 4EBP1. In embodiments, the method includes inhibiting the phosphorylation of S6. In embodiments, the method includes inhibiting the activity of Vacuolar H + -ATPase protein complex. In embodiments, the method includes increasing autophagy.
  • the method includes inhibiting the Rag-A/B Rag-C/D complex interaction with Raptor in mTORC1. In embodiments, the method includes inhibiting the phosphorylation of ULK1 kinase. In embodiments, the method includes increasing the nuclear translocation and/or activation of TFEB transcription factor. [0483] In an aspect is provided a method for increasing autophagy in a subject in need thereof, the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0484] In an aspect is provided a method for increasing autophagy in a subject in need thereof, the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein.
  • a compound described herein, or a pharmaceutically acceptable salt thereof for use in a method of increasing autophagy including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof.
  • Vacuolar H + -ATPase protein complex covalently bonded to a compound described herein, or a pharmaceutically acceptable salt thereof, which may be referred to herein as a Vacuolar H + -ATPase protein complex-compound complex.
  • a Vacuolar H + -ATPase protein complex covalently bonded to a compound described herein, which may be referred to herein as a Vacuolar H + -ATPase protein complex-compound complex.
  • the Vacuolar H + -ATPase protein complex is a human Vacuolar H + -ATPase protein complex.
  • the compound is provided in a therapeutically effective amount.
  • the compound contacts an amino acid corresponding to C277 of human ATP6V1A in the Vacuolar H + -ATPase protein complex.
  • the compound covalently binds an amino acid corresponding to C277 of human ATP6V1A in the Vacuolar H + -ATPase protein complex.
  • an ATP6V1A in a Vacuolar H + -ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex) is covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein).
  • a compound e.g., compound described herein or a portion of a compound described herein.
  • an ATP6V1A in a Vacuolar H + -ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex) is irreversibly covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein).
  • an ATP6V1A in a Vacuolar H + -ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex) is reversibly covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein).
  • an ATP6V1A in a Vacuolar H + -ATPase protein complex e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex
  • an ATP6V1A in a Vacuolar H + -ATPase protein complex is covalently bonded to a portion of a compound (e.g., compound described herein).
  • an ATP6V1A in a Vacuolar H + -ATPase protein complex (e.g., human
  • ATP6V1A in a human Vacuolar H + -ATPase protein complex is irreversibly covalently bonded to a portion of a compound described herein.
  • an ATP6V1A in a Vacuolar H + -ATPase protein complex e.g., human ATP6V1A in a human Vacuolar H + - ATPase protein complex
  • the compound described herein is bonded to a cysteine residue (e.g., residue corresponding to Cys277 of human ATP6V1A) of the ATP6V1A protein (e.g., human ATP6V1A protein).
  • the ATP6V1A in a Vacuolar H + -ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex) covalently bonded to a compound described herein is the product of a reaction between the ATP6V1A in a Vacuolar H + -ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex) and a compound described herein.
  • a Vacuolar H + -ATPase protein complex e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex
  • the covalently bonded ATP6V1A in a Vacuolar H + -ATPase protein complex e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex
  • compound described herein are the remnants of the reactant ATP6V1A in a Vacuolar H + -ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex) and compound, wherein each reactant now participates in the covalent bond between the ATP6V1A in a Vacuolar H + - ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex) and compound.
  • the remnant of the E substitutent is a linker including a covalent bond between the ATP6V1A in a Vacuolar H + -ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex) and the remainder of the compound described herein.
  • an ATP6V1A in a Vacuolar H + -ATPase protein complex e.g., human
  • ATP6V1A in a human Vacuolar H + -ATPase protein complex is covalently bonded to a compound described herein, the compound described herein forms a remnant of the pre- reacted compound wherein a bond connects the remnant of the compound to the remnant of the ATP6V1A in a Vacuolar H + -ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H + -ATPase protein complex) (e.g., cysteine sulfur, sulfur of amino acid
  • the ATP6V1A protein is a human ATP6V1A protein.
  • human ATP6V1A protein has a sequence described herein.
  • the compound is provided in a therapeutically effective amount.
  • the compound contacts an amino acid corresponding to C277 of human ATP6V1A.
  • the compound covalently binds an amino acid corresponding to C277 of human ATP6V1A.
  • an ATP6V1A protein e.g., human ATP6V1A
  • a compound e.g., compound described herein or a portion of a compound described herein.
  • an ATP6V1A protein (e.g., human ATP6V1A) is irreversibly covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein).
  • the ATP6V1A protein (e.g., human ATP6V1A) is reversibly covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein).
  • the ATP6V1A protein (e.g., human ATP6V1A) is covalently bonded to a portion of a compound (e.g., compound described herein).
  • the ATP6V1A protein (e.g., human ATP6V1A) is irreversibly covalently bonded to a portion of a compound described herein.
  • the ATP6V1A protein (e.g., human ATP6V1A) is reversibly covalently bonded to a portion of a compound described herein.
  • the compound described herein is bonded to a cysteine residue (e.g., residue corresponding to Cys277 of human ATP6V1A) of the ATP6V1A protein (e.g., human ATP6V1A).
  • the ATP6V1A protein covalently bonded to a compound described herein is the product of a reaction between the ATP6V1A protein and a compound described herein.
  • the covalently bonded ATP6V1A protein and compound described herein are the remnants of the reactant ATP6V1A protein and compound, wherein each reactant now participates in the covalent bond between the ATP6V1A protein and or compound.
  • the remnant of the E substitutent is a linker including a covalent bond between the ATP6V1A protein and the remainder of the compound described herein.
  • Embodiment P A compound having the formula:
  • Ring A is a phenyl or 5 to 6 membered heteroaryl
  • Ring B is a phenyl or 5 to 6 membered heteroaryl
  • L 1 is independently a bond, -S(O) 2 -, -N(R 5 )-, -O-, -S-, -C(O)-, -C(O)N(R 5 )-, -N(R 5 )C(O)-, -N(R 5 )C(O)NH-, -NHC(O)N(R 5 )-, -C(O)O-, -OC(O)-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene; R 5 is independently hydrogen
  • R 2 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 , -NH C(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3
  • R 1A , R 1B , R 1C , and R 1D are independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NHC(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3
  • L 1 is independently a bond, -S(O) 2 -, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene;
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -
  • Embodiment P3 The compound of embodiment P1, having the formula:
  • L 1 is independently a bond, -S(O) 2 -, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene;
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -
  • Embodiment P4 The compound of one of embodiments P1 to P3, wherein R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 ,
  • Embodiment P5. The compound of one of embodiments P1 to P3, wherein R 1 is independently halogen.
  • Embodiment P6 The compound of one of embodiments P1 to P3, wherein R 1 is -F.
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI
  • Embodiment P8 The compound of one of embodiments P1 to P6, wherein R 4 is independently halogen.
  • Embodiment P9 The compound of one of embodiments P1 to P6, wherein R 4 is -F.
  • Embodiment P10 The compound of one of embodiments P1 to P9, wherein L 1 is independently -S(O) 2 -, -NH-, or substituted or unsubstituted 5 to 6 membered
  • Embodiment P11 The compound of one of embodiments P1 to P9, wherein L 1 is independently -S(O) 2 -, -NH-, unsubstituted pyrrolidinylene, unsubstituted piperidinylene, or unsubstituted piperazinylene.
  • Embodiment P12 The compound of one of embodiments P1 to P9, wherein L 1 is independently -NH-.
  • Embodiment P13 The compound of one of embodiments P1 to P12 wherein E is
  • R 16 is independently hydrogen, halogen, -CX 16 3 , -CHX 16 2 , -CH 2 X 16 , -CN,
  • R 17 is independently hydrogen, halogen, -CX 17 3 , -CHX 17 2 , -CH 2 X 17 , -CN, -SO n17 R 17A , -SO v17 NR 17A R 17B , -NH NR 17A R 17B , -ONR 17A R 17B , -NHC(O)NHNR 17A R 17B ,
  • R 18 is independently hydrogen, halogen, -CX 18 3 , -CHX 18 2 , -CH 2 X 18 , -CN, -SO n18 R 18A , -SO v18 NR 18A R 18B , -NH NR 18A R 18B , -ONR 18A R 18B , -NHC(O)NHNR 18A R 18B ,
  • R 19 is independently hydrogen, halogen, -CX 19 3 , -CHX 19 2 , -CH 2 X 19 , -CN, -SO n19 R 19A , -SO v19 NR 19A R 19B , -NH NR 19A R 19B , -ONR 19A R 19B , -NHC(O)NHNR 19A R 19B ,
  • R 16A , R 16B , R 17A , R 17B , R 18A , R 18B , R 19A , and R 19B are independently
  • R 16A and R 16B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;
  • R 17A and R 17B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;
  • Embodiment P15 The compound of one of embodiments P1 to P14, wherein the
  • Embodiment P16 A pharmaceutical composition comprising a compound of one of embodiments P1 to P15 and a pharmaceutically acceptable excipient.
  • Embodiment P17 A method for treating cancer in a subject in need thereof, said method comprising administering to the subject in need thereof a therapeutically effective amount of a compound of one of embodiments P1 to P15.
  • Embodiment P18 The method of embodiment P17, wherein said cancer is renal cell carcinoma, follicular lymphoma, glioblastoma, colorectal cancer, endometrial, or lung cancer.
  • Embodiment P19 Embodiment P19.
  • a method of reducing the level of activity of mTORC1 in a subject in need thereof comprising administering to the subject in need thereof an effective amount of a compound of one of embodiments P1 to P15.
  • Embodiment P20 A method of reducing the level of activity of mTORC1 in a cell, the method comprising contacting a Vacuolar H + -ATPase protein complex in said cell with a compound of one of embodiments P1 to P15.
  • Embodiment P21 A method of reducing the level of activity of mTORC1 in a cell, the method comprising contacting an ATP6V1A in said cell with a compound of one of embodiments P1 to P15.
  • Embodiment P22 A method of reducing the level of activity of a Vacuolar H + - ATPase protein complex, the method comprising contacting an ATP6V1A in the Vacuolar H + -ATPase protein complex with a compound of one of embodiments P1 to P15. VII. Additional embodiments
  • Embodiment 1 A compound, or a pharmaceutically acceptable salt thereof, having the formula:
  • Ring A is a phenyl or 5 to 6 membered heteroaryl
  • Ring B is a phenyl or 5 to 6 membered heteroaryl
  • L 1 is independently a bond, -S(O) 2 -, -N(R 5 )-, -O-, -S-, -C(O)-, -C(O)N(R 5 )-,
  • R 5 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl,
  • heterocycloalkyl substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent -L 1 -R 1 substituents may optionally be joined to form a substituted or
  • R 2 is independently hydrogen, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl,
  • R 1A , R 1B , R 1C , and R 1D are independently hydrogen, halogen, -CCl 3 , -CBr 3 ,
  • -CF 3 -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NH NH 2 , -ONH 2 ,
  • L 1 is independently a bond, -S(O) 2 -, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-,
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br,
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br,
  • Embodiment 3 The compound of embodiment 1, having the formula:
  • L 1 is independently a bond, -S(O) 2 -, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-,
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br,
  • L 1 is independently a bond, -S(O) 2 -, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-,
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br,
  • L 1 is independently a bond, -S(O) 2 -, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-,
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br,
  • Embodiment 6 The compound of one of embodiments 1, 4, and 5, wherein R 3 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3
  • Embodiment 7 The compound of one of embodiments 1, 4, and 5, wherein R 3 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , or -CI 3 .
  • Embodiment 8. The compound of one of embodiments 1, 4, and 5, wherein R 3 is independently–Br or -CF 3 .
  • R 1 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 ,
  • Embodiment 10 The compound of one of embodiments 1 to 8, wherein R 1 is independently halogen.
  • Embodiment 11 The compound of one of embodiments 1 to 8, wherein R 1 is independently -F.
  • R 4 is independently halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO 2 , -SH, -SO 3 H, -SO 4 H, -SO 2 NH 2 , -NHNH 2 , -ONH 2 , -NHC(O)NHNH 2 , -NH C(O)NH 2 , -NHSO 2 H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl 3 , -OCBr 3 , -OCF 3 , -OCI 3 ,
  • Embodiment 13 The compound of one of embodiments 1 to 11, wherein R 4 is independently halogen.
  • Embodiment 14 The compound of one of embodiments 1 to 11, wherein R 4 is independently -F.
  • Embodiment 15 The compound of one of embodiments 1 to 14, wherein L 1 is independently -S(O) 2 -, -NH-, or substituted or unsubstituted 5 to 6 membered
  • Embodiment 16 The compound of one of embodiments 1 to 14, wherein L 1 is independently -S(O) 2 -, -NH-, unsubstituted pyrrolidinylene, unsubstituted piperidinylene, or unsubstituted piperazinylene.
  • Embodiment 17 The compound of one of embodiments 1 to 14, wherein L 1 is independently -NH-.
  • Embodiment 18 The compound of one of embodiments 1 to 17, wherein
  • R 16 is independently hydrogen, halogen, -CX 16 3 , -CHX 16 2 , -CH 2 X 16 ,
  • R 17 is independently hydrogen, halogen, -CX 17 3, -CHX 17 2, -CH 2 X 17 , -CN,
  • R 18 is independently hydrogen, halogen, -CX 18 3 , -CHX 18 2 , -CH 2 X 18 , -CN,
  • R 19 is independently hydrogen, halogen, -CX 19 3 , -CHX 19 2 , -CH 2 X 19 , -CN,
  • R 16A , R 16B , R 17A , R 17B , R 18A , R 18B , R 19A , and R 19B are independently
  • R 16A and R 16B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;
  • R 17A and R 17B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;
  • Embodiment 20 The compound of one of embodiments 1 to 17, wherein E is
  • Embodiment 21 The compound of one of embodiments 1 to 3, wherein the
  • Embodiment 22 A pharmaceutical composition comprising a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof, and a
  • Embodiment 23 A method for treating cancer in a subject in need thereof, said method comprising administering to the subject in need thereof a therapeutically effective amount of a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof.
  • Embodiment 24 The method of embodiment 23, wherein said cancer is renal cell carcinoma, follicular lymphoma, glioblastoma, colorectal cancer, endometrial cancer, or lung cancer.
  • Embodiment 25 Embodiment 25.
  • a method of reducing the level of activity of mTORC1 in a subject in need thereof comprising administering to the subject in need thereof an effective amount of a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof.
  • Embodiment 26 A method of reducing the level of activity of mTORC1 in a cell, the method comprising contacting a Vacuolar H + -ATPase protein complex in said cell with a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof.
  • Embodiment 28 A method of reducing the level of activity of a Vacuolar H + - ATPase protein complex, the method comprising contacting an ATP6V1A in the Vacuolar H + -ATPase protein complex with a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof.
  • Example 1 Covalent targeting of the vacuolar H + -ATPase enhances cellular clearance through inhibition of lysosomal mTORC1 signaling
  • Autophagy is a lysosomal degradation pathway that eliminates aggregated proteins and damaged organelles to maintain cellular homeostasis.
  • a major route for activating autophagy involves inhibition of the mTORC1 kinase, but selective and complete mTORC1 inhibition remains beyond the reach of current mTORC1-targeting compounds.
  • EN6 a small-molecule in vivo activator of autophagy that covalently and selectively targets cysteine 277 in the ATP6V1A subunit of the lysosomal v-ATPase, which mediates mTORC1 activation at the lysosome.
  • EN6-mediated ATP6V1A modification impairs mTORC1 lysosomal recruitment via the Rag guanosine triphosphatases, activates autophagy and increases lysosomal acidification. Consistently, EN6 clears TDP-43 aggregates, a causative agent in frontotemporal dementia, in an autophagy-dependent manner. Our results provide insight into how the v-ATPase regulates mTORC1, and reveal a unique approach for enhancing cellular clearance based on covalent inhibition of lysosomal mTORC1 signaling. [0547] Autophagy is central to the maintenance of organismal homeostasis in both physiological and pathological situations.
  • mTORC1 rapamycin complex 1
  • mTORC1 phosphorylates and inhibits a master switch for autophagosome formation, the ULK1 kinase (5,6).
  • mTORC1 blocks the nuclear translocation and activation of the TFEB transcription factors, which functions as a‘master regulator’ of catabolism by coordinately promoting the expression of genes required for autophagosome formation and lysosomal function (5-9).
  • pharmacological activators of autophagy can be beneficial in both cell and animal models of these diseases, by both degrading intracytoplasmic aggregates and by preventing associated cell death (12-15).
  • agents have been discovered that either inhibit or activate autophagy, many of these compounds do not possess the required specificity to activate autophagy in a selective manner, either due to off-target effects or due to multiple functions of a specific target.
  • the allosteric mTORC1 inhibitor, rapamycin results in the relatively specific inhibition of mTORC1 by causing its binding to FK506-binding protein 1A (FKBP1A).
  • rapamycin is an incomplete mTORC1 inhibitor; most notably it largely fails at blocking mTORC1-dependent inhibitory phosphorylation of ULK1 and TFEB and at triggering their pro-catabolic programs.
  • rapamycin-based drugs Rostyroxine-based drugs
  • the recently developed‘ATP-competitive’ compounds block the kinase activity of mTOR toward virtually all substrates. The higher potency and broader range of ATP-competitive mTOR inhibitors has led to promising results in cancer clinical trials;
  • Akt signaling which is an essential survival signal for neuronal cells (19-22).
  • the limitations of current mTOR inhibitors thus create an urgent need to identify new targets that could lead to selective activation of autophagy while avoiding unacceptable toxicities.
  • mTORC1 needs to translocate to the lysosome membrane (5,6).
  • Nutrients primarily amino acids, directly regulate the lysosomal recruitment of mTORC1 by modulating the nucleotide state of the Rag GTPases.
  • the Rags assemble as obligate heterodimers composed of RagA or RagB (which are highly similar to each other) associated with RagC or RagD, and are tethered to the lysosomal membrane by the pentameric
  • Ragulator complex composed of the LAMTOR1-5 proteins (23-25).
  • the Rag GTPases become active by adopting a nucleotide state in which Rag-A/B is GTP-loaded and Rag-C/D is GDP-loaded, and mediate the lysosomal attachment of mTORC1 by directly interacting with the mTORC1 subunit Raptor (23-25).
  • v-ATPase vacuolar H+ ATPase
  • v-ATPase vacuolar H+ ATPase
  • the v-ATPase forms a physical supercomplex with Ragulator and the Rag GTPases, and its integrity and activity are essential for lysosomal mTORC1 recruitment in response to amino acids (28-31).
  • v-ATPase represents a prime target for discovery of small molecules that may simultaneously block mTORC1 activation and enhance autophagic function.
  • chemoproteomics and covalent ligand screening we have discovered a small-molecule activator of autophagy that acts through covalently targeting a unique regulatory cysteine on ATP6V1A, resulting in the complete and selective inactivation of mTORC1 and enhanced cellular clearance of toxic protein aggregates.
  • EN6 The primary site of EN6 was identified as cysteine 277 (C277) of ATP6V1A, the catalytic subunit of the lysosomal v- ATPase (FIG.2B). This site showed an isotopic light-to-heavy (control-to-EN6-treated) ratio of >50 indicating high target engagement of this site compared to other targets.
  • EN6 displaces iodoacetamide-rhodamine (IA-rhodamine) labeling from recombinant human ATP6V1A protein with an IC 50 of 1.7 mM (FIG.2C).
  • v-ATPase interacts with Ragulator-Rags to enable amino acid-dependent recruitment of mTORC1 to the lysosome (28,42). Consistent with an inhibitory mechanism towards this pathway, EN6 treatment completely abrogated amino acid-induced mTORC1 recruitment to LAMP2-positive lysosomes (FIG.3E).
  • amino acids modulate the interaction of FLAG-tagged Ragulator subunit p14 with the v-ATPase (FIG.4A).
  • EN6 decreased the overall binding between the v-ATPase and Ragulator, and rendered this interaction insensitive to amino acids (FIG.4A).
  • TDP43 Tar-binding protein 43
  • EN6-mediated clearance of TDP-43 aggregates was lysosome- and v-ATPase-dependent, as it was prevented by co-treatment with bafilomycin A1 (FIG.5A, FIG.5B).
  • bafilomycin A1 FIG.5A, FIG.5B
  • EN6 is capable of clearing toxic protein aggregates in an autophagy-dependent manner.
  • Three mice cohorts were injected intraperitoneally with vehicle, rapamycin or EN6, and analyzed after 4 hours.
  • mTORC1 signaling was significantly impaired across the heart, kidney, and skeletal muscle, as demonstrated by reduced phosphorylation of S6, whereas autophagy was strongly activated, as shown by heightened LC3BII levels (FIGS.6A-6C).
  • EN6 was somewhat less potent than rapamycin in shutting down p-S6, it was significantly more effective than rapamycin at inhibiting phosphorylation of 4EBP1, consistent with our data in cell lines (FIG.6A).
  • EN6 functions as a complete and selective mTORC1 inhibitor both in cells and in vivo.
  • rapalogues pharmacological modulators of autophagy that mostly act through directly targeting the kinase function mTORC1, such as with rapalogues and ATP-competitive inhibitors. While both rapalogues and ATP-competitive mTORC1 inhibitors have potential therapeutic activity, their clinical utility is hampered by their incomplete mTORC1 inhibition (rapalogues) and concomitant inhibition of mTORC2 (ATP competitors) (44-47). Chronic exposure to rapalogues also inhibits mTORC2, leading to metabolic dysregulation (48,49).
  • EN6 shows promising cellular and in vivo activity
  • this covalent ligand is an early hit that still requires further medicinal chemistry efforts to optimize potency, selectivity, and in vivo bioavailability and efficacy.
  • isoTOP-ABPP studies here show that C277 of ATP6V1A is one of the primary and most highly engaged targets of EN6 in cells
  • EN6 may possess additional off-targets that either exhibit lower degree of engagement or act through reversible interactions.
  • Development of an alkyne-functionalized EN6 probe will aid in future assessment of EN6 selectivity and provide a foundation for additional medicinal chemistry, target engagement, and screening efforts to identify improved ligands against this site.
  • MEF cells stably expressing GFP-LC3-RFP- LC3DG were plated on 96-well plates (Corning; 3904) at 30,000 cells/well and allowed to grow in complete medium overnight. The cells were then incubated with covalent ligands (50 ⁇ M or at indicated concentrations), rapamycin (100 nM), Torin 1 (250 nM) or DMSO solvent control in complete medium (100 ⁇ L) for 24 h.
  • the medium was aspirated and the cells were fixed with 4% paraformaldehyde in PBS (100 ⁇ L) for 10 min, washed with PBS (100 ⁇ L) and assayed in PBS (100 ⁇ L) by SpectraMax i3 (Molecular Devices).
  • GFP fluorescence was measured with excitation and emission at 488 ⁇ 9 nm and 514 ⁇ 15 nm respectively, while RFP fluorescence was measured with excitation and emission at 584 ⁇ 9 nm and 612 ⁇ 15 nm respectively.
  • HEK293A cells stably expressing GFP-LC3-RFP-LC3DG before they were seeded, 96-well plates were coated with fibronectin in PBS (5 ⁇ g/mL, 75 ⁇ L/well) for 1 h at 37 o C. The solution was then aspirated, and cells were plated at 30,000 cells/well, allowed to grow in complete medium overnight, treated and assayed with the same protocol as described above for MEF cells.
  • solutions were aspirated after treatment with the compounds, and the cells were fixed and stained by Hoechst 33342 (13.3 ⁇ g/mL) in formalin (100 ⁇ L) for 15 min.
  • IsoTOP-ABPP chemoproteomic studies IsoTOP-ABPP studies were done as previously reported (35,36). Cells were lysed by probe sonication in PBS and protein concentrations were measured by BCA assay (54). For in situ experiments, cells were treated for 90 min with either DMSO vehicle or covalently-acting small molecule (from 1000X DMSO stock) before cell collection and lysis.
  • proteome samples diluted in PBS 4 mg of proteome per biological replicate
  • a DMSO vehicle or covalently-acting small-molecule for 30 min at room temperature.
  • Proteomes were subsequently labeled with IA-alkyne labeling (100 mM) for 1 h at room temperature.
  • CuAAC was used by sequential addition of tris(2-carboxyethyl)phosphine (1 mM, Sigma), tris[(1- benzyl-1H-1,2,3-triazol-4-yl)methyl]amine (34 mM, Sigma), copper (II) sulfate (1 mM, Sigma), and biotin-linker-azide—the linker functionalized with a TEV protease recognition sequence as well as an isotopically light or heavy valine for treatment of control or treated proteome, respectively.
  • proteomes were precipitated by centrifugation at 6500 x g, washed in ice-cold methanol, combined in a 1:1 control/treated ratio, washed again, then denatured and resolubilized by heating in 1.2% SDS/PBS to 80 °C for 5 minutes.
  • Insoluble components were precipitated by centrifugation at 6500 x g and soluble proteome was diluted in 5 mL 0.2% SDS/PBS. Labeled proteins were bound to avidin-agarose beads (170 ml resuspended beads/sample, Thermo Pierce) while rotating overnight at 4 °C. Bead- linked proteins were enriched by washing three times each in PBS and water, then
  • Peptides were diluted in water and acidified with formic acid (1.2 M, Spectrum) and prepared for analysis. [0571] Mass spectrometry analysis. Peptides from all chemoproteomic experiments were pressure-loaded onto a 250 mm inner diameter fused silica capillary tubing packed with 4 cm of Aqua C18 reverse-phase resin (Phenomenex # 04A-4299) which was previously equilibrated on an Agilent 600 series HPLC using gradient from 100% buffer A to 100% buffer B over 10 min, followed by a 5 min wash with 100% buffer B and a 5 min wash with 100% buffer A.
  • Aqua C18 reverse-phase resin Phenomenex # 04A-4299
  • Heated capillary temperature was set to 200 °C and the nanospray voltage was set to 2.75 kV.
  • Data were extracted in the form of MS1 and MS2 files using Raw Extractor 1.9.9.2 (The Scripps Research Institute) and searched against the Uniprot human database using ProLuCID search methodology in IP2 v.3 (Integrated Proteomics Applications, Inc.) (55). Cysteine residues were searched with a static modification for carboxyaminomethylation (+57.02146) and up to two differential modifications for methionine oxidation and either the light or heavy TEV tags (+464.28596 or +470.29977, respectively). Peptides were required to have at least one tryptic end and to contain the TEV modification.
  • ProLUCID data was filtered through DTASelect to achieve a peptide false-positive rate below 5%. Only those probe-modified peptides that were evident across all two out of three biological replicates were interpreted for their isotopic light to heavy ratios. Those probe-modified peptides that showed ratios >4 were further analyzed as potential targets of the covalently-acting small- molecule. For modified peptides with ratios >4, we filtered these hits for peptides were present in all three biological replicates. For those probe-modified peptide ratios >4, only those peptides with 3 ratios >4 were interpreted, and otherwise replaced with the lowest ratio.
  • lentiviral plasmids and packaging plasmids were transfected into HEK293T cells using PEI transfection method. Viral supernatant was collected 48 hours after transfection and filtered with 0.45 mm filter. The viruses were further concentrated using Lenti-X Concentrator (Clontech, 631231) according to the manufacturer’s instructions. Target cells were plated in 6-well or 10 cm plates with 8 mg/mL polybrene (Millipore, TR-1003-G) and incubated with virus containing media. 24 hours later, the media was changed to fresh media containing 2 mg/mL puromycin
  • Covalent ligand library The synthesis and characterization of the covalent ligands screened here have been previously reported (33-37,59). Compounds starting with“EN” were purchased from Enamine LLC. [0577] Antibodies and reagents for biological experiments.
  • Goat anti-rabbit IgG superclonal secondary antibody-Alexa Fluor 647 was from Thermo Fisher Scientific.
  • IRDye® 800CW Goat anti-Rabbit IgG H + L; 926-32211 was from Li-Cor.
  • Recombinant human ATP6V1A protein (ab132441) was from Abcam; Tetramethylrhodamine-5-iodoacetamide dihydroiodide (6222) was from Setareh Biotech.; Normal goat serum (10%; 50062Z), Hoechst 33342 (H3570) and LysoSensor Yellow/Blue DND-160 (L7545) were from Thermo Fisher Scientific.
  • DMEM Dulbecco's Modified Eagle’s Medium
  • FBS fetal bovine serum
  • Sequencing grade modified trypsin was from Promega.
  • Amino acid starvation and stimulation Sub-confluent cells were rinsed and incubated with RPMI without amino acids supplemented with 2% dialyzed FBS for 50 min, as described (27). Stimulation with amino acids (concentration as in RPMI) was performed for 10 min. Where drug treatment was performed, cells were incubated during the 50 min starvation period and the 10 min stimulation period.
  • Western blotting and immunoprecipitation was performed.
  • Cells were washed twice with ice-cold phosphate-buffered saline (PBS) and lysed in lysis buffer (1% Triton X-100, 10 mM b- glycerol phosphate, 10 mM sodium pyrophosphate, 4 mM EDTA, 40 mM HEPES at pH 7.4, and 1 tablet of EDTA-free protease inhibitors per 50 mL). Cell lysates were cleared by centrifugation in a microcentrifuge at 17,000 g for 10 minutes at 4 °C.
  • lysis buffer 1% Triton X-100, 10 mM b- glycerol phosphate, 10 mM sodium pyrophosphate, 4 mM EDTA, 40 mM HEPES at pH 7.4, and 1 tablet of EDTA-free protease inhibitors per 50 mL.
  • HEK293T cells stably expressing Flag-tagged proteins were lysed as above and 30 mL of a well-mixed 50% slurry of anti-FLAG M2 Affinity Gel (Sigma A2220) was added to each lysate (1 mg/mL) and incubated at 4 °C in a shaker for 1 hour.
  • Immunoprecipitates were washed four times, three times with lysis buffer and once with lysis buffer containing 400 mM NaCl. Immunoprecipitated proteins were denatured by addition of 50 mL of sample buffer and heating to 95 °C for 5 minutes, resolved by SDS-PAGE, and analyzed by immunoblotting.
  • the cells were then incubated with EN6 (at indicated concentrations), Torin 1 (250 nM) or DMSO control for indicated time intervals. After aspiration of the solution, the cells were washed with PBS (350 ⁇ L) and fixed with methanol for 15 min at -20 o C. The cells were rinsed three times with PBS (350 ⁇ L each), and incubated with PBS containing 5% normal goat serum and 0.3% Triton X-100 (300 ⁇ L) for 1 h.
  • EN6 at indicated concentrations
  • Torin 1 250 nM
  • DMSO control DMSO control
  • the cells were washed three times with PBS (350 ⁇ L each) and stained with Hoechst 33342 (5 ⁇ g/mL) in PBS in dark at room temperature for 15 min. After washing with PBS three times (350 ⁇ L each), the cells were imaged in PBS by Zeiss laser scanning microscope (LSM) 710 with a 20 ⁇ or 63 ⁇ oil-immersion objective lens.
  • LSM Zeiss laser scanning microscope
  • Hoechst 33342 was excited with a 405 nm diode laser, and emission was collected on a META detector between 410 and 587 nm.
  • Alexa Fluor 647 was excited with a 633 nm HeNe laser, and emission was collected on a META detector between 638 and 755 nm.
  • HEK-293T or Hela cells were seeded on fibronectin-coated glass coverslips and allowed to attach overnight. On the following day, cells were subjected to either amino acid starvation and stimulation with or without drug incubation and fixed in 4% paraformaldehyde (PFA) for 15 minutes at room temperature. The coverslips were rinsed twice with PBS and cells were permeabilized with 0.1% (w/v) saponin in PBS for 10 minutes.
  • PFA paraformaldehyde
  • the slides were incubated with primary antibodies in 5% normal donkey serum (Jackson ImmunoResearch, 017-000-121) for 1 hour at room temperature, rinsed four times with PBS, and incubated with fluorophore conjugated secondary antibodies derived from goat or donkey (Life Technologies, diluted 1:400 in 5% normal donkey serum) for 1 hour at room
  • HEK293A cells were plated on fibronectin-coated (5 ⁇ g/mL) 8-well Lab Tek borosilicate chambered coverglass slides (Nunc) at 40,000 cells/well and allowed to grow in complete medium overnight.
  • the cells were then incubated with DMSO control, EN6 (50 ⁇ M), bafilomycin A1 (0.2 ⁇ M), or a mixture of EN6 and bafilomycin A1 (50 and 0.2 ⁇ M respectively) at 37 o C for 4 h. After that, LysoSensor DND-160 (2 ⁇ M final concentration) was added to the solution and the cells were stained at 37 o C for 5 min. The solution was then replaced by DPBS and the live cells were imaged by Zeiss LSM 880 with a 40 ⁇ water-immersion objective lens.
  • the ratiometric images, F yellow / F blue were generated by Ratio Plus plugin of ImageJ. For quantification, a threshold value was set as background and the average intensity of the whole image was measured by ImageJ. All experiments were performed in triplicate, and statistical analyses were performed with a two-tailed Student’s t-test (MS Excel).
  • RNA extraction and quantitative RT-PCR were performed using AurumTM Total RNA Mini Kit (Bio-rad) and reverse transcription was performed from 1 mg total RNAs using iScriptTM Reverse Transcription for RT-qPCR (Bio-rad) according to manufacturer’s instruction. All real-time qPCR(qRT-PCR) analyses were performed using StepOnePlus machine (Applied Biosystems) with SsoAdbancedTM
  • the cells were incubated with DMSO control, isopropylthio-b-galactoside (IPTG; 50 ⁇ M), a mixture of EN6 (25 ⁇ M) and IPTG (50 ⁇ M), or a mixture of EN6 (25 ⁇ M), IPTG (50 ⁇ M) and bafilomycin A1 (0.2 ⁇ M) at 37 o C for 7 h.
  • IPTG isopropylthio-b-galactoside
  • EN6 25 ⁇ M
  • IPTG IPTG
  • bafilomycin A1 0.2 ⁇ M
  • the cells were imaged in PBS by Zeiss laser scanning microscope (LSM) 710 with a 20 ⁇ or 63 ⁇ oil-immersion objective lens.
  • LSM Zeiss laser scanning microscope
  • Hoechst 33342 was excited with a 405 nm diode laser, and emission was collected on a META detector between 410 and 483 nm.
  • GFP was excited with a 488 nm Ar laser, and emission was collected on a META detector between 493 and 598 nm.
  • Image analysis was performed by use of ImageJ. A threshold was first set for selection of GFP-TDP-43 aggregate, and a region of interest (ROI) was created over a single cell.
  • ROI region of interest
  • mice were euthanized, and tissues were harvested and lysed in lysis buffer (1% Triton X-100, 10 mM b- glycerol phosphate, 10 mM sodium pyrophosphate, 4 mM EDTA, 40 mM HEPES at pH 7.4, and 1 tablet of EDTA-free protease inhibitors per 50 ml) at 4 o C for 30 min.
  • lysis buffer 1% Triton X-100, 10 mM b- glycerol phosphate, 10 mM sodium pyrophosphate, 4 mM EDTA, 40 mM HEPES at pH 7.4, and 1 tablet of EDTA-free protease inhibitors per 50 ml
  • the lysates were cleared by centrifugation in a microcentrifuge at 21,130 g for 10 minutes at 4°C and protein concentration of supernatant was determined by BCA assay (Thermo Fisher Scientific).
  • the lysates was then diluted to 1.5 mg/mL, mixed with 4 x sample buffer, heated at 95 °C for 5 minutes, resolved by precast 4-20% TGX gels, and analyzed by immunoblotting.
  • Antibodies were obtained from various commercial sources and dilutions were prepared per

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Abstract

Described herein, inter alia, are compounds and methods useful for increasing autophagy.

Description

mTORC1 INHIBITORS FOR ACTIVATING AUTOPHAGY CROSS-REFERENCES TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional Application No.62/791,655, filed January 11, 2019, which is incorporated herein by reference in their entirety and for all purposes. REFERENCE TO A "SEQUENCE LISTING," A TABLE, OR A COMPUTER
PROGRAM LISTING APPENDIX SUBMITTED AS AN ASCII FILE
[0002] The Sequence Listing written in file 052103- 519001WO_Sequence_Listing_ST25.txt, created January 6, 2020, 44,632 bytes, machine format IBM-PC, MS Windows operating system, is hereby incorporated by reference. STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT
[0003] This invention was made with government support under grant no. CA195761 awarded by the National Institutes of Health. The government has certain rights in the invention. BACKGROUND
[0004] Autophagy is central to the maintenance of organismal homeostasis in both physiological and pathological situations. It is an essential, conserved lysosomal degradation pathway that controls the quality of the cytoplasm by eliminating aggregated proteins and damaged organelles. Accordingly, alterations in autophagy have been linked to a wide range of diseases and conditions, including aging, cancer, metabolic disorders, and
neurodegenerative diseases (1-3). Throughout the past decade, autophagy has attracted considerable attention as a target for the development of novel therapeutics. Disclosed herein, inter alia, are solutions to these and other problems in the art. BRIEF SUMMARY
[0005] In an aspect is provided a compound, or a pharmaceutically acceptable salt thereof, having the formula:
Figure imgf000004_0001
[0006] Ring A is a phenyl or 5 to 6 membered heteroaryl. [0007] Ring B is a phenyl or 5 to 6 membered heteroaryl. [0008] L1 is independently a bond, -S(O)2-, -N(R5)-, -O-, -S-, -C(O)-, -C(O)N(R5)-, -N(R5)C(O)-, -N(R5)C(O)NH-, -NHC(O)N(R5)-, -C(O)O-, -OC(O)-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene. [0009] R5 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. [0010] R1 is independently halogen, -CX1 3, -CHX1 2, -CH2X1, -OCX1 3, -OCH2X1,
-OCHX1 2, -CN, -SOn1R1D, -SOv1NR1AR1B, -NHC(O)NR1AR1B, -N(O)m1, -NR1AR1B, -C(O)R1C, -C(O)-OR1C, -C(O)NR1AR1B, -OR1D, -NR1ASO2R1D, -NR1AC(O)R1C, -NR1AC(O)OR1C, -NR1AOR1C, -N3, E, substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent -L1-R1 substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0011] E is an electrophilic moiety. [0012] R2 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. [0013] R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
unsubstituted heteroaryl. [0014] R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
unsubstituted heteroaryl; two adjacent R4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0015] In embodiments, R3 and R4 are independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0016] R1A, R1B, R1C, and R1D are independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R1A and R1B substituents bonded to the same nitrogen atom may be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl. [0017] In embodiments, R1A, R1B, R1C, and R1D are independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0018] X1 is independently–F, -Cl, -Br, or–I. [0019] n1 is independently an integer from 0 to 4. [0020] m1 and v1 are independently 1 or 2. [0021] z1 is independently an integer from 0 to 5. [0022] z3 is independently an integer from 0 to 2. [0023] z4 is independently an integer from 0 to 5. [0024] In an aspect is provided a pharmaceutical composition including a compound described herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. [0025] In an aspect is provided a method for treating cancer in a subject in need thereof, the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0026] In an aspect is provided a method for treating a neurodegenerative disease, the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0027] In an aspect is provided a method for treating a metabolic disease, the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0028] In an aspect is provided a method for treating aging, the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0029] In an aspect is provided a method of reducing the level of activity of mTORC1 in a subject in need thereof, the method including administering to the subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0030] In an aspect is provided a method of reducing the level of activity of mTORC1 in a cell, the method including contacting a Vacuolar H+-ATPase in the cell with a compound as described herein, or a pharmaceutically acceptable salt thereof. [0031] In an aspect is provided a method of reducing the level of activity of a Vacuolar H+- ATPase, the method including contacting the Vacuolar H+-ATPase with a compound described herein, or a pharmaceutically acceptable salt thereof. [0032] In an aspect is provided a method of reducing the level of activity of a Vacuolar H+- ATPase protein complex, the method including contacting a ATP6V1A in the Vacuolar H+- ATPase protein complex with a compound described herein, or a pharmaceutically acceptable salt thereof. [0033] In an aspect is provided a method of reducing the level of activity of mTORC1 in a cell, the method including contacting a ATP6V1A in the cell with a compound as described herein, or a pharmaceutically acceptable salt thereof. [0034] In an aspect is provided a method of reducing the level of activity of an ATP6V1A, the method including contacting the ATP6V1A with a compound described herein, or a pharmaceutically acceptable salt thereof. [0035] In an aspect is provided a method for increasing autophagy in a subject in need thereof, the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0036] In an aspect is provided a Vacuolar H+-ATPase protein complex covalently bonded to a compound described herein, or a pharmaceutically acceptable salt thereof, which may be referred to herein as a Vacuolar H+-ATPase protein complex-compound complex. [0037] In an aspect is provided a ATP6V1A protein covalently bonded to a compound described herein, or a pharmaceutically acceptable salt thereof, which may be referred to herein as a ATP6V1A protein-compound complex. BRIEF DESCRIPTION OF THE DRAWINGS
[0038] FIGS.1A-1F. Covalent ligand screen for autophagy activators. FIG.1A: A covalent ligand screen in MEF cells. MEF cells expressing a fluorescent probe GFP-LC3- RFP-LC3DG to measure autophagic flux 32, were treated with vehicle DMSO or a covalent ligand (50 mM) for 24 h and GFP/RFP ratios were analyzed. From left to right, the covalent ligand or vehicle is: Torin 1, TRH 1-194, Rapamycin, EN6, KEA 1-37, DKM 3-16, DKM 2- 37, DKM 2-98, TRH 1-170, DKM 3-30, TRH 1-168, TRH 1-60, EN2, KEA 1-69, KEA 1- 100, TRH 1-57, DKM 3-3, KEA 1-46, TRH 1-179, TRH 1-58, TRH 1-140, TRH 1-152, EN59, EN53, KEA1-31, TRH 1-78, EN84, TRH 1-20, DKM 3-12, KEA 1-98, KEA 1-40, EN51, TRH 1-12, TRH 1-27, DKM 2-47, DKM 3-36, DKM 3-9, EN8, EN71, DKM 3-7, TRH 1-156, TRH 1-65, DKM 2-85, DKM 2-116, DKM 2-43, KEA 1-91, TRH 1-54, DKM 2- 71, EN62, TRH 1-59, EN54, KEA 1-95, EN48, TRH 1-189, TRH 1-177, KEA 1-45, DKM 3- 29, TRH 1-68, KEA 1-39, DKM 2-94, DKM 2-93, EN37, KEA 1-42, TRH 1-178, KEA 1-97, DKM 3-42, KEA 1-58, TRH 1-53, KEA 1-38, EN58, DKM 3-11, EN10, TRH 1-68, DKM 3- 10, TRH 1-32, EN50, TRH 1-19, KEA 1-85, KEA 1-63, KEA 1-94, EN4, TRH 1-70, TRH 1- 162, EN20, EN70, DKM 2-117, DKM 2-42, DKM 2-114, DKM 3-43, KEA 1-70, EN65, EN66, KEA 1-93, DKM 2-83, KEA 1-48, DKM 3-31, TRH 1-59, TRH 1-56, DKM 2-108, TRH 1-57, EN60, DKM 2-119, DKM 2-50, DKM 3-32, YP 1-42, KEA 1-77, KEA 1-60, KEA 1-67, DKM 3-5, TRH 1-196, EN52, DKM 2-80, TRH 1-58, TRH 1-134, DKM 2-52, EN46, EN75, EN61, EN67, EN26, DMSO, KEA 1-59, EN43, DKM 3-42, EN1, KEA 1-23, DKM 2-76, KEA 1-62, DKM 2-40, TRH 1-56, EN69, DKM 2-97, DKM 2-113, KEA 1-43, TRH 1-65, TRH 1-163, KEA 1-71, TRH 1-135, KEA 1-54, DKM 2-100, TRH 1-135, TRH 1- 27, EN47, KEA 1-22, KEA 1-30, KEA 1-50, KEA 1-78, DKM 3-4, DKM 2-101, TRH 1-149, DKM 3-41, EN18, TRH 1-176, KEA 1-99, EN29, TRH 1-167, KEA 1-56, TRH 1-54, EN3, DKM 2-107, TRH 1-32, KEA 1-32, KEA 1-55, YP 1-36, KEA 1-49, EN68, EN45, KEA 1- 72, DKM 3-8, TRH 1-133, KEA 1-90, DKM 3-15, KEA 1-47, EN57, KEA 1-81, EN40, DKM 2-106, EN64, EN80, DKM 2-49, EN7, DKM 2-60, DKM 2-33, TRH 1-160, DKM 2- 58, KEA 1-61, DKM 3-36, DKM 2-110, DKM 2-48, EN12, KEA 1-68, DKM 2-59, EN49, DKM 2-32, DKM 2-31, DKM 3-32, EN5, EN15, TRH 1-55, DKM 2-47, EN16, EN55, EN19, KEA 1-87, KEA 1-64, KEA 1-53, EN9, EN17, KEA 1-57, DKM 2-34, DKM 2-109, DKM 3-43, EN13, KEA 1-73, EN32, TRH 1-13, EN103, EN21, EN25, KEA 1-83, EN36, KEA 1-84, EN86, DKM 2-86, KEA 1-41, DKM 2-111, KEA 1-88, EN33, DKM 2-62, KEA 1-74, EN44, KEA 1-79, TRH 1-155, DKM 2-103, EN38, EN24, DKM 3-13, EN23, DKM 2- 120, EN22, DKM 3-70, EN63, EN27, DKM 2-95, EN39, EN14, EN85, DKM 2-102, EN30, DKM 2-87, KEA 1-75, DKM 2-84, KEA 1-80, EN35, and EN28. FIG.1B: Compounds that showed significantly (p<0.05 compared to vehicle-treated controls) lower GFP/RFP ratios in MEF cells were screened in HEK293A cells expressing the same fluorescent autophagic flux probe. From left to right, the covalent ligand or vehicle is: Torin1, EN6, DKM 3-16, Rapamycin, EN2, DKM 3-30, DKM 3-70, DKM 2-84, KEA 1-46, TRH 1-168, EN14, KEA 1-100, DKM 2-72, KEA 1-80, KEA 1-36, KEA 1-75, TRH 1-170, DKM 2-102, DKM 2-95, EN30, TRH 1-170, TRH 1-60, TRH 1-140, EN28, KEA 1-37, KEA 1-79, TRH 1-194, DMSO, DKM 3-3, DKM 2-89, KEA 1-69, DKM 2-37, TRH 1-50, DKM 2-98, and TRH 1- 155. FIG.1C: Structure of cysteine-reactive covalent ligand hit EN6 that shows autophagy activating in both MEF and HEK293A cells. FIG.1D: Dose-response of EN6 in HEK293A cells expressing the fluorescent autophagic flux probe. FIG.1E: LC3B levels in HEK293A cells treated with EN6 (50 mM). FIG.1F: LC3B puncta in HEK293 cells treated with vehicle DMSO, EN6 (50 mM), or Torin1 (0.25 mM). Data shown in FIG.1A, FIG.1B, FIG.1D, and FIG.1F are average ± sem, n=3-25 biological replicates/group. Statistical significance was calculated with unpaired two-tailed Student’s t-tests. Significance is expressed as *p<0.05 compared to vehicle-treated controls. [0039] FIGS.2A-2C. Chemoproteomic profiling to identify targets of EN6. FIG.2A: Schematic of isoTOP-ABPP in which cells were pre-treated with DMSO or EN6 (50 mM, 4 h in situ) prior to labeling of proteomes in vitro with IA-alkyne (100 mM, 1 h), followed by appendage of isotopically light (for DMSO-treated) or heavy (for EN6-treated) TEV protease cleavable biotin-azide tags by copper-catalyzed azide-alkyne cycloaddition (CuAAC).
Control and treated proteomes were subsequently combined in a 1:1 ratio, probe-labeled proteins were avidin-enriched, digested with trypsin, and probe-modified tryptic peptides were eluted by TEV protease, analyzed by LC-MS/MS, and light to heavy probe-modified peptide ratios were quantified. FIG.2B: isoTOP-ABPP analysis of EN6 (50 mM) in MEF cells in situ analyzed as described in FIG.2A. FIG.2C: Gel-based ABPP analysis of EN6 interactions with recombinant ATP6V1A. Vehicle DMSO or EN6 were pre-incubated with recombinant human ATP6V1A (1 h) followed by labeling with a rhodamine-functionalized iodoacetamide probe (IA-rhodamine) (1 µM, 1 h) after which probe-labeled proteins were read-out by SDS/PAGE and in-gel fluorescence. Data shown in FIG.2C are average ± sem from n=3 biological replicates/group. [0040] FIGS.3A-3E. EN6 inhibits mTORC1 signaling and lysosomal recruitment. FIG. 3A: mTORC1 signaling with EN6 treatment in HEK293A cells. HEK293A cells, starved or stimulated with amino acids, were treated with vehicle DMSO or EN6 (20 mM) for 1 h and mTORC1 signaling was assessed by Western blotting. FIG.3B: AKT signaling in HEK293 cells treated with vehicle DMSO, rapamycin (0.1 mM), Torin1 (0.25 mM), or EN6 (25 mM) for 4 h. AKT signaling was assessed by Western blotting. FIG.3C: ATP6V1A knockdown by short hairpin (shRNA) assessed by Western blotting. FIG.3D: LC3B levels and mTORC1 signaling in Hela cells treated with EN6. Endogenous ATP6V1A was knocked down with shRNA and replaced with a Flag-tagged wild-type or C277A mutant ATP6V1A and these cells were treated with EN6 (25 mM) for 4 h. FIG.3E: mTORC1 localization in HEK293T cells treated with vehicle DMSO or EN6 (25 mM) for 1 h under amino acid starvation or stimulation. Shown are representative microscopy images of mTORC1 or the lysosomal marker LAMP2. Gels and microscopy images shown in FIGS.3A-3E are representative gels of n=2-3 biological replicates/group. [0041] FIGS.4A-4E. EN6 effects on v-ATPase and TFEB. FIG.4A: Co- immunoprecipitation experiments between stably expressed, FLAG-tagged Ragulator subunit p14 and endogenous v-ATPase components in HEK293T cells, in the absence or presence of amino acids treated with vehicle DMSO or EN6 (25 mM) for 1 h. Blots shown in FIG.4A are representative gels from n=3 biological replicates/group. FIG.4B: Localization of TFEB- GFP in Hela cells treated with vehicle DMSO or EN6 (25 mM, 4 h). Cells were stained with Hoechst 33342 and GFP-TFEB were imaged by microscopy. Shown are representative microscopy images and quantification of percentage of nuclear TFEB from n=6-7 biological replicates/group. FIG.4C: Gene expression of TFEB target genes in Hela cells treated with EN6 (25 mM) for 0 or 8 h, assessed by qRT-PCR from n=3 biological replicates/group. FIG. 4D: Lysosomal acidification of HEK293A cells treated with vehicle DMSO, bafilomycin A1 (0.2 mM), EN6 (50 mM), or with co-treatment of EN6 and bafilomycin A1 for 4 h, readout by LysoSensor DND-160. Microscopy images shown in FIG.4D are representative images from n=4 biological replicates/group. FIG.4E: Quantification of lysosomal acidification from experiment described in FIG.4D. Statistical significance calculated with unpaired two- tailed Student’s t-tests. Significance in FIG.4B and FIG.4C expressed as *p<0.05 compared to vehicle-treated controls or 0 h EN6-treated controls, respectively. Significance in FIG.4E is expressed as *p<0.05 compared to the vehicle-treated group, #p<0.05 compared to EN6- treated group. [0042] FIGS.5A-5B. EN6 improves clearance of TDP-43 aggregates in cells. Effect of EN6 and bafilomycin treatment on TDP-43 aggregate clearance. U2OS cells expressing an IPTG-inducible GFP-TDP-43 were co-treated with vehicle DMSO, IPTG (50 mM), IPTG and EN6 (25 mM), or IPTG, EN6, and bafilomycin (0.2 mM) for 7 h. Cells were stained with Hoechst 33342 and GFP-TDP-43 puncta were imaged by microscopy in FIG.5A.
Microscopy images are representative images from n=26 biological replicates/group. Data was quantified using ImageJ in FIG.5B and data shown as average ± sem. [0043] FIGS.6A-6C. EN6 inhibits mTORC1 signaling in mice. mTORC1 signaling in mouse heart (FIG.6A), kidney (FIG.6B), and skeletal muscle (FIG.6C). C57BL/6 male mice were treated intraperitoneally with vehicle (18:1:1 saline:ethanol:PEG40), rapamycin (10 mg/kg) or EN6 (50 mg/kg) for 4 h. mTORC1 signaling and LC3B levels were measured by Western blotting and quantified by densitometry. LC3B was normalized to actin loading controls, pS6 was normalized to total S6 levels, p4EBP1 was normalized to total 4EBP1 levels, and pAKT was normalized to total AKT levels. All normalized values were then normalized to vehicle-treated control levels. Data shown in are average ± sem, n=4 mice/group. Statistical significance was calculated with unpaired two-tailed Student’s t-tests. Significance is expressed as *p<0.05 compared to the vehicle-treated controls. [0044] FIG.7. Scheme of v-ATPase/mTORC1 regulation of autophagy and action of EN6. [0045] FIG.8. Transcript levels of genes unrelated to TFEB transcriptional programming. Gene expression of genes that are not TFEB target genes in Hela cells treated with EN6 (25 mM) for 0 or 8 h, assessed by qRT-PCR from n=3 biological replicates/group. DETAILED DESCRIPTION
I. Definitions
[0046] The abbreviations used herein have their conventional meaning within the chemical and biological arts. The chemical structures and formulae set forth herein are constructed according to the standard rules of chemical valency known in the chemical arts. [0047] Where substituent groups are specified by their conventional chemical formulae, written from left to right, they equally encompass the chemically identical substituents that would result from writing the structure from right to left, e.g., -CH2O- is equivalent to -OCH2-. [0048] The term“alkyl,” by itself or as part of another substituent, means, unless otherwise stated, a straight (i.e., unbranched) or branched carbon chain (or carbon), or combination thereof, which may be fully saturated, mono- or polyunsaturated and can include mono-, di-, and multivalent radicals. The alkyl may include a designated number of carbons (e.g., C1-C10 means one to ten carbons). Alkyl is an uncyclized chain. Examples of saturated hydrocarbon radicals include, but are not limited to, groups such as methyl, ethyl, n-propyl, isopropyl, n- butyl, t-butyl, isobutyl, sec-butyl, methyl, homologs and isomers of, for example, n-pentyl, n- hexyl, n-heptyl, n-octyl, and the like. An unsaturated alkyl group is one having one or more double bonds or triple bonds. Examples of unsaturated alkyl groups include, but are not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(1,4- pentadienyl), ethynyl, 1- and 3-propynyl, 3-butynyl, and the higher homologs and isomers. An alkoxy is an alkyl attached to the remainder of the molecule via an oxygen linker (-O-). An alkyl moiety may be an alkenyl moiety. An alkyl moiety may be an alkynyl moiety. An alkyl moiety may be fully saturated. An alkenyl may include more than one double bond and/or one or more triple bonds in addition to the one or more double bonds. An alkynyl may include more than one triple bond and/or one or more double bonds in addition to the one or more triple bonds. [0049] The term“alkylene,” by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkyl, as exemplified, but not limited by, -CH2CH2CH2CH2-. Typically, an alkyl (or alkylene) group will have from 1 to 24 carbon atoms, with those groups having 10 or fewer carbon atoms being preferred herein. A“lower alkyl” or“lower alkylene” is a shorter chain alkyl or alkylene group, generally having eight or fewer carbon atoms. The term“alkenylene,” by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkene. [0050] The term“heteroalkyl,” by itself or in combination with another term, means, unless otherwise stated, a stable straight or branched chain, or combinations thereof, including at least one carbon atom and at least one heteroatom (e.g., O, N, P, Si, and S), and wherein the nitrogen and sulfur atoms may optionally be oxidized, and the nitrogen heteroatom may optionally be quaternized. The heteroatom(s) (e.g., N, S, Si, or P) may be placed at any interior position of the heteroalkyl group or at the position at which the alkyl group is attached to the remainder of the molecule. Heteroalkyl is an uncyclized chain. Examples include, but are not limited to: -CH2-CH2-O-CH3, -CH2-CH2-NH-CH3,
-CH2-CH2-N(CH3)-CH3, -CH2-S-CH2-CH3, -S-CH2-CH2, -S(O)-CH3, -CH2-CH2-S(O)2-CH3, -CH=CH-O-CH3, -Si(CH3)3, -CH2-CH=N-OCH3, -CH=CH-N(CH3)-CH3, -O-CH3,
-O-CH2-CH3, and -CN. Up to two or three heteroatoms may be consecutive, such as, for example, -CH2-NH-OCH3 and -CH2-O-Si(CH3)3. A heteroalkyl moiety may include one heteroatom (e.g., O, N, S, Si, or P). A heteroalkyl moiety may include two optionally different heteroatoms (e.g., O, N, S, Si, or P). A heteroalkyl moiety may include three optionally different heteroatoms (e.g., O, N, S, Si, or P). A heteroalkyl moiety may include four optionally different heteroatoms (e.g., O, N, S, Si, or P). A heteroalkyl moiety may include five optionally different heteroatoms (e.g., O, N, S, Si, or P). A heteroalkyl moiety may include up to 8 optionally different heteroatoms (e.g., O, N, S, Si, or P). The term “heteroalkenyl,” by itself or in combination with another term, means, unless otherwise stated, a heteroalkyl including at least one double bond. A heteroalkenyl may optionally include more than one double bond and/or one or more triple bonds in additional to the one or more double bonds. The term“heteroalkynyl,” by itself or in combination with another term, means, unless otherwise stated, a heteroalkyl including at least one triple bond. A
heteroalkynyl may optionally include more than one triple bond and/or one or more double bonds in additional to the one or more triple bonds. In embodiments, a heteroalkyl (or heteroalkylene) group will have from 2 to 24 atoms including at least one carbon atom and at least one heteroatom (e.g., O, N, P, Si, and S), with those groups having 10 or fewer atoms being preferred herein. [0051] Similarly, the term“heteroalkylene,” by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from heteroalkyl, as exemplified, but not limited by, -CH2-CH2-S-CH2-CH2- and -CH2-S-CH2-CH2-NH-CH2-. For
heteroalkylene groups, heteroatoms can also occupy either or both of the chain termini (e.g., alkyleneoxy, alkylenedioxy, alkyleneamino, alkylenediamino, and the like). Still further, for alkylene and heteroalkylene linking groups, no orientation of the linking group is implied by the direction in which the formula of the linking group is written. For example, the formula -C(O)2R'- represents both -C(O)2R'- and -R'C(O)2-. As described above, heteroalkyl groups, as used herein, include those groups that are attached to the remainder of the molecule through a heteroatom, such as -C(O)R', -C(O)NR', -NR'R'', -OR', -SR', and/or -SO2R'. Where “heteroalkyl” is recited, followed by recitations of specific heteroalkyl groups, such as - NR'R'' or the like, it will be understood that the terms heteroalkyl and -NR'R'' are not redundant or mutually exclusive. Rather, the specific heteroalkyl groups are recited to add clarity. Thus, the term“heteroalkyl” should not be interpreted herein as excluding specific heteroalkyl groups, such as -NR'R'' or the like. [0052] The terms“cycloalkyl” and“heterocycloalkyl,” by themselves or in combination with other terms, mean, unless otherwise stated, cyclic versions of“alkyl” and“heteroalkyl,” respectively. Cycloalkyl and heterocycloalkyl are not aromatic. Additionally, for heterocycloalkyl, a heteroatom can occupy the position at which the heterocycle is attached to the remainder of the molecule. Examples of cycloalkyl include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl, and the like. Examples of heterocycloalkyl include, but are not limited to, 1- (1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 4-morpholinyl, 3- morpholinyl, tetrahydrofuran-2-yl, tetrahydrofuran-3-yl, tetrahydrothien-2-yl,
tetrahydrothien-3-yl, 1-piperazinyl, 2-piperazinyl, and the like. A“cycloalkylene” and a “heterocycloalkylene,” alone or as part of another substituent, means a divalent radical derived from a cycloalkyl and heterocycloalkyl, respectively. In embodiments, a cycloalkyl (or cycloalkylene) group will have from 3 to 8 carbon atoms. In embodiments, a
heterocycloalkyl (or heterocycloalkylene) group will have from 3 to 8 atoms including at least one carbon atom and at least one heteroatom (e.g., O, N, P, Si, and S). [0053] The terms“halo” or“halogen,” by themselves or as part of another substituent, mean, unless otherwise stated, a fluorine, chlorine, bromine, or iodine atom. Additionally, terms such as“haloalkyl” are meant to include monohaloalkyl and polyhaloalkyl. For example, the term“halo(C1-C4)alkyl” includes, but is not limited to, fluoromethyl, difluoromethyl, trifluoromethyl, 2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the like. [0054] The term“acyl” means, unless otherwise stated, -C(O)R where R is a substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0055] The term“aryl” means, unless otherwise stated, a polyunsaturated, aromatic, hydrocarbon substituent, which can be a single ring or multiple rings (preferably from 1 to 3 rings) that are fused together (i.e., a fused ring aryl) or linked covalently. A fused ring aryl refers to multiple rings fused together wherein at least one of the fused rings is an aryl ring. The term“heteroaryl” refers to aryl groups (or rings) that contain at least one heteroatom such as N, O, or S, wherein the nitrogen and sulfur atoms are optionally oxidized, and the nitrogen atom(s) are optionally quaternized. Thus, the term“heteroaryl” includes fused ring heteroaryl groups (i.e., multiple rings fused together wherein at least one of the fused rings is a heteroaromatic ring). A 5,6-fused ring heteroarylene refers to two rings fused together, wherein one ring has 5 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring. Likewise, a 6,6-fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring. And a 6,5-fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 5 members, and wherein at least one ring is a heteroaryl ring. A heteroaryl group can be attached to the remainder of the molecule through a carbon or heteroatom. Non-limiting examples of aryl and heteroaryl groups include phenyl, naphthyl, pyrrolyl, pyrazolyl, pyridazinyl, triazinyl, pyrimidinyl, imidazolyl, pyrazinyl, purinyl, oxazolyl, isoxazolyl, thiazolyl, furyl, thienyl, pyridyl, pyrimidyl, benzothiazolyl, benzoxazoyl benzimidazolyl, benzofuran,
isobenzofuranyl, indolyl, isoindolyl, benzothiophenyl, isoquinolyl, quinoxalinyl, quinolyl, 1- naphthyl, 2-naphthyl, 4-biphenyl, 1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2- imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5- benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl, 1-isoquinolyl, 5-isoquinolyl, 2- quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and 6-quinolyl. Substituents for each of the above noted aryl and heteroaryl ring systems are selected from the group of acceptable substituents described below. An“arylene” and a“heteroarylene,” alone or as part of another substituent, mean a divalent radical derived from an aryl and heteroaryl, respectively. A heteroaryl group substituent may be -O- bonded to a ring heteroatom nitrogen. In embodiments, an aryl (or arylene) group will have from 6 to 10 carbon atoms. In embodiments, a heteroaryl (or heteroarylene) group will have from 5 to 10 atoms including at least one carbon atom and at least one heteroatom (e.g., O, N, P, Si, and S). [0056] Spirocyclic rings are two or more rings wherein adjacent rings are attached through a single atom. The individual rings within spirocyclic rings may be identical or different. Individual rings in spirocyclic rings may be substituted or unsubstituted and may have different substituents from other individual rings within a set of spirocyclic rings. Possible substituents for individual rings within spirocyclic rings are the possible substituents for the same ring when not part of spirocyclic rings (e.g., substituents for cycloalkyl or
heterocycloalkyl rings). Spirocylic rings may be substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heterocycloalkylene and individual rings within a spirocyclic ring group may be any of the immediately previous list, including having all rings of one type (e.g., all rings being substituted heterocycloalkylene wherein each ring may be the same or different substituted heterocycloalkylene). When referring to a spirocyclic ring system, heterocyclic spirocyclic rings means a spirocyclic rings wherein at least one ring is a heterocyclic ring and wherein each ring may be a different ring. When referring to a spirocyclic ring system, substituted spirocyclic rings means that at least one ring is substituted and each substituent may optionally be different. [0057] The symbol“ ” denotes the point of attachment of a chemical moiety to the
Figure imgf000016_0001
remainder of a molecule or chemical formula. [0058] The term“oxo,” as used herein, means an oxygen that is double bonded to a carbon atom. [0059] The term“alkylarylene” as an arylene moiety covalently bonded to an alkylene moiety (also referred to herein as an alkylene linker). In embodiments, the alkylarylene group has the formula:
Figure imgf000017_0001
[0060] An alkylarylene moiety may be substituted (e.g., with a substituent group) on the alkylene moiety or the arylene linker (e.g., at carbons 2, 3, 4, or 6) with halogen, oxo, -N3, -CF3, -CCl3, -CBr3, -CI3, -CN, -CHO, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO2CH3, -SO3H, -OSO3H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, substituted or
unsubstituted C1-C5 alkyl or substituted or unsubstituted 2 to 5 membered heteroalkyl). In embodiments, the alkylarylene is unsubstituted. [0061] Each of the above terms (e.g.,“alkyl,”“heteroalkyl,”“cycloalkyl,”
“heterocycloalkyl,”“aryl,” and“heteroaryl”) includes both substituted and unsubstituted forms of the indicated radical. Preferred substituents for each type of radical are provided below. [0062] Substituents for the alkyl and heteroalkyl radicals (including those groups often referred to as alkylene, alkenyl, heteroalkylene, heteroalkenyl, alkynyl, cycloalkyl, heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl) can be one or more of a variety of groups selected from, but not limited to, -OR', =O, =NR', =N-OR', -NR'R'', -SR', halogen, -SiR'R''R''', -OC(O)R', -C(O)R', -CO2R', -CONR'R'', -OC(O)NR'R'', -NR''C(O)R',
-NR'-C(O)NR''R''', -NR''C(O)2R', -NR-C(NR'R''R''')=NR'''', -NR-C(NR'R'')=NR''', -S(O)R', -S(O)2R', -S(O)2NR'R'', -NRSO2R', -NR'NR''R''', -ONR'R'', -NR'C(O)NR''NR'''R'''', -CN, -NO2, -NR'SO2R'', -NR'C(O)R'', -NR'C(O)-OR'', -NR'OR'', in a number ranging from zero to (2m'+1), where m' is the total number of carbon atoms in such radical. R, R', R'', R''', and R'''' each preferably independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl (e.g., aryl substituted with 1-3 halogens), substituted or unsubstituted heteroaryl, substituted or unsubstituted alkyl, alkoxy, or thioalkoxy groups, or arylalkyl groups. When a compound described herein includes more than one R group, for example, each of the R groups is independently selected as are each R', R'', R''', and R'''' group when more than one of these groups is present. When R' and R'' are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 4-, 5-, 6-, or 7- membered ring. For example, -NR'R'' includes, but is not limited to, 1-pyrrolidinyl and 4- morpholinyl. From the above discussion of substituents, one of skill in the art will understand that the term“alkyl” is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (e.g., -CF3 and -CH2CF3) and acyl (e.g., -C(O)CH3, -C(O)CF3, -C(O)CH2OCH3, and the like). [0063] Similar to the substituents described for the alkyl radical, substituents for the aryl and heteroaryl groups are varied and are selected from, for example: -OR', -NR'R'', -SR', halogen, -SiR'R''R''', -OC(O)R', -C(O)R', -CO2R', -CONR'R'', -OC(O)NR'R'', -NR''C(O)R', -NR'-C(O)NR''R''', -NR''C(O)2R', -NR-C(NR'R''R''')=NR'''', -NR-C(NR'R'')=NR''', -S(O)R', -S(O)2R', -S(O)2NR'R'', -NRSO2R', -NR'NR''R''', -ONR'R'', -NR'C(O)NR''NR'''R'''', -CN, -NO2, -R', -N3, -CH(Ph)2, fluoro(C1-C4)alkoxy, and fluoro(C1-C4)alkyl, -NR'SO2R'',
-NR'C(O)R'', -NR'C(O)-OR'', -NR'OR'', in a number ranging from zero to the total number of open valences on the aromatic ring system; and where R', R'', R''', and R'''' are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl. When a compound described herein includes more than one R group, for example, each of the R groups is independently selected as are each R', R'', R''', and R'''' groups when more than one of these groups is present. [0064] Substituents for rings (e.g., cycloalkyl, heterocycloalkyl, aryl, heteroaryl, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene) may be depicted as substituents on the ring rather than on a specific atom of a ring (commonly referred to as a floating substituent). In such a case, the substituent may be attached to any of the ring atoms (obeying the rules of chemical valency) and in the case of fused rings or spirocyclic rings, a substituent depicted as associated with one member of the fused rings or spirocyclic rings (a floating substituent on a single ring), may be a substituent on any of the fused rings or spirocyclic rings (a floating substituent on multiple rings). When a substituent is attached to a ring, but not a specific atom (a floating substituent), and a subscript for the substituent is an integer greater than one, the multiple substituents may be on the same atom, same ring, different atoms, different fused rings, different spirocyclic rings, and each substituent may optionally be different. Where a point of attachment of a ring to the remainder of a molecule is not limited to a single atom (a floating substituent), the attachment point may be any atom of the ring and in the case of a fused ring or spirocyclic ring, any atom of any of the fused rings or spirocyclic rings while obeying the rules of chemical valency. Where a ring, fused rings, or spirocyclic rings contain one or more ring heteroatoms and the ring, fused rings, or spirocyclic rings are shown with one more floating substituents (including, but not limited to, points of attachment to the remainder of the molecule), the floating substituents may be bonded to the heteroatoms. Where the ring heteroatoms are shown bound to one or more hydrogens (e.g., a ring nitrogen with two bonds to ring atoms and a third bond to a hydrogen) in the structure or formula with the floating substituent, when the heteroatom is bonded to the floating substituent, the substituent will be understood to replace the hydrogen, while obeying the rules of chemical valency. [0065] Two or more substituents may optionally be joined to form aryl, heteroaryl, cycloalkyl, or heterocycloalkyl groups. Such so-called ring-forming substituents are typically, though not necessarily, found attached to a cyclic base structure. In one
embodiment, the ring-forming substituents are attached to adjacent members of the base structure. For example, two ring-forming substituents attached to adjacent members of a cyclic base structure create a fused ring structure. In another embodiment, the ring-forming substituents are attached to a single member of the base structure. For example, two ring- forming substituents attached to a single member of a cyclic base structure create a spirocyclic structure. In yet another embodiment, the ring-forming substituents are attached to non-adjacent members of the base structure. [0066] Two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally form a ring of the formula -T-C(O)-(CRR')q-U-, wherein T and U are
independently -NR-, -O-, -CRR'-, or a single bond, and q is an integer of from 0 to 3.
Alternatively, two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -A-(CH2)r-B-, wherein A and B are independently -CRR'-, -O-, -NR-, -S-, -S(O) -, -S(O)2-, -S(O)2NR'-, or a single bond, and r is an integer of from 1 to 4. One of the single bonds of the new ring so formed may optionally be replaced with a double bond. Alternatively, two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -(CRR')s-X'- (C''R''R''')d-, where s and d are independently integers of from 0 to 3, and X' is -O-, -NR'-, -S-, -S(O)-, -S(O)2-, or -S(O)2NR'-. The substituents R, R', R'', and R''' are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl. [0067] As used herein, the terms“heteroatom” or“ring heteroatom” are meant to include oxygen (O), nitrogen (N), sulfur (S), phosphorus (P), and silicon (Si). [0068] A“substituent group,” as used herein, means a group selected from the following moieties: (A) oxo, halogen, -CCl3, -CBr3, -CF3, -CI3, -CHCl2, -CHBr2, -CHF2, -CHI2, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCF3, -OCBr3, -OCI3, -OCHCl2, -OCHBr2, -OCHI2, -OCHF2, -OCH2Cl, -OCH2Br, -OCH2I, -OCH2F, -N3,
unsubstituted alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), unsubstituted aryl (e.g., C6- C10 aryl, C10 aryl, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), and (B) alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered
heteroalkyl), cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), substituted with at least one substituent selected from: (i) oxo, halogen, -CCl3, -CBr3, -CF3, -CI3, -CHCl2, -CHBr2, -CHF2, -CHI2, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCF3, -OCBr3, -OCI3, -OCHCl2, -OCHBr2, -OCHI2, -OCHF2, -OCH2Cl, -OCH2Br, -OCH2I, -OCH2F, -N3, unsubstituted alkyl (e.g., - C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), unsubstituted aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), and (ii) alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), aryl (e.g., C6- C10 aryl, C10 aryl, or phenyl), heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), substituted with at least one substituent selected from: (a) oxo, halogen, -CCl3, -CBr3, -CF3, -CI3, -CHCl2, -CHBr2, -CHF2, -CHI2, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCF3, -OCBr3, -OCI3, -OCHCl2, -OCHBr2, -OCHI2, -OCHF2, -OCH2Cl, -OCH2Br, -OCH2I, -OCH2F, -N3, unsubstituted alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), unsubstituted aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), and (b) alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), aryl (e.g., C6- C10 aryl, C10 aryl, or phenyl), heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), substituted with at least one substituent selected from: oxo, halogen, -CCl3, -CBr3, -CF3, -CI3, -CHCl2, -CHBr2, -CHF2, -CHI2, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCF3, -OCBr3, -OCI3, -OCHCl2, -OCHBr2, -OCHI2, -OCHF2, -OCH2Cl, -OCH2Br, -OCH2I, -OCH2F, -N3, unsubstituted alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), unsubstituted aryl (e.g., C6- C10 aryl, C10 aryl, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl). [0069] A“size-limited substituent” or“ size-limited substituent group,” as used herein, means a group selected from all of the substituents described above for a“substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted C1-C20 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 10 membered heteroaryl. [0070] A“lower substituent” or“ lower substituent group,” as used herein, means a group selected from all of the substituents described above for a“substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted C1-C8 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3- C7 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 9 membered heteroaryl. [0071] In some embodiments, each substituted group described in the compounds herein is substituted with at least one substituent group. More specifically, in some embodiments, each substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene described in the compounds herein are substituted with at least one substituent group. In other embodiments, at least one or all of these groups are substituted with at least one size-limited substituent group. In other embodiments, at least one or all of these groups are substituted with at least one lower substituent group. [0072] In other embodiments of the compounds herein, each substituted or unsubstituted alkyl may be a substituted or unsubstituted C1-C20 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered
heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6- C10 aryl, and/or each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 10 membered heteroaryl. In some embodiments of the compounds herein, each substituted or unsubstituted alkylene is a substituted or unsubstituted C1-C20 alkylene, each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 20 membered
heteroalkylene, each substituted or unsubstituted cycloalkylene is a substituted or
unsubstituted C3-C8 cycloalkylene, each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 8 membered heterocycloalkylene, each substituted or unsubstituted arylene is a substituted or unsubstituted C6-C10 arylene, and/or each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 10 membered
heteroarylene. [0073] In some embodiments, each substituted or unsubstituted alkyl is a substituted or unsubstituted C1-C8 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C7 cycloalkyl, each substituted or unsubstituted
heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and/or each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 9 membered heteroaryl. In some embodiments, each substituted or unsubstituted alkylene is a substituted or unsubstituted C1-C8 alkylene, each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 8 membered heteroalkylene, each substituted or
unsubstituted cycloalkylene is a substituted or unsubstituted C3-C7 cycloalkylene, each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 7 membered heterocycloalkylene, each substituted or unsubstituted arylene is a substituted or unsubstituted C6-C10 arylene, and/or each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 9 membered heteroarylene. In some embodiments, the compound is a chemical species set forth in the Examples section, figures, or tables below. [0074] In embodiments, a substituted or unsubstituted moiety (e.g., substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, and/or substituted or unsubstituted heteroarylene) is unsubstituted (e.g., is an unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl, unsubstituted alkylene, unsubstituted heteroalkylene, unsubstituted cycloalkylene, unsubstituted heterocycloalkylene, unsubstituted arylene, and/or unsubstituted heteroarylene, respectively). In embodiments, a substituted or unsubstituted moiety (e.g., substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, and/or substituted or unsubstituted heteroarylene) is substituted (e.g., is a substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene, respectively). [0075] In embodiments, a substituted moiety (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene) is substituted with at least one substituent group, wherein if the substituted moiety is substituted with a plurality of substituent groups, each substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of substituent groups, each substituent group is different. [0076] In embodiments, a substituted moiety (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene) is substituted with at least one size-limited substituent group, wherein if the substituted moiety is substituted with a plurality of size-limited substituent groups, each size-limited substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of size-limited substituent groups, each size-limited substituent group is different. [0077] In embodiments, a substituted moiety (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene) is substituted with at least one lower substituent group, wherein if the substituted moiety is substituted with a plurality of lower substituent groups, each lower substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of lower substituent groups, each lower substituent group is different. [0078] In embodiments, a substituted moiety (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted moiety is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group is different. [0079] In a recited claim or chemical formula description herein, each R substituent or L linker that is described as being“substituted” without reference as to the identity of any chemical moiety that composes the“substituted” group (also referred to herein as an“open substitution” on an R substituent or L linker or an“openly substituted” R substituent or L linker), the recited R substituent or L linker may, in embodiments, be substituted with one or more first substituent groups as defined below. [0080] The first substituent group is denoted with a corresponding first decimal point numbering system such that, for example, R1 may be substituted with one or more first substituent groups denoted by R1.1, R2 may be substituted with one or more first substituent groups denoted by R2.1, R3 may be substituted with one or more first substituent groups denoted by R3.1, R4 may be substituted with one or more first substituent groups denoted by R4.1, R5 may be substituted with one or more first substituent groups denoted by R5.1, and the like up to or exceeding an R100 that may be substituted with one or more first substituent groups denoted by R100.1. As a further example, R1A may be substituted with one or more first substituent groups denoted by R1A.1, R2A may be substituted with one or more first substituent groups denoted by R2A.1, R3A may be substituted with one or more first substituent groups denoted by R3A.1, R4A may be substituted with one or more first substituent groups denoted by R4A.1, R5A may be substituted with one or more first substituent groups denoted by R5A.1 and the like up to or exceeding an R100A may be substituted with one or more first substituent groups denoted by R100A.1. As a further example, L1 may be substituted with one or more first substituent groups denoted by RL1.1, L2 may be substituted with one or more first substituent groups denoted by RL2.1, L3 may be substituted with one or more first substituent groups denoted by RL3.1, L4 may be substituted with one or more first substituent groups denoted by RL4.1, L5 may be substituted with one or more first substituent groups denoted by RL5.1 and the like up to or exceeding an L100 which may be substituted with one or more first substituent groups denoted by RL100.1. Thus, each numbered R group or L group
(alternatively referred to herein as RWW or LWW wherein“WW” represents the stated superscript number of the subject R group or L group) described herein may be substituted with one or more first substituent groups referred to herein generally as RWW.1 or RLWW.1, respectively. In turn, each first substituent group (e.g., R1.1, R2.1, R3.1, R4.1, R5.1… R100.1; R1A.1, R2A.1, R3A.1, R4A.1, R5A.1… R100A.1; RL1.1, RL2.1, RL3.1, RL4.1, RL5.1… RL100.1) may be further substituted with one or more second substituent groups (e.g., R1.2, R2.2, R3.2, R4.2, R5.2… R100.2; R1A.2, R2A.2, R3A.2, R4A.2, R5A.2… R100A.2; RL1.2, RL2.2, RL3.2, RL4.2, RL5.2… RL100.2, respectively). Thus, each first substituent group, which may alternatively be represented herein as RWW.1 as described above, may be further substituted with one or more second substituent groups, which may alternatively be represented herein as RWW.2. [0081] Finally, each second substituent group (e.g., R1.2, R2.2, R3.2, R4.2, R5.2… R100.2; R1A.2, R2A.2, R3A.2, R4A.2, R5A.2… R100A.2; RL1.2, RL2.2, RL3.2, RL4.2, RL5.2… RL100.2) may be further substituted with one or more third substituent groups (e.g., R1.3, R2.3, R3.3, R4.3, R5.3… R100.3; R1A.3, R2A.3, R3A.3, R4A.3, R5A.3… R100A.3; RL1.3, RL2.3, RL3.3, RL4.3, RL5.3… RL100.3;
respectively). Thus, each second substituent group, which may alternatively be represented herein as RWW.2 as described above, may be further substituted with one or more third substituent groups, which may alternatively be represented herein as RWW.3. Each of the first substituent groups may be optionally different. Each of the second substituent groups may be optionally different. Each of the third substituent groups may be optionally different. [0082] Thus, as used herein, RWW represents a substituent recited in a claim or chemical formula description herein which is openly substituted.“WW” represents the stated superscript number of the subject R group (1, 2, 3, 1A, 2A, 3A, 1B, 2B, 3B, etc.). Likewise, LWW is a linker recited in a claim or chemical formula description herein which is openly substituted. Again,“WW” represents the stated superscript number of the subject L group (1, 2, 3, 1A, 2A, 3A, 1B, 2B, 3B, etc.). As stated above, in embodiments, each RWW may be unsubstituted or independently substituted with one or more first substituent groups, referred to herein as RWW.1; each first substituent group, RWW.1, may be unsubstituted or independently substituted with one or more second substituent groups, referred to herein as RWW.2; and each second substituent group may be unsubstituted or independently substituted with one or more third substituent groups, referred to herein as RWW.3. Similarly, each LWW linker may be unsubstituted or independently substituted with one or more first substituent groups, referred to herein as RLWW.1; each first substituent group, RLWW.1, may be unsubstituted or
independently substituted with one or more second substituent groups, referred to herein as RLWW.2; and each second substituent group may be unsubstituted or independently substituted with one or more third substituent groups, referred to herein as RLWW.3. Each first substituent group is optionally different. Each second substituent group is optionally different. Each third substituent group is optionally different. For example, if RWW is phenyl, the said phenyl group is optionally substituted by one or more RWW.1 groups as defined herein below, e.g., when RWW.1 is RWW.2-substituted alkyl, examples of groups so formed include but are not limited to itself optionally substituted by 1 or more RWW.2, which RWW.2 is optionally substituted by one or more RWW.3. By way of example when RWW.1 is alkyl, groups that could be formed, include but are not limited to:
Figure imgf000028_0001
. [0083] RWW.1 is independently oxo, halogen, -CXWW.13, -CHXWW.12, -CH2XWW.1,
-OCXWW.13, -OCH2XWW.1, -OCHXWW.12, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C=(O)NHNH2, -NH C=(O)NH2,
-NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, RWW.2-substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), RWW.2-substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), RWW.2-substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5- C6), RWW.2-substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), RWW.2-substituted or unsubstituted aryl (e.g., C6-C12, C6-C10, or phenyl), or RWW.2-substituted or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered). In embodiments, RWW.1 is independently oxo, halogen, -CXWW.1 3, -CHXWW.1 2, -CH2XWW.1, -OCXWW.13, -OCH2XWW.1, -OCHXWW.12, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C=(O)NHNH2,
-NHC=(O)NH2, -NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C12, C6-C10, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). XWW.1 is
independently–F, -Cl, -Br, or–I. [0084] RWW.2 is independently oxo, halogen, -CXWW.23, -CHXWW.22, -CH2XWW.2,
-OCXWW.23, -OCH2XWW.2, -OCHXWW.22, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C=(O)NHNH2, -NH C=(O)NH2,
-NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, RWW.3-substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), RWW.3-substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), RWW.3-substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5- C6), RWW.3-substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), RWW.3-substituted or unsubstituted aryl (e.g., C6-C12, C6-C10, or phenyl), or RWW.3-substituted or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered). In embodiments, RWW.2 is independently oxo, halogen, -CXWW.23, -CHXWW.22, -CH2XWW.2, -OCXWW.23, -OCH2XWW.2, -OCHXWW.22, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C=(O)NHNH2,
-NHC=(O)NH2, -NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C12, C6-C10, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). XWW.2 is
independently–F, -Cl, -Br, or–I. [0085] RWW.3 is independently oxo, halogen, -CXWW.3 3, -CHXWW.3 2, -CH2XWW.3,
-OCXWW.33, -OCH2XWW.3, -OCHXWW.32, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C=(O)NHNH2, -NH C=(O)NH2,
-NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3- C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C12, C6- C10, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). XWW.3 is independently–F, -Cl, -Br, or–I. [0086] Where two different RWW substituents are joined together to form an openly substituted ring (e.g. substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl or substituted heteroaryl), in embodiments the openly substituted ring may be independently substituted with one or more first substituent groups, referred to herein as RWW.1; each first substituent group, RWW.1, may be unsubstituted or independently substituted with one or more second substituent groups, referred to herein as RWW.2; and each second substituent group, RWW.2, may be unsubstituted or independently substituted with one or more third substituent groups, referred to herein as RWW.3; and each third substituent group, RWW.3, is unsubstituted. Each first substituent group is optionally different. Each second substituent group is optionally different. Each third substituent group is optionally different. In the context of two different RWW substituents joined together to form an openly substituted ring, the“WW” symbol in the RWW.1, RWW.2 and RWW.3 refers to the designated number of one of the two different RWW substituents. For example, in embodiments where R100A and R100B are optionally joined together to form an openly substituted ring, RWW.1 is R100A.1, RWW.2 is R100A.2, and RWW.3 is R100A.3. Alternatively, in embodiments where R100A and R100B are optionally joined together to form an openly substituted ring, RWW.1 is R100B.1, RWW.2 is R100B.2, and RWW.3 is R100B.3. RWW.1, RWW.2 and RWW.3 in this paragraph are as defined in the preceding paragraphs. [0087] RLWW.1 is independently oxo, halogen, -CXLWW.13, -CHXLWW.12, -CH2XLWW.1, -OCXLWW.1 3, -OCH2XLWW.1, -OCHXLWW.1 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C=(O)NHNH2, -NH C=(O)NH2, - NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, RLWW.2-substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), RLWW.2-substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), RLWW.2-substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5- C6), RLWW.2-substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), RLWW.2-substituted or unsubstituted aryl (e.g., C6-C12, C6-C10, or phenyl), or RLWW.2-substituted or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered). In embodiments, RLWW.1 is independently oxo, halogen, -CXLWW.1 3,
-CHXLWW.12, -CH2XLWW.1, -OCXLWW.13, -OCH2XLWW.1, -OCHXLWW.1 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC=(O)NHNH2, -NH C=(O) NH2, -NHSO2H, -NHC= (O)H, -NHC(O)-OH, -NHOH, -N3, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C12, C6-C10, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). XLWW.1 is independently–F, -Cl, -Br, or–I. [0088] RLWW.2 is independently oxo, halogen, -CXLWW.23, -CHXLWW.22, -CH2XLWW.2, -OCXLWW.2 3, -OCH2XLWW.2, -OCHXLWW.2 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C=(O)NHNH2, -NH C=(O)NH2,
-NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, RLWW.3-substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), RLWW.3-substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), RWW.3-substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5- C6), RLWW.3-substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), RLWW.3-substituted or unsubstituted aryl (e.g., C6-C12, C6-C10, or phenyl), or RLWW.3-substituted or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered). In embodiments, RLWW.2 is independently oxo, halogen, -CXLWW.23,
-CHXLWW.2 2, -CH2XLWW.2, -OCXLWW.2 3, -OCH2XLWW.2, -OCHXLWW.2 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC=(O)NHNH2, -NH C=(O)NH2, -NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C12, C6-C10, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). XLWW.2 is independently–F, -Cl, -Br, or–I. [0089] RLWW.3 is independently oxo, halogen, -CXLWW.3 3, -CHXLWW.3 2, -CH2XLWW.3, -OCXLWW.33, -OCH2XLWW.3, -OCHXLWW.32, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C=(O)NHNH2, -NH C=(O)NH2,
-NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3- C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C12, C6- C10, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). XLWW.3 is independently–F, -Cl, -Br, or–I. [0090] In the event that any R group recited in a claim or chemical formula description set forth herein (RWW substituent) is not specifically defined in this disclosure, then that R group (RWW group) is hereby defined as independently oxo, halogen, -CXWW3, -CHXWW2,
-CH2XWW, -OCXWW3, -OCH2XWW, -OCHXWW2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C=(O)NHNH2, -NH C=(O)NH2, - NHSO2H, -NHC=(O)H, -NHC(O)-OH, -NHOH, -N3, RWW.1-substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), RWW.1-substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), RWW.1-substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5- C6), RWW.1-substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), RWW.1-substituted or unsubstituted aryl (e.g., C6-C12, C6-C10, or phenyl), or RWW.1-substituted or unsubstituted heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered). XWW is independently–F, -Cl, -Br, or–I. Again,“WW” represents the stated superscript number of the subject R group (e.g., 1, 2, 3, 1A, 2A, 3A, 1B, 2B, 3B, etc.).
RWW.1, RWW.2, and RWW.3 are as defined above. [0091] In the event that any L linker group recited in a claim or chemical formula description set forth herein (i.e., an LWW substituent) is not explicitly defined, then that L group (LWW group) is herein defined as independently a bond,–O-, -NH-, -C(O)-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, -C(O)O-, -OC(O)-, -S-, -SO2NH-, RLWW.1-substituted or unsubstituted alkylene (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), RLWW.1-substituted or unsubstituted heteroalkylene (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), RLWW.1-substituted or unsubstituted cycloalkylene (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), RLWW.1-substituted or unsubstituted heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), RLWW.1-substituted or unsubstituted arylene (e.g., C6-C12, C6-C10, or phenyl), or RLWW.1- substituted or unsubstituted heteroarylene (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). Again,“WW” represents the stated superscript number of the subject L group (1, 2, 3, 1A, 2A, 3A, 1B, 2B, 3B, etc.). RLWW.1, as well as RLWW.2 and RLWW.3 are as defined above. [0092] Certain compounds of the present disclosure possess asymmetric carbon atoms (optical or chiral centers) or double bonds; the enantiomers, racemates, diastereomers, tautomers, geometric isomers, stereoisometric forms that may be defined, in terms of absolute stereochemistry, as (R)-or (S)- or, as (D)- or (L)- for amino acids, and individual isomers are encompassed within the scope of the present disclosure. The compounds of the present disclosure do not include those that are known in art to be too unstable to synthesize and/or isolate. The present disclosure is meant to include compounds in racemic and optically pure forms. Optically active (R)- and (S)-, or (D)- and (L)-isomers may be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques. When the compounds described herein contain olefinic bonds or other centers of geometric asymmetry, and unless specified otherwise, it is intended that the compounds include both E and Z geometric isomers. [0093] As used herein, the term“isomers” refers to compounds having the same number and kind of atoms, and hence the same molecular weight, but differing in respect to the structural arrangement or configuration of the atoms. [0094] The term“tautomer,” as used herein, refers to one of two or more structural isomers which exist in equilibrium and which are readily converted from one isomeric form to another. [0095] It will be apparent to one skilled in the art that certain compounds of this disclosure may exist in tautomeric forms, all such tautomeric forms of the compounds being within the scope of the disclosure. [0096] Unless otherwise stated, structures depicted herein are also meant to include all stereochemical forms of the structure; i.e., the R and S configurations for each asymmetric center. Therefore, single stereochemical isomers as well as enantiomeric and diastereomeric mixtures of the present compounds are within the scope of the disclosure. [0097] Unless otherwise stated, structures depicted herein are also meant to include compounds which differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures except for the replacement of a hydrogen by a deuterium or tritium, or the replacement of a carbon by 13C- or 14C-enriched carbon are within the scope of this disclosure. [0098] The compounds of the present disclosure may also contain unnatural proportions of atomic isotopes at one or more of the atoms that constitute such compounds. For example, the compounds may be radiolabeled with radioactive isotopes, such as for example tritium (3H), iodine-125 (125I), or carbon-14 (14C). All isotopic variations of the compounds of the present disclosure, whether radioactive or not, are encompassed within the scope of the present disclosure. [0099] It should be noted that throughout the application that alternatives are written in Markush groups, for example, each amino acid position that contains more than one possible amino acid. It is specifically contemplated that each member of the Markush group should be considered separately, thereby comprising another embodiment, and the Markush group is not to be read as a single unit. [0100] As used herein, the terms“bioconjugate” and“bioconjugate linker” refer to the resulting association between atoms or molecules of bioconjugate reactive groups or bioconjugate reactive moieties. The association can be direct or indirect. For example, a conjugate between a first bioconjugate reactive group (e.g.,–NH2,–COOH,–N- hydroxysuccinimide, or–maleimide) and a second bioconjugate reactive group (e.g., sulfhydryl, sulfur-containing amino acid, amine, amine sidechain containing amino acid, or carboxylate) provided herein can be direct, e.g., by covalent bond or linker (e.g., a first linker of second linker), or indirect, e.g., by non-covalent bond (e.g., electrostatic interactions (e.g., ionic bond, hydrogen bond, halogen bond), van der Waals interactions (e.g., dipole-dipole, dipole-induced dipole, London dispersion), ring stacking (pi effects), hydrophobic interactions and the like). In embodiments, bioconjugates or bioconjugate linkers are formed using bioconjugate chemistry (i.e., the association of two bioconjugate reactive groups) including, but are not limited to nucleophilic substitutions (e.g., reactions of amines and alcohols with acyl halides, active esters), electrophilic substitutions (e.g., enamine reactions) and additions to carbon-carbon and carbon-heteroatom multiple bonds (e.g., Michael reaction, Diels-Alder addition). These and other useful reactions are discussed in, for example, March, ADVANCED ORGANIC CHEMISTRY, 3rd Ed., John Wiley & Sons, New York, 1985; Hermanson, BIOCONJUGATE TECHNIQUES, Academic Press, San Diego, 1996; and Feeney et al., MODIFICATION OF PROTEINS; Advances in Chemistry Series, Vol.198, American Chemical Society, Washington, D.C., 1982. In embodiments, the first bioconjugate reactive group (e.g., maleimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl). In embodiments, the first bioconjugate reactive group (e.g., haloacetyl moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl). In embodiments, the first bioconjugate reactive group (e.g., pyridyl moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl). In embodiments, the first bioconjugate reactive group (e.g.,–N- hydroxysuccinimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., an amine). In embodiments, the first bioconjugate reactive group (e.g., maleimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., a sulfhydryl). In embodiments, the first bioconjugate reactive group (e.g.,–sulfo–N-hydroxysuccinimide moiety) is covalently attached to the second bioconjugate reactive group (e.g., an amine). [0101] Useful bioconjugate reactive moieties used for bioconjugate chemistries herein include, for example: (a) carboxyl groups and various derivatives thereof including, but not limited to, N- hydroxysuccinimide esters, N-hydroxybenztriazole esters, acid halides, acyl imidazoles, thioesters, p-nitrophenyl esters, alkyl, alkenyl, alkynyl and aromatic esters; (b) hydroxyl groups which can be converted to esters, ethers, aldehydes, etc.; (c) haloalkyl groups wherein the halide can be later displaced with a nucleophilic group such as, for example, an amine, a carboxylate anion, thiol anion, carbanion, or an alkoxide ion, thereby resulting in the covalent attachment of a new group at the site of the halogen atom; (d) dienophile groups which are capable of participating in Diels-Alder reactions such as, for example, maleimido or maleimide groups; (e) aldehyde or ketone groups such that subsequent derivatization is possible via formation of carbonyl derivatives such as, for example, imines, hydrazones, semicarbazones or oximes, or via such mechanisms as Grignard addition or alkyllithium addition; (f) sulfonyl halide groups for subsequent reaction with amines, for example, to form sulfonamides; (g) thiol groups, which can be converted to disulfides, reacted with acyl halides, or bonded to metals such as gold, or react with maleimides; (h) amine or sulfhydryl groups (e.g., present in cysteine), which can be, for example, acylated, alkylated or oxidized; (i) alkenes, which can undergo, for example, cycloadditions, acylation, Michael addition, etc; (j) epoxides, which can react with, for example, amines and hydroxyl compounds; (k) phosphoramidites and other standard functional groups useful in nucleic acid synthesis; (l) metal silicon oxide bonding; (m) metal bonding to reactive phosphorus groups (e.g., phosphines) to form, for example, phosphate diester bonds; (n) azides coupled to alkynes using copper catalyzed cycloaddition click chemistry; and (o) biotin conjugate can react with avidin or strepavidin to form a avidin-biotin complex or streptavidin-biotin complex. [0102] The bioconjugate reactive groups can be chosen such that they do not participate in, or interfere with, the chemical stability of the conjugate described herein. Alternatively, a reactive functional group can be protected from participating in the crosslinking reaction by the presence of a protecting group. In embodiments, the bioconjugate comprises a molecular entity derived from the reaction of an unsaturated bond, such as a maleimide, and a sulfhydryl group. [0103] “Analog,”“analogue,” or“derivative” is used in accordance with its plain ordinary meaning within Chemistry and Biology and refers to a chemical compound that is structurally similar to another compound (i.e., a so-called“reference” compound) but differs in composition, e.g., in the replacement of one atom by an atom of a different element, or in the presence of a particular functional group, or the replacement of one functional group by another functional group, or the absolute stereochemistry of one or more chiral centers of the reference compound. Accordingly, an analog is a compound that is similar or comparable in function and appearance but not in structure or origin to a reference compound. [0104] The terms“a” or“an,” as used in herein means one or more. In addition, the phrase “substituted with a[n],” as used herein, means the specified group may be substituted with one or more of any or all of the named substituents. For example, where a group, such as an alkyl or heteroaryl group, is“substituted with an unsubstituted C1-C20 alkyl, or unsubstituted 2 to 20 membered heteroalkyl,” the group may contain one or more unsubstituted C1-C20 alkyls, and/or one or more unsubstituted 2 to 20 membered heteroalkyls. [0105] Moreover, where a moiety is substituted with an R substituent, the group may be referred to as“R-substituted.” Where a moiety is R-substituted, the moiety is substituted with at least one R substituent and each R substituent is optionally different. Where a particular R group is present in the description of a chemical genus (such as Formula (I)), a Roman alphabetic symbol may be used to distinguish each appearance of that particular R group. For example, where multiple R13 substituents are present, each R13 substituent may be distinguished as R13A, R13B, R13C, R13D, etc., wherein each of R13A, R13B, R13C, R13D, etc. is defined within the scope of the definition of R13 and optionally differently. [0106] Descriptions of compounds of the present disclosure are limited by principles of chemical bonding known to those skilled in the art. Accordingly, where a group may be substituted by one or more of a number of substituents, such substitutions are selected so as to comply with principles of chemical bonding and to give compounds which are not inherently unstable and/or would be known to one of ordinary skill in the art as likely to be unstable under ambient conditions, such as aqueous, neutral, and several known physiological conditions. For example, a heterocycloalkyl or heteroaryl is attached to the remainder of the molecule via a ring heteroatom in compliance with principles of chemical bonding known to those skilled in the art thereby avoiding inherently unstable compounds. [0107] The term“pharmaceutically acceptable salts” is meant to include salts of the active compounds that are prepared with relatively nontoxic acids or bases, depending on the particular substituents found on the compounds described herein. When compounds of the present disclosure contain relatively acidic functionalities, base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt. When compounds of the present disclosure contain relatively basic functionalities, acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic,
monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic, p- tolylsulfonic, citric, tartaric, oxalic, methanesulfonic, and the like. Also included are salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, for example, Berge et al.,“Pharmaceutical Salts”, Journal of Pharmaceutical Science, 1977, 66, 1-19). Certain specific compounds of the present disclosure contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts. [0108] Thus, the compounds of the present disclosure may exist as salts, such as with pharmaceutically acceptable acids. The present disclosure includes such salts. Non-limiting examples of such salts include hydrochlorides, hydrobromides, phosphates, sulfates, methanesulfonates, nitrates, maleates, acetates, citrates, fumarates, proprionates, tartrates (e.g., (+)-tartrates, (-)-tartrates, or mixtures thereof including racemic mixtures), succinates, benzoates, and salts with amino acids such as glutamic acid, and quaternary ammonium salts (e.g., methyl iodide, ethyl iodide, and the like). These salts may be prepared by methods known to those skilled in the art. [0109] The neutral forms of the compounds are preferably regenerated by contacting the salt with a base or acid and isolating the parent compound in the conventional manner. The parent form of the compound may differ from the various salt forms in certain physical properties, such as solubility in polar solvents. [0110] In addition to salt forms, the present disclosure provides compounds, which are in a prodrug form. Prodrugs of the compounds described herein are those compounds that readily undergo chemical changes under physiological conditions to provide the compounds of the present disclosure. Prodrugs of the compounds described herein may be converted in vivo after administration. Additionally, prodrugs can be converted to the compounds of the present disclosure by chemical or biochemical methods in an ex vivo environment, such as, for example, when contacted with a suitable enzyme or chemical reagent. [0111] Certain compounds of the present disclosure can exist in unsolvated forms as well as solvated forms, including hydrated forms. In general, the solvated forms are equivalent to unsolvated forms and are encompassed within the scope of the present disclosure. Certain compounds of the present disclosure may exist in multiple crystalline or amorphous forms. In general, all physical forms are equivalent for the uses contemplated by the present disclosure and are intended to be within the scope of the present disclosure. [0112] A polypeptide, or a cell is“recombinant” when it is artificial or engineered, or derived from or contains an artificial or engineered protein or nucleic acid (e.g., non-natural or not wild type). For example, a polynucleotide that is inserted into a vector or any other heterologous location, e.g., in a genome of a recombinant organism, such that it is not associated with nucleotide sequences that normally flank the polynucleotide as it is found in nature is a recombinant polynucleotide. A protein expressed in vitro or in vivo from a recombinant polynucleotide is an example of a recombinant polypeptide. Likewise, a polynucleotide sequence that does not appear in nature, for example a variant of a naturally occurring gene, is recombinant. [0113] As used herein, the term“about” means a range of values including the specified value, which a person of ordinary skill in the art would consider reasonably similar to the specified value. In embodiments, about means within a standard deviation using
measurements generally acceptable in the art. In embodiments, about means a range extending to +/- 10% of the specified value. In embodiments, about includes the specified value. [0114] “Co-administer” is meant that a composition described herein is administered at the same time, just prior to, or just after the administration of one or more additional therapies. The compounds of the invention can be administered alone or can be coadministered to the patient. Co-administration is meant to include simultaneous or sequential administration of the compounds individually or in combination (more than one compound). Thus, the preparations can also be combined, when desired, with other active substances (e.g., to reduce metabolic degradation). The compositions of the present invention can be delivered transdermally, by a topical route, or formulated as applicator sticks, solutions, suspensions, emulsions, gels, creams, ointments, pastes, jellies, paints, powders, and aerosols. [0115] A“cell” as used herein, refers to a cell carrying out metabolic or other function sufficient to preserve or replicate its genomic DNA. A cell can be identified by well-known methods in the art including, for example, presence of an intact membrane, staining by a particular dye, ability to produce progeny or, in the case of a gamete, ability to combine with a second gamete to produce a viable offspring. Cells may include prokaryotic and eukaroytic cells. Prokaryotic cells include but are not limited to bacteria. Eukaryotic cells include but are not limited to yeast cells and cells derived from plants and animals, for example mammalian, insect (e.g., spodoptera) and human cells. Cells may be useful when they are naturally nonadherent or have been treated not to adhere to surfaces, for example by trypsinization. [0116] The terms“treating” or“treatment” refers to any indicia of success in the treatment or amelioration of an injury, disease, pathology or condition, including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the injury, pathology or condition more tolerable to the patient; slowing in the rate of
degeneration or decline; making the final point of degeneration less debilitating; improving a patient’s physical or mental well-being. The treatment or amelioration of symptoms can be based on objective or subjective parameters; including the results of a physical examination, neuropsychiatric exams, and/or a psychiatric evaluation. For example, the certain methods presented herein successfully treat cancer by decreasing the incidence of cancer and or causing remission of cancer. In some embodiments of the compositions or methods described herein, treating cancer includes slowing the rate of growth or spread of cancer cells, reducing metastasis, or reducing the growth of metastatic tumors. The term“treating” and conjugations thereof, include prevention of an injury, pathology, condition, or disease. In embodiments, treating is preventing. In embodiments, treating does not include preventing. In embodiments, the treating or treatment is no prophylactic treatment. [0117] An“effective amount” is an amount sufficient for a compound to accomplish a stated purpose relative to the absence of the compound (e.g., achieve the effect for which it is administered, treat a disease, reduce enzyme activity, increase enzyme activity, reduce signaling pathway, reduce one or more symptoms of a disease or condition (e.g., reduce signaling pathway stimulated by an autophagy adapter protein, reduce the signaling pathway activity of an autophagy protein). An example of an“effective amount” is an amount sufficient to contribute to the treatment, prevention, or reduction of a symptom or symptoms of a disease, which could also be referred to as a“therapeutically effective amount” when referred to in this context. A“reduction” of a symptom or symptoms (and grammatical equivalents of this phrase) means decreasing of the severity or frequency of the symptom(s), or elimination of the symptom(s). A“prophylactically effective amount” of a drug is an amount of a drug that, when administered to a subject, will have the intended prophylactic effect, e.g., preventing or delaying the onset (or reoccurrence) of an injury, disease, pathology or condition, or reducing the likelihood of the onset (or reoccurrence) of an injury, disease, pathology, or condition, or their symptoms. The full prophylactic effect does not necessarily occur by administration of one dose, and may occur only after administration of a series of doses. Thus, a prophylactically effective amount may be administered in one or more administrations. An“activity decreasing amount,” as used herein, refers to an amount of antagonist required to decrease the activity of an enzyme relative to the absence of the antagonist. A“function disrupting amount,” as used herein, refers to the amount of antagonist required to disrupt the function of an enzyme or protein relative to the absence of the antagonist. The exact amounts will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman,
Pharmaceutical Dosage Forms (vols.1-3, 1992); Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999); Pickar, Dosage Calculations (1999); and Remington: The Science and Practice of Pharmacy, 20th Edition, 2003, Gennaro, Ed., Lippincott, Williams & Wilkins). [0118] “Control” or“control experiment” is used in accordance with its plain ordinary meaning and refers to an experiment in which the subjects or reagents of the experiment are treated as in a parallel experiment except for omission of a procedure, reagent, or variable of the experiment. In some instances, the control is used as a standard of comparison in evaluating experimental effects. In some embodiments, a control is the measurement of the activity (e.g., signaling pathway) of a protein in the absence of a compound as described herein (including embodiments, examples, figures, or Tables). [0119] “Contacting” is used in accordance with its plain ordinary meaning and refers to the process of allowing at least two distinct species (e.g., chemical compounds including biomolecules, or cells) to become sufficiently proximal to react, interact or physically touch. It should be appreciated; however, the resulting reaction product can be produced directly from a reaction between the added reagents or from an intermediate from one or more of the added reagents which can be produced in the reaction mixture. [0120] The term“contacting” may include allowing two species to react, interact, or physically touch, wherein the two species may be a compound as described herein and a cellular component (e.g., protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, virus, lipid droplet, vesicle, small molecule, protein complex, protein aggregate, or macromolecule). In some embodiments contacting includes allowing a compound described herein to interact with a cellular component (e.g., protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, virus, lipid droplet, organelle, cellular compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or macromolecule) that is involved in a signaling pathway. [0121] As defined herein, the term“inhibition,”“inhibit,”“inhibiting” and the like in reference to a cellular component-inhibitor interaction means negatively affecting (e.g., decreasing) the activity or function of the cellular component (e.g., decreasing the signaling pathway stimulated by a cellular component (e.g., protein, ion, lipid, virus, lipid droplet, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or
macromolecule)), relative to the activity or function of the cellular component in the absence of the inhibitor. In some embodiments inhibition refers to reduction of a disease or symptoms of disease. In some embodiments, inhibition refers to a reduction in the activity of a signal transduction pathway or signaling pathway (e.g., reduction of a pathway involving the cellular component). Thus, inhibition includes, at least in part, partially or totally blocking stimulation, decreasing, preventing, or delaying activation, or inactivating, desensitizing, or down-regulating the signaling pathway or enzymatic activity or the amount of a cellular component. [0122] The term“modulator” refers to a composition that increases or decreases the level of a target molecule or the function of a target molecule or the physical state of the target of the molecule (e.g., a target may be a cellular component (e.g., protein, ion, lipid, virus, lipid droplet, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular
compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or macromolecule)) relative to the absence of the composition. [0123] The term“modulate” is used in accordance with its plain ordinary meaning and refers to the act of changing or varying one or more properties.“Modulation” refers to the process of changing or varying one or more properties. For example, as applied to the effects of a modulator on a target protein, to modulate means to change by increasing or decreasing a property or function of the target molecule or the amount of the target molecule. [0124] “Patient” or“subject in need thereof” refers to a living organism suffering from or prone to a disease or condition that can be treated by administration of a pharmaceutical composition as provided herein. Non-limiting examples include humans, other mammals, bovines, rats, mice, dogs, monkeys, goat, sheep, cows, deer, and other non-mammalian animals. In some embodiments, a patient is human. [0125] “Disease” or“condition” refer to a state of being or health status of a patient or subject capable of being treated with the compounds or methods provided herein. In some embodiments, the disease is a disease related to (e.g., caused by) a cellular component (e.g., protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, vesicle, small molecule, protein complex, protein aggregate, or macromolecule). [0126] As used herein, the term“cancer” refers to all types of cancer, neoplasm or malignant tumors found in mammals (e.g., humans), including leukemia, lymphoma, carcinomas and sarcomas. Exemplary cancers that may be treated with a compound or method provided herein include cancer of the thyroid, endocrine system, brain, breast, cervix, colon, head & neck, liver, kidney, lung, non-small cell lung, melanoma, mesothelioma, ovary, sarcoma, stomach, uterus, Medulloblastoma, colorectal cancer, pancreatic cancer. Additional examples include, Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer,
rhabdomyosarcoma, primary thrombocytosis, primary macroglobulinemia, primary brain tumors, cancer, malignant pancreatic insulanoma, malignant carcinoid, urinary bladder cancer, premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer,
neuroblastoma, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, endometrial cancer, adrenal cortical cancer, neoplasms of the endocrine or exocrine pancreas, medullary thyroid cancer, medullary thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid cancer, hepatocellular carcinoma, or prostate cancer. [0127] The term“leukemia” refers broadly to progressive, malignant diseases of the blood- forming organs and is generally characterized by a distorted proliferation and development of leukocytes and their precursors in the blood and bone marrow. Leukemia is generally clinically classified on the basis of (1) the duration and character of the disease-acute or chronic; (2) the type of cell involved; myeloid (myelogenous), lymphoid (lymphogenous), or monocytic; and (3) the increase or non-increase in the number abnormal cells in the blood- leukemic or aleukemic (subleukemic). Exemplary leukemias that may be treated with a compound or method provided herein include, for example, acute nonlymphocytic leukemia, chronic lymphocytic leukemia, acute granulocytic leukemia, chronic granulocytic leukemia, acute promyelocytic leukemia, adult T-cell leukemia, aleukemic leukemia, a leukocythemic leukemia, basophylic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross’ leukemia, hairy-cell leukemia, hemoblastic leukemia, hemocytoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenous leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, micromyeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myelocytic leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Naegeli leukemia, plasma cell leukemia, multiple myeloma, plasmacytic leukemia, promyelocytic leukemia, Rieder cell leukemia, Schilling’s leukemia, stem cell leukemia, subleukemic leukemia, or undifferentiated cell leukemia. [0128] As used herein, the term“lymphoma” refers to a group of cancers affecting hematopoietic and lymphoid tissues. It begins in lymphocytes, the blood cells that are found primarily in lymph nodes, spleen, thymus, and bone marrow. Two main types of lymphoma are non-Hodgkin lymphoma and Hodgkin’s disease. Hodgkin’s disease represents approximately 15% of all diagnosed lymphomas. This is a cancer associated with Reed- Sternberg malignant B lymphocytes. Non-Hodgkin’s lymphomas (NHL) can be classified based on the rate at which cancer grows and the type of cells involved. There are aggressive (high grade) and indolent (low grade) types of NHL. Based on the type of cells involved, there are B-cell and T-cell NHLs. Exemplary B-cell lymphomas that may be treated with a compound or method provided herein include, but are not limited to, small lymphocytic lymphoma, Mantle cell lymphoma, follicular lymphoma, marginal zone lymphoma, extranodal (MALT) lymphoma, nodal (monocytoid B-cell) lymphoma, splenic lymphoma, diffuse large cell B-lymphoma, Burkitt’s lymphoma, lymphoblastic lymphoma,
immunoblastic large cell lymphoma, or precursor B-lymphoblastic lymphoma. Exemplary T- cell lymphomas that may be treated with a compound or method provided herein include, but are not limited to, cunateous T-cell lymphoma, peripheral T-cell lymphoma, anaplastic large cell lymphoma, mycosis fungoides, and precursor T-lymphoblastic lymphoma. [0129] The term“sarcoma” generally refers to a tumor which is made up of a substance like the embryonic connective tissue and is generally composed of closely packed cells embedded in a fibrillar or homogeneous substance. Sarcomas that may be treated with a compound or method provided herein include a chondrosarcoma, fibrosarcoma,
lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abemethy's sarcoma, adipose sarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, chorio carcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, immunoblastic sarcoma of B cells, lymphoma,
immunoblastic sarcoma of T-cells, Jensen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukosarcoma, malignant mesenchymoma sarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma, serocystic sarcoma, synovial sarcoma, or telangiectaltic sarcoma. [0130] The term“melanoma” is taken to mean a tumor arising from the melanocytic system of the skin and other organs. Melanomas that may be treated with a compound or method provided herein include, for example, acral-lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Cloudman's melanoma, S91 melanoma, Harding-Passey melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungal melanoma, or superficial spreading melanoma. [0131] The term“carcinoma” refers to a malignant new growth made up of epithelial cells tending to infiltrate the surrounding tissues and give rise to metastases. Exemplary carcinomas that may be treated with a compound or method provided herein include, for example, medullary thyroid carcinoma, familial medullary thyroid carcinoma, acinar carcinoma, acinous carcinoma, adenocystic carcinoma, adenoid cystic carcinoma, carcinoma adenomatosum, carcinoma of adrenal cortex, alveolar carcinoma, alveolar cell carcinoma, basal cell carcinoma, carcinoma basocellulare, basaloid carcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma, bronchogenic carcinoma, cerebriform carcinoma, cholangiocellular carcinoma, chorionic carcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform carcinoma, carcinoma en cuirasse, carcinoma cutaneum, cylindrical carcinoma, cylindrical cell carcinoma, duct carcinoma, carcinoma durum, embryonal carcinoma, encephaloid carcinoma, epiermoid carcinoma, carcinoma epitheliale adenoides, exophytic carcinoma, carcinoma ex ulcere, carcinoma fibrosum, gelatiniforni carcinoma, gelatinous carcinoma, giant cell carcinoma, carcinoma gigantocellulare, glandular carcinoma, granulosa cell carcinoma, hair-matrix carcinoma, hematoid carcinoma, hepatocellular carcinoma, Hurthle cell carcinoma, hyaline carcinoma, hypernephroid carcinoma, infantile embryonal carcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelial carcinoma, Krompecher's carcinoma, Kulchitzky-cell carcinoma, large-cell carcinoma, lenticular carcinoma, carcinoma lenticulare, lipomatous carcinoma, lymphoepithelial carcinoma, carcinoma medullare, medullary carcinoma, melanotic carcinoma, carcinoma molle, mucinous carcinoma, carcinoma muciparum, carcinoma mucocellulare, mucoepidermoid carcinoma, carcinoma mucosum, mucous carcinoma, carcinoma myxomatodes, nasopharyngeal carcinoma, oat cell carcinoma, carcinoma ossificans, osteoid carcinoma, papillary carcinoma, periportal carcinoma, preinvasive carcinoma, prickle cell carcinoma, pultaceous carcinoma, renal cell carcinoma of kidney, reserve cell carcinoma, carcinoma sarcomatodes, schneiderian carcinoma, scirrhous carcinoma, carcinoma scroti, signet-ring cell carcinoma, carcinoma simplex, small-cell carcinoma, solanoid carcinoma, spheroidal cell carcinoma, spindle cell carcinoma, carcinoma spongiosum, squamous carcinoma, squamous cell carcinoma, string carcinoma, carcinoma telangiectaticum, carcinoma telangiectodes, transitional cell carcinoma, carcinoma tuberosum, tuberous carcinoma, verrucous carcinoma, or carcinoma villosum. [0132] As used herein, the term“autoimmune disease” refers to a disease or condition in which a subject’s immune system has an aberrant immune response against a substance that does not normally elicit an immune response in a healthy subject. Examples of autoimmune diseases that may be treated with a compound, pharmaceutical composition, or method described herein include Acute Disseminated Encephalomyelitis (ADEM), Acute necrotizing hemorrhagic leukoencephalitis, Addison’s disease, Agammaglobulinemia, Alopecia areata, Amyloidosis, Ankylosing spondylitis, Anti-GBM/Anti-TBM nephritis, Antiphospholipid syndrome (APS), Autoimmune angioedema, Autoimmune aplastic anemia, Autoimmune dysautonomia, Autoimmune hepatitis, Autoimmune hyperlipidemia, Autoimmune immunodeficiency, Autoimmune inner ear disease (AIED), Autoimmune myocarditis, Autoimmune oophoritis, Autoimmune pancreatitis, Autoimmune retinopathy, Autoimmune thrombocytopenic purpura (ATP), Autoimmune thyroid disease, Autoimmune urticaria, Axonal or neuronal neuropathies, Balo disease, Behcet’s disease, Bullous pemphigoid, Cardiomyopathy, Castleman disease, Celiac disease, Chagas disease, Chronic fatigue syndrome, Chronic inflammatory demyelinating polyneuropathy (CIDP), Chronic recurrent multifocal ostomyelitis (CRMO), Churg-Strauss syndrome, Cicatricial pemphigoid/benign mucosal pemphigoid, Crohn’s disease, Cogans syndrome, Cold agglutinin disease,
Congenital heart block, Coxsackie myocarditis, CREST disease, Essential mixed
cryoglobulinemia, Demyelinating neuropathies, Dermatitis herpetiformis, Dermatomyositis, Devic’s disease (neuromyelitis optica), Discoid lupus, Dressler’s syndrome, Endometriosis, Eosinophilic esophagitis, Eosinophilic fasciitis, Erythema nodosum, Experimental allergic encephalomyelitis, Evans syndrome, Fibromyalgia, Fibrosing alveolitis, Giant cell arteritis (temporal arteritis), Giant cell myocarditis, Glomerulonephritis, Goodpasture’s syndrome, Granulomatosis with Polyangiitis (GPA) (formerly called Wegener’s Granulomatosis), Graves’ disease, Guillain-Barre syndrome, Hashimoto’s encephalitis, Hashimoto’s thyroiditis, Hemolytic anemia, Henoch-Schonlein purpura, Herpes gestationis,
Hypogammaglobulinemia, Idiopathic thrombocytopenic purpura (ITP), IgA nephropathy, IgG4-related sclerosing disease, Immunoregulatory lipoproteins, Inclusion body myositis, Interstitial cystitis, Juvenile arthritis, Juvenile diabetes (Type 1 diabetes), Juvenile myositis, Kawasaki syndrome, Lambert-Eaton syndrome, Leukocytoclastic vasculitis, Lichen planus, Lichen sclerosus, Ligneous conjunctivitis, Linear IgA disease (LAD), Lupus (SLE), Lyme disease, chronic, Meniere’s disease, Microscopic polyangiitis, Mixed connective tissue disease (MCTD), Mooren’s ulcer, Mucha-Habermann disease, Multiple sclerosis, Myasthenia gravis, Myositis, Narcolepsy, Neuromyelitis optica (Devic’s), Neutropenia, Ocular cicatricial pemphigoid, Optic neuritis, Palindromic rheumatism, PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcus), Paraneoplastic cerebellar degeneration, Paroxysmal nocturnal hemoglobinuria (PNH), Parry Romberg syndrome, Parsonnage-Turner syndrome, Pars planitis (peripheral uveitis), Pemphigus, Peripheral neuropathy, Perivenous encephalomyelitis, Pernicious anemia, POEMS syndrome,
Polyarteritis nodosa, Type I, II, & III autoimmune polyglandular syndromes, Polymyalgia rheumatica, Polymyositis, Postmyocardial infarction syndrome, Postpericardiotomy syndrome, Progesterone dermatitis, Primary biliary cirrhosis, Primary sclerosing cholangitis, Psoriasis, Psoriatic arthritis, Idiopathic pulmonary fibrosis, Pyoderma gangrenosum, Pure red cell aplasia, Raynauds phenomenon, Reactive Arthritis, Reflex sympathetic dystrophy, Reiter’s syndrome, Relapsing polychondritis, Restless legs syndrome, Retroperitoneal fibrosis, Rheumatic fever, Rheumatoid arthritis, Sarcoidosis, Schmidt syndrome, Scleritis, Scleroderma, Sjogren’s syndrome, Sperm & testicular autoimmunity, Stiff person syndrome, Subacute bacterial endocarditis (SBE), Susac’s syndrome, Sympathetic ophthalmia,
Takayasu’s arteritis, Temporal arteritis/Giant cell arteritis, Thrombocytopenic purpura (TTP), Tolosa-Hunt syndrome, Transverse myelitis, Type 1 diabetes, Ulcerative colitis,
Undifferentiated connective tissue disease (UCTD), Uveitis, Vasculitis, Vesiculobullous dermatosis, Vitiligo, or Wegener’s granulomatosis (i.e., Granulomatosis with Polyangiitis (GPA). [0133] As used herein, the term“neurodegenerative disease” refers to a disease or condition in which the function of a subject’s nervous system becomes impaired. Examples of neurodegenerative diseases that may be treated with a compound, pharmaceutical composition, or method described herein include Alexander's disease, Alper's disease, Alzheimer's disease, Amyotrophic lateral sclerosis, Ataxia telangiectasia, Batten disease (also known as Spielmeyer-Vogt-Sjogren-Batten disease), Bovine spongiform encephalopathy (BSE), Canavan disease, Cockayne syndrome, Corticobasal degeneration, Creutzfeldt-Jakob disease, frontotemporal dementia, Gerstmann-Sträussler-Scheinker syndrome, Huntington's disease, HIV-associated dementia, Kennedy's disease, Krabbe's disease, kuru, Lewy body dementia, Machado-Joseph disease (Spinocerebellar ataxia type 3), Multiple sclerosis, Multiple System Atrophy, Narcolepsy, Neuroborreliosis, Parkinson's disease, Pelizaeus- Merzbacher Disease, Pick’s disease, Primary lateral sclerosis, Prion diseases, Refsum’s disease, Sandhoff's disease, Schilder's disease, Subacute combined degeneration of spinal cord secondary to Pernicious Anaemia, Schizophrenia, Spinocerebellar ataxia (multiple types with varying characteristics), Spinal muscular atrophy, Steele-Richardson-Olszewski disease, or Tabes dorsalis. [0134] As used herein, the term“metabolic disease” or“metabolic disorder” refers to a disease or condition in which a subject’s metabolism or metabolic system (e.g., function of storing or utilizing energy) becomes impaired. Examples of metabolic diseases that may be treated with a compound, pharmaceutical composition, or method described herein include diabetes (e.g., type I or type II), obesity, metabolic syndrome, or a mitochondrial disease (e.g., dysfunction of mitochondria or aberrant mitochondrial function). [0135] The term“cellular component associated disease” (e.g., the cellular component may be a protein, ion, lipid, nucleic acid, nucleotide, amino acid, protein, particle, organelle, cellular compartment, microorganism, virus, vesicle, small molecule, protein complex, protein aggregate, or macromolecule; the disease may be a neurodegenerative disease, cancer, a metabolic disease, authoimmune disease, inflammatory disease, or infectious disease) (also referred to herein as“cellular component related disease”) refers to a disease caused by the celllular component. Other diseases that are associated with aberrant activity or level of the cellular component are well known in the art and determining such diseases are within the skill of a person of skill in the art. [0136] “Pharmaceutically acceptable excipient” and“pharmaceutically acceptable carrier” refer to a substance that aids the administration of an active agent to and absorption by a subject and can be included in the compositions of the present invention without causing a significant adverse toxicological effect on the patient. Non-limiting examples of
pharmaceutically acceptable excipients include water, NaCl, normal saline solutions, lactated Ringer’s, normal sucrose, normal glucose, binders, fillers, disintegrants, lubricants, coatings, sweeteners, flavors, salt solutions (such as Ringer's solution), alcohols, oils, gelatins, carbohydrates such as lactose, amylose or starch, fatty acid esters, hydroxymethycellulose, polyvinyl pyrrolidine, and colors, and the like. Such preparations can be sterilized and, if desired, mixed with auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, and/or aromatic substances and the like that do not deleteriously react with the compounds of the invention. One of skill in the art will recognize that other pharmaceutical excipients are useful in the present invention. [0137] The term“preparation” is intended to include the formulation of the active compound with encapsulating material as a carrier providing a capsule in which the active component with or without other carriers, is surrounded by a carrier, which is thus in association with it. Similarly, cachets and lozenges are included. Tablets, powders, capsules, pills, cachets, and lozenges can be used as solid dosage forms suitable for oral administration. [0138] As used herein, the term“administering” means oral administration, administration as a suppository, topical contact, intravenous, intraperitoneal, intramuscular, intralesional, intrathecal, intranasal or subcutaneous administration, or the implantation of a slow-release device, e.g., a mini-osmotic pump, to a subject. Administration is by any route, including parenteral and transmucosal (e.g., buccal, sublingual, palatal, gingival, nasal, vaginal, rectal, or transdermal). Parenteral administration includes, e.g., intravenous, intramuscular, intra- arteriole, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial. Other modes of delivery include, but are not limited to, the use of liposomal formulations, intravenous infusion, transdermal patches, etc. By“co-administer” it is meant that a composition described herein is administered at the same time, just prior to, or just after the administration of one or more additional therapies, for example cancer therapies such as chemotherapy, hormonal therapy, radiotherapy, or immunotherapy. The compounds of the invention can be administered alone or can be coadministered to the patient.
Coadministration is meant to include simultaneous or sequential administration of the compounds individually or in combination (more than one compound). Thus, the
preparations can also be combined, when desired, with other active substances (e.g., to reduce metabolic degradation). The compositions of the present invention can be delivered by transdermally, by a topical route, formulated as applicator sticks, solutions, suspensions, emulsions, gels, creams, ointments, pastes, jellies, paints, powders, and aerosols. [0139] The compounds described herein can be used in combination with one another, with other active agents known to be useful in treating a disease associated with cells expressing a disease associated cellular component, or with adjunctive agents that may not be effective alone, but may contribute to the efficacy of the active agent. [0140] In some embodiments, co-administration includes administering one active agent within 0.5, 1, 2, 4, 6, 8, 10, 12, 16, 20, or 24 hours of a second active agent. Co- administration includes administering two active agents simultaneously, approximately simultaneously (e.g., within about 1, 5, 10, 15, 20, or 30 minutes of each other), or sequentially in any order. In some embodiments, co-administration can be accomplished by co-formulation, i.e., preparing a single pharmaceutical composition including both active agents. In other embodiments, the active agents can be formulated separately. In another embodiment, the active and/or adjunctive agents may be linked or conjugated to one another. [0141] As a non-limiting example, the compounds described herein can be co-administered with conventional chemotherapeutic agents including alkylating agents (e.g.,
cyclophosphamide, ifosfamide, chlorambucil, busulfan, melphalan, mechlorethamine, uramustine, thiotepa, nitrosoureas, etc.), anti-metabolites (e.g., 5-fluorouracil, azathioprine, methotrexate, leucovorin, capecitabine, cytarabine, floxuridine, fludarabine, gemcitabine, pemetrexed, raltitrexed, etc.), plant alkaloids (e.g., vincristine, vinblastine, vinorelbine, vindesine, podophyllotoxin, paclitaxel, docetaxel, etc.), topoisomerase inhibitors (e.g., irinotecan, topotecan, amsacrine, etoposide (VP16), etoposide phosphate, teniposide, etc.), antitumor antibiotics (e.g., doxorubicin, adriamycin, daunorubicin, epirubicin, actinomycin, bleomycin, mitomycin, mitoxantrone, plicamycin, etc.), platinum-based compounds (e.g., cisplatin, oxaloplatin, carboplatin, etc.), and the like. [0142] The compounds described herein can also be co-administered with conventional hormonal therapeutic agents including, but not limited to, steroids (e.g., dexamethasone), finasteride, aromatase inhibitors, tamoxifen, and gonadotropin-releasing hormone agonists (GnRH) such as goserelin. [0143] Additionally, the compounds described herein can be co-administered with conventional immunotherapeutic agents including, but not limited to, immunostimulants (e.g., Bacillus Calmette-Guérin (BCG), levamisole, interleukin-2, alpha-interferon, etc.), monoclonal antibodies (e.g., anti-CD20, anti-HER2, anti-CD52, anti-HLA-DR, and anti- VEGF monoclonal antibodies), immunotoxins (e.g., anti-CD33 monoclonal antibody- calicheamicin conjugate, anti-CD22 monoclonal antibody-pseudomonas exotoxin conjugate, etc.), and radioimmunotherapy (e.g., anti-CD20 monoclonal antibody conjugated to 111In, 90Y, or 131I, etc.). [0144] In a further embodiment, the compounds described herein can be co-administered with conventional radiotherapeutic agents including, but not limited to, radionuclides such as 47Sc, 64Cu, 67Cu, 89Sr, 86Y, 87Y, 90Y, 105Rh, 111Ag, 111In, 117mSn, 149Pm, 153Sm, 166Ho, 177Lu, 186Re, 188Re, 211At, and 212Bi, optionally conjugated to antibodies directed against tumor antigens. [0145] In therapeutic use for the treatment of a disease, compound utilized in the pharmaceutical compositions of the present invention may be administered at the initial dosage of about 0.001 mg/kg to about 1000 mg/kg daily. A daily dose range of about 0.01 mg/kg to about 500 mg/kg, or about 0.1 mg/kg to about 200 mg/kg, or about 1 mg/kg to about 100 mg/kg, or about 10 mg/kg to about 50 mg/kg, can be used. The dosages, however, may be varied depending upon the requirements of the patient, the severity of the condition being treated, and the compound or drug being employed. For example, dosages can be empirically determined considering the type and stage of cancer diagnosed in a particular patient. The dose administered to a patient, in the context of the present invention, should be sufficient to affect a beneficial therapeutic response in the patient over time. The size of the dose will also be determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of a compound in a particular patient. Determination of the proper dosage for a particular situation is within the skill of the practitioner. Generally, treatment is initiated with smaller dosages which are less than the optimum dose of the compound. Thereafter, the dosage is increased by small increments until the optimum effect under circumstances is reached. For convenience, the total daily dosage may be divided and administered in portions during the day, if desired. [0146] The compounds described herein can be used in combination with one another, with other active agents known to be useful in treating cancer or with adjunctive agents that may not be effective alone, but may contribute to the efficacy of the active agent. [0147] The term“associated” or“associated with” in the context of a substance or substance activity or function associated with a disease (e.g., a protein associated disease, disease associated with a cellular component) means that the disease (e.g., neurodegenerative disease, cancer) is caused by (in whole or in part), or a symptom of the disease is caused by (in whole or in part) the substance or substance activity or function or the disease or a symptom of the disease may be treated by modulating (e.g., inhibiting or activating) the substance (e.g., cellular component). For example, a neurodegenerative disease associated with a protein aggregate may be a neurodegenerative disease that results (entirely or partially) from aberrant protein aggregation or a neurodegenerative disease wherein a particular symptom of the disease is caused (entirely or partially) by aberrant protein aggregation. As used herein, what is described as being associated with a disease, if a causative agent, could be a target for treatment of the disease. For example, a neurodegenerative disease associated with aberrant protein aggregation or a protein aggregate associated neurodegenerative disease, may be treated with a protein aggregate modulator or protein aggregate targeted autophagy degrader, in the instance where increased protein aggregation causes the neurodegenerative disease. [0148] The term“aberrant” as used herein refers to different from normal. When used to describe enzymatic activity, aberrant refers to activity that is greater or less than a normal control or the average of normal non-diseased control samples. Aberrant activity may refer to an amount of activity that results in a disease, wherein returning the aberrant activity to a normal or non-disease-associated amount (e.g., by administering a compound or using a method as described herein), results in reduction of the disease or one or more disease symptoms. [0149] “Anti-cancer agent” is used in accordance with its plain ordinary meaning and refers to a composition (e.g., compound, drug, antagonist, inhibitor, modulator) having
antineoplastic properties or the ability to inhibit the growth or proliferation of cells. In some embodiments, an anti-cancer agent is a chemotherapeutic. In some embodiments, an anti- cancer agent is an agent identified herein having utility in methods of treating cancer. In some embodiments, an anti-cancer agent is an agent approved by the FDA or similar regulatory agency of a country other than the USA, for treating cancer. In embodiments, an anti-cancer agent is an inhibitor of K-Ras, RAF, MEK, Erk, PI3K, Akt, RTK, or mTOR. In embodiments, an anti-cancer agent is an MDM2 inhibitor or a genotoxic anti-cancer agent. In embodiments, an anti-cancer agent is nutlin-1, nutlin-2, nutlin-3, nutlin-3a, nutlin-3b, YH239-EE, MI-219, MI-773, MI-77301, MI-888, MX69, RG7112, RG7388, RITA, idasanutlin, DS-3032b, or AMG232. In embodiments, an anti-cancer agent is an alkylating agent, intercalating agent, or DNA replication inhibitor. Examples of anti-cancer agents include, but are not limited to, MEK (e.g., MEK1, MEK2, or MEK1 and MEK2) inhibitors (e.g., XL518, CI-1040, PD035901, selumetinib/ AZD6244, GSK1120212/ trametinib, GDC- 0973, ARRY-162, ARRY-300, AZD8330, PD0325901, U0126, PD98059, TAK-733, PD318088, AS703026, BAY 869766), alkylating agents (e.g., cyclophosphamide, ifosfamide, chlorambucil, busulfan, melphalan, mechlorethamine, uramustine, thiotepa, nitrosoureas, nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, meiphalan), ethylenimine and methylmelamines (e.g., hexamethlymelamine, thiotepa), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomusitne, semustine, streptozocin), triazenes (decarbazine)), anti-metabolites (e.g., 5- azathioprine, leucovorin, capecitabine, fludarabine, gemcitabine, pemetrexed, raltitrexed, folic acid analog (e.g., methotrexate), or pyrimidine analogs (e.g., fluorouracil, floxouridine, Cytarabine), purine analogs (e.g., mercaptopurine, thioguanine, pentostatin), etc.), plant alkaloids (e.g., vincristine, vinblastine, vinorelbine, vindesine, podophyllotoxin, paclitaxel, docetaxel, etc.), topoisomerase inhibitors (e.g., irinotecan, topotecan, amsacrine, etoposide (VP16), etoposide phosphate, teniposide, etc.), antitumor antibiotics (e.g., doxorubicin, adriamycin, daunorubicin, epirubicin, actinomycin, bleomycin, mitomycin, mitoxantrone, plicamycin, etc.), platinum-based compounds (e.g., cisplatin, oxaloplatin, carboplatin), anthracenedione (e.g., mitoxantrone), substituted urea (e.g., hydroxyurea), methyl hydrazine derivative (e.g., procarbazine), adrenocortical suppressant (e.g., mitotane, aminoglutethimide), epipodophyllotoxins (e.g., etoposide), antibiotics (e.g., daunorubicin, doxorubicin, bleomycin), enzymes (e.g., L-asparaginase), inhibitors of mitogen-activated protein kinase signaling (e.g., U0126, PD98059, PD184352, PD0325901, ARRY-142886, SB239063, SP600125, BAY 43-9006, wortmannin, or
LY294002, Syk inhibitors, mTOR inhibitors, antibodies (e.g., rituxan), gossyphol, genasense, polyphenol E, Chlorofusin, all trans-retinoic acid (ATRA), bryostatin, tumor necrosis factor- related apoptosis-inducing ligand (TRAIL), 5-aza-2'-deoxycytidine, all trans retinoic acid, doxorubicin, vincristine, etoposide, gemcitabine, imatinib (Gleevec.RTM.), geldanamycin, 17-N-Allylamino-17-Demethoxygeldanamycin (17-AAG), flavopiridol, LY294002, bortezomib, trastuzumab, BAY 11-7082, PKC412, PD184352, 20-epi-1, 25
dihydroxyvitamin D3; 5-ethynyluracil; abiraterone; aclarubicin; acylfulvene; adecypenol; adozelesin; aldesleukin; ALL-TK antagonists; altretamine; ambamustine; amidox;
amifostine; aminolevulinic acid; amrubicin; amsacrine; anagrelide; anastrozole;
andrographolide; angiogenesis inhibitors; antagonist D; antagonist G; antarelix; anti- dorsalizing morphogenetic protein-1; antiandrogen, prostatic carcinoma; antiestrogen;
antineoplaston; antisense oligonucleotides; aphidicolin glycinate; apoptosis gene modulators; apoptosis regulators; apurinic acid; ara-CDP-DL-PTBA; arginine deaminase; asulacrine; atamestane; atrimustine; axinastatin 1; axinastatin 2; axinastatin 3; azasetron; azatoxin;
azatyrosine; baccatin III derivatives; balanol; batimastat; BCR/ABL antagonists;
benzochlorins; benzoylstaurosporine; beta lactam derivatives; beta-alethine; betaclamycin B; betulinic acid; bFGF inhibitor; bicalutamide; bisantrene; bisaziridinylspermine; bisnafide; bistratene A; bizelesin; breflate; bropirimine; budotitane; buthionine sulfoximine;
calcipotriol; calphostin C; camptothecin derivatives; canarypox IL-2; capecitabine;
carboxamide-amino-triazole; carboxyamidotriazole; CaRest M3; CARN 700; cartilage derived inhibitor; carzelesin; casein kinase inhibitors (ICOS); castanospermine; cecropin B; cetrorelix; chlorins; chloroquinoxaline sulfonamide; cicaprost; cis-porphyrin; cladribine; clomifene analogues; clotrimazole; collismycin A; collismycin B; combretastatin A4;
combretastatin analogue; conagenin; crambescidin 816; crisnatol; cryptophycin 8;
cryptophycin A derivatives; curacin A; cyclopentanthraquinones; cycloplatam; cypemycin; cytarabine ocfosfate; cytolytic factor; cytostatin; dacliximab; decitabine; dehydrodidemnin B; deslorelin; dexamethasone; dexifosfamide; dexrazoxane; dexverapamil; diaziquone;
didemnin B; didox; diethylnorspermine; dihydro-5-azacytidine; 9-dioxamycin; diphenyl spiromustine; docosanol; dolasetron; doxifluridine; droloxifene; dronabinol; duocarmycin SA; ebselen; ecomustine; edelfosine; edrecolomab; eflornithine; elemene; emitefur;
epirubicin; epristeride; estramustine analogue; estrogen agonists; estrogen antagonists;
etanidazole; etoposide phosphate; exemestane; fadrozole; fazarabine; fenretinide; filgrastim; finasteride; flavopiridol; flezelastine; fluasterone; fludarabine; fluorodaunorunicin
hydrochloride; forfenimex; formestane; fostriecin; fotemustine; gadolinium texaphyrin;
gallium nitrate; galocitabine; ganirelix; gelatinase inhibitors; gemcitabine; glutathione inhibitors; hepsulfam; heregulin; hexamethylene bisacetamide; hypericin; ibandronic acid; idarubicin; idoxifene; idramantone; ilmofosine; ilomastat; imidazoacridones; imiquimod; immunostimulant peptides; insulin-like growth factor-1 receptor inhibitor; interferon agonists; interferons; interleukins; iobenguane; iododoxorubicin; ipomeanol, 4-; iroplact; irsogladine; isobengazole; isohomohalicondrin B; itasetron; jasplakinolide; kahalalide F; lamellarin-N triacetate; lanreotide; leinamycin; lenograstim; lentinan sulfate; leptolstatin; letrozole; leukemia inhibiting factor; leukocyte alpha interferon;
leuprolide+estrogen+progesterone; leuprorelin; levamisole; liarozole; linear polyamine analogue; lipophilic disaccharide peptide; lipophilic platinum compounds; lissoclinamide 7; lobaplatin; lombricine; lometrexol; lonidamine; losoxantrone; lovastatin; loxoribine;
lurtotecan; lutetium texaphyrin; lysofylline; lytic peptides; maitansine; mannostatin A;
marimastat; masoprocol; maspin; matrilysin inhibitors; matrix metalloproteinase inhibitors; menogaril; merbarone; meterelin; methioninase; metoclopramide; MIF inhibitor;
mifepristone; miltefosine; mirimostim; mismatched double stranded RNA; mitoguazone; mitolactol; mitomycin analogues; mitonafide; mitotoxin fibroblast growth factor-saporin; mitoxantrone; mofarotene; molgramostim; monoclonal antibody, human chorionic gonadotrophin; monophosphoryl lipid A+myobacterium cell wall sk; mopidamol; multiple drug resistance gene inhibitor; multiple tumor suppressor 1-based therapy; mustard anticancer agent; mycaperoxide B; mycobacterial cell wall extract; myriaporone; N-acetyldinaline; N- substituted benzamides; nafarelin; nagrestip; naloxone+pentazocine; napavin; naphterpin; nartograstim; nedaplatin; nemorubicin; neridronic acid; neutral endopeptidase; nilutamide; nisamycin; nitric oxide modulators; nitroxide antioxidant; nitrullyn; O6-benzylguanine;
octreotide; okicenone; oligonucleotides; onapristone; ondansetron; ondansetron; oracin; oral cytokine inducer; ormaplatin; osaterone; oxaliplatin; oxaunomycin; palauamine;
palmitoylrhizoxin; pamidronic acid; panaxytriol; panomifene; parabactin; pazelliptine;
pegaspargase; peldesine; pentosan polysulfate sodium; pentostatin; pentrozole; perflubron; perfosfamide; perillyl alcohol; phenazinomycin; phenylacetate; phosphatase inhibitors; picibanil; pilocarpine hydrochloride; pirarubicin; piritrexim; placetin A; placetin B;
plasminogen activator inhibitor; platinum complex; platinum compounds; platinum-triamine complex; porfimer sodium; porfiromycin; prednisone; propyl bis-acridone; prostaglandin J2; proteasome inhibitors; protein A-based immune modulator; protein kinase C inhibitor;
protein kinase C inhibitors, microalgal; protein tyrosine phosphatase inhibitors; purine nucleoside phosphorylase inhibitors; purpurins; pyrazoloacridine; pyridoxylated hemoglobin polyoxyethylerie conjugate; raf antagonists; raltitrexed; ramosetron; ras farnesyl protein transferase inhibitors; ras inhibitors; ras-GAP inhibitor; retelliptine demethylated; rhenium Re 186 etidronate; rhizoxin; ribozymes; RII retinamide; rogletimide; rohitukine; romurtide; roquinimex; rubiginone B1; ruboxyl; safingol; saintopin; SarCNU; sarcophytol A;
sargramostim; Sdi 1 mimetics; semustine; senescence derived inhibitor 1; sense
oligonucleotides; signal transduction inhibitors; signal transduction modulators; single chain antigen-binding protein; sizofuran; sobuzoxane; sodium borocaptate; sodium phenylacetate; solverol; somatomedin binding protein; sonermin; sparfosic acid; spicamycin D;
spiromustine; splenopentin; spongistatin 1; squalamine; stem cell inhibitor; stem-cell division inhibitors; stipiamide; stromelysin inhibitors; sulfinosine; superactive vasoactive intestinal peptide antagonist; suradista; suramin; swainsonine; synthetic glycosaminoglycans;
tallimustine; tamoxifen methiodide; tauromustine; tazarotene; tecogalan sodium; tegafur; tellurapyrylium; telomerase inhibitors; temoporfin; temozolomide; teniposide;
tetrachlorodecaoxide; tetrazomine; thaliblastine; thiocoraline; thrombopoietin;
thrombopoietin mimetic; thymalfasin; thymopoietin receptor agonist; thymotrinan; thyroid stimulating hormone; tin ethyl etiopurpurin; tirapazamine; titanocene bichloride; topsentin; toremifene; totipotent stem cell factor; translation inhibitors; tretinoin; triacetyluridine;
triciribine; trimetrexate; triptorelin; tropisetron; turosteride; tyrosine kinase inhibitors;
tyrphostins; UBC inhibitors; ubenimex; urogenital sinus-derived growth inhibitory factor; urokinase receptor antagonists; vapreotide; variolin B; vector system, erythrocyte gene therapy; velaresol; veramine; verdins; verteporfin; vinorelbine; vinxaltine; vitaxin; vorozole; zanoterone; zeniplatin; zilascorb; zinostatin stimalamer, Adriamycin, Dactinomycin, Bleomycin, Vinblastine, Cisplatin, acivicin; aclarubicin; acodazole hydrochloride; acronine; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa;
azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan;
cactinomycin; calusterone; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; carzelesin; cedefingol; chlorambucil; cirolemycin; cladribine; crisnatol mesylate; cyclophosphamide; cytarabine; dacarbazine; daunorubicin hydrochloride;
decitabine; dexormaplatin; dezaguanine; dezaguanine mesylate; diaziquone; doxorubicin; doxorubicin hydrochloride; droloxifene; droloxifene citrate; dromostanolone propionate; duazomycin; edatrexate; eflornithine hydrochloride; elsamitrucin; enloplatin; enpromate; epipropidine; epirubicin hydrochloride; erbulozole; esorubicin hydrochloride; estramustine; estramustine phosphate sodium; etanidazole; etoposide; etoposide phosphate; etoprine; fadrozole hydrochloride; fazarabine; fenretinide; floxuridine; fludarabine phosphate;
fluorouracil; fluorocitabine; fosquidone; fostriecin sodium; gemcitabine; gemcitabine hydrochloride; hydroxyurea; idarubicin hydrochloride; ifosfamide; iimofosine; interleukin I1 (including recombinant interleukin II, or rlL.sub.2), interferon alfa-2a; interferon alfa-2b; interferon alfa-n1; interferon alfa-n3; interferon beta-1a; interferon gamma-1b; iproplatin; irinotecan hydrochloride; lanreotide acetate; letrozole; leuprolide acetate; liarozole hydrochloride; lometrexol sodium; lomustine; losoxantrone hydrochloride; masoprocol; maytansine; mechlorethamine hydrochloride; megestrol acetate; melengestrol acetate;
melphalan; menogaril; mercaptopurine; methotrexate; methotrexate sodium; metoprine; meturedepa; mitindomide; mitocarcin; mitocromin; mitogillin; mitomalcin; mitomycin; mitosper; mitotane; mitoxantrone hydrochloride; mycophenolic acid; nocodazoie;
nogalamycin; ormaplatin; oxisuran; pegaspargase; peliomycin; pentamustine; peplomycin sulfate; perfosfamide; pipobroman; piposulfan; piroxantrone hydrochloride; plicamycin; plomestane; porfimer sodium; porfiromycin; prednimustine; procarbazine hydrochloride; puromycin; puromycin hydrochloride; pyrazofurin; riboprine; rogletimide; safingol; safingol hydrochloride; semustine; simtrazene; sparfosate sodium; sparsomycin; spirogermanium hydrochloride; spiromustine; spiroplatin; streptonigrin; streptozocin; sulofenur; talisomycin; tecogalan sodium; tegafur; teloxantrone hydrochloride; temoporfin; teniposide; teroxirone; testolactone; thiamiprine; thioguanine; thiotepa; tiazofurin; tirapazamine; toremifene citrate; trestolone acetate; triciribine phosphate; trimetrexate; trimetrexate glucuronate; triptorelin; tubulozole hydrochloride; uracil mustard; uredepa; vapreotide; verteporfin; vinblastine sulfate; vincristine sulfate; vindesine; vindesine sulfate; vinepidine sulfate; vinglycinate sulfate; vinleurosine sulfate; vinorelbine tartrate; vinrosidine sulfate; vinzolidine sulfate; vorozole; zeniplatin; zinostatin; zorubicin hydrochloride, agents that arrest cells in the G2-M phases and/or modulate the formation or stability of microtubules, (e.g., Taxol.TM (i.e. paclitaxel), Taxotere.TM, compounds comprising the taxane skeleton, Erbulozole (i.e., R- 55104), Dolastatin 10 (i.e., DLS-10 and NSC-376128), Mivobulin isethionate (i.e., as CI- 980), Vincristine, NSC-639829, Discodermolide (i.e., as NVP-XX-A-296), ABT-751 (Abbott, i.e., E-7010), Altorhyrtins (e.g., Altorhyrtin A and Altorhyrtin C), Spongistatins (e.g., Spongistatin 1, Spongistatin 2, Spongistatin 3, Spongistatin 4, Spongistatin 5,
Spongistatin 6, Spongistatin 7, Spongistatin 8, and Spongistatin 9), Cemadotin hydrochloride (i.e., LU-103793 and NSC-D-669356), Epothilones (e.g., Epothilone A, Epothilone B, Epothilone C (i.e., desoxyepothilone A or dEpoA), Epothilone D (i.e., KOS-862, dEpoB, and desoxyepothilone B), Epothilone E, Epothilone F, Epothilone B N-oxide, Epothilone A N- oxide, 16-aza-epothilone B, 21-aminoepothilone B (i.e., BMS-310705), 21- hydroxyepothilone D (i.e., Desoxyepothilone F and dEpoF), 26-fluoroepothilone, Auristatin PE (i.e., NSC-654663), Soblidotin (i.e., TZT-1027), LS-4559-P (Pharmacia, i.e., LS-4577), LS-4578 (Pharmacia, i.e., LS-477-P), LS-4477 (Pharmacia), LS-4559 (Pharmacia), RPR- 112378 (Aventis), Vincristine sulfate, DZ-3358 (Daiichi), FR-182877 (Fujisawa, i.e. WS- 9885B), GS-164 (Takeda), GS-198 (Takeda), KAR-2 (Hungarian Academy of Sciences), BSF-223651 (BASF, i.e., ILX-651 and LU-223651), SAH-49960 (Lilly/Novartis), SDZ- 268970 (Lilly/Novartis), AM-97 (Armad/Kyowa Hakko), AM-132 (Armad), AM-138 (Armad/Kyowa Hakko), IDN-5005 (Indena), Cryptophycin 52 (i.e., LY-355703), AC-7739 (Ajinomoto, i.e., AVE-8063A and CS-39.HCl), AC-7700 (Ajinomoto, i.e., AVE-8062, AVE- 8062A, CS-39-L-Ser.HCl, and RPR-258062A), Vitilevuamide, Tubulysin A, Canadensol, Centaureidin (i.e., NSC-106969), T-138067 (Tularik, i.e., T-67, TL-138067 and TI-138067), COBRA-1 (Parker Hughes Institute, i.e., DDE-261 and WHI-261), H10 (Kansas State University), H16 (Kansas State University), Oncocidin A1 (i.e., BTO-956 and DIME), DDE- 313 (Parker Hughes Institute), Fijianolide B, Laulimalide, SPA-2 (Parker Hughes Institute), SPA-1 (Parker Hughes Institute, i.e., SPIKET-P), 3-IAABU (Cytoskeleton/Mt. Sinai School of Medicine, i.e., MF-569), Narcosine (also known as NSC-5366), Nascapine, D-24851 (Asta Medica), A-105972 (Abbott), Hemiasterlin, 3-BAABU (Cytoskeleton/Mt. Sinai School of Medicine, i.e., MF-191), TMPN (Arizona State University), Vanadocene acetylacetonate, T- 138026 (Tularik), Monsatrol, lnanocine (i.e., NSC-698666), 3-IAABE (Cytoskeleton/Mt. Sinai School of Medicine), A-204197 (Abbott), T-607 (Tuiarik, i.e., T-900607), RPR-115781 (Aventis), Eleutherobins (such as Desmethyleleutherobin, Desaetyleleutherobin,
lsoeleutherobin A, and Z-Eleutherobin), Caribaeoside, Caribaeolin, Halichondrin B, D-64131 (Asta Medica), D-68144 (Asta Medica), Diazonamide A, A-293620 (Abbott), NPI-2350 (Nereus), Taccalonolide A, TUB-245 (Aventis), A-259754 (Abbott), Diozostatin, (-)- Phenylahistin (i.e., NSCL-96F037), D-68838 (Asta Medica), D-68836 (Asta Medica), Myoseverin B, D-43411 (Zentaris, i.e., D-81862), A-289099 (Abbott), A-318315 (Abbott), HTI-286 (i.e., SPA-110, trifluoroacetate salt) (Wyeth), D-82317 (Zentaris), D-82318
(Zentaris), SC-12983 (NCI), Resverastatin phosphate sodium, BPR-OY-007 (National Health Research Institutes), and SSR-250411 (Sanofi)), steroids (e.g., dexamethasone), finasteride, aromatase inhibitors, gonadotropin-releasing hormone agonists (GnRH) such as goserelin or leuprolide, adrenocorticosteroids (e.g., prednisone), progestins (e.g., hydroxyprogesterone caproate, megestrol acetate, medroxyprogesterone acetate), estrogens (e.g., diethlystilbestrol, ethinyl estradiol), antiestrogen (e.g., tamoxifen), androgens (e.g., testosterone propionate, fluoxymesterone), antiandrogen (e.g., flutamide), immunostimulants (e.g., Bacillus Calmette- Guérin (BCG), levamisole, interleukin-2, alpha-interferon, etc.), monoclonal antibodies (e.g., anti-CD20, anti-HER2, anti-CD52, anti-HLA-DR, and anti-VEGF monoclonal antibodies), immunotoxins (e.g., anti-CD33 monoclonal antibody-calicheamicin conjugate, anti-CD22 monoclonal antibody-pseudomonas exotoxin conjugate, etc.), radioimmunotherapy (e.g., anti-CD20 monoclonal antibody conjugated to 111In, 90Y, or 131I, etc.), triptolide,
homoharringtonine, dactinomycin, doxorubicin, epirubicin, topotecan, itraconazole, vindesine, cerivastatin, vincristine, deoxyadenosine, sertraline, pitavastatin, irinotecan, clofazimine, 5-nonyloxytryptamine, vemurafenib, dabrafenib, erlotinib, gefitinib, EGFR inhibitors, epidermal growth factor receptor (EGFR)-targeted therapy or therapeutic (e.g., gefitinib (Iressa™), erlotinib (Tarceva™), cetuximab (Erbitux™), lapatinib (Tykerb™), panitumumab (Vectibix™), vandetanib (Caprelsa™), afatinib/BIBW2992, CI- 1033/canertinib, neratinib/HKI-272, CP-724714, TAK-285, AST-1306, ARRY334543, ARRY-380, AG-1478, dacomitinib/PF299804, OSI-420/desmethyl erlotinib, AZD8931, AEE788, pelitinib/EKB-569, CUDC-101, WZ8040, WZ4002, WZ3146, AG-490, XL647, PD153035, BMS-599626), sorafenib, imatinib, sunitinib, dasatinib, or the like. A moiety of an anti-cancer agent is a monovalent anti-cancer agent (e.g., a monovalent form of an agent listed above). [0150] “Chemotherapeutic” or“chemotherapeutic agent” is used in accordance with its plain ordinary meaning and refers to a chemical composition or compound having antineoplastic properties or the ability to inhibit the growth or proliferation of cells. [0151] The term“electrophilic” as used herein refers to a chemical group that is capable of accepting electron density. An“electrophilic substituent,”“electrophilic chemical moiety,” or“electrophic moiety” refers to an electron-poor chemical group, substitutent, or moiety (monovalent chemical group), which may react with an electron-donating group, such as a nucleophile, by accepting an electron pair or electron density to form a bond. In some embodiments, the electrophilic substituent of the compound is capable of reacting with a cysteine residue. In some embodiments, the electrophilic substituent is capable of forming a covalent bond with a cysteine residue (e.g., ATP6V1A) and may be referred to as a“covalent cysteine modifier moiety” or“covalent cysteine modifier substituent.” The covalent bond formed between the electrophilic substituent and the sulfhydryl group of the cysteine may be a reversible or irreversible bond. In some embodiments, the electrophilic substituent of the compound is capable of reacting with a lysine residue. In some embodiments, the electrophilic substituent of the compound is capable of reacting with a serine residue. In some embodiments, the electrophilic substituent of the compound is capable of reacting with a methionine residue. [0152] “Nucleophilic” as used herein refers to a chemical group that is capable of donating electron density. [0153] An amino acid residue in a protein“corresponds” to a given residue when it occupies the same essential structural position within the protein as the given residue. For example, a selected residue in a selected protein corresponds to C277 of human Vacuolar H+- ATPase protein when the selected residue occupies the same essential spatial or other structural relationship as C277 in human Vacuolar H+-ATPase protein. In some
embodiments, where a selected protein is aligned for maximum homology with the human Vacuolar H+-ATPase protein, the position in the aligned selected protein aligning with C277 is said to correspond to C277. Instead of a primary sequence alignment, a three dimensional structural alignment can also be used, e.g., where the structure of the selected protein is aligned for maximum correspondence with the human Vacuolar H+-ATPase protein and the overall structures compared. In this case, an amino acid that occupies the same essential position as C277 in the structural model is said to correspond to the C277 residue. [0154] An amino acid residue in a protein“corresponds” to a given residue when it occupies the same essential structural position within the protein as the given residue. For example, a selected residue in a selected protein corresponds to C277 of human ATP6V1A protein when the selected residue occupies the same essential spatial or other structural relationship as C277 in human ATP6V1A protein. In some embodiments, where a selected protein is aligned for maximum homology with the human ATP6V1A protein, the position in the aligned selected protein aligning with C277 is said to correspond to C277. Instead of a primary sequence alignment, a three dimensional structural alignment can also be used, e.g., where the structure of the selected protein is aligned for maximum correspondence with the human ATP6V1A protein and the overall structures compared. In this case, an amino acid that occupies the same essential position as C277 in the structural model is said to correspond to the C277 residue. [0155] The term“isolated,” when applied to a nucleic acid or protein, denotes that the nucleic acid or protein is essentially free of other cellular components with which it is associated in the natural state. It can be, for example, in a homogeneous state and may be in either a dry or aqueous solution. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein that is the predominant species present in a preparation is substantially purified. [0156] The term“amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, g- carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid. The terms“non-naturally occurring amino acid” and“unnatural amino acid” refer to amino acid analogs, synthetic amino acids, and amino acid mimetics which are not found in nature. [0157] Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes. [0158] The terms“polypeptide,”“peptide,” and“protein” are used interchangeably herein to refer to a polymer of amino acid residues, wherein the polymer may in embodiments be conjugated to a moiety that does not consist of amino acids. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymers. [0159] “Percentage of sequence identity” is determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. [0160] The terms“identical” or percent“identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI web site http://www.ncbi.nlm.nih.gov/BLAST/ or the like). Such sequences are then said to be“substantially identical.” This definition also refers to, or may be applied to, the compliment of a test sequence. The definition also includes sequences that have deletions and/or additions, as well as those that have substitutions. As described below, the preferred algorithms can account for gaps and the like. Preferably, identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length. [0161] “Percentage of sequence identity” is determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. [0162] An amino acid or nucleotide base“position” is denoted by a number that sequentially identifies each amino acid (or nucleotide base) in the reference sequence based on its position relative to the N-terminus (or 5'-end). Due to deletions, insertions, truncations, fusions, and the like that must be taken into account when determining an optimal alignment, in general the amino acid residue number in a test sequence determined by simply counting from the N-terminus will not necessarily be the same as the number of its corresponding position in the reference sequence. For example, in a case where a variant has a deletion relative to an aligned reference sequence, there will be no amino acid in the variant that corresponds to a position in the reference sequence at the site of deletion. Where there is an insertion in an aligned reference sequence, that insertion will not correspond to a numbered amino acid position in the reference sequence. In the case of truncations or fusions there can be stretches of amino acids in either the reference or aligned sequence that do not correspond to any amino acid in the corresponding sequence. [0163] The terms“numbered with reference to” or“corresponding to,” when used in the context of the numbering of a given amino acid or polynucleotide sequence, refers to the numbering of the residues of a specified reference sequence when the given amino acid or polynucleotide sequence is compared to the reference sequence. [0164] The term“protein complex” is used in accordance with its plain ordinary meaning and refers to a protein which is associated with an additional substance (e.g., another protein, protein subunit, or a compound). Protein complexes typically have defined quaternary structure. The association between the protein and the additional substance may be a covalent bond. In embodiments, the association between the protein and the additional substance (e.g., compound) is via non-covalent interactions. In embodiments, a protein complex refers to a group of two or more polypeptide chains. Proteins in a protein complex are linked by non-covalent protein–protein interactions. A non-limiting example of a protein complex is the proteasome. [0165] The term“protein aggregate” is used in accordance with its plain ordinary meaning and refers to an abberrant collection or accumulation of proteins (e.g., misfolded proteins). Protein aggregates are often associated with diseases (e.g., amyloidosis). Typically, when a protien misfolds as a result of a change in the amino acid sequence or a change in the native environment which disrupts normal non-covalent interactions, and the misfolded protein is not corrected or degraded, the unfolded/misfolded protein may aggregate. There are three main types of protein aggregates that may form: amorphous aggregates, oligomers, and amyloid fibrils. In embodiments, protein aggregates are termed aggresomes. In
embodiments, the protein aggregate is TDP43, HTT, APP, SNCA, or MAPT. In
embodiments, the protein aggregate includes the protein Beta amyloid, Amyloid precursor protein, IAPP (Amylin), Alpha-synuclein, PrPSc, PrPSc, Huntingtin, Calcitonin, Atrial natriuretic factor, Apolipoprotein AI, Serum amyloid A, Medin, Prolactin, Transthyretin, Lysozyme, Beta-2 microglobulin, Gelsolin, Keratoepithelin, Beta amyloid, Cystatin, Immunoglobulin light chain AL, TDP43, or S-IBM. [0166] The term“vesicle” is used in accordance with its plain ordinary meaning and refers to a small membrane enclosed compartment within a cell. Vesicles are typically involved in transport, buoyancy control, or enzyme storage within a cell. Some vesicles, for example a lysosome, may include enzymes, proteins, polysaccharides, lipids, nucleic acids, or organelles within the compartment. Vesicles are typically formed within cells as a result of exocytosis or phagocytosis, however some vesicles are formed at the Golgi complex and transported to the cell membrane. Vesicles may be unilamellar or multilamellar. [0167] The term“vacuolar H+-ATPase,”“V-type proton ATPase,”“vacuolar H+-ATPase protein complex,” or“v-ATPase” refers to an enzyme that acidifies a wide array of intracellular organelles (e.g., lysosomes) and pump protons across the plasma membranes of cells. V-ATPases, including ATP6V1A as a component, couple the energy of ATP hydrolysis to proton transport across intracellular and plasma membranes of eukaryotic cells. [0168] The term“V-type proton ATPase catalytic subunit A” or“ATP6V1A” refers to a gene that encodes a component of vacuolar ATPase (v-ATPase), which is an enzyme that mediates amino acid-dependent recruitment of mTORC1 to the lysosome. In some embodiments ATP6V1A refers to UniProt P38606-1. In embodiments, ATP6V1A refers to human ATP6V1A. In embodiments, ATP6V1A refers to Entrez 523. In embodiments, ATP6V1A refers to RefSeq NM_001690.3. In embodiments, ATP6V1A refers to RefSeq NP_001681.2. In some embodiments, ATP6V1A has the sequence:
MDFSKLPKILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGD MATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPR GVNVSALSRDIKWDFTPCKNLRVGSHITGGDIYGIVSENSLIKHKIMLPPRNRGTVTYIA PPGNYDTSDVVLELEFEGVKEKFTMVQVWPVRQVRPVTEKLPANHPLLTGQRVLDALFPC VQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDG KVESIMKRTALVANTSNMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALRE ISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDP VTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAK EILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIKDDFLQQNGYTPYDRFCPFYKTVGM LSNMIAFYDMARRAVETTAQSDNKITWSIIREHMGDILYKLSSMKFKDPLKDGEAKIKSD YAQLLEDMQNAFRSLED (SEQ ID NO:1). [0169] The term“mTOR” refers to the protein“mechanistic target of rapamycin
(serine/threonine kinase)” or“mammalian target of rapamycin.” The term“mTOR” may refer to the nucleotide sequence or protein sequence of human mTOR (e.g., Entrez 2475, Uniprot P42345, RefSeq NM_004958, or RefSeq NP_004949). The term“mTOR” includes both the wild-type form of the nucleotide sequences or proteins as well as any mutants thereof. In some embodiments,“mTOR” is wild-type mTOR. In some embodiments, “mTOR” is one or more mutant forms. The term“mTOR” XYZ refers to a nucleotide sequence or protein of a mutant mTOR wherein the Y numbered amino acid of mTOR that normally has an X amino acid in the wildtype, instead has a Z amino acid in the mutant. In embodiments, an mTOR is the human mTOR. In embodiments, the mTOR has the following amino acid sequence:
MLGTGPAAATTAATTSSNVSVLQQFASGLKSRNEETRAKAAKELQHYVTMELREMSQEES TRFYDQLNHHIFELVSSSDANERKGGILAIASLIGVEGGNATRIGRFANYLRNLLPSNDP VVMEMASKAIGRLAMAGDTFTAEYVEFEVKRALEWLGADRNEGRRHAAVLVLRELAISVP TFFFQQVQPFFDNIFVAVWDPKQAIREGAVAALRACLILTTQREPKEMQKPQWYRHTFEE AEKGFDETLAKEKGMNRDDRIHGALLILNELVRISSMEGERLREEMEEITQQQLVHDKYC KDLMGFGTKPRHITPFTSFQAVQPQQSNALVGLLGYSSHQGLMGFGTSPSPAKSTLVESR CCRDLMEEKFDQVCQWVLKCRNSKNSLIQMTILNLLPRLAAFRPSAFTDTQYLQDTMNHV LSCVKKEKERTAAFQALGLLSVAVRSEFKVYLPRVLDIIRAALPPKDFAHKRQKAMQVDA TVFTCISMLARAMGPGIQQDIKELLEPMLAVGLSPALTAVLYDLSRQIPQLKKDIQDGLL KMLSLVLMHKPLRHPGMPKGLAHQLASPGLTTLPEASDVGSITLALRTLGSFEFEGHSLT QFVRHCADHFLNSEHKEIRMEAARTCSRLLTPSIHLISGHAHVVSQTAVQVVADVLSKLL VVGITDPDPDIRYCVLASLDERFDAHLAQAENLQALFVALNDQVFEIRELAICTVGRLSS MNPAFVMPFLRKMLIQILTELEHSGIGRIKEQSARMLGHLVSNAPRLIRPYMEPILKALI LKLKDPDPDPNPGVINNVLATIGELAQVSGLEMRKWVDELFIIIMDMLQDSSLLAKRQVA LWTLGQLVASTGYVVEPYRKYPTLLEVLLNFLKTEQNQGTRREAIRVLGLLGALDPYKHK VNIGMIDQSRDASAVSLSESKSSQDSSDYSTSEMLVNMGNLPLDEFYPAVSMVALMRIFR DQSLSHHHTMVVQAITFIFKSLGLKCVQFLPQVMPTFLNVIRVCDGAIREFLFQQLGMLV SFVKSHIRPYMDEIVTLMREFWVMNTSIQSTIILLIEQIVVALGGEFKLYLPQLIPHMLR VFMHDNSPGRIVSIKLLAAIQLFGANLDDYLHLLLPPIVKLFDAPEAPLPSRKAALETVD RLTESLDFTDYASRIIHPIVRTLDQSPELRSTAMDTLSSLVFQLGKKYQIFIPMVNKVLV RHRINHQRYDVLICRIVKGYTLADEEEDPLIYQHRMLRSGQGDALASGPVETGPMKKLHV STINLQKAWGAARRVSKDDWLEWLRRLSLELLKDSSSPSLRSCWALAQAYNPMARDLFNA AFVSCWSELNEDQQDELIRSIELALTSQDIAEVTQTLLNLAEFMEHSDKGPLPLRDDNGI VLLGERAAKCRAYAKALHYKELEFQKGPTPAILESLISINNKLQQPEAAAGVLEYAMKHF GELEIQATWYEKLHEWEDALVAYDKKMDTNKDDPELMLGRMRCLEALGEWGQLHQQCCE KWTLVNDETQAKMARMAAAAAWGLGQWDSMEEYTCMIPRDTHDGAFYRAVLALHQDLF SLAQQCIDKARDLLDAELTAMAGESYSRAYGAMVSCHMLSELEEVIQYKLVPERREIIRQIW WERLQGCQRIVEDWQKILMVRSLVVSPHEDMRTWLKYASLCGKSGRLALAHKTLVLLLGV DPSRQLDHPLPTVHPQVTYAYMKNMWKSARKIDAFQHMQHFVQTMQQQAQHAIATEDQQ HKQELHKLMARCFLKLGEWQLNLQGINESTIPKVLQYYSAATEHDRSWYKAWHAWAVMN FEAVLHYKHQNQARDEKKKLRHASGANITNATTAATTAATATTTASTEGSNSESEAESTENS PTPSPLQKKVTEDLSKTLLMYTVPAVQGFFRSISLSRGNNLQDTLRVLTLWFDYGHWPDVN EALVEGVKAIQIDTWLQVIPQLIARIDTPRPLVGRLIHQLLTDIGRYHPQALIYPLTVAS KSTTTARHNAANKILKNMCEHSNTLVQQAMMVSEELIRVAILWHEMWHEGLEEASRLYFG ERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEWCRKYMKSGNVKDLTQ AWDLYYHVFRRISKQLPQLTSLELQYVSPKLLMCRDLELAVPGTYDPNQPIIRIQSIAPSL QVITSKQRPRKLTLMGSNGHEFVFLLKGHEDLRQDERVMQLFGLVNTLLANDPTSLRKNL SIQRYAVIPLSTNSGLIGWVPHCDTLHALIRDYREKKKILLNIEHRIMLRMAPDYDHLTL MQKVEVFEHAVNNTAGDDLAKLLWLKSPSSEVWFDRRTNYTRSLAVMSMVGYILGLGDRH PSNLMLDRLSGKILHIDFGDCFEVAMTREKFPEKIPFRLTRMLTNAMEVTGLDGNYRITC HTVMEVLREHKDSVMAVLEAFVYDPLLNWRLMDTNTKGNKRSRTRTDSYSAGQSVEILDG VELGEPAHKKTGTTVPESIHSFIGDGLVKPEALNKKAIQIINRVRDKLTGRDFSHDDTLD VPTQVELLIKQATSHENLCQCYIGWCPFW (SEQ ID NO:2). [0170] The term“mTORC1” refers to the protein complex including mTOR and Raptor (regulatory-associated protein of mTOR). mTORC1 may also include MLST8 (mammalian lethal with SEC13 protein 8), PRAS40, and/or DEPTOR. mTORC1 may function as a nutrient/energy/redox sensor and regulator of protein synthesis. The term“mTORC1 pathway” or“mTORC1 signal transduction pathway” refers to a cellular pathway including mTORC1. An mTORC1 pathway includes the pathway components upstream and downstream from mTORC1. An mTORC1 pathway is a signaling pathway that is modulated by modulation of mTORC1 activity. In embodiments, an mTORC1 pathway is a signaling pathway that is modulated by modulation of mTORC1 activity but not by modulation of mTORC2 activity. In embodiments, an mTORC1 pathway is a signaling pathway that is modulated to a greater extent by modulation of mTORC1 activity than by modulation of mTORC2 activity. [0171] The term“mTORC2” refers to the protein complex including mTOR and RICTOR (rapamycin-insensitive companion of mTOR). mTORC2 may also include GbL, mSIN1 (mammalian stress-activated protein kinase interacting protein 1), Protor 1/2, DEPTOR, TTI1, and/or TEL2. mTORC2 may regulate cellular metabolism and the cytoskeleton. The term“mTORC2 pathway” or“mTORC2 signal transduction pathway” refers to a cellular pathway including mTORC2. An mTORC2 pathway includes the pathway components upstream and downstream from mTORC2. An mTORC2 pathway is a signaling pathway that is modulated by modulation of mTORC2 activity. In embodiments, an mTORC2 pathway is a signaling pathway that is modulated by modulation of mTORC2 activity but not by modulation of mTORC1 activity. In embodiments, an mTORC2 pathway is a signaling pathway that is modulated to a greater extent by modulation of mTORC2 activity than by modulation of mTORC1 activity. [0172] The term“Sequestosome-1” or“SQSTM1” or“p62/SQSTM1” or“ubiquitin- binding protein p62” or“p62” refers to an autophagosome cargo protein (including homologs, isoforms, and functional fragments thereof) that targets other proteins that bind to it for selective autophagy. p62 harbors active nuclear import and export signals and shuttles between the nucleus and cytoplasm. The term“p62” refers to the nucleotide sequences or proteins of human p62. The term“p62” includes both the wild-type form of the nucleotide sequences or proteins as well as any mutants thereof. In some embodiments,“p62” is wild- type p62. In some embodiments,“p62” is one or more mutant forms. The term“p62” XYZ refers to a nucleotide sequence or protein of a mutant p62 wherein the Y numbered amino acid of p62 that has an X amino acid in the wildtype instead has a Z amino acid in the mutant. In embodiments, p62 is a functional fragment thereof. In some embodiments p62 refers to UniProt C9J6J8, having the sequence: MASLTVKAYLLGKEDAAREIRRFSFCCSPEPEAEAEAAAGPGPCERLLSRVAALFPAL RPGGFQAHYRGGGFR (SEQ ID NO:3). [0173] In embodiments, p62 refers to Entrez 8878. In embodiments, p62 refers to RefSeq NM_001142298.1, RefSeq NM_001142299.1, RefSeq NM_003900.4, RefSeq
NP_001135770.1, RefSeq NP_001135771.1, or RefSeq NP_003891.1. In some
embodiments p62 refers to UniProt Q13501, having the sequence:
MASLTVKAYLLGKEDAAREIRRFSFCCSPEPEAEAEAAAGPGPCERLLSRVAALFPALRP GGFQAHYRDEDGDLVAFSSDEELTMAMSYVKDDIFRIYIKEKKECRRDHRPPCAQEAPRN MVHPNVICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKGLHRGHTKLAFPSPFGHLSEGFS HSRWLRKVKHGHFGWPGWEMGPPGNWSPRPPRAGEARPGPTAESASGPSEDPSVNFLKNV GESVAAALSPLGIEVDIDVEHGGKRSRLTPVSPESSSTEEKSSSQPSSCCSDPSKPGGNV EGATQSLAEQMRKIALESEGRPEEQMESDNCSGGDDDWTHLSSKEVDPSTGELQSLQMPE SEGPSSLDPSQEGPTGLKEAALYPHLPPEADPRLIESLSQMLSMGFSDEGGWLTRLLQTK NYDIGAALDTIQYSKHPPPL (SEQ ID NO:4). [0174] In some embodiments p62 refers to the sequence: RFSFCCSPEPEAEAEAAAGPGPCERL (SEQ ID NO:5). [0175] The term“LC3B” or“microtubule-associated proteins 1A/1B light chain 3B” refers to a central protein in the autophagy pathway, where it functions, for example, in autophagy substrate selection. The term“LC3B” may refer to the nucleotide sequence or protein sequence of human LC3B. In embodiments, LC3B is LC3BII. In embodiments, LC3B is Entrez 81631, Uniprot Q9GZQ8, RefSeq NM_022818.4, or RefSeq NP_073729.1. In embodiments, the LC3B has the following amino acid sequence:
MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNM SELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYASQETFG MKLSV (SEQ ID NO:6). [0176] The term“4EBP1” or“eukaryotic translation initiation factor 4E-binding protein 1” refers to a protein that interacts with eukaryotic translation initiation factor 4E, which is a component of the multisubunit complex that recruits 40S ribosomal subunits to the 5’ end of mRNAs. The term“4EBP1” may refer to the nucleotide sequence or protein sequence of human 4EBP1. In embodiments, 4EBP1 is Entrez 1978, Uniprot Q13541, RefSeq
NM_004095.3, or RefSeq NP_004086.1. In embodiments, the 4EBP1 has the following amino acid sequence:
MSGGSSCSQTPSRAIPATRRVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRKFLM ECRNSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKRAGGEESQFEMDI (SEQ ID NO:7). [0177] The term“TFEB” or“transcription factor EB” refers to a protein involved in lysosomal biogenesis. The TFEB protein coordinates, for example, expression of lysosomal hydrolases, membrane proteins, and genes involved in autophagy. The TFEB protein is encoded by the TFEB gene. The term“TFEB” may refer to the nucleotide sequence or protein sequence of human TFEB. In embodiments, TFEB is Entrez 7942, Uniprot P19484, RefSeq NM_001167827.2, RefSeq NM_001271943.1, RefSeq NM_001271944.1, RefSeq NM_001271945.1, RefSeq NM_007162.2, RefSeq NP_001161299.2, RefSeq
NP_001258872.1, RefSeq NP_001258873.1, RefSeqNP_001258874.1, or RefSeq
NP_009093.1. In embodiments, the TFEB has the following amino acid sequence:
MASRIGLRMQLMREQAQQEEQRERMQQQAVMHYMQQQQQQQQQQLGGPPTPAINTPVHF QSPPPVPGEVLKVQSYLENPTSYHLQQSQHQKVREYLSETYGNKFAAHISPAQGSPKPPPA ASPGVRAGHVLSSSAGNSAPNSPMAMLHIGSNPERELDDVIDNIMRLDDVLGYINPEMQM PNTLPLSSSHLNVYSSDPQVTASLVGVTSSSCPADLTQKRELTDAESRALAKERQKKDNH NLIERRRRFNINDRIKELGMLIPKANDLDVRWNKGTILKASVDYIRRMQKDLQKSRELEN HSRRLEMTNKQLWLRIQELEMQARVHGLPTTSPSGMNMAELAQQVVKQELPSEEGPGEAL MLGAEVPDPEPLPALPPQAPLPLPTQPPSPFHHLDFSHSLSFGGREDEGPPGYPEPLAPG HGSPFPSLSKKDLDLMLLDDSLLPLASDPLLSTMSPEASKASSRRSSFSMEEGDVL (SEQ ID NO:8). [0178] The term“TFE3” or“transcription factor E3” refers to a protein that activates expression of CD30L in T-cells. The TFE3 protein is encoded by the TFE3 gene. The term “TFE3” may refer to the nucleotide sequence or protein sequence of human TFE3. In embodiments, TFE3 is Entrez 7030, Uniprot P19532, RefSeq NM_001282142.1, RefSeq NM_006521.5, RefSeq NP_001269071.1, or RefSeq NP_006512.2. In embodiments, the TFE3 has the following amino acid sequence:
MSHAAEPARDGVEASAEGPRAVFVLLEERRPADSAQLLSLNSLLPESGIVADIELENVLD PDSFYELKSQPLPLRSSLPISLQATPATPATLSASSSAGGSRTPAMSSSSSSRVLLRQQL MRAQAQEQERRERREQAAAAPFPSPAPASPAISVVGVSAGGHTLSRPPPAQVPREVLKVQ THLENPTRYHLQQARRQQVKQYLSTTLGPKLASQALTPPPGPASAQPLPAPEAAHTTGPT GSAPNSPMALLTIGSSSEKEIDDVIDEIISLESSYNDEMLSYLPGGTTGLQLPSTLPVSG NLLDVYSSQGVATPAITVSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERRRRF NINDRIKELGTLIPKSSDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLEQAN RSLQLRIQELELQAQIHGLPVPPTPGLLSLATTSASDSLKPEQLDIEEEGRPGAATFHVG GGPAQNAPHQQPPAPPSDALLDLHFPSDHLGDLGDPFHLGLEDILMEEEEGVVGGLSGGA LSPLRAASDPLLSSVSPAVSKASSRRSSFSMEEES (SEQ ID NO:9). [0179] The term“autophagosome” is used in accordance with its plain ordinary meaning and refers to a vesicle that contains a cellular component slated to be degraded by autophagy. In embodiments, autophagosome formation is a multistep process that includes the biogenesis of the phagophore, followed by its elongation and closure. In embodiments, more than 15 autophagy-related ATG proteins, as well as class III PI3 kinases, may be required to construct the autophagosome, including the transmembrane ATG protein ATG9, along with
membranes from multiple sources cellular sources. [0180] “Nucleic acid” refers to nucleotides (e.g., deoxyribonucleotides or ribonucleotides) and polymers thereof in either single-, double- or multiple-stranded form, or complements thereof; or nucleosides (e.g., deoxyribonucleosides or ribonucleosides). In embodiments, “nucleic acid” does not include nucleosides. The terms“polynucleotide,”“oligonucleotide,” “oligo,” or the like refer, in the usual and customary sense, to a linear sequence of
nucleotides. Oligonucleotides are typically from about 5, 6, 7, 8, 9, 10, 12, 15, 25, 30, 40, 50 or more nucleotides in length, up to about 100 nucleotides in length. Nucleic acids and polynucleotides are a polymers of any length, including longer lengths, e.g., 200, 300, 500, 1000, 2000, 3000, 5000, 7000, 10,000, etc. In certain embodiments the nucleic acids herein contain phosphodiester bonds. In other embodiments, nucleic acid analogs are included that may have alternate backbones, comprising, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O-methylphosphoroamidite linkages (see, Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press); and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones, and non-ribose backbones, including those described in U.S. Patent Nos.5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580,
Carbohydrate Modifications in Antisense Research, Sanghui & Cook, eds. Nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half-life of such molecules in physiological environments or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs can be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made. A residue of a nucleic acid, as referred to herein, is a monomer of the nucleic acid (e.g., a nucleotide). The term“nucleoside” refers, in the usual and customary sense, to a glycosylamine including a nucleobase and a five-carbon sugar (ribose or deoxyribose). Non limiting examples, of nucleosides include, cytidine, uridine, adenosine, guanosine, thymidine and inosine. Nucleosides may be modified at the base and/or and the sugar. The term“nucleotide” refers, in the usual and customary sense, to a single unit of a polynucleotide, i.e., a monomer. Nucleotides can be ribonucleotides, deoxyribonucleotides, or modified versions thereof. Examples of polynucleotides contemplated herein include single and double stranded DNA, single and double stranded RNA, and hybrid molecules having mixtures of single and double stranded DNA and RNA. Examples of nucleic acid, e.g., polynucleotides contemplated herein include any types of RNA, e.g., mRNA, siRNA, miRNA, and guide RNA and any types of DNA, genomic DNA, plasmid DNA, and minicircle DNA, and any fragments thereof. The term“duplex” in the context of polynucleotides refers, in the usual and customary sense, to double strandedness. Nucleic acids can be linear or branched. For example, nucleic acids can be a linear chain of nucleotides or the nucleic acids can be branched, e.g., such that the nucleic acids comprise one or more arms or branches of nucleotides. Optionally, the branched nucleic acids are repetitively branched to form higher ordered structures such as dendrimers and the like. [0181] “Nucleotide,” as used herein, refers to a nucleoside-5’-polyphosphate compound, or a structural analog thereof, which can be incorporated (e.g., partially incorporated as a nucleoside-5’-monophosphate or derivative thereof) by a nucleic acid polymerase to extend a growing nucleic acid chain (such as a primer). Nucleotides may comprise bases such as A, C, G, T, U, or analogues thereof, and may comprise 2, 3, 4, 5, 6, 7, 8, or more phosphates in the phosphate group. Nucleotides may be modified at one or more of the base, sugar, or phosphate group. A nucleotide may have a label or tag attached (a“labeled nucleotide” or “tagged nucleotide”). [0182] The terms also encompass nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non- naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphodiester derivatives including, e.g.,
phosphoramidate, phosphorodiamidate, phosphorothioate (also known as phosphothioate having double bonded sulfur replacing oxygen in the phosphate), phosphorodithioate, phosphonocarboxylic acids, phosphonocarboxylates, phosphonoacetic acid, phosphonoformic acid, methyl phosphonate, boron phosphonate, or O-methylphosphoroamidite linkages (see, Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press) as well as modifications to the nucleotide bases such as in 5-methyl cytidine or
pseudouridine; and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones, modified sugars, and non-ribose backbones (e.g., phosphorodiamidate morpholino oligos or locked nucleic acids (LNA) as known in the art), including those described in U.S. Patent Nos.5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, Carbohydrate Modifications in Antisense Research, Sanghui & Cook, eds. Nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half-life of such molecules in physiological environments or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs can be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made. In embodiments, the internucleotide linkages in DNA are phosphodiester, phosphodiester derivatives, or a combination of both. [0183] Nucleic acids can include nonspecific sequences. As used herein, the term “nonspecific sequence” refers to a nucleic acid sequence that contains a series of residues that are not designed to be complementary to or are only partially complementary to any other nucleic acid sequence. By way of example, a nonspecific nucleic acid sequence is a sequence of nucleic acid residues that does not function as an inhibitory nucleic acid when contacted with a cell or organism. [0184] An“antisense nucleic acid” as referred to herein is a nucleic acid (e.g., DNA or RNA molecule) that is complementary to at least a portion of a specific target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) and is capable of reducing transcription of the target nucleic acid (e.g., mRNA from DNA), reducing the translation of the target nucleic acid (e.g., mRNA), altering transcript splicing (e.g., single stranded morpholino oligo), or interfering with the
endogenous activity of the target nucleic acid. See, e.g., Weintraub, Scientific American, 262:40 (1990). Typically, synthetic antisense nucleic acids (e.g., oligonucleotides) are generally between 15 and 25 bases in length. Thus, antisense nucleic acids are capable of hybridizing to (e.g., selectively hybridizing to) a target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein). In embodiments, the antisense nucleic acid hybridizes to the target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) in vitro. In embodiments, the antisense nucleic acid hybridizes to the target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) in a cell. In embodiments, the antisense nucleic acid hybridizes to the target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) in an organism. In embodiments, the antisense nucleic acid hybridizes to the target nucleic acid (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) under physiological conditions. Antisense nucleic acids may comprise naturally occurring nucleotides or modified nucleotides such as, e.g., phosphorothioate, methylphosphonate, and -anomeric sugar- phosphate, backbonemodified nucleotides. [0185] In the cell, the antisense nucleic acids hybridize to the corresponding RNA (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) forming a double-stranded molecule. The antisense nucleic acids interfere with the endogenous behavior of the RNA (e.g., a nucleic acid coding for one or more amino acids corresponding to C277 of human ATP6V1A protein) and inhibit its function relative to the absence of the antisense nucleic acid. Furthermore, the double-stranded molecule may be degraded via the RNAi pathway. The use of antisense methods to inhibit the in vitro translation of genes is well known in the art (Marcus-Sakura, Anal. Biochem., 172:289, (1988)). Further, antisense molecules which bind directly to the DNA may be used.
Antisense nucleic acids may be single or double stranded nucleic acids. Non-limiting examples of antisense nucleic acids include siRNAs (including their derivatives or pre- cursors, such as nucleotide analogs), short hairpin RNAs (shRNA), micro RNAs (miRNA), saRNAs (small activating RNAs) and small nucleolar RNAs (snoRNA) or certain of their derivatives or pre-cursors. [0186] The term“complement,” as used herein, refers to a nucleotide (e.g., RNA or DNA) or a sequence of nucleotides capable of base pairing with a complementary nucleotide or sequence of nucleotides. As described herein and commonly known in the art the complementary (matching) nucleotide of adenosine is thymidine and the complementary (matching) nucleotide of guanidine is cytosine. Thus, a complement may include a sequence of nucleotides that base pair with corresponding complementary nucleotides of a second nucleic acid sequence. The nucleotides of a complement may partially or completely match the nucleotides of the second nucleic acid sequence. Where the nucleotides of the complement completely match each nucleotide of the second nucleic acid sequence, the complement forms base pairs with each nucleotide of the second nucleic acid sequence. Where the nucleotides of the complement partially match the nucleotides of the second nucleic acid sequence only some of the nucleotides of the complement form base pairs with nucleotides of the second nucleic acid sequence. Examples of complementary sequences include coding and a non-coding sequences, wherein the non-coding sequence contains complementary nucleotides to the coding sequence and thus forms the complement of the coding sequence. A further example of complementary sequences are sense and antisense sequences, wherein the sense sequence contains complementary nucleotides to the antisense sequence and thus forms the complement of the antisense sequence. [0187] As described herein the complementarity of sequences may be partial, in which only some of the nucleic acids match according to base pairing, or complete, where all the nucleic acids match according to base pairing. Thus, two sequences that are complementary to each other, may have a specified percentage of nucleotides that are the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region). [0188] The term“antibody” refers to a polypeptide encoded by an immunoglobulin gene or functional fragments thereof that specifically binds and recognizes an antigen. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively. [0189] An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one“heavy” chain (about 50-70 kDa). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms“variable heavy chain,”“VH,” or“VH” refer to the variable region of an immunoglobulin heavy chain, including an Fv, scFv, dsFv, or Fab; while the terms“variable light chain,”“VL,” or“VL” refer to the variable region of an immunoglobulin light chain, including of an Fv, scFv, dsFv, or Fab. [0190] Examples of antibody functional fragments include, but are not limited to, complete antibody molecules, antibody fragments, such as Fv, single chain Fv (scFv), complementarity determining regions (CDRs), VL (light chain variable region), VH (heavy chain variable region), Fab, F(ab)2' and any combination of those or any other functional portion of an immunoglobulin peptide capable of binding to target antigen (see, e.g., FUNDAMENTAL IMMUNOLOGY (Paul ed., 4th ed.2001). As appreciated by one of skill in the art, various antibody fragments can be obtained by a variety of methods, for example, digestion of an intact antibody with an enzyme, such as pepsin; or de novo synthesis. Antibody fragments are often synthesized de novo either chemically or by using recombinant DNA methodology. Thus, the term antibody, as used herein, includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty et al., (1990) Nature 348:552). The term“antibody” also includes bivalent or bispecific molecules, diabodies, triabodies, and tetrabodies. Bivalent and bispecific molecules are described in, e.g., Kostelny et al. (1992) J. Immunol.148:1547, Pack and Pluckthun (1992) Biochemistry 31:1579, Hollinger et al. (1993), PNAS. USA 90:6444, Gruber et al. (1994) J. Immunol.152:5368, Zhu et al. (1997) Protein Sci.6:781, Hu et al. (1996) Cancer Res.56:3055, Adams et al. (1993) Cancer Res.53:4026, and McCartney, et al.
(1995) Protein Eng.8:301. [0191] The term“irreversible covalent bond” is used in accordance with its plain ordinary meaning in the art and refers to the resulting association between atoms or molecules of (e.g., electrophilic chemical moiety and nucleophilic moiety) wherein the probability of dissociation is low. In embodiments, the irreversible covalent bond does not easily dissociate under normal biological conditions. In embodiments, the irreversible covalent bond is formed through a chemical reaction between two species (e.g., electrophilic chemical moiety and cysteine). II. Compounds
[0192] In an aspect is provided a compound, or a pharmaceutically acceptable salt thereof, having the formula:
Figure imgf000076_0001
[0193] Ring A is a phenyl or 5 to 6 membered heteroaryl. [0194] Ring B is a phenyl or 5 to 6 membered heteroaryl. [0195] L1 is independently a bond, -S(O)2-, -N(R5)-, -O-, -S-, -C(O)-, -C(O)N(R5)-, -N(R5)C(O)-, -N(R5)C(O)NH-, -NHC(O)N(R5)-, -C(O)O-, -OC(O)-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene. [0196] R5 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0197] R1 is independently halogen, -CX1 3, -CHX1 2, -CH2X1, -OCX1 3, -OCH2X1,
-OCHX12, -CN, -SOn1R1D, -SOv1NR1AR1B, -NHC(O)NR1AR1B, -N(O)m1, -NR1AR1B, -C(O)R1C, -C(O)OR1C, -C(O)NR1AR1B, -OR1D, -NR1ASO2R1D, -NR1AC(O)R1C, -NR1AC(O)OR1C, -NR1AOR1C, -N3, E, substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent -L1-R1 substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0198] E is an electrophilic moiety. [0199] R2 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0200] R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
unsubstituted heteroaryl. [0201] R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
unsubstituted heteroaryl; two adjacent R4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0202] R1A, R1B, R1C, and R1D are independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R1A and R1B substituents bonded to the same nitrogen atom may be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl. [0203] X1 is independently–F, -Cl, -Br, or–I. [0204] n1 is independently an integer from 0 to 4. [0205] m1 and v1 are independently 1 or 2. [0206] z1 is independently an integer from 0 to 5. [0207] z3 is independently an integer from 0 to 2. [0208] z4 is independently an integer from 0 to 5. [0209] In an aspect is provided a compound having the formula:
Ring A, Ring B, L1, R1, R2, R3, z3, R4
Figure imgf000078_0001
, and z4 are as described herein, including in embodiments. [0210] In embodiments, the compound has the formula:
Figure imgf000078_0002
L1, E, R1, z1, R4, and z4 are as described herein, including in embodiments. [0211] In embodiments, the compound has the formula:
Figure imgf000079_0001
L1, E, R1, and R4 are as described herein, including in embodiments.
[0212] In embodiments, the compound has the formula:
L1, E, R1, and R4 are as described herein, including in
Figure imgf000079_0002
embodiments.
[0213] In embodiments, the compound has the formula:
L1, E, R1, z1, R3, R4, and z4 are as described herein,
Figure imgf000079_0003
including in embodiments.
[0214] In embodiments, the compound has the formula:
L1, E, R1, z1, R3, R4, and z4 are as described
Figure imgf000079_0004
herein, including in embodiments. [0215] In embodiments, the compound has the formula:
Figure imgf000080_0001
L1, E, R1, R3, and R4 are as described herein, including in embodiments.
[0216] In embodiments, the compound has the formula:
L1, E, R1, R3, and R4 are as described herein,
Figure imgf000080_0002
including in embodiments.
[0217] In embodiments, the compound has the formula:
Figure imgf000080_0003
L1, E, R1, R3, and R4 are as described herein, including in embodiments.
[0218] In embodiments, the compound has the formula:
Figure imgf000081_0001
L1, E, R1, R3, and R4 are as described herein, including in embodiments. [0219] In embodiments, the compound has the formula:
Figure imgf000081_0002
L1, E, R1, z1, R2, R4, and z4 are as described herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In
embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl. [0220] In embodiments, the compound has the formula:
L1, E, R1, R2, and R4 are as described herein, including in
Figure imgf000081_0003
embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl. [0221] In embodiments, the compound has the formula:
Figure imgf000082_0001
L1, E, R1, R2, and R4 are as described herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl. [0222] In embodiments, the compound has the formula:
L1, E, R1, z1, R2, R3, R4, and z4 are as described herein,
Figure imgf000082_0002
including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In
embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl. [0223] In embodiments, the compound has the formula:
Figure imgf000082_0003
L1, E, R1, z1, R2, R3, R4, and z4 are as described herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl. [0224] In embodiments, the compound has the formula:
Figure imgf000083_0001
L1, E, R1, R2, R3, and R4 are as described herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl. [0225] In embodiments, the compound has the formula:
Figure imgf000083_0002
L1, E, R1, R2, R3, and R4 are as described herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl. [0226] In embodiments, the compound has the formula:
L1, E, R1, R2, R3, and R4 are as described
Figure imgf000083_0003
herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl. [0227] In embodiments, the compound has the formula:
Figure imgf000084_0001
L1, E, R1, R2, R3, and R4 are as described herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl. [0228] In embodiments, L1 is independently a bond, -S(O)2-, -N(R5)-, -O-, -S-, -C(O)-, -C(O)N(R5)-, -N(R5)C(O)-, -N(R5)C(O)NH-, -NHC(O)N(R5)-, -C(O)O-, -OC(O)-, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkylene (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkylene (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkylene (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted arylene (e.g., C6-C10 or phenylene), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroarylene (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0229] In embodiments, a substituted L1 (e.g., substituted alkylene, substituted
heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted L1 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In
embodiments, when L1 is substituted, it is substituted with at least one substituent group. In embodiments, when L1 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when L1 is substituted, it is substituted with at least one lower substituent group. [0230] In embodiments, L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene. [0231] In embodiments, L1 is independently -S(O)2-, -NH-, or substituted or unsubstituted 5 to 6 membered heterocycloalkylene. [0232] In embodiments, L1 is independently -S(O)2-, -NH-, unsubstituted pyrrolidinylene, unsubstituted piperidinylene, or unsubstituted piperazinylene. [0233] In embodiments, L1 is independently -NH-. [0234] In embodiments, L1 is independently -N(R5)-, and R5 is as described herein, including in embodiments. In embodiments, L1 is independently -N(R5)-, and R5 is independently hydrogen or unsubstituted alkyl. In embodiments, L1 is independently -N(R5)-, and R5 is independently hydrogen or substituted or unsubstituted alkyl. In embodiments, L1 is independently -N(R5)-, and R5 is independently hydrogen or
unsubstituted alkyl. In embodiments, L1 is independently -N(R5)-, and R5 is independently hydrogen or unsubstituted C1-C4 alkyl. In embodiments, L1 is independently -N(R5)-, and R5 is independently hydrogen or unsubstituted methyl. [0235] In embodiments, R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0236] In embodiments, a substituted R1 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R1 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R1 is substituted, it is substituted with at least one substituent group. In embodiments, when R1 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R1 is substituted, it is substituted with at least one lower substituent group. [0237] In embodiments, R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6- C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0238] In embodiments, two adjacent R1 substituents are joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0239] In embodiments, two adjacent R1 substituents are joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0240] In embodiments, a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by joining two adjacent R1 substituents is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R1 substituents is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R1 substituents is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R1 substituents is substituted, it is substituted with at least one lower substituent group. [0241] In embodiments, R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl. [0242] In embodiments, R1 is independently halogen. In embodiments, R1 is independently –F. In embodiments, R1 is independently–Cl. In embodiments, R1 is independently–Br. In embodiments, R1 is independently–I. [0243] In embodiments, R1 is independently halogen. [0244] In embodiments, R1 is -F. [0245] In embodiments, R1 is independently halogen, -CX1 3, -CHX1 2, -CH2X1, -OCX1 3, -OCH2X1, -OCHX1 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted 2 to 6 membered heteroalkyl, substituted or unsubstituted C3-C8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted phenyl, or substituted or unsubstituted 5 to 6 membered heteroaryl. In embodiments, R1 is
independently halogen, -CX1 3, -CHX1 2, -CH2X1, -OH, -SH, -OCX1 3, -OCHX1 2, -OCH2X1, -CH3, -CH2CH3, -OCH3, -OCH2CH3, -SCH3, or -SCH2CH3. In embodiments, R1 is independently halogen, -CF3, -CHF2, -CH2F, -OH, -SH, -OCF3, -OCHF2, -OCH2F, -CH3, -CH2CH3, -OCH3, -OCH2CH3, -SCH3, or -SCH2CH3. In embodiments, R1 is substituted or unsubstituted C1-C6 alkyl. In embodiments, R1 is substituted or unsubstituted 2 to 6 membered heteroalkyl. In embodiments, R1 is substituted or unsubstituted C3-C8 cycloalkyl. In embodiments, R1 is substituted or unsubstituted 3 to 8 membered heterocycloalkyl. In embodiments, R1 is substituted or unsubstituted phenyl. In embodiments, R1 is substituted or unsubstituted 5 to 6 membered heteroaryl. In embodiments, R1 is independently halogen. In embodiments, R1 is independently -CX1 3. In embodiments, R1 is independently -CHX1 2. In embodiments, R1 is independently -CH2X1. In embodiments, R1 is independently -OCX13. In embodiments, R1 is independently -OCH2X1. In embodiments, R1 is independently
-OCHX1 2. In embodiments, R1 is independently -OCH2X1. In embodiments, R1 is independently -CN. In embodiments, R1 is independently -SOn1R1D. In embodiments, R1 is independently -SOv1NR1AR1B. In embodiments, R1 is independently -NHC(O)NR1AR1B. In embodiments, R1 is independently -N(O)m1. In embodiments, R1 is independently -NR1AR1B. In embodiments, R1 is independently -C(O)R1C. In embodiments, R1 is independently -C(O)OR1C. In embodiments, R1 is independently -C(O)NR1AR1B. In embodiments, R1 is independently -OR1D. In embodiments, R1 is independently -NR1ASO2R1D. In embodiments, R1 is independently -NR1AC(O)R1C. In embodiments, R1 is independently -NR1AC(O)OR1C. In embodiments, R1 is independently -NR1AOR1C. In embodiments, R1 is independently -OH. In embodiments, R1 is independently -NH2. In embodiments, R1 is independently -COOH. In embodiments, R1 is independently -CONH2. In embodiments, R1 is independently -NO2. In embodiments, R1 is independently -SH. In embodiments, R1 is independently -CF3. In embodiments, R1 is independently -CHF2. In embodiments, R1 is independently -CH2F. In embodiments, R1 is independently -OCF3. In embodiments, R1 is independently -OCH2F. In embodiments, R1 is independently -OCHF2. In embodiments, R1 is independently–OCH3. In embodiments, R1 is independently–OCH2CH3. In embodiments, R1 is independently –OCH2CH2CH3. In embodiments, R1 is independently–OCH(CH3)2. In embodiments, R1 is independently–OC(CH3)3. In embodiments, R1 is independently–SCH3. In embodiments, R1 is independently–SCH2CH3. In embodiments, R1 is independently–SCH2CH2CH3. In embodiments, R1 is independently–SCH(CH3)2. In embodiments, R1 is independently –SC(CH3)3. In embodiments, R1 is independently–CH3. In embodiments, R1 is
independently–CH2CH3. In embodiments, R1 is independently–CH2CH2CH3. In
embodiments, R1 is independently–CH(CH3)2. In embodiments, R1 is independently –C(CH3)3. In embodiments, R1 is independently–F. In embodiments, R1 is independently –Cl. In embodiments, R1 is independently–Br. In embodiments, R1 is independently–I. In embodiments, R1 is independently unsubstituted methyl. In embodiments, R1 is
independently unsubstituted ethyl. In embodiments, R1 is independently unsubstituted propyl. In embodiments, R1 is independently unsubstituted n-propyl. In embodiments, R1 is independently unsubstituted isopropyl. In embodiments, R1 is independently unsubstituted butyl. In embodiments, R1 is independently unsubstituted n-butyl. In embodiments, R1 is independently unsubstituted isobutyl. In embodiments, R1 is independently unsubstituted tert-butyl. In embodiments, R1 is independently unsubstituted pentyl. [0246] In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0247] In embodiments, a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by joining two adjacent -L1-R1 substituents is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent -L1-R1 substituents is substituted, it is substituted with at least one substituent group. In
embodiments, when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent -L1-R1 substituents is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent -L1-R1 substituents is substituted, it is substituted with at least one lower substituent group. [0248] In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted cycloalkyl. In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or
unsubstituted heterocycloalkyl. In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted aryl. In embodiments, two adjacent R1 substituents are joined to form a substituted or unsubstituted heteroaryl. In embodiments, two
adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted C3-C8 cycloalkyl. In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted 3 to 8 membered heterocycloalkyl. In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted C6-C10 aryl. In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted 5 to 10 membered heteroaryl. In embodiments, two adjacent R1 substituents are joined to form a substituted or unsubstituted C3-C6 cycloalkyl. In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted 3 to 6 membered
heterocycloalkyl. In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted phenyl. In embodiments, two adjacent -L1-R1 substituents are joined to form a substituted or unsubstituted 5 to 6 membered heteroaryl. It will be understood that when two adjacent L1 substituents are a bond, two adjacent -L1-R1 substituents that are joined are equivalent to two adjacent -R1 substituents being joined and may be depicted as such in a formula. [0249] In embodiments, R1A, R1B, R1C, and R1D are independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0250] In embodiments, R1A is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1- C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0251] In embodiments, a substituted R1A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R1A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R1A is substituted, it is substituted with at least one substituent group. In embodiments, when R1A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R1A is substituted, it is substituted with at least one lower substituent group. [0252] In embodiments, R1A is independently hydrogen. In embodiments, R1A is independently -CX1A 3. In embodiments, R1A is independently -CHX1A 2. In embodiments, R1A is independently -CH2X1A. In embodiments, R1A is independently -CN. In
embodiments, R1A is independently -COOH. In embodiments, R1A is independently
-CONH2. X1A is independently–F, -Cl, -Br, or -I. [0253] In embodiments, R1A is independently substituted or unsubstituted alkyl (e.g., C1- C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1A is independently substituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1A is independently unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1A is independently unsubstituted methyl. In embodiments, R1A is independently unsubstituted ethyl. In embodiments, R1A is independently unsubstituted propyl. In embodiments, R1A is independently unsubstituted isopropyl. In embodiments, R1A is independently unsubstituted tert-butyl. In embodiments, R1A is independently substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1A is independently substituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1A is independently unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1A is independently substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1A is independently substituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1A is independently unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1A is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1A is independently substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1A is independently unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1A is
independently substituted or unsubstituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1A is independently substituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1A is
independently unsubstituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1A is
independently substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1A is independently substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1A is independently unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0254] In embodiments, R1B is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1- C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0255] In embodiments, a substituted R1B (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R1B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R1B is substituted, it is substituted with at least one substituent group. In embodiments, when R1B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R1B is substituted, it is substituted with at least one lower substituent group. [0256] In embodiments, R1B is independently hydrogen. In embodiments, R1B is independently -CX1B 3. In embodiments, R1B is independently -CHX1B 2. In embodiments, R1B is independently -CH2X1B. In embodiments, R1B is independently -CN. In embodiments, R1B is independently -COOH. In embodiments, R1B is independently -CONH2. X1B is independently–F, -Cl, -Br, or -I. [0257] In embodiments, R1B is independently substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1B is independently substituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1B is independently unsubstituted alkyl (e.g., C1- C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1B is independently unsubstituted methyl. In embodiments, R1B is independently unsubstituted ethyl. In embodiments, R1B is
independently unsubstituted propyl. In embodiments, R1B is independently unsubstituted isopropyl. In embodiments, R1B is independently unsubstituted tert-butyl. In embodiments, R1B is independently substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1B is independently substituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1B is independently unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1B is independently substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1B is independently substituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1B is independently unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1B is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1B is independently substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1B is independently unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1B is
independently substituted or unsubstituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1B is independently substituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1B is
independently unsubstituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1B is independently substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1B is independently substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1B is independently unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0258] In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form a substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1A and R1B
substituents bonded to the same nitrogen atom may be joined to form an unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). [0259] In embodiments, a substituted heterocycloalkyl formed by joining R1A and R1B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when a substituted heterocycloalkyl formed by joining R1A and R1B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heterocycloalkyl formed by joining R1A and R1B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heterocycloalkyl formed by joining R1A and R1B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group. [0260] In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form a substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form a substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form an unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). [0261] In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1A and R1B
substituents bonded to the same nitrogen atom may be joined to form a substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form an unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0262] In embodiments, a substituted heteroaryl formed by joining R1A and R1B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when a substituted heteroaryl formed by joining R1A and R1B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heteroaryl formed by joining R1A and R1B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heteroaryl formed by joining R1A and R1B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group. [0263] In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form a substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form a substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1A and R1B substituents bonded to the same nitrogen atom may be joined to form an unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0264] In embodiments, R1C is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1- C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0265] In embodiments, a substituted R1C (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R1C is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R1C is substituted, it is substituted with at least one substituent group. In embodiments, when R1C is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R1C is substituted, it is substituted with at least one lower substituent group. [0266] In embodiments, R1C is independently hydrogen. In embodiments, R1C is independently -CX1C 3. In embodiments, R1C is independently -CHX1C 2. In embodiments, R1C is independently -CH2X1C. In embodiments, R1C is independently -CN. In embodiments, R1C is independently -COOH. In embodiments, R1C is independently -CONH2. X1C is independently–F, -Cl, -Br, or -I. [0267] In embodiments, R1C is independently substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1C is independently substituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1C is independently unsubstituted alkyl (e.g., C1- C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1C is independently unsubstituted methyl. In embodiments, R1C is independently unsubstituted ethyl. In embodiments, R1C is
independently unsubstituted propyl. In embodiments, R1C is independently unsubstituted isopropyl. In embodiments, R1C is independently unsubstituted tert-butyl. In embodiments, R1C is independently substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1C is independently substituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1C is independently unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1C is independently substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1C is independently substituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1C is independently unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1C is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1C is independently substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1C is independently unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1C is
independently substituted or unsubstituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1C is independently substituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1C is
independently unsubstituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1C is
independently substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1C is independently substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1C is independently unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0268] In embodiments, R1D is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1- C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0269] In embodiments, a substituted R1D (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R1D is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R1D is substituted, it is substituted with at least one substituent group. In embodiments, when R1D is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R1D is substituted, it is substituted with at least one lower substituent group. [0270] In embodiments, R1D is independently hydrogen. In embodiments, R1D is independently -CX1D3. In embodiments, R1D is independently -CHX1D2. In embodiments, R1D is independently -CH2X1D. In embodiments, R1D is independently -CN. In
embodiments, R1D is independently -COOH. In embodiments, R1D is independently
-CONH2. X1D is independently–F, -Cl, -Br, or -I. [0271] In embodiments, R1D is independently substituted or unsubstituted alkyl (e.g., C1- C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1D is independently substituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1D is independently unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2). In embodiments, R1D is independently unsubstituted methyl. In embodiments, R1D is independently unsubstituted ethyl. In embodiments, R1D is independently unsubstituted propyl. In embodiments, R1D is independently unsubstituted isopropyl. In embodiments, R1D is independently unsubstituted tert-butyl. In embodiments, R1D is independently substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1D is independently substituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1D is independently unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered). In embodiments, R1D is independently substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1D is independently substituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1D is independently unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, R1D is independently substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1D is independently substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1D is independently unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, R1D is
independently substituted or unsubstituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1D is independently substituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1D is
independently unsubstituted aryl (e.g., C6-C10 or phenyl). In embodiments, R1D is
independently substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1D is independently substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1D is independently unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0272] In embodiments, R1 is independently halogen, -CX1 3, -CHX1 2, -CH2X1, -OCX1 3, -OCH2X1, -OCHX1 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC=(O)NHNH2, -NH C=(O)NH2, -NHSO2H, -NHC=(O)H, -NHC(O)OH, -NHOH, R10-substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), R10-substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), R10-substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), R10-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), R10-substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or R10-substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R1 is independently halogen, -CX1 3, -CHX1 2, -CH2X1, -OCX1 3, -OCH2X1, -OCHX1 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C=(O)NHNH2, -NH C=(O)NH2, -NHSO2H, -NHC=(O)H, -NHC(O)OH, -NHOH, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1- C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3- C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C10 or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). X1 is independently–F, -Cl, -Br, or–I. In embodiments, R1 is independently unsubstituted methyl. In embodiments, R1 is independently unsubstituted ethyl. In embodiments, R1 is independently R10-substituted 2 membered heteroalkyl. In embodiments, R1 is independently R10-substituted methoxy. [0273] In embodiments, two adjacent–L1-R1 substituents are joined to form a R10- substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), R10-substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), R10-substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or R10-substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, two adjacent–L1-R1 substituents are joined to form an unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C10 or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, two adjacent–L1-R1 substituents are joined to form a R10-substituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, two adjacent–L1-R1 substituents are joined to form a R10-substituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, two adjacent–L1-R1 substituents are joined to form a R10-substituted aryl (e.g., C6-C10 or phenyl). In
embodiments, two adjacent–L1-R1 substituents are joined to form a R10-substituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, two adjacent–L1-R1 substituents are joined to form an unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6). In embodiments, two adjacent–L1-R1 substituents are joined to form an unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered). In embodiments, two adjacent–L1-R1 substituents are joined to form an unsubstituted aryl (e.g., C6-C10 or phenyl). In
embodiments, two adjacent–L1-R1 substituents are joined to form an unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0274] R10 is independently oxo, halogen, -CX10 3, -CHX10 2, -CH2X10, -OCX10 3, -OCH2X10, -OCHX10 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC=(O)NHNH2, -NHC=(O)NH2, -NHSO2H, -NHC=(O)H,
-NHC(O)OH, -NHOH, -N3, R11-substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), R11-substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), R11-substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), R11-substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), R11-substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or R11-substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). X10 is independently–F, -Cl, -Br, or–I. In embodiments, R10 is independently unsubstituted methyl. In embodiments, R10 is independently
unsubstituted ethyl. [0275] R11 is independently oxo, halogen, -CX11 3, -CHX11 2, -CH2X11, -OCX11 3, -OCH2X11, -OCHX11 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC=(O)NHNH2, -NHC=(O)NH2, -NHSO2H, -NHC=(O)H,
-NHC(O)OH, -NHOH, -N3, R12-substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), R12-substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), R12-substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), R12-substituted or
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), R12-substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or R12-substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). X11 is independently–F, -Cl, -Br, or–I. In embodiments, R11 is independently unsubstituted methyl. In embodiments, R11 is independently
unsubstituted ethyl. [0276] R12 is independently oxo, halogen, -CX12 3, -CHX12 2, -CH2X12, -OCX12 3, -OCH2X12, -OCHX12 2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC=(O)NHNH2, -NHC=(O)NH2, -NHSO2H, -NHC=(O)H,
-NHC(O)OH, -NHOH, -N3, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5- C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C10 or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). X12 is independently–F, -Cl, -Br, or–I. In embodiments, R12 is independently unsubstituted methyl. In embodiments, R12 is independently unsubstituted ethyl. [0277] In embodiments, n1 is 0. In embodiments, n1 is 1. In embodiments, n1 is 2. In embodiments, n1 is 3. In embodiments, n1 is 4. In embodiments, m1 is 1. In embodiments, m1 is 2. In embodiments, v1 is 1. In embodiments, v1 is 2. [0278] In embodiments, z1 is independently an integer from 0 to 4. In embodiments, z1 is 0. In embodiments, z1 is 1. In embodiments, z1 is 2. In embodiments, z1 is 3. In embodiments, z1 is 4. In embodiments, z1 is 5. [0279] In embodiments, R2 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1- C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0280] In embodiments, a substituted R2 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R2 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R2 is substituted, it is substituted with at least one substituent group. In embodiments, when R2 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R2 is substituted, it is substituted with at least one lower substituent group. [0281] In embodiments, R2 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R2 is
independently hydrogen. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently unsubstituted propyl. In embodiments, R2 is independently unsubstituted n-propyl. In embodiments, R2 is independently unsubstituted isopropyl. In embodiments, R2 is independently unsubstituted butyl. In embodiments, R2 is independently unsubstituted n- butyl. In embodiments, R2 is independently unsubstituted isobutyl. In embodiments, R2 is independently unsubstituted tert-butyl. In embodiments, R2 is independently unsubstituted pentyl. [0282] In embodiments, R2 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. [0283] In embodiments, R2 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C10 or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0284] In embodiments, R2 is independently hydrogen. In embodiments, R2 is
independently -CCl3. In embodiments, R2 is independently -CBr3. In embodiments, R2 is independently -CF3. In embodiments, R2 is independently -CI3. In embodiments, R2 is independently -CH2Cl. In embodiments, R2 is independently -CH2Br. In embodiments, R2 is independently -CH2F. In embodiments, R2 is independently -CH2I. In embodiments, R2 is independently -CHCl2. In embodiments, R2 is independently -CHBr2. In embodiments, R2 is independently -CHF2. In embodiments, R2 is independently -CHI2. In embodiments, R2 is independently unsubstituted C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently unsubstituted propyl. In embodiments, R2 is independently unsubstituted n-propyl. In embodiments, R2 is independently unsubstituted isopropyl. In embodiments, R2 is independently unsubstituted butyl. In embodiments, R2 is independently unsubstituted n-butyl. In embodiments, R2 is independently unsubstituted isobutyl. In embodiments, R2 is independently unsubstituted tert-butyl. In embodiments, R2 is independently unsubstituted pentyl. In embodiments, R2 is independently unsubstituted hexyl. In embodiments, R2 is independently unsubstituted C3-C6 cycloalkyl. [0285] In embodiments, R3 and R4 are independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0286] In embodiments, R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0287] In embodiments, a substituted R3 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R3 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R3 is substituted, it is substituted with at least one substituent group. In embodiments, when R3 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R3 is substituted, it is substituted with at least one lower substituent group. [0288] In embodiments, R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6- C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0289] In embodiments, R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C10 or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0290] In embodiments, R3 is independently halogen. In embodiments, R3 is independently –F. In embodiments, R3 is independently–Cl. In embodiments, R3 is independently–Br. In embodiments, R3 is independently–I. In embodiments, R3 is independently -CCl3. In embodiments, R3 is independently -CBr3. In embodiments, R3 is independently -CF3. In embodiments, R3 is independently -CI3. In embodiments, R3 is independently -CH2Cl. In embodiments, R3 is independently -CH2Br. In embodiments, R3 is independently -CH2F. In embodiments, R3 is independently -CH2I. In embodiments, R3 is independently -CHCl2. In embodiments, R3 is independently -CHBr2. In embodiments, R3 is independently -CHF2. In embodiments, R3 is independently -CHI2. In embodiments, R3 is independently unsubstituted C1-C4 alkyl. In embodiments, R3 is independently unsubstituted methyl. In embodiments, R3 is independently unsubstituted methyl. In embodiments, R3 is independently unsubstituted ethyl. In embodiments, R3 is independently unsubstituted propyl. In embodiments, R3 is independently unsubstituted n-propyl. In embodiments, R3 is independently unsubstituted isopropyl. In embodiments, R3 is independently unsubstituted butyl. In embodiments, R3 is independently unsubstituted n-butyl. In embodiments, R3 is independently unsubstituted isobutyl. In embodiments, R3 is independently unsubstituted tert-butyl. [0291] In embodiments, z3 is 0. In embodiments, z3 is 1. In embodiments, z3 is 2. [0292] In embodiments, R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered); two adjacent R4 substituents may optionally be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size- limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0293] In embodiments, a substituted R4 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R4 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R4 is substituted, it is substituted with at least one substituent group. In embodiments, when R4 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R4 is substituted, it is substituted with at least one lower substituent group. [0294] In embodiments, a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by joining two adjacent R4 substituents is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R4 substituents is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R4 substituents is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, or substituted heteroaryl formed by two adjacent R4 substituents is substituted, it is substituted with at least one lower substituent group. [0295] In embodiments, R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0296] In embodiments, R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl. [0297] In embodiments, R4 is independently halogen. In embodiments, R4 is independently –F. In embodiments, R4 is independently–Cl. In embodiments, R4 is independently–Br. In embodiments, R4 is independently–I. In embodiments, R4 is independently–OH. In embodiments, R4 is independently unsubstituted C1-C4 alkyl. In embodiments, R4 is independently unsubstituted methyl. In embodiments, R4 is independently unsubstituted ethyl. In embodiments, R4 is independently unsubstituted propyl. In embodiments, R4 is independently unsubstituted n-propyl. In embodiments, R4 is independently unsubstituted isopropyl. In embodiments, R4 is independently unsubstituted butyl. In embodiments, R4 is independently unsubstituted n-butyl. In embodiments, R4 is independently unsubstituted isobutyl. In embodiments, R4 is independently unsubstituted tert-butyl. [0298] In embodiments, R4 is independently halogen. [0299] In embodiments, R4 is independently -F. [0300] In embodiments, R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6- C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0301] In embodiments, R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C10 or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0302] In embodiments, z4 is independently an integer from 0 to 5. [0303] In embodiments, z4 is 0. In embodiments, z4 is 1. In embodiments, z4 is 2. In embodiments, z4 is 3. In embodiments, z4 is 4. In embodiments, z4 is 5. [0304] In embodiments, R5 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0305] In embodiments, a substituted R5 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R5 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R5 is substituted, it is substituted with at least one substituent group. In embodiments, when R5 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R5 is substituted, it is substituted with at least one lower substituent group. [0306] In embodiments, R5 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). In embodiments, R5 is
independently hydrogen. In embodiments, R5 is independently unsubstituted methyl. In embodiments, R5 is independently unsubstituted ethyl. In embodiments, R5 is independently unsubstituted propyl. In embodiments, R5 is independently unsubstituted n-propyl. In embodiments, R5 is independently unsubstituted isopropyl. In embodiments, R5 is independently unsubstituted butyl. In embodiments, R5 is independently unsubstituted n- butyl. In embodiments, R5 is independently unsubstituted isobutyl. In embodiments, R5 is independently unsubstituted tert-butyl. In embodiments, R5 is independently unsubstituted pentyl. [0307] In embodiments, R5 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. [0308] In embodiments, R5 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), unsubstituted aryl (e.g., C6-C10 or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0309] In embodiments, E is
Figure imgf000114_0001
In embodiments, E is
Figure imgf000114_0002
[0310] R16 is independently hydrogen, halogen, -CX163, -CHX162, -CH2X16, -CN,
-SOn16R16A, -SOv16NR16AR16B, -NHNR16AR16B, -ONR16AR16B, -NH C(O)NHNR16AR16B, -NHC(O)NR16AR16B, -N(O)m16, -NR16AR16B, -C(O)R16A, -C(O)-OR16A, -C(O)NR16AR16B, -OR16A, -NR16ASO2R16B, -NR16AC(O)R16B, -NR16AC(O)OR16B, -NR16AOR16B, -OCX163, -OCHX16 2, -OCH2X16, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0311] R17 is independently hydrogen, halogen, -CX17 3, -CHX17 2, -CH2X17, -CN,
-SOn17R17A, -SOv17NR17AR17B, -NHNR17AR17B, -ONR17AR17B, -NH C(O)NHNR17AR17B, -NHC(O)NR17AR17B, -N(O)m17, -NR17AR17B, -C(O)R17A, -C(O)-OR17A, -C(O)NR17AR17B, -OR17A, -NR17ASO2R17B, -NR17AC(O)R17B, -NR17AC(O)OR17B, -NR17AOR17B, -OCX17 3, -OCHX172, -OCH2X17, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0312] R18 is independently hydrogen, halogen, -CX18 3, -CHX18 2, -CH2X18, -CN,
-SOn18R18A, -SOv18NR18AR18B, -NHNR18AR18B, -ONR18AR18B, -NH C(O)NHNR18AR18B, -NHC(O)NR18AR18B, -N(O)m18, -NR18AR18B, -C(O)R18A, -C(O)-OR18A, -C(O)NR18AR18B, -OR18A, -NR18ASO2R18B, -NR18AC(O)R18B, -NR18AC(O)OR18B, -NR18AOR18B, -OCX18 3, -OCHX18 2, -OCH2X18, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0313] R19 is independently hydrogen, halogen, -CX19 3, -CHX19 2, -CH2X19, -CN,
-SOn19R19A, -SOv19NR19AR19B, -NHNR19AR19B, -ONR19AR19B, -NH C(O)NHNR19AR19B, -NHC(O)NR19AR19B, -N(O)m19, -NR19AR19B, -C(O)R19A, -C(O)-OR19A, -C(O)NR19AR19B, -OR19A, -NR19ASO2R19B, -NR19AC(O)R19B, -NR19AC(O)OR19B, -NR19AOR19B, -OCX19 3, -OCHX19 2, -OCH2X19, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0314] R16A, R16B, R17A, R17B, R18A, R18B, R19A, and R19B are independently hydrogen, -CX3, -CHX2, -CH2X, -CN, -OH, -COOH, -CONH2, substituted or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered); R16A and R16B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R17A and R17B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R18A and R18B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R19A and R19B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl. [0315] X, X16, X17, X18 and X19 are independently–F, -Cl, -Br, or–I. [0316] n16, n17, n18, and n19 are independently an integer from 0 to 4. [0317] m16, m17, m18, m19, v16, v17, v18, and v19 are independently 1 or 2. [0318] In embodiments, E is
Figure imgf000117_0001
.
[0319] In embodiments, E is a covalent cysteine modifier moiety.
[0320] In embodiments, E is
Figure imgf000117_0002
In embodiments, E is
Figure imgf000117_0003
. In
embodiments, E is
Figure imgf000117_0004
. In embodiments, E is
Figure imgf000117_0005
. In
embodiments, E is
Figure imgf000117_0006
. In embodiments, E is
Figure imgf000117_0007
In
embodiments, E is
Figure imgf000117_0008
. In embodiments, E is
Figure imgf000117_0009
In
embodiments, E is
Figure imgf000117_0010
. In embodiments, E is
Figure imgf000117_0011
In embodiments, E is
Figure imgf000117_0012
. In embodiments, E is
Figure imgf000117_0013
In embodiments, E is
Figure imgf000117_0014
. In embodiments, E is
Figure imgf000117_0015
. In embodiments, E is R16,
Figure imgf000117_0016
R17, R18, R19, and X17 are as described herein. [0321] In embodiments, R1 is independently
Figure imgf000118_0001
Figure imgf000118_0008
or
Figure imgf000118_0009
. In embodiments,
R1 is independently
Figure imgf000118_0002
. R16, R17, R18, R19, and X17 are as described herein. [0322] In embodiments, R1 is independently
Figure imgf000118_0010
, or
Figure imgf000118_0011
[0323] In embodiments, R1 is independently a covalent cysteine modifier moiety.
[0324] In embodiments, R1 is independently
Figure imgf000118_0003
. In embodiments, R1 is
independently
Figure imgf000118_0012
. In embodiments, R1 is independently
Figure imgf000118_0013
In
embodiments, R1 is independently
Figure imgf000118_0004
. In embodiments, R1 is independently
Figure imgf000118_0005
. In embodiments, R1 is independently
Figure imgf000118_0006
. In
embodiments, R1 is independently
Figure imgf000118_0007
. In embodiments, R1 is independently
Figure imgf000119_0002
. In embodiments, R1 is independently
Figure imgf000119_0001
. In
embodiments, R1 is independently
Figure imgf000119_0006
. In embodiments, R1 is independently
Figure imgf000119_0007
. In embodiments, R1 is independently
Figure imgf000119_0008
. In embodiments, R1 is
independently
Figure imgf000119_0004
embodiments, R1 is independently
Figure imgf000119_0003
. In
embodiments, R1 is independently
Figure imgf000119_0005
. R16, R17, R18, R19, and X17 are as described herein. [0325] X may independently be–F. X may independently be–Cl. X may independently be–Br. X may independently be–I. X16 may independently be–F. X16 may independently be–Cl. X16 may independently be–Br. X16 may independently be–I. X17 may
independently be–F. X17 may independently be–Cl. X17 may independently be–Br. X17 may independently be–I. X18 may independently be–F. X18 may independently be–Cl. X18 may independently be–Br. X18 may independently be–I. X19 may independently be–F. X19 may independently be–Cl. X19 may independently be–Br. X19 may independently be–I. [0326] n16 may independently be 0. n16 may independently be 1. n16 may independently be 2. n16 may independently be 3. n16 may independently be 4. n17 may independently be 0. n17 may independently be 1. n17 may independently be 2. n17 may independently be 3. n17 may independently be 4. n18 may independently be 0. n18 may independently be 1. n18 may independently be 2. n18 may independently be 3. n18 may independently be 4. n19 may independently be 0. n19 may independently be 1. n19 may independently be 2. n19 may independently be 3. n19 may independently be 4. [0327] v16 may independently be 1. v16 may independently be 2. v17 may independently be 1. v17 may independently be 2. v18 may independently be 1. v18 may independently be 2. v19 may independently be 1. v19 may independently be 2. [0328] m16 may independently be 1. m16 may independently be 2. m17 may
independently be 1. m17 may independently be 2. m18 may independently be 1. m18 may independently be 2. m19 may independently be 1. m19 may independently be 2. [0329] In embodiments, R16A, R16B, R17A, R17B, R18A, R18B, R19A, and R19B are
independently hydrogen, -CX3, -CHX2, -CH2X, -CN, -OH, -COOH, -CONH2, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered); R16A and R16B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered) or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered); R17A and R17B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered) or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered); R18A and R18B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered) or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered); R19A and R19B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered) or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0330] In embodiments, a substituted R16A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R16A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R16A is substituted, it is substituted with at least one substituent group. In embodiments, when R16A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R16A is substituted, it is substituted with at least one lower substituent group. [0331] In embodiments, a substituted R16B (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R16B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R16B is substituted, it is substituted with at least one substituent group. In embodiments, when R16B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R16B is substituted, it is substituted with at least one lower substituent group. [0332] In embodiments, a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R16A and R16B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl or the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R16A and R16B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R16A and R16B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R16A and R16B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group. [0333] In embodiments, a substituted R17A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R17A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R17A is substituted, it is substituted with at least one substituent group. In embodiments, when R17A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R17A is substituted, it is substituted with at least one lower substituent group. [0334] In embodiments, a substituted R17B (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R17B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R17B is substituted, it is substituted with at least one substituent group. In embodiments, when R17B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R17B is substituted, it is substituted with at least one lower substituent group. [0335] In embodiments, a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R17A and R17B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl or the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R17A and R17B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R17A and R17B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R17A and R17B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group. [0336] In embodiments, a substituted R18A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R18A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R18A is substituted, it is substituted with at least one substituent group. In embodiments, when R18A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R18A is substituted, it is substituted with at least one lower substituent group. [0337] In embodiments, a substituted R18B (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R18B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R18B is substituted, it is substituted with at least one substituent group. In embodiments, when R18B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R18B is substituted, it is substituted with at least one lower substituent group. [0338] In embodiments, a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R18A and R18B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl or the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R18A and R18B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R18A and R18B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R18A and R18B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group. [0339] In embodiments, a substituted R19A (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R19A is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R19A is substituted, it is substituted with at least one substituent group. In embodiments, when R19A is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R19A is substituted, it is substituted with at least one lower substituent group. [0340] In embodiments, a substituted R19B (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R19B is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R19B is substituted, it is substituted with at least one substituent group. In embodiments, when R19B is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R19B is substituted, it is substituted with at least one lower substituent group. [0341] In embodiments, a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R19A and R19B bonded to the same nitrogen is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted heterocycloalkyl or the substituted heteroaryl is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R19A and R19B bonded to the same nitrogen is substituted, it is substituted with at least one substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R19A and R19B bonded to the same nitrogen is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when a substituted heterocycloalkyl or a substituted heteroaryl formed by joining R19A and R19B bonded to the same nitrogen is substituted, it is substituted with at least one lower substituent group. [0342] In embodiments, R16 is independently hydrogen, halogen, -CX16 3, -CHX16 2, -CH2X16, -CN, -SOn16R16A, -SOv16NR16AR16B, -NH NR16AR16B, -ONR16AR16B,
-NHC(O)NHNR16AR16B, -NH C(O)NR16AR16B, -N(O)m16, -NR16AR16B, -C(O)R16A,
-C(O)-OR16A, -C(O)NR16AR16B, -OR16A, -NR16ASO2R16B, -NR16AC(O)R16B,
-NR16AC(O)OR16B, -NR16AOR16B, -OCX16 3, -OCHX16 2, -OCH2X16, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0343] In embodiments, a substituted R16 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R16 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R16 is substituted, it is substituted with at least one substituent group. In embodiments, when R16 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R16 is substituted, it is substituted with at least one lower substituent group. [0344] In embodiments, R16 is independently hydrogen. In embodiments, R16 is independently halogen. In embodiments, R16 is independently–CN. In embodiments, R16 is independently unsubstituted methyl. In embodiments, R16 is independently unsubstituted ethyl. In embodiments, R16 is independently unsubstituted propyl. In embodiments, R16 is independently unsubstituted isopropyl. In embodiments, R16 is independently unsubstituted butyl. In embodiments, R16 is independently unsubstituted tert-butyl. In embodiments, R16 is independently–CH2Ph. In embodiments, R16 is independently -F. In embodiments, R16 is independently -Cl. In embodiments, R16 is independently -Br. In embodiments, R16 is independently -I. In embodiments, R16 is independently unsubstituted methoxy. In embodiments, R16 is independently unsubstituted ethoxy. In embodiments, R16 is
independently -CF3. In embodiments, R16 is independently -CCl3. In embodiments, R16 is independently -CX16 3. In embodiments, R16 is independently -OH. In embodiments, R16 is independently -NH2. In embodiments, R16 is independently -COOH. In embodiments, R16 is independently -CONH2. In embodiments, R16 is independently -NO2. In embodiments, R16 is independently -SH. In embodiments, R16 is independently -SO3H. In embodiments, R16 is independently -SO4H. In embodiments, R16 is independently -SO2NH2. In embodiments, R16 is independently -NH NH2. In embodiments, R16 is independently -ONH2. In embodiments, R16 is independently -NH C(O)NHNH2. In embodiments, R16 is independently
-NHC(O)NH2. In embodiments, R16 is independently -NHSO2H. In embodiments, R16 is independently -NHC(O)H. In embodiments, R16 is independently -NHC(O)OH. In embodiments, R16 is independently -NHOH. [0345] In embodiments, R16A is independently hydrogen. In embodiments, R16A is independently -CX3. In embodiments, R16A is independently -CN. In embodiments, R16A is independently -COOH. In embodiments, R16A is independently -CONH2. In embodiments, R16A is independently -CHX2. In embodiments, R16A is independently -CH2X. In
embodiments, R16A is independently unsubstituted methyl. In embodiments, R16A is independently unsubstituted ethyl. In embodiments, R16A is independently unsubstituted propyl. In embodiments, R16A is independently unsubstituted isopropyl. In embodiments, R16A is independently unsubstituted butyl. In embodiments, R16A is independently unsubstituted tert-butyl. [0346] In embodiments, R16B is independently hydrogen. In embodiments, R16B is independently -CX3. In embodiments, R16B is independently -CN. In embodiments, R16B is independently -COOH. In embodiments, R16B is independently -CONH2. In embodiments, R16B is independently -CHX2. In embodiments, R16B is independently -CH2X. In
embodiments, R16B is independently unsubstituted methyl. In embodiments, R16B is independently unsubstituted ethyl. In embodiments, R16B is independently unsubstituted propyl. In embodiments, R16B is independently unsubstituted isopropyl. In embodiments, R16B is independently unsubstituted butyl. In embodiments, R16B is independently unsubstituted tert-butyl. [0347] In embodiments, R17 is independently hydrogen, halogen, -CX173, -CHX172, -CH2X17, -CN, -SOn17R17A, -SOv17NR17AR17B, -NH NR17AR17B, -ONR17AR17B,
-NHC(O)NHNR17AR17B, -NH C(O)NR17AR17B, -N(O)m17, -NR17AR17B, -C(O)R17A,
-C(O)-OR17A, -C(O)NR17AR17B, -OR17A, -NR17ASO2R17B, -NR17AC(O)R17B,
-NR17AC(O)OR17B, -NR17AOR17B, -OCX17 3, -OCHX17 2, -OCH2X17, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0348] In embodiments, a substituted R17 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R17 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R17 is substituted, it is substituted with at least one substituent group. In embodiments, when R17 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R17 is substituted, it is substituted with at least one lower substituent group. [0349] In embodiments, R17 is independently hydrogen. In embodiments, R17 is independently halogen. In embodiments, R17 is independently–CN. In embodiments, R17 is independently unsubstituted methyl. In embodiments, R17 is independently unsubstituted ethyl. In embodiments, R17 is independently unsubstituted propyl. In embodiments, R17 is independently unsubstituted isopropyl. In embodiments, R17 is independently unsubstituted butyl. In embodiments, R17 is independently unsubstituted tert-butyl. In embodiments, R17 is independently–CH2Ph. In embodiments, R17 is independently -F. In embodiments, R17 is independently -Cl. In embodiments, R17 is independently -Br. In embodiments, R17 is independently -I. In embodiments, R17 is independently unsubstituted methoxy. In embodiments, R17 is independently unsubstituted ethoxy. In embodiments, R17 is
independently -CF3. In embodiments, R17 is independently -CCl3. In embodiments, R17 is independently -CX17 3. In embodiments, R17 is independently -OH. In embodiments, R17 is independently -NH2. In embodiments, R17 is independently -COOH. In embodiments, R17 is independently -CONH2. In embodiments, R17 is independently -NO2. In embodiments, R17 is independently -SH. In embodiments, R17 is independently -SO3H. In embodiments, R17 is independently -SO4H. In embodiments, R17 is independently -SO2NH2. In embodiments, R17 is independently -NH NH2. In embodiments, R17 is independently -ONH2. In embodiments, R17 is independently -NH C(O)NHNH2. In embodiments, R17 is independently
-NHC(O)NH2. In embodiments, R17 is independently -NHSO2H. In embodiments, R17 is independently -NHC(O)H. In embodiments, R17 is independently -NHC(O)OH. In embodiments, R17 is independently -NHOH. [0350] In embodiments, R17A is independently hydrogen. In embodiments, R17A is independently -CX3. In embodiments, R17A is independently -CN. In embodiments, R17A is independently -COOH. In embodiments, R17A is independently -CONH2. In embodiments, R17A is independently -CHX2. In embodiments, R17A is independently -CH2X. In
embodiments, R17A is independently unsubstituted methyl. In embodiments, R17A is independently unsubstituted ethyl. In embodiments, R17A is independently unsubstituted propyl. In embodiments, R17A is independently unsubstituted isopropyl. In embodiments, R17A is independently unsubstituted butyl. In embodiments, R17A is independently unsubstituted tert-butyl. [0351] In embodiments, R17B is independently hydrogen. In embodiments, R17B is independently -CX3. In embodiments, R17B is independently -CN. In embodiments, R17B is independently -COOH. In embodiments, R17B is independently -CONH2. In embodiments, R17B is independently -CHX2. In embodiments, R17B is independently -CH2X. In
embodiments, R17B is independently unsubstituted methyl. In embodiments, R17B is independently unsubstituted ethyl. In embodiments, R17B is independently unsubstituted propyl. In embodiments, R17B is independently unsubstituted isopropyl. In embodiments, R17B is independently unsubstituted butyl. In embodiments, R17B is independently unsubstituted tert-butyl. [0352] In embodiments, R18 is independently hydrogen, halogen, -CX183, -CHX182, -CH2X18, -CN, -SOn18R18A, -SOv18NR18AR18B, -NH NR18AR18B, -ONR18AR18B,
-NHC(O)NHNR18AR18B, -NH C(O)NR18AR18B, -N(O)m18, -NR18AR18B, -C(O)R18A,
-C(O)-OR18A, -C(O)NR18AR18B, -OR18A, -NR18ASO2R18B, -NR18AC(O)R18B,
-NR18AC(O)OR18B, -NR18AOR18B, -OCX18 3, -OCHX18 2, -OCH2X18, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0353] In embodiments, a substituted R18 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R18 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R18 is substituted, it is substituted with at least one substituent group. In embodiments, when R18 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R18 is substituted, it is substituted with at least one lower substituent group. [0354] In embodiments, R18 is independently hydrogen. In embodiments, R18 is independently halogen. In embodiments, R18 is independently–CN. In embodiments, R18 is independently unsubstituted methyl. In embodiments, R18 is independently unsubstituted ethyl. In embodiments, R18 is independently unsubstituted propyl. In embodiments, R18 is independently unsubstituted isopropyl. In embodiments, R18 is independently unsubstituted butyl. In embodiments, R18 is independently unsubstituted tert-butyl. In embodiments, R18 is independently–CH2Ph. In embodiments, R18 is independently -F. In embodiments, R18 is independently -Cl. In embodiments, R18 is independently -Br. In embodiments, R18 is independently -I. In embodiments, R18 is independently unsubstituted methoxy. In embodiments, R18 is independently unsubstituted ethoxy. In embodiments, R18 is independently -CF3. In embodiments, R18 is independently -CCl3. In embodiments, R18 is independently -CX18 3. In embodiments, R18 is independently -OH. In embodiments, R18 is independently -NH2. In embodiments, R18 is independently -COOH. In embodiments, R18 is independently -CONH2. In embodiments, R18 is independently -NO2. In embodiments, R18 is independently -SH. In embodiments, R18 is independently -SO3H. In embodiments, R18 is independently -SO4H. In embodiments, R18 is independently -SO2NH2. In embodiments, R18 is independently -NH NH2. In embodiments, R18 is independently -ONH2. In embodiments, R18 is independently -NH C(O)NHNH2. In embodiments, R18 is independently
-NHC(O)NH2. In embodiments, R18 is independently -NHSO2H. In embodiments, R18 is independently -NHC(O)H. In embodiments, R18 is independently -NHC(O)OH. In embodiments, R18 is independently -NHOH. [0355] In embodiments, R18A is independently hydrogen. In embodiments, R18A is independently -CX3. In embodiments, R18A is independently -CN. In embodiments, R18A is independently -COOH. In embodiments, R18A is independently -CONH2. In embodiments, R18A is independently -CHX2. In embodiments, R18A is independently -CH2X. In
embodiments, R18A is independently unsubstituted methyl. In embodiments, R18A is independently unsubstituted ethyl. In embodiments, R18A is independently unsubstituted propyl. In embodiments, R18A is independently unsubstituted isopropyl. In embodiments, R18A is independently unsubstituted butyl. In embodiments, R18A is independently unsubstituted tert-butyl. [0356] In embodiments, R18B is independently hydrogen. In embodiments, R18B is independently -CX3. In embodiments, R18B is independently -CN. In embodiments, R18B is independently -COOH. In embodiments, R18B is independently -CONH2. In embodiments, R18B is independently -CHX2. In embodiments, R18B is independently -CH2X. In
embodiments, R18B is independently unsubstituted methyl. In embodiments, R18B is independently unsubstituted ethyl. In embodiments, R18B is independently unsubstituted propyl. In embodiments, R18B is independently unsubstituted isopropyl. In embodiments, R18B is independently unsubstituted butyl. In embodiments, R18B is independently unsubstituted tert-butyl. [0357] In embodiments, R19 is independently hydrogen, halogen, -CX193, -CHX192, -CH2X19, -CN, -SOn19R19A, -SOv19NR19AR19B, -NH NR19AR19B, -ONR19AR19B, -NHC(O)NHNR19AR19B, -NH C(O)NR19AR19B, -N(O)m19, -NR19AR19B, -C(O)R19A,
-C(O)-OR19A, -C(O)NR19AR19B, -OR19A, -NR19ASO2R19B, -NR19AC(O)R19B,
-NR19AC(O)OR19B, -NR19AOR19B, -OCX19 3, -OCHX19 2, -OCH2X19, substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted alkyl (e.g., C1-C8, C1-C6, C1-C4, or C1-C2), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted cycloalkyl (e.g., C3-C8, C3-C6, C4-C6, or C5-C6), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted aryl (e.g., C6-C10 or phenyl), or substituted (e.g., substituted with at least one substituent group, size-limited substituent group, or lower substituent group) or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered). [0358] In embodiments, a substituted R19 (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, and/or substituted heteroaryl) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted R19 is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, when R19 is substituted, it is substituted with at least one substituent group. In embodiments, when R19 is substituted, it is substituted with at least one size-limited substituent group. In embodiments, when R19 is substituted, it is substituted with at least one lower substituent group. [0359] In embodiments, R19 is independently hydrogen. In embodiments, R19 is independently halogen. In embodiments, R19 is independently–CN. In embodiments, R19 is independently unsubstituted methyl. In embodiments, R19 is independently unsubstituted ethyl. In embodiments, R19 is independently unsubstituted propyl. In embodiments, R19 is independently unsubstituted isopropyl. In embodiments, R19 is independently unsubstituted butyl. In embodiments, R19 is independently unsubstituted tert-butyl. In embodiments, R19 is independently–CH2Ph. In embodiments, R19 is independently -F. In embodiments, R19 is independently -Cl. In embodiments, R19 is independently -Br. In embodiments, R19 is independently -I. In embodiments, R19 is independently unsubstituted methoxy. In embodiments, R19 is independently unsubstituted ethoxy. In embodiments, R19 is
independently -CF3. In embodiments, R19 is independently -CCl3. In embodiments, R19 is independently -CX19 3. In embodiments, R19 is independently -OH. In embodiments, R19 is independently -NH2. In embodiments, R19 is independently -COOH. In embodiments, R19 is independently -CONH2. In embodiments, R19 is independently -NO2. In embodiments, R19 is independently -SH. In embodiments, R19 is independently -SO3H. In embodiments, R19 is independently -SO4H. In embodiments, R19 is independently -SO2NH2. In embodiments, R19 is independently -NH NH2. In embodiments, R19 is independently -ONH2. In embodiments, R19 is independently -NH C(O)NHNH2. In embodiments, R19 is independently
-NHC(O)NH2. In embodiments, R19 is independently -NHSO2H. In embodiments, R19 is independently -NHC(O)H. In embodiments, R19 is independently -NHC(O)OH. In embodiments, R19 is independently -NHOH. [0360] In embodiments, R19A is independently hydrogen. In embodiments, R19A is independently -CX3. In embodiments, R19A is independently -CN. In embodiments, R19A is independently -COOH. In embodiments, R19A is independently -CONH2. In embodiments, R19A is independently -CHX2. In embodiments, R19A is independently -CH2X. In
embodiments, R19A is independently unsubstituted methyl. In embodiments, R19A is independently unsubstituted ethyl. In embodiments, R19A is independently unsubstituted propyl. In embodiments, R19A is independently unsubstituted isopropyl. In embodiments, R19A is independently unsubstituted butyl. In embodiments, R19A is independently unsubstituted tert-butyl. [0361] In embodiments, R19B is independently hydrogen. In embodiments, R19B is independently -CX3. In embodiments, R19B is independently -CN. In embodiments, R19B is independently -COOH. In embodiments, R19B is independently -CONH2. In embodiments, R19B is independently -CHX2. In embodiments, R19B is independently -CH2X. In
embodiments, R19B is independently unsubstituted methyl. In embodiments, R19B is independently unsubstituted ethyl. In embodiments, R19B is independently unsubstituted propyl. In embodiments, R19B is independently unsubstituted isopropyl. In embodiments, R19B is independently unsubstituted butyl. In embodiments, R19B is independently unsubstituted tert-butyl. [0362] In embodiments, when R1 is substituted, R1 is substituted with one or more first substituent groups denoted by R1.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R1.1 substituent group is substituted, the R1.1 substituent group is substituted with one or more second substituent groups denoted by R1.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R1.2 substituent group is substituted, the R1.2 substituent group is substituted with one or more third substituent groups denoted by R1.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R1, R1.1, R1.2, and R1.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R1, R1.1, R1.2, and R1.3, respectively. [0363] In embodiments, when two adjacent R1 substituents are optionally joined to form a moiety that is substituted (e.g., a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R1.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R1.1 substituent group is substituted, the R1.1 substituent group is substituted with one or more second substituent groups denoted by R1.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R1.2 substituent group is substituted, the R1.2 substituent group is substituted with one or more third substituent groups denoted by R1.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R1, R1.1, R1.2, and R1.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R1, R1.1, R1.2, and R1.3, respectively. [0364] In embodiments, when two adjacent -L1-R1 substituents are optionally joined to form a moiety that is substituted (e.g., a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R1.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R1.1 substituent group is substituted, the R1.1 substituent group is substituted with one or more second substituent groups denoted by R1.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R1.2 substituent group is substituted, the R1.2 substituent group is substituted with one or more third substituent groups denoted by R1.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, -L1-R1, R1.1, R1.2, and R1.3 have values corresponding to the values of LWW, RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein LWW, RWW, RWW.1, RWW.2, and RWW.3 correspond to L1, R1, R1.1, R1.2, and R1.3, respectively. [0365] In embodiments, when R1A is substituted, R1A is substituted with one or more first substituent groups denoted by R1A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R1A.1 substituent group is substituted, the R1A.1 substituent group is substituted with one or more second substituent groups denoted by R1A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R1A.2 substituent group is substituted, the R1A.2 substituent group is substituted with one or more third substituent groups denoted by R1A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R1A, R1A.1, R1A.2, and R1A.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R1A, R1A.1, R1A.2, and R1A.3, respectively. [0366] In embodiments, when R1B is substituted, R1B is substituted with one or more first substituent groups denoted by R1B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R1B.1 substituent group is substituted, the R1B.1 substituent group is substituted with one or more second substituent groups denoted by R1B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R1B.2 substituent group is substituted, the R1B.2 substituent group is substituted with one or more third substituent groups denoted by R1B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R1B, R1B.1, R1B.2, and R1B.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R1B, R1B.1, R1B.2, and R1B.3, respectively. [0367] In embodiments, when R1A and R1B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R1A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R1A.1 substituent group is substituted, the R1A.1 substituent group is substituted with one or more second substituent groups denoted by R1A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R1A.2 substituent group is substituted, the R1A.2 substituent group is substituted with one or more third substituent groups denoted by R1A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R1A, R1A.1, R1A.2, and R1A.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R1A, R1A.1, R1A.2, and R1A.3, respectively. [0368] In embodiments, when R1A and R1B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R1B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R1B.1 substituent group is substituted, the R1B.1 substituent group is substituted with one or more second substituent groups denoted by R1B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R1B.2 substituent group is substituted, the R1B.2 substituent group is substituted with one or more third substituent groups denoted by R1B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R1B, R1B.1, R1B.2, and R1B.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R1B, R1B.1, R1B.2, and R1B.3, respectively. [0369] In embodiments, when R1C is substituted, R1C is substituted with one or more first substituent groups denoted by R1C.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R1C.1 substituent group is substituted, the R1C.1 substituent group is substituted with one or more second substituent groups denoted by R1C.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R1C.2 substituent group is substituted, the R1C.2 substituent group is substituted with one or more third substituent groups denoted by R1C.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R1C, R1C.1, R1C.2, and R1C.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R1C, R1C.1, R1C.2, and R1C.3, respectively. [0370] In embodiments, when R1D is substituted, R1D is substituted with one or more first substituent groups denoted by R1D.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R1D.1 substituent group is substituted, the R1D.1 substituent group is substituted with one or more second substituent groups denoted by R1D.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R1D.2 substituent group is substituted, the R1D.2 substituent group is substituted with one or more third substituent groups denoted by R1D.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R1D, R1D.1, R1D.2, and R1D.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R1D, R1D.1, R1D.2, and R1D.3, respectively. [0371] In embodiments, when R2 is substituted, R2 is substituted with one or more first substituent groups denoted by R2.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R2.1 substituent group is substituted, the R2.1 substituent group is substituted with one or more second substituent groups denoted by R2.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R2.2 substituent group is substituted, the R2.2 substituent group is substituted with one or more third substituent groups denoted by R2.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R2, R2.1, R2.2, and R2.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R2, R2.1, R2.2, and R2.3, respectively. [0372] In embodiments, when R3 is substituted, R3 is substituted with one or more first substituent groups denoted by R3.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R3.1 substituent group is substituted, the R3.1 substituent group is substituted with one or more second substituent groups denoted by R3.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R3.2 substituent group is substituted, the R3.2 substituent group is substituted with one or more third substituent groups denoted by R3.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R3, R3.1, R3.2, and R3.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R3, R3.1, R3.2, and R3.3, respectively. [0373] In embodiments, when R4 is substituted, R4 is substituted with one or more first substituent groups denoted by R4.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R4.1 substituent group is substituted, the R4.1 substituent group is substituted with one or more second substituent groups denoted by R4.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R4.2 substituent group is substituted, the R4.2 substituent group is substituted with one or more third substituent groups denoted by R4.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R4, R4.1, R4.2, and R4.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R4, R4.1, R4.2, and R4.3, respectively. [0374] In embodiments, when two adjacent R4 substituents are optionally joined to form a moiety that is substituted (e.g., a substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R4.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R4.1 substituent group is substituted, the R4.1 substituent group is substituted with one or more second substituent groups denoted by R4.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R4.2 substituent group is substituted, the R4.2 substituent group is substituted with one or more third substituent groups denoted by R4.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R4, R4.1, R4.2, and R4.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R4, R4.1, R4.2, and R4.3, respectively. [0375] In embodiments, when R5 is substituted, R5 is substituted with one or more first substituent groups denoted by R5.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R5.1 substituent group is substituted, the R5.1 substituent group is substituted with one or more second substituent groups denoted by R5.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R5.2 substituent group is substituted, the R5.2 substituent group is substituted with one or more third substituent groups denoted by R5.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R5, R5.1, R5.2, and R5.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R5, R5.1, R5.2, and R5.3, respectively. [0376] In embodiments, when R10 is substituted, R10 is substituted with one or more first substituent groups denoted by R10.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R10.1 substituent group is substituted, the R10.1 substituent group is substituted with one or more second substituent groups denoted by R10.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R10.2 substituent group is substituted, the R10.2 substituent group is substituted with one or more third substituent groups denoted by R10.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R10, R10.1, R10.2, and R10.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R10, R10.1, R10.2, and R10.3, respectively. [0377] In embodiments, when R11 is substituted, R11 is substituted with one or more first substituent groups denoted by R11.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R11.1 substituent group is substituted, the R11.1 substituent group is substituted with one or more second substituent groups denoted by R11.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R11.2 substituent group is substituted, the R11.2 substituent group is substituted with one or more third substituent groups denoted by R11.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R11, R11.1, R11.2, and R11.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R11, R11.1, R11.2, and R11.3, respectively. [0378] In embodiments, when R12 is substituted, R12 is substituted with one or more first substituent groups denoted by R12.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R12.1 substituent group is substituted, the R12.1 substituent group is substituted with one or more second substituent groups denoted by R12.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R12.2 substituent group is substituted, the R12.2 substituent group is substituted with one or more third substituent groups denoted by R12.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R12, R12.1, R12.2, and R12.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R12, R12.1, R12.2, and R12.3, respectively. [0379] In embodiments, when R16 is substituted, R16 is substituted with one or more first substituent groups denoted by R16.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R16.1 substituent group is substituted, the R16.1 substituent group is substituted with one or more second substituent groups denoted by R16.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R16.2 substituent group is substituted, the R16.2 substituent group is substituted with one or more third substituent groups denoted by R16.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R16, R16.1, R16.2, and R16.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R16, R16.1, R16.2, and R16.3, respectively. [0380] In embodiments, when R16A is substituted, R16A is substituted with one or more first substituent groups denoted by R16A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R16A.1 substituent group is substituted, the R16A.1 substituent group is substituted with one or more second substituent groups denoted by R16A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R16A.2 substituent group is substituted, the R16A.2 substituent group is substituted with one or more third substituent groups denoted by R16A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R16A, R16A.1, R16A.2, and R16A.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R16A, R16A.1, R16A.2, and R16A.3, respectively. [0381] In embodiments, when R16B is substituted, R16B is substituted with one or more first substituent groups denoted by R16B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R16B.1 substituent group is substituted, the R16B.1 substituent group is substituted with one or more second substituent groups denoted by R16B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R16B.2 substituent group is substituted, the R16B.2 substituent group is substituted with one or more third substituent groups denoted by R16B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R16B, R16B.1, R16B.2, and R16B.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R16B, R16B.1, R16B.2, and R16B.3, respectively. [0382] In embodiments, when R16A and R16B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R16A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R16A.1 substituent group is substituted, the R16A.1 substituent group is substituted with one or more second substituent groups denoted by R16A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R16A.2 substituent group is substituted, the R16A.2 substituent group is substituted with one or more third substituent groups denoted by R16A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R16A, R16A.1, R16A.2, and R16A.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R16A, R16A.1, R16A.2, and R16A.3, respectively. [0383] In embodiments, when R16A and R16B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R16B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R16B.1 substituent group is substituted, the R16B.1 substituent group is substituted with one or more second substituent groups denoted by R16B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R16B.2 substituent group is substituted, the R16B.2 substituent group is substituted with one or more third substituent groups denoted by R16B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R16B, R16B.1, R16B.2, and R16B.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R16B, R16B.1, R16B.2, and R16B.3, respectively. [0384] In embodiments, when R17 is substituted, R17 is substituted with one or more first substituent groups denoted by R17.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R17.1 substituent group is substituted, the R17.1 substituent group is substituted with one or more second substituent groups denoted by R17.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R17.2 substituent group is substituted, the R17.2 substituent group is substituted with one or more third substituent groups denoted by R17.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R17, R17.1, R17.2, and R17.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R17, R17.1, R17.2, and R17.3, respectively. [0385] In embodiments, when R17A is substituted, R17A is substituted with one or more first substituent groups denoted by R17A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R17A.1 substituent group is substituted, the R17A.1 substituent group is substituted with one or more second substituent groups denoted by R17A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R17A.2 substituent group is substituted, the R17A.2 substituent group is substituted with one or more third substituent groups denoted by R17A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R17A, R17A.1, R17A.2, and R17A.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R17A, R17A.1, R17A.2, and R17A.3, respectively. [0386] In embodiments, when R17B is substituted, R17B is substituted with one or more first substituent groups denoted by R17B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R17B.1 substituent group is substituted, the R17B.1 substituent group is substituted with one or more second substituent groups denoted by R17B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R17B.2 substituent group is substituted, the R17B.2 substituent group is substituted with one or more third substituent groups denoted by R17B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R17B, R17B.1, R17B.2, and R17B.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R17B, R17B.1, R17B.2, and R17B.3, respectively. [0387] In embodiments, when R17A and R17B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R17A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R17A.1 substituent group is substituted, the R17A.1 substituent group is substituted with one or more second substituent groups denoted by R17A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R17A.2 substituent group is substituted, the R17A.2 substituent group is substituted with one or more third substituent groups denoted by R17A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R17A, R17A.1, R17A.2, and R17A.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R17A, R17A.1, R17A.2, and R17A.3, respectively. [0388] In embodiments, when R17A and R17B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R17B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R17B.1 substituent group is substituted, the R17B.1 substituent group is substituted with one or more second substituent groups denoted by R17B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R17B.2 substituent group is substituted, the R17B.2 substituent group is substituted with one or more third substituent groups denoted by R17B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R17B, R17B.1, R17B.2, and R17B.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R17B, R17B.1, R17B.2, and R17B.3, respectively. [0389] In embodiments, when R18 is substituted, R18 is substituted with one or more first substituent groups denoted by R18.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R18.1 substituent group is substituted, the R18.1 substituent group is substituted with one or more second substituent groups denoted by R18.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R18.2 substituent group is substituted, the R18.2 substituent group is substituted with one or more third substituent groups denoted by R18.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R18, R18.1, R18.2, and R18.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R18, R18.1, R18.2, and R18.3, respectively. [0390] In embodiments, when R18A is substituted, R18A is substituted with one or more first substituent groups denoted by R18A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R18A.1 substituent group is substituted, the R18A.1 substituent group is substituted with one or more second substituent groups denoted by R18A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R18A.2 substituent group is substituted, the R18A.2 substituent group is substituted with one or more third substituent groups denoted by R18A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R18A, R18A.1, R18A.2, and R18A.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R18A, R18A.1, R18A.2, and R18A.3, respectively. [0391] In embodiments, when R18B is substituted, R18B is substituted with one or more first substituent groups denoted by R18B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R18B.1 substituent group is substituted, the R18B.1 substituent group is substituted with one or more second substituent groups denoted by R18B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R18B.2 substituent group is substituted, the R18B.2 substituent group is substituted with one or more third substituent groups denoted by R18B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R18B, R18B.1, R18B.2, and R18B.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R18B, R18B.1, R18B.2, and R18B.3, respectively. [0392] In embodiments, when R18A and R18B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R18A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R18A.1 substituent group is substituted, the R18A.1 substituent group is substituted with one or more second substituent groups denoted by R18A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R18A.2 substituent group is substituted, the R18A.2 substituent group is substituted with one or more third substituent groups denoted by R18A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R18A, R18A.1, R18A.2, and R18A.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R18A, R18A.1, R18A.2, and R18A.3, respectively. [0393] In embodiments, when R18A and R18B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R18B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R18B.1 substituent group is substituted, the R18B.1 substituent group is substituted with one or more second substituent groups denoted by R18B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R18B.2 substituent group is substituted, the R18B.2 substituent group is substituted with one or more third substituent groups denoted by R18B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R18B, R18B.1, R18B.2, and R18B.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R18B, R18B.1, R18B.2, and R18B.3, respectively. [0394] In embodiments, when R19 is substituted, R19 is substituted with one or more first substituent groups denoted by R19.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R19.1 substituent group is substituted, the R19.1 substituent group is substituted with one or more second substituent groups denoted by R19.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R19.2 substituent group is substituted, the R19.2 substituent group is substituted with one or more third substituent groups denoted by R19.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R19, R19.1, R19.2, and R19.3 have values corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R19, R19.1, R19.2, and R19.3, respectively. [0395] In embodiments, when R19A is substituted, R19A is substituted with one or more first substituent groups denoted by R19A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R19A.1 substituent group is substituted, the R19A.1 substituent group is substituted with one or more second substituent groups denoted by R19A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R19A.2 substituent group is substituted, the R19A.2 substituent group is substituted with one or more third substituent groups denoted by R19A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R19A, R19A.1, R19A.2, and R19A.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R19A, R19A.1, R19A.2, and R19A.3, respectively. [0396] In embodiments, when R19B is substituted, R19B is substituted with one or more first substituent groups denoted by R19B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R19B.1 substituent group is substituted, the R19B.1 substituent group is substituted with one or more second substituent groups denoted by R19B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R19B.2 substituent group is substituted, the R19B.2 substituent group is substituted with one or more third substituent groups denoted by R19B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R19B, R19B.1, R19B.2, and R19B.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R19B, R19B.1, R19B.2, and R19B.3, respectively. [0397] In embodiments, when R19A and R19B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R19A.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R19A.1 substituent group is substituted, the R19A.1 substituent group is substituted with one or more second substituent groups denoted by R19A.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R19A.2 substituent group is substituted, the R19A.2 substituent group is substituted with one or more third substituent groups denoted by R19A.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R19A, R19A.1, R19A.2, and R19A.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R19A, R19A.1, R19A.2, and R19A.3, respectively. [0398] In embodiments, when R19A and R19B substituents that are bonded to the same nitrogen atom are joined to form a moiety that is substituted (e.g., a substituted
heterocycloalkyl or substituted heteroaryl), the moiety is substituted with one or more first substituent groups denoted by R19B.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an R19B.1 substituent group is substituted, the R19B.1 substituent group is substituted with one or more second substituent groups denoted by R19B.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an R19B.2 substituent group is substituted, the R19B.2 substituent group is substituted with one or more third substituent groups denoted by R19B.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, R19B, R19B.1, R19B.2, and R19B.3 have values
corresponding to the values of RWW, RWW.1, RWW.2, and RWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein RWW, RWW.1, RWW.2, and RWW.3 correspond to R19B, R19B.1, R19B.2, and R19B.3, respectively. [0399] In embodiments, when L1 is substituted, L1 is substituted with one or more first substituent groups denoted by RL1.1 as explained in the definitions section above in the description of“first substituent group(s)”. In embodiments, when an RL1.1 substituent group is substituted, the RL1.1 substituent group is substituted with one or more second substituent groups denoted by RL1.2 as explained in the definitions section above in the description of “first substituent group(s)”. In embodiments, when an RL1.2 substituent group is substituted, the RL1.2 substituent group is substituted with one or more third substituent groups denoted by RL1.3 as explained in the definitions section above in the description of“first substituent group(s)”. In the above embodiments, L1, RL1.1, RL1.2, and RL1.3 have values corresponding to the values of LWW, RLWW.1, RLWW.2, and RLWW.3, respectively, as explained in the definitions section above in the description of“first substituent group(s)”, wherein LWW, RLWW.1, RLWW.2, and RLWW.3 are L1, RL1.1, RL1.2, and RL1.3, respectively. [0400] In embodiments, the compound is
Figure imgf000149_0001
, wherein R1, R2, and R4 are as described herein, including in embodiments. In embodiments, R1 and R4 are each independently halogen. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl.
[0401] In embodiments, the compound is
Figure imgf000149_0002
wherein R2 is as described herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl.
[0402] In embodiments, the compound is
Figure imgf000149_0003
wherein R2 is as described herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl.
[0403] In embodiments, the compound is
Figure imgf000149_0004
wherein R2 is as described herein, including in embodiments. In embodiments, R2 is independently C1-C6 alkyl. In embodiments, R2 is independently unsubstituted C1-C4 alkyl. In embodiments, R2 is independently unsubstituted methyl. In embodiments, R2 is independently unsubstituted ethyl. In embodiments, R2 is independently C3-C6 cycloalkyl.
[0404] In embodiments, the compound is
Figure imgf000150_0001
wherein R1 and R4 are each independently halogen.
[0405] In embodiments, the compound is
Figure imgf000150_0002
[0406] In embodiments, the compound is
Figure imgf000150_0003
[0407] In embodiments, the compound is
Figure imgf000150_0004
[0408] In embodiments, the compound is
Figure imgf000150_0005
[0409] In embodiments, the compound is
Figure imgf000150_0006
[0410] In embodiments, the compound is
Figure imgf000151_0001
[0411] In embodiments, the compound is
Figure imgf000151_0002
[0412] In embodiments, the compound is
Figure imgf000151_0003
.
[0413] In embodiments, the compound is
Figure imgf000151_0004
[0414] In embodiments, the compound is
Figure imgf000151_0005
[0415] In embodiments, the compound is
Figure imgf000151_0006
[0416] In embodiments, the compound is
Figure imgf000151_0007
[0417] In embodiments, the compound is
Figure imgf000151_0008
[0418] In embodiments, the compound is
Figure imgf000151_0009
[0419] In embodiments, the compound is
Figure imgf000152_0001
.
[0420] In embodiments, the compound is
Figure imgf000152_0002
[0421] In embodiments, the compound is a compound described herein. In embodiments, the compound, or a pharmaceutically acceptable salt thereof, is the compound described herein. In embodiments, the compound, or a pharmaceutically acceptable salt thereof, is the pharmaceutically acceptable salt of a compound described herein.
[0422] In embodiments, the compound is not wherein R1
Figure imgf000152_0003
and R4 are each independently halogen.
[0423] In embodiments, the compound is not
Figure imgf000152_0004
[0424] In embodiments, the compound is not
Figure imgf000152_0005
[0425] In embodiments, the compound is not
Figure imgf000152_0006
[0426] In embodiments, the compound is not
Figure imgf000153_0001
.
[0427] In embodiments, the compound is not
Figure imgf000153_0002
, wherein R16, R17, and R18 are as defined herein. [0428] In embodiments, R1 is not–F. In embodiments, R4 is not–F. In embodiments, when R1 is independently–F, R4 is not–F. In embodiments, when R4 is independently–F, R1 is not–F. III. Pharmaceutical compositions
[0429] In an aspect is provided a pharmaceutical composition including a compound described herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. [0430] In an aspect is provided a pharmaceutical composition including a compound described herein and a pharmaceutically acceptable excipient. [0431] In embodiments, the pharmaceutical composition includes an effective amount of the compound. In embodiments, the pharmaceutical composition includes a therapeutically effective amount of the compound. In embodiments, the pharmaceutical composition includes a second agent (e.g., an anti-cancer agent). In embodiments of the pharmaceutical compositions, the pharmaceutical composition includes a second agent in a therapeutically effective amount. IV. Methods of use
[0432] In an aspect is provided a method for treating cancer in a subject in need thereof, the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0433] In an aspect is provided a method for treating cancer in a subject in need thereof, the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein. [0434] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in a method of treating cancer including administering to a subject in need thereof a therapeutically effective amount of the compound, or a
pharmaceutically acceptable salt thereof. [0435] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for the treatment of cancer, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0436] In embodiments, the cancer is renal cell carcinoma, follicular lymphoma, glioblastoma, colorectal cancer, endometrial cancer, or lung cancer. [0437] In embodiments, the cancer is renal cell carcinoma. In embodiments, the cancer is follicular lymphoma. In embodiments, the cancer is glioblastoma. In embodiments, the cancer is colorectal cancer. In embodiments, the cancer is endometrial cancer. In
embodiments, the cancer is lung cancer. In embodiments, the cancer is pancreatic cancer. In embodiments, the cancer is melanoma. In embodiments, the cancer is breast cancer. In embodiments, the cancer is acute myeloid leukemia. In embodiments, the cancer is endometrial cancer. In embodiments, the cancer is non-Hodgkin lymphoma. In
embodiments, the cancer is mantle cell lymphoma. In embodiments, the method includes immunomodulation. In embodiments, the method includes cancer immunotherapy. [0438] In an aspect is provided a method for treating a neurodegenerative disease, the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0439] In an aspect is provided a method for treating a neurodegenerative disease, the method including administering to a subject in need thereof an effective amount of a compound described herein. In embodiments, the compound is included in a therapeutically effective amount. In embodiments, the method is a method of treating nerve damage, the method including administering to a subject in need thereof an effective amount of a compound described herein. In embodiments, the neurodegenerative disease is Huntington Disease. In embodiments, the neurodegenerative disease is Alzheimer Disease. In embodiments, the neurodegenerative disease is Parkinson’s Disease. In embodiments, the neurodegenerative disease is frontotemporal dementia. In embodiments, the method includes reducing protein aggregates (e.g., in the brain). In embodiments, the method includes reducing TDP-43 aggregates (e.g., in the brain). In embodiments, the neurodegenerative disease is amyotrophic lateral sclerosis. In embodiments, the neurodegenerative disease is chronic traumatic encephalopathy. In embodiments, the neurodegenerative disease is traumatic brain injury (e.g., concussion). [0440] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in a method of treating a neurodegenerative disease including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0441] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for the treatment of a
neurodegenerative disease, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0442] In an aspect is provided a method for treating a metabolic disease, the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0443] In an aspect is provided a method for treating a metabolic disease, the method including administering to a subject in need thereof an effective amount of a compound described herein. In embodiments, the compound is included in a therapeutically effective amount. In embodiments, the metabolic disease is diabetes. In embodiments, the metabolic disease is type I diabetes. In embodiments, the metabolic disease is type II diabetes. In embodiments, the metabolic disease is obesity. In embodiments, the metabolic disease is metabolic syndrome. In embodiments, the metabolic disease is a mitochondrial disease (e.g., dysfunction of mitochondria or aberrant mitochondrial function). [0444] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in a method of treating a metabolic disease including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0445] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for the treatment of a metabolic disease, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0446] In an aspect is provided a method for treating aging, the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0447] In an aspect is provided a method for treating aging, the method including administering to a subject in need thereof an effective amount of a compound described herein. [0448] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in a method of treating aging including administering to a subject in need thereof a therapeutically effective amount of the compound, or a
pharmaceutically acceptable salt thereof. [0449] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for the treatment of aging, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0450] In another aspect is provided a method of extending lifespan (e.g., increased 1 day, increased 2 days, increased 3 days, increased 7 days, increased 1 month, increased 6 months, increased 12 months, increased 2 years, increased 5 years, etc.) or inducing longevity, the method including administering to a subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0451] In another aspect is provided a method of extending lifespan (e.g., increased 1 day, increased 2 days, increased 3 days, increased 7 days, increased 1 month, increased 6 months, increased 12 months, increased 2 years, increased 5 years, etc.) or inducing longevity, the method including administering to a subject in need thereof an effective amount of a compound described herein. [0452] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in a method of extending lifespan (e.g., increased 1 day, increased 2 days, increased 3 days, increased 7 days, increased 1 month, increased 6 months, increased 12 months, increased 2 years, increased 5 years, etc.) or inducing longevity, including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0453] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for extending lifespan (e.g., increased 1 day, increased 2 days, increased 3 days, increased 7 days, increased 1 month, increased 6 months, increased 12 months, increased 2 years, increased 5 years, etc.) or inducing longevity, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0454] In an aspect is provided a method of reducing the level of activity of mTORC1 in a subject in need thereof, the method including administering to the subject in need thereof an effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0455] In an aspect is provided a method of reducing the level of activity of mTORC1 in a subject in need thereof, the method including administering to the subject in need thereof an effective amount of a compound described herein. [0456] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of mTORC1 including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0457] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for reducing the level of activity of mTORC1, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0458] In an aspect is provided a method of reducing the level of activity of mTORC1 in a cell, the method including contacting a Vacuolar H+-ATPase in the cell with a compound as described herein, or a pharmaceutically acceptable salt thereof. [0459] In an aspect is provided a method of reducing the level of activity of mTORC1 in a cell, the method including contacting a Vacuolar H+-ATPase in the cell with a compound as described herein. [0460] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of mTORC1 in a cell including contacting a Vacuolar H+-ATPase in the cell with the compound, or a
pharmaceutically acceptable salt thereof. [0461] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for reducing the level of activity of mTORC1 in a cell, the use including contacting a Vacuolar H+-ATPase in the cell with the compound, or a pharmaceutically acceptable salt thereof. [0462] In embodiments, the method includes dephosphorylation and/or nuclear
translocation of TFEB (e.g., RefSeq NM_007162.2 or RefSeq NP_009093.1) in a cell or subject. In embodiments, the method includes increasing the level of TFEB transcriptional targets in a cell or subject. In embodiments, the method includes increasing the level of CTSA (e.g., RefSeq NM_000308.3 or RefSeq NP_000299.2), CTSB (e.g., RefSeq
NM_001908.4 or RefSeq NP_001899.1), CTSF (e.g., RefSeq NM_003793.3 or RefSeq NP_003784.2), HEXB (e.g., RefSeq NM_000521.4 or RefSeq NP_000512.2), CLN3 (e.g., RefSeq NM_000086.2 or RefSeq NP_000077.1), CLCN7 (e.g., RefSeq NM_001287.5 or RefSeq NP_001278.1), ATP6V0D1 (e.g., RefSeq NM_004691.4 or RefSeq NP_004682.2), ATP6V0E1 (e.g., RefSeq NM_003945.3 or RefSeq NP_003936.1), LAMP1 (e.g., RefSeq NM_005561.3 or RefSeq NP_005552.3), or p62 (e.g., RefSeq NM_003900.4 or RefSeq NP_003891.1) in a cell or subject. In embodiments, the method includes increasing the level of LC3BII in a cell or subject. [0463] In embodiments, the method includes dephosphorylation and/or nuclear
translocation of TFE3 (e.g., RefSeq NM_006521.5 or RefSeq NP_006512.2) in a cell or subject. In embodiments, the method includes increasing the level of TFE3 transcriptional targets in a cell or subject. [0464] In an aspect is provided a method of reducing the level of activity of a Vacuolar H+- ATPase, the method including contacting the Vacuolar H+-ATPase with a compound described herein, or a pharmaceutically acceptable salt thereof. [0465] In an aspect is provided a method of reducing the level of activity of a Vacuolar H+- ATPase, the method including contacting the Vacuolar H+-ATPase with a compound described herein. [0466] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of a Vacuolar H+-ATPase including contacting contacting the Vacuolar H+-ATPase with the compound, or a pharmaceutically acceptable salt thereof. [0467] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for reducing the level of activity of a Vacuolar H+-ATPase, the use including contacting the Vacuolar H+-ATPase with the compound, or a pharmaceutically acceptable salt thereof. [0468] In an aspect is provided a method of reducing the level of activity of a Vacuolar H+- ATPase protein complex, the method including contacting an ATP6V1A in the Vacuolar H+- ATPase protein complex with a compound described herein, or a pharmaceutically acceptable salt thereof. [0469] In an aspect is provided a method of reducing the level of activity of a Vacuolar H+- ATPase protein complex, the method including contacting an ATP6V1A in the Vacuolar H+- ATPase protein complex with a compound described herein. [0470] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of a Vacuolar H+-ATPase protein complex including contacting contacting an ATP6V1A in the Vacuolar H+-ATPase protein complex with the compound, or a pharmaceutically acceptable salt thereof. [0471] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for reducing the level of activity of a Vacuolar H+-ATPase protein complex, the use including contacting an ATP6V1A in the Vacuolar H+-ATPase protein complex with the compound, or a pharmaceutically acceptable salt thereof. [0472] In an aspect is provided a method of reducing the level of activity of mTORC1 in a cell, the method including contacting an ATP6V1A in the cell with a compound as described herein, or a pharmaceutically acceptable salt thereof. [0473] In an aspect is provided a method of reducing the level of activity of mTORC1 in a cell, the method including contacting an ATP6V1A in the cell with a compound as described herein. [0474] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of mTORC1 in a cell including contacting an ATP6V1A in the cell with the compound, or a pharmaceutically acceptable salt thereof. [0475] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for reducing the level of activity of mTORC1 in a cell, the use including contacting an ATP6V1A in the cell with the compound, or a pharmaceutically acceptable salt thereof. [0476] In an aspect is provided a method of reducing the level of activity of an ATP6V1A, the method including contacting the ATP6V1A with a compound described herein, or a pharmaceutically acceptable salt thereof. [0477] In an aspect is provided a method of reducing the level of activity of an ATP6V1A, the method including contacting the ATP6V1A with a compound described herein. [0478] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in reducing the level of activity of an ATP6V1A including contacting the ATP6V1A with the compound, or a pharmaceutically acceptable salt thereof. [0479] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for reducing the level of activity of an ATP6V1A, the use including contacting the ATP6V1A with the compound, or a pharmaceutically acceptable salt thereof. [0480] In embodiments, the method includes reducing the activity of mTORC1 more than reducing the activity of mTORC2 (e.g., at least 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9.2, 3, 4, 5, 6, 7, 8,910, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 100000, 1000000-fold more). In embodiments, the method includes reducing the activity of mTORC1 more than reducing the activity of mTORC2 (e.g., about 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9.2, 3, 4, 5, 6, 7, 8,910, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 100000, 1000000-fold more). In embodiments, the method includes reducing the activity of mTORC1 more than reducing the activity of mTORC2 (e.g., 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9.2, 3, 4, 5, 6, 7, 8,910, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 100000, 1000000-fold more). [0481] In embodiments, the method includes reducing (e.g., reduced relative to a control) mTORC1 signaling by preventing mTORC1 localization to the lysosome. In embodiments, the method includes modulating (e.g., preventing the formation) of the Ragulator complex. In embodiments, the method includes reducing (e.g., reduced relative to a control) mTORC1 signaling by causing an accumulation of Ragulator complex in the lysosome. In
embodiments, the method includes preventing the activation of the Ragulator complex. In embodiments, the method includes preventing the binding of mTORC1 to the Ragulator complex. In embodiments, the method includes preventing the formation of the Ragulator complex. [0482] In embodiments, the method includes inhibiting the activation of the Ragulator complex. In embodiments, the method includes inhibiting the binding of mTORC1 to the Ragulator complex. In embodiments, the method includes inhibiting the formation of the Ragulator complex. In embodiments, the method includes inhibiting the amino-acid-induced localization of mTORC1 to the lysosome. In embodiments, the method includes inhibiting the binding between the Vacuolar H+-ATPase protein complex and the Ragulator. In embodiments, the method includes inhibiting the activity of Rag activity. In embodiments, the method includes inhibiting the GTPase activity of Rag. In embodiments, the method includes inhibiting the Rag GTPase-induced localization of mTORC1 to the lysosome. In embodiments, the method includes increased acidification of a lysosome. In embodiments, the method includes inhibiting the phosphorylation of 4EBP1. In embodiments, the method includes inhibiting the phosphorylation of S6. In embodiments, the method includes inhibiting the activity of Vacuolar H+-ATPase protein complex. In embodiments, the method includes increasing autophagy. In embodiments, the method includes inhibiting the Rag-A/B Rag-C/D complex interaction with Raptor in mTORC1. In embodiments, the method includes inhibiting the phosphorylation of ULK1 kinase. In embodiments, the method includes increasing the nuclear translocation and/or activation of TFEB transcription factor. [0483] In an aspect is provided a method for increasing autophagy in a subject in need thereof, the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein, or a pharmaceutically acceptable salt thereof. [0484] In an aspect is provided a method for increasing autophagy in a subject in need thereof, the method including administering to the subject in need thereof a therapeutically effective amount of a compound described herein. [0485] In an aspect is provided a compound described herein, or a pharmaceutically acceptable salt thereof, for use in a method of increasing autophagy including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. [0486] In an aspect is provided use of a compound described herein, or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for increasing autophagy, the use including administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof. V. Vacuolar H+-ATPase
[0487] In an aspect is provided a Vacuolar H+-ATPase protein complex covalently bonded to a compound described herein, or a pharmaceutically acceptable salt thereof, which may be referred to herein as a Vacuolar H+-ATPase protein complex-compound complex. [0488] In an aspect is provided a Vacuolar H+-ATPase protein complex covalently bonded to a compound described herein, which may be referred to herein as a Vacuolar H+-ATPase protein complex-compound complex. In embodiments, the Vacuolar H+-ATPase protein complex is a human Vacuolar H+-ATPase protein complex. In embodiments, the compound is provided in a therapeutically effective amount. In embodiments, the compound contacts an amino acid corresponding to C277 of human ATP6V1A in the Vacuolar H+-ATPase protein complex. In embodiments, the compound covalently binds an amino acid corresponding to C277 of human ATP6V1A in the Vacuolar H+-ATPase protein complex. [0489] In embodiments, an ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) is covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein). In embodiments, an ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) is irreversibly covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein). In embodiments, an ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) is reversibly covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein). In embodiments, an ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) is covalently bonded to a portion of a compound (e.g., compound described herein). In embodiments, an ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human
ATP6V1A in a human Vacuolar H+-ATPase protein complex) is irreversibly covalently bonded to a portion of a compound described herein. In embodiments, an ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+- ATPase protein complex) is reversibly covalently bonded to a portion of a compound described herein. In embodiments, the compound described herein is bonded to a cysteine residue (e.g., residue corresponding to Cys277 of human ATP6V1A) of the ATP6V1A protein (e.g., human ATP6V1A protein). [0490] In embodiments, the ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) covalently bonded to a compound described herein is the product of a reaction between the ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) and a compound described herein. It will be understood that the covalently bonded ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) and compound described herein are the remnants of the reactant ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) and compound, wherein each reactant now participates in the covalent bond between the ATP6V1A in a Vacuolar H+- ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) and compound. In embodiments of the covalently bonded ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) and compound described herein, the remnant of the E substitutent is a linker including a covalent bond between the ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) and the remainder of the compound described herein. It will be understood by a person of ordinary skill in the art that when an ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human
ATP6V1A in a human Vacuolar H+-ATPase protein complex) is covalently bonded to a compound described herein, the compound described herein forms a remnant of the pre- reacted compound wherein a bond connects the remnant of the compound to the remnant of the ATP6V1A in a Vacuolar H+-ATPase protein complex (e.g., human ATP6V1A in a human Vacuolar H+-ATPase protein complex) (e.g., cysteine sulfur, sulfur of amino acid
corresponding to C277 of human ATP6V1A in a Vacuolar H+-ATPase protein complex). [0491] In an aspect is provided an ATP6V1A protein covalently bonded to a compound described herein, or a pharmaceutically acceptable salt thereof, which may be referred to herein as an ATP6V1A protein-compound complex. [0492] In an aspect is provided an ATP6V1A protein covalently bonded to a compound described herein, which may be referred to herein as an ATP6V1A protein-compound complex. In embodiments, the ATP6V1A protein is a human ATP6V1A protein. In embodiments, human ATP6V1A protein has a sequence described herein. In embodiments, the compound is provided in a therapeutically effective amount. In embodiments, the compound contacts an amino acid corresponding to C277 of human ATP6V1A. In embodiments, the compound covalently binds an amino acid corresponding to C277 of human ATP6V1A. [0493] In embodiments, an ATP6V1A protein (e.g., human ATP6V1A) is covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein). In embodiments, an ATP6V1A protein (e.g., human ATP6V1A) is irreversibly covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein). In embodiments, the ATP6V1A protein (e.g., human ATP6V1A) is reversibly covalently bonded to a compound (e.g., compound described herein or a portion of a compound described herein). In embodiments, the ATP6V1A protein (e.g., human ATP6V1A) is covalently bonded to a portion of a compound (e.g., compound described herein). In embodiments, the ATP6V1A protein (e.g., human ATP6V1A) is irreversibly covalently bonded to a portion of a compound described herein. In
embodiments, the ATP6V1A protein (e.g., human ATP6V1A) is reversibly covalently bonded to a portion of a compound described herein. In embodiments, the compound described herein is bonded to a cysteine residue (e.g., residue corresponding to Cys277 of human ATP6V1A) of the ATP6V1A protein (e.g., human ATP6V1A). [0494] In embodiments, the ATP6V1A protein covalently bonded to a compound described herein is the product of a reaction between the ATP6V1A protein and a compound described herein. It will be understood that the covalently bonded ATP6V1A protein and compound described herein are the remnants of the reactant ATP6V1A protein and compound, wherein each reactant now participates in the covalent bond between the ATP6V1A protein and or compound. In embodiments of the covalently bonded ATP6V1A protein and compound described herein, the remnant of the E substitutent is a linker including a covalent bond between the ATP6V1A protein and the remainder of the compound described herein. It will be understood by a person of ordinary skill in the art that when a ATP6V1A protein is covalently bonded to a compound described herein, the compound described herein forms a remnant of the pre-reacted compound wherein a bond connects the remnant of the compound to the remnant of the ATP6V1A protein (e.g., cysteine sulfur, sulfur of amino acid corresponding to C277 of human ATP6V1A). [0495] It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes. VI. Embodiments
[0496] Embodiment P1. A compound having the formula:
Figure imgf000165_0001
wherein, Ring A is a phenyl or 5 to 6 membered heteroaryl; Ring B is a phenyl or 5 to 6 membered heteroaryl; L1 is independently a bond, -S(O)2-, -N(R5)-, -O-, -S-, -C(O)-, -C(O)N(R5)-, -N(R5)C(O)-, -N(R5)C(O)NH-, -NHC(O)N(R5)-, -C(O)O-, -OC(O)-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene; R5 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl; R1 is independently halogen, -CX1 3, -CHX1 2, -CH2X1, -OCX1 3, -OCH2X1, -OCHX1 2, -CN, -SOn1R1D, -SOv1NR1AR1B, -NHC(O)NR1AR1B, -N(O)m1, -NR1AR1B, -C(O)R1C, -C(O)-OR1C, -C(O)NR1AR1B, -OR1D, -NR1ASO2R1D, -NR1AC(O)R1C, -NR1AC(O)OR1C, -NR1AOR1C, -N3, E, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent -L1-R1 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
unsubstituted heteroaryl; E is an electrophilic moiety; R2 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl; R3 and R4 are independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
unsubstituted heteroaryl; R1A, R1B, R1C, and R1D are independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; X1 is independently–F, -Cl, -Br, or–I; n1 is independently an integer from 0 to 4; m1 and v1 are independently 1 or 2; z1 is independently an integer from 0 to 6; z3 is independently an integer from 0 to 2; and z4 is independently an integer from 0 to 6. [0497] Embodiment P2. The compound of embodiment P1, having the formula:
Figure imgf000167_0001
wherein, L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene; R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent R1 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; E is an electrophilic moiety; R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H,
-NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
unsubstituted heteroaryl; z1 is independently an integer from 0 to 4; and z4 is independently an integer from 0 to 5. [0498] Embodiment P3. The compound of embodiment P1, having the formula:
Figure imgf000168_0001
wherein, L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene; R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H,
-NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; E is an electrophilic moiety; and R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H,
-NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
unsubstituted heteroaryl. [0499] Embodiment P4. The compound of one of embodiments P1 to P3, wherein R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl. [0500] Embodiment P5. The compound of one of embodiments P1 to P3, wherein R1 is independently halogen. [0501] Embodiment P6. The compound of one of embodiments P1 to P3, wherein R1 is -F. [0502] Embodiment P7. The compound of one of embodiments P1 to P6 , wherein R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl. [0503] Embodiment P8. The compound of one of embodiments P1 to P6, wherein R4 is independently halogen. [0504] Embodiment P9. The compound of one of embodiments P1 to P6, wherein R4 is -F. [0505] Embodiment P10. The compound of one of embodiments P1 to P9, wherein L1 is independently -S(O)2-, -NH-, or substituted or unsubstituted 5 to 6 membered
heterocycloalkylene. [0506] Embodiment P11. The compound of one of embodiments P1 to P9, wherein L1 is independently -S(O)2-, -NH-, unsubstituted pyrrolidinylene, unsubstituted piperidinylene, or unsubstituted piperazinylene. [0507] Embodiment P12. The compound of one of embodiments P1 to P9, wherein L1 is independently -NH-. [0508] Embodiment P13. The compound of one of embodiments P1 to P12 wherein E is
or
Figure imgf000170_0001
wherein R16 is independently hydrogen, halogen, -CX16 3, -CHX16 2, -CH2X16, -CN,
-SOn16R16A, -SOv16NR16AR16B, -NHNR16AR16B, -ONR16AR16B, -NH C(O)NHNR16AR16B, -NHC(O)NR16AR16B, -N(O)m16, -NR16AR16B, -C(O)R16A, -C(O)-OR16A, -C(O)NR16AR16B, -OR16A, -NR16ASO2R16B, -NR16AC(O)R16B, -NR16AC(O)OR16B, -NR16AOR16B, -OCX163, -OCHX162, -OCH2X16, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl; R17 is independently hydrogen, halogen, -CX17 3, -CHX17 2, -CH2X17, -CN, -SOn17R17A, -SOv17NR17AR17B, -NH NR17AR17B, -ONR17AR17B, -NHC(O)NHNR17AR17B,
-NHC(O)NR17AR17B, -N(O)m17, -NR17AR17B, -C(O)R17A, -C(O)-OR17A, -C(O)NR17AR17B, -OR17A, -NR17ASO2R17B, -NR17AC(O)R17B, -NR17AC(O)OR17B, -NR17AOR17B, -OCX173, -OCHX17 2, -OCH2X17, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl; R18 is independently hydrogen, halogen, -CX18 3, -CHX18 2, -CH2X18, -CN, -SOn18R18A, -SOv18NR18AR18B, -NH NR18AR18B, -ONR18AR18B, -NHC(O)NHNR18AR18B,
-NHC(O)NR18AR18B, -N(O)m18, -NR18AR18B, -C(O)R18A, -C(O)-OR18A, -C(O)NR18AR18B, -OR18A, -NR18ASO2R18B, -NR18AC(O)R18B, -NR18AC(O)OR18B, -NR18AOR18B, -OCX18 3, -OCHX18 2, -OCH2X18, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl; R19 is independently hydrogen, halogen, -CX19 3, -CHX19 2, -CH2X19, -CN, -SOn19R19A, -SOv19NR19AR19B, -NH NR19AR19B, -ONR19AR19B , -NHC(O)NHNR19AR19B,
-NHC(O)NR19AR19B, -N(O)m19, -NR19AR19B, -C(O)R19A, -C(O)-OR19A, -C(O)NR19AR19B, -OR19A, -NR19ASO2R19B, -NR19AC(O)R19B, -NR19AC(O)OR19B, -NR19AOR19B, -OCX193, -OCHX192, -OCH2X19, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl; R16A, R16B, R17A, R17B, R18A, R18B, R19A, and R19B are independently
hydrogen, -CX3, -CHX2, -CH2X, -CN, -OH, -COOH, -CONH2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R16A and R16B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R17A and R17B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R18A and R18B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R19A and R19B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; each X1, X16, X17, X18, and X19 is independently–F, -Cl, -Br, or–I; n16, n17, n18, and n19 are independently an integer from 0 to 4; and m16, m17, m18, m19, v16, v17, v18, and v19 are independently 1 or 2. [0509] Embodiment P14. The compound of one of embodiments P1 to P12, wherein E is
Figure imgf000172_0001
or
Figure imgf000172_0002
[0510] Embodiment P15. The compound of one of embodiments P1 to P14, wherein the
compound is not
Figure imgf000172_0003
[0511] Embodiment P16. A pharmaceutical composition comprising a compound of one of embodiments P1 to P15 and a pharmaceutically acceptable excipient. [0512] Embodiment P17. A method for treating cancer in a subject in need thereof, said method comprising administering to the subject in need thereof a therapeutically effective amount of a compound of one of embodiments P1 to P15. [0513] Embodiment P18. The method of embodiment P17, wherein said cancer is renal cell carcinoma, follicular lymphoma, glioblastoma, colorectal cancer, endometrial, or lung cancer. [0514] Embodiment P19. A method of reducing the level of activity of mTORC1 in a subject in need thereof, the method comprising administering to the subject in need thereof an effective amount of a compound of one of embodiments P1 to P15. [0515] Embodiment P20. A method of reducing the level of activity of mTORC1 in a cell, the method comprising contacting a Vacuolar H+-ATPase protein complex in said cell with a compound of one of embodiments P1 to P15. [0516] Embodiment P21. A method of reducing the level of activity of mTORC1 in a cell, the method comprising contacting an ATP6V1A in said cell with a compound of one of embodiments P1 to P15. [0517] Embodiment P22. A method of reducing the level of activity of a Vacuolar H+- ATPase protein complex, the method comprising contacting an ATP6V1A in the Vacuolar H+-ATPase protein complex with a compound of one of embodiments P1 to P15. VII. Additional embodiments
[0518] Embodiment 1. A compound, or a pharmaceutically acceptable salt thereof, having the formula:
Figure imgf000173_0001
wherein Ring A is a phenyl or 5 to 6 membered heteroaryl; Ring B is a phenyl or 5 to 6 membered heteroaryl; L1 is independently a bond, -S(O)2-, -N(R5)-, -O-, -S-, -C(O)-, -C(O)N(R5)-,
-N(R5)C(O)-, -N(R5)C(O)NH-, -NHC(O)N(R5)-, -C(O)O-, -OC(O)-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene; R5 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl,
-CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl; R1 is independently halogen, -CX13, -CHX12, -CH2X1, -OCX13, -OCH2X1,
-OCHX12, -CN, -SOn1R1D, -SOv1NR1AR1B, -NHC(O)NR1AR1B, -N(O)m1, -NR1AR1B, -C(O)R1C, -C(O)-OR1C, -C(O)NR1AR1B, -OR1D, -NR1ASO2R1D, -NR1AC(O)R1C, -NR1AC(O)OR1C, -NR1AOR1C, -N3, E, substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent -L1-R1 substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; E is an electrophilic moiety; R2 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl,
-CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl; R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent R4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R1A, R1B, R1C, and R1D are independently hydrogen, halogen, -CCl3, -CBr3,
-CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; X1 is independently–F, -Cl, -Br, or–I; n1 is independently an integer from 0 to 4; m1 and v1 are independently 1 or 2; z1 is independently an integer from 0 to 5; z3 is independently an integer from 0 to 2; and z4 is independently an integer from 0 to 5. [0519] Embodiment 2. The compound of embodiment 1, having the formula:
Figure imgf000175_0001
wherein L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-,
-NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene; R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent R1 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; E is an electrophilic moiety; R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent R4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; z1 is independently an integer from 0 to 4; and z4 is independently an integer from 0 to 5. [0520] Embodiment 3. The compound of embodiment 1, having the formula:
Figure imgf000176_0001
wherein L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-,
-NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene; R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; E is an electrophilic moiety; and R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0521] Embodiment 4. The compound of embodiment 1, having the formula:
Figure imgf000177_0001
wherein L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-,
-NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene; R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; E is an electrophilic moiety; R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent R4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; z1 is independently an integer from 0 to 4; and z4 is independently an integer from 0 to 5. [0522] Embodiment 5. The compound of embodiment 1, having the formula:
Figure imgf000179_0001
wherein L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-,
-NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene; R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; E is an electrophilic moiety; R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br,
-CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. [0523] Embodiment 6. The compound of one of embodiments 1, 4, and 5, wherein R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl. [0524] Embodiment 7. The compound of one of embodiments 1, 4, and 5, wherein R3 is independently halogen, -CCl3, -CBr3, -CF3, or -CI3. [0525] Embodiment 8. The compound of one of embodiments 1, 4, and 5, wherein R3 is independently–Br or -CF3. [0526] Embodiment 9. The compound of one of embodiments 1 to 8, wherein R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl. [0527] Embodiment 10. The compound of one of embodiments 1 to 8, wherein R1 is independently halogen. [0528] Embodiment 11. The compound of one of embodiments 1 to 8, wherein R1 is independently -F. [0529] Embodiment 12. The compound of one of embodiments 1 to 11, wherein R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl. [0530] Embodiment 13. The compound of one of embodiments 1 to 11, wherein R4 is independently halogen. [0531] Embodiment 14. The compound of one of embodiments 1 to 11, wherein R4 is independently -F. [0532] Embodiment 15. The compound of one of embodiments 1 to 14, wherein L1 is independently -S(O)2-, -NH-, or substituted or unsubstituted 5 to 6 membered
heterocycloalkylene. [0533] Embodiment 16. The compound of one of embodiments 1 to 14, wherein L1 is independently -S(O)2-, -NH-, unsubstituted pyrrolidinylene, unsubstituted piperidinylene, or unsubstituted piperazinylene. [0534] Embodiment 17. The compound of one of embodiments 1 to 14, wherein L1 is independently -NH-. [0535] Embodiment 18. The compound of one of embodiments 1 to 17, wherein
E is
Figure imgf000181_0001
or
Figure imgf000181_0002
wherein R16 is independently hydrogen, halogen, -CX16 3, -CHX16 2, -CH2X16,
-CN, -SOn16R16A, -SOv16NR16AR16B, -NHNR16AR16B, -ONR16AR16B, -NHC(O)NHNR16AR16B, -NHC(O)NR16AR16B, -N(O)m16, -NR16AR16B, -C(O)R16A, -C(O)-OR16A, -C(O)NR16AR16B, -OR16A, -NR16ASO2R16B, -NR16AC(O)R16B, -NR16AC(O)OR16B, -NR16AOR16B, -OCX16 3, -OCHX162, -OCH2X16, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl; R17 is independently hydrogen, halogen, -CX173, -CHX172, -CH2X17, -CN,
-SOn17R17A, -SOv17NR17AR17B, -NHNR17AR17B, -ONR17AR17B, -NH C(O)NHNR17AR17B, -NHC(O)NR17AR17B, -N(O)m17, -NR17AR17B, -C(O)R17A, -C(O)-OR17A, -C(O)NR17AR17B, -OR17A, -NR17ASO2R17B, -NR17AC(O)R17B, -NR17AC(O)OR17B, -NR17AOR17B, -OCX173, -OCHX17 2, -OCH2X17, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl; R18 is independently hydrogen, halogen, -CX18 3, -CHX18 2, -CH2X18, -CN,
-SOn18R18A, -SOv18NR18AR18B, -NHNR18AR18B, -ONR18AR18B, -NH C(O)NHNR18AR18B, -NHC(O)NR18AR18B, -N(O)m18, -NR18AR18B, -C(O)R18A, -C(O)-OR18A, -C(O)NR18AR18B, -OR18A, -NR18ASO2R18B, -NR18AC(O)R18B, -NR18AC(O)OR18B, -NR18AOR18B, -OCX18 3, -OCHX182, -OCH2X18, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl; R19 is independently hydrogen, halogen, -CX19 3, -CHX19 2, -CH2X19, -CN,
-SOn19R19A, -SOv19NR19AR19B, -NHNR19AR19B, -ONR19AR19B, -NH C(O)NHNR19AR19B, -NHC(O)NR19AR19B, -N(O)m19, -NR19AR19B, -C(O)R19A, -C(O)-OR19A, -C(O)NR19AR19B, -OR19A, -NR19ASO2R19B, -NR19AC(O)R19B, -NR19AC(O)OR19B, -NR19AOR19B, -OCX19 3, -OCHX19 2, -OCH2X19, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl; R16A, R16B, R17A, R17B, R18A, R18B, R19A, and R19B are independently
hydrogen, -CX3, -CHX2, -CH2X, -CN, -OH, -COOH, -CONH2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R16A and R16B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R17A and R17B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R18A and R18B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R19A and R19B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; each X1, X16, X17, X18, and X19 is independently–F, -Cl, -Br, or–I; n16, n17, n18, and n19 are independently an integer from 0 to 4; and m16, m17, m18, m19, v16, v17, v18, and v19 are independently 1 or 2. [0536] Embodiment 19. The compound of one of embodiments 1 to 17, wherein E is
or
Figure imgf000183_0002
Figure imgf000183_0001
. [0537] Embodiment 20. The compound of one of embodiments 1 to 17, wherein E is
Figure imgf000183_0003
[0538] Embodiment 21. The compound of one of embodiments 1 to 3, wherein the
compound is not
Figure imgf000183_0004
[0539] Embodiment 22. A pharmaceutical composition comprising a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof, and a
pharmaceutically acceptable excipient. [0540] Embodiment 23. A method for treating cancer in a subject in need thereof, said method comprising administering to the subject in need thereof a therapeutically effective amount of a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof. [0541] Embodiment 24. The method of embodiment 23, wherein said cancer is renal cell carcinoma, follicular lymphoma, glioblastoma, colorectal cancer, endometrial cancer, or lung cancer. [0542] Embodiment 25. A method of reducing the level of activity of mTORC1 in a subject in need thereof, the method comprising administering to the subject in need thereof an effective amount of a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof. [0543] Embodiment 26. A method of reducing the level of activity of mTORC1 in a cell, the method comprising contacting a Vacuolar H+-ATPase protein complex in said cell with a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof. [0544] Embodiment 27. A method of reducing the level of activity of mTORC1 in a cell, the method comprising contacting an ATP6V1A in said cell with a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof. [0545] Embodiment 28. A method of reducing the level of activity of a Vacuolar H+- ATPase protein complex, the method comprising contacting an ATP6V1A in the Vacuolar H+-ATPase protein complex with a compound of one of embodiments 1 to 21, or a pharmaceutically acceptable salt thereof. EXAMPLES
Example 1: Covalent targeting of the vacuolar H+-ATPase enhances cellular clearance through inhibition of lysosomal mTORC1 signaling
[0546] Autophagy is a lysosomal degradation pathway that eliminates aggregated proteins and damaged organelles to maintain cellular homeostasis. A major route for activating autophagy involves inhibition of the mTORC1 kinase, but selective and complete mTORC1 inhibition remains beyond the reach of current mTORC1-targeting compounds. Here, we have coupled screening of a covalent ligand library with activity-based protein profiling to discover EN6, a small-molecule in vivo activator of autophagy that covalently and selectively targets cysteine 277 in the ATP6V1A subunit of the lysosomal v-ATPase, which mediates mTORC1 activation at the lysosome. EN6-mediated ATP6V1A modification impairs mTORC1 lysosomal recruitment via the Rag guanosine triphosphatases, activates autophagy and increases lysosomal acidification. Consistently, EN6 clears TDP-43 aggregates, a causative agent in frontotemporal dementia, in an autophagy-dependent manner. Our results provide insight into how the v-ATPase regulates mTORC1, and reveal a unique approach for enhancing cellular clearance based on covalent inhibition of lysosomal mTORC1 signaling. [0547] Autophagy is central to the maintenance of organismal homeostasis in both physiological and pathological situations. It is an essential, conserved lysosomal degradation pathway that controls the quality of the cytoplasm by eliminating aggregated proteins and damaged organelles. Accordingly, alterations in autophagy have been linked to a wide range of diseases and conditions, including aging, cancer, metabolic disorders, and
neurodegenerative diseases (1-3). Throughout the past decade, autophagy has attracted considerable attention as a target for the development of novel therapeutics (3,4). [0548] The activity of the autophagic machinery is tightly linked to upstream signals, nutrients and stressors through mechanistic target of rapamycin complex 1 (mTORC1) protein kinase. mTORC1 phosphorylates and inhibits a master switch for autophagosome formation, the ULK1 kinase (5,6). Moreover, mTORC1 blocks the nuclear translocation and activation of the TFEB transcription factors, which functions as a‘master regulator’ of catabolism by coordinately promoting the expression of genes required for autophagosome formation and lysosomal function (5-9). Inhibition of mTORC1 resulting from starvation or chemical inhibitors triggers autophagy by simultaneously unleashing the activity of ULK1 and TFEB. Most autophagy-modulators that have entered clinical development either target the mTOR pathway or impinge on poorly understood mTORC1-independent mechanisms, and their efficacy is predicted to be modest at best, versus their potential for significant off- target toxicological actions. [0549] Most protein misfolding diseases are associated with intracytoplasmic deposition of aggregate-prone proteins in neurons and non-neuronal cells, which impair essential cellular pathways for transport, energy production and quality control (10,11). Over recent years, evidence has accumulated to demonstrate that upregulation of autophagy is protective against neurodegeneration. Numerous studies have demonstrated that aggregate-prone proteins at the heart of neurodegenerative disease toxicity are autophagy substrates, and that
pharmacological activators of autophagy can be beneficial in both cell and animal models of these diseases, by both degrading intracytoplasmic aggregates and by preventing associated cell death (12-15). [0550] While many agents have been discovered that either inhibit or activate autophagy, many of these compounds do not possess the required specificity to activate autophagy in a selective manner, either due to off-target effects or due to multiple functions of a specific target. The allosteric mTORC1 inhibitor, rapamycin, results in the relatively specific inhibition of mTORC1 by causing its binding to FK506-binding protein 1A (FKBP1A). However, rapamycin is an incomplete mTORC1 inhibitor; most notably it largely fails at blocking mTORC1-dependent inhibitory phosphorylation of ULK1 and TFEB and at triggering their pro-catabolic programs. Thus, despite some early success in vitro, rapamycin-based drugs (Rapalogues) have proven ineffective in reducing neurotoxic protein aggregates (16-18). The recently developed‘ATP-competitive’ compounds block the kinase activity of mTOR toward virtually all substrates. The higher potency and broader range of ATP-competitive mTOR inhibitors has led to promising results in cancer clinical trials;
however, these compounds have shown considerable toxicity and the ability to cause substantial toxicity to pancreatic b-cell islets leading to b-cell death. Most relevant in the context of neurodegenerative disease, ATP competitive mTOR inhibitors strongly suppress Akt signaling, which is an essential survival signal for neuronal cells (19-22). The limitations of current mTOR inhibitors thus create an urgent need to identify new targets that could lead to selective activation of autophagy while avoiding unacceptable toxicities. [0551] To be activated, mTORC1 needs to translocate to the lysosome membrane (5,6). Nutrients, primarily amino acids, directly regulate the lysosomal recruitment of mTORC1 by modulating the nucleotide state of the Rag GTPases. The Rags assemble as obligate heterodimers composed of RagA or RagB (which are highly similar to each other) associated with RagC or RagD, and are tethered to the lysosomal membrane by the pentameric
Ragulator complex, composed of the LAMTOR1-5 proteins (23-25). Under amino acid sufficiency, the Rag GTPases become active by adopting a nucleotide state in which Rag-A/B is GTP-loaded and Rag-C/D is GDP-loaded, and mediate the lysosomal attachment of mTORC1 by directly interacting with the mTORC1 subunit Raptor (23-25). [0552] A key but poorly understood player in Rag-mTORC1 activation is the vacuolar H+ ATPase (v-ATPase), an evolutionarily conserved ATP-driven rotary proton pump that couples ATP hydrolysis by its peripheral V1 domain to proton translocation through membrane integral V0 domain to acidify the lysosome and enable its degradative functions (26,27). The v-ATPase forms a physical supercomplex with Ragulator and the Rag GTPases, and its integrity and activity are essential for lysosomal mTORC1 recruitment in response to amino acids (28-31). Although its precise role in Rag-mTORC1 activation is not completely understood, the v-ATPase represents a prime target for discovery of small molecules that may simultaneously block mTORC1 activation and enhance autophagic function. In this study, through the coupling of chemoproteomics and covalent ligand screening, we have discovered a small-molecule activator of autophagy that acts through covalently targeting a unique regulatory cysteine on ATP6V1A, resulting in the complete and selective inactivation of mTORC1 and enhanced cellular clearance of toxic protein aggregates. [0553] To simultaneously discover new targets, druggable hotspots and small-molecule modulators for activating autophagy, we screened a library of 217 cysteine- and lysine- reactive ligands based on acrylamide, chloroacetamide, and dichlorotriazine scaffolds in a cell-based autophagic flux assay that utilizes a dual-color, cleavable LC3B reporter (32-37). By running this screen in mouse embryonic fibroblast (MEF) cells, we identified several covalent ligands that increased LC3B processing and thus potentially increased autophagy activation (FIG.1A, Table 1). mTORC1 inhibitors rapamycin and Torin1 also demonstrated expected efficacy in this assay. Upon replication in HEK293 cells, the screen yielded the cysteine-reactive acrylamide EN6 as an inducer of LC3B degradation to a comparable degree to direct mTORC1 inhibitors, rapamycin and Torin1 (FIGS.1B-1D). We validated these findings by showing that, in HEK293 cells, EN6 treatment increased the levels of processed LC3BII (FIG.1E), and triggered formation of LC3 puncta to a similar degree to Torin1 treatment (FIG.1F). [0554] We next mapped the proteome-wide cysteine-reactivity of EN6 in MEF cells using competitive isotopic tandem orthogonal proteolysis-enabled activity-based protein profiling (isoTOP-ABPP) to discover the mechanism of action of this compound (FIG.2A). Upon in situ treatment of cells with vehicle or EN6, we labeled the resulting cell lysates with the cysteine-reactive alkyne-functionalized iodoacetamide probe (IA-alkyne) followed by the isoTOP-ABPP chemoproteomics pipeline (35,36,38-41). The primary site of EN6 was identified as cysteine 277 (C277) of ATP6V1A, the catalytic subunit of the lysosomal v- ATPase (FIG.2B). This site showed an isotopic light-to-heavy (control-to-EN6-treated) ratio of >50 indicating high target engagement of this site compared to other targets. We confirmed this interaction by demonstrating that EN6 displaces iodoacetamide-rhodamine (IA-rhodamine) labeling from recombinant human ATP6V1A protein with an IC50 of 1.7 mM (FIG.2C). [0555] Previous studies showed that the lysosomal v-ATPase physically interacts with the Ragulator-Rag complex in an amino acid-regulated manner and enables Ragulator-Rags to recruit mTORC1, leading to activation of anabolic programs and inhibition of autophagy initiation (28,42). We thus asked whether, by binding to the ATP6V1A subunit of the v- ATPase, EN6 may disrupt mTORC1 recruitment to the lysosome, thus leading to its observed autophagy-activating effect. Consistent with this premise, we found that EN6 treatment in cells led to complete inactivation of mTORC1 signaling as shown by reduced levels of phosphorylated canonical substrates, S6 kinase 1 (S6K1) and 4EBP1 (FIG.3A). Notably, consistent with specific mTORC1 inhibition by EN6, treatment with Torin1, but not EN6, blocked mTORC2-dependent AKT phosphorylation (FIG.3B). Confirming that mTORC1 inhibition by EN6 involves modification of C277 of ATP6V1A, phosphorylation of S6K and ULK1 were completely resistant to EN6-mediated inhibition in cells in which endogenous ATP6V1A was knocked down and replaced with the non-modifiable C277A mutant (FIG. 3C, FIG.3D). In these cells, EN6-induced LC3BII accumulation and p62/SQSTM1 degradation were also prevented by the C277A substitution, indicating that autophagy activation by EN6 is also strictly dependent on C277 modification (FIG.3C, FIG.3D). [0556] The v-ATPase interacts with Ragulator-Rags to enable amino acid-dependent recruitment of mTORC1 to the lysosome (28,42). Consistent with an inhibitory mechanism towards this pathway, EN6 treatment completely abrogated amino acid-induced mTORC1 recruitment to LAMP2-positive lysosomes (FIG.3E). [0557] As previously shown, amino acids modulate the interaction of FLAG-tagged Ragulator subunit p14 with the v-ATPase (FIG.4A). Notably, EN6 decreased the overall binding between the v-ATPase and Ragulator, and rendered this interaction insensitive to amino acids (FIG.4A). An explanation for this result is that covalent modification of C277 of ATP6V1A by EN6 causes a conformational change in the v-ATPase that partially decouples it from Ragulator-Rag and prevents activation of the latter complex by amino acids. Collectively, these data reveal that, by targeting C277 of ATP6V1A, EN6 impairs Rag GTPase-mediated recruitment of mTORC1 to the lysosome, leading to constitutive activation of autophagy. [0558] mTORC1 inhibition leads to upregulation of the catabolic functions of the lysosome through dephosphorylation and nuclear translocation of TFEB (5,7-9). Consistently, upon EN6 treatment we observed greatly enhanced nuclear translocation of TFEB and significantly increased levels of several lysosomal gene transcripts that are direct TFEB transcriptional targets, including v-ATPase components (FIG.4B, FIG.4C). We also showed that transcriptional targets measured that are not regulated by TFEB are not changed (FIG.8). Consistent with these transcriptional changes, EN6 treatment led to significantly increased acidification of the lysosome, as shown by lysosensor staining, and this heightened acidification was blocked by the v-ATPase inhibitor bafilomycin A1 (FIG.4D, FIG.4E). [0559] To determine whether EN6-mediated inhibition of mTORC1 and activation of autophagy could aid in boosting cellular clearance, we tested the effect of EN6 in clearing toxic Tar-binding protein 43 (TDP43) protein aggregates, which drive the development of amyotrophic lateral sclerosis (ALS) (43). In an IPTG-inducible GFP-TDP43 U2OS osteosarcoma cell line model, IPTG stimulation led to the rapid formation of TDP-43 aggregates, which were reduced by 75 % upon 7 hour EN6 treatment. EN6-mediated clearance of TDP-43 aggregates was lysosome- and v-ATPase-dependent, as it was prevented by co-treatment with bafilomycin A1 (FIG.5A, FIG.5B). Thus, our results indicate that EN6 is capable of clearing toxic protein aggregates in an autophagy-dependent manner. [0560] We next tested whether EN6 is able to inhibit mTORC1 and activate autophagy in vivo. Three mice cohorts were injected intraperitoneally with vehicle, rapamycin or EN6, and analyzed after 4 hours. mTORC1 signaling was significantly impaired across the heart, kidney, and skeletal muscle, as demonstrated by reduced phosphorylation of S6, whereas autophagy was strongly activated, as shown by heightened LC3BII levels (FIGS.6A-6C). While EN6 was somewhat less potent than rapamycin in shutting down p-S6, it was significantly more effective than rapamycin at inhibiting phosphorylation of 4EBP1, consistent with our data in cell lines (FIG.6A). Thus, due to its unique mechanism of action, EN6 functions as a complete and selective mTORC1 inhibitor both in cells and in vivo. [0561] Our study identifies a covalent ligand, EN6, which selectively targets a unique druggable hotspot—C277 within the v-ATPase subunit ATP6V1A—to activate autophagy by selectively and completely inhibiting mTORC1 signaling through disrupting mTORC1 localization to the lysosome (FIG.7). This is a distinct mechanism from other
pharmacological modulators of autophagy that mostly act through directly targeting the kinase function mTORC1, such as with rapalogues and ATP-competitive inhibitors. While both rapalogues and ATP-competitive mTORC1 inhibitors have potential therapeutic activity, their clinical utility is hampered by their incomplete mTORC1 inhibition (rapalogues) and concomitant inhibition of mTORC2 (ATP competitors) (44-47). Chronic exposure to rapalogues also inhibits mTORC2, leading to metabolic dysregulation (48,49). While EN6 shows promising cellular and in vivo activity, this covalent ligand is an early hit that still requires further medicinal chemistry efforts to optimize potency, selectivity, and in vivo bioavailability and efficacy. Furthermore, while isoTOP-ABPP studies here show that C277 of ATP6V1A is one of the primary and most highly engaged targets of EN6 in cells, EN6 may possess additional off-targets that either exhibit lower degree of engagement or act through reversible interactions. Development of an alkyne-functionalized EN6 probe will aid in future assessment of EN6 selectivity and provide a foundation for additional medicinal chemistry, target engagement, and screening efforts to identify improved ligands against this site. Nonetheless, our study convincingly demonstrates that the EN6 signaling impairments are driven through the targeting of C277 of ATP6V1A. [0562] A key question is how covalent modification of C277 within ATP6V1A affects v- ATPase function and mTORC1 regulation. By inspecting the previously reported crystal structures of the v-ATPase from Thermus Termophilus and Enterococcus Hirae (50,51), we note that the equivalent residues to human C277, C255 in Thermus and C259 in Enterococcus V1A subunits, respectively, lie in the core of the catalytic B-A interface, in close proximity to residues that are critical for catalysis, such as E279 in human (E257 in Thermus and E261 in Enterococcus, respectively). Because the side chain of C277 points away from the nucleotide, this residue is unlikely to play a direct role in catalysis, however, covalent modification of this cysteine could affect the rate of ATP hydrolysis and, therefore, proton pumping, ultimately impacting lysosomal acidification (52). Moreover, the conformational change induced by covalent modification of C277 could propagate to the Ragulator-Rag binding interface, thus interfering with their activation and ability to recruit mTORC1.
Future structural biology efforts with EN6 and v-ATPase will yield additional insights into the mechanism through which the v-ATPase interacts with the Ragulator-Rag complex to enable mTORC1 recruitment to the lysosome, and into how covalent modification by EN6 disrupts this process. [0563] A major challenge of chemical genetic screens is identifying the targets of leads that arise from screens. Oftentimes, lead compounds must be derivatized to bear biorthogonal and photoaffinity handles or conjugated to beads to facilitate chemoproteomic target identification. These approaches require additional synthetic efforts to make analogs of the lead molecule and alter the structure of the molecule, which may hinder or prevent target identification. Previous studies have highlighted the utility of covalent ligands and chemoproteomics in accessing unique ligandable sites within classically undruggable protein targets (34-36,41,53). [0564] Our study once again highlights the utility of chemoproteomics-enabled covalent ligand screening platforms to rapidly deconvolute the mechanism of action of cellular phenotypic screening hits and uncover unique and novel ligandable sites and druggable modalities that would not be predicted a priori. In this study, we reveal a cell and in vivo- active covalent ligand EN6 that uniquely targets a novel ligandable cysteine within the ATP6V1A v-ATPase complex to inhibit mTORC1 signaling and activate autophagy to improve cellular clearance. Example 2: Methods
[0565] Cell culture [0566] Human embryonic kidney HEK293T and HEK293A cells, mouse embryonic fibroblasts (MEF), HEK293A cells stably expressing GFP-LC3-RFP-LC3DG, MEF cells stably expressing GFP-LC3-RFP-LC3DG and human bone osteosarcoma epithelial U2OS cells stably expressing GFP-TDP43 were maintained in DMEM supplemented with 10 vol% FBS and 1 vol% GlutaMax. All cells were incubated in 5% CO2 humidified air, and subcultured when 80% confluence was reached. [0567] Screening for autophagy modulators. MEF cells stably expressing GFP-LC3-RFP- LC3DG were plated on 96-well plates (Corning; 3904) at 30,000 cells/well and allowed to grow in complete medium overnight. The cells were then incubated with covalent ligands (50 µM or at indicated concentrations), rapamycin (100 nM), Torin 1 (250 nM) or DMSO solvent control in complete medium (100 µL) for 24 h. After that, the medium was aspirated and the cells were fixed with 4% paraformaldehyde in PBS (100 µL) for 10 min, washed with PBS (100 µL) and assayed in PBS (100 µL) by SpectraMax i3 (Molecular Devices). GFP fluorescence was measured with excitation and emission at 488 ±9 nm and 514 ±15 nm respectively, while RFP fluorescence was measured with excitation and emission at 584 ±9 nm and 612 ±15 nm respectively. [0568] For HEK293A cells stably expressing GFP-LC3-RFP-LC3DG, before they were seeded, 96-well plates were coated with fibronectin in PBS (5 µg/mL, 75 µL/well) for 1 h at 37 oC. The solution was then aspirated, and cells were plated at 30,000 cells/well, allowed to grow in complete medium overnight, treated and assayed with the same protocol as described above for MEF cells. [0569] For checking cell viability, solutions were aspirated after treatment with the compounds, and the cells were fixed and stained by Hoechst 33342 (13.3 µg/mL) in formalin (100 µL) for 15 min. After that, cells were washed with PBS (100 µL) and assayed in PBS (100 µL) by SpectraMax i3 with excitation and emission at 350 ±9 nm and 461 ±15 nm respectively. [0570] IsoTOP-ABPP chemoproteomic studies. IsoTOP-ABPP studies were done as previously reported (35,36). Cells were lysed by probe sonication in PBS and protein concentrations were measured by BCA assay (54). For in situ experiments, cells were treated for 90 min with either DMSO vehicle or covalently-acting small molecule (from 1000X DMSO stock) before cell collection and lysis. For in vitro experiments, proteome samples diluted in PBS (4 mg of proteome per biological replicate) were treated with a DMSO vehicle or covalently-acting small-molecule for 30 min at room temperature. Proteomes were subsequently labeled with IA-alkyne labeling (100 mM) for 1 h at room temperature. CuAAC was used by sequential addition of tris(2-carboxyethyl)phosphine (1 mM, Sigma), tris[(1- benzyl-1H-1,2,3-triazol-4-yl)methyl]amine (34 mM, Sigma), copper (II) sulfate (1 mM, Sigma), and biotin-linker-azide—the linker functionalized with a TEV protease recognition sequence as well as an isotopically light or heavy valine for treatment of control or treated proteome, respectively. After CuAAC, proteomes were precipitated by centrifugation at 6500 x g, washed in ice-cold methanol, combined in a 1:1 control/treated ratio, washed again, then denatured and resolubilized by heating in 1.2% SDS/PBS to 80 °C for 5 minutes.
Insoluble components were precipitated by centrifugation at 6500 x g and soluble proteome was diluted in 5 mL 0.2% SDS/PBS. Labeled proteins were bound to avidin-agarose beads (170 ml resuspended beads/sample, Thermo Pierce) while rotating overnight at 4 °C. Bead- linked proteins were enriched by washing three times each in PBS and water, then
resuspended in 6 M urea/PBS (Sigma) and reduced in TCEP (1 mM, Sigma), alkylated with iodoacetamide (IA) (18 mM, Sigma), then washed and resuspended in 2 M urea and trypsinized overnight with 0.5 mg/mL sequencing grade trypsin (Promega). Tryptic peptides were eluted off. Beads were washed three times each in PBS and water, washed in TEV buffer solution (water, TEV buffer, 100 mM dithiothreitol) and resuspended in buffer with Ac-TEV protease and incubated overnight. Peptides were diluted in water and acidified with formic acid (1.2 M, Spectrum) and prepared for analysis. [0571] Mass spectrometry analysis. Peptides from all chemoproteomic experiments were pressure-loaded onto a 250 mm inner diameter fused silica capillary tubing packed with 4 cm of Aqua C18 reverse-phase resin (Phenomenex # 04A-4299) which was previously equilibrated on an Agilent 600 series HPLC using gradient from 100% buffer A to 100% buffer B over 10 min, followed by a 5 min wash with 100% buffer B and a 5 min wash with 100% buffer A. The samples were then attached using a MicroTee PEEK 360 mm fitting (Thermo Fisher Scientific #p-888) to a 13 cm laser pulled column packed with 10 cm Aqua C18 reverse-phase resin and 3 cm of strong-cation exchange resin for isoTOP-ABPP studies. Samples were analyzed using an Q Exactive Plus mass spectrometer (Thermo Fisher
Scientific) using a 5-step Multidimensional Protein Identification Technology (MudPIT) program, using 0%, 25%, 50%, 80%, and 100% salt bumps of 500 mM aqueous ammonium acetate and using a gradient of 5-55% buffer B in buffer A (buffer A: 95:5 water:acetonitrile, 0.1% formic acid; buffer B 80:20 acetonitrile:water, 0.1% formic acid). Data were collected in data-dependent acquisition mode with dynamic exclusion enabled (60 s). One full MS (MS1) scan (400-1800 m/z) was followed by 15 MS2 scans (ITMS) of the nth most abundant ions. Heated capillary temperature was set to 200 °C and the nanospray voltage was set to 2.75 kV. [0572] Data were extracted in the form of MS1 and MS2 files using Raw Extractor 1.9.9.2 (The Scripps Research Institute) and searched against the Uniprot human database using ProLuCID search methodology in IP2 v.3 (Integrated Proteomics Applications, Inc.) (55). Cysteine residues were searched with a static modification for carboxyaminomethylation (+57.02146) and up to two differential modifications for methionine oxidation and either the light or heavy TEV tags (+464.28596 or +470.29977, respectively). Peptides were required to have at least one tryptic end and to contain the TEV modification. ProLUCID data was filtered through DTASelect to achieve a peptide false-positive rate below 5%. Only those probe-modified peptides that were evident across all two out of three biological replicates were interpreted for their isotopic light to heavy ratios. Those probe-modified peptides that showed ratios >4 were further analyzed as potential targets of the covalently-acting small- molecule. For modified peptides with ratios >4, we filtered these hits for peptides were present in all three biological replicates. For those probe-modified peptide ratios >4, only those peptides with 3 ratios >4 were interpreted, and otherwise replaced with the lowest ratio. MS1 peak shapes of any resulting probe-modified peptides with ratios >3 were then manually confirmed to be of good quality for interpreted peptides across all biological replicates. [0573] Constructing knockdown lines. We used short-hairpin oligonucleotides to knock down the expression of ATP6V1A in Hela cells using previously described methods (56). The pLKO.1 lentiviral vector (TRC, Broad institute) was used to express the shRNA against ATP6V1A (TRCN0000029542). ATP6V1A WT or C277A resistant to the shRNA was cloned into pLKO.1 shRNA vector under the hPGK promoter. For lentivirus production, lentiviral plasmids and packaging plasmids (pMD2.5G, Addgene #12259 and psPAX2, Addgene #12260) were transfected into HEK293T cells using PEI transfection method. Viral supernatant was collected 48 hours after transfection and filtered with 0.45 mm filter. The viruses were further concentrated using Lenti-X Concentrator (Clontech, 631231) according to the manufacturer’s instructions. Target cells were plated in 6-well or 10 cm plates with 8 mg/mL polybrene (Millipore, TR-1003-G) and incubated with virus containing media. 24 hours later, the media was changed to fresh media containing 2 mg/mL puromycin
(Calbiochem, 540411) and selected for over 3 days. Knockdown and protein expression were confirmed by immunoblotting. [0574] Gel-based ABPP. Gel-based ABPP methods were performed as previously described (36,38,57,58). Recombinant pure human ATP6V1A protein was purchased from Abcam (ab132441). Pure protein (0.1 mg) was pre-treated with DMSO vehicle or covalently- acting small molecules for 1 h at 37 oC in an incubation volume of 50 mL PBS, and were subsequently treated with tetramethylrhodamine-5-iodoacetamide dihydroiodide (IA- rhodamine; 1 mM final concentration) for 1 h at room temperature. Samples were then diluted with 30 mL of 4 x reducing Laemmli SDS sample loading buffer (Alfa Aesar) and heated at 90 °C for 5 min. The samples were separated on precast 4-20% TGX gels (Bio-Rad Laboratories, Inc.) and scanned by ChemiDoc MP (Bio-Rad Laboratories, Inc.). Inhibition of target labeling was assessed by densitometry using ImageJ. [0575] Resynthesis and characterization of EN6. The initial autophagy screen shown in FIG.1A used EN6 from our screening plates. All subsequent uses of EN6 in this study are either from resupplied EN6 or resynthesized EN6. See Example 3 for experimental details. [0576] Covalent ligand library. The synthesis and characterization of the covalent ligands screened here have been previously reported (33-37,59). Compounds starting with“EN” were purchased from Enamine LLC. [0577] Antibodies and reagents for biological experiments. Antibodies to phospho-T389- S6K1 (9234), S6K1 (2708), phospho-S65-4E-BP1(9451), phospho-T37/464E-BP1 (2855), 4E-BP1 (9644), phospho-T308-Akt (13038), phospho-S473-Akt (4060), Akt (4691), phospho-S757-ULK1 (14202), ULK1 (8054), S6 (9202), phospho-S240/244 S6 (5364), LC3B (3868), p62/SQSTM1 (39749), ATP6V1B2 (14488) and FLAG epitope (2368) were from Cell Signaling Technology; Antibody to ATP6V1A (ab137574) was from Abcam; Antibodies to LAMP2 (sc-18822) and ATP6V1D (sc-390164) were from Santa Cruz
Biotechnology. Goat anti-rabbit IgG superclonal secondary antibody-Alexa Fluor 647 (A27040) was from Thermo Fisher Scientific. IRDye® 800CW Goat anti-Rabbit IgG (H + L; 926-32211) was from Li-Cor. Recombinant human ATP6V1A protein (ab132441) was from Abcam; Tetramethylrhodamine-5-iodoacetamide dihydroiodide (6222) was from Setareh Biotech.; Normal goat serum (10%; 50062Z), Hoechst 33342 (H3570) and LysoSensor Yellow/Blue DND-160 (L7545) were from Thermo Fisher Scientific. Amino acids, Flag-M2 affinity gel (A2220) and Bafilomycin A1 (B1793) from Sigma-Aldrich. Torin 1 (4247) from Tocris Biosciences. Rapamycin was from Selleckchem. Pierce Protease Inhibitor Tablets (A32965) from ThermoFisher Scientific. Amino acid-free RPMI (R9010-01) from US Biologicals. Dulbecco's Modified Eagle’s Medium (DMEM; 10-013-CV) and fetal bovine serum (FBS; 35-015-CV) were from Corning. 0.25% Trypsin-EDTA (1 x; 25200-056) and GluatMax (100 x; 25030-081) were from Thermo Fisher Scientific. Sequencing grade modified trypsin (V51111) was from Promega. [0578] Amino acid starvation and stimulation. Sub-confluent cells were rinsed and incubated with RPMI without amino acids supplemented with 2% dialyzed FBS for 50 min, as described (27). Stimulation with amino acids (concentration as in RPMI) was performed for 10 min. Where drug treatment was performed, cells were incubated during the 50 min starvation period and the 10 min stimulation period. [0579] Western blotting and immunoprecipitation. Cells were washed twice with ice-cold phosphate-buffered saline (PBS) and lysed in lysis buffer (1% Triton X-100, 10 mM b- glycerol phosphate, 10 mM sodium pyrophosphate, 4 mM EDTA, 40 mM HEPES at pH 7.4, and 1 tablet of EDTA-free protease inhibitors per 50 mL). Cell lysates were cleared by centrifugation in a microcentrifuge at 17,000 g for 10 minutes at 4 °C. Cell lysate samples were prepared by addition of 5X sample buffer, heated at 95 °C for 5 minutes, resolved by 10% or 12% SDS-PAGE, and analyzed by immunoblotting. Antibodies were obtained from various commercial sources and dilutions were prepared per recommended manufacturers’ procedures. [0580] For FLAG immunoprecipitations, HEK293T cells stably expressing Flag-tagged proteins were lysed as above and 30 mL of a well-mixed 50% slurry of anti-FLAG M2 Affinity Gel (Sigma A2220) was added to each lysate (1 mg/mL) and incubated at 4 °C in a shaker for 1 hour. Immunoprecipitates were washed four times, three times with lysis buffer and once with lysis buffer containing 400 mM NaCl. Immunoprecipitated proteins were denatured by addition of 50 mL of sample buffer and heating to 95 °C for 5 minutes, resolved by SDS-PAGE, and analyzed by immunoblotting. [0581] Imaging LC3B puncta in EN6-treated HEK293A cells by confocal fluorescence microscopy. HEK293A cells were plated on fibronectin-coated (5 µg/mL) 8-well Lab Tek borosilicate chambered coverglass slides (Nunc) at 40,000 cells/well and allowed to grow in complete medium overnight. The cells were then incubated with EN6 (at indicated concentrations), Torin 1 (250 nM) or DMSO control for indicated time intervals. After aspiration of the solution, the cells were washed with PBS (350 µL) and fixed with methanol for 15 min at -20 oC. The cells were rinsed three times with PBS (350 µL each), and incubated with PBS containing 5% normal goat serum and 0.3% Triton X-100 (300 µL) for 1 h. The cells were washed with PBS (350 µL) and incubated with anti-LC3B (Cell Signaling Technology #3868; v/v, 1:200) in PBS containing 1% BSA and 0.3%Triton X-100 at 4 oC overnight. After that, the cells were washed three times with PBS (350 µL each), and incubated with anti-rabbit superclonal secondary antibody-Alexa Fluor 647 (Thermo Fisher Scientific A27040; v/v = 1:500) in PBS containing 1% BSA and 0.3%Triton X-100 in dark at room temperature for 1 h. The cells were washed three times with PBS (350 µL each) and stained with Hoechst 33342 (5 µg/mL) in PBS in dark at room temperature for 15 min. After washing with PBS three times (350 µL each), the cells were imaged in PBS by Zeiss laser scanning microscope (LSM) 710 with a 20× or 63× oil-immersion objective lens. Hoechst 33342 was excited with a 405 nm diode laser, and emission was collected on a META detector between 410 and 587 nm. Alexa Fluor 647 was excited with a 633 nm HeNe laser, and emission was collected on a META detector between 638 and 755 nm. [0582] Image analysis was performed by use of ImageJ. A threshold of 100 -255 (for 8-bit images) was first set for selection of LC3B puncta, and a region of interest (ROI) was created over a single cell. The number of cellular LC3B puncta was then quantified by“Analyze Particles” using size and circularity of 0.1 -infinity and 0.0 -1.0 respectively.25 individual cells of each group from triplicate experiments were analyzed, and the statistical analyses were performed with a two-tailed Student’s t-test (MS Excel). [0583] Imaging lysosomal recruitment of mTORC1 by immunofluorescence. HEK-293T or Hela cells were seeded on fibronectin-coated glass coverslips and allowed to attach overnight. On the following day, cells were subjected to either amino acid starvation and stimulation with or without drug incubation and fixed in 4% paraformaldehyde (PFA) for 15 minutes at room temperature. The coverslips were rinsed twice with PBS and cells were permeabilized with 0.1% (w/v) saponin in PBS for 10 minutes. After rinsing twice with PBS, the slides were incubated with primary antibodies in 5% normal donkey serum (Jackson ImmunoResearch, 017-000-121) for 1 hour at room temperature, rinsed four times with PBS, and incubated with fluorophore conjugated secondary antibodies derived from goat or donkey (Life Technologies, diluted 1:400 in 5% normal donkey serum) for 1 hour at room
temperature in the dark. The coverslips were then washed four times with PBS, mounted on glass slides using Vectashield (Vector Laboratories) and imaged on a spinning disk confocal system built upon a Nikon Eclipse Ti microscope with Andor Zyla-4.5 sCMOS camera. [0584] Imaging lysosomal pH by LysoSensor DND-160. HEK293A cells were plated on fibronectin-coated (5 µg/mL) 8-well Lab Tek borosilicate chambered coverglass slides (Nunc) at 40,000 cells/well and allowed to grow in complete medium overnight. The cells were then incubated with DMSO control, EN6 (50 µM), bafilomycin A1 (0.2 µM), or a mixture of EN6 and bafilomycin A1 (50 and 0.2 µM respectively) at 37 oC for 4 h. After that, LysoSensor DND-160 (2 µM final concentration) was added to the solution and the cells were stained at 37 oC for 5 min. The solution was then replaced by DPBS and the live cells were imaged by Zeiss LSM 880 with a 40× water-immersion objective lens. The blue fluorescence of DND-160, Fblue, was excited with a two-photon laser at 760 nm and emission was collected on a META detector between 400 and 490 nm. The yellow fluorescence of DND-160, Fyellow, was excited with a two-photon laser at 760 nm and emission was collected on a META detector between 514 and 649 nm. [0585] The ratiometric images, Fyellow / Fblue, were generated by Ratio Plus plugin of ImageJ. For quantification, a threshold value was set as background and the average intensity of the whole image was measured by ImageJ. All experiments were performed in triplicate, and statistical analyses were performed with a two-tailed Student’s t-test (MS Excel). [0586] RNA extraction and quantitative RT-PCR (qRT-PCR). Total RNAs were extracted using AurumTM Total RNA Mini Kit (Bio-rad) and reverse transcription was performed from 1 mg total RNAs using iScriptTM Reverse Transcription for RT-qPCR (Bio-rad) according to manufacturer’s instruction. All real-time qPCR(qRT-PCR) analyses were performed using StepOnePlus machine (Applied Biosystems) with SsoAdbancedTM
Universal SYBR Green supermix (Bio-rad). [0587] The quantity of mRNA was calculated using the DDCt method and normalized to b- actin. All reactions were performed as triplicates. [0588] Assessing TDP-43 aggregates. U2OS cells stably expressing GFP-TDP-43 were plated on fibronectin-coated (5 µg/mL) 8-well Lab Tek borosilicate chambered coverglass slides (Nunc) at 30,000 cells/well and allowed to grow in complete medium overnight. The cells were incubated with DMSO control, isopropylthio-b-galactoside (IPTG; 50 µM), a mixture of EN6 (25 µM) and IPTG (50 µM), or a mixture of EN6 (25 µM), IPTG (50 µM) and bafilomycin A1 (0.2 µM) at 37 oC for 7 h. The cells were washed with PBS (350 µL) and fixed with 4% paraformaldehyde (PFA) for 15 minutes at room temperature. After fixation, the cells were washed three times with PBS (350 µL each) and stained with Hoechst 33342 (0.5 µg/mL) in PBS in dark at room temperature for 15 min. After washing with PBS three times (350 µL each), the cells were imaged in PBS by Zeiss laser scanning microscope (LSM) 710 with a 20× or 63× oil-immersion objective lens. Hoechst 33342 was excited with a 405 nm diode laser, and emission was collected on a META detector between 410 and 483 nm. GFP was excited with a 488 nm Ar laser, and emission was collected on a META detector between 493 and 598 nm. [0589] Image analysis was performed by use of ImageJ. A threshold was first set for selection of GFP-TDP-43 aggregate, and a region of interest (ROI) was created over a single cell. The number of cellular aggregates was then quantified by“Analyze Particles” using size and circularity of 5 -infinity and 0.0 -1.0 respectively. 26 individual cells of each group from triplicate experiments were analyzed, and the statistical analyses were performed with a two-tailed Student’s t-test (MS Excel). [0590] Assessing mTORC1 inhibition in vivo in mice. 6-week-old male C57BL/6 mice (Jackson Laboratory) were injected intraperitoneally with solvent control, EN6 (50 mg/kg) or rapamycin (10 mg/kg) in PBS/ethanol/PEG-40 (v/v/v = 18:1:1). After 6 h, mice were euthanized, and tissues were harvested and lysed in lysis buffer (1% Triton X-100, 10 mM b- glycerol phosphate, 10 mM sodium pyrophosphate, 4 mM EDTA, 40 mM HEPES at pH 7.4, and 1 tablet of EDTA-free protease inhibitors per 50 ml) at 4 oC for 30 min. The lysates were cleared by centrifugation in a microcentrifuge at 21,130 g for 10 minutes at 4°C and protein concentration of supernatant was determined by BCA assay (Thermo Fisher Scientific). The lysates was then diluted to 1.5 mg/mL, mixed with 4 x sample buffer, heated at 95 °C for 5 minutes, resolved by precast 4-20% TGX gels, and analyzed by immunoblotting. Antibodies were obtained from various commercial sources and dilutions were prepared per
recommended manufacturers’ procedures. Animal experiments were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committees of the University of California, Berkeley. Example 3: Methods for chemical syntheses
[0591] Materials and reagents for chemical syntheses. 2-Fluoro-5-nitroaniline was purchased from AK Scientific. 1-(2-Fluorophenyl)-1H-pyrazole-4-carboxylic acid was purchased from Enamine LLC. Acryloyl chloride, potassium carbonate, iron powder, ammonium chloride and N,N-diisopropylethylamine (DIPEA) were purchased from Sigma- Aldrich. All the solvents were of HPLC grade and were from Sigma-Aldrich. All other reagents were of analytical grade and were used without further purification. MilliQ water was used in all experiments unless otherwise stated. [0592] Physical Measurements and Instrumentation. 1H NMR and 13C{1H} spectra were collected at 25 °C on Bruker AVB-400, AVQ-400 and AV-300 at the College of Chemistry NMR Facility at the University of California, Berkeley. All chemical shifts are reported in the standard d notation of parts per million relative to residual solvent peak as an internal reference. Splitting patterns are indicated as follows: br, broad; s, singlet; d, doublet; t, triplet; m, multiplet; dd, doublet of doublets. High-resolution mass spectra were collected at the QB3/Chemistry Mass Spectrometry Facility at the University of California, Berkeley. Fluorescence from microplates were recorded on SpectraMax i3 (Molecular Devices). In-gel fluorescence images were recorded on ChemiDoc MP Gel Imaging system (Bio-Rad).
Fluorescence from western blots were imaged by Odyssey Infrared Imager (Li-Cor).
Confocal microscopy images were recorded on a Zeiss laser scanning microscope (LSM) 710 with a 20× or 63× oil-immersion objective lens, and a Zeiss LSM 880 with a 40× water- immersion objective lens at the CRL Molecular Imaging Center at the University of
California, Berkeley. [0593] Synthesis of EN6.
Figure imgf000200_0001
[0594] CC-2-26. K2CO3 (936.6 mg, 6.8 mmol) was added to 2-fluoro-5-nitroaniline (529.4 mg, 3.4 mmol) in dry THF (20 mL). At 0 oC, acryloyl chloride (300 µL, 3.8 mmol) in dry THF (10 mL) was added dropwise to the solution mixture with vigorous stirring. The solution mixture was further stirred at 0 oC for 1 h, and then the reaction was quenched by addition of water. Any organic volatile was removed by evaporation under reduced pressure, and the aqueous layer was extracted with ethyl acetate. The ethyl acetate layer was then washed by saturated NaCl solution, dried by MgSO4 and filtered. Volatile organic solvent was evaporated under reduced pressure, and the crude product was purified by column chromatography on silica gel using hexane/ethyl acetate (4:1, v/v) as eluent, yielding CC-2- 26 as yellow solid (643 mg, 90%). 1H NMR (CDCl3, 400 MHz): d 9.34-9.44 (1H, m), 7.97- 8.04 (1H, m), 7.55 (1H, br), 7.26 (1H, t, J = 9.5 Hz), 6.50-6.56 (1H, m), 6.27-6.35 (1H, m), 5.89-5.92 (1H, m). 13C{1H} NMR ([D6]DMSO, 100 MHz) d 164.1, 143.7, 130.8, 128.7, 127.4, 127.3, 120.5, 120.4, 118.0, 116.8, 116.5.19F{1H} NMR (CDCl3, 376 MHz) d = 119.0. HRMS (ESI) m/z [M -H] - calcd for C9H7FN2O3: 209.0363; found: 209.0371. [0595] CC-2-27. CC-2-26 (343 mg, 1.63 mmol) and ammonium chloride (873 mg, 16.3 mmol) were dissolved in EtOH/H2O mixture (50 mL; v/v = 4:1) with heating. Iron powder (911.5 mg, 16.3 mmol) was then added and the reaction mixture was heated under reflux for 3 h. After complete consumption of CC-2-26 as indicated by TLC, the reaction mixture was cooled to room temperature and any undissolved solid was filtered off. The filtrate was evaporated under reduced pressure, and the aqueous solution was extracted with ethyl acetate three times. The combined organic layer was dried by MgSO4 and filtered. Volatile organic solvent was evaporated under reduced pressure, and the crude product was purified by column chromatography on silica gel using hexane/ethyl acetate (3:2, v/v) as eluent, yielding CC-2-27 as pale yellow solid (211.5 mg, 72%). 1H NMR ([D6]DMSO, 400 MHz): d 9.66 (1H, s), 7.26 (1H, d, J = 5.3 Hz), 6.89 (1H, t, J = 9.4 Hz), 6.60 (1H, dd, J = 5.1 and 17.0 Hz), 6.27-6.33 (1H, m), 6.24 (1H, d, J = 17.0 Hz), 5.73 (1H, d, J = 10.2 Hz), 5.13 (2H, br).
13C{1H} NMR ([D6]DMSO, 100 MHz) d 163.3, 144.8, 131.7, 127.0, 125.9, 125.8, 115.3, 115.1, 110.1, 109.1. HRMS (ESI) m/z [M+H]+ calcd for C9H10FN2O: 181.0777; found: 181.07772. [0596] EN6. 1-(2-Fluorophenyl)-1H-pyrazole-4-carboxylic acid (57.2 mg, 0.28 mmol) and HATU (127.6 mg, 0.33 mmol) were dissolved in anhydrous DMF (2 mL) and the mixture was stirred at room temperature for 15 min. CC-2-27 (50 mg, 0.28 mmol) in anhydrous DMF (1 mL) was then added, followed by the addition of DIPEA (146 µL, 0.84 mmol). After reaction overnight, the solvent was evaporated under reduced pressure and the crude product was dissolved in ethyl acetate. The organic solution was washed with sat. NaHCO3(aq) solution and sat. NaCl(aq) solution, dried by MgSO4 and filtered. Volatile organic solvent was evaporated under reduced pressure, and the crude product was purified by column chromatography on silica gel using dichloromethane/methanol (24:1, v/v) as eluent, yielding the desired product as an off-white solid (38 mg, 37%). 1H NMR ([D6]DMSO, 400 MHz): d 10.13 (1H, s), 9.98 (1H, s), 8.88 (1H, s), 8.37 (1H, d, J = 6.2 Hz), 8.34 (1H, s), 7.87 (1H, t, J = 7.6 Hz), 7.61-7.68 (1H, m), 7.45-7.57 (2H, m), 7.40 (1H , t, J = 7.6 Hz), 7.26 (1H, t, J = 9.6 Hz), 6.60-6.71 (1H, m), 6.30 (1H, d, J = 17.0 Hz), 5.79 (1H, d, J = 10.1 Hz). 13C{1H} NMR ([D6]DMSO, 100 MHz) d 163.5, 159.9, 154.7, 152.2, 150.9, 148.5, 141.0, 135.2, 135.1, 132.9, 132.9, 131.4, 129.6, 129.5, 127.5, 127.4, 127.3, 125.9, 125.8, 125.5, 125.5, 125.0, 120.4, 117.3, 117.1, 117.0, 116.9, 115.8, 115.4, 115.2. HRMS (ESI) m/z [M+Na+]+ calcd for C19H14F2N4O2Na: 391.0983; found: 391.0977. Table 1: Structures of covalent ligands screened for autophagy activation
[0597]
Figure imgf000202_0001
Figure imgf000203_0001
Figure imgf000204_0001
Figure imgf000205_0001
Figure imgf000206_0001
Figure imgf000206_0002
Figure imgf000207_0001
Figure imgf000208_0001
Figure imgf000209_0001
Figure imgf000210_0001
Figure imgf000211_0001
Figure imgf000212_0001
Figure imgf000213_0001
Figure imgf000214_0001
Figure imgf000215_0001
Figure imgf000216_0001
Figure imgf000217_0001
Figure imgf000218_0001
Figure imgf000219_0001
Figure imgf000220_0001
Figure imgf000221_0003
Example 4: Additional analogs
[0598] Liquid Chromatography-Mass Spectrometry (LCMS) [0599] The following instrumentation and conditions were used for LCMS analysis:
Figure imgf000221_0001
[0600] LCMS condition A:
Figure imgf000221_0002
Figure imgf000222_0001
[0601] NMR spectra were run on Bruker AVANCE 300MHz, 400MHz or 600MHz NMR spectrometers using ICON-NMR, under TopSpin program control. Spectra were measured at 298K, unless indicated otherwise, and were referenced relative to the solvent resonance. [0602] Cell culture. Huh7 cells were cultured and analyzed in phenol red-free DMEM medium, supplemented with 10 vol% FCS, 1x MEM minimum essential amino acids, Penicillin Streptomycin and Glutamine. [0603] Antibodies and reagents for biological experiments. Primary antibodies include rabbit monoclonal anti-human TFE3 (Abcam ab179804). Secondary antibodies include Alexa488-conjugated donkey anti-rabbit (Thermo Fischer A21206). [0604] Synthesis of EN6.
Figure imgf000223_0001
[0605] CC-2-26. K2CO3 (936.6 mg, 6.8 mmol) was added to 2-fluoro-5-nitroaniline (529.4 mg, 3.4 mmol) in dry THF (20 mL). At 0 oC, acryloyl chloride (300 µL, 3.8 mmol) in dry THF (10 mL) was added dropwise to the solution mixture with vigorous stirring. The solution mixture was further stirred at 0 oC for 1 h, and then the reaction was quenched by addition of water. Any organic volatile was removed by evaporation under reduced pressure, and the aqueous layer was extracted with ethyl acetate. The ethyl acetate layer was then washed by saturated NaCl solution, dried by MgSO4 and filtered. Volatile organic solvent was evaporated under reduced pressure, and the crude product was purified by column chromatography on silica gel using hexane/ethyl acetate (4:1, v/v) as eluent, yielding CC-2- 26 as yellow solid (643 mg, 90%). 1H NMR (CDCl3, 400 MHz): d 9.34-9.44 (1H, m), 7.97- 8.04 (1H, m), 7.55 (1H, br), 7.26 (1H, t, J = 9.5 Hz), 6.50-6.56 (1H, m), 6.27-6.35 (1H, m), 5.89-5.92 (1H, m). 13C{1H} NMR ([D6]DMSO, 100 MHz) d 164.1, 143.7, 130.8, 128.7, 127.4, 127.3, 120.5, 120.4, 118.0, 116.8, 116.5. 19F{1H} NMR (CDCl3, 376 MHz) d = 119.0. HRMS (ESI) m/z [M -H] ^ calcd for C9H7FN2O3: 209.0363; found: 209.0371. [0606] CC-2-27. CC-2-26 (343 mg, 1.63 mmol) and ammonium chloride (873 mg, 16.3 mmol) were dissolved in EtOH/H2O mixture (50 mL; v/v = 4:1) with heating. Iron powder (911.5 mg, 16.3 mmol) was then added and the reaction mixture was heated under reflux for 3 h. After complete consumption of CC-2-26 as indicated by TLC, the reaction mixture was cooled to room temperature and any undissolved solid was filtered off. The filtrate was evaporated under reduced pressure, and the aqueous solution was extracted with ethyl acetate three times. The combined organic layer was dried by MgSO4 and filtered. Volatile organic solvent was evaporated under reduced pressure, and the crude product was purified by column chromatography on silica gel using hexane/ethyl acetate (3:2, v/v) as eluent, yielding CC-2-27 as pale yellow solid (211.5 mg, 72%). 1H NMR ([D6]DMSO, 400 MHz): d 9.66 (1H, s), 7.26 (1H, d, J = 5.3 Hz), 6.89 (1H, t, J = 9.4 Hz), 6.60 (1H, dd, J = 5.1 and 17.0 Hz), 6.27-6.33 (1H, m), 6.24 (1H, d, J = 17.0 Hz), 5.73 (1H, d, J = 10.2 Hz), 5.13 (2H, br).
13C{1H} NMR ([D6]DMSO, 100 MHz) d 163.3, 144.8, 131.7, 127.0, 125.9, 125.8, 115.3, 115.1, 110.1, 109.1. HRMS (ESI) m/z [M+H]+ calcd for C9H10FN2O: 181.0777; found: 181.07772. [0607] EN6. 1-(2-Fluorophenyl)-1H-pyrazole-4-carboxylic acid (57.2 mg, 0.28 mmol) and HATU (127.6 mg, 0.33 mmol) were dissolved in anhydrous DMF (2 mL) and the mixture was stirred at room temperature for 15 min. CC-2-27 (50 mg, 0.28 mmol) in anhydrous DMF (1 mL) was then added, followed by the addition of DIPEA (146 µL, 0.84 mmol). After reaction overnight, the solvent was evaporated under reduced pressure and the crude product was dissolved in ethyl acetate. The organic solution was washed with sat. NaHCO3(aq) solution and sat. NaCl(aq) solution, dried by MgSO4 and filtered. Volatile organic solvent was evaporated under reduced pressure, and the crude product was purified by column chromatography on silica gel using dichloromethane/methanol (24:1, v/v) as eluent, yielding the desired product as an off-white solid (38 mg, 37%). 1H NMR ([D6]DMSO, 400 MHz): d 10.13 (1H, s), 9.98 (1H, s), 8.88 (1H, s), 8.37 (1H, d, J = 6.2 Hz), 8.34 (1H, s), 7.87 (1H, t, J = 7.6 Hz), 7.61-7.68 (1H, m), 7.45-7.57 (2H, m), 7.40 (1H , t, J = 7.6 Hz), 7.26 (1H, t, J = 9.6 Hz), 6.60-6.71 (1H, m), 6.30 (1H, d, J = 17.0 Hz), 5.79 (1H, d, J = 10.1 Hz). 13C{1H} NMR ([D6]DMSO, 100 MHz) d 163.5, 159.9, 154.7, 152.2, 150.9, 148.5, 141.0, 135.2, 135.1, 132.9, 132.9, 131.4, 129.6, 129.5, 127.5, 127.4, 127.3, 125.9, 125.8, 125.5, 125.5, 125.0, 120.4, 117.3, 117.1, 117.0, 116.9, 115.8, 115.4, 115.2. HRMS (ESI) m/z [M+Na+]+ calcd for C19H14F2N4O2Na: 391.0983; found: 391.0977. [0608]
Figure imgf000224_0001
[0609] N-(3-acrylamido-4-fluorophenyl)-3-bromo-1-phenyl-1H-pyrazole-4-carboxamide (1-1). [0610] Step 1: 3-bromo-1-phenyl-1H-pyrazole-4-carboxylic acid. To a solution of ethyl 3- bromo-1-phenyl-1H-pyrazole-4-carboxylate (prepared as described in WO2017/7756, 2017, A1) (10.0 g, 33.9 mmol) in a 160 mL mixture of MeOH and THF (1:1) was added the solution of sodium hydroxide (6.78 g, 169.4 mmol) in 40 mL of water and the reaction mixture was stirred at rt for 16 h. The reaction was monitored by TLC. After completion of the reaction, the reaction solution was concentrated under reduced pressure, the residue was diluted with water, extracted with Et2O. The aqueous layer was collected, acidified with 4N HCl and extracted with EtOAc. The combined EtOAc layer was washed with brine, anhydrous sodium sulfate, and the solvent was evaporated under reduced pressure to afford a white residue. The residue was triturated with 5% CHCl3- hexane to get the product as white solid (8.2 g, 91%). [0611] Step 2: N-(3-acrylamido-4-fluorophenyl)-3-bromo-1-phenyl-1H-pyrazole-4- carboxamide (1-2). To a stirred solution of 3-bromo-1-phenyl-1H-pyrazole-4-carboxylic acid (0.15 g, 0.561 mmol) in 5.0 mL DMF was added CC-2-27 (0.165 mg, 0.561 mmol) and DIPEA (0.4 mL, 2.25 mmol). The reaction was stirred at rt for 15 min. Next, HATU (0.32 g, 0.842 mmol) and reaction mixture was stirred at rt for 16 h. The reaction was monitored by TLC. The reaction was concentrated under reduced pressure added NaHCO3 solution and extracted with EtOAc. The organic layer was washed with brine solution, dried over Na2SO4, filtered, concentrated and purified by combi-flash column chromatography eluting with 20- 30% EtOAc in DCM to afford the desired product as a light brown solid. The material further purified by preparative HPLC to afford a white solid, (28 mg, 26%). 1H NMR
(CDCl3, 600 MHz): d 8.38 (1H, s), 8.24 (1H, s), 8.01 (1H, s), 7.88 (1H, d), 7.56-7.47 (7H, m), 7.13-7.12 (2H, m), 6.49-6.46 (1H, d), 6.31-6.27 (1H, m). [0612]
Figure imgf000225_0001
[0613] N-(3-acrylamido-4-fluorophenyl)-1-(p-tolyl)-5-(trifluoromethyl)-1H-pyrazole-4- carboxamide (1-2). CC-2-27 (60.0 mg, 0.204 mmol), 1-(p-tolyl)-5-(trifluoromethyl)-1H- pyrazole-4-carboxylic acid (66.1 mg, 0.245 mmol), DIPEA (89 µl, 0.510 mmol) and 2.0 mL DMF were combined and stirred at rt for 10 min. HATU (116 mg, 0.306 mmol) was added and stirred at rt for 16 h. Reaction mixture was filtered and purified by preperative HPLC. Desired fractions were concentrated and lyopholized to afford a white solid (12 mg, 13%). LCMS Rt = 2.30 min (Condition A), MS (M+H) = 433.0. 1H NMR (400 MHz, DMSO-d6): d 10.60 (s, 1H), 9.98 (s, 1H), 8.39 (dd, J = 7.2, 2.6 Hz, 1H), 8.29 (s, 1H), 7.54 (ddd, J = 8.9, 4.4, 2.7 Hz, 1H), 7.41 (s, 5H), 7.28 (dd, J = 10.7, 8.9 Hz, 1H), 6.64 (dd, J = 17.0, 10.2 Hz, 1H), 6.30 (dd, J = 17.0, 2.0 Hz, 1H), 5.80 (dd, J = 10.2, 2.0 Hz, 1H), 2.43 (s, 3H). HRMS (ESI) m/z [M+H]+ calcd for C19H17F4N4O2: 433.1288; found: 433.1323. [0614]
Figure imgf000226_0001
[0615] N-(3-acrylamido-4-fluorophenyl)-1-phenyl-5-(trifluoromethyl)-1H-pyrazole-4- carboxamide (1-3). CC-2-27 (60.0 mg, 0.204 mmol), 1-phenyl-5-(trifluoromethyl)-1H- pyrazole-4-carboxylic acid (62.7 mg, 0.245 mmol), DIPEA (89 µl, 0.510 mmol) were combined in 2.5 mL DMF and stirred for 10 min. HATU (116 mg, 0.306 mmol) was added and stirred at rt for 16 h. The reaction mixture was filtered and purified by preperative HPLC to afford a white solid (14 mg, 16%). LCMS Rt = 2.18 min (Condition A), MS (M+H) = 417.3. 1H NMR (400 MHz, DMSO-d6): d 10.61 (s, 1H), 9.99 (s, 1H), 8.40 (dd, J = 7.5, 2.6 Hz, 1H), 8.32 (s, 1H), 7.66-7.59 (m, 3H), 7.55 (dd, J = 6.8, 3.2 Hz, 3H), 7.28 (dd, J = 10.7, 8.9 Hz, 1H), 6.64 (dd, J = 17.0, 10.2 Hz, 1H), 6.30 (dd, J = 17.0, 2.0 Hz, 1H), 5.80 (dd, J = 10.2, 2.0 Hz, 1H). HRMS (ESI) m/z [M+H]+ calcd for C20H15F4N4O2: 419.3532; found: 419.1156. [0616]
Figure imgf000226_0002
[0617] N-(3-acrylamido-4-fluorophenyl)-1-(4-hydroxyphenyl)-5-(trifluoromethyl)-1H- pyrazole-4-carboxamide (1-4). [0618] Step 1: 1-(4-hydroxyphenyl)-5-(trifluoromethyl)-1H-pyrazole-4-carboxylic acid. Ethyl 1-(4-methoxyphenyl)-5-(trifluoromethyl)-1H-pyrazole-4-carboxylate (prepared as described in: Gentile, D.; Rathinaswamy, M.; Jenkins, M.; Moss, S.; Siempelkamp, B.; Renslo, A.; Burke, J.; Shokat, K. Cell Chem. Bio.2017, 24, 1455-1466) (113 g, 359 mmol, 1 eq) in pyridine hydrochloride (291 g, 2.52 mol, 7 eq) was stirred at 180 °C for 8 h. LCMS showed desired MS was observed as major peak. The reaction mixture was cooled down, quenched with water 1000 mL, the solid was collected by filter and the solid was dissolved in 10% MeOH/EtOAc (2000 mL) and passed through a short silica gel column, the column was washed with EtOAc (1000 mL). The filtrate was concentrated and the residue was triturated with EtOAc (200 mL) to give c 1-(4-hydroxyphenyl)-5-(trifluoromethyl)-1H-pyrazole-4- carboxylic acid (65.0 g, 65%) as a gray solid. [0619] Step 2: CC-2-27 (60.0 mg, 0.204 mmol), 1-(4-hydroxyphenyl)-5-(trifluoromethyl)- 1H-pyrazole-4-carboxylic acid (66.6 mg, 0.245 mmol), DIPEA (89 µl, 0.510 mmol) and 1.0 mL DMF were combined and stirred at rt for 10 min. HATU (116 mg, 0.306 mmol) was added and stirred at rt for 16 h. Reaction mixture was filtered and purified by preperative HPLC to afford a white solid (4.5 mg, 5%). LCMS Rt = 1.77 min (Condition A), MS (M+H) = 435.1. 1H NMR (400 MHz, DMSO-d6): d 10.57 (s, 1H), 10.10 (s, 1H), 9.98 (s, 1H), 8.38 (d, J = 7.3 Hz, 1H), 8.24 (s, 1H), 7.60-7.45 (m, 1H), 7.31 (dd, J = 7.6, 5.5 Hz, 2H), 7.28-7.23 (m, 1H), 6.96-6.89 (m, 2H), 6.63 (dd, J = 17.0, 10.1 Hz, 1H), 6.30 (dd, J = 17.0, 2.0 Hz, 1H), 5.80 (dd, J = 10.2, 2.0 Hz, 1H). HRMS (ESI) m/z [M+H]+ calcd for C20H15F4N4O3:
435.3526; found: 435.1093. [0620] The following compounds were prepared in a similar procedure as EN-6.
Figure imgf000227_0001
Figure imgf000228_0001
[0621] Synthesis of N-(4-fluoro-3-(N-methylacrylamido)phenyl)-1-(2-fluorophenyl)- 1Hpyrazole-4-carboxamide (1-11).
Figure imgf000229_0001
[0622] N-(4-fluoro-3-(N-methylacrylamido)phenyl)-1-(2-fluorophenyl)-1Hpyrazole-4- carboxamide (1-11). [0623] Step 1: 2-fluoro-N-methyl-5-nitroaniline. To a stirred solution of 2-fluoro-5- nitroaniline (1.0 g, 6.41 mmol) in MeOH (20 mL), paraformaldahyde (0.769 g, 25.62 mmol) dissolved in MeOH (20 mL) was added slowly, the reaction was stirred at rt, then NaOMe (0.173 g, 3.02 mmol) in MeOH (10 mL) was added dropwise and the reaction was stirred at rt for 16 h. Completion of the reaction was monitored by TLC. After completion of reaction, the mixture was poured into 1M KOH aqueous solution and stirred to precipitate a yellow solid, the precipitate was filtered. Crude precipitate was purified by combi-flash column chromatography using EtOAc in Hexane. Product eluted 18% EtOAc in Hexane and 2- fluoro-N-methyl-5-nitroaniline was isolated as yellow solid (0.80 g, 73%). [0624] Step 2: N-(2-fluoro-5-nitrophenyl)-N-methylacrylamide. To a stirred solution of 2- fluoro-N-methyl-5-nitroaniline (0.60 g, 3.53 mmol) in THF (10 mL), DIPEA (1.3 mL, 7.05 mmol) was added then the reaction was stirred at rt for 10 min, then cooled to 0 °C, acryloyl chloride (0.317 g, 3.53 mmol) in THF (5 mL) added dropwise to the reaction mixture, then the reaction mixutre was stirred at rt for 2 h. The reaction was monitored by TLC and after completion the reaction was quenched with water, extracted using EtOAc, then washed with brine solution, dried over Na2SO4 and concentrated. The residue product was purified by combi-flash column chromatography using EtOAc in Hexane. N-(2-fluoro-5-nitrophenyl)-N- methylacrylamide eluted 15% EtOAc in Hexane as a yellow oil (0.60 g, 75%). [0625] Step 3: N-(5-amino-2-fluorophenyl)-N-methylacrylamide. To a stirred solution of N-(2-fluoro-5-nitrophenyl)-N-methylacrylamide (0.60 g, 2.68 mmol) in 10 mL of THF at 0 °C, was added NH4Cl (1.14 g, 21.5 mmol) dissolved in 3.0 mL MeOH and 1.0 mL H2O and stirred the reaction for 10 min. Followed by addition of zinc dust (1.4 g, 21.5 mmol) was added to the reaction and it was stirred for 3 h at rt. The reaction was monitored by TLC and upon completion the reaction mixture was filtered through pad of cellite and washed with ethyl acetate. The aqueous layer was extracted with ethyl acetate. The combined organic layers were washed with water, washed with brine solution, and then dried over anhydrous sodium sulphate, filtered and concentrated to afford product as yellow solid (0.45 g, 86%). [0626] Step 4: N-(4-fluoro-3-(N-methylacrylamido)phenyl)-1-(2-fluorophenyl)-1H- pyrazole-4-carboxamide (1-11). To a solution of N-(5-amino-2-fluorophenyl)-N- methylacrylamide (0.10 g, 0.514 mmol) in 3.0 mL DMF, was added 1-(2-fluorophenyl)-1H- pyrazole-4-carboxylic acid (0.106 g, 0.514 mmol) followed by DIPEA (0.9 mL, 2.57 mmol). Then reaction was stirred for 10 min and HATU (0.293 g, 0.771 mmol) was added. The reaction mixture was stirred at rt for 16 h. Completion of the reaction monitored by TLC. The reaction mixture was diluted with water and a solid was formed, and it was filtered and dried. Crude product was purified by combi-flash column chromatography using EtOAc in Hexane; compound eluted 30% EtOAc in Hexane. N-(4-fluoro-3-(N- methylacrylamido)phenyl)-1-(2-fluorophenyl)-1H-pyrazole-4-carboxamide (1-13) was isolated as pale pink solid (0.08 g, 40%) 1H NMR (DMSO-d6 , 300 MHz): d 10.22 (1H, s), 8.861 (1H, d), 8.33 (1H, s), 7.87 (1H, t), 7.79–7.77 (2H,. d), 7.51 (2H, m), 7.43–7.40 (2H, d), 6.199–6.19 (1H, d), 6.15 (1H, m), 5.65 (1H, d), 3.22 (1H, t). [0627] Synthesis of N-(3-acrylamido-4-fluorophenyl)-1-(2-fluorophenyl)-N-methyl-1H- pyrazole-4-carboxamide (1-12).
Figure imgf000230_0001
[0628] N-(3-acrylamido-4-fluorophenyl)-1-(2-fluorophenyl)-N-methyl-1H-pyrazole-4- carboxamide (1-12). [0629] Step 1: 4-fluoro-N-methyl-3-nitroaniline. To a stirred solution of 4-fluoro-3- nitroaniline (1.0 g, 6.41 mmol) in MeOH (20 mL), was slowly added paraformaldehyde (0.769 g, 25.6 mmol) dissolved in MeOH (20 mL). Upon completion of the addition, the reaction mixture was stirred at rt, while NaOMe (0.173 g, 3.02 mmol) in MeOH (10 mL) was slowly added dropwise. Upon completion of the addition, the reaction mixture was stirred at rt for 16 h. Completion of the reaction was monitored by TLC. After completion of reaction, the reaction mixture was poured into 1M KOH aqueous solution and stirred to precipitate a yellow solid. The precipitate was filtered and was dried. The precipitate was purified by combi-flash column chromatography using EtOAc in Hexane. Product eluted with 22% EtOAc in Hexane and was isolated as yellow solid (0.6 g, 55%). [0630] Step 2: N-(4-fluoro-3-nitrophenyl)-1-(2-fluorophenyl)-N-methyl-1H-pyrazole-4- carboxamide. To a stirred solution of 1-(2-fluorophenyl)-1H-pyrazole-4-carboxylic acid (0.20 g, 0.97 mmol) in 5.0 mL dichloromethane, thionyl chloride (0.1 mL) was added slowly at 0 °C, then catalytic amount DMF (5 drops) was added and stirred for 1 h. Then reaction mixture was concentrated under N2 atmosphere, then crude was dissolved in THF (5 mL), cooled to 0 °C, then DIPEA (0.35 mL, 1.94 mmol) was added to the reaction at 0 °C, followed by 4-fluoro-N-methyl-3-nitroaniline (0.165 g, 0.97 mmmol) dissolved in THF (5 mL). The reaction was stirred for 3 h at rt and was monitored by TLC. Upon completion, the reaction was quenched with water and extracted using EtOAc (3x). The organic layer was washed with water, washed with brine solution, and dried over anhydrous Na2SO4, filtered and concentrated to afford a yellow solid. The solid residue was purified by combi-flash column on eluting with 20% EtOAc in Hexane as eluent to isolate the product as a yellow solid (0.16 g, 46%). [0631] Step 3: N-(3-amino-4-fluorophenyl)-1-(2-fluorophenyl)-N-methyl-1H-pyrazole-4- carboxamide. To the stirred solution of N-(4-fluoro-3-nitrophenyl)-1-(2-fluorophenyl)-N- methyl-1H-pyrazole-4-carboxamide (0.16 g, 0.446 mmol) in THF:MeOH (7 mL : 3 mL) at 0 °C, was added ammonium chloride (0.191 g, 3.57 mmol) dissolved in 2.0 mL water and stirred the reaction for 10 min. Zinc dust (0.233 g, 3.57 mmol) was added to the resulting reaction mixture and it was stirred for 3 h at rt. The reaction was monitored by TLC. Upon completion of the reaction, the mixture was filtered through pad of cellite and washed with EtOAc. The combined washes were washed with water, washed with brine solution, and dried over anhydrous sodium sulphate, filtered and concentrated to obtain product as yellow solid (0.12 g, 92%). [0632] Step 4: N-(3-acrylamido-4-fluorophenyl)-1-(2-fluorophenyl)-N-methyl-1H-pyrazole- 4-carboxamide (1-12). To a solution of N-(3-amino-4-fluorophenyl)-1-(2-fluorophenyl)-N- methyl-1H-pyrazole-4-carboxamide (0.12 g, 0.365 mmol) in methylene chloride (9 mL) was added triethylamine (0.15 mL, 1.1 mmol). To the reaction mixture was added acryloyl chloride (0.033 g, 0.365 mmol) in methylene chloride (1 mL) at rt. The reaction mixture was stirred at rt for 2 h. The reaction was monitored by TLC and upon completion, the reaction mixture was concentrated. The residue was redissolved in EtOAc and washed with water and brine solution. The EtOAc layer was concentrated and the residue was purified by combi- flash column on eluting with 20% EtOAc in Hexane as eluent to afford N-(3-acrylamido-4- fluorophenyl)-1-(2-fluorophenyl)-N-methyl-1H-pyrazole-4-carboxamide as an off-white solid (0.10 g, 71%). 1H NMR (CDCl3, 300 MHz): d 8.50 (1H, dd), 7.78–7.77 (2H, t), 7.52 (1H, s), 7.27–7.23 (1H, m), 7.22–7.12 (1H, m), 6.96–6.95 (1H, m), 6.49–6.43 (1H, d), 6.32–6.23 (1H, m), 5.86–5.82 (1H, d), 3.43 (1H, s). [0633] Activity of Compounds [0634] TFE3 assay. For the TFE3 nuclear translocation assay, 3000 Huh7 cells were seeded in a volume of 50 µl medium into wells of black clear bottom 384-well plates
(Greiner). One day post plating, cells were treated for 4 h with a compound dose response, ranging from 80 to 0.63 µM. Compounds were added with the Echo instrument (LabCyte) using acoustic compound transfer. After 4 h, cells were fixed for 10 min at room temperature in 4% paraformaldehyde, washed 3 times with PBS, permeabilized by incubating four times 5 min in PBS containing 0.1% Triton X-100, and blocked for 1 h in blocking buffer (PBS containing 0.1% Triton X-100 and 2% BSA). TFE3 was stained overnight at 4 °C with rabbit monoclonal anti-human TFE3 antibody (Abcam ab179804) diluted 1:400 in blocking buffer. Cells were then washed 3 times with PBS and incubated in blocking buffer containing Alexa 488-conjugated donkey anti-rabbit secondary antibody (Thermo Fischer A21206, 1:2000) and Hoechst dye (Thermo Fisher H3570, 1:5000). After 3 washing steps in PBS, plates were imaged with an automated IN Cell Analyzer 2000 (GE Healthcare). Hoechst and Alexa488 fluorescence images were captured in 4 fields per well using a 20x objective. Image analysis was performed using CellProfiler (reference: PMID 17076895). Nuclei were first detected in the Hoechst image using Adaptative Otsu thresholding. The cell area was then defined by extending 10 pixels around the nuclear area. The cytoplasmic area was defined as cell area excluding the nuclear area. The mean intensity of the TFE3 staining in the nuclear versus cytoplasmic area was determined in the Alexa488 image and represented as ratio relative to DMSO-treated control cells.
[0635] Table 2. The measured TFE3 translocation activity.
Figure imgf000233_0001
[0636] Table 3. Compounds from TFE3 Translocation assay.
Figure imgf000233_0002
Figure imgf000234_0001
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Claims

WHAT IS CLAIMED IS: 1. A compound, or a pharmaceutically acceptable salt thereof, having the formula:
Figure imgf000238_0001
wherein
Ring A is a phenyl or 5 to 6 membered heteroaryl;
Ring B is a phenyl or 5 to 6 membered heteroaryl;
L1 is independently a bond, -S(O)2-, -N(R5)-, -O-, -S-, -C(O)-, -C(O)N(R5)-, -N(R5)C(O)-, -N(R5)C(O)NH-, -NHC(O)N(R5)-, -C(O)O-, -OC(O)-, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene;
R5 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl;
R1 is independently halogen, -CX1 3, -CHX1 2, -CH2X1, -OCX1 3, -OCH2X1, -OCHX1 2, -CN, -SOn1R1D, -SOv1NR1AR1B, -NHC(O)NR1AR1B, -N(O)m1, -NR1AR1B, -C(O)R1C, -C(O)-OR1C, -C(O)NR1AR1B, -OR1D, -NR1ASO2R1D, -NR1AC(O)R1C, -NR1AC(O)OR1C, -NR1AOR1C, -N3, E, substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent -L1-R1 substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; E is an electrophilic moiety;
R2 is independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NHC(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl;
R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent R4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R1A, R1B, R1C, and R1D are independently hydrogen, halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2,
-NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
X1 is independently–F, -Cl, -Br, or–I;
n1 is independently an integer from 0 to 4;
m1 and v1 are independently 1 or 2;
z1 is independently an integer from 0 to 5;
z3 is independently an integer from 0 to 2; and
z4 is independently an integer from 0 to 5.
2. The compound of claim 1, having the formula:
Figure imgf000240_0001
wherein
L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene;
R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent R1 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
E is an electrophilic moiety;
R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent R4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
z1 is independently an integer from 0 to 4; and
z4 is independently an integer from 0 to 5.
3. The compound of claim 1, having the formula:
Figure imgf000241_0001
wherein
L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene;
R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
E is an electrophilic moiety; and
R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
4. The compound of claim 1, having the formula:
Figure imgf000242_0001
wherein
L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene;
R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
E is an electrophilic moiety;
R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; two adjacent R4 substituents may optionally be joined to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
z1 is independently an integer from 0 to 4; and
z4 is independently an integer from 0 to 5.
5. The compound of claim 4, wherein E is
Figure imgf000243_0001
.
6. The compound of claim 1, having the formula:
Figure imgf000243_0002
wherein
L1 is independently a bond, -S(O)2-, -NH-, -O-, -S-, -C(O)NH-, -NHC(O)-, -NHC(O)NH-, substituted or unsubstituted heteroalkylene, substituted or unsubstituted heterocycloalkylene, or substituted or unsubstituted heteroarylene;
R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
E is an electrophilic moiety;
R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and
R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NHNH2, -ONH2, -NH C(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
7. The compound of claim 6, wherein E is
Figure imgf000244_0001
8. The compound of claim 1, wherein R3 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl.
9. The compound of claim 1, wherein R3 is independently halogen, -CCl3, -CBr3, -CF3, or -CI3.
10. The compound of claim 1, wherein R3 is independently–Br or -CF3.
11. The compound of claim 1, wherein R1 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, -N3, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl.
12. The compound of claim 1, wherein R1 is independently halogen.
13. The compound of claim 1, wherein R1 is independently -F.
14. The compound of claim 1, wherein R4 is independently halogen, -CCl3, -CBr3, -CF3, -CI3, -CH2Cl, -CH2Br, -CH2F, -CH2I, -CHCl2, -CHBr2, -CHF2, -CHI2, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, -SO4H, -SO2NH2, -NH NH2, -ONH2, -NHC(O)NHNH2, -NH C(O)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -OCCl3, -OCBr3, -OCF3, -OCI3, -OCH2Cl, -OCH2Br, -OCH2F, -OCH2I, -OCHCl2, -OCHBr2, -OCHF2, -OCHI2, substituted or unsubstituted C1-C4 alkyl, or substituted or unsubstituted 2 to 4 membered heteroalkyl.
15. The compound of claim 1, wherein R4 is independently halogen.
16. The compound of claim 1, wherein R4 is independently -F.
17. The compound of claim 1, wherein L1 is independently -S(O)2-, -NH-, or substituted or unsubstituted 5 to 6 membered heterocycloalkylene.
18. The compound of claim 1, wherein L1 is independently -S(O)2-, -NH-, unsubstituted pyrrolidinylene, unsubstituted piperidinylene, or unsubstituted piperazinylene.
19. The compound of claim 1, wherein L1 is independently -NH-.
20. The compound of claim 1, wherein E is
Figure imgf000246_0001
Figure imgf000246_0002
, or
Figure imgf000246_0003
wherein R16 is independently hydrogen, halogen, -CX163, -CHX162, -CH2X16, -CN, -SOn16R16A, -SOv16NR16AR16B, -NHNR16AR16B, -ONR16AR16B, -NHC(O)NHNR16AR16B, -NHC(O)NR16AR16B, -N(O)m16, -NR16AR16B, -C(O)R16A, -C(O)-OR16A, -C(O)NR16AR16B, -OR16A, -NR16ASO2R16B, -NR16AC(O)R16B, -NR16AC(O)OR16B, -NR16AOR16B, -OCX16 3, -OCHX16 2, -OCH2X16, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl;
R17 is independently hydrogen, halogen, -CX17 3, -CHX17 2, -CH2X17, -CN, -SOn17R17A, -SOv17NR17AR17B, -NHNR17AR17B, -ONR17AR17B, -NH C(O)NHNR17AR17B, -NHC(O)NR17AR17B, -N(O)m17, -NR17AR17B, -C(O)R17A, -C(O)-OR17A, -C(O)NR17AR17B, -OR17A, -NR17ASO2R17B, -NR17AC(O)R17B, -NR17AC(O)OR17B, -NR17AOR17B, -OCX17 3, -OCHX17 2, -OCH2X17, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl;
R18 is independently hydrogen, halogen, -CX18 3, -CHX18 2, -CH2X18, -CN, -SOn18R18A, -SOv18NR18AR18B, -NHNR18AR18B, -ONR18AR18B, -NH C(O)NHNR18AR18B, -NHC(O)NR18AR18B, -N(O)m18, -NR18AR18B, -C(O)R18A, -C(O)-OR18A, -C(O)NR18AR18B, -OR18A, -NR18ASO2R18B, -NR18AC(O)R18B, -NR18AC(O)OR18B, -NR18AOR18B, -OCX18 3, -OCHX18 2, -OCH2X18, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl;
R19 is independently hydrogen, halogen, -CX193, -CHX192, -CH2X19, -CN, -SOn19R19A, -SOv19NR19AR19B, -NHNR19AR19B, -ONR19AR19B, -NH C(O)NHNR19AR19B, -NHC(O)NR19AR19B, -N(O)m19, -NR19AR19B, -C(O)R19A, -C(O)-OR19A, -C(O)NR19AR19B, -OR19A, -NR19ASO2R19B, -NR19AC(O)R19B, -NR19AC(O)OR19B, -NR19AOR19B, -OCX19 3, -OCHX192, -OCH2X19, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl;
R16A, R16B, R17A, R17B, R18A, R18B, R19A, and R19B are independently hydrogen, -CX3, -CHX2, -CH2X, -CN, -OH, -COOH, -CONH2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; R16A and R16B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R17A and R17B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R18A and R18B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl; R19A and R19B substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;
each X1, X16, X17, X18, and X19 is independently–F, -Cl, -Br, or–I;
n16, n17, n18, and n19 are independently an integer from 0 to 4; and m16, m17, m18, m19, v16, v17, v18, and v19 are independently 1 or 2.
21. The compound of claim 1, wherein E is
Figure imgf000247_0001
, ,
or
Figure imgf000247_0004
Figure imgf000247_0005
22. The compound of claim 1, wherein E is
Figure imgf000247_0002
.
23. The compound of claim 1, wherein the compound is not
Figure imgf000247_0003
.
24. A pharmaceutical composition comprising a compound of one of claims 1 to 23, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
25. A method for treating cancer in a subject in need thereof, said method comprising administering to the subject in need thereof a therapeutically effective amount of a compound of one of claims 1 to 23, or a pharmaceutically acceptable salt thereof.
26. The method of claim 25, wherein said cancer is renal cell carcinoma, follicular lymphoma, glioblastoma, colorectal cancer, endometrial cancer, or lung cancer.
27. A method of reducing the level of activity of mTORC1 in a subject in need thereof, the method comprising administering to the subject in need thereof an effective amount of a compound of one of claims 1 to 23, or a pharmaceutically acceptable salt thereof.
28. A method of reducing the level of activity of mTORC1 in a cell, the method comprising contacting a Vacuolar H+-ATPase protein complex in said cell with a compound of one of claims 1 to 23, or a pharmaceutically acceptable salt thereof.
29. A method of reducing the level of activity of mTORC1 in a cell, the method comprising contacting an ATP6V1A in said cell with a compound of one of claims 1 to 23, or a pharmaceutically acceptable salt thereof.
30. A method of reducing the level of activity of a Vacuolar H+-ATPase protein complex, the method comprising contacting an ATP6V1A in the Vacuolar H+- ATPase protein complex with a compound of one of claims 1 to 23, or a pharmaceutically acceptable salt thereof.
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