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WO2011094628A1 - Compositions and methods for treating toxoplasmosis. cryptosporidiosis and other apicomplexan protozoan related diseases - Google Patents

Compositions and methods for treating toxoplasmosis. cryptosporidiosis and other apicomplexan protozoan related diseases Download PDF

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Publication number
WO2011094628A1
WO2011094628A1 PCT/US2011/023047 US2011023047W WO2011094628A1 WO 2011094628 A1 WO2011094628 A1 WO 2011094628A1 US 2011023047 W US2011023047 W US 2011023047W WO 2011094628 A1 WO2011094628 A1 WO 2011094628A1
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alkyl
groups
optionally substituted
compound
haloalkyl
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PCT/US2011/023047
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French (fr)
Inventor
Wesley C. Van Voorhis
Wilhelmus G.J. Hol
Eric T. Larson
Dustin James Maly
Ethan Merritt
Kayode K. Ojo
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University Of Washington
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Priority to EP11705328.0A priority Critical patent/EP2528919B1/en
Publication of WO2011094628A1 publication Critical patent/WO2011094628A1/en
Priority to US13/561,896 priority patent/US9765037B2/en
Priority to US15/686,839 priority patent/US10544104B2/en
Priority to US16/740,095 priority patent/US11247972B2/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04—Ortho-condensed systems
    • 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
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/4985—Pyrazines or piperazines ortho- or peri-condensed with heterocyclic ring systems
    • 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
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P33/00—Antiparasitic agents
    • A61P33/02—Antiprotozoals, e.g. for leishmaniasis, trichomoniasis, toxoplasmosis
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the present disclosure is generally directed to compositions and methods for treating apicomplexan protozoan related disease, such as toxoplasmosis and cryptosporidiosis.
  • C. parvum and C. hominus are infectious parasites of major health concern in humans as they are a common cause of illness transmitted by water.
  • C. parvum and C. hominus infections result in debilitating diarrhea that can be life-threatening in immunocompromised patients.
  • gondii may be the most common infectious eukaryotic parasite in humans, based on serosurveys. (See Montoya et al., Chapter 276: Toxoplasma gondii in Mandell, Bennett, & Dolin: Principles and Practice of Infectious Diseases, 6th ed. Publ: Churchill Livingston (2005)) Transmitted primarily through undercooked meat or accidental ingestion of cat feces, T. gondii infection presents major health concerns in immunocompromised hosts, where it causes toxoplasmic encephalitis, and in pregnancy, where it can result in severe birth defects or miscarriage. Sulfadiazine and pyrimethamine are the current therapies for toxoplasmosis, but they can cause nephrotoxicity, rash, and additional complications in pregnancy. Thus, new therapies for treating infections caused by both parasites are greatly needed.
  • T. gondii calcium-regulated signaling is associated with a number of cellular functions such as secretion, gliding motility and host cell invasion.
  • cellular functions such as secretion, gliding motility and host cell invasion.
  • Calcium-dependent signaling and kinases in apicomplexan parasites The proper control of intracellular calcium levels is important for host cell invasion and T. gondii use several mechanisms for the uptake and release of calcium.
  • this organism contains specialized calcium-regulated signaling enzymes, including a unique family of calcium-dependent protein kinases (CDPKs) which are present in plants, ciliates and green algae but not in animals.
  • CDPKs calcium-dependent protein kinases
  • kinases as targets for antimalarial intervention: kinomics, structure-based design, transmission-blockade, and targeting host cell enzymes. Biophysica et Biochimica Acta - Proteins and Proteomics 1754, 132-150 (2005)
  • These kinases are believed to be mediators of secretion, invasion, and gliding motility.
  • T. gondii, C. parvum, and C. hominus are highly related obligate intracellular parasites. While much less is known about the role of calcium signaling in C. parvum and C. hominus, it appears that many calcium-regulated signaling processes are conserved from T. gondii to C. parvum. (See Chen et al., Apical Organelle discharge by Cryptosporidium parvum is temperature, cytoskeleton, and intracellular calcium dependent and required for host cell invasion. Infect. Immun. 72, 6806-16 (2004)) C. parvum and C. hominus also possess CDP s that are believed to play important roles in calcium-regulated processes and they are virtually identical in these two spp. Thus inhibitors of C. parvum CDPKs would be expected to inhibit C. hominus CDPK.
  • CDPKs The roles that CDPKs play in calcium signaling in T. gondii, C. parvum and C. hominus make this family of kinases intriguing targets for the development of anti-parasitic agents.
  • the present disclosure is generally directed to compositions and methods for the treatment of apicomplexan-related disorders, including but not limited to toxoplasmosis, caused by the infectious eukaryotic parasite Toxoplasma gondii (T. gondii,) and cryptosporidiosis, caused by the infectious eukaryotic parasites Cryptosporidium parvum (C. parvum) and Cryptosporidium hominus (C. hominus).
  • the present disclosure is directed to compositions and methods for inhibiting apicomplexan calcium dependent protein kinases, including but not limited to T. gondii calcium dependent protein kinases ( gCDPKs) or C. parvum and C.
  • hominus calcium dependent protein kinases Q?CDPKs
  • Imidazo[l,5- a]pyrazine inhibitors both classes of compounds designed to be inactive against mammalian kinases.
  • the present disclosure rovides compounds of the formula (I),
  • R 1 , R 3 , X, Y, and Z are defined herein.
  • the present disclosure provides methods for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either (i) a bumped kinase inhibitor or (ii) a pharmaceutical composition comprising a bumped kinase inhibitor and a pharmaceutically acceptable excipient, carrier, or diluent.
  • the present disclosure provides methods for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either (i) a bumped kinase inhibitor or (ii) a pharmaceutical composition comprising a bumped kinase inhibitor and a pharmaceutically acceptable excipient, carrier, or diluent.
  • the present disclosure provides methods for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either a compound of formula (II) or (ii) a pharmaceutical composition comprising a compound of formula (II) and a pharmaceutically acce table exci ient carrier or diluent wherein the compound of formula (II) is
  • Figure 1 is a graphical representation of calcium-dependence of JgCDPKl activity. Enzyme activity was measured at a constant concentration of 0.5 mM EGTA with increasing concentrations of CaCl 2 using the luciferase based assay format. The precise quantity of free Ca 2+ was determined by measuring fluorescence intensity of Fluo-3 and Calcium green dyes (Invitrogen Corp. Carlsbad, USA) in the reaction buffer at excitation and emission wave lengths of 506 and 526 nM (Fluo-3) and 503 and 532 nM (Calcium green).
  • Figure 2 is a graphical representation of the crystal structure of calcium-free gCDPKl.
  • Animal CDPKs tend to have large gatekeeper residues such as phenylalanine,
  • (c and d) Stereo view of the active site with the bumped kinase inhibitors NA-PP2 (c) and NM-PP1 (d) bound. The orientation is as in panel la. Residues within 6 A of the inhibitor are shown as sticks. The unusual glycine gatekeeper residue that permits inhibition by bumped kinase inhibitors is highlighted in cyan. Difference electron density, contoured at +3.5 ⁇ (green mesh) and -3.5 ⁇ (pink mesh), was calculated after omission of the inhibitor, (e) TgCDPKl active site in the vicinity of the gatekeeper residue.
  • gCDPKl The surface of gCDPKl is shown in white and is slabbed through to show the adenine pocket of the ATPbinding site.
  • the glycine at the gatekeeper position of gCDPKl enlarges the active site pocket and facilitates binding of bumped kinase inhibitors (NA-PP2 is magenta sticks and NM-PP1 is violet sticks).
  • Larger amino acids, such as Met shown here (brown sticks and protruding surface) from superposition of a C. parvum ortholog (PDB ID 3hko; bound AMP-PNP shown as brown sticks) are more typical at this gatekeeper position, and prevent binding of compounds with large, hydrophobic "bumps" on the adenine ring. This is apparent by the brown surface protrusion of the Met clearly clashing with the "bump" of each of the BKIs in our crystal structures.
  • FIG. 3 is a graphical representation of the nuclear and cytosolic localization of TgCDPKl in T. gondii.
  • Live T. gondii cells transiently transfected with wild type JgCDPKl- GFP were fixed in 4% paraformaldehyde.
  • Samples were probed with anti-GFP followed by anti-rabbit Ig coupled to Texas red, stained with DAPI and viewed.
  • GFP green; DAPI, blue.
  • Figure 4 is a graphical representation demonstrating the effects of bumped kinase inhibitors on T. gondii binding to and invasion of mammalian cells.
  • T. gondii expressing ⁇ -galactosidase (10 3 per well) were allowed to infect fibroblasts in a 96 well plate.
  • invasion assays (a) compounds were added to the wells before infection with T. gondii.
  • growth assays
  • ⁇ -galactosidase activity was assessed by adding 0.5 mM chlorophenol red-fi-d- galactoside (CPRG), incubating at 37°C, and then measuring absorbance at 595 nm.
  • CPRG chlorophenol red-fi-d- galactoside
  • FIG. 5 is a graphical representation demonstrating IgCDPK gatekeeper mutant reduction of sensitivity to B Is.
  • T. gondii clonal lines expressing HA-tagged versions of JgCDPKl or a G128M mutant along with GFP and ⁇ -galactosidase were generated.
  • Anti-GFP served as a loading control.
  • Invasion assays were performed with increasing concentrations of BKIs NA-PP2 (b) and NM-PP1 (c) using the parental cell line and the transfectants additionally expressing wild type gCDPKl and rgCDPKl(G128M). Assays were done in triplicate and mean and standard deviations normalized to the no compound (vehicle alone) control are presented.
  • Figure 6 is a K m plot of ATP for IgCDPKl (2nM) using the SPA assay to measure phosphorylation of a biotinylated peptide substrate by labeled ⁇ -phosphate of ATP after 90 minutes incubation at 30°C.
  • Figure 7 is a K m plot of Syntide 2 substrate for T&CDPKl (2nM) using the SPA assay to measure phosphorylation of a biotinylated peptide substrate by labeled ⁇ -phosphate of ATP after 90 minutes incubation at 30°C.
  • Figure 8 is a Km plot of ATP using the luciferase based KinaseGlo assay that measures consumption of ATP after JgCDPKl (2nM) phosphorylation of peptide substrate Syntide 2 at 30oC during a 90 minute reaction time. Remaining ATP in the reaction was measured after addition of KinaseGlo reagent by luminescence light production. Omitting peptide substrate or enzyme led to virtually no consumption of ATP (not shown).
  • Figure 9 is: Km plot of Syntide 2 substrate using the luciferase based KinaseGlo assay as described for Figure 8.
  • Figure 10(a) is a representative image from the untreated CDPK-GFP dataset.
  • Intracellular parasites are marked by asterisks.
  • Figure 10(b) shows the change in the number of intracellular parasites upon drug treatment.
  • the number of intracellular parasites was determined by subtracting the number of extracellular parasites (SAG+) by the number of total parasites (GFP+) and expressed as a ratio to the number of host cells observed (as measured by DAPIstained nuclei). Each sample was normalized to the untreated control of the same line.
  • Figure 10(c) shows the data used to derive the graph in Figure 8(b). Note that cells expressing the gatekeeper mutant CDPK1(G128M) are less sensitive to the drug. The drug additionally appears to affect adhesion.
  • Figure 11(a) is a representative set of images of CDPK1(G128M)-GFP mixed with wild type, in the absence of drug. Vacuoles containing multiple GFP-expressing parasites are marked with * and wild type vacuoles are marked with - .
  • Figure 11(b) shows the number of vacuoles with wild type (GFP-) or transfectedparasites (GFP+), per host cell nucleus, in the absence and presence of drug for the three cell mixtures.
  • Figure 11(c) shows the data used to derive the graphs. Note that the parasite line overexpressing CDPK1(G128M)-GFP wasresistant to the effects of 1 ⁇ NA-PP2, as compared to the co-cultured wild type control.
  • FIG. 12 IgCDPKl and QJCDPKI inhibitors 1-3. IC 50 values shown are the average of three assays ⁇ (SEM).
  • B C. parvum parasite numbers (Y axis) present after 24 hours of infection of human intestinal cells (HCT-8) with C. parvum sporozoites (1 :1 ratio HCT-8 cells:C. parvum sporozoites) in the presence of varying concentrations of inhibitors 1- 3.
  • HCT-8 human intestinal cells
  • C. parvum sporozoites (1 :1 ratio HCT-8 cells:C. parvum sporozoites
  • Figure 13 is a graphical representation of the crystal structure of (left panel) Superposition of the active sites of TgCDPKl-3 (green sticks and light green ball-and-sticks) and Q?CDPKl-3 (orange sticks and ball-and-sticks) complexes (Pdb entries 3i7b and 3ncg). (right panel) Overlay of the ZgCDPKl-Sh and Q?CDPKl-5h complexes (Pdb entries 3n51 and 3mwu). Only residues within 6 A of the bound inhibitors are shown and the unique glycine gatekeeper residue is shown as ball-and-sticks.
  • Figure 14 shows in vitro activities of previously-described kinase inhibitors against
  • JgCDPKl Values shown are the average of three assays.
  • Figure 15 shows the structure of calcium-free, inactive CDPKl versus calcium bound, activated CDPKl.
  • the kinase domains of calcium-free IgCDPKl (green cartoon) and calcium-bound Q?CDPK1 (orange cartoon) are superimposed to highlight the dramatic conformational change that occurs in the CDPK activating domain (CAD) upon calcium activation.
  • CAD CDPK activating domain
  • the present disclosure provides compounds of the formula (I),
  • X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
  • R 1 is C 2 -6 alkyl, C 1-6 haloalkyl, -C 1-4 alkyl-R 12 , C 2 . 6 alkenyl, C 2 - 6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein
  • cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R 11 groups;
  • each R 11 is independently C w alkyl, Ci -6 haloalkyl, -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 NR 2 , or -S(0) 2 R;
  • R 12 is -OR, -SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R,
  • -OC(0)OR -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, -N(R)C(0)NR 2 , phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3.8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci- 6 alkyl, Ci- 6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 ;
  • R is one of the formulas
  • n 0, 1, or 2;
  • R Q is -0-, -S-, or -N(R Q )- , wherein R Q is hydrogen or Ci- 6 alkyl;
  • R 33 is Ci-6 alkyl, C 2-6 alkenyl, Ci- 6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi-6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_ 6 haloalkyl, -OR 20 , -SR 20 , -N(R 20 ) 2 , -C(0)R 20 , -C(0)OR 20 , -C(O)N(R 20 ) 2 , -S(0) 2 R 20 , -OC(0)R 20 , -OC(0)OR 20 , -OC(O)N(R 20 ) 2 , -N(R 0 )C(O)R
  • each R is independently halogen, cyano, nitro, Ci_ 6 alkyl, Ci- 6 haloalkyl,
  • each R is independently hydrogen or C 1-6 alkyl
  • R 35 is hydrogen or Ci- 6 alkyl; each R is independently hydrogen, C 1-6 alkyl, C2-6 alkenyl, C 1-6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi_6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, Ci_6 haloalkyl, -OR 0 , -SR°, -N(R°) 2 , -C(0)R°, -C(0)OR°, -C(0)N(R°) 2 , -S(0) 2 R°, -OC(0)R°, -OC(0)OR°, -OC(0)N(R°) 2 , -N(R°)C
  • R 1 is selected from one of the following groups (la) - (lii):
  • R 1 is C2-4 alkyl, -C 1-4 alkyl-R 12 , C2-4 alkynyl, C3.8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R 11 groups,
  • R 1 is C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R 11 groups,
  • R 1 is C3-8 cycloalkyl; or a monocyclic heterocyclyl optionally substituted with one R 11 group.
  • R 1 is C3-8 cycloalkyl.
  • R 1 is monocyclic heterocyclyl optionally substituted with one R 11 group.
  • R 1 is piperidinyl or tetrahydropyranyl, each optionally substituted with one R 11 group.
  • R 1 is phenyl optionally substituted with one or two R 11 groups,
  • R 1 is C 2 -6 alkyl.
  • R 1 is C2-4 alkyl.
  • R 1 is isopropyl or t-butyl.
  • R 1 is isopropyl.
  • R 1 is C 2 -6 alkyl or -C 1 .4 alkyl-R 12 .
  • R 1 is -Ci.4 alkyl-R 12 .
  • R 1 is -Ci-2 alkyl-R 12 .
  • R 12 is -C(0)OR or -C(0)NR 2 .
  • R 12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • (lt) Any one of groups (lm) - (lp), wherein R is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one or two groups that are each independently halogen, Ci_ 6 alkyl, -C(0)R, -C(0)0R, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -0C(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is phenyl or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci -6 alkyl, Ci -6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is monocyclic heterocyclyl optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci- 6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is monocyclic heterocyclyl optionally substituted by one or two groups that are each independently halogen, Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is piperidinyl or tetrahydropyranyl, each optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_ 6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, - OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci- 6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently Ci- 6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen, C 1-6 alkyl, C 2-6 alkenyl, Ci- 6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi-6 alkyl, heteroaryl, or heteroarylCi-6 alkyl.
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently Ci_ 6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen or Ci_ 6 alkyl.
  • Ci.6 alkyl -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen or Ci_6 alkyl.
  • R B is hydrogen, alkyl, -C(0)R A or -S(0) 2 R A , wherein each R A is independently hydrogen or Ci- 6 alkyl.
  • R is selected from one of the following groups (2a) - (2aa):
  • R is one of groups (R -a) through (R -g) as defined above.
  • R 3 is through (R 3 -g) as defined above.
  • R 33 is Ci. 6 alkyl, C 2 -6 alkenyl, C 1-6 haloalkyl, C3-8 cycloalkyl, aryl, or arylCi-6 alkyl.
  • R 33 is C 1-6 alkyl, C 1-6 haloalkyl, C3-8 cycloalkyl, phenyl, or benzyl.
  • n and R are selected from one of the following groups (4a) - (4x):
  • n 0 or 1 and R 32 is as defined for formula (I).
  • n is 0 or 1 and R 32 is halogen, cyano, nitro, C 1-6 alkyl, or C 1-6 haloalkyl.
  • n is 0 or 1 and R 32 is halogen, C 1-6 alkyl, or C 1-6 haloalkyl.
  • n is 0 or 1 and each R 32 is -OR 34 , -SR 34 , -N(R 34 ) 2 , -C(0)R 34 , -C(0)OR 34 , -C(0)N(R 4 ) 2 , -S(0) 2 R 34 , -OC(0)R 34 , -OC(0)OR 34 , -OC(0)N(R 34 ) 2 , -N(R 34 )C(0)R 34 , -N(R 34 )C(0)OR 34 , or -N(R 4 )C(0)N(R 34 ) 2, wherein each R 34 is independently hydrogen or C 1-6 alkyl.
  • n is 0 or 1 and R 32 is -OR 34 , -SR 34 , -N(R 34 ) 2 , wherein each R 34 is independently hydrogen or C 1-6 alkyl.
  • n is 0 or 1 and R 32 is -C(0)R 34 , -C(0)OR 34 , -C(0)N(R 34 ) 2 , or -S(0) 2 R 34 , wherein each
  • R 34 is independently hydrogen or C 1-6 alkyl.
  • n is as defined for formula (I) and each R 32 is independently halogen, cyano, nitro,
  • n is as defined for formula (I) and each R 32 is independently halogen, C 1-6 alkyl, or
  • Ci-6 haloalkyl Ci-6 haloalkyl
  • n is as defined for formula (I) and each R 32 is independently -OR 34 , -SR 34 , -N(R 34 ) 2 , -C(0)R 34 , -C(0)OR 34 , -C(0)N(R 34 ) 2 , -S(0) 2 R 34 , -OC(0)R 34 , -OC(0)OR 34 , -OC(0)N(R 34 ) 2 , -N(R 34 )C(0)R 34 , -N(R 34 )C(0)OR 34 , or -N(R 34 )C(0)N(R 34 ) 2 , wherein each R 34 is independently hydrogen or C 1-6 alkyl.
  • n is as defined for formula (I) and each R 32 is independently -OR 34 , -SR 34 , -N(R 34 ) 2 , wherein each R 34 is independently hydrogen or C 1-6 alkyl.
  • n is as defined for formula (I) and each R 32 is independently -C(0)R 34 , -C(0)OR 34 , -C(0)N(R 4 ) 2 , or -S(0) 2 R l4 , wherein each R 34 is independently hydrogen or C 1-6 alkyl.
  • n 1 or 2 and each R 32 is as defined for formula (I).
  • n is 1 or 2 and each R 32 is independently halogen, cyano, nitro, C 1-6 alkyl, or C 1-6 haloalkyl.
  • n is 1 or 2 and each R 32 is independently halogen, C 1-6 alkyl, or C 1-6 haloalkyl.
  • n is 1 or 2 and each R 32 is independently -OR 34 , -SR 34 , -N(R 34 ) 2 , -C(0)R 34 , -C(0)OR 34 , -C(0)N(R 34 ) 2 , -S(0) 2 R 34 , -OC(0)R 34 , -OC(0)OR 34 , -OC(0)N(R 34 ) 2 , -N(ir)C(0)R , -N(R J4 )C(0)0R , or -N(R i4 )C(0)N(R J4 ) 2 , wherein each R is independently hydrogen or C 1-6 alkyl.
  • n is 1 or 2 and each R 32 is independently -OR 34 , -SR 34 , -N(R 34 ) 2 , wherein each R 34 is independently hydrogen or C 1-6 alkyl.
  • n is 1 or 2 and each R 32 is independently -C(0)R 34 , -C(0)OR 34 , -C(0)N(R 34 ) 2 , or
  • each R 34 is independently hydrogen or C 1-6 alkyl.
  • n is 1 and R j2 is halogen, cyano, nitro, C 1-6 alkyl, or C 1-6 haloalkyl.
  • n is 1 and R j2 is halogen, C 1-6 alkyl, or C 1-6 haloalkyl.
  • n is 1 and R 32 is -OR 34 , -SR 34 , -N(R 34 ) 2 , -C(0)R 34 , -C(0)OR 34 , -C(0)N(R 34 ) 2 , -S(0) 2 R 34 , -OC(0)R 34 , -OC(0)OR 34 , -OC(0)N(R 34 ) 2 , -N(R 34 )C(0)R 34 , -N(R 34 )C(0)OR 34 , or -N(R 34 )C(0)N(R 34 ) 2 , wherein each R 34 is independently hydrogen or C 1-6 alkyl.
  • n is 1 and R 32 is-OR 34 , -SR 34 , -N(R 34 ) 2 , wherein each R 34 is independently hydrogen or Ci-6 alkyl.
  • n is 1 and R 32 is -C(0)R 34 , -C(0)OR 34 , -C(0)N(R 34 ) 2 , or -S(0) 2 R 34 , wherein each R 34 is independently hydrogen or C 1-6 alkyl.
  • R 33 is selected from one of the following groups (5a) - (5t);
  • R 33 is Ci-6 alkyl, C 2 . 6 alkenyl, arylCi_6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, C 1-6 haloalkyl, -OR 20 , -SR 20 , -N(R 20 ) 2 , -C(0)R 20 , -C(0)OR 2 °, -C(O)N(R 20 ) 2 , -S(0) 2 R 20 , -0C(0)R 20 , -OC(0)OR 20 , -OC(O)N(R 0 ) 2 , -N(R 20 )C(O)R 20 , -N(R 20 )C(O)OR 20 , or -N(R 20 )C(O)N(R 20 )
  • R 33 is Ci-6 alkyl, C 2 . 6 alkenyl, arylCi_6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, C 1-6 haloalkyl, -OR 20 , -SR 20 , -N(R 20 ) 2 , -C(0)R 20 , -C(0)OR 20 , -C(O)N(R 20 ) 2 , -S(0) 2 R 20 , -OC(0)R 20 , -OC(0)OR 20 , -OC(O)N(R 20 ) 2 , -N(R 20 )C(O)R 20 , -N(R 0 )C(O)OR 20 , or -N(R 20 )C(O)N(R 20 ) 2 ,
  • (5c) is Ci-6 alkyl, C 2 -6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one or two groups that are each independently halogen, Ci_6 alkyl, or Ci_6 haloalkyl.
  • R 33 is Ci-6 alkyl, C 2 -6 alkenyl, arylCi- 6 alkyl, or heteroarylCi- 6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one or two groups that are each independently halogen, Ci- 6 alkyl, or Ci- 6 haloalkyl.
  • R 33 is C 2 -6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci- 6 alkyl, Ci- 6 haloalkyl, -OR 20 , -SR 20 , -N(R 20 ) 2 , -C(0)R 20 , -C(0)OR 20 , -C(O)N(R 20 ) 2 , -S(0) 2 R 2 °, -OC(0)R 2 °, -OC(0)OR 20 , -OC(O)N(R 20 ) 2 , -N(R 20 )C(O)R 20 , -N(R 20 )C(O)OR 20 , or -N(R 20 )C(O)N(R 20 ) 2 , wherein
  • each R is independently hydrogen or Ci- 6 alkyl.
  • R is C 2 _6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one, two, three, or four groups that are each
  • 20 20 20 independently halogen, cyano, nitro, Ci_ 6 alkyl, Ci- 6 haloalkyl, -OR , -SR , -N(R ) 2 , -C(0)R 20 , -C(0)OR 20 , -C(O)N(R 20 ) 2 , -S(0) 2 R 2 °, -OC(0)R 2 °, -OC(0)OR 20 , -OC(O)N(R 20 ) 2 , -N(R 20 )C(O)R 20 , -N(R 20 )C(O)OR 20 , or -N(R 20 )C(O)N(R 20 ) 2 , wherein each R 20 is independently hydrogen or Ci- 6 alkyl.
  • R 33 is C 2- 6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one or two groups that are each independently halogen, Ci- 6 alkyl, or Ci- 6 haloalkyl.
  • R 33 is C 2 _6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one or two groups that are each independently halogen, Ci_6 alkyl, or Ci_6 haloalkyl.
  • R 33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR 20 , -SR 20 , -N(R 20 ) 2 , -C(0)R 20 , -C(0)OR 20 , -C(O)N(R 20 ) 2 , -S(0) 2 R 20 , -OC(0)R 20 , -OC(0)OR 20 , -OC(O)N(R 20 ) 2 , -N(R 20 )C(O)R 20 , -N(R 20 )C(O)OR 20 , or -N(R 20 )C(O)N(R 20 ) 2 , wherein each R 20 is independently hydrogen or C 1-6 alkyl.
  • R 33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each are each substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci- 6 alkyl, Ci_6 haloalkyl, -OR 20 , -SR 20 , -N(R 20 ) 2 , -C(0)R 20 , -C(0)OR 20 , -C(O)N(R 20 ) 2 , -S(0) 2 R 20 , -OC(0)R , -OC(0)OR , -OC(0)N(R u ) 2 , -N(R u )C(0)R , -N(R u )C(0)OR , or -N(R 20 )C(O)N(R 20 ) 2 , wherein each R 20 is independently hydrogen or Ci_ 6 alkyl
  • R 33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each optionally substituted with one or two groups that are each independently halogen, C 1-6 alkyl, or C 1-6 haloalkyl.
  • R 33 is arylCi-e alkyl or heteroarylC ⁇ alkyl, each substituted with one or two groups that are each independently halogen, C 1-6 alkyl, or C 1-6 haloalkyl.
  • R 33 is arylCi-6 alkyl optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, C 1-6 haloalkyl, -OR 20 , -SR 20 , -N(R 20 ) 2 , -C(0)R 20 , -C(0)OR 20 , -C(O)N(R 20 ) 2 , -S(0) 2 R 2 °, -OC(0)R 2 °, -OC(0)OR 20 , -OC(O)N(R 0 ) 2 , -N(R 20 )C(O)R 20 , -N(R 20 )C(O)OR 20 , or -N(R 20 )C(O)N(R 20 ) 2 , wherein each R 20 is independently hydrogen or C 1-6 alkyl.
  • R is arylCi-6 alkyl substituted with one, two, three, or four groups that are each
  • R 33 is arylCi-6 alkyl optionally substituted with one or two groups that are each independently halogen, C 1-6 alkyl, or C 1-6 haloalkyl.
  • R 33 is arylCi-6 alkyl substituted with one or two groups that are each independently halogen, C 1-6 alkyl, or C 1-6 haloalkyl.
  • R 33 is benzyl optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, C 1-6 haloalkyl, -OR 20 , -SR 20 , -N(R 20 ) 2 , -C(0)R 20 , -C(0)OR 20 , -C(O)N(R 20 ) 2 , -S(0) 2 R 2 °, -OC(0)R 2 °, -OC(0)OR 20 , -OC(O)N(R 20 ) 2 , -N(R 20 )C(O)R 20 , -N(R 0 )C(O)OR 20 , or -N(R 0 )C(O)N(R 20 ) 2 , wherein each R 20 is independently hydrogen or C 1-6 alkyl.
  • R 33 is benzyl substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci -6 alkyl, Ci- ⁇ haloalkyl, -OR 20 , -SR 20 , -N(R 20 ) 2 , -C(0)R 20 , -C(0)OR 20 , -C(O)N(R 20 ) 2 , -S(0) 2 R 20 , -OC(0)R 2 °, -OC(0)OR 20 , -OC(O)N(R 20 ) 2 , -N(R 20 )C(O)R 20 , -N(R 20 )C(O)OR 20 , or -N(R 20 )C(O)N(R 20 ) 2 , wherein each R 20 is independently hydrogen or C 1-6 alkyl.
  • R 33 is benzyl optionally substituted with one or two groups that are each independently halogen, C 1-6 alkyl, or C 1-6 haloalkyl.
  • R 33 is benzyl substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci- 6 haloalkyl.
  • Particular embodiments of this aspect of the invention include compounds of any one of the formulae (I), (la), and (lb), each as defined in each of the following rows, wherein each entry is a group number as defined above (e.g., (3c) refers to Q is -0-), a dash "-" indicates that the variable is as defined for formula (I) or defined according to any one of the applicable variable definitions (la)-(5t) [e.g., when R 1 is a dash, it can be either as defined for Formula (I) or any one of definitions (la)-(lii)]; and an "x" indicates that the variable is not applicable to the particular embodiment (e.g., when R J is (2o), then Q and R 33 are not necessary):
  • the compound is one of the compounds in Table A:
  • X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
  • R is C2-6 alkyl or -C 1-4 alkyl-R , wherein
  • R J is a monocyclic heterocyclyl optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 ;
  • R 3 is one of the formulas
  • n 0, 1, or 2;
  • R Q is -0- or -N(R Q )- , wherein R Q is hydrogen or Ci_6 alkyl;
  • R 33 is Ci-6 alkyl, C 2 - 6 alkenyl, arylCi_6 alkyl, or heteroarylCi-6 alkyl wherein the arylalkyl and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, Ci. 6 alkyl, Ci. 6 haloalkyl,
  • each R is independently hydrogen or Ci-6 alkyl.
  • each R is independently halogen, Ci_ 6 alkyl, or -OR , wherein R is Ci- 6 alkyl;
  • R 35 is hydrogen or Ci- 6 alkyl
  • each R is independently hydrogen or Ci- 6 alkyl.
  • the disclosure further comprises subgenera of formula (III) in which the substituents are selected as any and all combinations of one or more of structural formula (III), n, Q, R , R , R , and R as defined herein, including without limitation, the following: Structural Formula III is one of formulae (Ilia) - (Hlb):
  • R 1 is selected from one of the following groups (8a) - (8u):
  • R 1 is C 2 -6 alkyl.
  • R 1 is C2-4 alkyl.
  • R 1 is isopropyl or t-butyl.
  • R 1 is t-butyl.
  • R 1 is isopropyl.
  • R 1 is -Ci_4 alkyl-R 12 .
  • R 1 is -Ci-2 alkyl-R 12 .
  • R 1 is -CH 2 -R 12 .
  • R 12 is monocyclic heterocyclyl optionally substituted by one or two groups that are each independently halogen, C 1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is piperidinyl or tetrahydropyranyl, each optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci_ 6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R is piperidinyl optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, - OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 . 12
  • R is piperidinyl optionally substituted by one or two groups that are each independently Ci_ 6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen, Ci_ 6 alkyl, C 2 - 6 alkenyl, C ⁇ -6 haloalkyl, C3.8 cycloalkyl, heterocyclyl, aryl, arylQ.e alkyl, heteroaryl, or heteroarylC ⁇ 6 alkyl.
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently Ci -6 alkyl, -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently C 1-6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen or Ci_ 6 alkyl.
  • Ci_6 alkyl -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R ⁇ is independently hydrogen or C 1-6 alkyl.
  • R is selecte from one of the following groups (9a) - (9g):
  • Q is selected from one of the following groups (10a) - (lOd);
  • Q is -O- or -N(H)-.
  • n 0 or 1 and R 32 is as defined for formula (III).
  • n 1 or 2 and R 32 is as defined for formula (III).
  • R is selected from one of the following groups (12a) - (12i):
  • R 33 is Ci-6 alkyl, C 2 . 6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one or two groups that are each independently halogen, Ci. 6 alkyl, or Ci. 6 haloalkyl.
  • R is Ci-6 alkyl, C 2 -6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one or two groups that are each independently halogen, Ci_6 alkyl, or Ci_6 haloalkyl.
  • R 33 is C 2 _6 alkenyl, arylC 1 _6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one or two groups that are each independently halogen, Ci- 6 alkyl, or Ci- 6 haloalkyl.
  • R 33 is C 2 -6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one or two groups that are each independently halogen, Ci- 6 alkyl, or Ci- 6 haloalkyl.
  • R 33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each optionally substituted with one or two groups that are each independently halogen, Ci- 6 alkyl, or Ci- 6 haloalkyl.
  • R 33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each substituted with one or two groups that are each independently halogen, Ci- 6 alkyl, or Ci- 6 haloalkyl.
  • R is arylCi-6 alkyl optionally substituted with one or two groups that are each independently halogen, Ci- 6 alkyl, or Ci- 6 haloalkyl.
  • R 33 is arylQ-6 alkyl substituted with one or two groups that are each independently halogen, Ci_6 alkyl, or Ci_6 haloalkyl.
  • R 33 is benzyl optionally substituted with one or two groups that are each independently halogen, Ci- 6 alkyl, or Ci- 6 haloalkyl.
  • R 33 is benzyl substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or C 1-6 haloalkyl.
  • Particular embodiments of this aspect of the invention include compounds of any one of the formulae (III), (Ilia), and (lllb), each as defined in each of the following rows, wherein each entry is a group number as defined above (e.g., (10b) refers to Q is -0-), and a dash "-" indicates that the variable is as defined for formula (III) or defined according to any one of the applicable variable definitions (8a)-(12j) [e.g., when R 1 is a dash, it can be either as defined for Formula (III) or any one of definitions (8a)-(8u)]; and an "x" indicates that the variable is not applicable to the particular embodiment (e.g., when R 3 is (9c), then Q and R 33 are not necessary):
  • JgCDPKl has a unique ATP -binding site with a small gatekeeper residue, as opposed to the large gatekeeper residues present in mammalian protein kinases.
  • This key difference in gatekeeper residues between mammalian kinases and JgCDPKl allowed us to use bumped kinase inhibitors (BKIs) to selectively inhibit JgCDPKl without untoward effects on the mammalian host cell.
  • BKIs bumped kinase inhibitors
  • the disclosure provides methods for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either (i) a bumped kinase inhibitor or (ii) a pharmaceutical composition comprising a bumped kinase inhibitor and a pharmaceutically acceptable excipient, carrier, or diluent.
  • the bumped kinase inhibitor is selected from one of the compounds of Figure 14, or a pharmaceutically acceptable salt thereof.
  • the bumped kinase inhibitor is according to of the formula (I) as defined above, or any embodiment thereof.
  • the bumped kinase inhibitor is of the formula (II),
  • X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
  • R 1 is Ci-6 alkyl, Ci- 6 haloalkyl, C 2 -6 alkenyl, C 2 -6 alkynyl, -Ci- 6 alkyl-R 12 , C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein
  • cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, and phenyl groups are each optionally substituted with one or two R 11 groups;
  • each R 11 is independently Ci_ 6 alkyl, Ci_ 6 haloalkyl, -C(0)R, -C(0)OR, -C(0)NR 2 , -
  • R 12 is -OR, -SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, -N(R)C(0)NR 2 , phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3.8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci. 6 alkyl, Ci.
  • L is a bond or -CH 2 -;
  • R 3 is aryl or heteroaryl, each optionally substituted with one, two, or three R 31 groups, wherein
  • each R 31 is independently halogen, cyano, nitro, Ci_6 alkyl, C 1-6 haloalkyl, aryl, heteroaryl, C3-8 cycloalkyl, heterocyclyl, arylCi-6 alkyl, heteroarylCi-6 alkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, -N(R)C(0)NR 2 or -N(R)S(0) 2 R, wherein the aryl, heteroaryl, C3-8 cycloalkyl, heterocyclyl, arylalkyl, and heteroarylalkyl groups are optionally substituted with one or two R 10 groups;
  • each R is independently hydrogen, Ci_6 alkyl, C 2 _ 6 alkenyl, Ci_6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one,
  • each R 10 is independently halogen, cyano, nitro, C 1-6 alkyl, C 1-6 haloalkyl, -OR 0 , -SR°, -N(R°) 2 , -C(0)R°, -C(0)OR°, -C(0)N(R°) 2 , -S(0) 2 R°, -OC(0)R°, -OC(0)OR°,
  • each R° is independently hydrogen or C 1-6 alkyl.
  • the disclosure further comprises subgenera of formula (II) in which the substituents are selected as any and all combinations of one or more of structural formula (II), R 1 , and R 3 , as defined herein, including without limitation, the following:
  • Structural Formula II is one of formulae (Ila) - (Ilh):
  • R 1 is selected from one of the following groups (6a) - (6ii);
  • R 1 is Ci-4 alkyl, -C1-4 alkyl-R 12 , C 2 . 4 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R 11 groups.
  • R 1 is C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R 11 groups.
  • (6c) 1 is C3-8 cycloalkyl; or a monocyclic heterocyclyl optionally substituted with one R 11 group.
  • R 1 is C3-8 cycloalkyl.
  • R 1 is monocyclic heterocyclyl optionally substituted with one R 11 group.
  • R 1 is piperidinyl or tetrahydropyranyl, each optionally substituted with one R 11 group.
  • R 1 is phenyl optionally substituted with one or two R 11 groups.
  • R 1 is C 2 -6 alkyl.
  • R 1 is Ci.4 alkyl.
  • R 1 is isopropyl or t-butyl.
  • R 1 is t-butyl
  • R 1 is isopropyl.
  • R 1 is C2-6 alkyl or -C 1-4 alkyl-R 12 .
  • R 1 is -CM alkyl-R 12 .
  • R 1 is -d_ 2 alkyl-R 12 .
  • R 1 is -CH2-R 12 .
  • R 12 is -C(0)OR, -C(0)NR 2 , phenyl, monocyclic heteroaryl, C3.8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_ 6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or - N(R)C(0)NR 2 ;
  • R 12 Any one of groups (6m) - (6p), R 12 is -C(0)OR or -C(0) R 2 .
  • R is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, 0 1-6 haloalkyl, -OR, - SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one or two groups that are each independently halogen, C 1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R is phenyl or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_ 6 alkyl, Ci_ 6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is monocyclic heterocyclyl optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci -6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, - OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)0R, or -N(R)C(0)NR 2 .
  • R 12 is monocyclic heterocyclyl optionally substituted by one or two groups that are each independently halogen, Ci- 6 alkyl, - C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , - N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R is piperidinyl or tetrahydropyranyl, each optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci_ 6 alkyl, d_ 6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)0R, or - N(R)C(0)NR 2 .
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently halogen, cyano, nitro, C 1-6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)0R, or -N(R)C(0)NR 2 .
  • R is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)0R A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen, C ⁇ -6 alkyl, C 2 . 6 alkenyl, Ci- 6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylQ-6 alkyl, heteroaryl, or heteroarylCi_6 alkyl.
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently C 1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently Ci- 6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen or Ci-6 alkyl.
  • (6cc) Any one of groups (6m) - (6p), wherein R 12 is piperidinyl optionally substituted by one or two groups that are each independently C 1-6 alkyl, -C(0)R, -C(0)OR, - C(0)NR 2 , or -S(0) 2 R.
  • (6dd) Any one of groups (6m) - (6p), wherein R 12 is piperidinyl optionally substituted by one or two groups that are each independently C 1-6 alkyl, -C(0)R A , or -S(0) 2 R A , wherein each R A is independently hydrogen or -6 alkyl.
  • Ci_6 alkyl -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen or Ci- 6 alkyl.
  • R 3 is selected from one of the following groups (7a) - (7x):
  • R 3 is naphthyl, quinolinyl, pyridyl, pyrimidinyl, indolyl, benzodioxolyl, 2,3- dihydrobenzodioxinyl, dibenzothienyl, chromanyl, or phenyl, each optionally substituted with one, two, or three R 31 groups.
  • R 3 is naphthyl, quinolinyl, indolyl, benzodioxolyl, 2,3-dihydrobenzodioxinyl, or chromanyl, each optionally substituted with one, two, or three R 31 groups.
  • R is quinolinyl, pyridyl, pyrimidinyl, or indolyl, each optionally substituted with one,
  • R is quinolinyl or indolyl, each optionally substituted with one, two, or three R groups.
  • R 3 is quinolinyl optionally substituted with one, two, or three R 31 groups.
  • R 3 is pyridyl or pyrimidinyl, each optionally substituted with one, two, or three R 31 groups.
  • R 3 is phenyl substituted with one, two, or three R 31 groups.
  • R 3 is phenyl optionally substituted with one or two R 31 groups, and substituted with one group that is halogen, Ci_ 6 alkyl,-OR, -SR, -NR 2 , -N(R)C(0)R, or-N(R)S(0) 2 R.
  • R 3 is phenyl optionally substituted with one or two R 31 groups, and substituted with one group that is -OR or -N(R)C(0)R.
  • R is phenyl optionally substituted with one or two R groups, and substituted with one group that is -OR 10 , wherein R 10 is benzyl optionally substituted with one, two, three, or four groups that are each independently halogen, Ci_ 6 alkyl, Ci- 6 haloalkyl, or -OR 0
  • R 3 is phenyl optionally substituted with one or two R 31 groups, and substituted with one group that is -N(H)C(0)R 20 , wherein R 20 is C 1-6 alkyl, C 2 . 6 alkenyl, Ci- 6 haloalkyl, aryl, or arylCi-6 alkyl.
  • R 3 is naphthyl optionally substituted with one, two, or three R 31 groups.
  • R 3 is naphthyl optionally substituted with one or two R 31 groups and substituted with one group that is -OR 15 , wherein R 15 is Ci. 6 alkyl or benzyl, wherein the benzyl is optionally substituted with one, two, three, or four groups that are each independently halogen, Ci_ 6 alkyl, Ci_ 6 haloalkyl, or -OR 0 .
  • R 3 is naphth-l-yl optionally substituted with one, two, or three R 31 groups.
  • R 3 is naphth-l-yl optionally substituted with one or two R 31 groups and substituted with one group that is -OR 15 , wherein R 15 is Ci_ 6 alkyl or benzyl, wherein the benzyl is optionally substituted with one, two, three, or four groups that are each independently halogen, C 1-6 alkyl, Ci_6 haloalkyl, or -OR 0 .
  • R 3 is naphth-2-yl optionally substituted with one, two, or three R 31 groups.
  • R 3 is naphth-2-yl optionally substituted with one or two R 31 groups and substituted with one group that is -OR 15 , wherein R 15 is C 1-6 alkyl or benzyl, wherein the benzyl is optionally substituted with one, two, three, or four groups that are each independently halogen, C 1-6 alkyl, C 1-6 haloalkyl, or -OR 0 .
  • R 3 is indolyl optionally substituted with one, two, or three R jl groups.
  • R 3 is indol-2-yl optionally substituted with one, two, or three R 31 groups.
  • R 3 is indol-3-yl optionally substituted with one, two, or three R 31 groups.
  • R 3 is indol-5-yl optionally substituted with one, two, or three R 31 groups.
  • R 3 is indol-6-yl optionally substituted with one, two, or three R 31 groups.
  • the compound of formula (II) is one of compounds of Table
  • the bumped kinase inhibitor is of the formula (IV),
  • X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
  • Ci-6 alkyl is Ci-6 alkyl, C 2 -6 alkynyl, -Ci_6 alkyl-R , C3-8 cycloalkyl, monocyclic heterocyclyl, or phenyl, wherein
  • each R 11 is independently Ci_ 6 alkyl, Ci_ 6 haloalkyl, -C(0)R, or -S(0) 2 R;
  • R 12 is -C(0)OR, -C(0)NR 2 , phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_ 6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, - OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or - N(R)C(0)NR 2 ;
  • L is a bond or -CH 2 -;
  • R 3 is aryl or heteroaryl, each optionally substituted with one, two, or three R 31 groups, wherein
  • each R is independently halogen, Ci_6 alkyl, Ci_6 haloalkyl, phenyl, benzyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -OC(0)R, -N(R)C(0)R, or -N(R)S(0) 2 R, wherein the phenyl and benzyl groups are optionally substituted with one or two R 10 groups;
  • each R is independently hydrogen, Ci- 6 alkyl, C 2 _ 6 alkenyl, Ci- 6 haloalkyl, C3-8 cycloalkyl, aryl, arylCi- 6 alkyl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one or two R 10 groups; and
  • each R 10 is independently halogen, cyano, Ci-6 alkyl, Ci- 6 haloalkyl, -OR 0 , -SR°, or -N(R°) 2 , wherein each R° is independently hydrogen or Ci_6 alkyl.
  • the disclosure further comprises subgenera of formula (IV) in which the substituents are selected as any and all combinations of one or more of structural formula (IV), R , and R 3 , as defined herein, including without limitation, the following:
  • Structural Formula II is one of formulae (IV a) - (IVh):
  • R 1 is selected from one of the following groups (13a) - (13ff):
  • R 1 is C3-8 cycloalkyl; or a monocyclic heterocyclyl optionally substituted with
  • R 1 is C3-8 cycloalkyl.
  • R 1 is monocyclic heterocyclyl optionally substituted with one R 11 group.
  • R 1 is piperidinyl or tetrahydropyranyl, each optionally substituted with one R 11 group.
  • R 1 is phenyl optionally substituted with one or two R 11 groups.
  • R 1 is C 2 -6 alkyl.
  • R 1 is Ci -4 alkyl.
  • R 1 is isopropyl or t-butyl.
  • R 1 is t-butyl
  • R 1 is isopropyl
  • R 1 is C 2 -6 alkyl or -Ci_ 4 alkyl-R 12 .
  • R 1 is -CM alkyl-R 12 .
  • R 1 is -Ci- 2 alkyl-R 12 .
  • R 1 is -CH 2 -R 12 .
  • R 12 is -C(0)OR or -C(0)NR 2 .
  • R 12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci- 6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, - OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • any one of groups (13k) - (13n), is phenyl or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_ 6 alkyl, Ci_ 6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is monocyclic heterocyclyl optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci -6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , - S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or - N(R)C(0)NR 2 .
  • R 12 is monocyclic heterocyclyl optionally substituted by one or two groups that are each independently halogen, Ci- 6 alkyl, - C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , - N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is piperidinyl or tetrahydropyranyl, each optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci_ 6 alkyl, d_ 6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)0R, or - N(R)C(0)NR 2 .
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci- 6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR 2 , -C(0)R, -C(0)OR,-C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen, Ci-6 alkyl, C 2 . 6 alkenyl, Ci- 6 haloalkyl, C 3 _8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl.
  • R 12 is piperidinyl optionally substituted by one or two groups that are each independently C 1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR 2 , -S(0) 2 R, -OC(0)R, -OC(0)OR, -OC(0)NR 2 , -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR 2 .
  • R is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , -OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen or Ci-6 alkyl.
  • R 12 is , wherein R B is hydrogen, Ci_ 6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , - OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen, Ci -6 alkyl, C 2 _ 6 alkenyl, Ci_ 6 haloalkyl, C 3-8 cycloalkyl, heterocyclyl, aryl, arylCi- 6 alkyl, heteroaryl, or heteroarylCi-6 alkyl.
  • R 12 is , wherein R is hydrogen, Ci_ 6 alkyl, -C(0)R A , -C(0)OR A , -C(0)N(R A ) 2 , -S(0) 2 R A , -OC(0)R A , - OC(0)OR A , -OC(0)N(R A ) 2 , -N(R A )C(0)R A , -N(R A )C(0)OR A , or -N(R A )C(0)N(R A ) 2 , wherein each R A is independently hydrogen or C 1-6 alkyl.
  • R 3 is naphthyl, quinolinyl, pyridyl, pyrimidinyl, indolyl, benzodioxolyl, 2,3- dihydrobenzodioxinyl, dibenzothienyl, chromanyl, or phenyl, each optionally substituted with one, two, or three R 31 groups.
  • R 3 is naphthyl, quinolinyl, indolyl, benzodioxolyl, 2,3-dihydrobenzodioxinyl, or chromanyl, each optionally substituted with one, two, or three R 31 groups.
  • R is quinolinyl, pyridyl, pyrimidinyl, or indolyl, each optionally substituted with one, two, or three R 31 groups.
  • R 3 is quinolinyl or indolyl, each optionally substituted with one, two, or three R 31 groups.
  • R 3 is quinolinyl optionally substituted with one, two, or three R 31 groups.
  • R 3 is pyridyl or pyrimidinyl, each optionally substituted with one, two, or three R 31 groups.
  • R 3 is phenyl substituted with one, two, or three R 31 groups.
  • R 3 is phenyl optionally substituted with one or two R 31 groups, and substituted with one group that is halogen, Ci_ 6 alkyl,-OR, -SR, -NR 2 , -N(R)C(0)R, or-N(R)S(0) 2 R.
  • R is phenyl optionally substituted with one or two R groups, and substituted with one group that is -OR or -N(R)C(0)R.
  • R 3 is phenyl optionally substituted with one or two R 31 groups, and substituted with one group that is -OR 10 , wherein R 10 is benzyl optionally substituted with one, two, three, or four groups that are each independently halogen, Ci- 6 alkyl, Ci- 6 haloalkyl, or -OR 0 .
  • R 3 is phenyl optionally substituted with one or two R 31 groups, and substituted with one group that is -N(H)C(0)R 20 , wherein R 20 is C 1-6 alkyl, C 2 _6 alkenyl, Ci- 6 haloalkyl, aryl, or arylCi-6 alkyl.
  • R 3 is naphthyl optionally substituted with one, two, or three R 31 groups.
  • R 3 is naphthyl optionally substituted with one or two R 31 groups and substituted with one group that is -OR 15 , wherein R 15 is Ci_6 alkyl or benzyl, wherein the benzyl is optionally substituted with one or two groups that are each independently halogen, Ci_
  • R 3 is naphth-l-yl optionally substituted with one, two, or three R 31 groups.
  • R 3 is naphth-l-yl optionally substituted with one or two R 31 groups and substituted with one group that is -OR 15 , wherein R 15 is C ⁇ - alkyl or benzyl, wherein the benzyl is optionally substituted with one or two groups that are each independently halogen,
  • Ci-6 alkyl Ci -6 haloalkyl, or -OR 0 .
  • R 3 is naphth-2-yl optionally substituted with one, two, or three R 31 groups.
  • R 3 is naphth-2-yl optionally substituted with one or two R 31 groups and substituted with one group that is -OR 15 , wherein R 15 is Ci_6 alkyl or benzyl, wherein the benzyl is optionally substituted with one or two groups that are each independently halogen, or -OR 0 .
  • R 3 is indolyl optionally substituted with one, two, or three R jl groups.
  • R is indol-2-yl optionally substituted with one, two, or three R groups.
  • R is indol-3-yl optionally substituted with one, two, or three R groups.
  • R is indol-5-yl optionally substituted with one, two, or three R groups.
  • R is indol-6-yl optionally substituted with one, two, or three R groups.
  • One embodiment of the present disclosure provide a method of treating a subject in need of treatment for an apicomplexan-related disease comprising administering an effective amount of a compound of any of formulas (I) - (IV) or any embodiment thereof, that inhibits the activity of an apicomplexan calcium dependent protein kinase (CDPK).
  • Particular embodiments of the present disclosure provide a method of treating cryptosporidiosis in a subject comprising administering an effective amount of a compound of any of formulas (I) - (IV) or any embodiment thereof, that inhibits the activity of Cryptosporidium parvum and C. hominus calcium dependent protein kinase 1 (Q?CDPK1).
  • T CDPKl calcium dependent protein kinase 1
  • the compound of any one of formulas (I) - (IV) or any embodiment thereof can be administered in combination with a second agent, such as agents specific for use against the specific apicomplexan-related disorder being treated.
  • a second agent such as agents specific for use against the specific apicomplexan-related disorder being treated.
  • the apicomplexan protozoan related disease is toxoplasmosis.
  • toxoplasmosis can encompass a number of pathologies, including, but not limited to, encephalitis, retinitis, lymphadenopathy, disseminated disease, and hepatitis.
  • Toxoplasmosis infects most genera of warm-blooded animals, including humans, but the primary host is the felid (cat) family.
  • Cats are the definitive host for the Toxoplasma organism. Infection with this protozoan parasite is fairly common, but actual disease caused by this parasite is relatively rare in cats. Cats can become infected by Toxoplasma by eating any of the three infective stages of the parasites. The most common route of infection is probably by ingestion of tissue cysts in infected prey or in other raw meat. Toxoplasma multiply in the small intestines and in approximately two to three weeks the oocysts are excreted in the infected cat's feces.
  • cats may be treated prophylactically for toxoplasmosis (e.g, a gastrointestinal infection) provided by providing a therapeutically effective amount of a compounds of any one of formulas (I) - (IV) or to eliminate the chance that they would shed infectious Toxoplasmodia oocyts and infect their owners.
  • infected cats may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat toxoplasmosis.
  • similar prophylactic and therapeutic methods for limiting development of or treating toxoplasmosis can be used in any animal that can be infected by Toxoplasma sp.
  • a young child can be 14 years old or younger; or 13 years old or younger; or 12 years old or younger; or 1 1 years old or younger; or 10 years old or younger; or 9 years old or younger; or 8 years old or younger; or 7 years old or younger; or 6 years old or younger; or 5 years old or younger; or 4 years old or younger; or 3 years old or younger; or 2 years old or younger; or 1 year old or younger. This can cause damage to the brain (encephalitis) or the eyes (necrotizing retinochoroiditis).
  • toxoplasmosis infants infected via placental transmission may be born with either of these problems, or with nasal malformations, although these complications are rare in newborns. In most immunocompetent patients, the infection enters a latent phase, during which only bradyzoites are present, forming cysts in nervous and muscle tissue. Most infants who are infected while in the womb have no symptoms at birth but may develop symptoms later in life.
  • the most common current therapy for toxoplasmosis is sulfadiazine/pyrimethamine combination therapy, but therapy is often limited by allergic reactions to the sulfa component, anemia and pancytopenia induced by blocking the folate pathway.
  • the apicomplexan protozoan related disease is cryptosporidiosis.
  • Cryptosporidiosis is caused by infection with the single-celled parasite (not bacterium) Cryptosporidium parvum. This parasite is found in many mammals including lambs, calves, goat kids, piglets and humans. Research so far has shown two basic types, the bovine type which affects most species, and a second human type which causes disease in humans only. Outbreaks of human disease, where large numbers of people are affected, are usually water-borne and usually associated with the bovine type of Cryptosporidium. Individual sporadic cases of cryptosporidiosis in humans are mostly (around 60%) associated with the human type of Cryptosporidium.
  • Cryptosporidiosis affects the intestines of mammals and is typically an acute short- term infection. It is spread through the fecal-oral route, often through contaminated water; the main symptom is self-limiting diarrhea in people with intact immune systems. In immunocompromised individuals, such as HIV/AIDS patients, the symptoms are particularly severe and often fatal. Cryptosporidium is the organism most commonly isolated in HIV positive patients presenting with diarrhea. Cryptosporidiosis is one of the most common waterborne diseases and is found worldwide. The parasite is transmitted by environmentally hardy microbial cysts (oocysts) that, once ingested, exist in the small intestine and result in an infection of intestinal epithelial tissue.
  • ocysts environmentally hardy microbial cysts
  • Infection is through contaminated material such as earth, water, uncooked or cross-contaminated food that has been in contact with the feces of an infected individual or animal. It is especially prevalent amongst those in regular contact with bodies of fresh water including recreational water such as swimming pools.
  • Other potential sources include insufficiently treated or insufficiently filtered water water supplies, contaminated food, or exposure to feces.
  • Symptoms appear from two to ten days after infection, and last for up to two weeks or more. In immunocompetent people, the disease can be asymptomatic or cause acute diarrhea or persistent diarrhea that can last for a few weeks. There is often stomach pain or cramping and a low fever. Other symptoms may include nausea, vomiting, malabsorption, and dehydration.
  • Nitazoxanide has been FDA-approved for treatment of diarrhea caused by Cryptosporidium in people with healthy immune systems and is available by prescription, however it only shortens the duration of diarrhea by a couple of days. The effectiveness of nitazoxanide in immunosuppressed individuals is unclear and multiple trials have shown no benefit.
  • the inhibitors described herein may have use in other apicoplexa protozoan related diseases, such as coccidiosis caused by Eimeria spp., cause infections and disease in poultry; which causes Babesiosis which is caused by Babesia spp. and results in a malaria-like disease, and malaria in humans and animals caused by Plasmodium spp.
  • apicoplexa protozoan related diseases such as coccidiosis caused by Eimeria spp., cause infections and disease in poultry; which causes Babesiosis which is caused by Babesia spp. and results in a malaria-like disease, and malaria in humans and animals caused by Plasmodium spp.
  • the term "subject”, “individual,” or “patient,” used interchangeably, refers to any animal, including mammals, preferably mice, rats, other rodents, rabbits, dogs, cats, birds, swine, horses, livestock (e.g., pigs, sheep, goats, cattle), primates or humans.
  • mammals preferably mice, rats, other rodents, rabbits, dogs, cats, birds, swine, horses, livestock (e.g., pigs, sheep, goats, cattle), primates or humans.
  • a subject “in need thereof refers to a subject that has the disorder or disease to be treated or is predisposed to or otherwise at risk of developing the disease or disorder.
  • treatment and "treating” means
  • prophylactic use for example, preventing or limiting development of a disease, condition or disorder in an individual who may be predisposed or otherwise at risk to the disease, condition or disorder but does not yet experience or display the pathology or symptomatology of the disease;
  • inhibiting the disease for example, inhibiting a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder;
  • ameliorating the referenced disease state for example, ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e., reversing or improving the pathology and/or symptomatology) such as decreasing the severity of disease; or
  • the individual may be immunocompromised
  • the methods may further comprise administering the compounds disclosed herein to subjects at risk of acquiring an apicomplexan-related disease, such as those with compromised immune systems or that are extremely young in high risk areas.
  • the compounds described herein can be used in prophylactic manner.
  • Cryptosporidiosis is usually seen in calves between one and two weeks of age and presents with diarrhea, colic and pain, depression, loss of appetite, and weight loss.
  • calves may be treated prophylactically by providing an effective amount of a compound of any one of formulas (I) - (IV) to limit the contraction or transmission of cryptosporidiosis.
  • the administering is done within the first 7-8 days after birth (day 1, 2, 3, 4, 5, 6, 7, or 8) when calves are most susceptible to Cryptosporidia infection. Such treatments may be repeated as necessary as would be understood by one skilled in the art.
  • infected cattle may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat cryptosporidiosis. Such treatments may be repeated as necessary as would be understood by one skilled in the art.
  • the compounds of the invention may be administered together with electrolytes if cattle become dehydrated. If disease is severe, halfuginone can be used in combination with the compounds of the invention to reduce disease severity and prevent spread to other animals.
  • lambs are susceptible to cryptosporidiosis and may be provided a therapeutically effective amount of a compounds of any one of formulas (I) - (IV) to limit the contraction or transmission of cryptosporidiosis.
  • any or all members of a herd may be provided a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to limit the contraction or transmission of toxoplasmosis or cryptosporidiosis or to rid the herd of cattle of toxoplasmosis or cryptosporidiosis.
  • goat kids may be treated prophylactically by providing an effective amount of a compound of any one of formulas (I) - (IV) to limit the contraction or transmission of cryptosporidiosis.
  • the administering is done within the first 7-8 days after birth (day 1, 2, 3, 4, 5, 6, 7, or 8) when kids are most susceptible to cryptosporidiosis .
  • Such treatments may be repeated as necessary as would be understood by one skilled in the art.
  • the extent to which a kid is infected seems to be dependent on its age and immune status. Younger animals are much more susceptible to infection than adults. In studies done with lambs, five-day-old lambs had diarrhea for 9-10 days and suffered from a high rate of mortality. Sixty-day-old lambs showed no symptoms when they were infected, and adult sheep completely resisted infection. There is an indication that adults develop an immunity to Cryptosporidium, yet this immunity does not seem to be passed to their offspring.
  • Immune-depressed goats are very susceptible to the disease. This refers to the total immune status, not just protection from cryptosporidiosis. Many situations can cause animals to lack immunity. Animals with severe infections are more susceptible to secondary infections. The most common problem with kids is receiving a deficient amount of colostral antibodies following birth. Whether caused by disease, an imbalanced ration or improper management, animals lacking adequate immunity are much more susceptible to cryptosporidiosis.
  • infected goats may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat cryptosporidiosis.
  • the goat is a kid.
  • pigs are susceptible to cryptosporidiosis and may be provided a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to limit the contraction or transmission of cryptosporidiosis.
  • the administering is done within the first 21 days after birth (day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21) when piglets are most susceptible to cryptosporidiosis and/or most likely
  • infected pigs may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat cryptosporidiosis.
  • the pig is a piglet.
  • birds such as turkeys and chickens
  • Cryptosporidium baileyi can cause respiratory disease in chickens and turkeys. The same species causes infections of the hindgut and cloacal bursa in chickens, turkeys, and ducks. C. meleagridis also infects both species. A further species causes respiratory disease in quail. The oocysts are excreted ready sporulated in the faeces and infection occurs by inhalation and ingestion.
  • infected birds may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat cryptosporidiosis.
  • birds such as turkeys and chickens
  • a parasitic disease caused by the development and multiplication of coccidiosis in the epithelial cells of the intestine.
  • Eimeria infections are ubiquitous; they are found wherever chickens or turkeys are reared (traditional, industrial, label or organic/bio farms).
  • Particular strains of Eimeria known to infect birds include, but are not limited to, Eimeria acervulina.
  • infected birds may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat coccidiosis
  • mammals such as goats, sheep, llamas, alpacas, cattle, rabbits, and mice, are susceptible to coccidiosis and may be provided an effective amount of a compounds of any one of formulas (I) - (IV) to limit the contraction or spreading of Eimeria.
  • Eimeria known to infect mammals include, but are not limited to, Eimeria ahsata, Eimeria alabamensis, Eimeria alijevi, Eimeria apsheronica, Eimeria arloingi, Eimeria arundeli, Eimeria bakuensis, Eimeria bovis, Eimeria cameli, Eimeria caprina, Eimeria caprovina, Eimeria christenseni, Eimeria clethrionomyis, Eimeria coecicola, Eimeria contorta, Eimeria couesii, Eimeria crandallis, Eimeria dammahensis, Eimeria dowleri, Eimeria exigua, Eimeria falciformis, Eimeria farasanii, Eimeria ferrisi, Eimeria flavescens, Eimeria gallatii, Eimeria granulosa, Eimeria hirci, Eimeria intestinalis,
  • the usual age range for animals suffering from coccidiosis is from three weeks to one year of age, but cattle remain susceptible to coccidiosis throughout their lives or until they develop acquired immunity.
  • the susceptibility of the animals is influenced by nutritional status (colostrum supply), stress (overstocking, transport, climate, hygiene, etc.), immune status and the occurrence of concurrent diseases.
  • Eimeria bovis Eimeria bovis
  • Eimeria zuernii pathogenic coccidia species may also affect the cattle in the stables, such as Eimeria alabamensis (animals fed on contaminated hay), which is commonly associated with diarrheic problems in animals that are released to pasture.
  • Carrier hosts shed relatively fewer oocysts and the susceptible “multiplier hosts” pick up the infection and shed many-fold oocysts into the environment. Exposure to multiplier hosts leads to subclinical or mildly clinical infection in animals exposed to a large number of oocysts in the environment. Calves exposed to a large number of oocysts are likely to develop severe coccidiosis. In feedlots where few oocysts are present, stress factors such as weaning, diet, temperature extremes and other variables may make the calves more susceptible to infection and under such conditions the reproductive potential of coccidia in the gut greatly increases.
  • the compounds disclosed herein can be used to treat coccidiosis in combination with standard treatments such as, but not limited to, replacing fluids by administering liquid nutritional supplement orally by nipple bottle until the animal is rehydrated.
  • Animals that have lost 5 percent of their body weight may require intravenous (IV) and'or electrolyte therapy.
  • Treatment may include IV or subcutaneous ly (SC) fluid therapy with a physiologically balanced electrolyte such as Ringer's, Plasmalyte-A, or Normosol-R.
  • Sulfas such as AlbonTM, SulmetTM, or Di-MethoxTM, can also be mixed in the drinking water or as a drench for individual goats.
  • An alternative is CORIDTM (amprolium).
  • the phrase "therapeutically effective amount” refers to the amount of active compound or pharmaceutical agent that elicits the biological or medicinal response that is being sought in a tissue, system, animal, individual or human by a researcher, veterinarian, medical doctor or other clinician, which includes one or more of the following: (1) preventing the disease; for example, preventing a disease, condition or disorder in an individual who may be predisposed to the disease, condition or disorder but does not yet experience or display the pathology or symptomatology of the disease; (2) inhibiting the disease; for example, inhibiting a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder; and (3) ameliorating the disease; for example, ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e., reversing the pathology and/or symptomatology) such as decreasing the severity of disease.
  • preventing the disease for example, preventing a disease, condition or disorder in an
  • the inventors have identified compounds for use in treating apicomplexan-related disorders. While not being bound by a specific mechanism of action, the inventors believe that the inhibitory activity is based on selective inhibition of apicomplexan protein kinases, specifically selective inhibitors against apicomplexan calcium- dependent protein kinases (CDPKs).
  • CDPKs apicomplexan protein kinases
  • the inventors have further identified a specific region of such CDPKs that the inhibitors bind to, exemplified by SEQ ID NO: l (from the T. gondii, CDPK (SEQ ID NO: 13); (TgCDPK))) and SEQ ID NO:2 (from the C. parvum CDPK (CpCDPK)(SEQ ID NOs: 14, 15, 16, 17)).
  • another aspect of the present disclosure provides a method of identifying a compound for treating an apicomplexan-related disease, including but not limited to those disclosed above, and most preferably toxoplasmosis and cryptosporidiosis.
  • the method comprises (a) contacting a polypeptide comprising an amino acid sequence according to SEQ ID NO. 1 or SEQ ID NO:2 with a compound to be tested for the ability to bind to the polypeptide under conditions suitable for binding to the polypeptide, and (b) identifying compounds that bind to the polypeptide.
  • Suitable conditions for such binding can be determined by one of skill in the art based on the teachings herein.
  • the methods may comprise suitable wash steps to remove unbound compounds.
  • the methods may be conducted in vitro, or the binding may be assayed in cells using appropriate reporter molecules.
  • the method comprises contacting the compound with the recited peptide.
  • the compound is contacted with TgCDPK or CpCDPK.
  • the compound is contacted with TgCDPK or CpCDPK under conditions for crystallizing the complex, as described in the examples that follow.
  • the method may further comprise comparing binding of the compound to a control. Any suitable control can be used.
  • the control comprises comparing binding of the polypeptide to binding of the compound to a control polypeptide. Any suitable control polypeptide may be used.
  • control polypeptide may comprise a mutated CDPK active region, such as TgCDPKl G128M (described below), or corresponding C.parvum CDPK mutated at the gatekeeper glycine residue (CpCDPK residue 150) (as described in detail herein).
  • a mutated CDPK active region such as TgCDPKl G128M (described below), or corresponding C.parvum CDPK mutated at the gatekeeper glycine residue (CpCDPK residue 150) (as described in detail herein).
  • the gatekeeper glycine residue in any TgCDPK or CpCDPK may be mutated as described herein to replace the glycine residue with alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, or valine.
  • those compounds that show selective binding to the polypeptide and little to no binding to the control peptide are identified as selective inhibitors against apicomplexan CDPKs. Exemplary methods according to this aspect of the invention are described in the examples that follow.
  • the methods may comprise a verification step (c), comprising applying a compound selected in (b) to the relevant apicomplexan species, such Toxoplasma gondii of C. parvum, to test for inhibitory activity.
  • a verification step (c) comprising applying a compound selected in (b) to the relevant apicomplexan species, such Toxoplasma gondii of C. parvum, to test for inhibitory activity. Exemplary such assays for inhibitory activity are described in the examples herein.
  • test compounds comprise polypeptide sequences
  • polypeptides may be chemically synthesized or recombinantly expressed. Recombinant expression can be accomplished using standard methods in the art, as disclosed above.
  • expression vectors can comprise bacterial or viral expression vectors, and such host cells can be prokaryotic or eukaryotic.
  • Synthetic polypeptides prepared using the well-known techniques of solid phase, liquid phase, or peptide condensation techniques, or any combination thereof, can include natural and unnatural amino acids.
  • Amino acids used for peptide synthesis may be standard Boc (Na-amino protected Na-t-butyloxycarbonyl) amino acid resin with standard deprotecting, neutralization, coupling and wash protocols, or standard base-labile Na-amino protected 9-fluorenylmethoxycarbonyl (Fmoc) amino acids. Both Fmoc and Boc Na-amino protected amino acids can be obtained from Sigma, Cambridge Research Biochemical, or other chemical companies familiar to those skilled in the art.
  • the polypeptides can be synthesized with other Na-protecting groups that are familiar to those skilled in this art. Solid phase peptide synthesis may be accomplished by techniques familiar to those in the art and provided, such as by using automated synthesizers.
  • test compounds comprise antibodies
  • such antibodies can be polyclonal or monoclonal.
  • the antibodies can be humanized, fully human, or murine forms of the antibodies.
  • Such antibodies can be made by well-known methods, such as described in Harlow and Lane, Antibodies; A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1988).
  • nucleic acids may be chemically synthesized or recombinantly expressed as well. Recombinant expression techniques are well known to those in the art (See, for example, Sambrook, et al., 1989, supra).
  • the nucleic acids may be DNA or RNA, and may be single stranded or double.
  • such nucleic acids can be chemically or enzymatically synthesized by manual or automated reactions, using standard techniques in the art. If synthesized chemically or by in vitro enzymatic synthesis, the nucleic acid may be purified prior to introduction into the cell.
  • the nucleic acids can be purified from a mixture by extraction with a solvent or resin, precipitation, electrophoresis, chromatography, or a combination thereof.
  • the nucleic acids may be used with no or a minimum of purification to avoid losses due to sample processing.
  • test compounds comprise compounds other than polypeptides, antibodies, or nucleic acids
  • such compounds can be made by any of the variety of methods in the art for conducting organic chemical synthesis.
  • compositions described herein generally comprise a combination of a compound described herein and a pharmaceutically acceptable carrier, diluent, or excipient. Such compositions are substantially free of non-pharmaceutically acceptable components, i.e., contain amounts of non-pharmaceutically acceptable components lower than permitted by US regulatory requirements at the time of filing this application.
  • the composition further optionally comprises an additional pharmaceutically acceptable carrier, diluent, or excipient.
  • the pharmaceutical compositions described herein are solid pharmaceutical compositions (e.g., tablet, capsules, etc.).
  • compositions can be prepared in a manner well known in the pharmaceutical art, and can be administered by a variety of routes, depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including intranasal, vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), ocular, oral or parenteral.
  • topical including ophthalmic and to mucous membranes including intranasal, vaginal and rectal delivery
  • pulmonary e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal
  • ocular oral or parenteral.
  • Methods for ocular delivery can include topical administration (eye drops), subconjunctival, periocular or intravitreal injection or introduction by balloon catheter or ophthalmic inserts surgically placed in the conjunctival sac.
  • Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration.
  • Parenteral administration can be in the form of a single bolus dose, or may be, for example, by a continuous perfusion pump.
  • Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
  • compositions can contain, as the active ingredient, one or more of the compounds described herein above in combination with one or more pharmaceutically acceptable carriers.
  • the active ingredient is typically mixed with an excipient, diluted by an excipient or enclosed within such a carrier in the form of, for example, a capsule, sachet, paper, or other container.
  • the excipient serves as a diluent, it can be a solid, semi-solid, or liquid material, which acts as a vehicle, carrier or medium for the active ingredient.
  • compositions can be in the form of tablets, pills, powders, lozenges, sachets, cachets, elixirs, suspensions, emulsions, solutions, syrups, aerosols (as a solid or in a liquid medium), ointments containing, for example, up to 10% by weight of the active compound, soft and hard gelatin capsules, suppositories, sterile injectable solutions, and sterile packaged powders.
  • the active compound can be milled to provide the appropriate particle size prior to combining with the other ingredients. If the active compound is substantially insoluble, it can be milled to a particle size of less than 200 mesh. If the active compound is substantially water soluble, the particle size can be adjusted by milling to provide a substantially uniform distribution in the formulation, e.g. about 40 mesh.
  • excipients include lactose, dextrose, sucrose, sorbitol, mannitol, starches, gum acacia, calcium phosphate, alginates, tragacanth, gelatin, calcium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrup, and methyl cellulose.
  • the formulations can additionally include: lubricating agents such as talc, magnesium stearate, and mineral oil; wetting agents; emulsifying and suspending agents; preserving agents such as methyl- and propylhydroxy-benzoates; sweetening agents; and flavoring agents.
  • the compositions described herein can be formulated so as to provide quick, sustained or delayed release of the active ingredient after administration to the patient by employing procedures known in the art.
  • compositions can be formulated in a unit dosage form, each dosage containing from about 5 to about 100 mg, more usually about 10 to about 30 mg, of the active ingredient.
  • unit dosage forms refers to physically discrete units suitable as unitary dosages for human subjects and other mammals, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect, in association with a suitable pharmaceutical excipient.
  • the active compound can be effective over a wide dosage range and is generally administered in a pharmaceutically effective amount. It will be understood, however, that the amount of the compound actually administered will usually be determined by a physician, according to the relevant circumstances, including the condition to be treated, the chosen route of administration, the actual compound administered, the age, weight, and response of the individual patient, the severity of the patient's symptoms, and the like.
  • the principal active ingredient is mixed with a pharmaceutical excipient to form a solid preformulation composition containing a homogeneous mixture of a compound described herein.
  • a solid preformulation composition containing a homogeneous mixture of a compound described herein.
  • the active ingredient is typically dispersed evenly throughout the composition so that the composition can be readily subdivided into equally effective unit dosage forms such as tablets, pills and capsules.
  • This solid preformulation is then subdivided into unit dosage forms of the type described above containing from, for example, 0.1 to about 500 mg of the active ingredient of a compound described herein.
  • the tablets or pills can be coated or otherwise compounded to provide a dosage form affording the advantage of prolonged action.
  • the tablet or pill can comprise an inner dosage and an outer dosage component, the latter being in the form of an envelope over the former.
  • the two components can be separated by an enteric layer which serves to resist disintegration in the stomach and permit the inner component to pass intact into the duodenum or to be delayed in release.
  • enteric layers or coatings such materials including a number of polymeric acids and mixtures of polymeric acids with such materials as shellac, cetyl alcohol, and cellulose acetate.
  • liquid forms in which the compounds and compositions can be incorporated for administration orally or by injection include aqueous solutions, suitably flavored syrups, aqueous or oil suspensions, and flavored emulsions with edible oils such as cottonseed oil, sesame oil, coconut oil, or peanut oil, as well as elixirs and similar pharmaceutical vehicles.
  • compositions for inhalation or insufflation include solutions and suspensions in pharmaceutically acceptable, aqueous or organic solvents, or mixtures thereof, and powders.
  • the liquid or solid compositions may contain suitable pharmaceutically acceptable excipients as described supra.
  • the compositions are administered by the oral or nasal respiratory route for local or systemic effect.
  • Compositions in can be nebulized by use of inert gases. Nebulized solutions may be breathed directly from the nebulizing device or the nebulizing device can be attached to a face masks tent, or intermittent positive pressure breathing machine. Solution, suspension, or powder compositions can be administered orally or nasally from devices which deliver the formulation in an appropriate manner.
  • compositions can be administered to a patient already suffering from a disease in an amount sufficient to cure or at least partially arrest the symptoms of the disease and its complications. Effective doses will depend on the disease condition being treated as well as by the judgment of the attending clinician depending upon factors such as the severity of the disease, the age, weight and general condition of the patient, and the like.
  • compositions administered to a patient can be in the form of pharmaceutical compositions described above. These compositions can be sterilized by conventional sterilization techniques, or may be sterile filtered. Aqueous solutions can be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile aqueous carrier prior to administration.
  • the pH of the compound preparations typically will be between 3 and 11, more preferably from 5 to 9 and most preferably from 7 to 8. It will be understood that use of certain of the foregoing excipients, carriers, or stabilizers will result in the formation of pharmaceutical salts.
  • the therapeutic dosage of the compounds can vary according to, for example, the particular use for which the treatment is made, the manner of administration of the compound, the health and condition of the patient, and the judgment of the prescribing physician.
  • the proportion or concentration of a compound described herein in a pharmaceutical composition can vary depending upon a number of factors including dosage, chemical characteristics (e.g., hydrophobicity), and the route of administration.
  • the compounds described herein can be provided in an aqueous physiological buffer solution containing about 0.1 to about 10% w/v of the compound for parenteral administration. Some typical dose ranges are from about 1 ⁇ g/kg to about 1 g/kg of body weight per day.
  • the dose range is from about 0.01 mg/kg to about 100 mg/kg of body weight per day.
  • the dosage is likely to depend on such variables as the type and extent of progression of the disease or disorder, the overall health status of the particular patient, the relative biological efficacy of the compound selected, formulation of the excipient, and its route of administration. Effective doses can be extrapolated from dose-response curves derived from in vitro or animal model test systems.
  • the compounds described herein can also be formulated in combination with one or more additional active ingredients which can include any pharmaceutical agent such as anti-viral agents, vaccines, antibodies, immune enhancers, immune suppressants, anti-inflammatory agents and the like.
  • alkenyl as used herein, means a straight or branched chain hydrocarbon containing from 2 to 10 carbons, unless otherwise specified, and containing at least one carbon-carbon double bond.
  • alkenyl include, but are not limited to, ethenyl, 2-propenyl, 2-methyl-2-propenyl, 3-butenyl, 4-pentenyl, 5-hexenyl, 2-heptenyl, 2-methyl-l-heptenyl, 3-decenyl, and 3,7-dimethylocta-2,6-dienyl.
  • alkyl as used herein, means a straight or branched chain hydrocarbon containing from 1 to 10 carbon atoms, unless otherwise specified.
  • Representative examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec -butyl, iso-butyl, tert-butyl, n-pentyl, isopentyl, neopentyl, n-hexyl, 3-methylhexyl, 2,2-dimethylpentyl, 2,3-dimethylpentyl, n-heptyl, n-octyl, n-nonyl, and n-decyl.
  • an “alkyl” group is a linking group between two other moieties, then it may also be a straight or branched chain; examples include, but are not limited to -CH 2 -, -CH 2 CH 2 -, -CH 2 CH 2 CHC(CH 3 )-, -CH 2 CH(CH 2 CH 3 )CH 2 -.
  • alkynyl as used herein, means a straight or branched chain hydrocarbon group containing from 2 to 10 carbon atoms and containing at least one carbon-carbon triple bond.
  • Representative examples of alkynyl include, but are not limited, to acetylenyl, 1-propynyl, 2-propynyl, 3-butynyl, 2-pentynyl, and 1-butynyl.
  • aryl means a phenyl (i.e., monocyclic aryl), a bicyclic ring system containing at least one phenyl ring or an aromatic bicyclic ring containing only carbon atoms in the aromatic bicyclic ring system or a multicyclic aryl ring system, provided that the bicyclic or multicyclic aryl ring system does not contain a heteroaryl ring when fully aromatic.
  • the bicyclic aryl can be azulenyl, naphthyl, or a phenyl fused to a monocyclic cycloalkyl, a monocyclic cycloalkenyl, or a monocyclic heterocyclyl.
  • the bicyclic aryl is attached to the parent molecular moiety through any carbon atom contained within the phenyl portion of the bicyclic system, or any carbon atom with the napthyl or azulenyl ring.
  • the fused monocyclic cycloalkyl or monocyclic heterocyclyl portions of the bicyclic aryl are optionally substituted with one or two oxo and/or thia groups.
  • bicyclic aryls include, but are not limited to, azulenyl, naphthyl, dihydroinden-l-yl, dihydroinden-2-yl, dihydroinden-3-yl, dihydroinden-4-yl, 2,3-dihydroindol-4-yl, 2,3-dihydroindol-5-yl, 2,3-dihydroindol-6-yl, 2,3-dihydroindol-7-yl, inden-l-yl, inden-2-yl, inden-3-yl, inden-4-yl, dihydronaphthalen-2-yl, dihydronaphthalen-3-yl, dihy dronaphthalen-4-y 1, dihy dronaphthalen- 1 -yl, 5,6,7 , 8-tetrahy dronaphthalen- 1 -y 1, 5,6,7,8-tetrahydronaphthalen-2-
  • the bicyclic aryl is (i) naphthyl or (ii) a phenyl ring fused to either a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclic heterocyclyl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • Multicyclic aryl groups are a phenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl, provided that when the base ring is fused to a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl, then the base ring is fused to the base ring of the a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocycly
  • multicyclic aryl is attached to the parent molecular moiety through any carbon atom contained within the base ring.
  • multicyclic aryl groups are a phenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl, provided that when the base ring is fused to a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl, then the base ring is fused to the base ring of the a bicyclic cycloalkyl, bicyclic cyclooalky
  • arylalkyl and “-alkylaryl” as used herein means an aryl group, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.
  • Representative examples of arylalkyl include, but are not limited to, benzyl, 2-phenylethyl, 3-phenylpropyl, and 2-naphth-2-ylethyl.
  • cyano and "nitrile” as used herein, mean a -CN group.
  • cycloalkyl as used herein, means a monocyclic, bicyclic, or a multicyclic cycloalkyl ring system.
  • Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups can be saturated or unsaturated, but not aromatic. In certain embodiments, cycloalkyl groups are fully saturated. Examples of monocyclic cycloalkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, and cyclooctyl.
  • Bicyclic cycloalkyl ring systems are bridged monocyclic rings or fused bicyclic rings.
  • Bridged monocyclic rings contain a monocyclic cycloalkyl ring where two non-adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form -(CH 2 ) W -, where w is 1, 2, or 3).
  • bicyclic ring systems include, but are not limited to, bicyclo[3.1.1]heptane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, bicyclo[3.3.1]nonane, and bicyclo[4.2.1]nonane.
  • Fused bicyclic cycloalkyl ring systems contain a monocyclic cycloalkyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl.
  • the bridged or fused bicyclic cycloalkyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkyl ring.
  • Cycloalkyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • the fused bicyclic cycloalkyl is a 5 or 6 membered monocyclic cycloalkyl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused bicyclic cycloalkyl is optionally substituted by one or two groups which are independently oxo or thia.
  • Multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other rings systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl.
  • multicyclic cycloalkyl is attached to the parent molecular moiety through any carbon atom contained within the base ring.
  • multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other rings systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl.
  • Examples of multicyclic cycloalkyl groups include, but are not limited to tetradecahydrophenanthrenyl, perhydrophenothiazin-l-yl,
  • Cycloalkenyl refers to a monocyclic, bicyclic, or a multicyclic cycloalkenyl ring system.
  • Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups are unsaturated (i.e., containing at least one annular carbon-carbon double bond), but not aromatic. Examples of monocyclic ring systems include cyclopentenyl and cyclohexenyl.
  • Bicyclic cycloalkenyl rings are bridged monocyclic rings or a fused bicyclic rings.
  • Bridged monocyclic rings contain a monocyclic cycloalkenyl ring where two non-adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form -(CH 2 ) W -, where w is 1, 2, or 3).
  • alkylene bridge of between one and three additional carbon atoms
  • bicyclic cycloalkenyls include, but are not limited to, norbornenyl and bicyclo[2.2.2]oct-2-enyl.
  • Fused bicyclic cycloalkenyl ring systems contain a monocyclic cycloalkenyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl.
  • the bridged or fused bicyclic cycloalkenyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkenyl ring.
  • Cycloalkenyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • Multicyclic cycloalkenyl rings contain a monocyclic cycloalkenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two rings systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl.
  • multicyclic cycloalkenyl is attached to the parent molecular moiety through any carbon atom contained within the base ring.
  • multicyclic cycloalkenyl rings contain a monocyclic cycloalkenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two rings systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl.
  • halo or halogen as used herein, means -CI, -Br, -I or -F.
  • haloalkyl as used herein, means at least one halogen, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.
  • Representative examples of haloalkyl include, but are not limited to, chloromethyl, 2-fluoroethyl, trifluoromethyl, pentafluoroethyl, and 2-chloro-3-fluoropentyl.
  • heteroaryl means a monocyclic, bicyclic, or a multicyclic heteroaryl ring system.
  • the monocyclic heteroaryl can be a 5 or 6 membered ring.
  • the 5 membered ring consists of two double bonds and one, two, three or four nitrogen atoms and optionally one oxygen or sulfur atom.
  • the 6 membered ring consists of three double bonds and one, two, three or four nitrogen atoms.
  • the 5 or 6 membered heteroaryl is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heteroaryl.
  • monocyclic heteroaryl include, but are not limited to, furyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl, oxazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, pyrazolyl, pyrrolyl, tetrazolyl, thiadiazolyl, thiazolyl, thienyl, triazolyl, and triazinyl.
  • the bicyclic heteroaryl consists of a monocyclic heteroaryl fused to a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl.
  • the fused cycloalkyl or heterocyclyl portion of the bicyclic heteroaryl group is optionally substituted with one or two groups which are independently oxo or thia.
  • the bicyclic heteroaryl contains a fused cycloalkyl, cycloalkenyl, or heterocyclyl ring
  • the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon or nitrogen atom contained within the monocyclic heteroaryl portion of the bicyclic ring system.
  • the bicyclic heteroaryl is a monocyclic heteroaryl fused to a phenyl ring or a monocyclic heteroaryl, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom within the bicyclic ring system.
  • bicyclic heteroaryl include, but are not limited to, benzimidazolyl, benzofuranyl, benzothienyl, benzoxadiazolyl, benzoxathiadiazolyl, benzothiazolyl, cinnolinyl, 5,6-dihydroquinolin-2-yl, 5,6-dihydroisoquinolin-l-yl, furopyridinyl, indazolyl, indolyl, isoquinolinyl, naphthyridinyl, quinolinyl, purinyl, 5,6,7,8-tetrahydroquinolin-2-yl, 5,6,7,8-tetrahydroquinolin-3-yl, 5,6,7,8-tetrahydroquinolin-4-yl, 5,6,7,8-tetrahydroisoquinolin-l-yl, thienopyridinyl, 4,5,6,7 -tetrahy d
  • the fused bicyclic heteroaryl is a 5 or 6 membered monocyclic heteroaryl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • the multicyclic heteroaryl group is a monocyclic heteroaryl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic heterocyclyl, a bicyclic cycloalkenyl, and a bicyclic cycloalkyl; or (ii) two ring systems selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic heterocyclyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic cycloalkyl.
  • multicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom contained within the base ring.
  • multicyclic heteroaryl groups are a monocyclic heteroaryl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic heterocyclyl, a bicyclic cycloalkenyl, and a bicyclic cycloalkyl; or (ii) two ring systems selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic heterocyclyl, a monocyclic cycloalkenyl, and a monocyclic cycloalkyl.
  • multicyclic heteroaryls include, but are not limited to 5H- [l,2,4]triazino[5,6-b]indol-5-yl, 2,3,4,9-tetrahydro-lH-carbazol-9-yl, 9H-pyrido[3,4-b]indol- 9-yl, 9H-carbazol-9-yl, acridin-9-yl,
  • heteroarylalkyl and "-alkylheteroaryl” as used herein, means a heteroaryl, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.
  • Representative examples of heteroarylalkyl include, but are not limited to, fur-3-ylmethyl, lH-imidazol-2-ylmethyl, lH-imidazol-4-ylmethyl, l-(pyridin-4-yl)ethyl, pyridin-3-ylmethyl, pyridin-4-ylmethyl, pyrimidin-5-ylmethyl, 2-(pyrimidin-2-yl)propyl, thien-2-ylmethyl, and thien-3-ylmethyl.
  • heterocyclyl as used herein, means a monocyclic, bicyclic, or multicyclic heterocycle.
  • the monocyclic heterocycle is a 3, 4, 5, 6 or 7 membered ring containing at least one heteroatom independently selected from the group consisting of 0, N, and S where the ring is saturated or unsaturated, but not aromatic.
  • the 3 or 4 membered ring contains 1 heteroatom selected from the group consisting of 0, N and S.
  • the 5 membered ring can contain zero or one double bond and one, two or three heteroatoms selected from the group consisting of 0, N and S.
  • the 6 or 7 membered ring contains zero, one or two double bonds and one, two or three heteroatoms selected from the group consisting of 0, N and S.
  • the monocyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the monocyclic heterocycle.
  • Representative examples of monocyclic heterocycle include, but are not limited to, azetidinyl, azepanyl, aziridinyl, diazepanyl, 1,3-dioxanyl, 1,3-dioxolanyl, 1,3-dithiolanyl, 1,3-dithianyl, imidazolinyl, imidazolidinyl, isothiazolinyl, isothiazolidinyl, isoxazolinyl, isoxazolidinyl, morpholinyl, oxadiazolinyl, oxadiazolidinyl, oxazolinyl, oxazolidinyl, piperazinyl, piperidinyl, pyranyl, pyrazolinyl, pyrazolidinyl, pyr
  • the bicyclic heterocycle is a monocyclic heterocycle fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocycle, or a monocyclic heteroaryl.
  • the bicyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the monocyclic heterocycle portion of the bicyclic ring system.
  • bicyclic heterocyclyls include, but are not limited to, 2,3-dihydrobenzofuran-2-yl, 2,3-dihydrobenzofuran-3-yl, indolin-l-yl, indolin-2-yl, indolin-3-yl, 2,3-dihydrobenzothien-2-yl, decahydroquinolinyl, decahydroisoquinolinyl, octahydro-lH-indolyl, and octahydrobenzofuranyl.
  • Heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.
  • the bicyclic heterocyclyl is a 5 or 6 membered monocyclic heterocyclyl ring fused to phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the bicyclic heterocyclyl is optionally substituted by one or two groups which are independently oxo or thia.
  • Multicyclic heterocyclyl ring systems are a monocyclic heterocyclyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other rings systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl.
  • multicyclic heterocyclyl is attached to the parent molecular moiety through any carbon atom or nitrogen atom contained within the base ring.
  • multicyclic heterocyclyl ring systems are a monocyclic heterocyclyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other rings systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl.
  • multicyclic heterocyclyl groups include, but are not limited to lOH-phenothiazin-10-yl, 9,10-dihydroacridin-9-yl, 9,10-dihydroacridin-lO-yl, 10H- phenoxazin-10-yl, 10, l l-dihydro-5H-dibenzo[b,f]azepin-5-yl, l,2,3,4-tetrahydropyrido[4,3- g]isoquinolin-2-yl, 12H-benzo[b]phenoxazin-12-yl, and dodecahydro-lH-carbazol-9-yl.
  • nitro as used herein, means a -N0 2 group.
  • saturated as used herein means the referenced chemical structure does not contain any multiple carbon-carbon bonds.
  • a saturated cycloalkyl group as defined herein includes cyclohexyl, cyclopropyl, and the like.
  • unsaturated means the referenced chemical structure contains at least one multiple carbon-carbon bond, but is not aromatic.
  • a unsaturated cycloalkyl group as defined herein includes cyclohexenyl, cyclopentenyl, cyclohexadienyl, and the like.
  • pharmaceutically acceptable salt refers to both pharmaceutically acceptable acid and base addition salts and solvates.
  • Such pharmaceutically acceptable salts include salts of acids such as hydrochloric, phosphoric, hydrobromic, sulfuric, sulfmic, formic, toluenesulfonic, methanesulfonic, nitric, benzoic, citric, tartaric, maleic, hydroiodic, alkanoic such as acetic, HOOC-(CH 2 ) n -COOH where n is 0-4, and the like.
  • Non-toxic pharmaceutical base addition salts include salts of bases such as sodium, potassium, calcium, ammonium, and the like. Those skilled in the art will recognize a wide variety of non-toxic pharmaceutically acceptable addition salts.
  • the two exemplary synthetic routes described below can be used to generate derivatives that contain varying substituents at the 1- and 3 -positions of the pyrazolopyrimidine core (Schemes 1 and 2).
  • the first series of analogs retain the naphthylmethylene substituent at the 3 -position and contain various alkyl groups at the 1- position. Synthesis of these analogs began with conversion of 1 -naphthalene acetyl chloride to pyrazolopyrimidine 4 in five steps (Scheme 1). (16)
  • the second series of derivatives can be generated with a synthetic route that allows various substituents to be introduced at the 3 -position of the pyrazolopyrimidine core (Scheme 2).
  • la-lab Iodinated pyrazolopyrimidine 6 can be generated in three steps from commercially available 5-amino-lH-pyrazole-4-carbonitrile.
  • Various aryl substituents can be introduced by coupling boronic acids and boronic esters to 6 using standard palladium-catalyzed cross- coupling conditions.
  • Flash chromatography was performed on prepacked columns of silica gel (Varian SF10-4g, Si 50) by IntelliFlash with EtOAc/hexanes or MeOH/CH 2 Cl 2 as eluent.
  • the purification by preparative HPLC was performed on Varian Dynamax Microsorb 100-5 CI 8 column (250 mm x 21.4 mm) with CH 3 CN/H 2 0 or MeOH/H 2 0 and 0.05% TFA as eluent.
  • the mass spectra were recorded with the Bruker Esquire Liquid Chromatograph - Ion Trap Mass Spectrometer.
  • the desired product was collected and subsequently deprotected by stirring in a mixture of trifluoroactetic acid (.5 mL) and dicholoromethane (.5 mL) for 2 h.
  • the reaction mixture was concentrated in vacuo to yield the final compound.
  • Acetaldehyde (10 equiv), sodium triacetoxyborohydride (3 equiv), diisopropylethylamine (0.75 equiv), and a catalytic amount of acetic acid were added to 5g-5i (.028 mmol) and dissolved in dichloroethane (200 ⁇ ). The reaction was allowed to stir at room temperature overnight. The reaction mixture was diluted with methanol and water and purified using reverse-phase preparative HPLC with a methanol/water gradient.
  • Example 38 Preparation of Compound 7g 7g was synthesized using 3-methylphenylboronic acid in General Procedure F.
  • MS (ESI) (M + H) + 268.4.
  • Example 59 Preparation of Compound 7ab 7ab was synthesized using 3-Methylthiophenylboronic acid in General Procedure F.
  • Example 71 General Procedure H Intermediates L or O (0.03 mmol), tetrakis(triphenylphosphine) palladium(O) (0.05 equiv), and sodium carbonate (2.3 equiv) were added to the appropriate boronic acid or pinacol ester (1.1 equiv) in dimethoxyethane (1 mL) and water (0.5 mL). The reaction was performed in a microwave at 85°C for one hour, followed by extraction with ethyl acetate and water. The organic layer was collected and concentrated in vacuo to yield the crude product. The crude product was then purified via flash chromatography with an ethyl acetate/hexanes gradient.
  • the two Ca -binding EF-hand lobes and connecting extended helical stem of the calmodulin-like regulatory domain lie along one face of the kinase domain, adjacent to the active site ( Figure 2a).
  • the kinase and regulatory domains are connected by an intervening helical junction domain characteristic of this class of kinases 18 .
  • the conformation represented by these structures is likely an inactive form of the enzyme since the calmodulin- like domain occludes the surface required for recognition of target proteins and peptides.
  • the ATP binding site remains accessible to small molecule substrates and inhibitors.
  • kinase inhibitors bind in the ATP-binding pocket of the active site 19,20 . These inhibitors exploit many of the same hydrophobic contacts as the purine ring of ATP and make at least one conserved hydrogen bond to the hinge region. Potent inhibitors also occupy at least one hydrophobic pocket adjacent to the ATP-binding site. These additional hydrophobic interactions increase both binding affinity and target selectivity of the inhibitor because there is substantial heterogeneity among different kinases in these regions.
  • Examination of the JgCDPKl sequence in the vicinity of the ATP-binding pocket shows that it contains a glycine residue at a position that has been termed the gatekeeper
  • IgCDPKl The glycine at this position in IgCDPKl (Gly 128) is expected to create a much larger pocket off the ATP-binding site than is typically seen in protein kinases and comparison of the IgCDPKl structure with other kinases shows that this is indeed the case. This difference in the active site architectures can be exploited for design of selective inhibitors against IgCDPKl .
  • BKIs are analogs of 4-amino-l-3 ⁇ 4/t- butyl-3-phenylpyrazolo[3,4-d]pyrimidine (Table 2) that are derivatized at C3 with bulky
  • JgCDPKl The mode of action of JgCDPKl is unknown but its localization in the cell might provide clues to its cellular function.
  • TgCDPKl was fused with green fluorescent protein (GFP) to facilitate its localization within live intracellular T. gondii.
  • GFP green fluorescent protein
  • TgCDPKl-GFP was found in both the cytosol and the nucleus ( Figure 3). Similar findings were obtained when the GFP tag was replaced with a C-terminal hemagglutinin (HA) tag.
  • HA hemagglutinin
  • T. gondii expressing CDPK1-GFP, CDPK1(G128M)-GFP, or GFP were mixed with the indicated concentration of NA-PP2 and added to the fibroblast monolayer for 15 min at 4 °C to allow binding (Kafsack et al). The samples were then raised to 37 °C for 4 min to allow invasion. Samples were fixed, washed, and stained with antibody to T. gondii surface antigens (SAG, Argene) to identify extracellular parasites.
  • Figure 8(a) is a representative image from the untreated CDPK-GFP dataset. Intracellular parasites are marked by asterisks.
  • Figure 8(b) shows the change in the number of intracellular parasites upon drug treatment.
  • the number of intracellular parasites was determined by subtracting the number of extracellular parasites (SAG+) by the number of total parasites (GFP+) and expressed as a ratio to the number of host cells observed (as measured by DAPIstained nuclei). Each sample was normalized to the untreated control of the same line.
  • Figure 8(c) shows the data used to derive the graph in panel b. Note that cells expressing the gatekeeper mutant CDPK1(G128M) are less sensitive to the drug. The drug additionally appears to affect adhesion.
  • T. gondii overexpressing CDPK1-GFP, CDPK1(G128M)-GFP, or GFP were mixed with wild type cells (105 of each) in medium with or without 1 ⁇ NA-PP2. Parasites were allowed to infect fibroblasts on cover slips and grown overnight. Samples were stained with DAPI to identify host and parasite nuclei and vacuoles with 2 or more T. gondii cells (only fully invaded parasites can replicate) were counted. Each vacuole was assessed for GFP expression by the parasites.
  • Figure 9(a) is a representative set of images of CDPK1(G128M)- GFP mixed with wild type, in the absence of drug.
  • Vacuoles containing multiple GFP- expressing parasites are marked with * and wild type vacuoles are marked with - .
  • Figure 9(b) shows the number of vacuoles with wild type (GFP-) or transfectedparasites (GFP+), per host cell nucleus, in the absence and presence of drug for the three cell mixtures.
  • Figure 9(c) shows Data used to derive the graphs. Note that the parasite line overexpressing CDPK1(G128M)-GFP wasresistant to the effects of 1 ⁇ NA-PP2, as compared to the co- cultured wild type control.
  • JgCDPKl is a promising drug target for the therapy of toxoplasmosis. Its kinase activity is uniquely sensitive to inhibition by BKIs, and BKI treatment in turn blocks entry of the parasite into mammalian cells. Blocking cell entry is important because T. gondii is an obligate intracellular parasite and cannot replicate without invasion. Moreover, these experimental findings address concerns about quantitative differences between enzyme inhibition and cellular effects thereby validating the utility of JgCDPKl structures in complex with BKIs to drive drug development for toxoplasmosis therapy. The concept of using BKIs for the therapy of toxoplasmosis is bolstered by the fact that BKIs have been used in mouse studies with no demonstration of toxicity or troublesome
  • BKIs have promise; as a selective drug for toxoplasmosis therapy because they are non-toxic to mammals but prevent cell entry and thus the replication of J. gondii.
  • TgCDPKl was localized in the cytoplasm, but also found in the nucleus. Some plant CDPKs are also partially localized to the nucleus. In those CDPKs, nuclear localization is mediated by a signal in the junction domain 18 , but the T. gondii protein is not homologous in this region and no nuclear localization signal is predicted by standard programs. Since the size of the protein is above the threshold for free diffusion through the nuclear pore, we propose that the protein could bear a non-canonical nuclear localization sequence or piggyback into the nucleus on another protein.
  • TgCDPKl gatekeeper Drug-resistant mutations of the TgCDPKl gatekeeper to a bulky residue could eventually emerge under selective pressure of BKI therapy.
  • One strategy to suppress the emergence of resistance is the co-administration of two drugs targeting different proteins.
  • TgCDPKl is not the target of any existing drug
  • the development of an anti-TgCDPKl compound could provide a partner drug for co-administration with another drug.
  • Most transmission of T. gondii is not from person-to-person (although this can occur in pregnancy, transplantation, or transfusion), but rather through zoonotic cycles where drug pressure is not exerted . This suggests that if drug resistance emerges it will largely be confined to the individual, posing little threat to the utility of the drug in other infected persons.
  • TgCDPKl (GI: 12484153, ToxoDB ID 162.m00001) or its G128M mutant, cloned into pAVA0421, was expressed in BL21 *(DE3) E. coli (Invitrogen Corp. Carlsbad, USA) for 72 hours at 20°C in a LEX Bioreactor (Harbinger Biotechnology & Engineering Corp. Ontario Canada).
  • N terminal hexahistidine tag was removed by 3C protease cleavage at a 1 :50 mg ratio and dialyzed overnight at 4°C in 200mM NaCl, 20 mM HEPES, 5% glycerol, 1 mM TCEP, pH 7.0 with final separation on Ni 2+ SepharoseTM 6 Fast Flow resin. Fractions were analyzed for purity by SDS-polyacrylamide gel electrophoresis and found to be >99% pure.
  • ATP consumption kinase assays were performed using a nonradioactive inaseGlo ® luciferase assay (Promega Corp., Madison, WI, USA).
  • Kinase phosphorylation reactions were performed in a buffered medium containing 20 mM HEPES pH 7.5 (KOH), 0.1% BSA, lOmM MgCl 2 , ImM EGTA (pH 7.2), plus or minus 2mM CaCl 2 14 .
  • the phosphorylation reaction mixture of 40 ⁇ peptide substrate (Syntide-2, peptide sequence: Pro-Leu-Ala-Arg-Thr-Leu-Ser-Val-Ala-Gly-Leu-Pro-Gly-Lys-Lys (SEQ ID NO: 12)) (GenScript, Piscataway, USA), 19.48 nM ofl4 TgCDPKl, 90 to 0.0005 ⁇ serial dilutions of inhibitor in a total volume of 25 ⁇ , was initiated by the addition of 10 ⁇ ATP. The reaction was terminated after 30 minutes incubation at 30 C by addition of excess EGTA (5 mM final concentration). Internal positive and negative controls were included in each assay run.
  • Dpn I digested PCR products was transformed into XLIO-Gold ultracompetent E. coli cell (Stratagene) with selection on LB agar supplemented with 100 g/ml ampicillin. Mutant plasmids was recovered with alkaline denaturation method using the QIAGEN plasmid purification kits and verified by nucleotide sequence analysis before transformation into protein expression E. coli strain BL21 *(DE3) (Invitrogen Corp. Carlsbad, USA). Induction of expression and purification of mutant TgCDPKl(G128M) in E. coli BL21*(DE3) (Invitrogen Corp. Carlsbad, USA) was previously described 30 .
  • TgCDPKl protein was screened for crystallization leads using a Phoenix crystallization robot (Art Robbins Instruments, Sunnyvale, CA) and the JCSG+ Suite sparse
  • SSRL SSRL Automated mounting
  • SAM SSRL automated mounting
  • All data were collected at 100 K on a MarMosaic-325 CCD detector using the Blu-Ice software package 33 .
  • Single-wavelength anomalous dispersion (SAD) data were collected from a single crystal of SeMet protein 34 at a wavelength of 0.9792 A, the Se peak wavelength determined from a fluorescence scan of the crystal. All other datasets were also collected at or near the Se peak wavelength; apo (native) at 0.9792 A, NA-PP2 complex (SeMet) at 0.9791 A, and NM-PP1 complex (native) at 0.9795 A. All data were processed using HKL2000 35 . Data collection statistics are presented in Table 1.
  • SOLVE 38 located 12 of 14 expected selenium atoms and produced initial phases to approximately 2.7 A.
  • the resulting phases were input into RESOLVE 38 using the RESOLVE BUILD script (http://www.solve.lanl.gov/Resolve/html_resolve_manual/resolve_build.txt) for density modification and automated model building.
  • the model was significantly improved by bootstrapping the results back into the RESOLVE_BUILD script two more times for rebuilding. Iterated manual model building and restrained refinement continued using Coot39 and REFMAC5 40 .
  • the TgCDPKl coding region or its G128M mutant were amplified from the E. coli expression plasmids using primers to insert 3 adenine nucleotides before the start codon and mutate the second codon from glycine to alanine, allowing for enhanced expression in the parasite 49 .
  • the products were inserted into the Bglll/Avrll site of T. gondii transfection vector pCAT-GFP 50 or pHx-ACP-YFP 51 to yield in frame fusions with GFP or YFP, under the control of the tubA or Gral promoters respectively.
  • Plasmids encoding HA-tagged versions of the molecules were created by replacing the YFP sequence with one that specifies four C- terminal HA epitopes.
  • Linearized constructs were electroporated into RH strain T. gondii according to standard methods 52 and transfected parasites were used to infect human foreskin fibroblasts growing on cover slips.
  • T. gondii strain expressing ⁇ - galactosidase under control of the TubA promoter, as well as GFP under control of the GRA1 promoter was employed (kind gift of Gustavo Arrizabalaga) 53 .
  • T. gondii cells expressing ⁇ -galactosidase were grown in the presence of serial concentrations of BKIs. All assays were performed in triplicate and the mean and standard deviation are presented unless otherwise noted. In the growth assays, 10 3 parasites were allowed to infect a confluent layer of fibroblasts in each well of a 96 well plate. After 4 hr, drug was added to the indicated final concentration. To assess effects on invasion, compounds were added prior to the addition of the parasites. The cultures were incubated for
  • Cytotoxicity was analyzed by adding medium containing up to 50 ⁇ of each compound to a confluent layer of fibroblasts; plates were incubated at 37 C for 4 days. Alamar blue (Alamar Biosciences, Sacramento, CA) was added to each well and developed over night.
  • parvum sporozoites are observed with increasing concentrations of compounds 1-3 under both sets of conditions, with analogue 2 demonstrating the most potent effect on parasite proliferation similar to analogue 2's superior potency against Q?CDPK1.
  • the potencies of the pyrazolopyrimidine inhibitors were dramatically increased when they were added at the time of sporozoite infection rather than one hour after C. parvum had been incubated with HCT-8 host cells. This suggests that these inhibitors affect an early stage of C. parvum host cell invasion, which is similar to their effects on T. gondii invasion. In all cases, the relative ability of each inhibitor to block C. parvum proliferation correlates with its in vitro activity against CpCDPKl.
  • Derivatives containing smaller alkyl groups (5a-5c) were found to have reduced potencies for both enzymes relative to 3. Furthermore, a significant increase in potency was not observed for inhibitors that contain bulkier substituents at the 1 -position (5d-5f). However, the reduced potencies of compounds with larger substituents is not due to a size restriction in the ATP -binding pocket because derivatives that contain a basic piperidine group (derivatives 5g-5i) were found to be significantly more potent inhibitors of TgCDPKl and QJCDPKI .
  • compound 5h which contains a methylene linkage between the pyrazolopyrimidine core and piperidine ring, has an 8-fold and 16-fold lower IC50 for QJCDPKI and JgCDPKl than parent compound 3, respectively.
  • Derivatization of 5g-5i with an acetyl (5j-51), ethyl (5m-5o), or sulfonylmethyl (5p-5r) group reduces the enhanced potency that the piperidine substituent confers, with only modified versions of piperidine 5g showing similar inhibition as the parent compound.
  • most compounds from this series are near equipotent inhibitors of both TgCDP l and Q?CDPK1, demonstrating the overall similarity in this region of the ATP-binding pockets of both kinases.
  • Analogues that contain meta- and jwa-substituted aryl rings (7c, 7i, 7k, and 7m) are potent against both enzymes and show reduced selectivity for TgCDPKl .
  • pyrazolopyrimidine derivatives that contain a 2-naphthyl (7p-7r) or quinoline group (7t) are potent inhibitors of both enzymes.
  • bicyclic substituents that are not planar show reduced potency (7u-7w).
  • most inhibitors from this series are 2- to 12-fold selective for JgCDPKl over QJCDPKI.
  • several compounds for example, compounds 71, 7q and 7t are equipotent or slightly selective for CpCDPKl .
  • pyrazolopyrimidine inhibitors that contain smaller aryl groups at the 3- position (7c and 7e) are less selective for both parasite kinases due to their increased potency against SRC and ABL.
  • analogues that contain a substituted naphthyl (7q and 7r) or quinoline (7t) substituent at the 3-poisition are much more selective due the increased size of these functional groups.
  • the larger threonine gatekeeper residues of SRC and ABL restrict access of these inhibitors to Hydrophobic Pocket II.
  • substitution at the 1 -position affects the potency of these compounds against JgCDPKl and Q?CDPK1 relative to SRC and ABL.
  • piperidine-containing analogues 5m and 5p are less selective for JgCDPKl and Q?CDPK1 than parent compound 1.
  • several analogues restore the high selectivity of this class of compounds, with secondary piperidine 5h demonstrating over 1000-fold selectivity for the CDPKs.
  • JgCDPKl (U.S. Provisional Patent Application No. 61/299,286, and reference 9) Similar to the structures of other pyrazolopyrimidines bound to tyrosine kinases, these inhibitors occupy the ATP -binding cleft of JgCDPKl .
  • the pyrazolopyrimidine scaffold superimposes with the purine ring of ATP, with the exocyclic amine and nitrogen at the 5-position forming hydrogen-bonding interactions with the hinge region.
  • the glycine gatekeeper residue of JgCDPKl allows bulky substituents at the 3-position unobstructed access to Hydrophobic Pocket II.
  • inhibitors are able to bind the ATP-binding site of CDPK1 whether it is active or not. While structures of both enzymes bound to 2 and 3 provided direct insight into how large substituents can be accommodated at the 3 -position, we were interested in further exploring how substitution at the 1 -position affects the potencies of these inhibitors. Structures of inhibitor 5h bound to TgCDPKl and CpCDPKl show how increased potency can be obtained. While the pyrazolopyrimidine cores and 3-postition substituents of inhibitors 3 and 5h make identical contacts with both enzymes, the piperidine ring of 5h forms a salt bridge with a glutamate residue that lines the ATP-binding cleft.
  • this interaction is present in the structures of 5h bound to both TgCDPKl and CjpCDPKl.
  • alkylation, acetylation or sulfonylation of the piperidine ring disrupts this interaction and accounts for the lower potency of compounds 5j-5r.
  • the reduced potency of 5h against SRC and ABL demonstrates that these kinases cannot form a similar interaction.
  • inhibitors show minimal inhibition of the tyrosine kinases SRC and ABL and are not toxic to human cell lines.
  • other derivatives of pyrazolopyrimidine may be useful and such variations on the compounds discussed herein are contemplated.
  • optimized inhibitors may be able to be used to inhibit C. parvum host cell invasion.

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Abstract

Compositions and methods for the treatment of toxoplasmosis-, caused by the infectious eukaryotic parasite Toxoplasma gondii (T, gondii) and for the treatment of ciyptosporidiosis, caused by the infectious eukaryotic parasites Cryptosporidium parvum (C parvuai) and Cnγtosporidium homimus (C. hominus) are described. In particular, the present disclosure is directed to compositions and methods for inhibiting either T. gondii calcium dependent protein kinases (TgCDPKs) or C. parvum and C. hominus calcium dependent protein kinases (CpDPKS) using pyrazolopyriinidine and/or imidazo[l,5-a]pyraziαe inhibitors, of the formula.(I), wherein the variables X. Y, Z, L. R1. and R3 are defined herein.

Description

COMPOSITIONS AND METHODS FOR TREATING TOXOPLASMOSIS, CRYPTOSPORIDIOSIS AND OTHER APICOMPLEXAN PROTOZOAN RELATED
DISEASES
CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of the filing dates of U.S. Provisional Patent
Application Serial No. 61/299,286, filed January 28, 2010, and U.S. Provisional Patent Application Serial No. 61/358,045, filed June 24, 2010, each of which are hereby incorporated by reference in their entirety.
STATEMENT OF GOVERNMENT SUPPORT This invention was made with U.S. government support under P01 AI067921,
R01AI080625, and R01AI50506 awarded by the National Institutes of Health (MAID). The U.S. Government has certain rights in the invention.
FIELD OF THE INVENTION
The present disclosure is generally directed to compositions and methods for treating apicomplexan protozoan related disease, such as toxoplasmosis and cryptosporidiosis.
BACKGROUND OF THE INVENTION
The apicomplexan protozoans Cryptosporidium parvum and Toxoplasma gondii are ubiquitous parasites that infect humans and domesticated animals. Recently C. hominus was recognized to be distinct from C. parvum, and does not appear to infect domesticated animals, but rather appears limited to human infections. C. parvum and C. hominus are infectious parasites of major health concern in humans as they are a common cause of illness transmitted by water. (See White AC. Chapter 280: Cryptosporidiosis (Cryptosporidium hominis, Cryptosporidium parvum, and Other Species) in Mandell, Bennett, & Dolin: Principles and Practice of Infectious Diseases, 6th ed. Publ: Churchill Livingston (2005)) C. parvum and C. hominus infections result in debilitating diarrhea that can be life-threatening in immunocompromised patients.
Recent studies have implicated Cryptosporidium spp. in around 15-20% of childhood diarrheal disease in the developing world. (See Sarnie et al, Cryptosporidium species: preliminary descriptions of the prevalence and genotype distribution among school children and hospital patients in the Venda region, Limpopo Province, South Africa. Exp.Parasitol. 114, 314-322 (2006); and Ajjampur et al., Closing the diarrhea diagnostic gap in Indian children by the application of molecular techniques. J. Med. Microbiol. 57, 1364-1368 (2008)) Currently, nitazoxanide is the only approved therapy for cryptosporidiosis but it is expensive and has not been shown to be effective in treating immunocompromised hosts. T. gondii may be the most common infectious eukaryotic parasite in humans, based on serosurveys. (See Montoya et al., Chapter 276: Toxoplasma gondii in Mandell, Bennett, & Dolin: Principles and Practice of Infectious Diseases, 6th ed. Publ: Churchill Livingston (2005)) Transmitted primarily through undercooked meat or accidental ingestion of cat feces, T. gondii infection presents major health concerns in immunocompromised hosts, where it causes toxoplasmic encephalitis, and in pregnancy, where it can result in severe birth defects or miscarriage. Sulfadiazine and pyrimethamine are the current therapies for toxoplasmosis, but they can cause nephrotoxicity, rash, and additional complications in pregnancy. Thus, new therapies for treating infections caused by both parasites are greatly needed.
In T. gondii, calcium-regulated signaling is associated with a number of cellular functions such as secretion, gliding motility and host cell invasion. (See Nagamune and Sibley, Comparative genomic and phylogenetic analyses of calcium ATPases and calcium- regulated proteins in the apicomplexa. Mol. Biol. Evol. 23, 1613-1627 (2006); and Billker et al., Cell Host Microbe. 2009 Jun 18;5(6):612-22. Calcium-dependent signaling and kinases in apicomplexan parasites) The proper control of intracellular calcium levels is important for host cell invasion and T. gondii use several mechanisms for the uptake and release of calcium. Furthermore, this organism contains specialized calcium-regulated signaling enzymes, including a unique family of calcium-dependent protein kinases (CDPKs) which are present in plants, ciliates and green algae but not in animals. (See Doerig et al, Protein kinases as targets for antimalarial intervention: kinomics, structure-based design, transmission-blockade, and targeting host cell enzymes. Biophysica et Biochimica Acta - Proteins and Proteomics 1754, 132-150 (2005)) These kinases are believed to be mediators of secretion, invasion, and gliding motility. (See Nagamune and Sibley LD, supra; Billker et al., supra; and Kieschnick et al, C. Toxoplasma gondii attachment to host cells is regulated by a calmodulin-like domain protein kinase. J. Biol. Chem. 276, 12369-12377 (2001)) T. gondii, C. parvum, and C. hominus are highly related obligate intracellular parasites. While much less is known about the role of calcium signaling in C. parvum and C. hominus, it appears that many calcium-regulated signaling processes are conserved from T. gondii to C. parvum. (See Chen et al., Apical Organelle discharge by Cryptosporidium parvum is temperature, cytoskeleton, and intracellular calcium dependent and required for host cell invasion. Infect. Immun. 72, 6806-16 (2004)) C. parvum and C. hominus also possess CDP s that are believed to play important roles in calcium-regulated processes and they are virtually identical in these two spp. Thus inhibitors of C. parvum CDPKs would be expected to inhibit C. hominus CDPK.
The roles that CDPKs play in calcium signaling in T. gondii, C. parvum and C. hominus make this family of kinases intriguing targets for the development of anti-parasitic agents.
SUMMARY OF THE INVENTION The present disclosure is generally directed to compositions and methods for the treatment of apicomplexan-related disorders, including but not limited to toxoplasmosis, caused by the infectious eukaryotic parasite Toxoplasma gondii (T. gondii,) and cryptosporidiosis, caused by the infectious eukaryotic parasites Cryptosporidium parvum (C. parvum) and Cryptosporidium hominus (C. hominus). In one embodiment, the present disclosure is directed to compositions and methods for inhibiting apicomplexan calcium dependent protein kinases, including but not limited to T. gondii calcium dependent protein kinases ( gCDPKs) or C. parvum and C. hominus calcium dependent protein kinases (Q?CDPKs) using pyrazolopyrimidine inhibitors, or in another embodiment, Imidazo[l,5- a]pyrazine inhibitors, both classes of compounds designed to be inactive against mammalian kinases.
In one aspect, the present disclosure rovides compounds of the formula (I),
Figure imgf000004_0001
(I)
and pharmaceutically acceptable salts thereof, wherein R1, R3, X, Y, and Z are defined herein.
In another aspect, the present disclosure provides methods for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either (i) a bumped kinase inhibitor or (ii) a pharmaceutical composition comprising a bumped kinase inhibitor and a pharmaceutically acceptable excipient, carrier, or diluent. In another aspect, the present disclosure provides methods for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either (i) a bumped kinase inhibitor or (ii) a pharmaceutical composition comprising a bumped kinase inhibitor and a pharmaceutically acceptable excipient, carrier, or diluent.
In another aspect, the present disclosure provides methods for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either a compound of formula (II) or (ii) a pharmaceutical composition comprising a compound of formula (II) and a pharmaceutically acce table exci ient carrier or diluent wherein the compound of formula (II) is
Figure imgf000005_0001
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 is a graphical representation of calcium-dependence of JgCDPKl activity. Enzyme activity was measured at a constant concentration of 0.5 mM EGTA with increasing concentrations of CaCl2 using the luciferase based assay format. The precise quantity of free Ca2+ was determined by measuring fluorescence intensity of Fluo-3 and Calcium green dyes (Invitrogen Corp. Carlsbad, USA) in the reaction buffer at excitation and emission wave lengths of 506 and 526 nM (Fluo-3) and 503 and 532 nM (Calcium green). No activity was observed with equimolar concentrations of EGTA and CaCl2 (0 free Ca2+) but significant kinase activity was observed by gradually increasing the CaCl2 concentration in the mixture. The reaction reached maximal activity at approximately 18 μΜ free CaCl2.
Figure 2 is a graphical representation of the crystal structure of calcium-free gCDPKl. (a) Association of the kinase domain (green) and the calmodulin-like calcium regulatory domain (orange) buries approximately 1400 hi of accessible surface area per domain. The junction domain, connecting the kinase and regulatory domains, is shown in brown. This interaction surface between kinase and regulatory domains is entirely lost during the transition to the Ca2+-bound form in which the regulatory domain relocates to lie along the opposite surface of the kinase domain [Wernimont et al. submitted for publication, PDB accession number 3hx4], the left side in the orientation shown. The active site is shown with bound inhibitor, NA-PP2 (magenta), (b) Comparative analysis of the ATP binding pocket of kinases reveals the presence of a glycine in the position of the gatekeeper residue (bold) in TgCDPKl and a C. parvum CDPK1 ortholog. Medium-sized side chains, threonine and serine, are found at this position in other apicomplexan CDPKs, E. tenella (£YCDPK1) and P. falciparum (P/CDPK1 and /CDPK4). Animal CDPKs tend to have large gatekeeper residues such as phenylalanine, (c and d) Stereo view of the active site with the bumped kinase inhibitors NA-PP2 (c) and NM-PP1 (d) bound. The orientation is as in panel la. Residues within 6 A of the inhibitor are shown as sticks. The unusual glycine gatekeeper residue that permits inhibition by bumped kinase inhibitors is highlighted in cyan. Difference electron density, contoured at +3.5 σ (green mesh) and -3.5 σ (pink mesh), was calculated after omission of the inhibitor, (e) TgCDPKl active site in the vicinity of the gatekeeper residue. The surface of gCDPKl is shown in white and is slabbed through to show the adenine pocket of the ATPbinding site. The glycine at the gatekeeper position of gCDPKl enlarges the active site pocket and facilitates binding of bumped kinase inhibitors (NA-PP2 is magenta sticks and NM-PP1 is violet sticks). Larger amino acids, such as Met shown here (brown sticks and protruding surface) from superposition of a C. parvum ortholog (PDB ID 3hko; bound AMP-PNP shown as brown sticks) are more typical at this gatekeeper position, and prevent binding of compounds with large, hydrophobic "bumps" on the adenine ring. This is apparent by the brown surface protrusion of the Met clearly clashing with the "bump" of each of the BKIs in our crystal structures.
Figure 3 is a graphical representation of the nuclear and cytosolic localization of TgCDPKl in T. gondii. Live T. gondii cells transiently transfected with wild type JgCDPKl- GFP were fixed in 4% paraformaldehyde. Samples were probed with anti-GFP followed by anti-rabbit Ig coupled to Texas red, stained with DAPI and viewed. GFP, green; DAPI, blue.
Figure 4 is a graphical representation demonstrating the effects of bumped kinase inhibitors on T. gondii binding to and invasion of mammalian cells. For these assays, T. gondii expressing β-galactosidase (103 per well) were allowed to infect fibroblasts in a 96 well plate. For "invasion" assays (a), compounds were added to the wells before infection with T. gondii. For "growth" assays (b), compounds were added to the indicated final concentration, four hours after infection with T. gondii cells. After 20 hours, the cells were lysed and β-galactosidase activity was assessed by adding 0.5 mM chlorophenol red-fi-d- galactoside (CPRG), incubating at 37°C, and then measuring absorbance at 595 nm.
Figure 5 is a graphical representation demonstrating IgCDPK gatekeeper mutant reduction of sensitivity to B Is. T. gondii clonal lines expressing HA-tagged versions of JgCDPKl or a G128M mutant along with GFP and β-galactosidase were generated. Western blot (a) of protein separated on a 10% acrylamide gel and probed with anti-HA. Anti-GFP served as a loading control. Invasion assays were performed with increasing concentrations of BKIs NA-PP2 (b) and NM-PP1 (c) using the parental cell line and the transfectants additionally expressing wild type gCDPKl and rgCDPKl(G128M). Assays were done in triplicate and mean and standard deviations normalized to the no compound (vehicle alone) control are presented.
Figure 6 is a Km plot of ATP for IgCDPKl (2nM) using the SPA assay to measure phosphorylation of a biotinylated peptide substrate by labeled γ-phosphate of ATP after 90 minutes incubation at 30°C.
Figure 7 is a Km plot of Syntide 2 substrate for T&CDPKl (2nM) using the SPA assay to measure phosphorylation of a biotinylated peptide substrate by labeled γ-phosphate of ATP after 90 minutes incubation at 30°C.
Figure 8 is a Km plot of ATP using the luciferase based KinaseGlo assay that measures consumption of ATP after JgCDPKl (2nM) phosphorylation of peptide substrate Syntide 2 at 30oC during a 90 minute reaction time. Remaining ATP in the reaction was measured after addition of KinaseGlo reagent by luminescence light production. Omitting peptide substrate or enzyme led to virtually no consumption of ATP (not shown).
Figure 9 is: Km plot of Syntide 2 substrate using the luciferase based KinaseGlo assay as described for Figure 8.
Figure 10(a) is a representative image from the untreated CDPK-GFP dataset.
Intracellular parasites are marked by asterisks.
Figure 10(b) shows the change in the number of intracellular parasites upon drug treatment. The number of intracellular parasites was determined by subtracting the number of extracellular parasites (SAG+) by the number of total parasites (GFP+) and expressed as a ratio to the number of host cells observed (as measured by DAPIstained nuclei). Each sample was normalized to the untreated control of the same line. Figure 10(c) shows the data used to derive the graph in Figure 8(b). Note that cells expressing the gatekeeper mutant CDPK1(G128M) are less sensitive to the drug. The drug additionally appears to affect adhesion.
Figure 11(a) is a representative set of images of CDPK1(G128M)-GFP mixed with wild type, in the absence of drug. Vacuoles containing multiple GFP-expressing parasites are marked with * and wild type vacuoles are marked with - .
Figure 11(b) shows the number of vacuoles with wild type (GFP-) or transfectedparasites (GFP+), per host cell nucleus, in the absence and presence of drug for the three cell mixtures.
Figure 11(c) shows the data used to derive the graphs. Note that the parasite line overexpressing CDPK1(G128M)-GFP wasresistant to the effects of 1 μΜ NA-PP2, as compared to the co-cultured wild type control.
Figure 12. (A) IgCDPKl and QJCDPKI inhibitors 1-3. IC50 values shown are the average of three assays ± (SEM). (B) C. parvum parasite numbers (Y axis) present after 24 hours of infection of human intestinal cells (HCT-8) with C. parvum sporozoites (1 :1 ratio HCT-8 cells:C. parvum sporozoites) in the presence of varying concentrations of inhibitors 1- 3. (left graph) Cultures were exposed to each inhibitor at the time of infection, (right graph) Cultures were exposed to each inhibitor 1 hour after infection.
Figure 13 is a graphical representation of the crystal structure of (left panel) Superposition of the active sites of TgCDPKl-3 (green sticks and light green ball-and-sticks) and Q?CDPKl-3 (orange sticks and ball-and-sticks) complexes (Pdb entries 3i7b and 3ncg). (right panel) Overlay of the ZgCDPKl-Sh and Q?CDPKl-5h complexes (Pdb entries 3n51 and 3mwu). Only residues within 6 A of the bound inhibitors are shown and the unique glycine gatekeeper residue is shown as ball-and-sticks.
Figure 14 shows in vitro activities of previously-described kinase inhibitors against
JgCDPKl. Values shown are the average of three assays.
Figure 15 shows the structure of calcium-free, inactive CDPKl versus calcium bound, activated CDPKl. The kinase domains of calcium-free IgCDPKl (green cartoon) and calcium-bound Q?CDPK1 (orange cartoon) are superimposed to highlight the dramatic conformational change that occurs in the CDPK activating domain (CAD) upon calcium activation. In the absence of calcium, access to the active site (marked by bound inhibitors shown as ball-and-sticks) by protein substrates is occluded by the CAD (cyan cartoon). Upon binding calcium (gray spheres), the CAD (beige cartoon) is repositioned to the opposite surface of the kinase domain so that protein substrates may now bind. Despite this large conformational rearrangement of the CAD, the active site of the kinase domain in the vicinity of the bound inhibitors remains largely unchanged.
DETAILED DESCRIPTION OF THE INVENTION
The following description provides specific details for a thorough understanding of, and enabling description for, embodiments of the disclosure. However, one skilled in the art will understand that the disclosure may be practiced without these details. In other instances, well-known structures and functions have not been shown or described in detail to avoid unnecessarily obscuring the description of the embodiments of the disclosure.
In one aspect, the present disclosure provides compounds of the formula (I),
Figure imgf000009_0001
(I)
or a pharmaceutically acceptable salt thereof, wherein
X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
R1 is C2-6 alkyl, C1-6 haloalkyl, -C1-4 alkyl-R12, C2.6 alkenyl, C2-6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein
the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups;
each R11 is independently Cw alkyl, Ci-6 haloalkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2NR2, or -S(0)2R;
and
R12 is -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R,
-OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, -N(R)C(0)NR2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3.8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2;
R is one of the formulas,
Figure imgf000010_0001
(R3-e) (R3-f) (R -g) (R -h)
Figure imgf000010_0002
(R3-i)
wherein
n is 0, 1, or 2;
Q is -0-, -S-, or -N(RQ)- , wherein RQ is hydrogen or Ci-6 alkyl; and
R33 is Ci-6 alkyl, C2-6 alkenyl, Ci-6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi-6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R20, -OC(0)R20, -OC(0)OR20, -OC(O)N(R20)2, -N(R 0)C(O)R20, -N(R 0)C(O)OR20, or -N(R20)C(O)N(R 0)2, wherein each R20 is independently hydrogen or Ci_6 alkyl.
34 each R is independently halogen, cyano, nitro, Ci_6 alkyl, Ci-6 haloalkyl,
-SR , -N(RJ4)2, -C(0)R , -C(0)0R14, -C(0)N(RJ4)2, -S(0)2R , -OC(0)R , -OC(0)OR34, -OC(0)N(R34)2, -N(R34)C(0)R34, -N(R34)C(0)OR34, or
-N(R )C(0)N(R )2; wherein each R is independently hydrogen or C 1-6 alkyl;
and
R35 is hydrogen or Ci-6 alkyl; each R is independently hydrogen, C1-6 alkyl, C2-6 alkenyl, C1-6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi_6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C1-6 alkyl, Ci_6 haloalkyl, -OR0, -SR°, -N(R°)2, -C(0)R°, -C(0)OR°, -C(0)N(R°)2, -S(0)2R°, -OC(0)R°, -OC(0)OR°, -OC(0)N(R°)2, -N(R°)C(0)R°, -N(R°)C(0)OR°, or -N(R°)C(0)N(R°)2, wherein each R° is independently hydrogen or C1-6 alkyl, provided that the compound is not
Figure imgf000011_0001
Figure imgf000012_0001
.The disclosure further comprises subgenera of formula (I) in which the substituents are selected as any and all combinations of one or more of structural formula (I), n, Q, R1, R3, R32, and R33 as defined herein, including without limitation, the following: Structural Formula I is one of formulae (la) - (lb):
Figure imgf000012_0002
R1 is selected from one of the following groups (la) - (lii):
(la) R1 is C2-4 alkyl, -C1-4 alkyl-R12, C2-4 alkynyl, C3.8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups, (lb) R1 is C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups,
(lc) R1 is C3-8 cycloalkyl; or a monocyclic heterocyclyl optionally substituted with one R11 group.
(Id) R1 is C3-8 cycloalkyl.
(le) R1 is monocyclic heterocyclyl optionally substituted with one R11 group.
(If) R1 is piperidinyl or tetrahydropyranyl, each optionally substituted with one R11 group. (lg) 1 is phenyl optionally substituted with one or two R11 groups,
(lh) R1 is C2-6 alkyl.
(li) R1 is C2-4 alkyl.
(lj) R1 is isopropyl or t-butyl.
(Ik) R1 is t-butyl.
(11) R1 is isopropyl.
(lm) R1 is C2-6 alkyl or -C1.4 alkyl-R12.
(In) R1 is -Ci.4 alkyl-R12.
(lo) R1 is -Ci-2 alkyl-R12.
Figure imgf000013_0001
(lq) Any one of groups (lm) - (lp), wherein R12 is -C(0)OR, -C(0)NR2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C1_6 alkyl, C1_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2;
(lr) Any one of groups (lm) - (lp), R12 is -C(0)OR or -C(0)NR2.
(Is) Any one of groups (lm) - (lp), R12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
12
(lt)Any one of groups (lm) - (lp), wherein R is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one or two groups that are each independently halogen, Ci_6 alkyl, -C(0)R, -C(0)0R, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -0C(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(lu) Any one of groups (lm) - (lp), R12 is phenyl or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(lv) Any one of groups (lm) - (lp), R12 is monocyclic heterocyclyl optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(lw) Any one of groups (lm) - (lp), wherein R12 is monocyclic heterocyclyl optionally substituted by one or two groups that are each independently halogen, Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(lx) Any one of groups (lm) - (lp), R12 is piperidinyl or tetrahydropyranyl, each optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, - OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(ly) Any one of groups (lm) - (lp), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(lz) Any one of groups (lm) - (lp), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci-6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen, C1-6 alkyl, C2-6 alkenyl, Ci-6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi-6 alkyl, heteroaryl, or heteroarylCi-6 alkyl.
(laa) Any one of groups (lm) - (lp), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(lbb) Any one of groups (lm) - (lp), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen or Ci_ 6 alkyl.
(Ice) Any one of groups (lm) - (lp), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, or -S(0)2R. (ldd) Any one of groups (lm) - (lp), wherein R is piperidinyl optionally substituted by r t two groups that are each independently C1-6 alkyl, -C(0)RA, or -S(0)2RA, wherein each RA is independently hydrogen or Ci_6 alkyl.
(lee) Any one of groups (lm) - (lp), wherein R12 is
Figure imgf000015_0001
, wherein RB is hydrogen, Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2. "N'RB
(Iff) Any one of groups (lm) - (lp), wherein R12 is , wherein RB is hydrogen,
Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen, C1-6 alkyl, C2_6 alkenyl, C1-6 haloalkyl, C3_g cycloalkyl, heterocyclyl, aryl, arylCi-6 alkyl, heteroaryl, or heteroarylCi-6 alkyl.
(lgg) Any one of groups (lm) - (lp), wherein R12 is
Figure imgf000015_0002
, wherein RB is hydrogen,
Ci.6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen or Ci_6 alkyl.
(lhh) Any one of groups (lm) - (lp), wherein R12 is
Figure imgf000015_0003
, wherein R° is hydrogen,
Ci_6 alk l, -C(0)R, -C(0)OR, -C(0)NR2, or -S(0)2R.
Figure imgf000015_0004
wherein RB is hydrogen, alkyl, -C(0)RA or -S(0)2RA, wherein each RA is independently hydrogen or Ci-6 alkyl.
R is selected from one of the following groups (2a) - (2aa):
3 3 3
(2a) R is one of groups (R -a) through (R -g) as defined above.
(2b) R3 is through (R3-g) as defined above.
(2c) R3 is
Figure imgf000015_0005
Figure imgf000016_0001
R3is
(2p) R3is
Figure imgf000016_0002
5
Figure imgf000017_0001
(2t) R'is or
(2u) Any one of groups (21) - (2t), wherein R is hydrogen or methyl
(2v) Any one of groups (21) - (2t), wherein R35 is methyl
(2w) Any one of groups (21) - (2t), wherein R35 is hydrogen.
Figure imgf000017_0002
(2y) Group (2x) wherein R33 is Ci.6 alkyl, C2-6 alkenyl, C1-6 haloalkyl, C3-8 cycloalkyl, aryl, or arylCi-6 alkyl.
(2z) Group (2x) wherein R33 is C1-6 alkyl, C1-6 haloalkyl, C3-8 cycloalkyl, phenyl, or benzyl.
(2aa) Group (2x) wherein R33 is C1-4 alkyl, C1-4 haloalkyl, C5-6 cycloalkyl, phenyl, or benzyl. 0 is selected from one of the following groups (3a) - (3e):
(3a) Qis-0-or-N(RQ)-.
(3b) Qis-O-or-N(H)-.
(3c) Qis-O-.
(3d) Q is -N(RQ)-.
(3e) Qis-N(H)-. n and R are selected from one of the following groups (4a) - (4x):
(4a) n is 0.
(4b) n is 0 or 1 and R32 is as defined for formula (I).
(4c) n is 0 or 1 and R32 is halogen, cyano, nitro, C1-6 alkyl, or C1-6 haloalkyl.
(4d) n is 0 or 1 and R32 is halogen, C1-6 alkyl, or C1-6 haloalkyl.
(4e) n is 0 or 1 and each R32 is -OR34, -SR34, -N(R34)2, -C(0)R34, -C(0)OR34, -C(0)N(R 4)2, -S(0)2R34, -OC(0)R34, -OC(0)OR34, -OC(0)N(R34)2, -N(R34)C(0)R34, -N(R34)C(0)OR34, or -N(R 4)C(0)N(R34)2, wherein each R34 is independently hydrogen or C1-6 alkyl.
(4f) n is 0 or 1 and R32 is -OR34, -SR34, -N(R34)2, wherein each R34 is independently hydrogen or C1-6 alkyl.
(4g) n is 0 or 1 and R32 is -C(0)R34, -C(0)OR34, -C(0)N(R34)2, or -S(0)2R34, wherein each
R34 is independently hydrogen or C1-6 alkyl.
(4h) n is as defined for formula (I) and each R32 is independently halogen, cyano, nitro,
C\-6 alkyl, or d-6 haloalkyl.
(4i) n is as defined for formula (I) and each R32 is independently halogen, C1-6 alkyl, or
Ci-6 haloalkyl.
(4j) n is as defined for formula (I) and each R32 is independently -OR34, -SR34, -N(R34)2, -C(0)R34, -C(0)OR34, -C(0)N(R34)2, -S(0)2R34, -OC(0)R34, -OC(0)OR34, -OC(0)N(R34)2, -N(R34)C(0)R34, -N(R34)C(0)OR34, or -N(R34)C(0)N(R34)2, wherein each R34 is independently hydrogen or C1-6 alkyl.
(4k) n is as defined for formula (I) and each R32 is independently -OR34, -SR34, -N(R34)2, wherein each R34 is independently hydrogen or C1-6 alkyl.
(41) n is as defined for formula (I) and each R32 is independently -C(0)R34, -C(0)OR34, -C(0)N(R 4)2, or -S(0)2Rl4, wherein each R34 is independently hydrogen or C1-6 alkyl.
(4m) n is 1 or 2 and each R32 is as defined for formula (I).
(4n) n is 1 or 2 and each R32 is independently halogen, cyano, nitro, C1-6 alkyl, or C1-6 haloalkyl.
(4o) n is 1 or 2 and each R32 is independently halogen, C1-6 alkyl, or C1-6 haloalkyl.
(4p) n is 1 or 2 and each R32 is independently -OR34, -SR34, -N(R34)2, -C(0)R34, -C(0)OR34, -C(0)N(R34)2, -S(0)2R34, -OC(0)R34, -OC(0)OR34, -OC(0)N(R34)2, -N(ir)C(0)R , -N(RJ4)C(0)0R , or -N(Ri4)C(0)N(RJ4)2, wherein each R is independently hydrogen or C1-6 alkyl.
(4q) n is 1 or 2 and each R32 is independently -OR34, -SR34, -N(R34)2, wherein each R34 is independently hydrogen or C1-6 alkyl.
(4r) n is 1 or 2 and each R32 is independently -C(0)R34, -C(0)OR34, -C(0)N(R34)2, or
-S(0)2R34, wherein each R34 is independently hydrogen or C1-6 alkyl.
(4s) n is 1 and Rj2 is as defined for formula (I).
(4t) n is 1 and Rj2 is halogen, cyano, nitro, C1-6 alkyl, or C1-6 haloalkyl.
(4u) n is 1 and Rj2 is halogen, C1-6 alkyl, or C1-6 haloalkyl.
(4v) n is 1 and R32 is -OR34, -SR34, -N(R34)2, -C(0)R34, -C(0)OR34, -C(0)N(R34)2, -S(0)2R34, -OC(0)R34, -OC(0)OR34, -OC(0)N(R34)2, -N(R34)C(0)R34, -N(R34)C(0)OR34, or -N(R34)C(0)N(R34)2, wherein each R34 is independently hydrogen or C1-6 alkyl.
(4w) n is 1 and R32 is-OR34, -SR34, -N(R34)2, wherein each R34 is independently hydrogen or Ci-6 alkyl.
(4x) n is 1 and R32 is -C(0)R34, -C(0)OR34, -C(0)N(R34)2, or -S(0)2R34, wherein each R34 is independently hydrogen or C1-6 alkyl.
R33 is selected from one of the following groups (5a) - (5t);
(5a) R33 is Ci-6 alkyl, C2.6 alkenyl, arylCi_6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR2°, -C(O)N(R20)2, -S(0)2R20, -0C(0)R20, -OC(0)OR20, -OC(O)N(R 0)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or Ci_6 alkyl.
(5b) R33 is Ci-6 alkyl, C2.6 alkenyl, arylCi_6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R20, -OC(0)R20, -OC(0)OR20, -OC(O)N(R20)2, -N(R20)C(O)R20, -N(R 0)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or Ci-6 alkyl. (5c) is Ci-6 alkyl, C2-6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one or two groups that are each independently halogen, Ci_6 alkyl, or Ci_6 haloalkyl.
(5d) R33 is Ci-6 alkyl, C2-6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci-6 haloalkyl.
(5e) R33 is C2-6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R2°, -OC(0)R2°, -OC(0)OR20, -OC(O)N(R20)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein
20
each R is independently hydrogen or Ci-6 alkyl.
33
(5f) R is C2_6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one, two, three, or four groups that are each
20 20 20 independently halogen, cyano, nitro, Ci_6 alkyl, Ci-6 haloalkyl, -OR , -SR , -N(R )2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R2°, -OC(0)R2°, -OC(0)OR20, -OC(O)N(R20)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or Ci-6 alkyl.
(5g) R33 is C2-6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci-6 haloalkyl.
(5h) R33 is C2_6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one or two groups that are each independently halogen, Ci_6 alkyl, or Ci_6 haloalkyl.
(5i) R33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R20, -OC(0)R20, -OC(0)OR20, -OC(O)N(R20)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or C1-6 alkyl.
(5j) R33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each are each substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci_6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R20, -OC(0)R , -OC(0)OR , -OC(0)N(R u)2, -N(R u)C(0)R , -N(R u)C(0)OR , or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or Ci_6 alkyl
(5k) R33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each optionally substituted with one or two groups that are each independently halogen, C1-6 alkyl, or C1-6 haloalkyl.
(51) R33 is arylCi-e alkyl or heteroarylC^ alkyl, each substituted with one or two groups that are each independently halogen, C1-6 alkyl, or C1-6 haloalkyl.
(5m) R33 is arylCi-6 alkyl optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R2°, -OC(0)R2°, -OC(0)OR20, -OC(O)N(R 0)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or C1-6 alkyl.
33
(5n) R is arylCi-6 alkyl substituted with one, two, three, or four groups that are each
20 20 20 independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR , -SR , -N(R )2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R20, -OC(0)R2°, -OC(0)OR20, -OC(O)N(R 0)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or C1-6 alkyl
(5o) R33 is arylCi-6 alkyl optionally substituted with one or two groups that are each independently halogen, C1-6 alkyl, or C1-6 haloalkyl.
(5p) R33 is arylCi-6 alkyl substituted with one or two groups that are each independently halogen, C1-6 alkyl, or C1-6 haloalkyl.
(5q) R33 is benzyl optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R2°, -OC(0)R2°, -OC(0)OR20, -OC(O)N(R20)2, -N(R20)C(O)R20, -N(R 0)C(O)OR20, or -N(R 0)C(O)N(R20)2, wherein each R20 is independently hydrogen or C1-6 alkyl.
(5r) R33 is benzyl substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-β haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R20, -OC(0)R2°, -OC(0)OR20, -OC(O)N(R20)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or C1-6 alkyl.
(5s) R33 is benzyl optionally substituted with one or two groups that are each independently halogen, C1-6 alkyl, or C1-6 haloalkyl.
(5t) R33 is benzyl substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci-6 haloalkyl. Particular embodiments of this aspect of the invention include compounds of any one of the formulae (I), (la), and (lb), each as defined in each of the following rows, wherein each entry is a group number as defined above (e.g., (3c) refers to Q is -0-), a dash "-" indicates that the variable is as defined for formula (I) or defined according to any one of the applicable variable definitions (la)-(5t) [e.g., when R1 is a dash, it can be either as defined for Formula (I) or any one of definitions (la)-(lii)]; and an "x" indicates that the variable is not applicable to the particular embodiment (e.g., when RJ is (2o), then Q and R33 are not necessary):
Figure imgf000022_0001
Figure imgf000022_0002
R33 n & R33 n &
R1 R3 R32 Q R1 R3 Q
R32
(l)-47 lp 2b 5q 4n 3a (l)-77 lh 2b 5q 4c 3c
(l)-48 laa 2b 5q 4n 3a (l)-78 In 2b 5q 4c 3c
(l)-49 lh 2c 5a 4n 3a (l)-79 lp 2b 5q 4c 3c
(l)-50 In 2c 5a 4n 3a (l)-80 laa 2b 5q 4c 3c
(1)-51 lp 2c 5a 4n 3a (1)-81 lh 2c 5a 4c 3c
(l)-52 laa 2c 5a 4n 3a (l)-82 In 2c 5a 4c 3c
(l)-53 lh 2c 5e 4n 3a (l)-83 lp 2c 5a 4c 3c
(l)-54 In 2c 5e 4n 3a (l)-84 laa 2c 5a 4c 3c
(l)-55 lp 2c 5e 4n 3a (l)-85 lh 2c 5e 4c 3c
(l)-56 laa 2c 5e 4n 3a (l)-86 In 2c 5e 4c 3c
(l)-57 lh 2c 5i 4n 3a (l)-87 lp 2c 5e 4c 3c
(l)-58 In 2c 5i 4n 3a (l)-88 laa 2c 5e 4c 3c
(l)-59 lp 2c 5i 4n 3a (l)-89 lh 2c 5i 4c 3c
(l)-60 laa 2c 5i 4n 3a (l)-90 In 2c 5i 4c 3c
(1)-61 lh 2c 5q 4n 3a (1)-91 lp 2c 5i 4c 3c
(l)-62 In 2c 5q 4n 3a (l)-92 laa 2c 5i 4c 3c
(l)-63 lp 2c 5q 4n 3a (l)-93 lh 2c 5q 4c 3c
(l)-64 laa 2c 5q 4n 3a (l)-94 In 2c 5q 4c 3c
(l)-65 lh 2b 5a 4c 3c (l)-95 lp 2c 5q 4c 3c
(l)-66 In 2b 5a 4c 3c (l)-96 laa 2c 5q 4c 3c
(l)-67 lp 2b 5a 4c 3c (l)-97 lh 2b 5a 4n 3c
(l)-68 laa 2b 5a 4c 3c (l)-98 In 2b 5a 4n 3c
(l)-69 lh 2b 5e 4c 3c (l)-99 lp 2b 5a 4n 3c
(l)-70 In 2b 5e 4c 3c (1)-100 laa 2b 5a 4n 3c
(1)-71 lp 2b 5e 4c 3c (1)-101 lh 2b 5e 4n 3c
(l)-72 laa 2b 5e 4c 3c (1)-102 In 2b 5e 4n 3c
(l)-73 lh 2b 5i 4c 3c (1)-103 lp 2b 5e 4n 3c
(l)-74 In 2b 5i 4c 3c (1)-104 laa 2b 5e 4n 3c
(l)-75 lp 2b 5i 4c 3c (1)-105 lh 2b 5i 4n 3c
(l)-76 laa 2b 5i 4c 3c (1)-106 In 2b 5i 4n 3c
SUBSTITUTE R33 n & R33 n &
R1 R3 R32 Q R1 R3 Q
R32
(1)-107 lp 2b 5i 4n 3c (1)-137 lh 2b - - 3c
(1)-108 laa 2b 5i 4n 3c (1)-138 In 2b - - 3c
(1)-109 lh 2b 5q 4n 3c (1)-139 lp 2b - - 3c
(1)-110 In 2b 5q 4n 3c (1)-140 laa 2b - - 3c
(l)-lll lp 2b 5q 4n 3c (1)-141 lh 2c - - 3c
(1)-112 laa 2b 5q 4n 3c (1)-142 In 2c - - 3c
(1)-113 lh 2c 5a 4n 3c (1)-143 lp 2c - - 3c
(1)-114 In 2c 5a 4n 3c (1)-144 laa 2c - - 3c
(1)-115 lp 2c 5a 4n 3c (1)-145 lh 2b - - 3a
(1)-116 laa 2c 5a 4n 3c (1)-146 In 2b - - 3a
(1)-117 lh 2c 5e 4n 3c (1)-147 lp 2b - - 3a
(1)-118 In 2c 5e 4n 3c (1)-148 laa 2b - - 3a
(1)-119 lp 2c 5e 4n 3c (1)-149 lh 2c - - 3a
(1)-120 laa 2c 5e 4n 3c (1)-150 In 2c - - 3a
(1)-121 lh 2c 5i 4n 3c (1)-151 lp 2c - - 3a
(1)-122 In 2c 5i 4n 3c (1)-152 laa 2c - - 3a
(1)-123 lp 2c 5i 4n 3c (1)-153 - - 5a - 3a
(1)-124 laa 2c 5i 4n 3c (1)-154 - - 5e - 3a
(1)-125 lh 2c 5q 4n 3c (1)-155 - - 5i - 3a
(1)-126 In 2c 5q 4n 3c (1)-156 - - 5q - 3a
(1)-127 lp 2c 5q 4n 3c (1)-157 - - 5a - 3c
(1)-128 laa 2c 5q 4n 3c (1)-158 - - 5e - 3a
(1)-129 lh 2b - - - (1)-159 - - 5i - 3a
(1)-130 In 2b - - - (1)-160 - - 5q - 3a
(1)-131 lp 2b - - - (1)-161 - 2b 5a - 3a
(1)-132 laa 2b - - - (1)-162 - 2b 5e - 3a
(1)-133 lh 2c - - - (1)-163 - 2b 5i - 3a
(1)-134 In 2c - - - (1)-164 - 2b 5q - 3a
(1)-135 lp 2c - - - (1)-165 - 2b 5a - 3c
(1)-136 laa 2c - - - (1)-166 - 2b 5e - 3a
SUBSTITUTE R33 n & R33 n &
R1 R3 R32 Q R1 R3 R32 Q
(1)-167 - 2b 5i - 3a (1)-172 - 2c 5q - 3a
(1)-168 - 2b 5q - 3a (1)-173 - 2c 5a - 3c
(1)-169 - 2c 5a - 3a (1)-174 - 2c 5e - 3a
(1)-170 - 2c 5e - 3a (1)-175 - 2c 5i - 3a
(1)-171 - 2c 5i - 3a (1)-176 - 2c 5q - 3a
Figure imgf000025_0001
Figure imgf000025_0002
embodiment, the compound is one of the compounds in Table A:
Figure imgf000025_0003
Figure imgf000026_0001
Figure imgf000027_0001
Figure imgf000028_0001
Figure imgf000029_0001
and a pharmaceutically acceptable salts thereof. In another embodiment, the present disclosure provides compounds of the formula
(ΠΙ),
Figure imgf000030_0001
(III)
or a pharmaceutically acceptable salt thereof, wherein
X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
1 12
R is C2-6 alkyl or -C1-4 alkyl-R , wherein
R J is a monocyclic heterocyclyl optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C1-6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2;
R3 is one of the formulas,
Figure imgf000030_0002
(R3-a) (R3-j) (R -k)
wherein
n is 0, 1, or 2;
Q is -0- or -N(RQ)- , wherein RQ is hydrogen or Ci_6 alkyl; and
R33 is Ci-6 alkyl, C2-6 alkenyl, arylCi_6 alkyl, or heteroarylCi-6 alkyl wherein the arylalkyl and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, Ci.6 alkyl, Ci.6 haloalkyl,
20 20 20 20
-OR , -SR , or -N(R )2, wherein each R is independently hydrogen or Ci-6 alkyl.
32 34 34
each R is independently halogen, Ci_6 alkyl, or -OR , wherein R is Ci-6 alkyl; and
R35 is hydrogen or Ci-6 alkyl;
and
each R is independently hydrogen or Ci-6 alkyl. The disclosure further comprises subgenera of formula (III) in which the substituents are selected as any and all combinations of one or more of structural formula (III), n, Q, R , R , R , and R as defined herein, including without limitation, the following: Structural Formula III is one of formulae (Ilia) - (Hlb):
Figure imgf000031_0001
R1 is selected from one of the following groups (8a) - (8u):
(8a) R1 is C2-6 alkyl.
(8b) R1 is C2-4 alkyl.
(8c) R1 is isopropyl or t-butyl.
(8d) R1 is t-butyl.
(8e) R1 is isopropyl.
(8f) R1 is -Ci_4 alkyl-R12.
(8g) R1 is -Ci-2 alkyl-R12.
(8h) R1 is -CH2-R12.
(8i) Any one of groups (8f) - (8h), wherein R12 is monocyclic heterocyclyl optionally substituted by one or two groups that are each independently halogen, C1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(8j) Any one of groups (8f) - (8h), R12 is piperidinyl or tetrahydropyranyl, each optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(8k) 12
Any one of groups (8f) - (8h), wherein R is piperidinyl optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, - OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2. 12
(81)Any one of groups (8f) - (8h), wherein R is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen, Ci_6 alkyl, C2-6 alkenyl, C\-6 haloalkyl, C3.8 cycloalkyl, heterocyclyl, aryl, arylQ.e alkyl, heteroaryl, or heteroarylC^ 6 alkyl.
(8m) Any one of groups (8f) - (8h), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(8n) Any one of groups (8f) - (8h), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently C1-6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen or Ci_6 alkyl.
(80) Any one of groups (8f) - (8h), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently C\.e alkyl, -C(0)R, -C(0)OR, -C(0)NR2, or - S(0)2R.
(8p) Any one of groups (8f) - (8h), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci-6 alkyl, -C(0)RA, or -S(0)2RA, wherein each RA is independently hydrogen or Ci-6 alkyl.
(8q) Any one of groups (8f) - (8h), wherein R12 is
Figure imgf000032_0001
, wherein RB is hydrogen,
Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(8r) Any one of groups (8f) - (8h), wherein R12 is I"N'RB , wherein RB is hydrogen,
Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen, Ci-6 alkyl, C2-6 alkenyl, Ci-6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl.
(8s) Any one of groups (8f) - (8h), wherein R12 is
Figure imgf000032_0002
, wherein RB is hydrogen,
Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each R^ is independently hydrogen or C1-6 alkyl.
(8t) Any one of groups (8f) - (8h), wherein R12 is
Figure imgf000033_0001
, wherein R is hydrogen, Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, or -S(0)2R
(8u) Any one of groups (8f) - (8h), wherein R1Z is
Figure imgf000033_0002
, wherein RB is hydrogen,
Ci-6 alkyl, -C(0)RA, or -S(0)2RA, wherein each RA is independently hydrogen or C1-6 alkyl.
R is selecte from one of the following groups (9a) - (9g):
5
Figure imgf000033_0003
5
(9d) R3 is
(9e) Any one of groups (9b) - (9d), wherein R35 is hydrogen or methyl.
(9f) Any one of groups (9b) - (9d), wherein R35 is methyl.
(9g) Any one of groups (9b) - (9d), wherein R35 is hydrogen.
Q is selected from one of the following groups (10a) - (lOd);
(10a) Q is -O- or -N(H)-.
(10b) Q is -0-.
(10c) Q is -N(RQ)-. (10d) Q is -N(H)-. n and R are selected from one of the following groups (11a) - (lie):
(11a) n is 0.
(lib) n is 0 or 1 and R32 is as defined for formula (III).
(11c) n is 1 or 2 and R32 is as defined for formula (III).
R is selected from one of the following groups (12a) - (12i):
(12a) R33 is Ci-6 alkyl, C2.6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one or two groups that are each independently halogen, Ci.6 alkyl, or Ci.6 haloalkyl.
33
(12b) R is Ci-6 alkyl, C2-6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one or two groups that are each independently halogen, Ci_6 alkyl, or Ci_6 haloalkyl.
(12c) R33 is C2_6 alkenyl, arylC1_6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci-6 haloalkyl.
(12d) R33 is C2-6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are each substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci-6 haloalkyl.
(12e) R33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each optionally substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci-6 haloalkyl.
(12f) R33 is arylCi-6 alkyl or heteroarylCi-6 alkyl, each substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci-6 haloalkyl.
33
(12g) R is arylCi-6 alkyl optionally substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci-6 haloalkyl.
(12h) R33 is arylQ-6 alkyl substituted with one or two groups that are each independently halogen, Ci_6 alkyl, or Ci_6 haloalkyl.
(12i) R33 is benzyl optionally substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or Ci-6 haloalkyl.
(12j) R33 is benzyl substituted with one or two groups that are each independently halogen, Ci-6 alkyl, or C1-6 haloalkyl. Particular embodiments of this aspect of the invention include compounds of any one of the formulae (III), (Ilia), and (lllb), each as defined in each of the following rows, wherein each entry is a group number as defined above (e.g., (10b) refers to Q is -0-), and a dash "-" indicates that the variable is as defined for formula (III) or defined according to any one of the applicable variable definitions (8a)-(12j) [e.g., when R1 is a dash, it can be either as defined for Formula (III) or any one of definitions (8a)-(8u)]; and an "x" indicates that the variable is not applicable to the particular embodiment (e.g., when R3 is (9c), then Q and R33 are not necessary):
Figure imgf000035_0001
Figure imgf000035_0002
R33 n & R33 n &
R1 R3 Q R1 R3 R32 Q
(3)-47 - 9a 12e - 10b (3)-48 - 9a 12i - 10b embodiment of the preceding embodiments of formulas (I) and (III), the compound is not
Figure imgf000036_0001
METHODS FOR USE
Clinical toxoplasmosis is caused by the actively dividing tachyzoite form of the parasite, which exits its host cell and invades a new cell every few days. JgCDPKl has a unique ATP -binding site with a small gatekeeper residue, as opposed to the large gatekeeper residues present in mammalian protein kinases. This key difference in gatekeeper residues between mammalian kinases and JgCDPKl allowed us to use bumped kinase inhibitors (BKIs) to selectively inhibit JgCDPKl without untoward effects on the mammalian host cell.
Accordingly, the disclosure provides methods for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either (i) a bumped kinase inhibitor or (ii) a pharmaceutical composition comprising a bumped kinase inhibitor and a pharmaceutically acceptable excipient, carrier, or diluent.
In one embodiment, the bumped kinase inhibitor is selected from one of the compounds of Figure 14, or a pharmaceutically acceptable salt thereof.
In another embodiment, the bumped kinase inhibitor is according to of the formula (I) as defined above, or any embodiment thereof.
In another embodiment, the bumped kinase inhibitor is of the formula (II),
Figure imgf000037_0001
(Π)
or a pharmaceutically acceptable salt thereof, wherein
X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
R1 is Ci-6 alkyl, Ci-6 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, -Ci-6 alkyl-R12, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein
the cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups;
each R11 is independently Ci_6 alkyl, Ci_6 haloalkyl, -C(0)R, -C(0)OR, -C(0)NR2, -
S(0)2NR2, or -S(0)2R;
and
R12 is -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, -N(R)C(0)NR2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3.8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci.6 alkyl, Ci.6 haloalkyl, -OR, -SR, - NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2;
L is a bond or -CH2-;
R3 is aryl or heteroaryl, each optionally substituted with one, two, or three R31 groups, wherein
each R31 is independently halogen, cyano, nitro, Ci_6 alkyl, C1-6 haloalkyl, aryl, heteroaryl, C3-8 cycloalkyl, heterocyclyl, arylCi-6 alkyl, heteroarylCi-6 alkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, -N(R)C(0)NR2 or -N(R)S(0)2R, wherein the aryl, heteroaryl, C3-8 cycloalkyl, heterocyclyl, arylalkyl, and heteroarylalkyl groups are optionally substituted with one or two R10 groups;
each R is independently hydrogen, Ci_6 alkyl, C2_6 alkenyl, Ci_6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one,
10
two, three, or four R groups;
and
each R10 is independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR0, -SR°, -N(R°)2, -C(0)R°, -C(0)OR°, -C(0)N(R°)2, -S(0)2R°, -OC(0)R°, -OC(0)OR°,
-OC(0)N(R°)2, -N(R°)C(0)R°, -N(R°)C(0)OR°, or -N(R°)C(0)N(R°)2, wherein each R° is independently hydrogen or C1-6 alkyl.
The disclosure further comprises subgenera of formula (II) in which the substituents are selected as any and all combinations of one or more of structural formula (II), R1, and R3, as defined herein, including without limitation, the following:
Structural Formula II is one of formulae (Ila) - (Ilh):
Figure imgf000038_0001
R1 is selected from one of the following groups (6a) - (6ii);
(6a) R1 is Ci-4 alkyl, -C1-4 alkyl-R12, C2.4 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups.
(6b) R1 is C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups. (6c) 1 is C3-8 cycloalkyl; or a monocyclic heterocyclyl optionally substituted with one R11 group.
(6d) R1 is C3-8 cycloalkyl.
(6e) R1 is monocyclic heterocyclyl optionally substituted with one R11 group.
(6f) R1 is piperidinyl or tetrahydropyranyl, each optionally substituted with one R11 group. (6g) R1 is phenyl optionally substituted with one or two R11 groups.
(6h) R1 is C2-6 alkyl.
(6i) R1 is Ci.4 alkyl.
(6j) R1 is isopropyl or t-butyl.
(6k) R1 is t-butyl.
(61) R1 is isopropyl.
(6m) R1 is C2-6 alkyl or -C1-4 alkyl-R12.
(6n) R1 is -CM alkyl-R12.
(60) R1 is -d_2 alkyl-R12.
(6p) R1 is -CH2-R12.
(6q) Any one of groups (6m) - (6p), wherein R12 is -C(0)OR, -C(0)NR2, phenyl, monocyclic heteroaryl, C3.8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or - N(R)C(0)NR2;
(6r) Any one of groups (6m) - (6p), R12 is -C(0)OR or -C(0) R2.
12
(6s) Any one of groups (6m) - (6p), R is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C1-6 alkyl, 01-6 haloalkyl, -OR, - SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(6t) Any one of groups (6m) - (6p), wherein R12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one or two groups that are each independently halogen, C1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2. (6u) Any one of groups (6m) - (6p), R is phenyl or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(6v) Any one of groups (6m) - (6p), R12 is monocyclic heterocyclyl optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, - OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)0R, or -N(R)C(0)NR2.
(6w) Any one of groups (6m) - (6p), wherein R12 is monocyclic heterocyclyl optionally substituted by one or two groups that are each independently halogen, Ci-6 alkyl, - C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, - N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
12
(6x) Any one of groups (6m) - (6p), R is piperidinyl or tetrahydropyranyl, each optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, d_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)0R, or - N(R)C(0)NR2.
(6y) Any one of groups (6m) - (6p), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently halogen, cyano, nitro, C1-6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)0R, or -N(R)C(0)NR2.
12
(6z) Any one of groups (6m) - (6p), wherein R is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)0RA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen, C\-6 alkyl, C2.6 alkenyl, Ci-6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylQ-6 alkyl, heteroaryl, or heteroarylCi_6 alkyl.
(6aa) Any one of groups (6m) - (6p), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently C1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(6bb) Any one of groups (6m) - (6p), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci-6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen or Ci-6 alkyl.
(6cc) Any one of groups (6m) - (6p), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently C1-6 alkyl, -C(0)R, -C(0)OR, - C(0)NR2, or -S(0)2R.
(6dd) Any one of groups (6m) - (6p), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently C1-6 alkyl, -C(0)RA, or -S(0)2RA, wherein each RA is independently hydrogen or -6 alkyl.
(6ee) Any one of groups (6m) - (6p), wherein R12 is
Figure imgf000041_0001
; wherein RB is hydrogen,
Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(6ff) Any one of groups (6m) - (6p), wherein R12 is
Figure imgf000041_0002
, wherein RB is hydroge
Ci-e alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen, Ci_6 alkyl, C2_6 alkenyl, Ci_6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi-6 alkyl, heteroaryl, or heteroarylCi_6 alkyl.
(6gg) Any one of groups (6m) - (6p), wherein R12 is
Figure imgf000041_0003
wherein RB is hydrogen,
Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen or Ci-6 alkyl.
(6hh) Any one of groups (6m) - (6p), wherein R12 is
Figure imgf000041_0004
, wherein RB is hydrogen,
Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, or -S(0)2R. r"N'RB
(6ii) Any one of groups (6m) - (6p), wherein R12 is , wherein RB is hydrogen,
C\-6 alkyl, -C(0)RA, or -S(0)2RA, wherein each RA is independently hydrogen or C1-6 alkyl. R3 is selected from one of the following groups (7a) - (7x):
(7a) R3 is naphthyl, quinolinyl, pyridyl, pyrimidinyl, indolyl, benzodioxolyl, 2,3- dihydrobenzodioxinyl, dibenzothienyl, chromanyl, or phenyl, each optionally substituted with one, two, or three R31 groups.
(7b) R3 is naphthyl, quinolinyl, indolyl, benzodioxolyl, 2,3-dihydrobenzodioxinyl, or chromanyl, each optionally substituted with one, two, or three R31 groups.
(7c) R is quinolinyl, pyridyl, pyrimidinyl, or indolyl, each optionally substituted with one,
31
two, or three R groups.
3 31
(7d) R is quinolinyl or indolyl, each optionally substituted with one, two, or three R groups.
(7e) R3 is quinolinyl optionally substituted with one, two, or three R31 groups.
(7f) R3 is pyridyl or pyrimidinyl, each optionally substituted with one, two, or three R31 groups.
(7g) R3 is phenyl substituted with one, two, or three R31 groups.
(7h) R3 is phenyl optionally substituted with one or two R31 groups, and substituted with one group that is halogen, Ci_6 alkyl,-OR, -SR, -NR2, -N(R)C(0)R, or-N(R)S(0)2R. (7i) R3 is phenyl optionally substituted with one or two R31 groups, and substituted with one group that is -OR or -N(R)C(0)R.
3 31
(7j) R is phenyl optionally substituted with one or two R groups, and substituted with one group that is -OR10, wherein R10 is benzyl optionally substituted with one, two, three, or four groups that are each independently halogen, Ci_6 alkyl, Ci-6 haloalkyl, or -OR0
(7k) R3 is phenyl optionally substituted with one or two R31 groups, and substituted with one group that is -N(H)C(0)R20, wherein R20 is C1-6 alkyl, C2.6 alkenyl, Ci-6 haloalkyl, aryl, or arylCi-6 alkyl.
(71) R3 is naphthyl optionally substituted with one, two, or three R31 groups.
(7m) R3 is naphthyl optionally substituted with one or two R31 groups and substituted with one group that is -OR15, wherein R15 is Ci.6 alkyl or benzyl, wherein the benzyl is optionally substituted with one, two, three, or four groups that are each independently halogen, Ci_6 alkyl, Ci_6 haloalkyl, or -OR0.
(7n) R3 is naphth-l-yl optionally substituted with one, two, or three R31 groups.
(7o) R3 is naphth-l-yl optionally substituted with one or two R31 groups and substituted with one group that is -OR15, wherein R15 is Ci_6 alkyl or benzyl, wherein the benzyl is optionally substituted with one, two, three, or four groups that are each independently halogen, C1-6 alkyl, Ci_6 haloalkyl, or -OR0.
(7p) R3 is naphth-2-yl optionally substituted with one, two, or three R31 groups.
(7q) R3 is naphth-2-yl optionally substituted with one or two R31 groups and substituted with one group that is -OR15, wherein R15 is C1-6 alkyl or benzyl, wherein the benzyl is optionally substituted with one, two, three, or four groups that are each independently halogen, C1-6 alkyl, C1-6 haloalkyl, or -OR0.
Figure imgf000043_0001
(7s) R3 is indolyl optionally substituted with one, two, or three Rjl groups.
(7t) R3 is indol-2-yl optionally substituted with one, two, or three R31 groups.
(7u) R3 is indol-3-yl optionally substituted with one, two, or three R31 groups.
(7v) R3 is indol-5-yl optionally substituted with one, two, or three R31 groups.
(7w) R3 is indol-6-yl optionally substituted with one, two, or three R31 groups.
(7x) Any one of groups (2a) - (2aa) as defined above for formula (I).
Other particular embodiments of this aspect of the invention include compounds of any one of the formulae (II), (Ila) - (Ilh), each as defined in each of the following rows, wherein each entry is a group number as defined above (e.g., (7w) refers to R is indol-6-yl optionally substituted with one, two, or three R31 groups), and a dash "-" indicates that the variable is as defined for formula (II) or defined according to any one of the applicable variable definitions (6a)-(7x) [e.g., when R1 is a dash, it can be either as defined for Formula (II) or any one of definitions (6a)-(6ii)]:
Figure imgf000043_0002
Figure imgf000043_0003
Figure imgf000043_0004
Figure imgf000044_0001
In another embodiment, the compound of formula (II) is one of compounds of Table
B,
Figure imgf000044_0002
Figure imgf000045_0001
Figure imgf000046_0001
Figure imgf000047_0001
Figure imgf000048_0001
Figure imgf000049_0001
Figure imgf000050_0001
Figure imgf000051_0001
Figure imgf000052_0001
Figure imgf000053_0001
Figure imgf000054_0001
a- J d]pyrimidin-4-amine
Figure imgf000055_0001
Figure imgf000056_0001
Figure imgf000057_0001
Figure imgf000058_0001
Figure imgf000059_0001
In another embodiment, the bumped kinase inhibitor is of the formula (IV),
Figure imgf000059_0002
or a pharmaceutically acceptable salt thereof, wherein
X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
1 12
is Ci-6 alkyl, C2-6 alkynyl, -Ci_6 alkyl-R , C3-8 cycloalkyl, monocyclic heterocyclyl, or phenyl, wherein
the monocyclic heterocyclyl and phenyl groups are each optionally substituted with one or two R11 groups; each R11 is independently Ci_6 alkyl, Ci_6 haloalkyl, -C(0)R, or -S(0)2R;
and
R12 is -C(0)OR, -C(0)NR2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, - OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or - N(R)C(0)NR2;
L is a bond or -CH2-;
R3 is aryl or heteroaryl, each optionally substituted with one, two, or three R31 groups, wherein
31
each R is independently halogen, Ci_6 alkyl, Ci_6 haloalkyl, phenyl, benzyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -OC(0)R, -N(R)C(0)R, or -N(R)S(0)2R, wherein the phenyl and benzyl groups are optionally substituted with one or two R10 groups;
each R is independently hydrogen, Ci-6 alkyl, C2_6 alkenyl, Ci-6 haloalkyl, C3-8 cycloalkyl, aryl, arylCi-6 alkyl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one or two R10 groups; and
each R10 is independently halogen, cyano, Ci-6 alkyl, Ci-6 haloalkyl, -OR0, -SR°, or -N(R°)2, wherein each R° is independently hydrogen or Ci_6 alkyl.
The disclosure further comprises subgenera of formula (IV) in which the substituents are selected as any and all combinations of one or more of structural formula (IV), R , and R3, as defined herein, including without limitation, the following:
Structural Formula II is one of formulae (IV a) - (IVh):
Figure imgf000060_0001
Figure imgf000061_0001
R1 is selected from one of the following groups (13a) - (13ff):
(13a) R1 is C3-8 cycloalkyl; or a monocyclic heterocyclyl optionally substituted with
group.
(13b) R1 is C3-8 cycloalkyl.
(13c) R1 is monocyclic heterocyclyl optionally substituted with one R11 group.
(13d) R1 is piperidinyl or tetrahydropyranyl, each optionally substituted with one R11 group. (13e) R1 is phenyl optionally substituted with one or two R11 groups.
(13f) R1 is C2-6 alkyl.
(13g) R1 is Ci-4 alkyl.
(13h) R1 is isopropyl or t-butyl.
(13i) R1 is t-butyl.
(13j) R1 is isopropyl.
(13k) R1 is C2-6 alkyl or -Ci_4 alkyl-R12.
(131) R1 is -CM alkyl-R12.
(13m) R1 is -Ci-2 alkyl-R12.
(13n) R1 is -CH2-R12.
(13o) Any one of groups (13k) - (13n), R12 is -C(0)OR or -C(0)NR2.
(13p) Any one of groups (13k) - (13n)„ R12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, - OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(13q) Any one of groups (13k) - (13n), wherein R12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one or two groups that are each independently halogen, Ci_6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2. (13r) Any one of groups (13k) - (13n), is phenyl or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(13s) Any one of groups (13k) - (13n), R12 is monocyclic heterocyclyl optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, - S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or - N(R)C(0)NR2.
(13t) Any one of groups (13k) - (13n), wherein R12 is monocyclic heterocyclyl optionally substituted by one or two groups that are each independently halogen, Ci-6 alkyl, - C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, - N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(13u) Any one of groups (13k) - (13n), R12 is piperidinyl or tetrahydropyranyl, each optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, d_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)0R, or - N(R)C(0)NR2.
(13v) Any one of groups (13k) - (13n), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
(13w) Any one of groups (13k) - (13n), wherein R 12 is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen, Ci-6 alkyl, C2.6 alkenyl, Ci-6 haloalkyl, C3_8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl.
(13x) Any one of groups (13k) - (13n), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently C1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2. (13y) Any one of groups (13k) - (13n), wherein R is piperidinyl optionally substituted by one or two groups that are each independently Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, -OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen or Ci-6 alkyl.
(13z) Any one of groups (13k) - (13n), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci-6 alkyl, -C(0)R, -C(0)OR, - C(0)NR2, or -S(0)2R.
(13aa) Any one of groups (13k) - (13n), wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci-6 alkyl, -C(0)RA, or -S(0)2RA, wherein each RA is independently hydrogen or Ci-6 alkyl
(13bb)Any one of groups (13k) - (13n), wherein R12 is
Figure imgf000063_0001
5 wherein RB is hydrogen, C1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0
(13cc) Any one of groups (13k) - (13n), wherein R12 is
Figure imgf000063_0002
, wherein RB is hydrogen, Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, - OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen, Ci-6 alkyl, C2_6 alkenyl, Ci_6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi-6 alkyl, heteroaryl, or heteroarylCi-6 alkyl.
(13dd)Any one of groups (13k) - (13n), wherein R12 is
Figure imgf000063_0003
, wherein R is hydrogen, Ci_6 alkyl, -C(0)RA, -C(0)ORA, -C(0)N(RA)2, -S(0)2RA, -OC(0)RA, - OC(0)ORA, -OC(0)N(RA)2, -N(RA)C(0)RA, -N(RA)C(0)ORA, or -N(RA)C(0)N(RA)2, wherein each RA is independently hydrogen or C1-6 alkyl.
;e) Any one of groups (13k) - (13n), wherein R12 is
Figure imgf000063_0004
wherein RB is hydrogen, Ci-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, or -S(0)2R. (13ff) Any one of groups (13k) - (13n), wherein R12 is
Figure imgf000064_0001
, wherein RB is hydrogen, Ci.6 alkyl, -C(0)RA, or -S(0)2RA, wherein each RA is independently hydrogen or C1-6 alkyl. R~ is selected from one of the following groups (14a) - (14x):
(14a) R3 is naphthyl, quinolinyl, pyridyl, pyrimidinyl, indolyl, benzodioxolyl, 2,3- dihydrobenzodioxinyl, dibenzothienyl, chromanyl, or phenyl, each optionally substituted with one, two, or three R31 groups.
(14b) R3 is naphthyl, quinolinyl, indolyl, benzodioxolyl, 2,3-dihydrobenzodioxinyl, or chromanyl, each optionally substituted with one, two, or three R31 groups.
(14c) R is quinolinyl, pyridyl, pyrimidinyl, or indolyl, each optionally substituted with one, two, or three R31 groups.
(14d) R3 is quinolinyl or indolyl, each optionally substituted with one, two, or three R31 groups.
(14e) R3 is quinolinyl optionally substituted with one, two, or three R31 groups.
(14f) R3 is pyridyl or pyrimidinyl, each optionally substituted with one, two, or three R31 groups.
(14g) R3 is phenyl substituted with one, two, or three R31 groups.
(14h) R3 is phenyl optionally substituted with one or two R31 groups, and substituted with one group that is halogen, Ci_6 alkyl,-OR, -SR, -NR2, -N(R)C(0)R, or-N(R)S(0)2R.
(14i) R is phenyl optionally substituted with one or two R groups, and substituted with one group that is -OR or -N(R)C(0)R.
(14j) R3 is phenyl optionally substituted with one or two R31 groups, and substituted with one group that is -OR10, wherein R10 is benzyl optionally substituted with one, two, three, or four groups that are each independently halogen, Ci-6 alkyl, Ci-6 haloalkyl, or -OR0.
(14k) R3 is phenyl optionally substituted with one or two R31 groups, and substituted with one group that is -N(H)C(0)R20, wherein R20 is C1-6 alkyl, C2_6 alkenyl, Ci-6 haloalkyl, aryl, or arylCi-6 alkyl.
(141) R3 is naphthyl optionally substituted with one, two, or three R31 groups.
(14m) R3 is naphthyl optionally substituted with one or two R31 groups and substituted with one group that is -OR15, wherein R15 is Ci_6 alkyl or benzyl, wherein the benzyl is optionally substituted with one or two groups that are each independently halogen, Ci_
6 alkyl, Ci_6 haloalkyl, or -OR0.
(14n) R3 is naphth-l-yl optionally substituted with one, two, or three R31 groups.
(14o) R3 is naphth-l-yl optionally substituted with one or two R31 groups and substituted with one group that is -OR15, wherein R15 is C\- alkyl or benzyl, wherein the benzyl is optionally substituted with one or two groups that are each independently halogen,
Ci-6 alkyl, Ci-6 haloalkyl, or -OR0.
(14p) R3 is naphth-2-yl optionally substituted with one, two, or three R31 groups.
(14q) R3 is naphth-2-yl optionally substituted with one or two R31 groups and substituted with one group that is -OR15, wherein R15 is Ci_6 alkyl or benzyl, wherein the benzyl is optionally substituted with one or two groups that are each independently halogen, or -OR0.
Figure imgf000065_0001
(14s) R3 is indolyl optionally substituted with one, two, or three Rjl groups.
3 31
(14t) R is indol-2-yl optionally substituted with one, two, or three R groups.
3 31
(14u) R is indol-3-yl optionally substituted with one, two, or three R groups.
3 31
(14v) R is indol-5-yl optionally substituted with one, two, or three R groups.
3 31
(14w) R is indol-6-yl optionally substituted with one, two, or three R groups.
(14x) Any one of groups (2a) - (2aa) as defined above for formula (I).
Other particular embodiments of this aspect of the invention include compounds of any one of the formulae (IV), (IVa) - (IVh), each as defined in each of the following rows, wherein each entry is a group number as defined above (e.g., (14w) refers to R3 is indol-6-yl optionally substituted with one, two, or three R31 groups), and a dash "-" indicates that the variable is as defined for formula (IV) or defined according to any one of the applicable variable definitions (13a)-(14x) [e.g., when R1 is a dash, it can be either as defined for Formula (IV) or any one of definitions (13a)-(13ff)]:
Figure imgf000065_0003
Figure imgf000065_0004
Figure imgf000065_0002
Figure imgf000066_0001
In an embodiment of any of the preceding, the compound of formula (II) and (IV) one of the following compounds
Figure imgf000066_0002
Figure imgf000067_0001
One embodiment of the present disclosure provide a method of treating a subject in need of treatment for an apicomplexan-related disease comprising administering an effective amount of a compound of any of formulas (I) - (IV) or any embodiment thereof, that inhibits the activity of an apicomplexan calcium dependent protein kinase (CDPK). Particular embodiments of the present disclosure provide a method of treating cryptosporidiosis in a subject comprising administering an effective amount of a compound of any of formulas (I) - (IV) or any embodiment thereof, that inhibits the activity of Cryptosporidium parvum and C. hominus calcium dependent protein kinase 1 (Q?CDPK1).
Other particular embodiments of the present disclosure provide a method of treating cryptosporidiosis in a subject comprising administering an effective amount of a compound of any of formulas (I) - (IV) or any embodiment thereof, that inhibits the activity of T. gondii, calcium dependent protein kinase 1 (T CDPKl).
Optionally, the compound of any one of formulas (I) - (IV) or any embodiment thereof, can be administered in combination with a second agent, such as agents specific for use against the specific apicomplexan-related disorder being treated.
In one embodiment, the apicomplexan protozoan related disease is toxoplasmosis. As understood by one of ordinary skill in the art, toxoplasmosis can encompass a number of pathologies, including, but not limited to, encephalitis, retinitis, lymphadenopathy, disseminated disease, and hepatitis. Toxoplasmosis infects most genera of warm-blooded animals, including humans, but the primary host is the felid (cat) family.
Cats are the definitive host for the Toxoplasma organism. Infection with this protozoan parasite is fairly common, but actual disease caused by this parasite is relatively rare in cats. Cats can become infected by Toxoplasma by eating any of the three infective stages of the parasites. The most common route of infection is probably by ingestion of tissue cysts in infected prey or in other raw meat. Toxoplasma multiply in the small intestines and in approximately two to three weeks the oocysts are excreted in the infected cat's feces. In another example, cats may be treated prophylactically for toxoplasmosis (e.g, a gastrointestinal infection) provided by providing a therapeutically effective amount of a compounds of any one of formulas (I) - (IV) or to eliminate the chance that they would shed infectious Toxoplasmodia oocyts and infect their owners. In another embodiment, infected cats may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat toxoplasmosis. As will be understood by those of skill in the art, similar prophylactic and therapeutic methods for limiting development of or treating toxoplasmosis can be used in any animal that can be infected by Toxoplasma sp.
Animals are infected by eating infected meat, by ingestion of feces of a cat that has itself recently been infected, or by transmission from mother to fetus. While cats are often blamed for spreading toxoplasmosis, contact with raw meat is a more significant source of human infections in many countries, and fecal contamination of hands is a greater risk factor. Infection has two stages (1) acute toxoplasmosis; and (2) latent toxoplasmosis. During acute toxoplasmosis, symptoms are often influenza-like: swollen lymph nodes, or muscle aches and pains that last for a month or more. Rarely, a patient with a fully functioning immune system may develop eye damage from toxoplasmosis. Young children (15 years old or younger) and immunocompromised patients, such as those with HIV/AIDS, those taking certain types of chemotherapy, or those who have recently received an organ transplant, may develop severe toxoplasmosis. In an embodiment, a young child can be 14 years old or younger; or 13 years old or younger; or 12 years old or younger; or 1 1 years old or younger; or 10 years old or younger; or 9 years old or younger; or 8 years old or younger; or 7 years old or younger; or 6 years old or younger; or 5 years old or younger; or 4 years old or younger; or 3 years old or younger; or 2 years old or younger; or 1 year old or younger. This can cause damage to the brain (encephalitis) or the eyes (necrotizing retinochoroiditis). Infants infected via placental transmission may be born with either of these problems, or with nasal malformations, although these complications are rare in newborns. In most immunocompetent patients, the infection enters a latent phase, during which only bradyzoites are present, forming cysts in nervous and muscle tissue. Most infants who are infected while in the womb have no symptoms at birth but may develop symptoms later in life. The most common current therapy for toxoplasmosis is sulfadiazine/pyrimethamine combination therapy, but therapy is often limited by allergic reactions to the sulfa component, anemia and pancytopenia induced by blocking the folate pathway. When sulfadiazine cannot be used, clindamycin may be combined with pyrimethamine but most experts feel it does not work as well as sulfadiazine. Spiramycin has been used for toxoplasmosis during pregnancy but has issues with low efficacy and is no longer available in the United States. Thus few therapeutic alternatives are available.
In another embodiment, the apicomplexan protozoan related disease is cryptosporidiosis. Cryptosporidiosis is caused by infection with the single-celled parasite (not bacterium) Cryptosporidium parvum. This parasite is found in many mammals including lambs, calves, goat kids, piglets and humans. Research so far has shown two basic types, the bovine type which affects most species, and a second human type which causes disease in humans only. Outbreaks of human disease, where large numbers of people are affected, are usually water-borne and usually associated with the bovine type of Cryptosporidium. Individual sporadic cases of cryptosporidiosis in humans are mostly (around 60%) associated with the human type of Cryptosporidium.
Cryptosporidiosis affects the intestines of mammals and is typically an acute short- term infection. It is spread through the fecal-oral route, often through contaminated water; the main symptom is self-limiting diarrhea in people with intact immune systems. In immunocompromised individuals, such as HIV/AIDS patients, the symptoms are particularly severe and often fatal. Cryptosporidium is the organism most commonly isolated in HIV positive patients presenting with diarrhea. Cryptosporidiosis is one of the most common waterborne diseases and is found worldwide. The parasite is transmitted by environmentally hardy microbial cysts (oocysts) that, once ingested, exist in the small intestine and result in an infection of intestinal epithelial tissue. Infection is through contaminated material such as earth, water, uncooked or cross-contaminated food that has been in contact with the feces of an infected individual or animal. It is especially prevalent amongst those in regular contact with bodies of fresh water including recreational water such as swimming pools. Other potential sources include insufficiently treated or insufficiently filtered water water supplies, contaminated food, or exposure to feces. Symptoms appear from two to ten days after infection, and last for up to two weeks or more. In immunocompetent people, the disease can be asymptomatic or cause acute diarrhea or persistent diarrhea that can last for a few weeks. There is often stomach pain or cramping and a low fever. Other symptoms may include nausea, vomiting, malabsorption, and dehydration. Individuals who are asymptomatic (have no symptoms) are nevertheless infective. Immunocompromised people, as well as very young or very old people, can develop a more severe form of cryptosporidiosis. When Cryptosporidium spreads beyond the intestine, as it can predominantly in patients with AIDS, it can reach the lungs, middle ear, pancreas, and stomach. Thus, one symptom is pain in the right upper quadrant. The parasite can infect the biliary tract, causing biliary cryptosporidiosis. This can result in cholecystitis and cholangitis. Current treatment is symptomatic, with fluid rehydration, electrolyte correction and management of any pain. Nitazoxanide has been FDA-approved for treatment of diarrhea caused by Cryptosporidium in people with healthy immune systems and is available by prescription, however it only shortens the duration of diarrhea by a couple of days. The effectiveness of nitazoxanide in immunosuppressed individuals is unclear and multiple trials have shown no benefit.
The inhibitors described herein may have use in other apicoplexa protozoan related diseases, such as coccidiosis caused by Eimeria spp., cause infections and disease in poultry; which causes Babesiosis which is caused by Babesia spp. and results in a malaria-like disease, and malaria in humans and animals caused by Plasmodium spp.
As used herein, the term "subject", "individual," or "patient," used interchangeably, refers to any animal, including mammals, preferably mice, rats, other rodents, rabbits, dogs, cats, birds, swine, horses, livestock (e.g., pigs, sheep, goats, cattle), primates or humans.
As used here, a subject "in need thereof refers to a subject that has the disorder or disease to be treated or is predisposed to or otherwise at risk of developing the disease or disorder.
As used here, the terms "treatment" and "treating" means
(i) inhibiting the progression the disease;
(ii) prophylactic use for example, preventing or limiting development of a disease, condition or disorder in an individual who may be predisposed or otherwise at risk to the disease, condition or disorder but does not yet experience or display the pathology or symptomatology of the disease; (iii) inhibiting the disease; for example, inhibiting a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder;
(iv) ameliorating the referenced disease state, for example, ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e., reversing or improving the pathology and/or symptomatology) such as decreasing the severity of disease; or
(v) eliciting the referenced biological effect.
In various preferred embodiments, the individual may be immunocompromised
(having an immune system that has been impaired by disease or treatment, such as an HIV infected patient, and AIDS patient, or a patient receiving chemotherapy or an organ transplant), a pregnant female, fifteen years old or younger, fifty-five years old or older, exposed to contaminated water supplies, and/or exposed to other sources of contamination (fecal matter, blood transfusion, earth, food, etc.) The methods may further comprise administering the compounds disclosed herein to subjects at risk of acquiring an apicomplexan-related disease, such as those with compromised immune systems or that are extremely young in high risk areas.
In other embodiments, the compounds described herein can be used in prophylactic manner. Cryptosporidiosis is usually seen in calves between one and two weeks of age and presents with diarrhea, colic and pain, depression, loss of appetite, and weight loss. Thus, in one embodiment, calves may be treated prophylactically by providing an effective amount of a compound of any one of formulas (I) - (IV) to limit the contraction or transmission of cryptosporidiosis. In a preferred embodiment, the administering is done within the first 7-8 days after birth (day 1, 2, 3, 4, 5, 6, 7, or 8) when calves are most susceptible to Cryptosporidia infection. Such treatments may be repeated as necessary as would be understood by one skilled in the art.
In another embodiment, infected cattle may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat cryptosporidiosis. Such treatments may be repeated as necessary as would be understood by one skilled in the art. In this embodiment, the compounds of the invention may be administered together with electrolytes if cattle become dehydrated. If disease is severe, halfuginone can be used in combination with the compounds of the invention to reduce disease severity and prevent spread to other animals.
In another example, lambs are susceptible to cryptosporidiosis and may be provided a therapeutically effective amount of a compounds of any one of formulas (I) - (IV) to limit the contraction or transmission of cryptosporidiosis.
In another example, any or all members of a herd (e.g., cattle, goats, lambs, etc.), may be provided a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to limit the contraction or transmission of toxoplasmosis or cryptosporidiosis or to rid the herd of cattle of toxoplasmosis or cryptosporidiosis.
In another embodiment, goat kids may be treated prophylactically by providing an effective amount of a compound of any one of formulas (I) - (IV) to limit the contraction or transmission of cryptosporidiosis. In a preferred embodiment, the administering is done within the first 7-8 days after birth (day 1, 2, 3, 4, 5, 6, 7, or 8) when kids are most susceptible to cryptosporidiosis . Such treatments may be repeated as necessary as would be understood by one skilled in the art. The extent to which a kid is infected seems to be dependent on its age and immune status. Younger animals are much more susceptible to infection than adults. In studies done with lambs, five-day-old lambs had diarrhea for 9-10 days and suffered from a high rate of mortality. Sixty-day-old lambs showed no symptoms when they were infected, and adult sheep completely resisted infection. There is an indication that adults develop an immunity to Cryptosporidium, yet this immunity does not seem to be passed to their offspring.
Immune-depressed goats are very susceptible to the disease. This refers to the total immune status, not just protection from cryptosporidiosis. Many situations can cause animals to lack immunity. Animals with severe infections are more susceptible to secondary infections. The most common problem with kids is receiving a deficient amount of colostral antibodies following birth. Whether caused by disease, an imbalanced ration or improper management, animals lacking adequate immunity are much more susceptible to cryptosporidiosis.
In another embodiment, infected goats may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat cryptosporidiosis. In a preferred embodiment, the goat is a kid.
In another example, pigs are susceptible to cryptosporidiosis and may be provided a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to limit the contraction or transmission of cryptosporidiosis. In a preferred embodiment, the administering is done within the first 21 days after birth (day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21) when piglets are most susceptible to cryptosporidiosis and/or most likely
In another embodiment, infected pigs may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat cryptosporidiosis. In a preferred embodiment, the pig is a piglet.
In another example, birds, such as turkeys and chickens, are susceptible to cryptosporidiosis and may be provided an effective amount of a compounds of any one of formulas (I) - (IV) to prevent the contraction or transmission of cryptosporidiosis. In particular, Cryptosporidium baileyi can cause respiratory disease in chickens and turkeys. The same species causes infections of the hindgut and cloacal bursa in chickens, turkeys, and ducks. C. meleagridis also infects both species. A further species causes respiratory disease in quail. The oocysts are excreted ready sporulated in the faeces and infection occurs by inhalation and ingestion. Signs of cryptosporidiosis in poultry include snick, cough, swollen sinuses, low weight gain, and diarrhea. In another embodiment, infected birds may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat cryptosporidiosis.
In another example, birds, such as turkeys and chickens, are susceptible to coccidiosis due to Eimeria infections and may be provided an effective amount of a compounds of any one of formulas (I) - (IV) to limit the contraction or transmission of coccidiosis,. a parasitic disease caused by the development and multiplication of coccidia in the epithelial cells of the intestine. Eimeria infections are ubiquitous; they are found wherever chickens or turkeys are reared (traditional, industrial, label or organic/bio farms). Particular strains of Eimeria known to infect birds include, but are not limited to, Eimeria acervulina. Eimeria adenoeides, Eimeria brunette, Eimeria colchici, Eimeria curvata, Eimeria dispersa, Eimeria duodenali, Eimeria fraterculae, Eimeria gallopavonis, Eimeria praecox, Eimeria maxima, Eimeria meleagrimitis, Eimeria mitis, Eimeria necatrix, Eimeria phasiani, Eimeria procera, and Eimeria tenella. In another embodiment, infected birds may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat coccidiosis
In another example, mammals, such as goats, sheep, llamas, alpacas, cattle, rabbits, and mice, are susceptible to coccidiosis and may be provided an effective amount of a compounds of any one of formulas (I) - (IV) to limit the contraction or spreading of Eimeria. Particular strains of Eimeria known to infect mammals include, but are not limited to, Eimeria ahsata, Eimeria alabamensis, Eimeria alijevi, Eimeria apsheronica, Eimeria arloingi, Eimeria arundeli, Eimeria bakuensis, Eimeria bovis, Eimeria cameli, Eimeria caprina, Eimeria caprovina, Eimeria christenseni, Eimeria clethrionomyis, Eimeria coecicola, Eimeria contorta, Eimeria couesii, Eimeria crandallis, Eimeria dammahensis, Eimeria dowleri, Eimeria exigua, Eimeria falciformis, Eimeria farasanii, Eimeria ferrisi, Eimeria flavescens, Eimeria gallatii, Eimeria granulosa, Eimeria hirci, Eimeria intestinalis, Eimeria irresidua, Eimeria intricata, Eimeria jolchijevi, Eimeria krijgsmanni, Eimeria larimerensis, Eimeria macusaniensis, Eimeria magna, Eimeria marconii, Eimeria media, Eimeria melanuri, Eimeria myoxi, Eimeria nagpurensis, Eimeria ninakohlyaldmovae, Eimeria ovinoidalis, Eimeria pallida, Eimeria palustris, Eimeria papillata, Eimeria perforans, Eimeria phocae, Eimeria pileata, Eimeria pipistrellu, Eimeria piriformis, Eimeria prionotemni, Eimeria punctate, Eimeria roobroucki, Eimeria saudiensis, Eimeria sealanderi, Eimeria separate, Eimeria stiedae, Eimeria ursini, Eimeria vermiformis, Eimeria weybridgensis, Eimeria wobati, and Eimeria zuernii. In another embodiment, infected mammals may be treated by providing a therapeutically effective amount of a compound of any one of formulas (I) - (IV) to treat coccidiosis
The usual age range for animals suffering from coccidiosis is from three weeks to one year of age, but cattle remain susceptible to coccidiosis throughout their lives or until they develop acquired immunity. The susceptibility of the animals is influenced by nutritional status (colostrum supply), stress (overstocking, transport, climate, hygiene, etc.), immune status and the occurrence of concurrent diseases.
Infections with multiple Eimeria species (pathogenic and non-pathogenic) are common in real life situations. The most important species related to the clinical manifestation of the disease in the stable are Eimeria bovis and Eimeria zuernii, although other pathogenic coccidia species may also affect the cattle in the stables, such as Eimeria alabamensis (animals fed on contaminated hay), which is commonly associated with diarrheic problems in animals that are released to pasture.
"Carrier hosts" shed relatively fewer oocysts and the susceptible "multiplier hosts" pick up the infection and shed many-fold oocysts into the environment. Exposure to multiplier hosts leads to subclinical or mildly clinical infection in animals exposed to a large number of oocysts in the environment. Calves exposed to a large number of oocysts are likely to develop severe coccidiosis. In feedlots where few oocysts are present, stress factors such as weaning, diet, temperature extremes and other variables may make the calves more susceptible to infection and under such conditions the reproductive potential of coccidia in the gut greatly increases.
In goats, although the infection can occur in any goat herd raised under semi and intensive management practices, it is most frequently observed in kids 2 to 4 weeks postweaning. The infection occurs by ingesting the pathogenic sporulated oocyst (sporulated is a form of resistance of the Coccidia). Oocysts can be found in the water or in feed supplies contaminated with feces. Once ingested, oocysts penetrate the cells lining the intestine where they go through several stages of development and cause inflammation and destruction of intestinal cells. Stress is the predisposing factor in kids during the postweaning period. Outbreaks can occur during stressful conditions such as after shipping or when animals are relocated. Outbreaks can also occur during sudden weather changes, after a change in concentrated feed practices, when animals are recovering from a disease, or in worm burden cases. Although coccidiosis can occur year around, a higher incidence occurs during postweaning.
The compounds disclosed herein can be used to treat coccidiosis in combination with standard treatments such as, but not limited to, replacing fluids by administering liquid nutritional supplement orally by nipple bottle until the animal is rehydrated. Animals that have lost 5 percent of their body weight may require intravenous (IV) and'or electrolyte therapy. Treatment may include IV or subcutaneous ly (SC) fluid therapy with a physiologically balanced electrolyte such as Ringer's, Plasmalyte-A, or Normosol-R. Administer the solution (2 to 5 milliliters per pound) one to three times daily until the animal is rehydrated. Sulfas such as Albon™, Sulmet™, or Di-Methox™, can also be mixed in the drinking water or as a drench for individual goats. An alternative is CORID™ (amprolium).
As used herein, the phrase "therapeutically effective amount" refers to the amount of active compound or pharmaceutical agent that elicits the biological or medicinal response that is being sought in a tissue, system, animal, individual or human by a researcher, veterinarian, medical doctor or other clinician, which includes one or more of the following: (1) preventing the disease; for example, preventing a disease, condition or disorder in an individual who may be predisposed to the disease, condition or disorder but does not yet experience or display the pathology or symptomatology of the disease; (2) inhibiting the disease; for example, inhibiting a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder; and (3) ameliorating the disease; for example, ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e., reversing the pathology and/or symptomatology) such as decreasing the severity of disease.
METHODS FOR IDENTIFYING A COMPOUND
As disclosed herein, the inventors have identified compounds for use in treating apicomplexan-related disorders. While not being bound by a specific mechanism of action, the inventors believe that the inhibitory activity is based on selective inhibition of apicomplexan protein kinases, specifically selective inhibitors against apicomplexan calcium- dependent protein kinases (CDPKs). The inventors have further identified a specific region of such CDPKs that the inhibitors bind to, exemplified by SEQ ID NO: l (from the T. gondii, CDPK (SEQ ID NO: 13); (TgCDPK))) and SEQ ID NO:2 (from the C. parvum CDPK (CpCDPK)(SEQ ID NOs: 14, 15, 16, 17)). Thus, another aspect of the present disclosure provides a method of identifying a compound for treating an apicomplexan-related disease, including but not limited to those disclosed above, and most preferably toxoplasmosis and cryptosporidiosis. The method comprises (a) contacting a polypeptide comprising an amino acid sequence according to SEQ ID NO. 1 or SEQ ID NO:2 with a compound to be tested for the ability to bind to the polypeptide under conditions suitable for binding to the polypeptide, and (b) identifying compounds that bind to the polypeptide. Suitable conditions for such binding can be determined by one of skill in the art based on the teachings herein. For example, the methods may comprise suitable wash steps to remove unbound compounds. The methods may be conducted in vitro, or the binding may be assayed in cells using appropriate reporter molecules.
In one embodiment, the method comprises contacting the compound with the recited peptide. In another embodiment, the compound is contacted with TgCDPK or CpCDPK. In a further embodiment, the compound is contacted with TgCDPK or CpCDPK under conditions for crystallizing the complex, as described in the examples that follow. In all of these embodiments, the method may further comprise comparing binding of the compound to a control. Any suitable control can be used. In one embodiment, the control comprises comparing binding of the polypeptide to binding of the compound to a control polypeptide. Any suitable control polypeptide may be used. In one embodiment, the control polypeptide may comprise a mutated CDPK active region, such as TgCDPKl G128M (described below), or corresponding C.parvum CDPK mutated at the gatekeeper glycine residue (CpCDPK residue 150) (as described in detail herein). For example, the gatekeeper glycine residue in any TgCDPK or CpCDPK may be mutated as described herein to replace the glycine residue with alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, or valine. In these embodiments, those compounds that show selective binding to the polypeptide and little to no binding to the control peptide are identified as selective inhibitors against apicomplexan CDPKs. Exemplary methods according to this aspect of the invention are described in the examples that follow.
In a further embodiment, the methods may comprise a verification step (c), comprising applying a compound selected in (b) to the relevant apicomplexan species, such Toxoplasma gondii of C. parvum, to test for inhibitory activity. Exemplary such assays for inhibitory activity are described in the examples herein.
When the test compounds comprise polypeptide sequences, such polypeptides may be chemically synthesized or recombinantly expressed. Recombinant expression can be accomplished using standard methods in the art, as disclosed above. Such expression vectors can comprise bacterial or viral expression vectors, and such host cells can be prokaryotic or eukaryotic. Synthetic polypeptides, prepared using the well-known techniques of solid phase, liquid phase, or peptide condensation techniques, or any combination thereof, can include natural and unnatural amino acids. Amino acids used for peptide synthesis may be standard Boc (Na-amino protected Na-t-butyloxycarbonyl) amino acid resin with standard deprotecting, neutralization, coupling and wash protocols, or standard base-labile Na-amino protected 9-fluorenylmethoxycarbonyl (Fmoc) amino acids. Both Fmoc and Boc Na-amino protected amino acids can be obtained from Sigma, Cambridge Research Biochemical, or other chemical companies familiar to those skilled in the art. In addition, the polypeptides can be synthesized with other Na-protecting groups that are familiar to those skilled in this art. Solid phase peptide synthesis may be accomplished by techniques familiar to those in the art and provided, such as by using automated synthesizers.
When the test compounds comprise antibodies, such antibodies can be polyclonal or monoclonal. The antibodies can be humanized, fully human, or murine forms of the antibodies. Such antibodies can be made by well-known methods, such as described in Harlow and Lane, Antibodies; A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1988).
When the test compounds comprise nucleic acid sequences, such nucleic acids may be chemically synthesized or recombinantly expressed as well. Recombinant expression techniques are well known to those in the art (See, for example, Sambrook, et al., 1989, supra). The nucleic acids may be DNA or RNA, and may be single stranded or double. Similarly, such nucleic acids can be chemically or enzymatically synthesized by manual or automated reactions, using standard techniques in the art. If synthesized chemically or by in vitro enzymatic synthesis, the nucleic acid may be purified prior to introduction into the cell. For example, the nucleic acids can be purified from a mixture by extraction with a solvent or resin, precipitation, electrophoresis, chromatography, or a combination thereof. Alternatively, the nucleic acids may be used with no or a minimum of purification to avoid losses due to sample processing.
When the test compounds comprise compounds other than polypeptides, antibodies, or nucleic acids, such compounds can be made by any of the variety of methods in the art for conducting organic chemical synthesis.
PHARMACEUTICAL COMPOSITIONS
The pharmaceutical compositions described herein generally comprise a combination of a compound described herein and a pharmaceutically acceptable carrier, diluent, or excipient. Such compositions are substantially free of non-pharmaceutically acceptable components, i.e., contain amounts of non-pharmaceutically acceptable components lower than permitted by US regulatory requirements at the time of filing this application. In some embodiments of this aspect, if the compound is dissolved or suspended in water, the composition further optionally comprises an additional pharmaceutically acceptable carrier, diluent, or excipient. In other embodiments, the pharmaceutical compositions described herein are solid pharmaceutical compositions (e.g., tablet, capsules, etc.).
These compositions can be prepared in a manner well known in the pharmaceutical art, and can be administered by a variety of routes, depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including intranasal, vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), ocular, oral or parenteral. Methods for ocular delivery can include topical administration (eye drops), subconjunctival, periocular or intravitreal injection or introduction by balloon catheter or ophthalmic inserts surgically placed in the conjunctival sac. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Parenteral administration can be in the form of a single bolus dose, or may be, for example, by a continuous perfusion pump. Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
Also, pharmaceutical compositions can contain, as the active ingredient, one or more of the compounds described herein above in combination with one or more pharmaceutically acceptable carriers. In making the compositions described herein, the active ingredient is typically mixed with an excipient, diluted by an excipient or enclosed within such a carrier in the form of, for example, a capsule, sachet, paper, or other container. When the excipient serves as a diluent, it can be a solid, semi-solid, or liquid material, which acts as a vehicle, carrier or medium for the active ingredient. Thus, the compositions can be in the form of tablets, pills, powders, lozenges, sachets, cachets, elixirs, suspensions, emulsions, solutions, syrups, aerosols (as a solid or in a liquid medium), ointments containing, for example, up to 10% by weight of the active compound, soft and hard gelatin capsules, suppositories, sterile injectable solutions, and sterile packaged powders.
In preparing a formulation, the active compound can be milled to provide the appropriate particle size prior to combining with the other ingredients. If the active compound is substantially insoluble, it can be milled to a particle size of less than 200 mesh. If the active compound is substantially water soluble, the particle size can be adjusted by milling to provide a substantially uniform distribution in the formulation, e.g. about 40 mesh.
Some examples of suitable excipients include lactose, dextrose, sucrose, sorbitol, mannitol, starches, gum acacia, calcium phosphate, alginates, tragacanth, gelatin, calcium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrup, and methyl cellulose. The formulations can additionally include: lubricating agents such as talc, magnesium stearate, and mineral oil; wetting agents; emulsifying and suspending agents; preserving agents such as methyl- and propylhydroxy-benzoates; sweetening agents; and flavoring agents. The compositions described herein can be formulated so as to provide quick, sustained or delayed release of the active ingredient after administration to the patient by employing procedures known in the art.
The compositions can be formulated in a unit dosage form, each dosage containing from about 5 to about 100 mg, more usually about 10 to about 30 mg, of the active ingredient. The term "unit dosage forms" refers to physically discrete units suitable as unitary dosages for human subjects and other mammals, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect, in association with a suitable pharmaceutical excipient.
The active compound can be effective over a wide dosage range and is generally administered in a pharmaceutically effective amount. It will be understood, however, that the amount of the compound actually administered will usually be determined by a physician, according to the relevant circumstances, including the condition to be treated, the chosen route of administration, the actual compound administered, the age, weight, and response of the individual patient, the severity of the patient's symptoms, and the like.
For preparing solid compositions such as tablets, the principal active ingredient is mixed with a pharmaceutical excipient to form a solid preformulation composition containing a homogeneous mixture of a compound described herein. When referring to these preformulation compositions as homogeneous, the active ingredient is typically dispersed evenly throughout the composition so that the composition can be readily subdivided into equally effective unit dosage forms such as tablets, pills and capsules. This solid preformulation is then subdivided into unit dosage forms of the type described above containing from, for example, 0.1 to about 500 mg of the active ingredient of a compound described herein.
The tablets or pills can be coated or otherwise compounded to provide a dosage form affording the advantage of prolonged action. For example, the tablet or pill can comprise an inner dosage and an outer dosage component, the latter being in the form of an envelope over the former. The two components can be separated by an enteric layer which serves to resist disintegration in the stomach and permit the inner component to pass intact into the duodenum or to be delayed in release. A variety of materials can be used for such enteric layers or coatings, such materials including a number of polymeric acids and mixtures of polymeric acids with such materials as shellac, cetyl alcohol, and cellulose acetate.
The liquid forms in which the compounds and compositions can be incorporated for administration orally or by injection include aqueous solutions, suitably flavored syrups, aqueous or oil suspensions, and flavored emulsions with edible oils such as cottonseed oil, sesame oil, coconut oil, or peanut oil, as well as elixirs and similar pharmaceutical vehicles.
Compositions for inhalation or insufflation include solutions and suspensions in pharmaceutically acceptable, aqueous or organic solvents, or mixtures thereof, and powders. The liquid or solid compositions may contain suitable pharmaceutically acceptable excipients as described supra. In some embodiments, the compositions are administered by the oral or nasal respiratory route for local or systemic effect. Compositions in can be nebulized by use of inert gases. Nebulized solutions may be breathed directly from the nebulizing device or the nebulizing device can be attached to a face masks tent, or intermittent positive pressure breathing machine. Solution, suspension, or powder compositions can be administered orally or nasally from devices which deliver the formulation in an appropriate manner.
The amount of compound or composition administered to a patient will vary depending upon what is being administered, the purpose of the administration, such as prophylaxis or therapy, the state of the patient, the manner of administration, and the like. In therapeutic applications, compositions can be administered to a patient already suffering from a disease in an amount sufficient to cure or at least partially arrest the symptoms of the disease and its complications. Effective doses will depend on the disease condition being treated as well as by the judgment of the attending clinician depending upon factors such as the severity of the disease, the age, weight and general condition of the patient, and the like.
The compositions administered to a patient can be in the form of pharmaceutical compositions described above. These compositions can be sterilized by conventional sterilization techniques, or may be sterile filtered. Aqueous solutions can be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile aqueous carrier prior to administration. The pH of the compound preparations typically will be between 3 and 11, more preferably from 5 to 9 and most preferably from 7 to 8. It will be understood that use of certain of the foregoing excipients, carriers, or stabilizers will result in the formation of pharmaceutical salts.
The therapeutic dosage of the compounds can vary according to, for example, the particular use for which the treatment is made, the manner of administration of the compound, the health and condition of the patient, and the judgment of the prescribing physician. The proportion or concentration of a compound described herein in a pharmaceutical composition can vary depending upon a number of factors including dosage, chemical characteristics (e.g., hydrophobicity), and the route of administration. For example, the compounds described herein can be provided in an aqueous physiological buffer solution containing about 0.1 to about 10% w/v of the compound for parenteral administration. Some typical dose ranges are from about 1 μg/kg to about 1 g/kg of body weight per day. In some embodiments, the dose range is from about 0.01 mg/kg to about 100 mg/kg of body weight per day. The dosage is likely to depend on such variables as the type and extent of progression of the disease or disorder, the overall health status of the particular patient, the relative biological efficacy of the compound selected, formulation of the excipient, and its route of administration. Effective doses can be extrapolated from dose-response curves derived from in vitro or animal model test systems.
The compounds described herein can also be formulated in combination with one or more additional active ingredients which can include any pharmaceutical agent such as anti-viral agents, vaccines, antibodies, immune enhancers, immune suppressants, anti-inflammatory agents and the like.
DEFINITIONS
Unless the context clearly requires otherwise, throughout the description and the claims, the words 'comprise', 'comprising', and the like are to be construed in an inclusive sense as opposed to an exclusive or exhaustive sense; that is to say, in the sense of "including, but not limited to". Words using the singular or plural number also include the plural or singular number, respectively. Additionally, the words "herein," "above" and "below" and words of similar import, when used in this application, shall refer to this application as a whole and not to any particular portions of this application.
Terms used herein may be preceded and/or followed by a single dash, or a double dash, "=", to indicate the bond order of the bond between the named substituent and its parent moiety; a single dash indicates a single bond and a double dash indicates a double bond. In the absence of a single or double dash it is understood that a single bond is formed between the substituent and its parent moiety; further, substituents are intended to be read "left to right" unless a dash indicates otherwise. For example, Q-Cealkoxycarbonyloxy and -OC(0)Ci-C6alkyl indicate the same functionality; similarly arylalkyl and -alkylaryl indicate the same functionality.
The term "alkenyl" as used herein, means a straight or branched chain hydrocarbon containing from 2 to 10 carbons, unless otherwise specified, and containing at least one carbon-carbon double bond. Representative examples of alkenyl include, but are not limited to, ethenyl, 2-propenyl, 2-methyl-2-propenyl, 3-butenyl, 4-pentenyl, 5-hexenyl, 2-heptenyl, 2-methyl-l-heptenyl, 3-decenyl, and 3,7-dimethylocta-2,6-dienyl.
The term "alkyl" as used herein, means a straight or branched chain hydrocarbon containing from 1 to 10 carbon atoms, unless otherwise specified. Representative examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec -butyl, iso-butyl, tert-butyl, n-pentyl, isopentyl, neopentyl, n-hexyl, 3-methylhexyl, 2,2-dimethylpentyl, 2,3-dimethylpentyl, n-heptyl, n-octyl, n-nonyl, and n-decyl. When an "alkyl" group is a linking group between two other moieties, then it may also be a straight or branched chain; examples include, but are not limited to -CH2-, -CH2CH2-, -CH2CH2CHC(CH3)-, -CH2CH(CH2CH3)CH2-.
The term "alkynyl" as used herein, means a straight or branched chain hydrocarbon group containing from 2 to 10 carbon atoms and containing at least one carbon-carbon triple bond. Representative examples of alkynyl include, but are not limited, to acetylenyl, 1-propynyl, 2-propynyl, 3-butynyl, 2-pentynyl, and 1-butynyl.
The term "aryl," as used herein, means a phenyl (i.e., monocyclic aryl), a bicyclic ring system containing at least one phenyl ring or an aromatic bicyclic ring containing only carbon atoms in the aromatic bicyclic ring system or a multicyclic aryl ring system, provided that the bicyclic or multicyclic aryl ring system does not contain a heteroaryl ring when fully aromatic. The bicyclic aryl can be azulenyl, naphthyl, or a phenyl fused to a monocyclic cycloalkyl, a monocyclic cycloalkenyl, or a monocyclic heterocyclyl. The bicyclic aryl is attached to the parent molecular moiety through any carbon atom contained within the phenyl portion of the bicyclic system, or any carbon atom with the napthyl or azulenyl ring. The fused monocyclic cycloalkyl or monocyclic heterocyclyl portions of the bicyclic aryl are optionally substituted with one or two oxo and/or thia groups. Representative examples of the bicyclic aryls include, but are not limited to, azulenyl, naphthyl, dihydroinden-l-yl, dihydroinden-2-yl, dihydroinden-3-yl, dihydroinden-4-yl, 2,3-dihydroindol-4-yl, 2,3-dihydroindol-5-yl, 2,3-dihydroindol-6-yl, 2,3-dihydroindol-7-yl, inden-l-yl, inden-2-yl, inden-3-yl, inden-4-yl, dihydronaphthalen-2-yl, dihydronaphthalen-3-yl, dihy dronaphthalen-4-y 1, dihy dronaphthalen- 1 -yl, 5,6,7 , 8-tetrahy dronaphthalen- 1 -y 1, 5,6,7,8-tetrahydronaphthalen-2-yl, 2,3 -dihy drobenzofuran-4-yl, 2,3-dihydrobenzofuran-5-yl, 2,3-dihydrobenzofuran-6-yl, 2,3-dihydrobenzofuran-7-yl, benzo[d][l,3]dioxol-4-yl, benzo[d][l,3]dioxol-5-yl, 2H-chromen-2-on-5-yl, 2H-chromen-2-on-6-yl, 2H-chromen-2-on-7-yl, 2H-chromen-2-on-8-yl, isoindoline-l,3-dion-4-yl, isoindoline-l,3-dion-5-yl, inden-l-on-4-yl, inden-l-on-5-yl, inden-l-on-6-yl, inden-l-on-7-yl, 2,3-dihydrobenzo[b][l,4]dioxan-5-yl, 2,3-dihydrobenzo[b][l,4]dioxan-6-yl, 2H-benzo[b] [ 1 ,4]oxazin3 (4H)-on-5-yl, 2H-benzo[b] [ 1 ,4]oxazin3 (4H)-on-6-yl,
2H-benzo [b] [ 1 ,4] oxazin3 (4H)-on-7-yl, 2H-benzo[b] [ 1 ,4]oxazin3 (4H)-on-8-yl, benzo[d]oxazin-2(3H)-on-5-yl, benzo[d]oxazin-2(3H)-on-6-yl, benzo[d]oxazin-2(3H)-on-7-yl, benzo[d]oxazin-2(3H)-on-8-yl, quinazolin-4(3H)-on-5-yl, quinazolin-4(3H)-on-6-yl, quinazolin-4(3H)-on-7-yl, quinazolin-4(3H)-on-8-yl, quinoxalin-2(lH)-on-5-yl, quinoxalin-2(lH)-on-6-yl, quinoxalin-2(lH)-on-7-yl, quinoxalin-2(lH)-on-8-yl, benzo[d]thiazol-2(3H)-on-4-yl, benzo[d]thiazol-2(3H)-on-5-yl, benzo[d]thiazol-2(3H)-on-6-yl, and, benzo[d]thiazol-2(3H)-on-7-yl. In certain embodiments, the bicyclic aryl is (i) naphthyl or (ii) a phenyl ring fused to either a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclic heterocyclyl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. Multicyclic aryl groups are a phenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl, provided that when the base ring is fused to a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl, then the base ring is fused to the base ring of the a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl. The multicyclic aryl is attached to the parent molecular moiety through any carbon atom contained within the base ring. In certain embodiments, multicyclic aryl groups are a phenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ring systems independently selected from the group consisting of a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl, provided that when the base ring is fused to a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl, then the base ring is fused to the base ring of the a bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl. Examples of multicyclic aryl groups include but are not limited to anthracen-9-yl and phenanthren-9-yl.
The term "arylalkyl" and "-alkylaryl" as used herein, means an aryl group, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein. Representative examples of arylalkyl include, but are not limited to, benzyl, 2-phenylethyl, 3-phenylpropyl, and 2-naphth-2-ylethyl.
The terms "cyano" and "nitrile" as used herein, mean a -CN group.
The term "cycloalkyl" as used herein, means a monocyclic, bicyclic, or a multicyclic cycloalkyl ring system. Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups can be saturated or unsaturated, but not aromatic. In certain embodiments, cycloalkyl groups are fully saturated. Examples of monocyclic cycloalkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, and cyclooctyl. Bicyclic cycloalkyl ring systems are bridged monocyclic rings or fused bicyclic rings. Bridged monocyclic rings contain a monocyclic cycloalkyl ring where two non-adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form -(CH2)W-, where w is 1, 2, or 3). Representative examples of bicyclic ring systems include, but are not limited to, bicyclo[3.1.1]heptane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, bicyclo[3.3.1]nonane, and bicyclo[4.2.1]nonane. Fused bicyclic cycloalkyl ring systems contain a monocyclic cycloalkyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. The bridged or fused bicyclic cycloalkyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkyl ring. Cycloalkyl groups are optionally substituted with one or two groups which are independently oxo or thia. In certain embodiments, the fused bicyclic cycloalkyl is a 5 or 6 membered monocyclic cycloalkyl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused bicyclic cycloalkyl is optionally substituted by one or two groups which are independently oxo or thia. Multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other rings systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl. The multicyclic cycloalkyl is attached to the parent molecular moiety through any carbon atom contained within the base ring. In certain embodiments, multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other rings systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl. Examples of multicyclic cycloalkyl groups include, but are not limited to tetradecahydrophenanthrenyl, perhydrophenothiazin-l-yl, and perhydrophenoxazin- 1 -yl.
"Cycloalkenyl" as used herein refers to a monocyclic, bicyclic, or a multicyclic cycloalkenyl ring system. Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups are unsaturated (i.e., containing at least one annular carbon-carbon double bond), but not aromatic. Examples of monocyclic ring systems include cyclopentenyl and cyclohexenyl. Bicyclic cycloalkenyl rings are bridged monocyclic rings or a fused bicyclic rings. Bridged monocyclic rings contain a monocyclic cycloalkenyl ring where two non-adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form -(CH2)W-, where w is 1, 2, or 3). Representative examples of bicyclic cycloalkenyls include, but are not limited to, norbornenyl and bicyclo[2.2.2]oct-2-enyl. Fused bicyclic cycloalkenyl ring systems contain a monocyclic cycloalkenyl ring fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. The bridged or fused bicyclic cycloalkenyl is attached to the parent molecular moiety through any carbon atom contained within the monocyclic cycloalkenyl ring. Cycloalkenyl groups are optionally substituted with one or two groups which are independently oxo or thia. Multicyclic cycloalkenyl rings contain a monocyclic cycloalkenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two rings systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl. The multicyclic cycloalkenyl is attached to the parent molecular moiety through any carbon atom contained within the base ring. IN certain embodiments, multicyclic cycloalkenyl rings contain a monocyclic cycloalkenyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two rings systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl.
The term "halo" or "halogen" as used herein, means -CI, -Br, -I or -F.
The term "haloalkyl" as used herein, means at least one halogen, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein. Representative examples of haloalkyl include, but are not limited to, chloromethyl, 2-fluoroethyl, trifluoromethyl, pentafluoroethyl, and 2-chloro-3-fluoropentyl.
The term "heteroaryl," as used herein, means a monocyclic, bicyclic, or a multicyclic heteroaryl ring system. The monocyclic heteroaryl can be a 5 or 6 membered ring. The 5 membered ring consists of two double bonds and one, two, three or four nitrogen atoms and optionally one oxygen or sulfur atom. The 6 membered ring consists of three double bonds and one, two, three or four nitrogen atoms. The 5 or 6 membered heteroaryl is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heteroaryl. Representative examples of monocyclic heteroaryl include, but are not limited to, furyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl, oxazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, pyrazolyl, pyrrolyl, tetrazolyl, thiadiazolyl, thiazolyl, thienyl, triazolyl, and triazinyl. The bicyclic heteroaryl consists of a monocyclic heteroaryl fused to a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. The fused cycloalkyl or heterocyclyl portion of the bicyclic heteroaryl group is optionally substituted with one or two groups which are independently oxo or thia. When the bicyclic heteroaryl contains a fused cycloalkyl, cycloalkenyl, or heterocyclyl ring, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon or nitrogen atom contained within the monocyclic heteroaryl portion of the bicyclic ring system. When the bicyclic heteroaryl is a monocyclic heteroaryl fused to a phenyl ring or a monocyclic heteroaryl, then the bicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom within the bicyclic ring system. Representative examples of bicyclic heteroaryl include, but are not limited to, benzimidazolyl, benzofuranyl, benzothienyl, benzoxadiazolyl, benzoxathiadiazolyl, benzothiazolyl, cinnolinyl, 5,6-dihydroquinolin-2-yl, 5,6-dihydroisoquinolin-l-yl, furopyridinyl, indazolyl, indolyl, isoquinolinyl, naphthyridinyl, quinolinyl, purinyl, 5,6,7,8-tetrahydroquinolin-2-yl, 5,6,7,8-tetrahydroquinolin-3-yl, 5,6,7,8-tetrahydroquinolin-4-yl, 5,6,7,8-tetrahydroisoquinolin-l-yl, thienopyridinyl, 4,5,6,7 -tetrahy drobenzo [c] [ 1 ,2 ,5 ] oxadiazolyl, and 6,7-dihydrobenzo[c][l,2,5]oxadiazol-4(5H)-onyl. In certain embodiments, the fused bicyclic heteroaryl is a 5 or 6 membered monocyclic heteroaryl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. The multicyclic heteroaryl group is a monocyclic heteroaryl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic heterocyclyl, a bicyclic cycloalkenyl, and a bicyclic cycloalkyl; or (ii) two ring systems selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic heterocyclyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic cycloalkyl. The multicyclic heteroaryl group is connected to the parent molecular moiety through any carbon atom or nitrogen atom contained within the base ring. In certain embodiments, multicyclic heteroaryl groups are a monocyclic heteroaryl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic heterocyclyl, a bicyclic cycloalkenyl, and a bicyclic cycloalkyl; or (ii) two ring systems selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic heterocyclyl, a monocyclic cycloalkenyl, and a monocyclic cycloalkyl. Examples of multicyclic heteroaryls include, but are not limited to 5H- [l,2,4]triazino[5,6-b]indol-5-yl, 2,3,4,9-tetrahydro-lH-carbazol-9-yl, 9H-pyrido[3,4-b]indol- 9-yl, 9H-carbazol-9-yl, acridin-9-yl,
The term "heteroarylalkyl" and "-alkylheteroaryl" as used herein, means a heteroaryl, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein. Representative examples of heteroarylalkyl include, but are not limited to, fur-3-ylmethyl, lH-imidazol-2-ylmethyl, lH-imidazol-4-ylmethyl, l-(pyridin-4-yl)ethyl, pyridin-3-ylmethyl, pyridin-4-ylmethyl, pyrimidin-5-ylmethyl, 2-(pyrimidin-2-yl)propyl, thien-2-ylmethyl, and thien-3-ylmethyl.
The term "heterocyclyl" as used herein, means a monocyclic, bicyclic, or multicyclic heterocycle. The monocyclic heterocycle is a 3, 4, 5, 6 or 7 membered ring containing at least one heteroatom independently selected from the group consisting of 0, N, and S where the ring is saturated or unsaturated, but not aromatic. The 3 or 4 membered ring contains 1 heteroatom selected from the group consisting of 0, N and S. The 5 membered ring can contain zero or one double bond and one, two or three heteroatoms selected from the group consisting of 0, N and S. The 6 or 7 membered ring contains zero, one or two double bonds and one, two or three heteroatoms selected from the group consisting of 0, N and S. The monocyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the monocyclic heterocycle. Representative examples of monocyclic heterocycle include, but are not limited to, azetidinyl, azepanyl, aziridinyl, diazepanyl, 1,3-dioxanyl, 1,3-dioxolanyl, 1,3-dithiolanyl, 1,3-dithianyl, imidazolinyl, imidazolidinyl, isothiazolinyl, isothiazolidinyl, isoxazolinyl, isoxazolidinyl, morpholinyl, oxadiazolinyl, oxadiazolidinyl, oxazolinyl, oxazolidinyl, piperazinyl, piperidinyl, pyranyl, pyrazolinyl, pyrazolidinyl, pyrrolinyl, pyrrolidinyl, tetrahydrofuranyl, tetrahydrothienyl, thiadiazolinyl, thiadiazolidinyl, thiazolinyl, thiazolidinyl, thiomorpholinyl, 1, 1-dioxidothiomorpholinyl (thiomorpholine sulfone), thiopyranyl, and trithianyl. The bicyclic heterocycle is a monocyclic heterocycle fused to either a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocycle, or a monocyclic heteroaryl. The bicyclic heterocycle is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the monocyclic heterocycle portion of the bicyclic ring system. Representative examples of bicyclic heterocyclyls include, but are not limited to, 2,3-dihydrobenzofuran-2-yl, 2,3-dihydrobenzofuran-3-yl, indolin-l-yl, indolin-2-yl, indolin-3-yl, 2,3-dihydrobenzothien-2-yl, decahydroquinolinyl, decahydroisoquinolinyl, octahydro-lH-indolyl, and octahydrobenzofuranyl. Heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. In certain embodiments, the bicyclic heterocyclyl is a 5 or 6 membered monocyclic heterocyclyl ring fused to phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the bicyclic heterocyclyl is optionally substituted by one or two groups which are independently oxo or thia. Multicyclic heterocyclyl ring systems are a monocyclic heterocyclyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other rings systems independently selected from the group consisting of a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl. The multicyclic heterocyclyl is attached to the parent molecular moiety through any carbon atom or nitrogen atom contained within the base ring. In certain embodiments, multicyclic heterocyclyl ring systems are a monocyclic heterocyclyl ring (base ring) fused to either (i) one ring system selected from the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other rings systems independently selected from the group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic heterocyclyl. Examples of multicyclic heterocyclyl groups include, but are not limited to lOH-phenothiazin-10-yl, 9,10-dihydroacridin-9-yl, 9,10-dihydroacridin-lO-yl, 10H- phenoxazin-10-yl, 10, l l-dihydro-5H-dibenzo[b,f]azepin-5-yl, l,2,3,4-tetrahydropyrido[4,3- g]isoquinolin-2-yl, 12H-benzo[b]phenoxazin-12-yl, and dodecahydro-lH-carbazol-9-yl.
The term "nitro" as used herein, means a -N02 group.
The term "oxo" as used herein means a =0 group. The term "saturated" as used herein means the referenced chemical structure does not contain any multiple carbon-carbon bonds. For example, a saturated cycloalkyl group as defined herein includes cyclohexyl, cyclopropyl, and the like.
The term "thia" as used herein means a =S group.
The term "unsaturated" as used herein means the referenced chemical structure contains at least one multiple carbon-carbon bond, but is not aromatic. For example, a unsaturated cycloalkyl group as defined herein includes cyclohexenyl, cyclopentenyl, cyclohexadienyl, and the like.
As used herein, the phrase "pharmaceutically acceptable salt" refers to both pharmaceutically acceptable acid and base addition salts and solvates. Such pharmaceutically acceptable salts include salts of acids such as hydrochloric, phosphoric, hydrobromic, sulfuric, sulfmic, formic, toluenesulfonic, methanesulfonic, nitric, benzoic, citric, tartaric, maleic, hydroiodic, alkanoic such as acetic, HOOC-(CH2)n-COOH where n is 0-4, and the like. Non-toxic pharmaceutical base addition salts include salts of bases such as sodium, potassium, calcium, ammonium, and the like. Those skilled in the art will recognize a wide variety of non-toxic pharmaceutically acceptable addition salts.
SYNTHETIC METHODS
The two exemplary synthetic routes described below can be used to generate derivatives that contain varying substituents at the 1- and 3 -positions of the pyrazolopyrimidine core (Schemes 1 and 2). The first series of analogs retain the naphthylmethylene substituent at the 3 -position and contain various alkyl groups at the 1- position. Synthesis of these analogs began with conversion of 1 -naphthalene acetyl chloride to pyrazolopyrimidine 4 in five steps (Scheme 1). (16)
Sche
Figure imgf000091_0001
5g-5i
v. (a) Malononitrile, NaH, THF; (b) Dimethyl Sulfate, NaHC03; (c) H2NNH2, EtOH, heat; (d) Formamide, 180°C. ii: R2-Br, K2C03, DMF // : (a) R2-OH, PS- PPh3, DEAD, THF; (b) TFA, DCM. iv. Ac20, DIPEA, DMF v: CH3CHO, NaHB(OAc)3. vi: Methylsulfonyl chloride, DIPEA, DMF.
To introduce various alkyl substituents at the 1 -position, 4 can be derivatized with alkyl halides by direct nucleophilic displacement (5a-5e) or with alcohols using standard Mitsunobu reaction conditions (5a-5e). (17, 18) Notably, the use of support-bound triphenylphosphine for the Mitsunobu reaction can expedite the purification of alkylated products. (19) The N-Boc protecting groups can be removed from piperidine analogues 5f-5h and the resultant free amines can be acetylated, sulfonylated, or alkylated.
The second series of derivatives can be generated with a synthetic route that allows various substituents to be introduced at the 3 -position of the pyrazolopyrimidine core (Scheme 2).
Scheme 2.
Figure imgf000091_0002
la-lab Iodinated pyrazolopyrimidine 6 can be generated in three steps from commercially available 5-amino-lH-pyrazole-4-carbonitrile. Various aryl substituents can be introduced by coupling boronic acids and boronic esters to 6 using standard palladium-catalyzed cross- coupling conditions.
SYNTHETIC EXAMPLES
Commercially available reagents and anhydrous solvents were used without further purification unless otherwise specified. The final purity of all compounds was determined by analytical HPLC with an Agilent ZORBAX SB-C18 column (2.1 mm x 150 mm). Analytical HPLC data were generated by injecting 20 of sample solution in methanol and acetonitrile to a reverse phase HPLC system run over 30 min (2-100% acetonitrile/water with 0.05%TFA and 2-100% methanol/water with 0.05% TFA). The products were detected by UV at the detection frequency of 254 nm. All compounds were determined to be >95%> pure by this method. Flash chromatography was performed on prepacked columns of silica gel (Varian SF10-4g, Si 50) by IntelliFlash with EtOAc/hexanes or MeOH/CH2Cl2 as eluent. The purification by preparative HPLC was performed on Varian Dynamax Microsorb 100-5 CI 8 column (250 mm x 21.4 mm) with CH3CN/H20 or MeOH/H20 and 0.05% TFA as eluent. The mass spectra were recorded with the Bruker Esquire Liquid Chromatograph - Ion Trap Mass Spectrometer. NMR spectra were recorded with either a Bruker 300 MHz spectrometer or Bruker 500 MHz spectrometer at ambient temperature with the residual solvent peaks as internal standards. The chemical shifts are given in ppm (δ) and coupling constants are reported in Hz. ¾ resonances are referenced to CDCL (7.26 ppm), DMSO-d6 (2.54) or CD3OD (3.34). Example 1 Preparation of Intermediate A
Figure imgf000092_0001
To malononitrile (0.646 g, 9.8 mmol) in THF (15 mL) and sodium hydride (0.494 g, 19.5 mmol, 95% dispersion in paraffin oil), 1-naphthyleneacetyl chloride (2.0 g, 9.8 mmol) was added dropwise at 5-10 °C. After 3 h, the reaction mixture was warmed to room temperature and hydrochloric acid (45 mL) was added. The mixture was then extracted with ethyl acetate (3 x 75 mL) and the organic layer was dried over Na2S04 to yield A (1.71 g, 75%). lK NMR (CDCls, 300 MHz) δ 7.96-8.02 (m, 1H), 7.80-7.91 (m, 2H), 7.49-7.59 (m, 2H), 7.41-7.47 (m, 2H), 4.12 (s, 2H), 3.56 (s, 1H).
Example 2 Preparation of Intermediate B
Figure imgf000093_0001
To sodium hydrogen carbonate (6.112 g, 72.7 mmol) in 1,4-dioxane (12 mL) and water (2 mL), compound A (2.130 g, 9.1 mmol) and dimethyl sulfate (6.038 mL, 63.6 mmol) were added slowly. After stirring at 85 °C for 2.5 h, water (60 mL) was added. Extraction with tert-butyl methyl ether (4 x 50 mL), drying of the organic layer with Na2SC>4, and silica gel chromatography using an ethyl acetate-hexanes gradient yielded B (0.964 g, 43%). lR NMR (CDCI3, 300 MHz) δ 8.08-8.13 (m, 1H), 7.99-8.03 (m, 1H), 7.92-7.97 (m, 1H), 7.58- 7.70 (m, 2H), 7.49-7.56 (m, 1H), 7.25-7.30 (m, 1H), 4.63 (s, 2H), 3.98 (s, 3H).
Example 3 Preparation of Compound 4
Figure imgf000093_0002
To compound B (0.908 g, 3.66 mmol) in ethanol (10 mL), hydrazine hydrate (222
3.66 mmol, 80% hydrazine hydrate) and triethylamine (501 \L, 3.66 mmol) were added. After refluxing for 3.5 h the solvent was evaporated and water was added. The solid was collected and without any further purification, was refluxed in formamide (6 mL) overnight. The cold reaction mixture was diluted with water and the precipitate was collected. This precipitate was redissolved in chloroform and then purified by silica gel chromatography using a methanol-chloroform gradient to yield 4 (456 mg, 45%). 1H NMR (DMSO-d6, 300 MHz) δ 8.37 (s, 1H), 8.05-8.14 (m, 1H), 7.89-7.97 (m, 1H), 7.78-7.86 (m, 1H), 7.38-7.57 (m, 4H), 4.86 (s, 2H).
Example 4 General Procedure A
Figure imgf000094_0001
A mixture of 4 (0.073 mmol), K2C03 (4.0 equiv), and the appropriate alkyl halide (1.1 equiv) were dissolved in dimethylformamide (400 ί) and acetonitrile (1 mL). The reaction was heated to 5 °C below the boiling point of the alkyl halide overnight. Preparative HPLC with a methanol/water gradient was used to yield the final compound.
Example 5 Preparation of Compound 3
3 was synthesized using isopropyl iodide as the alkyl halide in General Procedure A. ¾ NMPv (CDCI3, 300 MHz) δ 8.04 (s, IH), 7.98-8.03 (m, IH), 7.84-7.92 (m, 2H), 7.40-7.56 (m, 3H), 7.30- 7.36 (m, IH), 5.14 (sept, J =6.9, IH), 4.76 (s, 2H), 1.62 (d, J=6.9, 6H). MS (ESI) (M + H)+= 318.4.
Example 6 Preparation of Compound 5 a
5a was synthesized using methyl iodide as the alkyl halide in General Procedure A. ¾ NMPv (CDC13, 300 MHz) δ 8.10 (s, IH), 7.90-8.02 (m, 3H), 7.46-7.61 (m, 3H), 7.36-7.42 (m, IH), 4.79 (s, 2H), 4.14 (s, 3H). (M + H)+= 290.4. Example 7 Preparation of Compound 5b
5b was synthesized using propargyl bromide as the alkyl halide in General Procedure A. ¾ NMR (CDCI3, 300 MHz) δ 8.12 (s, IH), 7.95-8.00 (m, IH), 7.87-7.92 (m, 2H), 7.46- 7.55 (m, 3H), 7.36- 7.40 (m, IH), 5.24 (m, 2H), 4.79 (s, 2H), 2.48 (m, IH). MS (ESI) (M + H)+= 314.4. Example 8 Preparation of Compound 5c
5c was synthesized using iodoacetamide as the alkyl halide in General Procedure A. ¾ NMR (CD3OD, 500 MHz) δ 8.31 (s, IH), 8.08-8.11 (m, IH), 7.88-7.92 (s, IH), 7.81-7.84 (m, IH), 7.50-7.54 (m, 2H), 7.41-7.46 (m, IH), 7.26-7.30 (m, IH), 5.06 (s, 2H), 4.79 (s, 2H). MS (ESI) (M + H)+= 333.4. Example 9 Preparation of Compound 5 e
5e was synthesized using benzyl bromide as the alkyl halide in General Procedure A. ¾ NMR (CDCI3, 300 MHz) δ 8.26 (s, 1H), 8.12-8.16 (m, 2H), 7.88-7.94 (m, 2H), 7.74-7.80 (m, 1H), 7.61- 7.65 (m, 2H), 7.40 (m, 5H), 5.65 (s, 2H) 4.79 (s, 2H). MS (ESI) (M + H)+ = 366.5.
Example 10 Preparation of Compound 5f
5f was synthesized using cyclohexyl iodide as the alkyl halide in General Procedure A. *H MR (CD3OD, 300 MHz) δ 8.18-8.23 (m, 1H), 8.16 (s, 1H), 7.88-7.93 (m, 1H), 7.78- 7.83 (m, 1H), 7.49-7.54 (m, 2H), 7.36-7.43 (m, 1H), 7.16-7.21 (m, 1H), 4.79 (s, 2H), 4.18- 4.24 (m, 1H), 3.66- 3.71 (m, 2H), 3.53-3.58 (m, 2H), 1.92-1.99 (m, 2H), 1.35-1.40 (m, 2H), 0.86-0.94 (m, 2H). MS (ESI) (M + H)+= 358.5.
Example 11 General Procedure B
Figure imgf000095_0001
A mixture of 4 (0.073 mmol), polymer-supported triphenylphosphine (2 equiv of 1.52 mmol/g PL-TPP from Varian Polymer Laboratories) and the appropriate alcohol (1.0 equiv) were dissolved in dry THF (1 mL) and stirred under N2. Diethyl azodicarboxylate (1.5 equiv) was then added at 0°C. After 15 min, the reaction mixture was warmed to room temperature and allowed to run overnight. The resin was filtered off and washed with dicholoromethane, concentrated in vacuo, and purified using reverse-phase preparative HPLC with a methanol/water gradient. The desired product was collected and subsequently deprotected by stirring in a mixture of trifluoroactetic acid (.5 mL) and dicholoromethane (.5 mL) for 2 h. The reaction mixture was concentrated in vacuo to yield the final compound.
Example 12 Preparation of Compound 5g
5g was synthesized using N-boc piperidine-4-ol as the alcohol in General Procedure B. JH NMR (DMSO-d6, 300 MHz) δ 8.33 (s, 1H), 8.15-8.20 (m, 1H), 7.91-7.96 (m, 1H), 7.80-7.84 (m, 1H), 7.51-7.57 (m, 2H), 7.37-7.44 (m, 1H), 7.19-7.23 (m, 1H), 4.95 (m, 1H), 4.84 (s, 2H), 3.32-3.41 (m, 2H), 3.05-3.20 (m, 2H), 2.1 1-2.26 (m, 2H), 1.95-2.05 (m, 2H). MS (ESI) (M + H)+= 359.4.
Example 13 Preparation of Compound 5h
5h was synthesized using N-boc piperidine-4-methanol as the alcohol in General Procedure B. lR NMR (CD3OD, 500 MHz) δ 8.12 (s, IH), 8.04-8.09 (m, IH), 7.93-7.97 (m, IH), 7.81-7.85 (m, IH), 7.48-7.52 (m, 2H), 7.40-7.44 (m, IH), 7.29-7.32 (m, IH), 4.75 (s, 2H), 4.16 (d, J=7.0, 2H), 2.83-2.90 (m, 2H), 2.17-2.24 (m, IH), 1.70-1.76 (m, 2H), 1.36-1.47 (m, 2H), 0.84-0.97 (m, 2H). MS (ESI) (M + H)+= 373.5.
Example 14 Preparation of Compound 5i 5i was synthesized using N-boc piperidine-4-ethanol as the alcohol in General
Procedure B. lR NMR (CD3OD, 300 MHz) δ 8.25 (s, IH), 7.98-8.02 (m, IH), 7.86-7.90 (m, IH), 7.78-7.82 (m, IH), 7.44-7.49 (m, 2H), 7.38-7.42 (m, IH), 7.28-7.32 (m, IH), 4.81 (s, 2H), 4.30-4.35 (m, 2H), 3.57-3.62 (m, 2H), 2.50-2.61 (m, 2H), 1.90-2.01 (m, 2H), 1.75-1.85 (m, 5H). MS (ESI) (M + H)+= 387.5. Example 15 General Procedure C
Figure imgf000096_0001
Acetic anhydride (1 equiv) and diisopropylethylamine (3 equiv) were added to compounds 5g-5i (.028 mmol) and dissolved in dimethylformamide (200 μΐ,). The reaction was allowed to stir at room temperature overnight. The reaction mixture was diluted with methanol and water and purified using reverse-phase preparative HPLC with a methanol/water gradient.
Example 16 Preparation of Compound 5j
5j was synthesized using 5g in General Procedure C. JH NMR (CDC13, 300 MHz) δ 8.09 (s, IH), 7.88-8.00 (m, 3H), 7.44-7.58 (m, 3H), 7.34-7.39 (m, IH), 4.95-5.05 (m, IH), 4.81-4.90 (m, IH), 4.76 (s, 2H), 4.04-4.13 (m, IH), 3.29-3.41 (m, IH), 2.81-2.91 (m, IH), 2.06-2.40 (m, 7H). MS (ESI) (M + H)+= 401.5. Example 17 Preparation of Compound 5k
5k was synthesized using 5h in General Procedure C. lR NMR (CD3OD, 300 MHz) δ
8.25 (s, IH), 8.04-8.10 (m, IH), 7.88-7.93 (m, IH), 7.81-7.85 (m , IH), 7.47-7.52 (m, 2H), 7.39-7.45 (m, IH), 7.29-7.33 (m, IH), 4.78 (s, 2H), 4.38-4.46 (m, IH), 4.24 (d, J=6.9, 2H), 3.79-3.87 (m, IH), 2.95-3.05 (m, IH), 2.45-2.58 (m, IH), 2.10-2.20 (m, IH), 2.05 (s, 3H), 1.46-1.60 (m, 2H), 1.32- 1.40 (m, 2H). MS (ESI) (M + H)+= 415.5.
Example 18 Preparation of Compound 51
51 was synthesized using 5i in General Procedure C. H NMR (CD3OD, 300 MHz) δ
8.26 (s, IH), 8.05-8.1 1 (m, IH), 7.89-7.94 (m, IH), 7.82-7.86 (m, IH), 7.48-7.54 (m, 2H), 7.41-7.46 (m, IH), 7.30-7.34 (m, IH), 4.82 (s, 2H), 4.33-4.40 (m, 2H), 3.72-3.77 (m, IH),
3.43-3.49 (m, IH), 2.71- 2.79 (m, IH), 2.26-2.33 (m, IH), 2.04 (s, 3H), 1.72-1.79 (m, 2H), 1.60-1.70 (m, 2H), 1.32-1.42 (m, 3H). MS (ESI) (M + H)+= 429.5.
Example 19 General Procedure D
Figure imgf000097_0001
Acetaldehyde (10 equiv), sodium triacetoxyborohydride (3 equiv), diisopropylethylamine (0.75 equiv), and a catalytic amount of acetic acid were added to 5g-5i (.028 mmol) and dissolved in dichloroethane (200 μΕ). The reaction was allowed to stir at room temperature overnight. The reaction mixture was diluted with methanol and water and purified using reverse-phase preparative HPLC with a methanol/water gradient.
Example 20 Preparation of Compound 5m
5m was synthesized using 5g in General Procedure D. lR NMR (CD3OD, 300 MHz) δ 8.22 (s, IH), 8.08-8.14 (m, IH), 7.87-7.92 (m, IH), 7.80-7.85 (m, IH), 7.49-7.54 (m, 2H), 7.42-7.47 (m, IH), 7.31-7.35 (m, IH), 4.89-4.96 (m, IH), 4.80 (s, 2H), 4.32-4.38 (m, 2H), 3.52-3.58 (m, 2H), 2.99-3.10 (m, 2H), 1.87-1.95 (m, 2H), 1.73-1.80 (m, 2H), 1.28-144 (m, 3H). MS (ESI) (M + H)+= 387.5. Example 21 Preparation of Compound 5n
5n was synthesized using 5h in General Procedure D. lE NMR (CD3OD, 300 MHz) δ 8.22 (s, IH), 8.08-8.14 (m, IH), 7.89-7.93 (m, IH), 7.81-7.85 (m, IH), 7.48-7.54 (m, 2H), 7.39-7.45 (m, IH), 7.28-7.33 (m, IH), 4.78 (s, 2H), 4.23-4.27 (m, 2H), 3.64-3.69 (m, 2H), 3.10-3.19 (m, 2H), 2.80-2.87 (m, IH), 2.17-2.24 (m, 2H), 1.78-1.84 (m, 2H), 1.57-1.66 (m, 2H), 1.28-1.42 (m, 3H). MS (ESI) (M + H)+= 401.5.
Example 22 Preparation of Compound 5o
5o was synthesized using 5i in General Procedure D. H NMR (CD3OD, 300 MHz) δ 8.26 (s, IH), 8.03-8.09 (m, IH), 7.88-7.94 (m, IH), 7.81-7.86 (m, IH), 7.48-7.54 (m, 2H), 7.40-7.46 (m, IH), 7.29-7.34 (m, IH), 4.76 (s, 2H), 4.33-4.41 (m, 2H), 3.66-3.72 (m, IH), 3.53-3.60 (m, 2H), 3.30- 3.38 (m, 2H), 3.02-3.10 (m, 2H), 2.39-2.51 (m, 2H), 1.86-1.97 (m, 2H), 1.73-1.82 (m, 2H), 1.28-1.42 (m, 3H). MS (ESI) (M + H)+= 415.6.
Example 23 General Procedure E
Figure imgf000098_0001
Methylsulfonyl chloride (1.0 equiv) and diisopropylethylamine (3.0 equiv) were added to 5g-5i (.028 mmol) and dissolved in dimethylformamide (200 μΐ). The reaction was allowed to stir at room temperature overnight. The reaction mixture was diluted with methanol and water and purified using reverse-phase preparative HPLC with a methanol/water gradient. Example 24 Preparation of Compound 5 g
5p was synthesized using 5g in General Procedure E. JH NMR (CDCI3, 300 MHz) δ 8.30 (s, IH), 8.08-8.14 (m, IH), 7.87-7.92 (m, IH), 7.80-7.85 (m, IH), 7.46-7.54 (m, 2H), 7.39-7.45 (m, IH), 7.25-7.30 (m, IH), 4.89-4.96 (m, IH), 4.80 (s, 2H), 3.64-3.73 (m, 2H), 2.94-3.05 (m, 2H), 2.76 (s, 3H), 2.13-2.28 (m, 2H), 2.00-2.10 (m, 2H). MS (ESI) (M + H)+= 437.6.
Example 25 Preparation of Compound 5q 5q was synthesized using 5h in General Procedure E. lU NMR (CD3OD, 300 MHz) δ 8.26 (s, 1H), 8.04-8.1 1 (m, 1H), 7.88-7.94 (m, 1H), 7.80-7.86 (m, 1H), 7.48-7.54 (m, 2H),
7.39- 7.45 (m, lH), 7.29-7.35 (m, 1H), 4.78 (s, 2H), 4.26 (d, J=6.9, 2H), 3.59-3.69 (m, 2H), 2.78 (s, 3H), 2.57- 2.68 (m, 2H), 1.98-2.06 (m, 1H), 1.55-1.63 (m, 2H), 1.34-1.40 (m, 2H). MS (ESI) (M + H)+= 451.6.
Example 26 Preparation of Compound 5r
5r was synthesized using 5i in General Procedure E. JH NMR (CD3OD, 300 MHz) δ 8.26 (s, 1H), 8.03-8.09 (m, 1H), 7.88-7.94 (m, 1H), 7.81-7.86 (m, 1H), 7.48-7.54 (m, 2H),
7.40- 7.46 (m, 1H), 7.29-7.34 (m, 1H), 4.76 (s, 2H), 4.34-4.41 (t, J=6.9, 2H), 3.50-3.59 (m, 2H), 2.76 (s, 3H), 2.31- 2.43 (m, 2H), 1.66-1.81 (m, 4H), 1.35-1.40 (m, 1H), 1.10-1.17 (m,
2H). MS (ESI) (M + H)+= 465.6.
Example 27 Preparation of Compound 5d
To compound B (0.107 g, 0.43 mmol) in ethanol (2 mL), t-butyl hydrazine hydrochloride (0.054 g, 0.43 mmol) and triethylamine (59 μΕ, 0.43 mmol) were added. After refluxing for 3.5 h, the solvent was evaporated and water was added. The solid was collected and then refluxed in formamide (6 mL) overnight. The cold reaction mixture was diluted with water and the precipitate was collected. This precipitate was re-dissolved in chloroform and then purified by silica gel chromatography using a methanol-chloroform gradient to yield 5d (0.025 g, 18%). JH NMR (DMSO- d6, 300 MHz) δ 8.24-8.32 (m, 2H), 7.93 (m, 1H), 7.81 (m, 1H), 7.52-7.58 (m, 2H), 7.39 (m, 1H), 7.13 (m, 1H), 4.81 (s, 2H), 1.66 (s, 9H). MS (ESI) (M + H)+= 332.4.
Example 28 Preparation of Intermediate C
Figure imgf000099_0001
Commercially available 5-amino-lH-pyrazole-4-carbonitrile (2.0 g, 18.5 mmol) was mixed with formamide (10 mL) and heated to 180°C overnight under nitrogen. The solution was cooled to rt, 60 mL of water was added, and the resulting precipitate was collected by vacuum filtration to yield C (2.367 g, 95%). ¾ NMR (DMSO-d6, 300 MHz) δ 8.13 (s, 1H), 8.06 (s, 1H). Example 29 Preparation of Intermediate D
Figure imgf000100_0001
Compound C (2.367 g, 17.5 mmol) and N-iodosuccinimide (4.810 g, 21.4 mmol) were added to dimethylformamide (60 mL) and stirred at 50°C for 24 hours. Another batch of N-iodosuccinimide (0.871 g, 3.8 mmol) was added to the reaction mixture and was allowed to stir for an additional 24 hours. The reaction mixture was cooled to room temperature and water (100 mL) was added, forming a precipitate that was collected by filtration to yield D (4.1 g, 89%). lR NMR (DMSO- d6, 300 MHz) δ 8.18 (s, 1H).
Example 30 Preparation of Compound 6
Figure imgf000100_0002
A mixture of D (1.0 g, 3.8 mmol), K2C03 (2.135 g, 15.4 mmol), and isopropyl iodide (421 μΕ, 4.2 mmol) were dissolved in dimethylformamide (7.5 mL). The reaction was heated to 80°C and left to run overnight. An extraction with saturated sodium acetate and ethyl acetate was performed. The organic layer was dried with sodium sulfate and concentrated in vacuo. The crude product was purified using silica gel chromatography with a methanol/dichloromethane gradient to yield 6 (673 mg, 58%). H NMR (DMSO-d6, 300 MHz) δ 8.19 (s, 1H), 4.93-5.03 (m, 1H), 1.43 (d, J=6.9, 6H).
Example 31 General Procedure F
Figure imgf000100_0003
Compound 6 (1 equiv), tetrakis(triphenylphosphine) palladium(O) (0.05 equiv), and sodium carbonate (2.3 equiv) were added to the appropriate boronic acid or pinacol ester (1.1 equiv) in dimethoxy ethane (1 mL) and water (0.5 mL). The reaction was performed in a microwave at 85°C for one hour, followed by extraction with ethyl acetate and water. The organic layer was collected and concentrated in vacuo to yield the crude product. The crude product was then purified via flash chromatography with an ethyl acetate/hexanes gradient.
Example 32 Preparation of Compound 7a
7a was synthesized using 4-chlorophenylboronic acid in General Procedure F. XH NM (CDCI3, 300 MHz) δ 8.32 (s, IH), 7.57 (m, 4H), 5.19 (sep, J=6.8, IH), 1.61 (d, J=6.8, 6H). MS (ESI) (M + H)+= 288.8.
Example 33 Preparation of Compound 7b
7b was synthesized using 3-chlorophenylboronic acid in General Procedure F. JH NMR (CDCI3, 300 MHz) δ 8.40 (s, IH), 7.76 (s, IH), 7.60 (m, IH), 7.46-7.50 (m, 2H), 5.21 (sep, J=6.7, IH), 1.62 (d, J=6.7, 6H). MS (ESI) (M + H)"=288.8.
Example 34 Preparation of Compound 7c
7c was synthesized using 3, 4-dichlorophenylboronic acid in General Procedure F. lR NMR (CDCI3, 300 MHz) δ 8.41 (s, IH), 7.86 (s, IH), 7.56-7.66 (m, 2H), 5.21 (sep, J=6.7, IH), 1.61 (d, 1=6.6, 6H). MS (ESI) (M + H)+=323.3. Example 35 Preparation of Compound 7d
7d was synthesized using 4-isopropylphenylboronic acid in General Procedure F. lK NMR (CDCI3, 300 MHz) δ 8.38 (s, IH), 7.64 (d, J=8.0, 2H), 7.41 (d, J=8.0, 2H), 5.20 (sep, J=6.8, IH), 3.01 (sep, J=6.8, IH), 1.61 (d, J=6.6, 6H), 1.32 (d, J=6.9 , 6H). MS (ESI) (M + H)+= 296.4. Example 36 Preparation of Compound 7e
7e was synthesized using 3-isopropylphenylboronic acid in General Procedure F. lH NMR (CDCI3, 300 MHz) δ 8.38 (s, IH), 7.38-7.68 (m, 4H), 5.20 (sep, J=6.8, IH), 3.01 (sep, J= 6.8, IH), 1.62 (d, J=6.8, 6H), 1.32 (d, J=6.8, 6H). MS (ESI) (M + H)+= 296.4.
Example 37 Preparation of Compound 7f 7f was synthesized using 4-methylphenylboronic acid in General Procedure F. JH
NMR (CDCI3, 300 MHz) δ 8.33 (s, IH), 7.59 (d, J=7.7, 2H), 7.36 (d, J=7.7, 2H), 5.20 (sep, J=6.8, IH), 2.46 (s, 3H), 1.62 (d, J=6.8, 6H). MS (ESI) (M + H)+= 268.4.
Example 38 Preparation of Compound 7g 7g was synthesized using 3-methylphenylboronic acid in General Procedure F. H NMR (CDCI3, 300 MHz) δ 8.37 (s, IH), 7.59 (m, 3H), 7.31 (s, IH), 5.16 (sep, J=6.8, IH), 2.43 (s, 3H), 1.61 (d, J=6.6, 6H). MS (ESI) (M + H)+= 268.4.
Example 39 Preparation of Compound 7h
7h was synthesized using 3, 4-dimethylphenylboronic acid in General Procedure F. JH NMR (CDCI3, 300 MHz) δ 8.37 (s, IH), 7.50 (m, 2H), 7.31 (s, IH), 5.19 (sep, J=6.6, IH), 2.37 (s, 3H), 2.35 (s, 3H), 1.61 (d, J=6.6, 6H). MS (ESI) (M + H)+= 282.4.
Example 40 Preparation of Compound 7i
7i was synthesized using 4-fluoro-3-methylphenylboronic acid in General Procedure F. JH NMR (CDCI3, 300 MHz) δ 8.38 (s, IH), 7.45-7.58 (m, 2H), 7.15 (m, IH), 5.19 (sep, J=6.8, IH), 2.39 (s, 3H), 1.61 (d, J=6.7, 6H). MS (ESI) (M + H)+= 286.4.
Example 41 Preparation of Compound 7j
7j was synthesized using 4-methoxyphenylboronic acid in General Procedure F. lR NMR (CDCI3, 300 MHz) δ 8.37 (s, IH), 7.59 (m, 2H), 7.08 (m, 2H), 5.19 (sept, J=6.8, IH), 3.90 (s, 3H), 1.61 (d, =6.8, 6H). MS (ESI) (M + H)+= 284.4.
Example 42 Preparation of Compound 7k
7k was synthesized using 3, 4-dimethoxyphenylboronic acid in General Procedure F. ¾ NMR (CDCI3, 300 MHz) δ 8.38 (s, IH), 7.21-7.27 (m, 2H), 7.02-7.06 (m, IH), 5.19 (sep, J=6.9, IH), 3.97 (m, 6H), 1.62 (d, J=6.9, 6H). MS (ESI) (M + H)+= 314.4.
Example 43 Preparation of Compound 71
71 was synthesized using 3,4,5-trimethoxyphenylboronic acid in General Procedure F. ¾ NMR (CDCI3, 300 MHz) δ 8.39 (s, IH), 6.91 (s, 2H), 5.22 (sep, J=6.9, IH), 3.95 (s, 6H), 3.92 (s, 3H), 1.62 (d, J=6.9, 6H). MS (ESI) (M + H)+= 344.5.
Example 44 Preparation of Compound 7m
7m was synthesized using 4-methoxy-3-methylphenylboronic acid in General Procedure F. l NMR (CDCI3, 300 MHz) δ 8.37 (s, IH), 7.49 (m, 2H), 6.99 (m, IH), 5.19 (sep, J=6.7, IH), 3.91 (s, 3H), 2.32 (s, 3H), 1.61 (d, J=6.7, 6H). MS (ESI) (M + H)+= 298.4. Example 45 Preparation of Compound 7n
7n was synthesized using 3-acetylphenylboronic acid in General Procedure F. lH NMR (CDCI3, 300 MHz) δ 8.41 (s, IH), 8.32 (s, IH), 8.08 (d, J=8.2, IH), 7.95 (d, J=8.2, IH), 7.67 (m, IH), 5.23 (sep, J=6.8, IH), 2.70 (s, 3H), 1.63 (d, J=6.6, 6H). MS (ESI) (M + H)+= 296.4.
Example 46 Preparation of Compound 7o
7o was synthesized using naphthalene- 1-boronic acid in General Procedure F. !H NMR (DMSO-de, 300 MHz δ 8.30 (s, IH), 8.03-8.1 1 (m, 2H), 7.85-7.90 (m, IH), 7.50-7.69 (m, 4H), 5.13 (septet, J=6.8, IH), 1.53 (d, J=6.8, 6H). MS (ESI) (M + H)+= 304.4. Example 47 Preparation of Compound 7p
7p was synthesized using naphthalene-2-boronic acid in General Procedure F. XH NMR (CDCI3, 300 MHz) δ 8.42 (s, IH), 8.19 (s, IH), 7.84-8.04 (m, 4H), 7.56-7.62 (m, 2H), 5.25 (septet, J=6.7, IH), 1.66 (d, J=6.7, 6H). MS (ESI) (M + H)+= 304.4.
Example 48 Preparation of Compound 7q 7q was synthesized using 6-methoxynaphthalene-2-boronic acid in General Procedure
F. JH NMR (300 MHz, CDC13) δ 8.27 (s, IH), 8.10 (s, IH), 7.77 - 7.94 (m, 2H), 7.64 - 7.73 (m, 2H), 7.21 (s, IH), 5.23 (septet, J=6.9, IH), 3.98 (s, 3H), 1.65 (d, J=6.9, 6H). MS (ESI) (M + H)+= 334.4.
Example 49 Preparation of Compound 7r 7r was synthesized using 6-ethoxynaphthalene-2-boronic acid in General Procedure
F. ¾ NMR (CDCI3, 300 MHz) δ 8.39 (s, IH), 8.10 (s, IH), 7.76-7.92 (m, 3H), 7.19-7.23 (m, 2H), 5.23 (sep, J=6.6, IH), 4.21 (q, J=6.9, 2H), 1.61 (d, J=6.6, 6H), 1.52 (t, J=6.9, 3H). MS (ESI) (M + H)+= 348.4.
Example 50 Preparation of Compound 7s 7s was synthesized using 2-methoxynapthalene-3-boronic acid in General Procedure
F. JH NMR (CDCI3, 300 MHz) δ 8.38 (s, IH), 8.03 (s, IH), 7.80-7.89 (m, 2H), 7.50-7.57 (m, 2H), 7.40-7.46 (m, IH), 5.23 (sep, J=6.8, IH), 3.98 (s, 3H), 1.66 (d, J=6.8, 6H). MS (ESI) (M + H)+= 334.4. Example 51 Preparation of Compound 7t
7t was synthesized using quinoline-3-boronic acid in General Procedure F. lH NMR (CDCI3, 300 MHz) δ 9.27 (s, IH), 8.46 (m, IH), 8.38 (s, IH), 8.17 (d, J= 8.4, IH), 7.91 (d, J=8.4, IH), 7.77 (m, IH), 7.62 (m, IH), 5.22 (sep, J=6.9, IH), 1.61 (d, J=6.9, 6H). MS (ESI) (M + H)+= 305.4.
Example 52 Preparation of Compound 7u
7u was synthesized using 3,4-methylenedioxyphenylboronic acid in General Procedure F. lR NMR (CDCI3, 300 MHz) δ 8.37 (s, IH), 7.14-7.21 (m, 2H), 6.95-7.00 (m, IH), 6.06 (s, 2H), 5.18 (sep, J=6.7, IH), 1.61 (d, J=6.7, 6H). MS (ESI) (M + H)+= 298.4. Example 53 Preparation of Compound 7v
7v was synthesized using l,4-benzodioxane-6-boronic acid in General Procedure F. ¾ NMR (CDCI3, 500 MHz) δ 8.30 (s, IH), 7.18 (s, IH), 7.06-7.14 (m, 2H), 5.20 (sep, J=6.7, IH), 4.36 (s, 4H), 1.63 (d, J=6.7, 6H). MS (ESI) (M + H)+= 312.4.
Example 54 Preparation of Compound 7w 7 was synthesized using 3,4-dihydrochromen-6-ylboronic acid in General Procedure
F. JH NMR (CDCI3, 300 MHz) δ 8.35 (s, IH), 7.35-7.41 (m, 2H), 6.92-6.98 (m, IH), 5.18 (sep, J=6.7, IH), 4.27 (t, J=5.2, 2H), 2.89 (t, J=5.2, 2H), 2.03-2.12 (m, 2H), 1.61 (d, J=6.7, 6H). MS (ESI) (M + H)+= 310.4.
Example 55 Preparation of Compound 7x 7x was synthesized using dibenzo[b,d]thiophen-4-ylboronic acid in General
Procedure F. lR NMR (CDCI3, 500 MHz) δ 8.47 (s, IH), 8.27 (s, IH), 7.72 (d, J =7.6, IH), 7.66 (d, J=7.6, IH), 7.54 (s, IH), 7.47 (t, j=7.6, IH), 7.39 (t, j=7.6, IH), 5.24 (sep, J=6.8, IH), 1.65 (d, j=6.8, 6H). MS (ESI) (M + H)+= 360.5.
Example 56 Preparation of Compound 7y 7y was synthesized using 3-Benzylphenylboronic acid pinacol ester in General
Procedure F. lU NMR (CDCI3, 300 MHz) δ 8.35 (s, IH), 7.56 (m, IH), 7.42-7.52 (m, 2H), 7.29-7.37 (m, 3H), 7.16-7.27 (m, 3H), 5.19 (sep, J=6.7, IH), 4.08 (s, 2H), 1.61 (d, J=6.7, 6H). MS (ESI) (M + H)+= 344.4. Example 57 Preparation of Compound 7z
7z was synthesized using 3-Biphenylboronic acid in General Procedure F. lH NMR (CDCI3, 300 MHz) δ 8.40 (s, 1H), 7.94 (s, 1H), 7.61-7.75 (m, 5H), 7.40-7.53 (m, 3H), 5.22 (sep, J=6.8, 1H), 1.64 (d, J=6.8, 6H). MS (ESI) (M + H)~= 330.4.
Example 58 Preparation of Compound 7aa
7aa was synthesized using 3-Benzyloxyphenylboronic acid in General Procedure F. ¾ NMR (300 MHz, CDC13) δ 8.40 (s, 1H), 8.10 (s, 1H), 7.37-7.55 (m, 5H), 7.15-7.26 (m, 3H), 5.14-5.27 (m, 3H), 1.64 (d, J=6.8, 6H). MS (ESI) (M + H)+= 360.5.
Example 59 Preparation of Compound 7ab 7ab was synthesized using 3-Methylthiophenylboronic acid in General Procedure F.
!H NMR (CDCI3, 300 MHz) δ 8.38 (s, 1H), 7.56 (s, 1H), 7.36-7.50 (m, 3H), 5.21 (sep, J=6.7, 1H), 2.56 (s, 3H), 1.63 (d, 3=6.1, 6H). MS (ESI) (M + H)+= 300.4.
Example 60 General Procedure G (compounds 1 and 2):
Figure imgf000105_0001
E F 1, 2
Intermediates E: To malononitrile (1.0 equiv) in THF (15 mL) and sodium hydride (2.0 equiv, 95% dispersion in paraffin oil), the appropriate acyl chloride (1.0 equiv) was added dropwise at 5-10°C. After 3 hours, the reaction mixture was warmed to room temperature and hydrochloric acid (45 mL) was added. The mixture was extracted with ethyl acetate (3 x 75 mL) and the organic layer was dried over Na2S04 to yield intermediate E.
Intermediates F: To sodium hydrogen carbonate (8.0 equiv) in 1,4-dioxane (12 mL) and water (2 mL), compound E (1.0 equiv) and dimethyl sulfate (7.0 equiv) were added slowly. After stirring at 85°C for 2.5 h, water (60 mL) was added. Extraction with tert-butyl methyl ether (4 x 50 mL), drying of the organic layer with Na2S04, and silica gel chromatography using an ethyl acetate/hexanes gradient yielded intermediate F.
Compounds 1 and 2: To compound F (1.0 equiv) in ethanol (2 mL), t-butyl hydrazine hydrochloride (1.0 equiv) and triethylamine (1.0 equiv) were added. After refluxing for 3.5 h, the solvent was evaporated and water was added. The solid was collected and then refluxed in formamide (6 mL) overnight. The cold reaction mixture was diluted with water and the precipitate was collected. This precipitate was re-dissolved in chloroform and then purified by silica gel chromatography using a methanol-chloroform gradient to yield final compound.
1 was synthesized using 1-naphthoyl chloride as the acyl chloride in General Procedure G. JH NMR (CDCI3, 300 MHz) δ 8.25 (s, 1H), 7.97-8.10 (m, 2H), 7.77-7.85 (m,
1H), 7.55-7.67 (m, 4H), 1.91 (s, 9H). MS (ESI) (M + H)+= 318.4.
2 was synthesized using 2-naphthoyl chloride as the acyl chloride in General Procedure G. LH NMR (DMSO-d6, 300 MHz) δ 8.33 (s, 1H), 8.19 (s, 1H), 7.98-8.10 (m, 3H), 7.78-7.83 (m, 1H), 7.57-7.62 (m, 2H), 1.79 (s, 9H). MS (ESI) (M + H)+= 318.4.
Example 61 Preparation of Intermediate G
Figure imgf000106_0001
Phthalimide (354 mg, 2.35 mmol), 3-chloropyrazin-2-yl methanol (284 mg, 1.96 mmol), and resin bound triphenylphosphine (1.55 g, 2.35 mmol) were added to anhydrous THF. To this reaction mixture, DIAD (507 mg, 2.35 mmol) was added dropwise. After 12 h the reaction mixture was concentrated. The crude product was purified using silica gel chromatography with a hexane/dichloromethane gradient to yield Intermediate G (300 mg, 56% yield). JH-NMR (300 MHz, CDC13) δ 5.17 (s, 2H), 7.77-7.83 (m, 2H), 7.87-7.97 (m, 2H), 8.29-8.34 (m, 2H). MS (ESI) (M+H)+ 274.2.
Example 62 Preparation of Intermediate H
Figure imgf000106_0002
Anhydrous hydrazine (0.05 mL, 1.37 mmol) was added to a solution of Intermediate G (150 mg, 0.5 mmol) in 3.0 mL of dichloromethane at rt under an inert atmosphere. After 2.5 h, 4.5 mL of MeOH was added and the reaction mixture was stirred at reflux for 19 h. The reaction mixture was cooled to rt and the white precipitate that formed was filtered off. The precipitate was washed with ether (3X) and the filtrate was concentrated in vacuo. The resultant solid was re-dissolved in EtOAc and filtered again. The solution was concentrated to afford 77 mg (97% yield) of pure product. ^- MR (300 MHz, MeOD) δ 4.08 (s, 2H), 8.34 (d, 1H, J= 2.7 Hz), 8.58 (d, 1H, J= 2.7 Hz). MS (ESI) (M+H)+ 143.9. Example 63 Intermediate I
Figure imgf000107_0001
Intermediate H (26 mg, 0.19 mmol), isobutyric acid (0.02 mL, 0.2 mmol), EDCI (50 mg, 0.25 mmol), DIEA (0.1 mL, 0.5 mmol), and DMAP (5.7 mg, 0.038 mmol) were dissolved in 2.0 mL of dichloromethane. The reaction mixture was stirred at rt overnight and then concentrated in vacuo. The resultant residue was dissolved in EtOAc, washed with water (2X), NaHC03 (IX), and brine (IX). The organic layer was dried over Na2S04, and concentrated in vacuo to afford 37 mg (93% yield) of pure Intermediate I. ¾-NMR (300 MHz, CDC13) δ 1.21-1.26 (m, 6H), 2.46-2.59 (m, 1H), 4.69 (d, 2H, J = 4.5 Hz), 8.32-8.34 (m, 1H), 8.46 (d, lH, J= 2.4 Hz).
Example 64 Intermediate J
Figure imgf000107_0002
POCl3 (0.08 ml, 0.90 mmol) was added to Intermediate I (37 mg, 0.18 mmol) dissolved in 0.78 mL of acetonitrile. A drop of DMF was added and the reaction mixture was stirred at 55 °C for 30 minutes. The reaction mixture was then concentrated in vacuo and the resultant solid was dissolved in 2 M ammonia in methanol followed by concentrating this solution in vacuo. The resultant solid was dissolved in a minimal amount of water and the product was extracted into dichloromethane (4X). The organic layers were combined and washed with saturated NaHC03, (IX), concentrated in vacuo, and dried over Na2S04. Concentration of the solution afforded 33 mg (98% yield) of Intermediate J. !H-NMR (300 MHz, CDC13) δ 1.46 (d, 6H, J = 6.9 Hz), 3.29-3.38 (m, 1H), 7.33 (d, 1H, J = 4.8 Hz), 7.61 (d, 1H, J= 5.1 Hz), 7.82 (s, 1H). MS (ESI) (M+H)+ 196. Example 65 Intermediate K
Figure imgf000108_0001
Intermediate J (33 mg, 0.17 mmol) dissolved in 0.18 mL of DMF was added to NIS (39 mg, 0.17 mmol) dissolved in 0.6 mL of DMF. The reaction mixture was heated to 60 °C for 3 h and then cooled to room temperature. The reaction mixture was partitioned between 1 M a2S03 and dichloromethane. The aqueous layer was then extracted with dichloromethane (3X). The organic layers were combined, dried over a2S04 and concentrated in vacuo to afford 34 mg (62% yield) of pure Intermediate K. !H-NMR (300 MHz, CDC13) δ 1.41 (d, 6H, / = 6.9 Hz), 3.20-3.31 (m, 1H), 7.28 (d, 1H, J= 5.1 Hz), 7.65 (d, 1H, J = 5.1 Hz). MS (ESI) (M+H)+ 322.1.
Example 66 Intermediate L
Figure imgf000108_0002
Intermediate K (33 mg, 0.10 mmol) and NH4OH were heated to 80 °C for 6 h in a microwave. The reaction mixture was concentrated in vacuo and purified using silica gel chromatography with a hexane/EtOAc gradient to yield Intermediate L (33 mg, 66% yield). ¾-NMR (300 MHz, CDC13) δ 1.4 (d, 6H, / = 5.4 Hz), 3.17-3.26 (m, 1H), 5.88 (br s, 2H), 7.02 (d, 1H, J= 5.1 Hz), 7.23 (d, 1H, J= 5.1 Hz). MS (ESI) (M+H)+ 303.2. Example 67 Intermediate M
Figure imgf000108_0003
Intermediate H (104 mg, 0.76 mmol), pivalic acid (0.08 mL, 0.8 mmol), EDCI (200 mg, 1.0 mmol), DIEA (0.4 mL, 2.0 mmol), and DMAP (22 mg, 0.15 mmol) were dissolved in 8.0 mL of dichloromethane. The reaction mixture was stirred at rt overnight and then concentrated in vacuo. The resultant residue was dissolved in EtOAc, washed with water (2X), NaHC03 (IX), and brine (IX). The organic layer was dried over Na2S04, and concentrated in vacuo to afford 145 mg (94% yield) of pure Intermediate M. H-NMR (300 MHz, CDC13) δ 1.15 (s, 9H), 4.59 (d, 2H, J= 4.8 Hz), 8.31-8.34 (m, 1H), 8.42 (d, 1H, J= 2.4 Hz).
Example 68 Intermediate N
Figure imgf000109_0001
POCl3 (0.12 ml, 1.35 mmol) was added to Intermediate M (54 mg, 0.27 mmol) dissolved in 1.2 mL of acetonitrile. A drop of DMF was added and the reaction mixture was stirred at 55 °C for 30 minutes. The reaction mixture was then concentrated in vacuo and the resultant solid was dissolved in 2 M ammonia in methanol followed by concentrating this solution in vacuo. The resultant solid was dissolved in a minimal amount of water and the product was extracted into dichloromethane (4X). The organic layers were combined and washed with saturated NaHC03 (IX), concentrated in vacuo, and dried over Na2S04. Concentration of the solution afforded 45 mg (95% yield) of Intermediate N. 1 H-NMR (300 MHz, CDC13) δ 1.35 (s, 9H), 7.38 (m, 1H), 7.66 (m, 1H), 7.87 (s, 1H). MS (ESI) (M+H)+ 210.1.
Example 69 Intermediate O
Figure imgf000109_0002
Intermediate N (45 mg, 0.25 mmol) dissolved in 0.23 mL of DMF was added to NIS (51 mg, 0.22 mmol) dissolved in 0.8 mL of DMF. The reaction mixture was heated to 60 °C for 3 h and then cooled to room temperature. The reaction mixture was partitioned between 1 M a2S03 and dichloromethane. The aqueous layer was then extracted with dichloromethane (3X). The organic layers were combined, dried over Na2S04 and concentrated in vacuo to afford 49 mg (70% yield) of pure Intermediate O. *H-NMR (300 MHz, CDC13) δ 1.31 (s, 9H), 7.23 (d, 1H, J= 5.1 Hz), 7.67 (d, 1H, J= 5.1 Hz). MS (ESI) (M+H)+ 336.4. Example 70 Intermediate P
Figure imgf000110_0001
Intermediate 0 (76 mg, 0.22 mmol) and NH4OH were heated to 80 °C for 6 h in a microwave. The reaction mixture was concentrated in vacuo and purified using silica gel chromatography with a hexane/EtOAc gradient to yield Intermediate P (76 mg, 66% yield). ¾-NM (300 MHz, CDC13) δ 1.32 (s, 9H), 5.28 (br s, 2H), 7.06 (d, 1H, J= 5.1 Hz), 7.21 (d, lH, J= 5.1 Hz). MS (ESI) (M+H)+ 317.1.
Example 71 General Procedure H Intermediates L or O (0.03 mmol), tetrakis(triphenylphosphine) palladium(O) (0.05 equiv), and sodium carbonate (2.3 equiv) were added to the appropriate boronic acid or pinacol ester (1.1 equiv) in dimethoxyethane (1 mL) and water (0.5 mL). The reaction was performed in a microwave at 85°C for one hour, followed by extraction with ethyl acetate and water. The organic layer was collected and concentrated in vacuo to yield the crude product. The crude product was then purified via flash chromatography with an ethyl acetate/hexanes gradient.
Example 72 Preparation of compounds 8-12 and 69-72
Compounds 8-12 and 69-72 were generated with General Procedure H using the appropriate substituted boronic acid as is familiar to those skilled in the art.
BIOLOGICAL EXAMPLES
Biological Example 1 Enzymology ofTgCDPKl
Two types of enzyme assays were developed to follow IgCDPKl activity, a radiometric scintillation proximity assay measured the labeled γ-phosphate of ATP added to a biotinylated peptide substrate and an ATP consumption assay where ATP consumption was monitored by luciferase and light production (KinaseGlo®, Promega Corp., Madison, WI). Both assays gave similar results for calcium dependence, Km of substrates (less than 2-fold differences in Km values; see Table 6 Figures 6, 7, 8, and 9), and inhibitor concentrations for 50% enzyme inhibition (IC50S; see, Tables 6 and 7).
Table 6. Km and IC50 values for TgCDPKl enzyme
Figure imgf000111_0001
Table 7. Inhibitor IC50 values at different JgCDPKl enzyme concentrations
Figure imgf000111_0002
As expected, activity of I CDPKl on the peptide substrates required addition of exogenous calcium (Figure 1). Indeed, calcium titration revealed that a concentration of 4.7 μΜ gave 50% of JgCDPKl kinase activity. The Km of ATP and peptide substrates were determined to be 10 and 14 μΜ, respectively. Biological Example 2 Structure ofTgCDPKl
2_|_
We have determined X-ray crystal structures of Ca -free J CDPKl in the apo form and in complex with two potent inhibitors (Table 1 and Figure 2).
Table 1. Data collection and refineiiieaf statistics.
SAD (SeMei) Apo fmfef A-FP2 M-PP1
Baia
Space group P2> :P2I
a,A c (A) 48.2, 72.0, 67.5 48.1, 71.9 4S.-, 72.S, S7.1 47.2, 72.?, 65.7 a, 3, y O 90.0, 102.9, 90.0 9 103.0, 50.0 90.0, 103J, 90.0 90.0, 98.8, 90.0
50-2.30 (23%- 50-2.84 (2.12- 5S-L§S ( - 50-1.99 (2.08-
Figure imgf000112_0001
U:li£ SJ€ jeffectisBS 28,324 (2,799) 3Q.0S03 <2,S¾¾ 30,350 (2,975)
0. 1 {&.¾) S. 5 ( .S7) 0.0? φ.Ίϋ) 0.OS <Q.74> 13.1 (2.4) 17.0 (2.4) 8.4 (2.1) 34.2 (1.9)
C«t3¾iteteaess {%) 108 nOQ)
7.7 (7.7} 4.2 (4.2) 3.7 δ) 4.2 (4.1)
Wiisois 3 i sctor (A2) 43.7 34.S 2S..S 29.7
36.S9-2.04 29 72- 1.96 35.72-i.99
No.. fdkcnei» 26Λ71 29,224 21797 o. reflectiaisi lest srt 1 ,431 1,556
0.213 ί 9.258 S.193 0.245 0192 .i G.22S
No. aiosjis
PiiitSlfi 3,c74 3,776 3743 oaprotem 79 194 167
^factors (A¾
Froteis (Mess B„ ÷ -?TL∑) 69.2 42.5 4S.7
&si f oieia Meaa ¾a) 27.7 27.1 24.0
.S1.S. devtatsoas
Boad esi f s (A) 8.09S Q.O07
Bosrf aagSfls O δ.97§ 0.873
3^^^
*Yatoes i& a-eati&ses are &r Mgkst-rejolstisn shell The structure of the catalytic domain is typical of serine/threonine type protein
2_|_
kinases. The two Ca -binding EF-hand lobes and connecting extended helical stem of the calmodulin-like regulatory domain lie along one face of the kinase domain, adjacent to the active site (Figure 2a). The kinase and regulatory domains are connected by an intervening helical junction domain characteristic of this class of kinases18. The conformation represented by these structures is likely an inactive form of the enzyme since the calmodulin- like domain occludes the surface required for recognition of target proteins and peptides. Importantly, the ATP binding site remains accessible to small molecule substrates and inhibitors. The group of Raymond Hui at the Toronto Structural Genomics Consortium has shown that when rgCDPKl is activated by calcium, the regulatory domain undergoes major structural rearrangement and is repositioned to lie against the opposite surface of the kinase domain (Wernimont et al. submitted for publication, PDB accession number 3hx4). This dramatic structural change allows access of the protein substrates to the active site.
Biological Example 3 Bumped Kinase Inhibitors (BKIs) and TgCDPKl
Most known kinase inhibitors bind in the ATP-binding pocket of the active site19,20. These inhibitors exploit many of the same hydrophobic contacts as the purine ring of ATP and make at least one conserved hydrogen bond to the hinge region. Potent inhibitors also occupy at least one hydrophobic pocket adjacent to the ATP-binding site. These additional hydrophobic interactions increase both binding affinity and target selectivity of the inhibitor because there is substantial heterogeneity among different kinases in these regions. Examination of the JgCDPKl sequence in the vicinity of the ATP-binding pocket (Figure 2b) shows that it contains a glycine residue at a position that has been termed the gatekeeper
21 23
residue because it constrains access to the ATP-binding site " . The glycine at this position in IgCDPKl (Gly 128) is expected to create a much larger pocket off the ATP-binding site than is typically seen in protein kinases and comparison of the IgCDPKl structure with other kinases shows that this is indeed the case. This difference in the active site architectures can be exploited for design of selective inhibitors against IgCDPKl .
Shokat and colleagues have shown that mutation of bulky gatekeeper residues to glycine renders mutant kinases uniquely susceptible to inhibition by a class of kinase inhibitors called "bumped kinase inhibitors" (BKIs). BKIs are analogs of 4-amino-l-¾/t- butyl-3-phenylpyrazolo[3,4-d]pyrimidine (Table 2) that are derivatized at C3 with bulky
24
aromatic groups .
t
Figure imgf000114_0001
G12SM JgCDPKl 21.44 IS
Figure imgf000114_0002
pei si ie t ree S mes τιΐΐ i e jaeaa s s B^sa. t asssy ¾ss p i nEe ¾ssag cssp ng nase i at 20 sM ¾€DPXi, 18 μ&ί ATP, 4& μΜ peptide, ¾td an lacubaiios fime of 30 s a.
The large sidechain of the gatekeeper residue in most kinases prevents access of the C3 bulky aromatic substituent to the more hydrophobic pocket at the back of the catalytic cleft rendering them insensitive to BKI inhibition21'22. Large gatekeeper amino acids like methionine or phenylalanine severely restrict access by the BKIs, while small residues such
2223 25 26
as the glycine present in JgCDPKl are most permissive ' ' ' . Studies with genetically engineered mice that express mutant kinases with small gatekeeper residues (glycine or alanine), have demonstrated that BKIs preferentially target the mutant kinases27"29. The well- documented lack of BKIs inhibition of mammalian kinases suggests that this class of compounds may be very selective for JgCDPKl during T. gondii infection27"29.
Based on structural and sequence analysis of the differences in ATP -binding sites of typical mammalian kinases and JgCDPKl with a small gatekeeper (Figures 2a and 2b), we synthesized three BKIs and demonstrated that two of three were low double digit nanomolar inhibitors of JgCDPKl (Table 2). To show that the glycine gatekeeper is the primary determinant of BKI inhibition, we created a glycine to methionine gatekeeper mutant of JgCDPKl (G128M). Indeed the wild type enzyme was inhibited significantly better by individual BKIs compared to the G128M mutant enzyme (Table 2). For NA-PP1, there was a 175-fold difference, for NA-PP2, a 1200-fold difference and for NM-PP1, a 550-fold difference between IC50 values for wild type versus the G128M mutant (Table 2).
The crystal structure of JgCDPKl in complex with two potent BKIs were determined
( A-PP2, Figure 2c; NM-PP1, Figure 2d) and, as predicted, these inhibitors bind in the ATP-binding site with the C3 bulky aromatic substituent occupying the pocket adjacent to the glycine gatekeeper. Superposition of an orthologous CDPK containing a methionine gatekeeper onto our BKI complexes showed impairment of the favorable binding mode observed for the BKIs in gCDPKl (Figure 2e). The bulky gatekeeper sidechain clashes with the C3 bulky aromatic substituent providing a structural basis for the insensitivity of typical kinases towards BKI inhibition, as verified experimentally with the G128M mutant of ZgCDPKl (Table 2). These results strongly implicate IgCDPKl with its unique glycine gatekeeper as a drug target for selective treatment of toxoplasmosis.
Biological Example 4 TgCDPKl Appears in the Cytoplasm and Nucleus ofl. gondii
Cells
The mode of action of JgCDPKl is unknown but its localization in the cell might provide clues to its cellular function. To this end, TgCDPKl was fused with green fluorescent protein (GFP) to facilitate its localization within live intracellular T. gondii. TgCDPKl-GFP was found in both the cytosol and the nucleus (Figure 3). Similar findings were obtained when the GFP tag was replaced with a C-terminal hemagglutinin (HA) tag. Thus CDPK1 may have targets in both cytosol and nucleus.
Biological Example 5 Effects of BKIs on Toxoplasma gondii Cell Entry and Growth We tested three BKIs for effects on host cell invasion and parasite growth since earlier work on TgCDPKl 14 suggested a key role for this enzyme in T. gondii invasion. As shown in Figure 4, BKIs profoundly reduced T. gondii proliferation if added simultaneously with cellular infection (Figure 4a), and modestly reduced proliferation when added 4 hr after the start of invasion (Figure 4b). Thus, inhibition of gCDPKl activity by BKIs has a stronger effect on invasion than on intracellular growth. This was confirmed by microscopic examination of invasion (see Figures 8(a)-8(c) and 9(a) - 9(c)) and is consistent with previous observations on the role of TgCDPKl 12,14
T. gondii expressing CDPK1-GFP, CDPK1(G128M)-GFP, or GFP were mixed with the indicated concentration of NA-PP2 and added to the fibroblast monolayer for 15 min at 4 °C to allow binding (Kafsack et al). The samples were then raised to 37 °C for 4 min to allow invasion. Samples were fixed, washed, and stained with antibody to T. gondii surface antigens (SAG, Argene) to identify extracellular parasites. Figure 8(a) is a representative image from the untreated CDPK-GFP dataset. Intracellular parasites are marked by asterisks. Figure 8(b) shows the change in the number of intracellular parasites upon drug treatment. The number of intracellular parasites was determined by subtracting the number of extracellular parasites (SAG+) by the number of total parasites (GFP+) and expressed as a ratio to the number of host cells observed (as measured by DAPIstained nuclei). Each sample was normalized to the untreated control of the same line. Figure 8(c) shows the data used to derive the graph in panel b. Note that cells expressing the gatekeeper mutant CDPK1(G128M) are less sensitive to the drug. The drug additionally appears to affect adhesion.
T. gondii overexpressing CDPK1-GFP, CDPK1(G128M)-GFP, or GFP were mixed with wild type cells (105 of each) in medium with or without 1 μΜ NA-PP2. Parasites were allowed to infect fibroblasts on cover slips and grown overnight. Samples were stained with DAPI to identify host and parasite nuclei and vacuoles with 2 or more T. gondii cells (only fully invaded parasites can replicate) were counted. Each vacuole was assessed for GFP expression by the parasites. Figure 9(a) is a representative set of images of CDPK1(G128M)- GFP mixed with wild type, in the absence of drug. Vacuoles containing multiple GFP- expressing parasites are marked with * and wild type vacuoles are marked with - . Figure 9(b) shows the number of vacuoles with wild type (GFP-) or transfectedparasites (GFP+), per host cell nucleus, in the absence and presence of drug for the three cell mixtures. Figure 9(c) shows Data used to derive the graphs. Note that the parasite line overexpressing CDPK1(G128M)-GFP wasresistant to the effects of 1 μΜ NA-PP2, as compared to the co- cultured wild type control.
We expect that longer exposure to B Is would increase the impact of the drug on T. gondii growth, as egressed parasites are prevented from invading new cells. Each BKI was tested for its effects on human fibroblast replication; the EC50S were found to be approximately 1000-fold higher (not shown) than those seen in the T. gondii "invasion" assay.
Biological Example 6 T. gondii Cell Expressing the G128M Gatekeeper Mutant
Demonstrate that BKIs Act Through JgCDPKl in vivo
We transfected the T. gondii cell line with expression plasmids encoding an HA tag fused to the C-terminus of either wild type ZgCDPKl or the G128M gatekeeper mutant. Immunoblot analysis showed that the wild type and G128M mutant TgCDPKls were expressed to similar levels (Figure 5a). Compared to the parental cell line, parasites expressing the G128M mutant were relatively resistant to BKIs NA-PP2 and NM-PP1 added prior to invasion (Figure 5b and 5c). In contrast, parasites overexpressing the wild type JgCDPKl protein showed only a small shift in resistance. Although NA-PP2 was somewhat less effective against wild-type parasites in this experiment, the results were identical in the relative potency of the inhibitors, in that A-PP2 was more potent than NM-PP1 in blocking T. gondii invasion, following the potency observed against IgCDPKl enzyme. Furthermore, in both a microscopic assay of invasion (see Figures 8(a) - 8(c)) 30 and in a mixed cellular infection using wild type and TgCDPKl(G128M) (see Figures 9(a) - 9(c)), parasites expressing the gatekeeper mutant were markedly resistant to NA-PP2 while cells expressing either wild type JgCDPKl or GFP controls were not. These findings demonstrate that BKIs are working primarily through the JgCDPKl target to prevent T. gondii mammalian cell entry.
We have shown that JgCDPKl is a promising drug target for the therapy of toxoplasmosis. Its kinase activity is uniquely sensitive to inhibition by BKIs, and BKI treatment in turn blocks entry of the parasite into mammalian cells. Blocking cell entry is important because T. gondii is an obligate intracellular parasite and cannot replicate without invasion. Moreover, these experimental findings address concerns about quantitative differences between enzyme inhibition and cellular effects thereby validating the utility of JgCDPKl structures in complex with BKIs to drive drug development for toxoplasmosis therapy. The concept of using BKIs for the therapy of toxoplasmosis is bolstered by the fact that BKIs have been used in mouse studies with no demonstration of toxicity or troublesome
27 29
effects to the animals " . Thus, BKIs have promise; as a selective drug for toxoplasmosis therapy because they are non-toxic to mammals but prevent cell entry and thus the replication of J. gondii.
Since the structure was determined for the inactive, Ca2+-free form of JgCDPK, there may be some concern that this form would not be optimal to guide the design of small molecule inhibitors with improved potency and selectivity. It is apparent from structural and biochemical studies presented here, however, that small molecule inhibitors can still access the ATP-binding site of the Ca2+-free conformation of JgCDPKl. Importantly, the structure of the active site near the ATP-binding pocket, particularly in the vicinity of the gatekeeper residue, is not significantly altered between the structures shown here and that of the Ca2+- bound enzyme in complex with AMP-PNP (Wernimont et al. submitted for publication, PDB 3hx4). Thus, structure-guided optimization of small molecule inhibitors that target this
2_|_
region is possible using the inactive, Ca -free form of TgCDPKl.
TgCDPKl was localized in the cytoplasm, but also found in the nucleus. Some plant CDPKs are also partially localized to the nucleus. In those CDPKs, nuclear localization is mediated by a signal in the junction domain18, but the T. gondii protein is not homologous in this region and no nuclear localization signal is predicted by standard programs. Since the size of the protein is above the threshold for free diffusion through the nuclear pore, we propose that the protein could bear a non-canonical nuclear localization sequence or piggyback into the nucleus on another protein. As noted earlier, Raymond Hui's group has demonstrated a Ca2+-dependent structural rearrangement that repositions the regulatory domain to the opposite side of the catalytic domain (Wernimont et al. submitted for publication, PDB accession number 3hx4). This observation of Ca -induced structural
2_|_
rearrangement raises the intriguing, but speculative, possibility that Ca could modulate localization by revealing or occluding the relevant region of the kinase. In any case, these results raise the possibility that TgCDPKl phosphorylates specific nuclear proteins in addition to its presumably cytosolic targets involved in gliding motility.
Drug-resistant mutations of the TgCDPKl gatekeeper to a bulky residue could eventually emerge under selective pressure of BKI therapy. One strategy to suppress the emergence of resistance is the co-administration of two drugs targeting different proteins. As TgCDPKl is not the target of any existing drug, the development of an anti-TgCDPKl compound could provide a partner drug for co-administration with another drug. Most transmission of T. gondii is not from person-to-person (although this can occur in pregnancy, transplantation, or transfusion), but rather through zoonotic cycles where drug pressure is not exerted . This suggests that if drug resistance emerges it will largely be confined to the individual, posing little threat to the utility of the drug in other infected persons.
As other apicomplexan pathogens employ CDPK enzymes with a small gatekeeper residue, this work may have broader applicability. For instance, the TgCDPKl ortholog in Cryptosporidium parvum also has a glycine residue at the gatekeeper position (Figure 2b), suggesting that BKIs targeting T. gondii could also be effective for the therapy of cryptosporidiosis, another potentially life-threatening infection with poor therapeutics. Other parasite CDPKs have small gatekeeper residues, such as threonine.. Indeed, an extended search of all reported human kinase ATP binding motifs found none with a glycine or alanine gatekeeper residue, and about -20% with threonine21. Thus, these findings may have implications in the rational design of anti-apicomplexan CDPK agents devoid of toxic side effects to the host cells.
Biological Example 7 Expression, Purification and Assay of Recombinant Mutant and
Wild Type TgCDPKl
TgCDPKl (GI: 12484153, ToxoDB ID 162.m00001) or its G128M mutant, cloned into pAVA0421, was expressed in BL21 *(DE3) E. coli (Invitrogen Corp. Carlsbad, USA) for 72 hours at 20°C in a LEX Bioreactor (Harbinger Biotechnology & Engineering Corp. Ontario Canada). Cells collected from 2 liters of culture were lysed in 200 ml of 30 mM imidazole, 500 mM NaCl, 25 mM HEPES, 5% glycerol, 0.025% azide, ImM TCEP, 10 mM MgCl2, 1 mM AEBSF, pH 7.0 and incubated with Benzonase® (Novagen, USA) for 30 min at room temperature before centrifugation at 14,000 rpm for 75 min and 4°C. Clarified
2_|_
supernatant was loaded onto 5ml Ni HisTrap FF resin columns pre-equilibrated with 30 mM imidazole, 500 mM NaCl, 25 mM HEPES, 5% glycerol, 0.025% azide, 1 mM TCEP. Recombinant histidine-tagged protein was eluted in 220 mM imidazole pH 7.0. Fractions were subsequently separated on AKTA Prime size exclusion columns (HiLoad™ 26/60 Superdex 75™ prep grade) pre-equilibrated 500 mM NaCl, 25 mM HEPES, 5% glycerol, 0.025% azide, 2 mM DTT, pH 7.0. The N terminal hexahistidine tag was removed by 3C protease cleavage at a 1 :50 mg ratio and dialyzed overnight at 4°C in 200mM NaCl, 20 mM HEPES, 5% glycerol, 1 mM TCEP, pH 7.0 with final separation on Ni2+ Sepharose™ 6 Fast Flow resin. Fractions were analyzed for purity by SDS-polyacrylamide gel electrophoresis and found to be >99% pure.
Two types of kinase assays were employed, an ATP consumption assay and a scintillation proximity assay. ATP consumption kinase assays were performed using a nonradioactive inaseGlo® luciferase assay (Promega Corp., Madison, WI, USA). Kinase phosphorylation reactions were performed in a buffered medium containing 20 mM HEPES pH 7.5 (KOH), 0.1% BSA, lOmM MgCl2, ImM EGTA (pH 7.2), plus or minus 2mM CaCl2 14. The phosphorylation reaction mixture of 40 μΜ peptide substrate (Syntide-2, peptide sequence: Pro-Leu-Ala-Arg-Thr-Leu-Ser-Val-Ala-Gly-Leu-Pro-Gly-Lys-Lys (SEQ ID NO: 12)) (GenScript, Piscataway, USA), 19.48 nM ofl4 TgCDPKl, 90 to 0.0005 μΜ serial dilutions of inhibitor in a total volume of 25 μΐ, was initiated by the addition of 10 μΜ ATP. The reaction was terminated after 30 minutes incubation at 30 C by addition of excess EGTA (5 mM final concentration). Internal positive and negative controls were included in each assay run. No activity was detected when the peptide substrate was left out of the reaction mixture. Unused ATP was measured in luminescence based readout as counts per seconds on the Chameleon 425-104 multi-label plate scintillation counter (Hidex, Oy, Turku Finland). A second enzyme assay, based on the scintillation proximity assay, directly measured the attachment of γ-phosphate to peptide substrate. The scintillation proximity assay was used for confirmation of enzymatic characteristics like Km for ATP and substrate and for confirmation of IC50s of the inhibitors. Phosphorylation of biotinated peptide substrate, (Bio-Syntide-2, American Peptide Company, Inc. Sunnyvale, CA) was determined by serial titrations in scintillation proximity assays using streptavidin coated Beads and [γ- l3P] ATP (PerkinElmer, Boston, USA) as previously described30.
Biological Example 8 Site-Directed Mutagenesis
Site-directed mutagenesis of the predicted gate keeper glycine residue to methionine was executed with Stratagene kit. PC amplification of pAVA0421-rgCDPKl plasmid DNA with page purified primers TgDPKmetS (GGC TAC TTC TAC CTC GTC ATG GAA GTG TAC ACG GGA GGC GAG TTG)(SEQ ID NO: 3) and TgDPKmetAS (CAA CTC GCC TCC CGT GTA CAC TTC CAT GAC GAG GTA GAA GTA GCC)(SEQ ID NO: 4) was carried out at 95°C (30 seconds), 95°C (30 seconds), 55°C (1 minute), 68°C (6:00 minutes) followed by 68°C (6:00 minutes) repeated in 16 cycles. Dpn I digested PCR products was transformed into XLIO-Gold ultracompetent E. coli cell (Stratagene) with selection on LB agar supplemented with 100 g/ml ampicillin. Mutant plasmids was recovered with alkaline denaturation method using the QIAGEN plasmid purification kits and verified by nucleotide sequence analysis before transformation into protein expression E. coli strain BL21 *(DE3) (Invitrogen Corp. Carlsbad, USA). Induction of expression and purification of mutant TgCDPKl(G128M) in E. coli BL21*(DE3) (Invitrogen Corp. Carlsbad, USA) was previously described30.
Biological Example 9 Protein Crystallization
Purified TgCDPKl protein was screened for crystallization leads using a Phoenix crystallization robot (Art Robbins Instruments, Sunnyvale, CA) and the JCSG+ Suite sparse
31
matrix crystallization screen (Qiagen, Valencia, CA) . A few leads were further optimized by finer grid screening around the initial hit using sitting-drop vapor diffusion at room temperature. Diffraction-quality crystals of native and selenomethionyl-derivatized (SeMet) protein (-18-26 mg/ml) were grown from mother liquor composed of 0.18-0.25 M (di- or tri-) ammonium citrate (pH 6.5-7.0), 22-26% polyethylene glycol (PEG) 3350, and 5 mM dithiothreitol. For inhibitor cocrystals, the crystallization drop was additionally supplemented with a final concentration of 4 mM inhibitor dissolved in dimethylsulfoxide. Thin pointed rods or plates approximately 50-150 μιη long typically grew within one week. Crystals were mounted in cryoloops (Hampton Research, Aliso Viejo, CA) and directly frozen in liquid nitrogen or were first transferred to a fresh drop of mother liquor containing 10-20% ethylene glycol for, typically, less than 20 seconds prior to freezing. For inhibitor co-crystals, 2-4 mM inhibitor was maintained in the cryoprotection solution.
Biological Example 10 Structure Determination
Crystals of TgCDPKl were screened at the Stanford Synchrotron Research
32
Lightsource (SSRL) on beamline 9-2 using the SSRL automated mounting (SAM) system . All data were collected at 100 K on a MarMosaic-325 CCD detector using the Blu-Ice software package33. Single-wavelength anomalous dispersion (SAD) data were collected from a single crystal of SeMet protein34 at a wavelength of 0.9792 A, the Se peak wavelength determined from a fluorescence scan of the crystal. All other datasets were also collected at or near the Se peak wavelength; apo (native) at 0.9792 A, NA-PP2 complex (SeMet) at 0.9791 A, and NM-PP1 complex (native) at 0.9795 A. All data were processed using HKL200035. Data collection statistics are presented in Table 1.
Initially, we were able to solve the structure of the kinase domain by molecular replacement (MR) using MOLREP36 or Phaser37 with the structure of the kinase domain of the orthologous protein from Cryptosporidium parvum (PDB ID 3dfa) as the search model. Although representing nearly two-thirds of the total protein content of the asymmetric unit, the resulting MR phases were not good enough to allow tracing of the novel calmodulin-like regulatory domain; despite significant effort at manual improvement of the MR solution and attempts to additionally place various calmodulin-like domains of very low sequence identity by MR. We thus turned to using SeMet protein in order to obtain experimental phase information to solve the complete structure. Using a SeMet SAD dataset, SOLVE38 located 12 of 14 expected selenium atoms and produced initial phases to approximately 2.7 A. The resulting phases were input into RESOLVE38 using the RESOLVE BUILD script (http://www.solve.lanl.gov/Resolve/html_resolve_manual/resolve_build.txt) for density modification and automated model building. The model was significantly improved by bootstrapping the results back into the RESOLVE_BUILD script two more times for rebuilding. Iterated manual model building and restrained refinement continued using Coot39 and REFMAC540. This model was transferred into the other datasets by MR using Phaser followed by a few rounds of model building and improvement in Coot and refinement with REFMAC5. The improved models were then submitted to ARP/wARP41 for rebuilding using and continued cycles of building and restrained refinement ensued. Based on the initial, unbiased difference density present in the active sites of the cocrystal structures, it was immediately clear that the inhibitors had bound the enzyme. Ideal coordinates and refinement restraints for use in REFMAC5 and Coot for these ligands were created with the PRODRG server42. In the final cycles of refinement, perturbational displacement of the protein was described by a multi-group translation/libration/screw (TLS) model, with group boundaries suggested by the TLSMD server43'44, that were refined prior to restrained refinement. Model quality was monitored and validated using Coot and MolProbity45. All final models display good Ramachandran statistics. For the final apo model, 97.6% of the residues are in favored regions of the Ramachandran plot with no outliers. The NA-PP2 complex model has 98.9% of residues in favored regions with no outliers and the NM-PP1 complex has 98.5% of residues in favored regions and Gly420 is an outlier. The CCP4 suite of programs46,47 was used for all steps from data preparation through refinement. Model refinement statistics are presented in Table 1. Structural figures were created and rendered using PyMOL (Delano Scientific, Palo Alto, CA).
Atomic coordinates and structure factors have been deposited in the Protein Data
48
Bank . (http://www.pdb.org) with accession numbers 3i79 (apo), 3i7c (NA-PP2 complex), and 3i7b (NM-PP1 complex).
Biological Example 11 T. gondii growth/invasion assay and expression of lgCDPKl-
HA and lgCDPKl(G128M)
The TgCDPKl coding region or its G128M mutant were amplified from the E. coli expression plasmids using primers to insert 3 adenine nucleotides before the start codon and mutate the second codon from glycine to alanine, allowing for enhanced expression in the parasite49. The products were inserted into the Bglll/Avrll site of T. gondii transfection vector pCAT-GFP50 or pHx-ACP-YFP51 to yield in frame fusions with GFP or YFP, under the control of the tubA or Gral promoters respectively. Plasmids encoding HA-tagged versions of the molecules were created by replacing the YFP sequence with one that specifies four C- terminal HA epitopes. Linearized constructs were electroporated into RH strain T. gondii according to standard methods52 and transfected parasites were used to infect human foreskin fibroblasts growing on cover slips. In some cases a T. gondii strain expressing β- galactosidase under control of the TubA promoter, as well as GFP under control of the GRA1 promoter, was employed (kind gift of Gustavo Arrizabalaga)53.
Immunofluorescence analysis was performed as described52 using rabbit anti-GFP (Invitrogen Corp. Carlsbad, USA) followed by goat anti-rabbit IgG coupled to Texas red (Southern Biotechnology). DNA was stained with DAPI. Samples were viewed on a Nikon Eclipse E600 using a Plan Apo 60X 1.4 na objective.
T. gondii cells expressing β-galactosidase were grown in the presence of serial concentrations of BKIs. All assays were performed in triplicate and the mean and standard deviation are presented unless otherwise noted. In the growth assays, 103 parasites were allowed to infect a confluent layer of fibroblasts in each well of a 96 well plate. After 4 hr, drug was added to the indicated final concentration. To assess effects on invasion, compounds were added prior to the addition of the parasites. The cultures were incubated for
20 hours at 37 C and β-galactosidase was assayed as earlier described using chlorophenol red
54 0 β-galactopyranose (CPRG, Sigma) as substrate . Plates were developed at 37 C for 4 hr (growth), 8 hr (invasion), or 10 hr (CDPK expression) and absorbance was measured at 595 nm on a Versamax microplate reader.
Cytotoxicity was analyzed by adding medium containing up to 50 μΜ of each compound to a confluent layer of fibroblasts; plates were incubated at 37 C for 4 days. Alamar blue (Alamar Biosciences, Sacramento, CA) was added to each well and developed over night.
Biological Example 12 QJCDPKI
The sensitivity of Q?CDPK1 to compounds 1-3 was determined with an in vitro activity assay (Figure 12A). Both J CDPKl and Q?CDPK1 show similar levels of inhibition by these compounds, with analog 2 as the most potent inhibitor. Next, the phenotypic response of C. parvum cells to compounds 1-3 was tested by measuring the amount of parasites present after 18 hours of infection of human intestinal cells (HCT-8) with C. parvum sporozoites in the presence of varying concentrations of these inhibitors. These assays were performed under two different sets of conditions: one in which the sporozoites were exposed to each inhibitor at the time of infection (Figure 12B, left graph) and a second assay in which the sporozoites were exposed to each inhibitor one hour after infection (Figure 12B, right graph). For each assay, the HCT-8 cells were lysed after 24 hours of culture and the amount of C. parvum rRNA was quantified using reverse transcriptase real time PCR. The amount of C. parvum rRNA was then related to the number of parasites using standard curves developed separately. Importantly, reduced levels of C. parvum sporozoites are observed with increasing concentrations of compounds 1-3 under both sets of conditions, with analogue 2 demonstrating the most potent effect on parasite proliferation similar to analogue 2's superior potency against Q?CDPK1. The potencies of the pyrazolopyrimidine inhibitors were dramatically increased when they were added at the time of sporozoite infection rather than one hour after C. parvum had been incubated with HCT-8 host cells. This suggests that these inhibitors affect an early stage of C. parvum host cell invasion, which is similar to their effects on T. gondii invasion. In all cases, the relative ability of each inhibitor to block C. parvum proliferation correlates with its in vitro activity against CpCDPKl.
Based on the ability of pyrazolopyrimidine inhibitors to block T. gondii and C. parvum host cell invasion, compounds were further optimized based on this scaffold as potent and selective dual inhibitors of gCDPKl and QJCDPKI. Two synthetic routes were used to generate derivatives that contain varying substituents at the 1- and 3 -positions of the pyrazolopyrimidine core as described in the preceding synthetic examples.
Inhibition of JgCDPKl and CpCDPKl was determined using a luminescent kinase assay which measures ATP depletion in the presence of the Syntide 2 peptide substrate (KinaseGlo). (U.S. Provisional Patent Application No. 61/299,286, and reference 9) Similar to IgCDPKl, exogenous calcium was necessary for CpCDPKl to possess maximum catalytic activity (data not shown). Notably, both kinases were tested at the same ATP concentration which allows direct comparison of inhibitor potencies due to these enzymes possessing similar Km for this cofactor. (20)
Encouraged by the similar potency of inhibitor 3 against gCDPKl (IC50 = 150 ± 20 nM) and Q7CDPKI (IC50 = 130 ± 40 nM), pyrazolopyrimidine analogues that contain a naphthylmethylene group at the 3-position and various alkyl substituents at the 1 -position were tested for their ability to inhibit both kinases (Table 3). Table 3. In vitro activities of 3, 5a-5r against JgCDPKl and Q?CDPK1. Values shown are the average of three assays ± (SEM).
Figure imgf000125_0001
_ 3 150 (20) 130 (40) -|- N^° 5j 100 ( 10) 91 (26)
(10)
Figure imgf000125_0002
Derivatives containing smaller alkyl groups (5a-5c) were found to have reduced potencies for both enzymes relative to 3. Furthermore, a significant increase in potency was not observed for inhibitors that contain bulkier substituents at the 1 -position (5d-5f). However, the reduced potencies of compounds with larger substituents is not due to a size restriction in the ATP -binding pocket because derivatives that contain a basic piperidine group (derivatives 5g-5i) were found to be significantly more potent inhibitors of TgCDPKl and QJCDPKI . Notably, compound 5h, which contains a methylene linkage between the pyrazolopyrimidine core and piperidine ring, has an 8-fold and 16-fold lower IC50 for QJCDPKI and JgCDPKl than parent compound 3, respectively. Derivatization of 5g-5i with an acetyl (5j-51), ethyl (5m-5o), or sulfonylmethyl (5p-5r) group reduces the enhanced potency that the piperidine substituent confers, with only modified versions of piperidine 5g showing similar inhibition as the parent compound. Notably, most compounds from this series are near equipotent inhibitors of both TgCDP l and Q?CDPK1, demonstrating the overall similarity in this region of the ATP-binding pockets of both kinases.
To further probe the hydrophobic pocket adjacent to the gatekeeper residue (Hydrophobic Pocket II) a series of analogs that contain an isopropyl group at the 1 -position and various aryl substituents at the 3-position were tested for their ability to inhibit both kinases (Table 4, compounds 7a-7ab). While many of these inhibitors were not expected to be as selective for Q?CDPK1 and JgCDPKl over mammalian kinases as naphthylmethylene derivatives 3 and 5a-5r, we felt that this series of compounds would provide insight into which substituents can be accommodated in this region. As shown in Table 4, a large number of aryl substituents are accommodated by both kinases. Almost all of the compounds from this series have an IC50 less than 1 μΜ, with several inhibitors demonstrating very high potency against both enzymes. Inhibitors that contain aryl rings that are mono-substituted with smaller substituents at the meta (7b, 7e, 7g, and 7ab) or para positions (7a, 7d, 7f, and 7j) are accommodated in the ATP-binding sites of both kinases but are more potent against TgCDPKl than CjpCDPKl . However, neither kinase is inhibited by compounds that contain aryl rings that are weftz-substituted with larger substituents at the 3-position (7y, 7z, and 7aa). Analogues that contain meta- and jwa-substituted aryl rings (7c, 7i, 7k, and 7m) are potent against both enzymes and show reduced selectivity for TgCDPKl . Consistent with this observation, pyrazolopyrimidine derivatives that contain a 2-naphthyl (7p-7r) or quinoline group (7t) are potent inhibitors of both enzymes. However, bicyclic substituents that are not planar show reduced potency (7u-7w). In general, most inhibitors from this series are 2- to 12-fold selective for JgCDPKl over QJCDPKI. However, several compounds (for example, compounds 71, 7q and 7t) are equipotent or slightly selective for CpCDPKl . This fact demonstrates that while the ATP-binding pockets of both kinases are very similar they are not identical. Table 4. In vitro activities of 7a-5ab against TgCDPKl and Q7CDPKI . Values shown are the average of three assays ± (SEM).
Figure imgf000127_0001
Key to the use of pyrazolopyrimidine-based kinase inhibitors as anti-parasitic agents is the potential to selectively inhibit IgCDPKl and Q?CDPK1 over mammalian kinases. To determine the potency of these compounds against mammalian kinases, a subset of inhibitors were tested against the tyrosine kinases SRC and ABL. We felt that these two kinases would be a suitable counter-screen because they both contain the most permissive gatekeeper residue found in mammalian kinases (threonine) and the pyrazolopyrimidine core was originally developed as a kinase inhibitor scaffold against SRC-family kinases. (21)
As shown in Table 5, most of the pyrazolopyrimidines tested have limited activity against SRC and ABL. Consistent with earlier studies, previously-characterized "bumped" inhibitors 1 and 3 do not potently inhibit SRC or ABL kinase. Despite the increased activity of analogue 2 against IgCDPKl and Q?CDPK1, this compound only weakly inhibits SRC and ABL (ICso >1 μΜ).
Table 5. Activities of various inhibitors against human kinases and human cell lines. Values shown are the average of three assays ± (SEM). ic50 (μΜ) GL 50 ( Μ)
Compound Abl Src CRL8155 III.60 HCC2998 SF539
Number
1 >20 1.3 (0.2) >10 >10 >10 >10
2 6.0 (1.5) 1.9 (0.2) >10 >10 >10 >10
3 7.9 (2.0) 8.8 (1.8) >10 >10 >10 >10
5d 7.7 (3.8) 2.2 (0.5) >10 >10 >10 >10
5h >20 >20 >10 >10 >10 >10
5m 0.36 (.05) 0.21 (.06) - - - -
5n >20 >20 >10 >10 >10 >10
5o >20 4.2 (2.1) - - - -
5p 0.090 (.019) 0.36 (.07) >10 >10 >10 >10
7c 0.07 (.02) 0.035 (.008) >10 >10 >10 >10
7e 0.20 (.02) 0.22 (.02) - - - -
7p 0.075 (.024) 0.065 (.009) >10 >10 -10 >10
7q 0.82 (.04) 0.77 (0.10) >10 >10 >10 >10
7r 1.7 (0.5) 0.20 (.03) - - - -
7t 0.86 (.06) 2.7 (0.6) >10 >10 >10 >10
As expected, pyrazolopyrimidine inhibitors that contain smaller aryl groups at the 3- position (7c and 7e) are less selective for both parasite kinases due to their increased potency against SRC and ABL. However, analogues that contain a substituted naphthyl (7q and 7r) or quinoline (7t) substituent at the 3-poisition are much more selective due the increased size of these functional groups. Presumably, the larger threonine gatekeeper residues of SRC and ABL restrict access of these inhibitors to Hydrophobic Pocket II. While the substituent at the 3 -position is the major contributor to inhibitor selectivity, substitution at the 1 -position affects the potency of these compounds against JgCDPKl and Q?CDPK1 relative to SRC and ABL. For example, piperidine-containing analogues 5m and 5p are less selective for JgCDPKl and Q?CDPK1 than parent compound 1. However, several analogues restore the high selectivity of this class of compounds, with secondary piperidine 5h demonstrating over 1000-fold selectivity for the CDPKs. To test the overall toxicity of our pyrazolopyrimidines inhibitors, they were assayed for their ability to inhibit the growth of four human cell lines (Table 5): glioma derived (SF539), human lymphocyte (CRL8155), human promyelocytic leukemia (HL-60) and colorectal carcinoma (HC 2998). For all four cell lines tested, the inhibitors showed little or no growth inhibition at the highest concentration tested (10 μΜ).
We have previously reported crystal structures of inhibitors 2 and 3 bound to
JgCDPKl. (U.S. Provisional Patent Application No. 61/299,286, and reference 9) Similar to the structures of other pyrazolopyrimidines bound to tyrosine kinases, these inhibitors occupy the ATP -binding cleft of JgCDPKl . The pyrazolopyrimidine scaffold superimposes with the purine ring of ATP, with the exocyclic amine and nitrogen at the 5-position forming hydrogen-bonding interactions with the hinge region. In addition, the glycine gatekeeper residue of JgCDPKl allows bulky substituents at the 3-position unobstructed access to Hydrophobic Pocket II. Replacing glycine with a larger amino acid at this position clearly creates a steric clash with the 2-naphthyl and 1-naphthylmethylene groups of inhibitors 2 and 3, respectively. (8) Based on the similar sensitivities of JgCDPKl and Q?CDPK1 to pyrazolopyrimidines we predicted that inhibitors of this class would bind in a similar orientation in both enzymes. The structure of compound 3 bound to CpCDPKl shows that this is indeed the case (Figure 13a). Superposition of the active sites of JgCDPKl and Q?CDPK1 bound to 3 shows that the inhibitor has an identical mode of binding in both kinases. Furthermore, all of the residues surrounding the inhibitor are nearly superimposable, which is remarkable because JgCDPKl is in the calcium- free inactive conformation while Q?CDPK1 is in the calcium-bound active conformation (Figure 15).
It is therefore clear that the inhibitors are able to bind the ATP-binding site of CDPK1 whether it is active or not. While structures of both enzymes bound to 2 and 3 provided direct insight into how large substituents can be accommodated at the 3 -position, we were interested in further exploring how substitution at the 1 -position affects the potencies of these inhibitors. Structures of inhibitor 5h bound to TgCDPKl and CpCDPKl show how increased potency can be obtained. While the pyrazolopyrimidine cores and 3-postition substituents of inhibitors 3 and 5h make identical contacts with both enzymes, the piperidine ring of 5h forms a salt bridge with a glutamate residue that lines the ATP-binding cleft. Importantly, this interaction is present in the structures of 5h bound to both TgCDPKl and CjpCDPKl. Presumably, alkylation, acetylation or sulfonylation of the piperidine ring disrupts this interaction and accounts for the lower potency of compounds 5j-5r. Furthermore, the reduced potency of 5h against SRC and ABL demonstrates that these kinases cannot form a similar interaction.
In conclusion, we have demonstrated that selective pyrazolopyrimidine kinase inhibitors are indeed potent inhibitors of Q?CDPK1 and that they are able to inhibit an early stage of C. parvum cell invasion. This class of compounds have a similar effect on the ability of T. gondii to invade human fibroblast cells. (U.S. Provisional Patent Application No. 61/299,286, and reference 9) Based on these results, a diverse panel of pyrazolopyrimidine analogues was generated and their activities against Q?CDPK1 and TgCDPKl were determined. By exploiting a unique sequence and structural variation in the ATP-binding clefts of TgCDPKl and TgCDPKl potent dual inhibitors of these enzymes were obtained. Importantly, many of these inhibitors show minimal inhibition of the tyrosine kinases SRC and ABL and are not toxic to human cell lines. Additionally, other derivatives of pyrazolopyrimidine may be useful and such variations on the compounds discussed herein are contemplated. For example, the potency and selectivity of these compounds and optimization their PK/ADME/Tox properties. Furthermore, optimized inhibitors may be able to be used to inhibit C. parvum host cell invasion.
Biological Example 13 TgCDPKl and CpCDPKl IC50 data
The following compounds were tested for inhibition of TgCDPKl and CpCDPKl according to the preceding methods:
Figure imgf000130_0001
Figure imgf000130_0002
ICso (μΜ) ICso (μΜ)
Cmpd # TgCDPKl CpCDPKl Cmpd # TgCDPKl CpCDPKl
5b 0.086 0.13 7n 1.483 2.068
5c 1.923 2.038 7o 0.326 0.62
5d 0.031 0.144 7 0.005 0.01
5e 1.848 > 3.0 7q 0.006 0.005
5f 0.946 2.416 7r 0.005 0.012
5g 0.059 0.056 7s 0.863 0.591
5h 0.015 0.009 7t 0.024 0.02
5i 0.052 0.034 7u 0.045 0.312
5j 0.091 0.103 7v 0.181 0.984
5k 0.208 0.36 7w 0.017 0.11
51 0.104 0.179 7x > 3.0 > 3.0
5m 0.036 0.05 7y 0.322 1.402
5n 0.269 0.163 7z 2.229 > 3.0
5o 0.093 0.103 7aa 1.058 1.894
5p 0.054 0.075 7ab 0.056 0.121
5q 0.563 0.691 8 0.0048 0.0078
5r 0.117 0.194 9 0.04 0.032
7a 0.018 0.216 10 0.078 0.0336
7b 0.02 0.1 15 11 0.0103 0.0573
7c 0.004 0.013 12 0.0032 0.0532
7d 0.048 0.213 13 0.553 0.894
7e 0.014 0.059 14 0.627 0.953
7f 0.013 0.087 15 0.149 0.265
7g 0.019 0.1 14 16 0.9609 > 3.0
7h 0.009 0.022 17 0.98 1.554
7i 0.009 0.053 18 > 3.0 > 3.0
7j 0.04 0.41 19 0.0638 0.3705
7k 0.037 0.173 20 0.0036 0.003
71 0.42 0.093 21 > 3.0 > 3.0
7m 0.005 0.017 22 1.142 > 3.0 ICso (μΜ) ICso (μΜ)
Cmpd # TgCDPKl CpCDPKl Cmpd # TgCDPKl CpCDPKl
23 > 3.0 > 3.0 50 0.0522 1.0316
24 0.0119 0.0704 51 0.0159 0.2624
25 0.0038 0.0073 52 0.0043 0.3728
26 0.0091 0.0162 53 0.012 0.2723
27 0.0569 0.6231 54 0.0159 0.1471
28 0.0049 0.0023 55 0.0163 0.0307
29 0.0038 0.0035 56 0.004 0.1052
30 0.1 144 0.0837 57 0.01 0.0134
31 0.1 168 0.0936 58 0.1357 0.5877
32 0.0038 0.0051 59 0.0997 0.8319
33 0.0026 0.0046 60 0.0666 0.9289
34 0.0023 0.0021 61 0.0684 0.9269
35 0.0037 0.0044 62 0.0409 0.6918
36 0.003 0.0032 63 0.0462 0.4168
37 0.0013 0.0008 64 0.1429 0.9285
38 0.0007 0.0006 65 0.1706 1.1576
39 0.0007 0.0004 66 0.1777 2.0183
40 0.0008 0.0497 67 0.1963 0.8222
41 0.0006 0.0041 68 >3 >3
42 0.0009 0.054 69 0.0046 0.0107
43 0.0054 0.244 70 0.0042 0.0022
44 0.0037 0.0067 71 0.0049 0.0053
45 0.015 0.092 72 0.0249 0.0123
46 0.0106 0.1017 73
47 0.0055 0.2717 74
48 0.1366 1.5858 75
49 0.0186 0.2102
Biological Example 14 Tyrosine Kinase IC50 data
The following compounds were tested for inhibition of human tyrosine kinases SrcKD, Src3D, AblKD, Abl3D, HckKD according to the preceding methods: ICso^M)
Cmpd#
SrcKD Src3D AblKD Abl3D HckKD
1 1.3 >20.0
2 1.9 6
3 8.8 7.9 1.382
5d 2.2 7.7
5h >20.0 >20.0 > 10.0
5m 0.21 0.36
5n >20.0 >20.0
5o 4.2 >20.0
5p 0.36 0.09
7c 0.035 0.07
7e 0.22 0.2
7p 0.065 0.075
0.77 0.576 0.82 0.375
7q
7r 0.2 0.549 1.7 0.218
7t 0.2 1.7
9 0.686 2.01
11 0.475 0.628 2.36 0.541
12 0.298 0.307 0.838 0.244
20 0.294 0.238
24 1.45 0.353
25 5.02 0.969
26 1.242 0.304
28 >20.0 >20.0 > 10.0
29 >20.0 >20.0 > 10.0
30 >20.0 >20.0
32 > 10.0 > 10.0 > 10.0
33 > 10.0 > 10.0 > 10.0
34 3.063 > 10.0 1.613
35 > 10.0 > 10.0 > 10.0
36 > 10.0 > 10.0 > 10.0 Ι^ο (μΜ)
Cmpd #
SrcKD Src3D AblKD Abl3D HckKD
37 1.759 > 10.0
38 0.375 0.497
39 1.551 > 10.0
40 0.038 0.043 0.316
41 0.199 0.675
42 0.784 1.68
43 0.263 1.153
44 > 10.0 7.34
45 > 10.0 7.326
48 0.8832 1.701
49 0.1118 0.0333
50 0.1966 1.073
51 0.4003 1.798
52 0.1067 1.267
53 0.191 1 1.23
54 0.1254 0.194
55 0.897 0.6492
57 >10 >10
68 >10 >10
69 3.9 >10
70 2.38 4.79
71 6.09 >10
72 >10 6.35
REFERENCES (BIOLOGICAL EXAMPLES 1 - 11)
The following references are herein incorporated by reference.
1. Montoya JG, Kovacs JA & Remington JS. Principles and Practice of Infectious Diseases.
Chapter 276 Mandell,B.&.D. (ed.) (Churchill Livingston, 2005).
2. Mead,P.S. et al. Food-related illness and death in the United States. Emerging Infectious Diseases 5, 607-625 (1999). 3. Baril,L. et al. Risk factors for toxoplasma infection in pregnancy: A case-control study in France. Scandinavian Journal of Infectious Diseases 31, 305-309 (1999).
4. Jones,J.L. et al. Toxoplasma gondii infection in the United States: Seroprevalence and risk factors. American Journal of Epidemiology 154, 357-365 (2001).
5. Wallace,M.R., Rossetti,R.J. & 01son,P.E. Cats and Toxoplasmosis Risk in Hiv-Infected Adults. Jama-Journal of the American Medical Association 269, 76-77 (1993).
6. Vastava,P.B. et al. MRI features of toxoplasma encephalitis in the immunocompetent host: a report of two cases. Neuroradiology 44, 834-838 (2002).
7. Hermentin,K., Hassl,A., Picher.O. & Aspock,H. Comparison of Different Serotests for Specific Toxoplasma Igm- Antibodies (Isaga, Spiha, Ifat) and Detection of Circulating
Antigen in 2 Cases of Laboratory Acquired Toxoplasma Infection. Zentralblatt fur Bakteriologie Mikrobiologie und Hygiene Series A-Medical Microbiology Infectious Diseases Virology Parasitology 270, 534-541 (1989).
8. Bach,M.C. & Armstrong,R.M. Acute Toxoplasmic Encephalitis in A Normal Adult.
Archives of Neurology 40, 596-597 (1983).
9. Pelphrey,P.M. et al. Highly efficient ligands for dihydrofolate reductase from
Cryptosporidium hominis and Toxoplasma gondii inspired by structural analysis. Journal of Medicinal Chemistry 50, 940-950 (2007).
10. Dannemann,B. et al. Treatment of Toxoplasmic Encephalitis in Patients with Aids - A Randomized Trial Comparing Pyrimethamine Plus Clindamycin to Pyrimethamine Plus
Sulfadiazine. Annals of Internal Medicine 116, 33-43 (1992).
11. JEFFREY MJACOBSON et al. Pyrimethamine Pharmacokinetics in Human
Immunodeficiency Virus-Positive Patients Seropositive for Toxoplasma gondii.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY 40, 1360-1365 (1996).
12. Nagamune,K. & Sibley,L.D. Comparative genomic and phylogenetic analyses of calcium ATPases and calcium-regulated proteins in the apicomplexa. Mol. Biol. Evol. 23, 1613- 1627 (2006).
13. Lovett,J.L. & Sibley,L.D. Intracellular calcium stores in Toxoplasma gondii govern
invasion of host cells. Journal of Cell Science 116, 3009-3016 (2003).
14. Kieschnick,H., Wakefield,T., Narducci,C.A. & Beckers,C. Toxoplasma gondii attachment to host cells is regulated by a calmodulin-like domain protein kinase. J. Biol. Chem. 276, 12369-12377 (2001).
15. Canduri,F., Perez,P.C, Caceres,R.A. & de Azevedo,W.F. Protein kinases as targets for antiparasitic chemotherapy drugs. Current Drug Targets 8, 389-398 (2007). 16. Doerig,C, Billker,0., Pratt,D. & EndicottJ. Protein kinases as targets for antimalarial intervention: kinomics, structure-based design, transmission-blockade, and targeting host cell enzymes. Biophysica et Biochimica Acta - Proteins and Proteomics 1754, 132-150 (2005).
17. Harper,J.F. & Harmon,A. Plants, symbiosis and parasites: A calcium signaling
connection. Nature Reviews Molecular Cell Biology 6, 555-566 (2005).
18. Raichaudhuri,A., Bhattacharyya,R., Chaudhuri,S., Chakrabarti,P. & Dasgupta,M. Domain analysis of a groundnut calcium-dependent protein kinase: nuclear localization sequence in the junction domain is coupled with nonconsensus calcium binding domains. J. Biol. Chem. 281, 10399-10409 (2006).
19. Noble,M.E., Endicott,J.A. & Johnson,L.N. Protein kinase inhibitors: insights into drug design from structure. Science 303, 1800-1805 (2004).
20. Knight,Z.A. & Shokat,K.M. Features of selective kinase inhibitors. Chemistry & Biology
12, 621-637 (2005).
21. Cohen,M.S., Zhang,C, Shokat, .M. & Taunton,! Structural bioinformatics-based design of selective, irreversible kinase inhibitors. Science 308, 1318-1321 (2005).
22. LiaOjJ.J. Molecular recognition of protein kinase binding pockets for design of potent and selective kinase inhibitors. J. Med. Chem. 50, 409-424 (2007).
23. Bishop,A.C. et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase.
Nature 407, 395-401 (2000).
24. Bishop,A.C. et al. Generation of monospecific nanomolar tyrosine kinase inhibitors via a chemical genetic approach. Journal of the American Chemical Society 121, 627-631 (1999).
25. Zhang,C. et al. A second-site suppressor strategy for chemical genetic analysis of diverse protein kinases. Nat. Methods 2, 435-441 (2005).
26. Bishop,A.C, Buzko,0. & Shokat,K.M. Magic bullets for protein kinases. Trends Cell Biol. 11, 167-172 (2001).
27. Johnson,A.W. et al. The brain-derived neurotrophic factor receptor TrkB is critical for the acquisition but not expression of conditioned incentive value. European Journal of Neuroscience 28, 997-1002 (2008).
28. Morgan,D.J. et al. Tissue-specific PKA inhibition using a chemical genetic approach and its application to studies on sperm capacitation. Proceedings of the National Academy of Sciences of the United States of America 105, 20740-20745 (2008). 29. Chen,X. et al. A chemical-genetic approach to studying neurotrophin signaling. Neuron 46, 13-21 (2005).
30. Ojo, .K. et al. Glycogen synthase kinase 3 is a potential drug target for African
trypanosomiasis therapy. Antimicrob. Agents Chemother. 52, 3710-3717 (2008).
31. Newman,! et al. Towards rationalization of crystallization screening for small- to
medium-sized academic laboratories: the PACT/JCSG plus strategy. Acta
Crystallographica Section D-Bio ogical Crystallography 61, 1426-1431 (2005).
32. Cohen,A.E., Ellis,P.J., Miller,M.D., Deacon,A.M. & Phizackerley,R.P. An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot. Journal of Applied Crystallography 35, 720-726 (2002).
33. McPhillips,T.M. et al. Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. Journal of Synchrotron Radiation 9, 401-406 (2002).
34. Hendrickson,W.A., Horton,J.R. & Lemaster,D.M. Selenomethionyl Proteins Produced for Analysis by Multiwavelength Anomalous Diffraction (Mad) - A Vehicle for Direct Determination of 3 -Dimensional Structure. Embo Journal 9, 1665-1672 (1990).
35. Otwinowski,Z. & Minor,W. Processing of X-ray diffraction data collected in oscillation mode. Macromolecular Crystallography, Pt A 276, 307-326 (1997).
36. Vagin,A. & Teplyakov,A. MOLREP: an automated program for molecular replacement.
Journal of Applied Crystallography 30, 1022-1025 (1997).
37. Mccoy,AJ. et al. Phaser crystallographic software. Journal of Applied Crystallography
40, 658-674 (2007).
38. Terwilliger,T. SOLVE and RESOLVE: automated structure solution, density
modification, and model building. Journal of Synchrotron Radiation 11, 49-52 (2004).
39. Emsley,P. & Cowtan, . Coot: model-building tools for molecular graphics. Acta
Crystallographica Section D-Biological Crystallography 60, 2126-2132 (2004).
40. Murshudov,G.N., Vagin,A.A. & Dodson,E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallographica Section D-Biological Crystallography 53, 240-255 (1997).
41. Cohen,S.X. et al ARP/wARP and molecular replacement: the next generation. Acta Crystallographica Section D-Biological Crystallography 64, 49-60 (2008). 42. Schuttelkopf,A-W. & van Aalten,D.M.F. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section DBiological Crystallography 60, 1355-1363 (2004).
43. Painter, J. & Merritt,E.A. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallographica Section D-Biological
Crystallography 62, 439-450 (2006).
44. Painter, J. & Merritt,E.A. TLSMD web server for the generation of multi-group TLS models. Journal of Applied Crystallography 39, 109-1 11 (2006).
45. Lovell,S.C. et al. Structure validation by C alpha geometry: phi,psi and C beta deviation.
Proteins-Structure Function and Genetics 50, 437-450 (2003).
46. Bailey,S. The Ccp4 Suite - Programs for Protein Crystallography. Acta Crystallographica Section D-Biological Ciystallography 50, 760-763 (1994).
47. Potterton,E., Briggs,P., Turkenburg,M. & Dodson,E. A graphical user interface to the CCP4 program suite. Acta Crystallographica Section D-Biological Crystallography 59, 1 131-1137 (2003).
48. Berman,H.M. et al. The Protein Data Bank. Nucleic Acids Research 28, 235-242 (2000).
49. Matrajt,M., Nishi,M., Fraunholz,M.J., Peter,0. & Roos,D.S. Amino-terminal control of transgenic protein expression levels in Toxoplasma gondii. Molecular and Biochemical Parasitology 120, 285-289 (2002).
50. Striepen,B., He,C.Y.X., Matrajt,M., Soldati,D. & Roos,D.S. Expression, selection, and organellar targeting of the green fluorescent protein in Toxoplasma gondii. Molecular and Biochemical Parasitology 92, 325-338 (1998).
51. DeRocher,A., Hagen,C.B., Froehlich .E., FeaginJ.E. & Parsons,M. Analysis of targeting sequences demonstrates that trafficking to the Toxoplasma gondii plastid branches off the secretory system. Journal of Cell Science 113, 3969-3977 (2000).
52. Karnataki,A. et al. Cell cycle-regulated vesicular trafficking of Toxoplasma APT1, a protein localized to multiple apicoplast membranes. Molecular Microbiology 63, 1653- 1668 (2007).
53. Fruth,I.A. & Arrizabalaga,G. Toxoplasma gondii: Induction of egress by the potassium ionophore nigericin. International Journal for Parasitology 37, 1559- 1567 (2007).
54. Seeber,F. & Boothroyd,J.C. Escherichia coli beta-galactosidase as an in vitro and in vivo reporter enzyme and stable transfection marker in the intracellular protozoan parasite Toxoplasma gondii. Gene 169, 39-45 (1996). REFERENCES (SYNTHETIC EXAMPLES AND BIOLOGICAL EXAMPLES 12 ETC.) The following references are herein incorporated by reference.
1. White AC. Chapter 280: Cryptosporidiosis (Cryptosporidium hominis, Cryptosporidium parvum, and Other Species) in Mandell, Bennett, & Dolin: Principles and Practice of Infectious Diseases, 6th ed. Publ: Churchill Livingston (2005).
2. Sarnie, A.; Bessong, P. O.; Obi, C. L.; Sevilleja, J. E.; Stroup, S.; Houpt, E.; Guerrant, R.
L. Cryptosporidium species: preliminary descriptions of the prevalence and genotype distribution among school children and hospital patients in the Venda region, Limpopo Province, South Africa. Exp.Parasitol. 114, 314-322 (2006).
3. Montoya JG, Kovacs JA, Remington JS. Chapter 276: Toxoplasma gondii in Mandell,
Bennett, & Dolin: Principles and Practice of Infectious Diseases, 6th ed. Publ: Churchill Livingston (2005).
4. Nagamune K, Sibley LD. Comparative genomic and phylogenetic analyses of calcium ATPases and calcium-regulated proteins in the apicomplexa. Mol. Biol. Evol. 23, 1613- 1627 (2006).
5. Billker O, Lourido S, Sibley LD. Cell Host Microbe. 2009 Jun 18;5(6):612-22. Calcium- dependent signaling and kinases in apicomplexan parasites.
6. Doerig C, Billker O, Pratt D, Endicott J. Protein kinases as targets for antimalarial
intervention: kinomics, structure-based design, transmission-blockade, and targeting host cell enzymes. Biophysica et Biochimica Acta - Proteins and Proteomics 1754, 132- 150 (2005).
7. Kieschnick H, WakefieldT, Narducci CA, Beckers, C. Toxoplasma gondii attachment to host cells is regulated by a calmodulin-like domain protein kinase. J. Biol. Chem. 276, 12369-12377 (2001).
8. Chen XM, O'Hara SP, Huang BQ, Nelson JB, Lin JJC, Zhu G, Ward HD, LaRusso NF.
Apical Organelle discharge by Cryptosporidium parvum is temperature, cytoskeleton, and intracellular calcium dependent and required for host cell invasion. Infect. Immun. 72, 6806-16 (2004).
9. Ojo K, Larson, ET, eyloun KR, Castaneda LJ, DeRocher AE, Inampudi K, Kim JE, Arakaki T, Murphy, RC, Zhang L, Napuli AJ, Maly DJ, Verlinde CLMJ, Buckner FS, Parsons M, Hoi WGJ, Merritt EA, Van Voorhis WC. Toxoplasma gondii calcium- dependent protein kinase 1 is a target for selective kinase inhibitors Nat. Struct. Mol Biol. 17, In Press. (2010). 10. Sugi T, Kato K, Kobayashi K, Watanabe S, Kurokawa H, Gong H, Pandey K, Takemae H, Akashi H. Use of the kinase inhibitor analog 1NM-PP 1 reveals a role for Toxoplasma gondii CDPK1 in the invasion step. Eukaryot. Cell 9, 667-70 (2010).
11. Liao, J.J. Molecular recognition of protein kinase binding pockets for design of potent and selective kinase inhibitors. J. Med. Chem. 50, 409-424 (2007).
12. Zhang, C. et al. A second-site suppressor strategy for chemical genetic analysis of diverse protein kinases. Nat. Methods 2, 435-441 (2005).
13. Cohen, M.S. et al. Structural bioinformatics-based design of selective, irreversible kinase inhibitors. Science , 1318-1321 (2005).
14. Bishop, A.C. et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase.
Nature 407, 395-401 (2000).
15. Bishop, A.C. et al. Design of allele-specific inhibitors to probe protein kinase signaling.
Curr. Biol. 8, 257-266 (1998).
16. Bishop, AC. et al. Generation of monospecific nanomolar tyrosine kinase inhibitors via a chemical genetic approach. J. Am. Chem. Soc. 121, 627-631 (1999).
17. Burchat AF, Calderwood DJ, Friedman MM, Hirst GC, Li B, Rafferty P, Ritter ,
Skinner BS. "Pyrazolo[3,4- ]pyrimidines containing an extended 3-substituent as potent inhibitors of Lck - a selectivity insight" Bioorg. Med. Chem. Lett., 12, 1687-1690 (2002).
18. Apsel, B, Blair, JA, Gonzalez B, Nazif TM, Feldman ME, Aizenstein B, Hoffman R, Williams R.L, Shokat KM, Knight ZA. "Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases" Nat. Chem. Biol., 4, 691-699 (2008).
19. Valeur, E.; Roche, D. Efficient, mild, parallel and purification-free synthesis of aryl ethers via Mitsunobu reaction. Tet. Lett. 49, 4182-4185 (2008).
20. QJCDPKI 'S and TfcCDPKl 's Kms for ATP are 9.0 μΜ and 10 μΜ, respectively
21. Hanke JH, Gardner JP, Dow RL, Changelian PL, Brissette WH, Weringer EJ, Pollok BA, Connelly PA. "Discovery of a novel, potent, and Src family-selective tyrosine kinase inhibitor. Study of Lck- and FynT-dependent T cell activation." J. Biol. Chem., 271, 695- 701 (1996).
22. Ajjampur, S. S.; Rajendran, P.; Ramani, S.; Banerjee, I.; Monica, B.; Sankaran, P.;
Rosario, V.; Arumugam, R.; Sarkar, R.; Ward, H.; Kang, G. Closing the diarrhea diagnostic gap in Indian children by the application of molecular techniques. J. Med. Microbiol. 57, 1364-1368 (2008).
CONCLUSION The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize.
All of the references cited herein are incorporated by reference. Aspects of the disclosure can be modified, if necessary, to employ the systems, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. These and other changes can be made to the disclosure in light of the detailed description.
Specific elements of any of the foregoing embodiments can be combined or substituted for elements in other embodiments. Furthermore, while advantages associated with certain embodiments of the disclosure have been described in the context of these embodiments, other embodiments may also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to fall within the scope of the disclosure. Accordingly, the disclosure is not limited, except as by the appended claims.

Claims

We Claim:
1. A method for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either
(i) a bumped kinase inhibitor or
(ii) a pharmaceutical composition comprising a bumped kinase inhibitor and a pharmaceutically acceptable excipient, carrier, or diluent.
Figure imgf000142_0001
The method of claim 1, wherein the bumped kinase inhibitor is of the formula,
Figure imgf000142_0002
or a pharmaceutically acceptable salt thereof, wherein X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
R1 is Ci-6 alkyl, Ci_6 haloalkyl, C2-6 alkenyl, C2-6 alkynyl, -Ci_6 alkyl-R12, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein
the cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups;
each R11 is independently Cw alkyl, Ci-6 haloalkyl, -C(0)R, -C(0)OR, -C(0)NR2,
-S(0)2NR2, or -S(0)2R;
and
R12 is -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, -N(R)C(0)NR2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2;
L is a bond or -CH2-;
R3 is aryl or heteroaryl, each optionally substituted with one, two, or three R31 groups, wherein each R31 is independently halogen, cyano, nitro, Ci_6 alkyl, C1-6 haloalkyl, aryl, heteroaryl, C3-8 cycloalkyl, heterocyclyl, arylCi-6 alkyl, heteroarylCi-6 alkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, -N(R)C(0)NR2 or -N(R)S(0)2R, wherein the aryl, heteroaryl, C3-8 cycloalkyl, heterocyclyl, arylalkyl, and heteroarylalkyl groups are optionally substituted with one or two R10 groups;
each R is independently hydrogen, Ci_6 alkyl, C2-6 alkenyl, Ci_6 haloalkyl, C3_8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four R10 groups;
and
each R10 is independently halogen, cyano, nitro, Ci-6 alkyl, Ci_6 haloalkyl, -OR0, -SR°, -N(R°)2, -C(0)R°, -C(0)OR°, -C(0)N(R°)2, -S(0)2R°, -OC(0)R°, -OC(0)OR°, -OC(0)N(R°)2, -N(R°)C(0)R°, -N(R°)C(0)OR°, or -N(R°)C(0)N(R°)2, wherein each R° is independently hydrogen or Ci-6 alkyl. 4. The method of claim 3 according to the formula,
5. The method of claim 3 according to the formula,
Figure imgf000144_0001
.
6. The method of any one of claims 3 - 5, wherein L is a bond.
7. The method of any one of claims 3 - 5, wherein L is -CH2-.
8. The method any one of claims 3 - 7, wherein R is naphthyl, quinolinyl, pyridyl, pyrimidinyl, indolyl, benzodioxolyl, 2,3-dihydrobenzodioxinyl, dibenzothienyl, chromanyl, or phenyl, each optionally substituted with one, two, or three R31 groups.
9. The method any one of claims 3 - 7, wherein R3 is naphthyl, quinolinyl, indolyl, benzodioxolyl, 2,3-dihydrobenzodioxinyl, or chromanyl, each optionally substituted
31
with one, two, or three R groups.
10. The method any one of claims 3 - 7, wherein RJ is phenyl substituted with one, two, or three Rjl groups.
11. The method any one of claims 3 - 7, wherein R3 is phenyl optionally substituted with one or two R31 groups, and substituted with one group that is halogen, C1-6 alkyl, -OR, -SR, -NR2, -N(R)C(0)R, or -N(R)S(0)2R.
12. The method any one of claims 3 - 7, wherein R is phenyl optionally substituted with
31
one or two R groups, and substituted with one group that is -OR or -N(R)C(0)R.
13. The method any one of claims 3 - 7, wherein R3 is phenyl optionally substituted with one or two R31 groups, and substituted with one group that is -OR10, wherein R10 is benzyl optionally substituted with one, two, three, or four groups that are each independently halogen, C1-6 alkyl, Ci.6 haloalkyl, or -OR0.
14. The method any one of claims 3 - 7, wherein R is phenyl optionally substituted with
31 20 one or two R groups, and substituted with one group that is -N(H)C(0)R , wherein R20 is Ci_6 alkyl, C2-6 alkenyl, Ci_6 haloalkyl, aryl, or arylCi_6 alkyl.
15. The method any one of claims 3 - 7, wherein R3 is naphthyl optionally substituted with one, two, or three R31 groups.
16. The method any one of claims 3 - 7, wherein R3 is naphthyl optionally substituted with one or two R31 groups and substituted with one group that is -OR15, wherein R15 is Ci-6 alkyl or benzyl, wherein the benzyl is optionally substituted with one, two, three, or four groups that are each independently halogen, C1-6 alkyl, C1-6 haloalkyl, or
-ORu
17. The method of claim 16, wherein R3 is
Figure imgf000145_0001
18. The method any one of claims 3 - 7, wherein R3 is indolyl optionally substituted with one, two, or three R31 groups.
19. The method of any one of claims 3 - 18, wherein R1 is C1-4 alkyl, -C1-4 alkyl-R12, C2-4 alkynyl, C3_8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups.
20. The method of any one of claims 3 - 18, wherein R1 is C3.8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups.
21. The method of any one of claims 3 - 18, wherein R1 is C3-8 cycloalkyl.
22. The method of any one of claims 3 - 18, wherein R1 is monocyclic heterocyclyl optionally substituted with one R11 group.
23. The method of any one of claims 3 - 18, wherein R1 is C1-4 alkyl.
24. The method of any one of claims 3 - 18, wherein R1 is isopropyl or t-butyl.
25. The method of any one of claims 3 - 18, wherein R1 is -C1-4 alkyl-R12.
26. The method of any one of claims 3 - 18, wherein 1 is -C alkyl-R 12 , wherein R 12 is -C(0)OR, -C(0)NR2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2;
27. The method of any one of claims 3 - 18, wherein R 1 is -C alkyl-R 12 , wherein R 12 is -C(0)OR or -C(0)NR2.
28. The method of any one of claims 3 - 18, wherein R1 is -CM alkyl-R12, wherein R12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, - N(R)C(0)OR, or -N(R)C(0)NR2.
29. The method of any one of claims 3 - 18, wherein R1 is -CM alkyl-R12, wherein R12 is phenyl or monocyclic heterocyclyl, each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
30. The method of any one of claims 3 - 18, wherein R1 is -CM alkyl-R12, wherein R12 is monocyclic heterocyclyl optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci-6 alkyl, C1-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
31. The method of any one of claims 3 - 18, wherein R1 is -CM alkyl-R12, wherein R12 is piperidinyl or tetrahydropyranyl, each optionally substituted by one or two groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR,-C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
32. The method of any one of claims 1- 31, wherein the apicomplexan protozoan related disease is toxoplasmosis.
33. The method of any one of claims 1- 31, wherein the apicomplexan protozoan related disease is cryptosporidiosis.
34. The method of any one of claims 1- 31, wherein the subject is a mammal.
35. The method of any one of claims 1- 31, wherein the subject is human.
36. The method of any one of claims 1- 31, wherein the subject is livestock.
37. The method of claim 1, wherein the compound is a compound of Table B.
38. A compound of the formula
Figure imgf000147_0001
or a pharmaceutically acceptable salt thereof, wherein
X, Y, and Z are defined by either: (i) X is N, Y is C, and Z is N; or (ii) X is C, Y is N, and Z is C(H);
1 is C2-6 alkyl, C1-6 haloalkyl, -C1-4 alkyl-R12, C2.6 alkenyl, C2-6 alkynyl, C3-8 cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl, wherein
the cycloalkyl, heterocyclyl, heteroaryl, and phenyl groups are each optionally substituted with one or two R11 groups;
each R11 is independently Cw alkyl, Ci-6 haloalkyl, -C(0)R, -C(0)OR, -C(0)NR2,
-S(0)2NR2, or -S(0)2R;
and
R12 is -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, -N(R)C(0)NR2, phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the aryl, heteroaryl, C3.8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2; i ne of the formulas,
Figure imgf000148_0001
wherein
n is 0, 1, or 2;
Q is -0-, -S-, or -N(RQ)- , wherein RQ is hydrogen or C1-6 alkyl; and
R33 is Ci-6 alkyl, C2-6 alkenyl, C1-6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi-6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R20, -OC(0)R20, -OC(0)OR20, -OC(O)N(R20)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R 0)C(O)N(R20)2, wherein each R20 is independently hydrogen or C1-6 alkyl,
each R32 is independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR34, -SR34, -N(R 4)2, -C(0)R34, -C(0)OR34, -C(0)N(R34)2, -S(0)2R34, -OC(0)R34, -OC(0)OR34, -OC(0)N(R34)2, -N(R34)C(0)R34, -N(R34)C(0)OR34, or -N(R34)C(0)N(R34)2, wherein each R34 is independently hydro gen or C1-6 alkyl;
and
35
R is hydrogen or Ci_6 alkyl;
and
each R is independently hydrogen, C1-6 alkyl, C2_6 alkenyl, C1-6 haloalkyl, C3-8 cycloalkyl, heterocyclyl, aryl, arylCi_6 alkyl, heteroaryl, or heteroarylCi-6 alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C1-6 alkyl, Ci_6 haloalkyl, -OR , -SR , -N(R")2, -C(0)R , -C(0)OR , -C(0)N(R")¾ -S(0)2R°, -OC(0)R°, -OC(0)OR°, -OC(0)N(R°)2, -N(R°)C(0)R°, -N(R°)C(0)OR°, or -N(R°)C(0)N(R°)2, wherein each R° is independently hydrogen or Ci_6 alkyl, provided that the compound is not
1 -cyclopentyl-3 -( 1 -methyl- 1 H-indol-5-yl)- 1 H-pyrazolo [3 ,4-d]pyrimidin-4-amine;
1 -cyclopentyl-3 -( 1 H-indol-5 -yl)- 1 H-pyrazolo [3 ,4-d]pyrimidin-4-amine;
1 -cyclopentyl-3 -( 1 H-indol-6-yl)- 1 H-pyrazolo [3 ,4-d]pyrimidin-4-amine;
6-(4-amino-l-cyclopentyl-lH-pyrazolo[3,4-d]pyrimidin-3-yl)-lH-indole-3-carbaldehyde;
3 -( 1 H-indol-5-yl)- 1 -isopropyl- 1 H-pyrazolo [3 ,4-d]pyrimidin-4-amine;
1 -isopropyl-3 -(1 -methyl- 1 H-indol-5 -yl)- 1 H-pyrazolo [3 ,4-d]pyrimidin-4-amine;
3 -( 1 H-indol-6-yl)- 1 -isopropyl- 1 H-pyrazolo [3 ,4-d]pyrimidin-4-amine;
2- (4-amino-l-isopropyl-lH-pyrazolo[3,4-d]pyrimidin-3-yl)-lH-indol-5-ol;
3 - ( 1 H-indol-4-yl)- 1 -isopropyl- 1 H-pyrazolo [3 ,4-d]pyrimidin-4-amine; and
l-cyclopentyl-3-(lH-indol-4-yl)-lH-pyrazolo[3,4-d]pyrimidin-4-amine.
39. The compound of claim 38 of the formula,
The compound of claim 38 of the formula,
Figure imgf000149_0001
41. The compound of any one of claims 38 - 40, wherein R is
Figure imgf000149_0002
42. The compound of claim 41, wherein Q is -0- or -N(RQ)-.
43. The compound of claim 41, wherein Q is -0-.
44. The compound of any one of claims 41 - 43, wherein R3i is Ci-6 alkyl, C2-6 alkenyl, arylCi-6 alkyl, or heteroarylCi-6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, Ci_6 alkyl, Ci_6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20 -C(0)OR20, -C(O)N(R20)2, -S(0)2R20, -OC(0)R20, -OC(0)OR20, -OC(O)N(R20)2, -N(EnC(0)lC , -N(R20)C(0)OR , or -N(R 0)C(0)N(R 0)2, wherein each R u is independently hydrogen or C1-6 alkyl.
45. The compound of any one of claims 41 - 43, wherein R33 is Ci_6 alkyl, C2-6 alkenyl, arylCi-6 alkyl, or heteroarylCi_6 alkyl, wherein the arylalkyl and heteroarylalkyl are optionally substituted with one or two groups that are each independently halogen, C\. 6 alkyl, or C1-6 haloalkyl.
46. The compound of any one of claims 41 - 43, wherein R3j is arylCi-6 alkyl or heteroarylCi-6 alkyl, each are optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR2°, -C(O)N(R20)2, -S(0)2R20, -OC(0)R20, -OC(0)OR20, -OC(O)N(R20)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or C1-6 alkyl.
47. The compound of any one of claims 41 - 43, wherein R3j is arylCi-6 alkyl or heteroarylCi-6 alkyl, each optionally substituted with one or two groups that are each independently halogen, C1-6 alkyl, or C1-6 haloalkyl.
48. The compound of any one of claims 41 - 43, wherein R33 is benzyl optionally substituted with one, two, three, or four groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1-6 haloalkyl, -OR20, -SR20, -N(R20)2, -C(0)R20, -C(0)OR20, -C(O)N(R20)2, -S(0)2R20, -OC(0)R20, -OC(0)OR20, -OC(O)N(R20)2, -N(R20)C(O)R20, -N(R20)C(O)OR20, or -N(R20)C(O)N(R20)2, wherein each R20 is independently hydrogen or C1-6 alkyl.
49. The compound of any one of claims 41 - 43, wherein R33 is benzyl optionally substituted with one or two groups that are each independently halogen, Ci_6 alkyl, or Ci-6 haloalkyl.
50. The compound of any one of claims 38 - 40, wherein R is
Figure imgf000150_0001
51. The compound of claim 50, wherein R is hydrogen.
52. The compound of claim 50 or 51, wherein n is 1 or 2.
53. The compound of claim 50 or 51, wherein n is 1.
54. The compound of claim 50 or 51, wherein n is 1 or 2, and each R32 is independently halogen, C1-6 alkyl, or C1-6 haloalkyl.
55. The compound of any one of claims 38- 54, wherein R1 is C2-6 alkyl or -C1-4 alkyl-R12. 1 12
56. The compound of claim 55, wherein is -C1-4 alkyl-R .
1 12
57. The compound of claim 56, wherein R is -CH2-R .
58. The compound of any one of claims 55-57, wherein R12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3.8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one, two, or three groups that are each independently halogen, cyano, nitro, C1-6 alkyl, C1.6 haloalkyl, -OR, -SR, -NR2, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
59. The compound of any one of claims 55-57, wherein R12 is phenyl, monocyclic heteroaryl, C3-8 cycloalkyl, or monocyclic heterocyclyl, wherein the phenyl, heteroaryl, C3-8 cycloalkyl, and heterocyclyl groups are each optionally substituted by one or two groups that are each independently halogen, Ci-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
60. The compound of any one of claims 55-57, wherein R12 is monocyclic heterocyclyl optionally substituted by one or two groups that are each independently halogen, C1-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
61. The compound of any one of claims 55-57, wherein R12 is piperidinyl optionally substituted by one or two groups that are each independently Ci-6 alkyl, -C(0)R, -C(0)OR, -C(0)NR2, -S(0)2R, -OC(0)R, -OC(0)OR, -OC(0)NR2, -N(R)C(0)R, -N(R)C(0)OR, or -N(R)C(0)NR2.
62. The compound of claim 55, wherein R1 is isopropyl or t-butyl.
63. The compound of claim 38 that is a compound of Table A.
64. A method for treating an apicomplexan protozoan related disease comprising providing to a patient in need of such treatment a therapeutically effective amount of either (i) a compound according to any one of claims 38-63; or (ii) a pharmaceutical composition comprising a compound according to any one of claims 38-63 and a pharmaceutically acceptable excipient, carrier, or diluent.
65. The method of claim 64, wherein the apicomplexan protozoan related disease is toxoplasmosis.
66. The method of claim 64, wherein the apicomplexan protozoan related disease is cryptosporidiosis.
67. The method of claim 64, wherein the apicomplexan protozoan related disease is coccidiosis.
68. The method of claim 64, wherein the subject is a mammal.
69. The method of claim 64, wherein the subject is human.
70. The method of claim 64, wherein the subject is livestock.
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Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014081922A1 (en) * 2012-11-21 2014-05-30 The Trustees Of The University Of Pennsylvania Compositions and methods useful in preventing and treating apicomplexa infections
WO2014189947A1 (en) 2013-05-20 2014-11-27 University Of Washington Through Its Center For Commercialization 5-aminopyrazole-4-carboxamide inhibitors of cdpk1 from t. gondii and c. parvum
WO2015079251A1 (en) * 2013-11-29 2015-06-04 Cancer Research Technology Limited Quinazoline compounds
WO2015146929A1 (en) * 2014-03-24 2015-10-01 武田薬品工業株式会社 Heterocyclic compound
JP2015532287A (en) * 2012-09-26 2015-11-09 ザ・リージエンツ・オブ・ザ・ユニバーシテイー・オブ・カリフオルニア IRE1 regulation
WO2016123152A1 (en) * 2015-01-26 2016-08-04 University Of Washington Compositions and methods for treating toxoplasmosis, cryptosporidiosis and other apicomplexan protozoan related diseases
US10196397B2 (en) 2014-11-19 2019-02-05 Sun Pharmaceutical Industries Limited Process for the preparation of ibrutinib
US10294227B2 (en) 2015-05-21 2019-05-21 University Court Of The University Of Edinburgh Compounds
US10844067B2 (en) 2016-04-15 2020-11-24 Cancer Research Technology Limited Heterocyclic compounds as RET kinase inhibitors
US10954241B2 (en) 2016-04-15 2021-03-23 Cancer Research Technology Limited Heterocyclic compounds as ret kinase inhibitors
US11352361B2 (en) 2017-04-13 2022-06-07 Cancer Research Technology Limited Compounds useful as RET inhibitors

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002076986A1 (en) * 2001-03-22 2002-10-03 Abbott Gmbh & Co. Kg Pyrazolopyrimidines as therapeutic agents
US20060084654A1 (en) * 2003-10-15 2006-04-20 Beck Patricia A Imidazopyrazine tyrosine kinase inhibitors
WO2007061737A2 (en) * 2005-11-17 2007-05-31 Osi Pharmaceuticals, Inc. FUSED BICYCLIC mTOR INHIBITORS
WO2008066755A2 (en) * 2006-11-22 2008-06-05 University Of Georgia Research Foundation, Inc. Tyrosine kinase inhibitors as anti-kinetolastid and anti-apicomplexan agents

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002076986A1 (en) * 2001-03-22 2002-10-03 Abbott Gmbh & Co. Kg Pyrazolopyrimidines as therapeutic agents
US20060084654A1 (en) * 2003-10-15 2006-04-20 Beck Patricia A Imidazopyrazine tyrosine kinase inhibitors
WO2007061737A2 (en) * 2005-11-17 2007-05-31 Osi Pharmaceuticals, Inc. FUSED BICYCLIC mTOR INHIBITORS
WO2008066755A2 (en) * 2006-11-22 2008-06-05 University Of Georgia Research Foundation, Inc. Tyrosine kinase inhibitors as anti-kinetolastid and anti-apicomplexan agents

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
BISHOP A C ET AL: "Generation of monospecific nanomolar tyrosine kinase inhibitors via a chemical genetic approach", JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 121, no. 4, 1 January 1999 (1999-01-01), AMERICAN CHEMICAL SOCIETY, WASHINGTON, DC; US, pages 627 - 631, XP002142032, ISSN: 0002-7863, DOI: 10.1021/JA983267V *
LOURIDO SEBASTIAN ET AL: "Calcium - dependent protein kinase 1 is an essential regulator of exocytosis in Toxoplasma", NATURE, vol. 465, no. 7296, 20 May 2010 (2010-05-20), NATURE PUBLISHING GROUP, LONDON, GB, pages 359 - 362, XP009147814, ISSN: 0028-0836, DOI: 10.1038/NATURE09022 *
OJO K K ET AL: "Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors", NATURE STRUCTURAL AND MOLECULAR BIOLOGY, vol. 17, no. 5, May 2010 (2010-05-01), NATURE PUBLISHING GROUP USA, pages 602 - 607+METHOD, XP002635429, ISSN: 1545-9993 *

Cited By (24)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2015532287A (en) * 2012-09-26 2015-11-09 ザ・リージエンツ・オブ・ザ・ユニバーシテイー・オブ・カリフオルニア IRE1 regulation
US11613544B2 (en) 2012-09-26 2023-03-28 The Regents Of The University Of California Substituted imidazo[1,5-a]pyrazines for modulation of IRE1
US10131668B2 (en) 2012-09-26 2018-11-20 The Regents Of The University Of California Substituted imidazo[1,5-a]pYRAZINES for modulation of IRE1
US10822340B2 (en) 2012-09-26 2020-11-03 The Regents Of The University Of California Substituted imidazolopyrazine compounds and methods of using same
WO2014081922A1 (en) * 2012-11-21 2014-05-30 The Trustees Of The University Of Pennsylvania Compositions and methods useful in preventing and treating apicomplexa infections
WO2014189947A1 (en) 2013-05-20 2014-11-27 University Of Washington Through Its Center For Commercialization 5-aminopyrazole-4-carboxamide inhibitors of cdpk1 from t. gondii and c. parvum
US9518026B2 (en) 2013-05-20 2016-12-13 University Of Washington Through Its Center For Commercialization 5-aminopyrazole-4-carboxamide inhibitors of CDPK1 from T. gondii and C. parvum
US9956214B2 (en) 2013-05-20 2018-05-01 University Of Washington Through Its Center For Commercialization 5-aminopyrazole-4-carboxamide inhibitors of CDPK1 from T. gondii and C. parvum
WO2015079251A1 (en) * 2013-11-29 2015-06-04 Cancer Research Technology Limited Quinazoline compounds
WO2015146929A1 (en) * 2014-03-24 2015-10-01 武田薬品工業株式会社 Heterocyclic compound
CN106459040A (en) * 2014-03-24 2017-02-22 武田药品工业株式会社 Heterocyclic compound
US10196397B2 (en) 2014-11-19 2019-02-05 Sun Pharmaceutical Industries Limited Process for the preparation of ibrutinib
US10307425B2 (en) 2015-01-26 2019-06-04 University Of Washington Compositions and methods for treating toxoplasmosis, cryptosporidiosis and other apicomplexan protozoan related diseases
US10350211B2 (en) 2015-01-26 2019-07-16 University Of Washington Bumped kinase inhibitor compositions and methods for treating cancer
US10632122B2 (en) 2015-01-26 2020-04-28 University Of Washington Compositions and methods for treating toxoplasmosis, cryptosporidiosis and other apicomplexan protozoan related diseases
AU2016211630B2 (en) * 2015-01-26 2021-03-25 University Of Washington Compositions and methods for treating toxoplasmosis, cryptosporidiosis and other apicomplexan protozoan related diseases
WO2016123152A1 (en) * 2015-01-26 2016-08-04 University Of Washington Compositions and methods for treating toxoplasmosis, cryptosporidiosis and other apicomplexan protozoan related diseases
US10294227B2 (en) 2015-05-21 2019-05-21 University Court Of The University Of Edinburgh Compounds
US10844067B2 (en) 2016-04-15 2020-11-24 Cancer Research Technology Limited Heterocyclic compounds as RET kinase inhibitors
US10954241B2 (en) 2016-04-15 2021-03-23 Cancer Research Technology Limited Heterocyclic compounds as ret kinase inhibitors
US11548896B2 (en) 2016-04-15 2023-01-10 Cancer Research Technology Limited Heterocyclic compounds as RET kinase inhibitors
US11661423B2 (en) 2016-04-15 2023-05-30 Cancer Research Technology Limited Heterocyclic compounds as RET kinase inhibitors
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US11680068B2 (en) 2017-04-13 2023-06-20 Cancer Research Technology Limited Compounds useful as RET inhibitors

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