WO2003051896A1

WO2003051896A1 - Cytidine libraries and compounds synthesized by solid-phase combinatorial strategies

Info

Publication number: WO2003051896A1
Application number: PCT/US2002/035558
Authority: WO
Inventors: Haoyun An; Jean-Luc Girardet; Yili Ding; Dinesh Barawkar; Zhi Hong
Original assignee: Ribapharm Inc.
Priority date: 2001-12-17
Filing date: 2002-11-05
Publication date: 2003-06-26
Also published as: AU2002340387A1

Abstract

Substituted cytidine nucleoside analog libraries and compounds in such libraries are prepared in a combinatorial library approach. Particularly preferred heterocyclic bases in such compounds and libraries include amino acid substituted cytidine nucleosides, 2'-O-substituted cytidine nucleosides, and N-substituted cytidine nucleosides, all of which may be useful in the treatment of various conditions, particularly viral infections and neoplastic diseases.

Description

CYTIDINE LIBRARIES AND COMPOUNDS SYNTHESIZED BY SOLID-PHASE

COMBINATORIAL STRATEGIES

Field of The Invention The field of the invention is combinatorial nucleoside libraries and related compounds.

Background of The Invention

Nucleosides and related compounds interact with many biological targets, and some nucleoside analogues have been used as antimetabolites for treatment of cancers and viral infections. After entry into the cell, many nucleoside analogues can be phosphorylated to monophosphates by nucleoside kinases, and then further phosphorylated by nucleoside monophosphate kinases and nucleoside diphosphate kinases to give nucleoside triphosphates. Once a nucleoside analogue is converted to its triphosphate inside the cell, it can be incorporated into DNA or RNA. Incorporation of certain unnatural nucleoside analogues into nucleic acid replicates or transcripts can interrupt gene expression by early chain termination, or by interfering with function of the modified nucleic acids. In addition, certain nucleoside analogue triphosphates are very potent, competitive inhibitors of DNA or RNA polymerases, which can significantly reduce the rate at which the natural nucleoside can be incorporated. Many anti-HIV nucleoside analogues fall into this category, including 3'-C-azido-3'- deoxythymidine, 2',3'-dideoxycytidine, 2',3'-dideoxyinosine, and 2',3'-didehydro-2',3'- dideoxythymidine.

Various nucleoside analogues can also act in other ways, for example, causing apoptosis of cancer cells and/or modulating immune systems. In addition to nucleoside antimetabolites, a number of nucleoside analogues that show very potent anticancer and antiviral activities act through still other mechanisms. Some well-known nucleoside anticancer drugs are thymidylate synthase inhibitors such as 5-fluorouridine, and adenosine deaminase inhibitors such as 2-chloroadenosine. A well-studied anticancer compound, neplanocin A, is an inhibitor of S-adenosylhomocysteine hydrolase, which shows potent anticancer and antiviral activities.

Among various nucleoside and nucleotide analogs, cytidine nucleoside analogs have shown significant antiviral and antineoplastic activity (see e.g., Carbone et al., Biochem Pharmacol. 2001 Jul 1;62(1):101-10; or Miura et al., Jpn J Cancer Res. 2001 May;92(5):562- 7; or Christensen et al., Antiviral Res. 2000 Nov;48(2):131-42). Many of those cytosine analogs, however, have relatively significant side effects. Moreover, numerous of the cytosine analogs have modifications in the sugar moiety while retaining the pyrimidine portion unchanged.

Unfortunately, many of the known nucleoside analogues that inhibit tumor growth or viral infections are also toxic to normal mammalian cells, primarily because these nucleoside analogues lack adequate selectivity between the normal cells and the virus-infected host cells or cancer cells. For this reason many otherwise promising nucleoside analogues fail to become therapeutics in the treatment of various diseases.

Selective inhibition of cancer cells or host cells infected by viruses has been an important subject for some time, and tremendous efforts have been made to search for more selective nucleoside analogues. In general, however, a large pool of nucleoside analogues is thought to be necessary in order to identify highly selective nucleoside analogues. Unfortunately, the classical method of synthesizing nucleosides and nucleotides having desired physiochemical properties, and then screening them individually, takes a significant amount of time to identify a lead molecule. Although thousands of nucleoside analogues were synthesized over the past decades, if both sugar and base modifications are considered, many additional analogues are still waiting to be synthesized.

During the last few years, combinatorial chemistry has been used to generate huge numbers of organic compounds other than nucleosides, nucleotides, and their analogs resulting in large compound libraries. If nucleosides, nucleotides, and their analogs could be made through a combinatorial chemistry approach, a large number of such compounds could be synthesized within months instead of decades, and large libraries could be developed.

A combinatorial chemistry approach to nucleosides may also encourage a focus beyond previously addressed biological targets. For example, in the past nucleoside analogues were usually designed as potential inhibitors of DNA or RNA polymerases and several other enzymes and receptors, including inosine monophosphate dehydrogenase, protein kinases, and adenosine receptors. If a vast number of diversified nucleoside analogues could be created, their use may be far beyond these previously recognized biological targets, which would open a new era for the use of nucleoside analogues as human therapeutics.

The generation of combinatorial libraries of chemical compounds by employing solid phase synthesis is well known in the art. For example, Geysen, et al. (Proc. Natl. Acac. Sci. USA, 3998 (1984)) describes the construction of a multi-amino acid peptide library; Houghton, et al. (Nature, 354, 84 (1991)) describes the generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery; and Lam, et al. (Nature, 354, 82 (1991)) describes a method of synthesis of linear peptides on a solid support such as polystyrene or polyacrylamide resin.

Although a combinatorial chemistry approach has been proven to work well with many types of compounds, there are numerous problems with the generation of nucleoside libraries. Among numerous other difficulties, most nucleoside analogues contain a sugar moiety and a nucleoside base, which are linked together through a glycosidic bond. The formation of the glycosidic bond can be achieved through a few types of condensation reactions. However, most of the reactions do not give a good yield of desired products, which may not be suitable to generations of nucleoside libraries. Moreover, the glycosidic bonds in many nucleosides are in labile to acidic condition, and many useful reactions in combinatorial chemistry approaches cannot be used in the generation of nucleoside analogue libraries. As a result, many researchers focused their attention to areas in pharmaceutical chemistry that appear to present easier access to potential therapeutic molecules, and there seems to be a lack of methods for generating libraries of nucleosides and nucleotides using solid phase synthesis. Therefore, there is still a need to provide methods for generation of nucleoside and nucleotide libraries, and especially substituted and modified cytidine libraries and library compounds.

Summary of the Invention The present invention is directed to cytidine libraries and library compounds within these libraries. In one aspect of the inventive subject matter, an amino acid substituted cytidine library will comprise library compounds according to Formula 1 A or IB

Formula 1A Formula IB'

wherein A, X, Y, Z, Ri, and R₂ are defined as in the respective portions of the detailed description below.

In another aspect of the inventive subject matter, a 2'-O-alkylcytidine library will comprise library compounds according to Formula 2C and 2D

ula 2D

wherein X, Y, R_t, R₂, and R₃ are defined as in the respective portions of the detailed description below. Additionally, further contemplated 2'-O-alkyl substituted libraries include libraries and compounds according to Formulae 2E and 2F (2'O-methyl-N4-substituted cytidines)

wherein the substituents OPG , •, and R are defined as in the respective portions of the detailed description below. Further contemplated libraries will comprise library compounds according to Formulae 2G and 2H

wherein the substituents R, Ri, and R₂ are defined as described in the respective portions of the detailed description.

In a still further aspect of the inventive subject matter, an N-substituted cytidine library will comprise library compounds according to Formulae 3 A and 3B

Formula 3A'

wherein X, Y, R, and R_\ through R_ό are defined as in the respective portions of the detailed description below.

In yet another aspect of the inventive subject matter, contemplated nucleoside libraries and compounds include compounds according to Formula 21, 2K, 2M, or 20

Formula 21 Formula 2K

Formula 20

wherein A, Ri, R₂, and R₃ are defined as in the respective portions of the detailed description below.

In still further aspects of the inventive subject matter, contemplated nucleoside libraries and compounds include compounds according to Formula 2U, 2V, or 2W

Structure 2U Structure 2V Structure 2W wherein X, Y, Z, R, Ri, R₂, R₃ and R4 are defined as in the respective portions of the detailed description below.

In yet another aspect of the inventive subject matter, contemplated nucleoside libraries and compounds include compounds according to Formula 2Z

Structure 2Z

wherein R is defined as in the respective portions of the detailed description below.

Various objects, features, aspects and advantages of the present invention will become more apparent from the following detailed description of preferred embodiments of the invention. Detailed Description

The term "nucleoside library" as used herein refers to a plurality of chemically distinct nucleosides, nucleotides, nucleoside analogs, and/or nucleotide analogs wherein at least some of the nucleosides, nucleotides, nucleoside analogs, and/or nucleotide analogs include, or have been synthesized from a common precursor.

For example, a plurality of nucleosides, nucleotides, nucleoside analogs, and/or nucleotide analogs that were prepared using l'-azido or l'-amino ribofuranose as a building block/precursor is considered a nucleoside library under the scope of this definition. Therefore, the term "common precursor" may encompass a starting material in a first step in a synthesis as well as a synthesis intermediate (i.e., a compound derived from a starting material). In another example, at least one step in the synthesis of one of the nucleosides, nucleotides, nucleoside analogs, and/or nucleotide analogs is concurrent with at least one step in the synthesis of another one of the nucleosides, nucleotides, nucleoside analogs, and/or nucleotide analogs, and synthesis is preferably at least partially automated. In contrast, a collection of individually synthesized nucleosides, nucleotides, nucleoside analogs, and/or nucleotide analogs, and especially a collection of compounds not obtained from a nucleoside library, is not considered a nucleoside library because such nucleosides, nucleotides, nucleoside analogs, and/or nucleotide analogs will not have a common precursor, and because such nucleosides, nucleotides, nucleoside analogs, and/or nucleotide analogs are not concurrently produced.

It is further generally contemplated that the complexity of contemplated libraries is at least 20 distinct nucleosides, nucleotide, nucleoside analogs, and/or nucleotide analogs, more typically at least 100 distinct nucleosides, nucleotide, nucleoside analogs, and/or nucleotide analogs, and most typically at least 1000 distinct nucleosides, nucleotide, nucleoside analogs, and/or nucleotide analogs. Consequently, a typical format of a nucleoside library will include multi-well plates, or a plurality of small volume (i.e., less than 1ml) vessels coupled to each other. The term "library compound" as used herein refers to a nucleoside, nucleotide, nucleoside analog, and/or nucleotide analog within a nucleoside library.

As also used herein, the terms "heterocycle" and "heterocyclic base" are used interchangeably herein and refer to any compound in which a plurality of atoms form a ring via a plurality of covalent bonds, wherein the ring includes at least one atom other than a carbon atom. Particularly contemplated heterocyclic bases include 5- and 6-membered rings with nitrogen, sulfur, or oxygen as the non-carbon atom (e.g., imidazole, pyrrole, triazole, dihydropyrimidine). Further contemplated heterocylces may be fused (i.e., covalently bound) to another ring or heterocycle, and are thus termed "fused heterocycle" or "fused heterocyclic base" as used herein. Especially contemplated fused heterocycles include a 5-membered ring fused to a 6-membered ring (e.g., purine, pyrrolo[2,3-d]pyrimidine), and a 6-membered ring fused to another 6-membered or higher ring (e.g., pyrido[4,5-d]pyrimidine, benzodiazepine). Examples of these and further preferred heterocyclic bases are given below. Still further contemplated heterocyclic bases may be aromatic, or may include one or more double or triple bonds. Moreover, contemplated heterocyclic bases and fused heterocycles may further be substituted in one or more positions (see below).

As further used herein, the term "sugar" refers to all carbohydrates and derivatives thereof, wherein particularly contemplated derivatives include deletion, substitution or addition of a chemical group or atom in the sugar. For example, especially contemplated deletions include 2'-deoxy and/or 3'-deoxy sugars. Especially contemplated substitutions include replacement of the ring-oxygen with sulfur or methylene, or replacement of a hydroxyl group with a halogen, an amino-, sulfhydryl-, or methyl group, and especially contemplated additions include methylene phosphonate groups. Further contemplated sugars also include sugar analogs (i.e., not naturally occurring sugars), and particularly carbocyclic ring systems. The term " carbocyclic ring system" as used herein refers to any molecule in which a plurality of carbon atoms form a ring, and in especially contemplated carbocyclic ring systems the ring is formed from 3, 4, 5, or 6 carbon atoms. Examples of these and further preferred sugars are given below.

The term "nucleoside" refers to all compounds in which a heterocyclic base is covalently coupled to a sugar, and an especially preferred coupling of the nucleoside to the sugar includes a Cl'-(glycosidic) bond of a carbon atom in a sugar to a carbon- or heteroatom (typically nitrogen) in the heterocyclic base. The term "nucleoside analog" as used herein refers to all nucleosides in which the sugar is not a ribofuranose and/or in which the heterocyclic base is not a naturally occurring base (e.g., A, G, C, T, I, etc.). Similarly, the term "nucleotide" refers to a nucleoside to which a phosphate group is coupled to the sugar. Likewise, the term "nucleotide analog" refers to a nucleoside analog to which a phosphate group is coupled to the sugar. It should further be particularly appreciated that the terms nucleoside, nucleotide, nucleoside analog, and/or nucleotide analog also includes all prodrug forms of a nucleoside, nucleotide, nucleoside analog, and/or nucleotide analog, wherein the prodrug form may be activated/converted to the active drug/nucleoside, nucleotide, nucleoside analog, and/or nucleotide analog in one or more than one step, and wherein the activation/conversion of the prodrug into the active drug/nucleoside, nucleotide, nucleoside analog, and/or nucleotide analog may occur intracellularly or extracellularly (in a single step or multiple steps). Especially contemplated prodrug forms include those that confer a particular specificity towards a diseased or infected cell or organ, and exemplary contemplated prodrug forms are described in "Prodrugs" by Kenneth B. Sloan (Marcel Dekker; ISBN: 0824786297), "Design of Prodrugs" by Hans Bundgaard (ASIN: 044480675X), or in copending US application number 09/594410, filed 06/16/2000, all of which are incorporated by reference herein. Particularly suitable prodrug forms of the above compounds may include a moiety that is covalently coupled to at least one of the C2'-OH, C3'-OH, and C5'-OH, wherein the moiety is preferentially cleaved from the compound in a target cell (e.g., Hepatocyte) or a target organ (e.g., liver). While not limiting to the inventive subject matter, it is preferred that cleavage of the prodrug into the active form of the drug is mediated (at least in part) by a cellular enzyme, and particularly receptor, transporter and cytochrome-associated enzyme systems (e.g., CYP- system).

Especially contemplated prodrugs comprise a cyclic phosphate, cyclic phosphonate and or a cyclic phosphoamidates, which are preferentially cleaved in a hepatocyte to produce contemplated compounds. There are numerous such prodrugs known in the art, and all of those are considered suitable for use herein. However, especially contemplated prodrug forms are disclosed in WO 01/47935 (Novel Bisamidate Phosphonate Prodrugs), WO 01/18013 (Prodrugs For Liver Specific Drug Delivery), WO 00/52015 (Novel Phosphorus-Containing Prodrugs), and WO 99/45016 (Novel Prodrugs For Phosphorus-Containing Compounds), all of which are incorporated by reference herein. Consequently, especially suitable prodrug forms include those targeting a hepatocyte or the liver.

Still further particularly preferred prodrugs include those described by Renze et al. in Nucleosides Nucleotides Nucleic Acids 2001 Apr-Jul;20(4-7):931-4, by Balzarini et al. in Mol Pharmacol 2000 Nov;58(5):928-35, or in U.S. Pat. No. 6,312,662 to Erion et al., U.S. Pat. No. 6,271,212 to Chu et al., U.S. Pat. No. 6,207,648 to Chen et al., U.S. Pat. No. 6,166,089 and U.S. Pat. No. 6,077,837 to Kozak, U.S. Pat. No. 5,728,684 to Chen, and published U.S. Patent Application with the number 20020052345 to Erion, all of which are incorporated by reference herein. Alternative contemplated prodrugs include those comprising a phosphate and/or phosphonate non-cyclic ester, and an exemplary collection of suitable prodrugs is described in U.S. Pat. No. 6,339,154 to Shepard et al., U.S. Pat. No. 6,352,991 to Zemlicka et al, and U.S. Pat. No. 6,348,587 to Schinazi et al. Still further particularly contemplated prodrug forms are described in FASEB J. 2000 Sep;14(12):1784- 92, Pharm. Res. 1999, Aug 16:8 1179-1185, and Antimicrob Agents Chemother 2000, Mar 44:3 477-483, all of which are incorporated by reference herein.

The terms "alkyl" and "unsubstituted alkyl" are used interchangeably herein and refer to any linear, branched, or cyclic hydrocarbon in which all carbon-carbon bonds are single bonds. The terms "alkenyl" and "unsubstituted alkenyl" are used interchangeably herein and refer to any linear, branched, or cyclic alkyl with at least one carbon-carbon double bond. Furthermore, the terms "alkynyl" and "unsubstituted alkynyl" are used interchangeably herein and refer to any linear, branched, or cyclic alkyl or alkenyl with at least one carbon-carbon triple bond. The terms "aryl" and "unsubstituted aryl" are used interchangeably herein and refer to any aromatic cyclic alkenyl or alkynyl. The term "alkaryl" is employed where an aryl is covalently bound to an alkyl, alkenyl, or alkynyl.

The term "substituted" as used herein refers to a replacement of an atom or chemical group (e.g. , H, NH₂, or OH) with a functional group, and particularly contemplated functional groups include nucleophilic groups (e.g., -NH₂, -OH, -SH, -NC, etc.), electrophilic groups (e.g., C(O)OR, C(X)OH, etc.), polar groups (e.g., -OH), non-polar groups (e.g., aryl, alkyl, alkenyl, alkynyl, etc.), ionic groups (e.g., -N *), and halogens (e.g., -F, -Cl), and all chemically reasonable combinations thereof. Thus, the term "functional group" as used herein refers to a nucleophilic group (e.g., -NH₂, -OH, -SH, -NC, -CN etc.), an electrophilic group (e.g., C(O)OR, C(X)OH, C(Halogen)OR, etc.), a polar group (e.g., -OH), a non-polar group {e.g., aryl, alkyl, alkenyl, alkynyl, etc.), an ionic group (e.g., -NH₃ ^-1;, and a halogen.

Contemplated Sugars

It is contemplated that suitable sugars will have a general formula of C_nH_2nO_n, wherein n is between 2 and 8, and wherein (where applicable) the sugar is in the D- or L-configuration. Moreover, it should be appreciated that there are numerous equivalent modifications of such sugars known in the art (sugar analogs), and all of such modifications are specifically included herein. For example, some contemplated alternative sugars will include sugars in which the heteroatom in the cyclic portion of the sugar is an atom other than oxygen (e.g., sulfur, carbon, or nitrogen) analogs, while other alternative sugars may not be cyclic but in a linear (open-chain) form. Suitable sugars may also include one or more double bonds. Still further specifically contemplated alternative sugars include those with one or more non-hydroxyl substituents, and particularly contemplated substituents include mono-, di-, and triphosphates (preferably as C₅' esters), alkyl groups, alkoxy groups, halogens, amino groups and amines, sulfur-containing substituents, etc. Particularly contemplated modifications include substituted ribofuranoses, wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atom, with R being Ci-io alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CC1₃, CC1₂H, CH₂OH, CN, COOR', and CONHR, and with R being C_MO alkyl, alkenyl, alkynyl, aryl. It is still further contemplated that all contemplated substituents (hydroxyl substituents and non-hydroxyl substituents) may be directed in the alpha or beta position.

Numerous of the contemplated sugars and sugar analogs are commercially available. However, where contemplated sugars are not commercially available, it should be recognized that there are various methods known in the art to synthesize such sugars. For example, suitable protocols can be found in "Modern Methods in Carbohydrate Synthesis" by Shaheer H. Khan (Gordon & Breach Science Pub; ISBN: 3718659212), in U.S. Pat Nos. 4,880,782 and 3,817,982, in WO88/00050, or in EP 199,451. An exemplary collection of further contemplated sugars and sugar analogs is depicted below, wherein all of the exemplary sugars may be in D- or L-configuration, and wherein at least one of the substituents may further be in either alpha or beta orientation.

H& tH₃/R/CF₃ HO* tlH Hef ^') H

N, S^)H

X, Y,Z = θ,S, Se, NH, NR, CH₂, CHR.P(O), P(0)OR

R = H,OH,NHR,halo,CH₂OH,COOH,N₃, alkyl, aryl, alkynyl, heterocycles, OR, SR, P(θ)(θ R)₂

OCOR.NHCOR, NHS0₂ ,NH₂NH₂, amidine, substituted amidine.quanidine, substituted gyanidine

An especially contemplated class of sugars comprises alkylated sugars, wherein one or more alkyl groups (or other substituents, including alkenyl, alkynyl, aryl, halogen, CF₃, CHF₂, CC1₃, CHCI₂, N₃, NH₂, etc.) are covalently bound to sugar at the C',, C^C^d, or C₅ atom. In such alkylated sugars, it is especially preferred that the sugar portion comprises a furanose (most preferably a D- or L-ribofuranose), and that at least one of the alkyl groups is a methyl group. Of course, it should be recognized that the alkyl group may or may not be substituted with one or more substituents. One exemplary class of preferred sugars is depicted below:

in which B is hydrogen, hydroxyl, or a heterocyclic base, R is independently hydrogen, hydroxyl, substituted or unsubstituted alkyl (branched, linear, or cyclic), with R including between one and twenty carbon atoms.

Contemplated Heterocyclic Bases It is generally contemplated that all compounds in which a plurality of atoms (wherein at least one atom is an atom other than a carbon atom) form a ring via a plurality of covalent bonds are considered a suitable heterocyclic base. However, particularly contemplated heterocyclic bases have between one and three rings, wherein especially preferred rings include 5- and 6-membered rings with nitrogen, sulfur, or oxygen as the non-carbon atom (e.g., imidazole, pyrrole, triazole, dihydropyrimidine). Further contemplated heterocylces may be fused (i.e., covalently bound) to another ring or heterocycle, and are thus termed "fused heterocycle" as used herein. Especially contemplated fused heterocycles include a 5- membered ring fused to a 6-membered ring (e.g., purine, pyrrolo[2,3-d]pyrimidine), and a 6-membered ring fused to another 6-membered or higher ring (e.g., pyrido[4,5-d]pyrimidine, benzodiazepine). While cytidine heterocyclic bases are especially contemplated, an exemplary collection of alternative heterocyclic bases is depicted below, wherein all of the depicted heterocyclic bases may further include one or more substituents, double and triple bonds, and any chemically reasonable combination thereof. It should further be appreciated that all of the contemplated heterocyclic bases may be coupled to contemplated sugars via a carbon atom or a non-carbon atom in the heterocyclic base.

Contemplated Solid Phases

It is generally contemplated that all known types of solid phases are suitable for use herein, so long as contemplated nucleosides (or sugar, or heterocyclic base) can be coupled to such solid phases, and so long as the coupled nucleoside (or sugar, or heterocyclic base) will remain coupled to the solid phase during at least one chemical reaction on the nucleoside (or sugar, or heterocyclic base). Especially contemplated solid phases (i.e., solid supports) include Merrifield resins, ArgoGel (available from Argonaut, San Francisco, CA), Sasrin resin (a polystyrene resin available from Bachem Bioscience, Switzerland), TentaGel S AC, TentaGel PHB, or TentaGel S NH₂ resin (polystyrene-polyethylene glycol copolymer resins available from Rappe Polymere, Tubingen, Germany). Alternatively, contemplated solid supports may also include glass, as described in U. S. Pat. No. 5,143,854. Another preferred solid support comprises a "soluble" polymer support, which may be fabricated by copolymerization of polyethylene glycol, polyvinylalcohol, or polyvinylalcohol with polyvinyl pyrrolidine or derivatives thereof (e.g., see Janda and Hyunsoo (1996) Methods Enzymol. 267:234-247; Gravert and Janda (1997) Chemical Reviews 97:489-509; and Janda and Hyunsoo, PCT publication No. WO 96/03418).

Consequently, it should be recognized that there are numerous methods of coupling nucleosides, sugars, or heterocyclic bases to solid phases that may be appropriate, and a particular method will generally depend on the particular type of solid phase and/or type of sugar. Thus, all of such known methods are contemplated suitable for use herein, and exemplary suitable solid phase coupling reactions are described, for example, in "Organic Synthesis on Solid Phase - Supports, Linkers, Reactions" by Florencio Zaragoza Dorwald et al. John Wiley & Sons; ISBN: 3527299505, or in "Solid-Phase Synthesis and Combinatorial Technologies" by Pierfausto Seneci, John Wiley & Sons; ISBN: 0471331953.

Contemplated Combinatorial Reactions

It is generally contemplated that all known types of combinatorial reactions and/or reaction sequences may be used in conjunction with the teaching presented herein so long as such combinatorial reactions between a substrate and at least two distinct reagents will result in at least two distinct products. Contemplated combinatorial reactions and/or reaction sequences may therefore be performed sequentially, in parallel, or in any chemically reasonable combination thereof. It is still further contemplated that suitable combinatorial reactions and/or reaction sequences may be performed in a single compartment or multiple compartments. Preferred combinatorial reactions and/or reaction sequences include at least one step in which a substrate or reaction intermediate is coupled to a solid phase (which may include the wall of the reaction compartment or a solid or soluble polymers), and that the solid phase is physically separated from another substrate on another solid phase. While not limiting to the inventive subject matter, it is generally preferred that contemplated solid phase synthesis is at least partially automated. There are numerous methods and protocols for combinatorial chemistry known in the art, and exemplary suitable protocols and methods are described in "Solid-Phase Synthesis and Combinatorial Technologies" by Pierfausto Seneci (John Wiley & Sons; ISBN: 0471331953) or in "Combinatorial Chemistry and Molecular Diversity in Drug Discovery" by Eric M. Gordon and James F. Kerwin (Wiley-Liss; ISBN: 0471155187).

Contemplated Libraries and Nucleosides

The inventors have discovered that nucleoside analog libraries, and especially cytidine nucleoside libraries, library compounds and their analogs can be prepared in various combinatorial library approaches. Particularly preferred approaches include those in which diverse heterocyclic bases and/or diverse nucleoside substituents are prepared from precursor nucleosides that are modified in a series of at least two subsequent and/or parallel modification reactions. Some of these exemplary libraries are described in more detail below.

Amino Acid substituted Cytidine Libraries

In a particularly preferred aspect of the inventive subject matter, the inventors have discovered that amino acid substituted cytidine libraries may be produced following a general synthetic procedure as described in Scheme 1 below. Here, 5-bromouridine is converted to the corresponding 5-amino uridine, which is then used as a nucleophilic substrate in a reaction with a first set of reagents (e.g. , activated and/or protected amino acids) to form a first set of amino acid derivatives of the nucleoside. The so produced amino acid derivatives of the nucleoside are then coupled to a solid phase and the remaining sugar hydroxyl groups are protected. Further diversification is then achieved by converting at least one of the two keto groups in the heterocyclic base into a leaving group (e.g., nitrotriazole), which is then replaced with a second set of substrates in a nucleophilic substitution reaction. Alternatively, the amino group in the amino acid (that is attached to the heterocyclic base) may be employed as a nucleophile to displace the leaving group and consequently to form a ring structure in an intramolecular reaction.

Schem e 1

With respect to the nucleoside, it should be recognized that 5-bromouridine is a preferred starting material and commercially available from various sources. However, it should also be appreciated that numerous alternative reagents are also suitable. For example, there are various 5-bromouracil analogs (e.g., substituted and unsubstituted deoxy- and dideoxy analogs) commercially available. Moreover, it should be recognized that suitable nucleoside analogs may also be prepared with sugar moieties other than a ribofuranose fiom a coupling reaction between (commercially available) 5-bromouracil and a suitable sugar following standard coupling procedures well known in the art.

Particularly contemplated sugars include various substituted ribofuranoses, carbocyclic ring systems with 5 or 6 carbon atoms, and arabinose, wherein the sugar is in a D-configuration or in an L-configuration. Further contemplated sugars include those previously described in the section entitled "Contemplated Sugars", and it is especially contemplated that where the sugar has a C₂' and/or C₃' substituent other than a hydroxyl group, alternative sugars may include hydrogen, a methyl group, a halogen, or an azide group in at least one of these positions (in either alpha or beta orientation).

Consequently, the nature of protecting groups for the sugar will vary considerably, and while it is particularly contemplated that suitable protection groups include benzyl-, acetyl-, and TBDMS groups, numerous alternative protection groups are also considered suitable. Among other groups, a collection of appropriate alternative protection groups and their reactions is described in Protective Groups in Organic Synthesis by Peter G. M. Wuts, Theodora W. Greene, John Wiley & Sons; ISBN: 0471160199.

Furthermore, the solid phase and methods of coupling the solid phase to the nucleoside will at least in part depend on the particular sugar and position of coupling. Therefore, it is contemplated that all known solid phases are suitable for use in conjunction with the teachings presented herein, and exemplary suitable solid phases are described, for example, in Organic Synthesis on Solid Phase - Supports, Linkers, Reactions; by Florencio Zaragoza Dorwald et al. John Wiley & Sons; ISBN: 3527299505, or in Solid-Phase Synthesis and Combinatorial Technologies by Pierfausto Seneci, John Wiley & Sons; ISBN: 0471331953. Preferred solid phases, however, include Merrifield resins, ArgoGel (available from Argonaut, San Francisco, CA), Sasrin resin (a polystyrene resin available from Bachem Bioscience, Switzerland), TentaGel S AC, TentaGel PHB, or TentaGel S NH₂ resin (polystyrene-polyethylene glycol copolymer resins available from Rappe Polymere, Tubingen, Germany).

It should further be appreciated that various alternative heterocyclic bases are also appropriate and particularly contemplated alternative heterocyclic bases include pyrimidine heterocyclic bases with at least one halogen substituent and at least one keto group. While not limiting to the inventive subject matter, alternative heterocyclic bases may further include substituents other than halogens and keto groups, and especially contemplated substituents include hydroxyls, amino groups, and azido groups. Suitable alternative heterocyclic bases include those listed above in the section entitled "Contemplated Heterocyclic Bases". With respect to the first set of reagents, it is generally preferred that such reagents are amino acids, which may be in D-or L-configuration. It should still further be appreciated that by coupling an amino acid to the heterocyclic base a chiral center may be introduced into the nucleoside. While it is generally preferred that suitable amino acids are naturally occurring amino acids, non-natural amino acids (e.g. , beta-amino acids, or amino acids including a halogen or heteroatom other than N, O, or S) are also contemplated. Among other compounds, suitable amino acids may have the general formula R-C(H)(NH₂)COOH, wherein R is hydrogen, a functional group, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl. Alternatively, suitable reagents may have the formula N(H)(R)COOH, N(H)(R)CSOH, or may be RSO H, wherein R is defined as above.

It is still further contemplated that numerous reagents other than amino acids are also suitable substrates for the first reaction with the amino group, so long as such reagents can react (with or without prior activation or catalyst) with the amino group of the heterocyclic base to form a covalent bond with the base. Consequently, an alternative first set of reagents especially include an electrophilic group (e.g., carboxylic acids which may or may not be branched, substituted, or include an aromatic moiety, and may have a general formula of R-COOH, wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl).

Similarly, a suitable second set of reagents will include all nucleophiles capable of reacting with the carbon atom in the heterocyclic base to which the nitrotriazole leaving group is attached to expel the leaving group from the base. Thus, particularly contemplated nucleophiles include R-NH₂, RR'NH, R-SH, or R-OH, wherein R can be hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl. Alternatively, suitable nucleophiles may also include Grignard reagents, or similarly reactive compounds.

Thus, it should be appreciated that nucleoside libraries with at least two library compounds can be synthesized, wherein one of the at least two library compounds has a structure according to Formula 1A with a first set of substituents A, X, Y, Ri, and R₂, wherein another one of the at least two library compounds has a structure according to Formula 1A with a second set of substituents A, X, Y, Ri, and R₂ Formula 1A

wherein A is a protected or unprotected sugar bound to a solid phase, Y is C=O, CONH, CSNH, or SO₂, and X is NH, NR', S, or O; and wherein R, R, and R₂ are independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl, and wherein not all of the substituents A, X, Y, Ri, and R₂ in the first set are the same as the substituents A, X, Y, Ri, and R₂ in the second set.

Thus, contemplated library compounds will include molecules according to formula 1 A (supra) wherein A is a protected or unprotected sugar, Y is C=O, CONH, CSNH, or SO₂, and X is NH, NR', S, or O; and wherein R', Ri and R₂ are independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl.

In especially preferred libraries, it is contemplated that the sugar is selected from the group consisting of a ribofuranose, a substituted ribofuranose, a carbocyclic ring system, and an arabinose, wherein the sugar is in a D-configuration or in an L-configuration, and wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atoms, with R being C_MO alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CC1₃, CC1₂H, CH₂OH, CN, COOR', and CONHR*, and with R being C ₀ alkyl, alkenyl, alkynyl, aryl.

2'-O-Alkyl-5-substituted Cytidine Libraries

In yet another aspect of the inventive subject matter, the inventors discovered that 2'-O-alkylcytidine libraries can be generated using a procedure as outlined in Scheme 2A below, in which a substituted dihydropyrimidine nucleoside (here: 5-iodouridine) is first converted to the corresponding 2'-O-substituted pyrimidine and bound to a solid phase. The 2'-O-substituted pyrimidine is further reacted with a first set of reagents in a Heck reaction to form a first set of products using a first set of reagents. At least one of the keto groups in the pyrimidine moiety of a first set of products is then reacted with TIPS to generate a leaving group, which is subsequently exchanged with a nucleophilic reagent (second set of reagents), thereby generating a second set of products that may further be derivatized if the reactive group is present (e.g., -NH₂ group).

R¹ O

TBD SC? CH₃

j TBAF I TBAF

Scheme 2 A

With respect to the nucleoside, it should be recognized that 5-iodouracil is a preferred starting material and commercially available from various sources. However, it should also be appreciated that numerous alternative reagents are also suitable. For example, there are various 5-iodouracil analogs (e.g., substituted and unsubstituted deoxy- and dideoxy analogs) commercially available. Moreover, it should be recognized that suitable nucleoside analogs may also be prepared with sugar moieties other than a ribofuranose from a coupling reaction between (commercially available) 5-iodouracil and a suitable sugar following standard coupling procedures well known in the art.

Particularly contemplated alternative sugars include various substituted ribofuranoses, carbocyclic ring systems with 5 or 6 carbon atoms, and arabinose, wherein the sugar is in a D-configuration or in an L-configuration. Further contemplated sugars include those previously described in the section entitled "Contemplated Sugars", and it is especially contemplated that where the sugar has a C₂' and/or C₃' substituent other than a hydroxyl group, alternative sugars may include hydrogen, a halogen, or an azide group in at least one of these positions (in either alpha or beta orientation).

Consequently, the nature of protecting groups for the sugar will vary considerably, and while it is particularly contemplated that suitable protection groups include benzyl-, acetyl-, and TBDMS groups, numerous alternative protection groups are also considered suitable. Among other groups, a collection of appropriate alternative protection groups and their reactions is described in Protective Groups in Organic Synthesis by Peter G. M. Wuts, Theodora W. Greene, John Wiley & Sons; ISBN: 0471160199. Furthermore, the solid phase and methods of coupling the solid phase to the nucleoside will at least in part depend on the particular sugar and position of coupling. Therefore, it is contemplated that all known solid phases are suitable for use in conjunction with the teachings presented herein, and exemplary suitable solid phases are described, for example, in Organic Synthesis on Solid Phase - Supports, Linkers, Reactions; by Florencio Zaragoza Dorwald et al. John Wiley & Sons; ISBN: 3527299505, or in Solid-Phase Synthesis and Combinatorial Technologies by Pierfausto Seneci, John Wiley & Sons; ISBN: 0471331953. Preferred solid phases, however, include Merrifield resins, ArgoGel (available from Argonaut, San Francisco, CA), Sasrin resin (a polystyrene resin available from Bachem Bioscience, Switzerland), TentaGel S AC, TentaGel PHB, or TentaGel S NH₂ resin (polystyrene-polyethylene glycol copolymer resins available from Rappe Polymere, Tubingen, Germany).

It should further be appreciated that various alternative heterocyclic bases are also appropriate and particularly contemplated alternative heterocyclic bases include pyrimidine heterocyclic bases with at least one halogen substituent and at least one keto group. While not limiting to the inventive subject matter, alternative heterocyclic bases may also include substituents other than halogens and keto groups, and especially contemplated substituents include hydroxyls, amino groups, and azido groups. Suitable alternative heterocyclic bases include those listed above in the section entitled "Contemplated Heterocyclic Bases".

Preferred first sets of reagents include all reagents that can react in a Heck reaction with the heterocyclic base at the 5 -position to form a covalent bond with the heterocyclic base. Therefore, generally preferred first sets of reagents include those with a double or a triple bond, and particularly preferred first reagents will have a general structure of R-C≡CH, wherein R is hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl.

Alternatively, first sets of reagents may also include reagents that can react in a Stille reaction (coupling of a halogenide with an tin-organic compound with Pd as catalyst). Thus, suitable first reagents also include reagents of the general formula RSnR'₃, wherein R is defined as above, and R' is typically butyl. Many of contemplated first sets of reagents are commercially available, and all of these are considered suitable for use herein. Furthermore, it should be appreciated that where first sets of reagents are not commercially available, all or almost all of them can be produced following procedures well known in the art without expenditure of undue experimentation (see e.g., Advanced Organic Chemistry: Structure and Mechanisms (Part A) by Francis A. Carey, Richard J. Sundberg; Plenum Pub Corp; ISBN: 0306462435; or Advanced Organic Chemistry : Reactions and Synthesis (Part B) by Francis Carey, Richard J. Sundberg; Plenum Pub Corp; ISBN: 0306434571, or Compendium of Organic Synthetic Methods, Volume 9, by Michael B. Smith, John Wiley & Sons; ISBN: 0471145793).

With respect to the second set of reagents it is contemplated that such reagents generally include all reagents that can displace the leaving group attached to the heterocyclic base and particularly include NH₃, NH₂OH, RNH₂, RNHR, RNHNH₂, RONH₂, RNHOH, RSO₂NH₂, CN, N₃, and guanidine, wherein R is hydrogen, a functional group, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl.

It should further be especially noted that where the introduction of the second reagent generates a primary amino group (e.g., -NH₂ or -NHNH₂), the amino group can further be reacted with an activated ester or other electrophilic compound, including RCoA, RCOC1, RCSC1, RSO2C1, and various isothiocyanates and isocyanates (wherein R is defined as above). Many of the compounds in the second set of reagents are commercially available, and all of these are contemplated suitable for use herein. Moreover, it should be appreciated that where first sets of reagents are not commercially available, all or almost all of them can be produced following procedures well known in the art without expenditure of undue experimentation (see e.g., Advanced Organic Chemistry: Structure and Mechanisms (Part A) by Francis A. Carey, Richard J. Sundberg; Plenum Pub Corp; ISBN: 0306462435; or Advanced Organic Chemistry : Reactions and Synthesis (Part B) by Francis Carey, Richard J. Sundberg; Plenum Pub Corp; ISBN: 0306434571, or Compendium of Organic Synthetic Methods, Volume 9, by Michael B. Smith, John Wiley & Sons; ISBN: 0471145793).

Furthermore, it should be recognized that all of the contemplated 2'-O-alkyl nucleoside libraries and library compounds need not be restricted to a methyl as the alkyl substituent in the sugar moiety, but it should be appreciated that alternative alkyls are also suitable. For example, appropriate alkyls include straight and branched alkyls, which may or may not be further substituted. Consequently, contemplated 2'-O-substituted libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2A with a first set of substituents X, Ri , R₂, and R₃, and wherein another one of the at least two library compounds has a structure according to Formula 2 A with a second set of substituents X, Ri, R₂, and R₃

rmula 2A

wherein X is NH, NHO, NHNH, or ONH, and Ri is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl; R₂ is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, and a heterocyclic base; and R is selected from the group consisting of hydrogen, methyl, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, O-alkynyl; wherein • comprises a solid phase, wherein not all of the substituents X, Ri, R₂, and R₃ in the first set are the same as the substituents X, Rj, R₂, and R in the second set; and with the proviso that that R_\ is not H or CH3, when X-R₂ is NH2.

Similarly, contemplated 2'-O-substituted libraries may also have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2B with a first set of substituents X, Y, Ri, R₂, and R₃, and wherein another one of the at least two library compounds has a structure according to Formula 2B with a second set of substituents X, Y, Ri, R2, and R₃

wherein X is NH, NHO, NHNH, or ONH, and Y is CO, CS, SO₂, CONH, CSNH; Ri is selected from the group consisting of hydrogen an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl; R₂ is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, and a heterocyclic base; and R₃ is selected from the group consisting of hydrogen, methyl, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, O-alkynyl; wherein • comprises a solid phase, wherein not all of the substituents X, Ri, R₂, and R₃ in the first set are the same as the substituents X, Ri , R₂, and R₃ in the second set; and with the proviso that that Ri is not H or CH₃, when X-R₂ is NH₂.

Consequently, contemplated compounds will have a structure according to Formula 2C or 2D

wherein X is NH, NHO, NHNH, or ONH, and Y is CO, CS, SO₂, CONH, CSNH; R, is selected from the group consisting of hydrogen an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl; R₂ is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, and a heterocyclic base; and R₃ is selected from the group consisting of hydrogen, methyl, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, O-alkynyl; with the proviso that that Ri is not H or CH₃, when X-R₂ is NH₂.

Moreover, it should be recognized that while the sugar C2'- and C3'-substituents in Formulae 2A-2D are oriented in alpha orientation, one or more of the substituents may also be in beta orientation. In especially preferred nucleosides and nucleoside libraries where the sugar is selected from the group consisting of a ribofuranose, a substituted ribofuranose, a carbocyclic ring system, and an arabinose, and/or wherein the sugar is in a D-configuration or in an L-configuration, it is contemplated that the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atoms, with R being C_MO alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CC1₃, CC1₂H, CH₂OH, CN, COOR', and

CONHR, and with R' being C ₀ alkyl, alkenyl, alkynyl, aryl. 2'-O-Alkyl-N4-substituted Cytidine Libraries

Furthermore, the inventors discovered that 2'-O-methyl-N4-substituted cytidine libraries may be generated in a library approach in which 2'-O-methyluridine is coupled via the C5'-position to a solid support. The remaining hydroxyl (here: 3'-hydroxyl) groups are protected, and at least one of the keto groups of the heterocyclic base is reacted with a (preferably bulky) leaving group (here: TPS-C1). The so prepared nucleoside may then be reacted with a set of amine reagents that will replace the leaving group, and thereby form the N4-substituted cytidine. After replacement, the nucleoside may then be deprotected and split from the solid support. An exemplary synthetic route is depicted in Scheme 2B below:

TBD

With respect to the sugar, the solid phase, the protection groups, and the coupling of the protection groups to the sugar, the same considerations as described above for the 2'-O- alkyl-5-substituted cytidine libraries apply. Similarly, while 2'-O-methyluridine is the preferred and commercially available starting material, it should be recognized that various alternative 2' -O-alkyl nucleosides are also contemplated and especially include those 2'-O- alkyl nucleosides that have a heterocyclic base with at least one keto group. Thus, especially suitable alternative heterocyclic bases include various naturally occurring nucleosides (A,C,G,T,U, hypoxanthine), and derivatives thereof. Further contemplated alternative heterocyclic bases are described in the section with the title "Contemplated Heterocyclic Bases" above, and suitable leaving groups are all groups with sufficient reactivity to replace a keto group, and numerous such leaving groups are well known in the art.

Furthermore, suitable reagents to replace the leaving group (preferably OTPS) include all nucleophilic reagents, and particularly include various primary and secondary amines. Numerous primary and secondary amines are known in the art, and many of those are commercially available. However, particularly preferred reagents have the formula R-NH2 or RR"NH, wherein R and R' are independently hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl, or a substituted aryl.

Consequently, contemplated 2'O-methyl-N4-substituted cytidine libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2E with a first substituent R, and wherein another one of the at least two library compounds has a structure according to Formula 2E with a second substituent R

Formula 2E

wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl, O^PG is a protected hydroxyl, and wherein • comprises a solid phase, and wherein R in the one library compound is different from R in the second library compound. Thus, contemplated libraries include compounds according to Formula 2F

Formula 2F

wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl.

Furthermore, it should be recognized that while the sugar C2'- and C3'-substituents in Formulae 2E and 2F are oriented in alpha orientation, one or more of the substituents may also be in beta orientation.

2'-O-alkyl-5-substituted Uridine Libraries

Still further, the inventors discovered that various 2'-O-alkyl-5-substituted uridine libraries may be generated in a library approach in which uridine is first converted to a 2'-O- methyluridine, which is subsequently acetylated on the remaining sugar hydroxyl groups (here: 3' and 5'). The so prepared nucleoside is then iodinated in the 5-position of the heterocyclic ring, and the 3',5'-diacetylated 5-iodo-2'-O-methyluridine is then reacted with a first set of reagents in a Stille-type reaction to form the corresponding 5-substituted-2'-O- methyluridine. An exemplary reaction scheme is shown in Scheme 2C below.

14 15 16

19 18 17

Scheme 2C

It should generally be appreciated that suitable sugars need not be restricted to the sugar shown in Scheme 2C (ribofuranose), and numerous alternative sugars are also contemplated, including substituted ribofuranose, substituted or unsubstituted arabinose, xylose, and glucose. Further contemplated sugars are included in the section with the title "Contemplated Sugars". Similarly, with respect to the heterocyclic base it should be recognized that various alternative bases are also suitable, and exemplary alternative heterocyclic bases are described in the section entitled "Contemplated Heterocyclic Bases" above. However, it is generally preferred that suitable heterocyclic bases include pyrimidine bases.

Furthermore, it is contemplated that the (non-2'-hydroxyl) groups in the sugar may be derivatized with various acyls, and especially contemplated acyls have the general structure R-C(O)-, wherein R may be a substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or alkaryl.

Especially preferred first sets of reagents include various alkynyls and alkynyl derivatives, however, it should be appreciated that many compounds other than the below listed alkynyls (see examples) are also considered suitable for use herein and generally include all compounds that can replace iodine (preferably in a nucleophilic aromatic substitution). Consequently, particularly contemplated reagents include reagents that may replace iodine in a Stille-type reaction.

Therefore, contemplated 2'O-methyl-5-substituted uridine libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2G with a first substituent R, and wherein another one of the at least two library compounds has a structure according to Formula 2G with a second substituent R

Formula 2G

wherein R is an alkynyl or a substituted alkynyl, and wherein R in the first library compound is not the same as R in the second library compound. Thus, contemplated library compounds will have a structure according to Formula G wherein R is an alkynyl or a substituted alkynyl.

2'-O-alkyl-4-,5-disubstituted Cytidine Libraries

The inventors further discovered that the 5-substituted 2'-O-methyluridine library compounds (supra) may be employed as substrates in a further sequence of reactions in which at least one keto group (preferably the 4-oxo group) is replaced with a second set of substrates as depicted in Scheme 2D below.

19 20

21

24 23 22

Scheme 2D

In this exemplary approach, the 5-substituted 2'-O-methyluridine library compounds are covalently coupled to a solid phase (preferably at the C5'-OH, however, alternative positions are also contemplated and include the C3'-OH), and remaining sugar hydroxyls are protected (e.g., via acetylation). Then, the 4-oxo group is reacted to form a leaving group (e.g., OTPS), which is subsequently replaced with a suitable second reagent from a second set of reagents. With respect to the solid phase, the protecting groups, and the coupling of the sugar to the solid phase the same considerations as described above for 2'-O-alkyl-5- substituted cytidine libraries apply.

Particularly preferred second reagents include primary and secondary amines (i.e., R-NH₂ and RR'NH, wherein R and R' are independently hydrogen, alkyl, alkenyl, alkynyl, aryl, and aralkyl, all of which may or may not be substituted), however, it should be appreciated that all nucleophilic reagents that will replace the leaving group are also considered suitable herein. For example, alternative second reagents include R-OH, R-SH, (R as defined above) and various Grignard compounds.

Thus, contemplated 2'-O-methyl-4,5-disubstituted cytidine libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2H with a first set of substituents

and R₂, and wherein another one of the at least two library compounds has a structure according to Formula 2H with a second set of substituents Ri and R₂

Formula 2H

wherein Ri is an alkynyl or a substituted alkynyl, and R₂ is NRR' with R and R independently being hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl.

Alternatively, N4-substituted cytidine libraries may be produced from a 5 -(substituted alkynyl) substituted protected uridine as depicted below in Scheme 2E. Here, a 2'-O-methyl- 3',5'-acetylated uridine with a 5-alkynyl-l-ol substituent is bound to a solid phase via the alcohol group in the substituent of the uridine ring. Then, under similar conditions as already described above (coupling of a solid phase to the nucleoside, reaction to form a leaving group, deprotection and cleavage off the solid phase), at least one of the oxo-groups in the uridine heterocyclic base is reacted with TIPS-C1 to form a leaving group, and the leaving group is then replaced with a nucleophilic substituent. With respect to the sugar, protecting groups, the heterocyclic base, the leaving group, and the nucleophilic reagent, the same considerations as described above apply.

25 26

28

Scheme 2E 27

4,5-,6-trisubstituted Uridine/Cytidine Nucleoside Libraries

In a still further contemplated aspect of the inventive subject matter, the inventors discovered that 4,5,6-trisubstituted Uridine/Cytidine nucleoside libraries can be prepared such that a commercially available nucleoside is employed as a starting material as depicted in Scheme 2F below.

Here, 5-iodouridine is first protected with suitable sugar hydroxyl protection groups to form a protected 5-iodouridine, which is subsequently reacted with a first reagent from a first set of reagents (preferably electrophilic reagents) to form a 6-substituted protected uridine. The 6-substituted protected uridine is then deprotected, the C5'-hydroxyl group of the sugar coupled to a solid support, and the remaining hydroxyl groups of the sugar (here: C2' and C3') again protected (here: acetylated). The iodine group on the heterocyclic base is then exchanged in a Stille-type reaction with a second reagent from a second set of substrates (typically organo-tin compounds) to yield a library of 5,6-disubstituted uridine nucleosides, which may further be reacted with nitrotriazole in the 4-position (and/or 2-position) of the heterocyclic base to form a leaving group that can be replaced with a nucleophilic reagent. A further reaction with a third reagent from a third set of reagents then yields a 4,5,6- trisubstituted uridine/cytidine nucleoside library.

R, = RS, RC(O), ROC(O)

TBAF

R₂ = alkyl, alkenyl, alkynyl, 35 aryl

With respect to the nucleoside, it should be recognized that 5-iodouridine is a preferred starting material and commercially available from various sources. However, it should also be appreciated that numerous alternative reagents are also suitable. For example, there are various 5-iodouridine analogs (e.g., substituted and unsubstituted deoxy- and dideoxy analogs) commercially available. Moreover, it should be recognized that suitable nucleoside analogs may also be prepared with sugar moieties other than a ribofuranose from a coupling reaction between (commercially available) 5-iodouracil and a suitable sugar following standard coupling procedures well known in the art.

Particularly contemplated sugars in alternative nucleosides include various substituted ribofuranoses, carbocyclic ring systems with 5 or 6 carbon atoms, and arabinose, wherein the sugar is in a D-configuration or in an L-configuration. Further contemplated sugars include those previously described in the section entitled "Contemplated Sugars", and it is especially preferred that where the sugar has a C₂' and/or C ' substituent other than a hydroxyl group, alternative C2^* and/or C₃' substituents include hydrogen, a halogen, or an azide group in either alpha or beta orientation.

Consequently, the nature of protecting groups for the sugar will vary considerably, and while it is particularly contemplated that suitable protection groups include benzyl-, acetyl-, and TBS groups, numerous alternative protection groups are also considered suitable. Among other groups, a collection of appropriate alternative protection groups and their reactions is described in Protective Groups in Organic Synthesis by Peter G. M. Wuts, Theodora W. Greene, John Wiley & Sons; ISBN: 0471160199.

It should still further be appreciated that various alternative heterocyclic bases are also appropriate and particularly contemplated alternative heterocyclic bases include pyrimidine heterocyclic bases with at least one acidic proton, at least one halogen substituent, and at least one keto group. While not limiting to the inventive subject matter, alternative heterocyclic bases may also include substituents other than halogens and keto groups, and especially contemplated substituents include hydroxyls, amino groups, and azido groups. With respect to the first set of reagents, it is generally preferred that such reagents are electrophilic reagents, and it is especially preferred that the first set of reagents have a structure RSX, RC(O)X, and/or ROC(O)X, wherein R is alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl, and wherein X is a halogen.

Similarly, a suitable second set of reagents will include all reagents capable of replacing a halogen (most typically an iodine) on the heterocyclic base in a Stille-type reaction (J. Org. Chem. (1983), 48: 4634 or Can. J. Chem (2000), 78: 957-962). Consequently, particularly contemplated second reagents include tin organic and/or tributyltin organic compounds in which the organic moiety may be an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl.

With respect to the third reagent, it is contemplated that all reagents capable of a nucleophilic substitution of a leaving group coupled to the heterocyclic base are considered suitable for use herein. However, particularly contemplated third reagents include various primary and secondary amines (R-NH₂ and RR"NH with R and R' independently as described above, wherein R=R'), various sulfides (R-SH with R as defined above), and various hydrazines (R-NHNH₂ with R as defined above).

Thus, contemplated 4,5,6-trisubstituted uridine libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 21 with a first set of substituents A, Ri, R₂, and R₃, and wherein another one of the at least two library compounds has a structure according to Formula 21 with a second set of substituents A, Ri, R₂, and R₃

Formula 21

wherein A is a protected or unprotected sugar bound to a solid phase, Rj is RS-, RC(O)-, or ROC(O)-, R₂ is R, and R₃ is RNH, RR'N, RNHNH, or RS, wherein R and R are independently hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl.

Consequently, contemplated 4,5,6-trisubstituted uridine/cytidine nucleosides may have a structure according to Formula 2J

Formula 2J

wherein A is a protected or unprotected sugar, R_\ is RS-, RC(O)-, or ROC(O)-, R₂ is R, and R₃ is RNH, RR'N, RNHNH, or RS-, wherein R and R' are independently an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl.

In particularly contemplated libraries and library compounds the sugar is selected from the group consisting of a ribofuranose, a substituted ribofuranose, an arabinose, and a xylofuranose, wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atom, with R being C_MO alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CC1₃, CC1₂H, CH₂OH, CN, COOR, and CONHR', and with R' being Ci-io alkyl, alkenyl, alkynyl, aryl.

5,6-disubstituted Uridine Nucleoside Libraries

Furthermore, it should be appreciated that following a substantially similar path as described in Scheme 2F above, 5,6-disubstituted uridine nucleoside libraries and compounds may be produced such that reaction of the library nucleosides with the third substrate is omitted, and in which the 5,6-disubstituted uridine nucleosides are deprotected and cleaved of the resin as shown in Scheme 2G below.

Here, the acetyl protection groups are removed via reaction with methanolamine, and the solid phase is cleaved from the nucleoside (library) with TFA. However, alternative deprotection and cleaving methods are also suitable and well known to a person of ordinary skill in the art. With respect to the sugar, the heterocyclic base, the solid phase, the coupling of the sugar to the solid phase, and the protection group, the same considerations as described above for the 4,5,6-trisubstituted uridine/cytidine libraries apply.

Thus, 5,6-disubstituted uridine libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2K with a first set of substituents A, Ri, and R₂, and wherein another one of the at least two library compounds has a structure according to Formula 2K with a second set of substituents

Formula 2K

wherein A is a protected or unprotected sugar bound to a solid phase, R_\ is RS, RC(O), or ROC(O), and R₂ is R, wherein R may be hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl, and wherein not all of the first set of substituents A, Ri, and R₂, are the same as the second set of substituents A, Ri, and R₂.

Consequently, contemplated 5,6-disubstituted uridine nucleosides may have a structure according to Formula 2L

Formula 2L

wherein A is a protected or unprotected sugar, Ri is RS, RC(O), or ROC(O), and R₂ is R, wherein R may be hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl. Particularly preferred sugars include substituted and unsubstituted ribofuranose, substituted and unsubstituted arabinose, and substituted and unsubstituted xylofuranose.

4,6-disubstituted Uridine/Cytidine Nucleoside Libraries The inventors still further discovered that 4,6-disubstituted uridine/cytidine libraries and compounds may be synthesized in a protocol in which commercially available uridine is employed as a starting material. In an exemplary route, as depicted in Scheme 2H, the sugar hydroxyl groups in the uridine are first protected with suitable protection groups to form a protected uridine, which is then reacted with a first reagent from a first set of reagents (preferably electrophilic compounds) to generate a first set of 6-substituted uridine nucleosides. In a further step, the protecting groups are cleaved from the sugar portion and the nucleoside is coupled to a solid phase (preferably via the C5' OH group) while the remaining sugar hydroxyl groups are again reacted with a protection group (here: acetyl). In a still further step, at least one oxo group in the heterocyclic base (preferably the oxo group in 4-position) is then reacted with a leaving group (preferably nitrotriazole), which is subsequently replaced by a second reagent from a second set of reagents (preferably nucleophiles) to further increase diversity of the nucleoside library. Then, the protecting groups may be removed from the sugar and the nucleoside may be cleaved from the solid support.

TBAF

Scheme 2H

With respect to the nucleoside, the protecting groups, and the solid phase, the same considerations as described above for the 4,5,6-trisubstituted Uridine/Cytidine nucleoside libraries apply. Preferred first sets of reagents include electrophilic reagents, and it is especially preferred that the first set of reagents have a structure RSX, RC(O)X, and/or ROC(O)X, wherein R is alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl, and wherein X is a halogen.

With respect to the second set of reagents, it is contemplated that all reagents capable of a nucleophilic substitution of a leaving group coupled to the heterocyclic base are considered suitable for use herein. However, particularly contemplated second reagents include various primary and secondary amines (R-NH₂ and RR"NH with R and R' as described above), various sulfides (R-SH with R as defined above), and various hydrazines (R-NHNH₂ with R as defined above).

Thus, contemplated 4,6-disubstituted uridine/cytidine libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2M with a first set of substituents A, Ri, and R₂, and wherein another one of the at least two library compounds has a structure according to Formula 2M with a second set of substituents A, Ri, and R₂

la 2M

wherein A is a protected or unprotected sugar bound to a solid phase, Ri is RS, RC(O), or ROC(O), R₂ is RNH, RR'N, RNHNH, or RS, wherein R and R are independently an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl, and wherein the first set of substituents A, Ri, and R₂ is not the same as the second set of substituents A, Ri, and R₂.

Consequently, contemplated 4,6-disubstituted uridine/cytidine nucleosides may have a structure according to Formula 2N

Formula 2N

wherein A is a protected or unprotected sugar, R) is RS, RC(O), or ROC(O), and R₂ is RNH, RR'N, RNHNH, or RS, wherein R and R' are independently an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl. Particularly preferred sugars include substituted and unsubstituted ribofuranose, substituted and unsubstituted arabinose, and substituted and unsubstituted xylofuranose.

4,5-disubstituted Uridine/Cytidine Nucleoside Libraries

The inventors yet further discovered that 4,5-disubstituted uridine/cytidine libraries and compounds may be synthesized in a protocol in which commercially available 5- iodouridine is employed as a starting material. In an exemplary route, as depicted in Scheme 21, the sugar hydroxyl groups in the 5-iodouridine are first protected with suitable protection groups to form a protected uridine, which is further coupled (preferably via the C5' OH group) to a solid phase. The 5-iodouridine is then reacted in a Stille-type reaction with a first reagent from a first set of reagents (preferably organo-tin compounds) to generate a first set of 5-substituted uridine nucleosides. In a further step, at least one oxo group in the heterocyclic base (preferably the oxo group in 4-position) is reacted with a leaving group (preferably nitrotriazole), which is subsequently replaced by a second reagent from a second set of reagents (preferably nucleophiles) to further increase diversity of the nucleoside library. Then, the protecting groups may be removed from the sugar and the nucleoside may be cleaved from the solid support to yield the corresponding 4,5-disubstituted nucleosides.

29 49 R₂ = alkyl, alkenyl, alkynyl, ^arV' 50

,

Again, with respect to the nucleoside, the protecting groups, and the solid phase, the same considerations as described above for the 4,6-disubstituted uridine/cytidine libraries apply. Preferred first sets of reagents include all reagents capable of replacing a halogen (most typically an iodine) on the heterocyclic base in a Stille-type reaction (J. Org. Chem. (1983), 48: 4634 or Can. J. Chem (2000), 78: 957-962). Consequently, particularly contemplated second reagents include tin organic and/or tributyl-tin organic compounds in which the organic moiety may be an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl.

With respect to the second set of reagents, it is contemplated that all reagents capable of a nucleophilic substitution of a leaving group coupled to the heterocyclic base are considered suitable for use herein. However, particularly contemplated second reagents include various primary and secondary amines (R-NH₂ and RR"NH with R and R as described above), various sulfides (R-SH with R as defined above), and various hydrazines (R-NHNH₂ with R as defined above).

Thus, contemplated 4,5-disubstituted uridine/cytidine libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2O with a first set of substituents A, R_\, and R₂, and wherein another one of the at least two library compounds has a structure according to Formula 2O with a second set of substituents A, Ri, and R2

Formula 20

wherein A is a protected or unprotected sugar bound to a solid phase, Ri is R, and R₂ is RNH, RR'N, RNHNH, or RS, wherein R and R' are independently an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl, and wherein the first set of substituents A, Ri, and R₂ is not the same as the second set of substituents A, Ri, and R₂.

Consequently, contemplated 4,5-disubstituted uridine/cytidine nucleosides may have a structure according to Formula 2P

Formula 2P

wherein A is a protected or unprotected sugar, Ri is R, and R₂ is RNH, RR'N, RNHNH, or RS, wherein R and R' are independently an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl. Particularly preferred sugars include substituted and unsubstituted ribofuranose, substituted and unsubstituted arabinose, and substituted and unsubstituted xylofuranose.

In still further alternative aspects, where it is particularly desirable to employ a starting nucleoside in which at least one of the substituents is oriented in beta orientation (and particularly the C3' substituent), 4,5-disubstituted cytosine nucleoside libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula IB with a first set of substituents Z, X, Ri, and R₂, wherein another one of the at least two library compounds has a structure according to Formula IB with a second set of substituents Z, X, Ri, and R₂

Formula IB

wherein X is NH, S, or O; Z is hydrogen, N₃, NH₂, OH, SH, or NHR wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl; and wherein Ri and R₂ are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl; wherein • comprises a solid phase, and wherein not all of the substituents Z, X, Ri, and R₂ in the first set are the same as the substituents Z, X, Ri, and R₂ in the second set. Thus, contemplated compounds may have a structure according to formula IB'

Formula IB'

wherein X is NH, S, or O; Z is hydrogen, N₃, NH , OH, SH, or NHR wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl; and wherein Ri and R₂ are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl.

With respect to the sugar, it should be appreciated that numerous sugars with at least one substituent in beta orientation are well known in the art and many of those are commercially available. Consequently, it is contemplated that such alternative sugars may be provided to synthesize the corresponding nucleoside in which the sugar substituent is in beta orientation by procedures well known in the art (see e.g., Handbook of Nucleoside Synthesis by Helmut Vorbruggen and Carmen Ruh-Pohlenz. Wiley-Interscience; ISBN: 0471093831). With respect to aspects of synthesis, solid phase and protecting groups, the same considerations as described above apply. Anhydro-Nucleoside Libraries and Compounds

In further particularly preferred aspects of the inventive subject matter, anhydrotriazine nucleoside libraries may be synthesized following an exemplary synthetic scheme as depicted in Scheme 2J below.

NH COR

D RCOCi

57 58

Scheme 2J

Here, synthesis may start from 4'-thio-3'-azido-5-aza-arabinocytidine, which may be synthesized by glycosylation of per-acetyl-4'-thioazidoarabinose with 5-azacytosine and subsequent deprotection with ammonia as described by Hanna et al. in Nucleosides Nucleotides (1997), 16, 129-144. In a further step, the 4'-thio-3'-azido-5-aza-arabinocytidine is coupled to a solid phase and the 2'-hydroxyl group is protected. The amino group in the heterocyclic base may then be reacted with a first set of reagents (e.g., an activated electrophilic reagent or electrophilic reagent in the presence of a catalyst). In a further step, the azido group is then reduced to the corresponding amino group with subsequent (or in some cases concurrent) formation of the corresponding anhydronucleoside and cleavage from the solid phase.

With respect to the starting material, it should be recognized that various nucleosides other that 4'-thio-3'-azido-5-aza-arabinocytidine are also suitable, and alternative starting materials particularly include nucleosides with modified sugar moiety and/or modified heterocyclic base (relative to 4'-thio-3'-azido-5-aza-arabinocytidine). For example, suitable modified sugar moieties include all natural and non-natural sugars so long as alternative sugars include a nucleophilic C'₂-substituent in alpha orientation that has sufficient reactivity to form a covalent bond in a reaction with the heterocyclic base. Exemplary suitable sugar moieties are depicted in structures 2Q and 2R below

Structure 2R

wherein W is S or O; B is the heterocyclic base or reactive group that can be employed to couple a heterocyclic base to the C'ι position in such sugars; Z is OH or NH₂; X is H, OH, SH, N₃, CN, NH₂, NHR', NHCOR', NHSO₂R', COOH, COOR', CH₂NO₂, Cl, F, Br, alkyl, alkenyl, or alkynyl; and R is alkyl, aryl, R'CO, R'SO₂, R'NHCO, RΗHCS, RΗH, SH, OH, N₃, R'O, or H; wherein R' is substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or aralkyl; and wherein R, is H, N₃, NH₂, RCO, or RCONH, and R₂ is H, CH₃, CF₃, CH=CH₂, or alkynyl.

In still further examples, numerous modified heterocyclic bases other than 5- azacytosine may also be used in the synthesis of contemplated compounds, and especially preferred alternative heterocyclic bases include 5-substituted cytosine as depicted in structures 2S and 2T below:

Structure 2T

wherein R_. is NH₂, NHR', R', halogen, or CH=CHR, wherein X is hydrogen or a sugar as indicated above, R is alkyl, aryl, R'CO, R'SO₂, R'NHCO, R'NHCS, RNH, SH, OH, N₃, R'O, H; wherein Z is N, S, or CH; and wherein R' is substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or aralkyl. With respect to the solid phase and the protecting group, the same considerations as described in the sections above apply.

Particularly preferred first sets of reagents include substituted and unsubstituted acid chlorides, which may or may not have at least one double bond (which may further be conjugated or not conjugated with another double bond), and which may have the general formula RCOC1, wherein R is substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or alkaryl. Alternatively, however, it is contemplated that suitable first set of reagents may also include numerous compounds other than substituted and unsubstituted acid chlorides, and it is generally preferred that such compounds will include an electrophilic center with sufficient reactivity to form a covalent bond with the amino group in the heterocyclic base.

Consequently, contemplated anhydronucleosides may have a structure according to Formula 2U

wherein R, is H, N₃, NH₂, R'CO, or R'CONH, R₂ is H, CH₃, CF₃, CH=CH₂, or alkynyl, R₃ is H, R', COR', SO R, or OCOR with R being hydrogen, substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, and aralkyl, and wherein _t is NH₂, NHR, R', halogen, or CH=CHR, with R' as defined above. It should further be appreciated that both D- and L-configuration are contemplated.

Additionally, contemplated compounds include the following compounds having a structure according to Formulae 2V and 2W, where the heterocyclic base is a triazine or purine base:

wherein X is H, OH, SH, N₃, CN, NH₂, NHR, NHCOR, NHSO₂R', COOH, COOR, CH₂NO₂, Cl, F, Br, alkyl, alkenyl, or alkynyl; Y is O, S, NH, CH₂, CHR; Z is N or CH; and R is independently alkyl, aryl, R'CO, R'SO₂, R'NHCO, R'NHCS, R'NH, SH, OH, N₃, R'O, H; and wherein R' is substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or aralkyl.

Triazine C-Nucleoside Libraries In a yet further preferred aspect of the inventive subject matter, triazine C-nucleoside libraries may be synthesized following an exemplary synthetic scheme as depicted in Scheme 2K below.

62 Scheme 2K ⁶³

Here, a 2',3 '-protected Cl'-aldehyde sugar is coupled to a solid phase, and the aldehyde is reacted with methanol to form the corresponding methoxy derivative, which is subsequently reacted with substituted diamine compound (or set of distinct substituted diamine compounds) to form the substituted triazine heterocyclic base. In a further step, the substituted triazine heterocyclic base is derivatized with a first set of reagents (various primary amines) to further increase the complexity of the so generated library. Deprotection of the sugar alcohol groups and cleavage of the library compounds from the solid phase will then yield triazine C-nucleoside libraries and their compounds.

In alternative aspects of the inventive subject matter, it is contemplated that numerous sugars other than a beta C'ι -aldehyde ribofuranose are also suitable, and particularly contemplated alternative sugars include substituted and unsubstituted alpha Ci-aldehyde ribofuranose, and various substituted and unsubstituted furanose and pyranose sugars with a C'ι-aldehyde group (which may be in alpha or beta orientation). Exemplary suitable sugars include those that are described in the section "Contemplated Sugars", and among those particularly sugars with a Ci-aldehyde group. Furthermore, it should be recognized that suitable sugars may be in the D- and/or L-configuration. With respect to the protection groups and the solid phase, the same considerations as described in the sections above apply.

Especially preferred substituted diamine compounds will have a general structure according to Structure 2X below

X

RHN Y Structure 2X

H₂N^"^^SCH₃

wherein R is R', X is O, S, or NHR', Y is N or CH, and wherein R is a substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or alkaryl. It is generally contemplated that many of the compounds according to Structure 2X are commercially available. Alternatively, suitable substituted diamines may be synthesized in a reaction in which a substituted isocyanate (R-N=C=O) is condensed at room temperature with H₂N-C(=NH)S-CH₃ as described by Piskala et al. in Nucleic Acid Chemistry (1978), 1, 443-449 [Editors: Townsend et al. Wiley N.Y., N.Y]. Alternatively, it should be recognized that such compounds may also be prepared following procedures well known in the art (see e.g., Advanced Organic Chemistry: Structure and Mechanisms (Part A) by Francis A. Carey, Richard J. Sundberg; Plenum Pub Corp; ISBN: 0306462435; or Advanced Organic Chemistry : Reactions and Synthesis (Part B) by Francis Carey, Richard J. Sundberg; Plenum Pub Corp; ISBN: 0306434571, or Compendium of Organic Synthetic Methods, Volume 9, by Michael B. Smith, John Wiley & Sons; ISBN: 0471145793).

Similarly, it should be recognized that the first set of reagents may vary considerably. However, it is generally preferred that such reagents are primary amines with the general formula R-NH₂, wherein R may be a substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or alkaryl. Exemplary primary amines are listed in the experimental section below.

Consequently, contemplated libraries and compounds will have a structure according to Structures 2Y and 2Z

wherein • is a solid phase, and wherein R may be hydrogen, a substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or alkaryl.

In further alternative aspects, and especially where the substituted diamine compound has a structure according to structure 2X' as depicted below, contemplated compounds may have a structure according to structure 2Y' and 2Z'.

wherein R is independently a substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or alkaryl, and X is N or CH.

4,5,6-trisubstituted Cytidine Nucleoside Libraries

The inventors further discovered that 4,5, 6-substituted cytidine libraries can be generated using a procedure as outlined in Scheme 3 below, in which a 5,6-disubstituted uracil nucleoside (or population of distinct substituted uracil nucleosides) is first converted to the corresponding protected 6-substituted uracil and bound to a solid phase. The protected and bound substituted uracil is further reacted with TPS-Cl to generate a leaving group, which is exchanged with a nucleophile, and more preferably an NH₂-containing reagent as indicated in the scheme, thereby generating a first set of N-substituted-6-substituted cytidine products. Where the 6-substituted uracil is in the 5-position, it is contemplated that such 5 -substituents may be introduced as described above (e.g., Heck- or Stille reaction from the corresponding 5-halogenated uracil). Contemplated 5-substituents therefore especially include an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl.

(or other ways)

With respect to the nucleoside, it should be recognized that 5,6-dialkyluracil is a preferred starting material and commercially available from various sources. It should also be appreciated that numerous alternative reagents are also suitable, including various 6- substituted analogs (e.g., 6-amino, 6-aza, 6-carboxy, or 6-propyl substituted uracil), most of which are commercially available. It is generally preferred, however, that the 6-substituent is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl or a substituted aryl. Where desired heterocyclic bases with particular 5- and 6-substituents are not commercially available, it should be appreciated that such heterocyclic bases may be produced from the corresponding pyrimidine base following protocols similar to those described in WO88/04662. Moreover, it should be recognized that suitable nucleoside analogs may also be prepared with sugar moieties other than a ribofuranose from a coupling reaction between (commercially available) 6-substituted uracil and a suitable sugar following standard coupling procedures well known in the art. Particularly contemplated sugars include various substituted ribofuranoses, carbocyclic ring systems with 5 or 6 carbon atoms, and arabinose, wherein the sugar is in a D-configuration or in an L-configuration. Further contemplated sugars include those previously described herein (supra), and it is especially contemplated that where the sugar has a C₂' and/or C ' substituent other than a hydroxyl group, alternative sugars may include hydrogen, a halogen, or an azide group in at least one of these positions (in either alpha or beta orientation). For example, especially preferred alternative sugars include an amino group at the C3' position, wherein the amino group may be mono- or disubstituted (-NH₂, -NHR, or -NRR').

Preferred nucleophiles that replace the leaving group on the heterocyclic base particularly include NH∑-containing reagents. For example, hydroxylamine, NH₃, primary amines (e.g. , R-NH₂, R-NHNH₂, RONH₂, RSO₂NH₂), and secondary amines (e.g. , R¹R²NH), wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl or a substituted aryl are considered suitable for use herein. However, it should be appreciated that numerous alternative amines are also contemplated so long as the exchange of the amine for the leaving group will transform the substituted uracil into an N-substituted cytidine.

Consequently, contemplated N-substituted cytidine libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 3A with a first set of substituents X, R, Ri, R₂, and R₃, and wherein another one of the at least two library compounds has a structure according to Formula 3 A with a second set of substituents X, R, Ri, R₂, and R

HO R₃

wherein X is NH, NHO, NHNH, or ONH, NHSO₂, R and R, are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl; an aryl and a substituted aryl; R₂ is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, and a heterocyclic base; and R₃ is selected from the group consisting of hydrogen, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, O-alkynyl, with the proviso that R and Ri is not H at the same time; wherein • comprises a solid phase, and wherein not all of the substituents X, R, Ri, R₂, and R₃ in the first set are the same as the substituents X, R, Ri, R₂, and R₃ in the second set.

Thus, contemplated library compounds may have a structure according to Formula 3A'

Formula 3A'

wherein X is NH, NHO, NHNH, or ONH, NHSO₂, R and Ri are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl; R₂ is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, and a heterocyclic base; and R₃ is selected from the group consisting of hydrogen, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, O-alkynyl, with the proviso that R and Ri is not H at the same time.

Additionally, contemplated N-substituted cytidine libraries may have at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 3B with a first set of substituents X, Y, R, Ri, R₂, R₃, R_t, R₅, and R , and wherein another one of the at least two library compounds has a structure according to Formula 3B with a second set of substituents X, Y, R, Ri, R₂, R₃, Rt, R₅, and R_

Formula 3B

wherein X is NH, NHO, NHNH, or ONH, NHSO₂, Y is C(O), CONH, CSNH, or SO₂, Ri, R₂, R_t, R₅, and R^ are independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl; R₃ is selected from the group consisting of hydrogen, OH, OCH₃, SH, SCH , O-alkyl, O-alkenyl, and O-alkynyl, and wherein not all of the substituents X, Y, Ri, R₂, R₃, R_t, R₅, and Re in the first set are the same as the substituents X, Y, Ri, R2, R₃, R_t, R₅, and R_ in the second set. Thus, contemplated library compounds may have a structure according to Formula 3B'

Formula 3B'

wherein X is NH, NHO, NHNH, or ONH, NHSO₂, Y is C(O), CONH, CSNH, or SO₂, Ri, R₂, R_t, R₅, and R are independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl; R₃ is selected from the group consisting of hydrogen, OH, OCH , SH, SCH₃, O-alkyl, O-alkenyl, and O-alkynyl.

It should generally be appreciated that in compounds according to Formulae 3B and 3B' the introduction of the substituents in the 4-, 5-, and 6-position in the heterocyclic base will generally follow reaction conditions similar to those described above (e.g. , 4,5,6-trisubstituted nucleosides). With respect to the substituents in the C2' and C3' position in the sugar, it should be recognized that the substituents may be introduced at any suitable time during the synthesis. However, it is preferred that the substituents in the C2' and C3' position in the sugar are already incorporated into the sugar moiety of the starting nucleoside.

Uses of contemplated libraries and compounds

In one preferred aspect, it is contemplated that the libraries according to the inventive subject matter may be used to facilitate structure-activity analysis of nucleoside-type compounds. For example, where it is known that an enzyme employs a nucleoside as substrate/co-substrate, and where an inhibitor or alternative substrate for the enzyme is desired, contemplated libraries will provide a researcher with rapid information on the impact of a particular substituent in a particular position of the library compound.

In a further example, it is contemplated that libraries according to the inventive subject matter will exhibit a significant source of revenue for a seller since in most cases purchase of a library of nucleosides, nucleoside analogs, nucleotides, and/or nucleotide analogs will be less costly to a user than individual synthesis of these compounds.

In yet another example, the library compounds may serve as in vitro and/or in vivo substrates or inhibitors with particularly desirable physicochemical and/or biological properties. Among other uses, the library compounds may act as inhibitors of DNA and/or RNA for various nucleoside-using enzymes, and especially polymerases, reverse transcriptases, and ligases. Therefore, contemplated nucleosides will exhibit particular usefulness as in vitro and/or in vivo antiviral agent, antineoplastic agent, or immunomodulatory agent. Still further, it is contemplated that nucleosides according to the inventive subject matter may be incorporated into oligo- or polynucleotides, which will then exhibit altered hybridization characteristics with single or double stranded DNA in vitro and in vivo.

Particularly contemplated antiviral activities include at least partial reduction of viral titers of respiratory syncytial virus (RSV), hepatitis B virus (HBV), hepatitis C virus (HCV), herpes simplex type 1 and 2, herpes genitalis, herpes keratitis, herpes encephalitis, herpes zoster, human immunodeficiency virus (HIV), influenza A virus, Hanta virus (hemorrhagic fever), human papilloma virus (HPV), and measles virus. Especially contemplated immunomodulatory activity includes at least partial reduction of clinical symptoms and signs in arthritis, psoriasis, inflammatory bowel disease, juvenile diabetes, lupus, multiple sclerosis, gout and gouty arthritis, rheumatoid arthritis, rejection of transplantation, giant cell arteritis, allergy and asthma, but also modulation of some portion of a mammal's immune system, and especially modulation of cytokine profiles of Type 1 and Type 2. Where modulation of Type 1 and Type 2 cytokines occurs, it is contemplated that the modulation may include suppression of both Type 1 and Type 2, suppression of Type 1 and stimulation of Type 2, or suppression of Type 2 and stimulation of Type 1.

Where contemplated nucleosides are administered in a pharmacological composition, it is contemplated that suitable nucleosides can be formulated in admixture with a pharmaceutically acceptable carrier. For example, contemplated nucleosides can be administered orally as pharmacologically acceptable salts, or intravenously in physiological saline solution (e.g. , buffered to a pH of about 7.2 to 7.5). Conventional buffers such as phosphates, bicarbonates or citrates can be used for this purpose. Of course, one of ordinary skill in the art may modify the formulations within the teachings of the specification to provide numerous formulations for a particular route of administration. In particular, contemplated nucleosides may be modified to render them more soluble in water or other vehicle, which for example, may be easily accomplished by minor modifications (salt formulation, esterification, etc.) that are well within the ordinary skill in the art. It is also well within the ordinary skill of the art to modify the route of administration and dosage regimen of a particular compound in order to manage the pharmacokinetics of the present compounds for maximum beneficial effect in a patient.

In certain pharmaceutical dosage forms, prodrug forms of contemplated nucleosides may be formed for various purposes, including reduction of toxicity, increasing the organ- or target cell specificity, etc. One of ordinary skill in the art will recognize how to readily modify the present compounds to pro-drug forms to facilitate delivery of active compounds to a target site within the host organism or patient (see above). One of ordinary skill in the art will also take advantage of favorable pharmacokinetic parameters of the pro-drug forms, where applicable, in delivering the present compounds to a targeted site within the host organism or patient to maximize the intended effect of the compound.

In addition, contemplated compounds may be administered alone or in combination with other agents for the treatment of various diseases or conditions. Combination therapies according to the present invention comprise the administration of at least one compound of the present invention or a functional derivative thereof and at least one other pharmaceutically active ingredient. The active ingredient(s) and pharmaceutically active agents may be administered separately or together and when administered separately this may occur simultaneously or separately in any order. The amounts of the active ingredient(s) and pharmaceutically active agent(s) and the relative timings of administration will be selected in order to achieve the desired combined therapeutic effect. Among other contemplated agents for combination with contemplated compounds, it is especially preferred that such agents include interferon, and particularly IFN-alpha or IFN-beta (or fragments thereof). Examples

5-Amino Substituted Cytidine Libraries (Scheme 1)

5-Amino Uridine (2): 5-Bromo Uridine (1) (3.23 gm, 10 mmol) was taken into a pre- cooled steel bomb and to this was added liquid ammonia (75 ml). This steel bomb was closed and kept for 24 hrs at 60°C. The bomb was opened after cooling in dry ice and left open overnight at room temperature for ammonia to evaporate. This solid 5-amino uridine was used for next step without further purification. 5-N-(Fmoc-NH-amino acid)-5-amino-uridine (3). To a solution of 5-amino uridine (2.59 gm, 10 mmol) in anhydrous DMF (100 ml) were added Fmoc-NH-amino acid (10 mmol), PyBOP (5.20 gm, 10 mmol), HOBt (1.35gm, 10 mmol) and DIPEA (1.74 ml, 10 mmol). The reaction mixture was stirred at room temperature for 20 hrs. After work up this was purified by column chromatography.

5-N-(Fmoc-amino acid)-5'-O-(MMTr-solid support)-uridine (4): A mixture of 5-N- (Fmoc-NH-amino acid)-5-amino-uridine (3) (1.25 mmol) inanhydrous pyridine (10 ml) and MMTr-Cl solid support (1 mmol) were allowed to shake at room temperature for 48 hrs. The resin was filtered and successively washed with DMF, MeOH and CH2CI2.

2',3'-O-t-Butyldimethylsilyl-5-N-(Fmoc-amino acid)-5'-O-(MMTr-solid support)- uridine (5): A mixture of 5-N-(Fmoc-amino acid)-5'-O-(MMTr-solid support)-uridine (4) (0.1 mmol) in anhydrous DMF (2 ml) t-butyldimthylsilyl chloride (1 mmol) and imidazole (2 mmol) were kept shaking at room temperature for 36 hrs and then successively washed with DMF, MeOH and CH₂C1₂.

3-Nitro-l,2,4-triazole (3.4 g, 30 mmol) was added to a suspension of resin 5 (5.0 mmol) in a mixture of pyridine (40 mL) and diphenylchlorophosphate (4.1 mL, 20 mmol). The reaction mixture was shaken at room temperature for 48 h, then the resin was filtered and washed with pyridine (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin 6 was dried under high vacuum at 40 °C.

4-N-substitution: 50 mg of resin 6 was added to each of the 96 wells on the ACT parallel synthesizer. 1 ml of base (0.3 M DMAP in pyridine containing diisopropylethylamine) and 0.65 ml of each of 96 amines (1 M in DMF) were added to each of the 96 reaction vessels. The sealed reaction vessels in the reaction block were shaken at room temperature for 6 hours. The solvent was filtered off by vacuum. The resins were washed 3 times with DMF, 3 times with DCM-MeOH, and 3 times with dichloromethane to give a library of 96 resins. 1 ml of DMF and 1 ml of tetrabutylammonium fluoride in THF (1 M) were added to each of the 96 reaction vessels. The reaction block was shaken at room temperature for 5 hours, filtered and washed 3 times with DMF, 3 times with 40% water in methanol, and 3 times with dichloromethane. The resins were treated with 20% piperidine for 2 h and washed with DMF and dichloromethane. The final compounds 7 were cleaved from resins by reacting with TFA for 5 minutes. The final libraries were characterized by LC-MS.

Building Blocks for 5-NH-position: Fmoc-Alanine-OH, N-_α-Fmoc-N_α-Methyl- Alanine-OH, Fmoc-NH-(CH₂)_n-COOH, Fmoc-Arginine(MMTr)-OH , Fmoc-

Aspargine(MMTr)-OH, Fmoc-Aspartic acid(OtBu)-OH, Fmoc-Citrulline-OH, Fmoc- Cysteine(MMTr)-OH, Fmoc-Glutamic acid(OtBu)-OH, Fmoc-Glutamine(MMTr)-OH, Fmoc- Glycine-OH, Fmoc-Histidine(MMTr)-OH, Fmoc-Homoserine(MMTr)-OH, Fmoc- Isonipecotic-OH, Fmoc-Leucine-OH, Fmoc-Lycine(Boc)-OH, Fmoc-Methionine-OH, Fmoc- Norleucine-OH, FmocNorvaline-OH, Fmoc-Phenylalanine-OH, Fmoc-Phenylglycine-OH, Fmoc-Sarcosine-OH, Fmoc-Serine(OtBu)-OH, Fmoc-Thienylalanine-OH, Fmoc- Threinine(OtBu)-OH, Fmoc-Tryptophan(Boc)-OH, Fmoc-Tyrosine(OtBu)-OH, Fmoc-Naline- OH, Fmoc-Alanine-OH. However, all natural, unnatural, α, β, γ, ω and other amino acids, heterocylic, aromatic, and aliphatic organic carboxylic acids are also suitable for use herein.

2' -O-Alkyl-5 -substituted Cytidine Libraries (Scheme 2 A)

Commercially available 5-iodouridine is converted to the corresponding 2-O-methyl- 5-iodouridine following procedures well known in the art. The so formed 2-O-methyl-5- iodouridine is subsequently coupled to a solid phase as described for various nucleosides below, and a Heck reaction is employed to replace the iodine with the desired substituent under conditions similar to those described in R.F. Heck. Org. React. Ν.Y. 27, 345 (1982); J.E. Plevyak and R.F. Heck. J. Org. Chem. 43, 2454 (1978); M. Hiroshige, J.R. Hauske, P. Zhou. J. Am. Chem. Soc. 117, 11590 (1995); or D.A. Goff and R.Ν. Zuckermann. J. Org. Chem. 60, 5748 (1995). Introduction of the second substituent (here amine reagent) via TPSC1 is performed under conditions similar to those described below in Scheme 2B or 3. Introduction of the third substituent (here e.g. : activated acids) is performed using conditions well known in the art. 2'0-methyl-N4-substituted cytidine libraries (Scheme 2B)

A solution of 2'-O-methyluridine (9) (2.17 g) in 25 ml of pyridine was added to a shakable funnel containing 4.05 g of 4-methyoxytrityl chloride resin (Novabiochem, loading capacity, 1.73 mmol/g). 4-N,N-Dimethylaminopyridine (DMAP) was added. The reaction mixture was shaken at room temperature for 2 days. The mixture was filtered and the resin was washed 4 times with pyridine-DMF (1 :1) and 4 times with dichlorormethane.

The resultant uridine-substituted resin was swelled in 20 ml of pyridine, 10 ml of dichloromethane and 3.0 ml of triethylamine. T-Butyldimethylsilychloride (5.27 g, 5 eq.) and imidazole (2.38 g, 5 eq) were added to the mixture followed by 5 ml of DMF to improve the solubility. The mixture was shaken at room temperature for 24 hours and filtered. The resin was washed 4 times with pyridine-DMF (1 :1) and 3 times with dichloromethane, and dried under vacuum to provide dried resin 10 loaded with protected cytidine.

A mixture of the above prepared resin, DMAP (100 mg), dichloromethane (30 ml) and triethylamine (6.8 ml) was shaken at room temperature for 30 minutes. 2,4,6- tris(isopropyl)benzenesulfonyl chloride (TIP-C1, 4.24 g, 2 eq) was added. The resultant mixture was shaken at room temperature for 24 hours. 2 ml of methanol was added to consume the excess amount of TIP-C1, shaken and filtered. The resin was washed 5 times with pyridine-DMF (1 :1) and 3 times with dichloromethane, and dried under vacuum to provide 7.2 g of resin 11 which is confirmed by MAS NMR spectrometry and ready for the parallel array synthesis of nucleoside library 13.

50 mg of resin 11 was added to each of the 96 wells on the ACT parallel synthesizer. 1 ml of base (0.3 M DMAP in pyridine containing diisopropylethylamine) and 0.65 ml of each of 96 amines (1 M in DMF) were added to each of the 96 reaction vessels. The sealed reaction vessels in the reaction block were shaken at room temperature for 6 hours. The solvent was filtered off by vacuum. The resins were washed 3 times with DMF, 3 times with DCM-MeOH, and 3 times with dichloromethane to give a library of 96 resins 12.

1 ml of DMF and 1 ml of tetrabutylammonium fluoride in THF (1 M) were added to each of the 96 reaction vessels. The reaction block was shaken at room temperature for 5 hours, filtered and washed 3 times with DMF, 3 times with 40% water in methanol, and 3 times with dichloromethane. To the reaction 96 vessels containing resins were added 1.5 ml of 2% trifluoroacetic acid solution in dichloroethane. After shaking for 2 minutes, the filtrates were collected into 96 different vials. The resins were further washed with methanol and the filtrates were combined with the corresponding 96 vials. The solutions of the 96 samples were dried to provide 96 nucleosides 13 in 20 - 30 mg. The samples were analyzed by TLC and LC-MS spectrometry. LC-MS analysis of these samples confirmed the integrity and purity. Sample purity of the samples range from 70-100%.

5 -(substituted acetylene)-2 '-O-methyl-3 .5 -di-O-acetyluridine analogues (Scheme

2C).

To a stirred solution of 5-iodo-2'-methyluridine (18) (Jasenka Matulic-Adamic, Andrew T. Daniher, Alexander Karpeisky, Peter Haeberli, David S weedier and Leonid

Beigelman, Bioorg. Med. Chem. Lett. 10 (2000), 1299-1302) (4.68 g, 10 mmol) in anhydrous dimethylformamide (40 mL) were added triethylamine (6 mL), the acetylene derivative (20 mmol), tris(dibenzylideneacetone)dipalladium(0) (200 mg), copper (I) iodide (50 mg), Ph₃P (400 mg). The mixture was stirred for 18 hours at room temperature under a nitrogen atomsphere. After being concentrated under vacuum, the resulting residue was purified by flash column chromatography. The appropriate fractions were combined, and the solvent was removed under vacuum to give the pure products 19. Exemplary alkynyl and alkynyl derivatives were prepared and characterized as follows:

5-(Phenylacetylene)-2'-O-methyl-3',5'-di-O-acetyluridine (19a). The above procedure was carried out using phenylacetylene (20 mmol). The desired product 19a (3 g, 65.5%) was obtained after chromatographic purification (hexane/ethyl acetate = 1 :1), and characterized by Η NMR (CDC1₃; 300 MHz) and ES MS.

5-(4-Methoxylphenylacetylene)-2'-O-methyl-3',5'-di-O-acetyluridine (19b). The above procedure was carried out using 4-methoxylphenylacetylene (20 mmol). The desired product 19b (3.5 g, 71.7%) was obtained after chromatographic purification (hexane/ethyl acetate = 1 :1), and characterized by Η NMR (CDC1₃; 300 MHz) as well as ES MS.

5-(4-Trifluoromethylphenylacetylene)-2'-O-methyl-3',5'-di-O-acetyluridine (19c). The above procedure was carried out using 4-trifluoromethylphenyleneacetylene (20 mmol). The desired product 19c (2.8 g, 53%) was obtained after chromatographic purification (hexane/ethyl acetate = 1 :1), and characterized by Η NMR (CDC1₃; 300 MHz) as well as ES MS.

5-(4-Fluorophenylacetylene)-2'-O-methyl-3',5'-di-O-acetyluridine (19d). The above procedure was carried out using 4-fluorophenylacetylene (20 mmol). The desired product 19d (3.0 g, 63%) was obtained after chromatographic purification (hexane/ethyl acetate = 1 :1), and characterized by Η NMR (CDC1₃; 300 MHz) as well as ES MS.

5 -(substituted acetylene)-2 -O-methyluridine libraries (20) (Scheme 2D).

To a solution of 5 -(substituted acetylene)-2'-O-methyl-3',5'-di-O-acetyluridine derivative 19 (8 mmol) in methanol (40 mL) was added sodium methoxide (IN, 1 mL). After stirring at room temperature for 4 hours, the mixture was neutralized by H⁺ resin. The solvent was removed, and the residue was purified on a silica gel column using dichloromethane and methanol (10:1) as eluents to give the pure products 20. Exemplary compounds are as follows:

5-(Phenylacetylene)-2'-O-methyluridine (20a). The procedure was carried out using compound 19a as starting material to give the product 20a as a solid (85%). The product was characterized by Η NMR (CDC1₃; 300 MHz) and ES MS.

5-(4-Methoxylphenylacetylene)-2'-O-methyluridine (20b). The procedure was carried out using compound 19b as starting material to give the product 20b as a solid (80%) which was characterized by Η NMR (CDC1₃; 300 MHz) and ES MS.

5-(4-Trifluoromethylphenylacetylene)-2'-O-methyluridine (20c). The procedure was carried out using compound 19c as starting material to give the product 20c as a solid (85%) which was characterized by Η NMR (CDC1₃; 300 MHz) and ES MS.

5-(4-Fluorophenylacetylene)-2'-O-methyl-uridine (20d). The procedure was carried out using compound 19d as starting material to give the product 20d as a solid (79%) which was characterized by Η NMR (CDC1₃; 300 MHz) and ES MS. 5 -(substituted acetylene) -4-N-substituted amine 2 '-O-methylcytidine libraries

(Scheme 2D- continued)

To a solution of 5-(substituted acetylene)-2'-O-methyluridine derivative 20 (5 mmol) in dry pyridine (40 mL) were added MMTC1 resin (4 g) and 4-DMAP (200 mg). The mixture was shaken for 48 hours. Methanol (2 mL) was added. After shaking for another 30 min., the resulting resin 21 was filtered, washed with pyridine and DMF, and dried. 5-(substituted acetylene)-2'-O-methyl-3'-O-acetyl-5'-O-MMT-resin uridine analogues (22). To a mixture of resin 21 in pyridine (20 mL) was added acetic anhydride (15 mL). After shaking at room temperature for 10 hours, the resulting resin 22 was filtered, washed, and dried. 5 -(substituted acetylene)-4-O-TIPS-2'-O-methyl-3'-O-acetyl-5'-O-MMT-resin cytidine analogues (23). To a mixture of resin 22 in dichloromethane (40 mL) were added triethylamine (6 mL) and 4- DMAP (150 mg). After shaking at room temperature for one hour, TIPSC1 (4.5 g) was added. The mixture was continued to shake for another six hours. The resulting resin 23 was filtered, washed, and dried. To 96 mixtures of resin 23 (60 mg) in IM of diisopropylethylamine in NMP (0.75 mL) were added 96 substituted amines (see amine building blocks) (0.75 mL, IM in NMP). These mixtures were shaken at room temperature for 12 hours, at 60°C for 12 hours, then at 90°C for 24 hours. The resins were washed with CH₂CI₂ and dried. The resins were then treated with CH₃NH2 in methanol (1 M) at room temperature for 12 hours, and washed with CH₂CI₂ and dried. The final compounds were obtained treating the resins with 1 % TFA in CH₂C1₂ for 2 min. The libraries were tested by LC-MS to have 70-95% purity.

Alternative route (Scheme 2E)

Reaction a: 25 (6 mmol), MMTCI resin (4 g), pyridine (50 mL), DAMP (100 mg), room temperature 48 hours. Reaction b: 26 (6 g), TIPC1 (4 equiv.), Et₃N (6 equiv.), DMAP (100 mg), CH₂C1₂, room temperature. Reaction c: 27 (60 mg), R'R"NH (1 M in DMF, 0.75 mL), DIEA (IM in DMF, 0.75 ml), room temperature 12 hours, 60°C for 12 hours, 90°C for 24 hours; then (CH₃)₂NH, methanol, 12 hours, 1% TFA in CH₂C1₂, 2 min.

4,5,6-trisubstituted Uridine/Cytidine Nucleoside Libaries (Scheme 2F)

Eert-butyldimethylsilyl chloride (4.3 g, 28 mmol) and imidazole (2.2 g, 32 mmol) were added to a solution of 5-iodouridine (29) (3.0 g, 8.1 mmol) in pyridine (32 mL). The reaction mixture was stirred at room temperature for 24 h. Ethanol (10 mL) was added, and the solvents were evaporated under reduced pressure. The residue was dissolved in ethyl acetate and a saturated aqueous solution of sodium bicarbonate were added. The organic layer was separated and washed with brine, then dried over sodium sulfate, filtered and evaporated. The residue was subjected to silica gel chromatography to give 30 (4.8 g, 83% yield).

Lithium diisopropylamide (2 M in tetrahydrofuran, 13 mL) was added to a stirred solution of 30 (3.6 g, 5.0 mmol) in tetrahydrofuran (30 mL) at -72 °C. After stirring for 2 h at this temperature, phenyldisulfide (2.2 g, 10 mmol) was slowly added, and the reaction mixture was stirred for an additional 3 h. Acetic acid (2 mL) was added, and the mixture was warmed to room temperature. Methylene chloride and a saturated aqueous solution of sodium bicarbonate was added. The organic layer was separated, washed with brine, then dried over sodium sulfate, filtered and evaporated. The residue was subjected to silica gel chromatography to give 31 (1.9 g, 45%).

Tetrabutylammonium fluoride (1 M in tetrahydrofuran, 4.3 mL) was added to a solution of 31 (1 g, 0.12 mmol) in tetrahydrofuran, and the reaction mixture was stirred at room temperature for 16 h. The solvent was evaporated, and the residue was subjected to silica gel chromatography to give 32 (0.5 g).

Compound 32 (14.8 g, 31 mmol) was added to a suspension of 4-methoxytrityl resin (10.5 g, 18 mmol) in pyridine (80 mL). The reaction mixture was shaken for 48 h at room temperature, then methanol (10 mL) was added. The reaction mixture was shaken for an additional 30 min, then the resin was filtered and washed with pyridine (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin was dried under high vacuum at 40 °C. Mass: 16.8 g (80% loading). Acetic anhydride (5.4 mL, 57 mmol) was added to a suspension of this resin (11 g, 11 mmol) in pyridine (90 mL), and the reaction mixture was shaken at rt for 24 h. The resin was filtered and washed with pyridine (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin was dried under high vacuum at 40 °C. Mass: 11.7 g (97% yield).

Triphenylphosphine (250 mg, 0.95 mmol), cupric iodide (180 mg, 0.95 mmol) and tris(dibenzylideneacetone)dipalladium(0) (390 mg, 0.43 mmol) were added to a suspension of resin 33 (5.6 g, 5.3 mmol) in a mixture of dimethylformamide (40 mL), triethylamine (1.8 mL, 13 mmol) and phenyl acetylene (2.0 mL, 19 mmol). The reaction mixture was shaken at 80 °C for 3 h, then the resin was filtered from the hot solution. The resin was washed with dimethylformamide (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin was dried under high vacuum at 40 °C. Mass: 5.3 g.

Triphenylphosphine (505 mg, 1.9 mmol), cupric iodide (370 mg, 1.9 mmol) and palladium(II) acetate (190 mg, 0.80 mmol) were added to a suspension of resin 3 (5.8 g, 5.5 mmol) in a mixture of dimethylformamide (20 mL) and 2-(tributylstannyl)furan (6.0 mL, 19 mmol) (Stille reaction). The reaction mixture was shaken at 70 °C for 16 h, then the resin was filtered from the hot solution. The resin was washed with dimethylformamide (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin was dried under high vacuum at 40 °C. Mass: 5.3 g.

3-Nitro-l,2,4-triazole (3.4 g, 30 mmol) was added to a suspension of resin 34 (5.0 mmol) in a mixture of pyridine (40 mL) and diphenylchlorophosphate (4.1 mL, 20 mmol). The reaction mixture was shaken at rt for 48 h, then the resin was filtered and washed with pyridine (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin was dried under high vacuum at 40 °C.

Cyclopropylamine (2 M in DMF, 0.25 mL) was added to a suspension of resin 35 (50 mg, 0.04 mmol) in DMF (0.75 mL). The reaction mixture was shaken at 95 °C for 24 h, then filtered. The resin was washed with DMF (3 x 1 mL), methanol (3 x 1 mL) and methylene chloride (3 x 1 mL).

A methylamine solution (1.0 M in methanol, 1 mL) was added to resin 36 and the reaction mixture was shaken at room temperature for 16 h, then filtered. The resin was washed with methanol (3 x 1 mL), and methylene chloride (3 x 1 mL).

A 1.5% solution of TFA in dichloroethane (1 mL) was added to the resin 37 and the reaction mixture was shaken for 2 min, then methanol (1 mL) was added and the resin was filtered. The resin was washed with methanol (3 x 0.25 mL). The filtrate was evaporated under high vacuum at room temperature to give the desired nucleoside. 5,6-Disubstituted Uridine Nucleosides (Scheme 2G)

A methylamine solution (1.0 M in methanol, 1 mL) was added to resin 34 (50 mg, 0.04 mmol) (for preparation of 34, see Scheme 2F) and the reaction mixture was shaken at room temperature for 16 h, then filtered. The resin 47 was washed with methanol (3 x 1 mL), and methylene chloride (3 x 1 mL). A 1.5% solution of TFA in dichloroethane (1 mL) was added to the resin 47 and the reaction mixture was shaken for 2 min, then methanol (1 mL) was added and the resin was filtered. The resin was washed with methanol (3 x 0.25 mL). The filtrate was evaporated under high vacuum at room temperature to give the desired nucleoside 48.

4, 6-disubstituted Uridine/Cytidine Nucleoside Libaries (Scheme 2H)

Eert-butyldimethylsilyl chloride (4.3 g, 28 mmol) and imidazole (2.2 g, 32 mmol) were added to a solution of uridine (14) (2.0 g, 8.1 mmol) in pyridine (32 mL). The reaction mixture was stirred at room temperature for 24 h. Ethanol (10 mL) was added, and the solvents were evaporated under reduced pressure. The residue was dissolved in ethyl acetate and a saturated aqueous solution of sodium bicarbonate was added. The organic layer was separated and washed with brine, then dried over sodium sulfate, filtered and evaporated. The residue was subjected to silica gel chromatography to give 39 (3.9 g, 83% yield).

Lithium diisopropylamide (2 M in tetrahydrofuran, 13 mL) was added to a solution of 39 (3.0 g, 5.0 mmol) in tetrahydrofuran (30 mL) stirred at -72 °C. After 2 h at this temperature, phenyldisulfide (2.2 g, 10 mmol) was slowly added, and the reaction mixture was stirred for an additional 3 h. Acetic acid (2 mL) was added, and the mixture was allowed to reach room temperature. Methylene chloride and a saturated aqueous solution of sodium bicarbonate was added. The organic layer was separated and washed with brine, then dried over sodium sulfate, filtered and evaporated. The residue was subjected to silica gel chromatography to give 40 (1.7 g, 50%).

Tetrabutylammonium fluoride (1 M in tetrahydrofuran, 4.3 mL) was added to a solution of 40 (0.85 g, 1.2 mmol) in tetrahydrofuran, and the reaction mixture was stirred at room temperature for 16 h. The solvent was evaporated, and the residue was subjected to silica gel chromatography to give 41 (0.4 g). Compound 41 (10.9 g, 31 mmol) was added to a suspension of 4-methoxytrityl resin (10.5 g, 18 mmol) in pyridine (80 mL). The reaction mixture was shaken for 48 h at room temperature, and then methanol (10 mL) was added. The reaction mixture was shaken for an extra 30 min, and then the resin 42 was filtered and washed with pyridine (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin was dried under high vacuum at 40 °C. Mass: 13.8 g (80% loading). Acetic anhydride (5.4 mL, 57 mmol) was added to a suspension of this resin (9.7 g, 11 mmol) in pyridine (90 mL), and the reaction mixture was shaken at room temperature for 24 h. The resin was filtered and washed with pyridine (3 x 10 mL), and methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin 42 was dried under high vacuum at 40 °C. Mass: 10.2 g (97% yield).

3-Nitro-l,2,4-triazole (3.4 g, 30 mmol) was added to a suspension of resin 42 (5.0 mmol) in a mixture of pyridine (40 mL) and diphenylchlorophosphate (4.1 mL, 20 mmol). The reaction mixture was shaken at rt for 48 h, then the resin was filtered and washed with pyridine (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin was dried under high vacuum at 40 °C.

Cyclopropylamine (2 M in DMF, 0.25 mL) was added to a suspension of resin 43 (50 mg, 0.04 mmol) in DMF (0.75 mL). The reaction mixture was shaken at 95 °C for 24 h, and then filtered. The resin was washed with DMF (3 x 1 mL), methanol (3 x 1 mL) and methylene chloride (3 x 1 mL).

A methylamine solution (1.0 M in methanol, 1 mL) was added to resin 44 and the reaction mixture was shaken at room temperature for 16 h, then filtered. The resin was washed with methanol (3 x 1 mL), and methylene chloride (3 x 1 mL). A 1.5% solution of TFA in dichloroethane (1 mL) was added to the resin 45 and the reaction mixture was shaken for 2 min, then methanol (1 mL) was added and the resin was filtered. The resin was washed with methanol (3 x 0.25 mL). The filtrate was evaporated under high vacuum at room temperature to give the desired nucleoside.

4,5-disubstituted Uridine/Cytidine Nucleoside Libaries (Scheme 21)

5-Iodouridine (29) (11.4 g, 31 mmol) was added to a suspension of 4-methoxytrityl resin (10.5 g, 18 mmol) in pyridine (80 mL). The reaction mixture was shaken for 48 h at room temperature, then methanol (10 mL) was added. The reaction mixture was shaken for an additional 30 min, then the resin was filtered and washed with pyridine (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin was dried under high vacuum at 40 °C. Mass: 15.7 g (88% loading). Acetic anhydride (5.4 mL, 57 mmol) was added to a suspension of this resin (10.4 g, 11 mmol) in pyridine (90 mL), and the reaction mixture was shaken at room temperature for 24 h. The resin was filtered and washed with pyridine (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). Resin 49 was dried under high vacuum at 40 °C. Mass: 11.1 g (97% yield).

Triphenylphosphine (250 mg, 0.95 mmol), cupric iodide (180 mg, 0.95 mmol) and tris(dibenzylideneacetone)dipalladium(0) (390 mg, 0.43 mmol) were added to a suspension of resin 49 (5.3 g, 5.3 mmol) in a mixture of dimethylformamide (40 mL), triethylamine (1.8 mL, 13 mmol) and phenyl acetylene (2.0 mL, 19 mmol). The reaction mixture was shaken at 80 °C for 3 h, then the resin was filtered from the hot solution. The resin 50a was washed with dimethylformamide (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin 50a was dried under high vacuum at 40 °C. Mass: 5.0 g.

Triphenylphosphine (270 mg, 1.0 mmol), cupric iodide (195 mg, 1.0 mmol) and tris(dibenzylideneacetone)dipalladium(0) (420 mg, 0.46 mmol) were added to a suspension of resin 49 (5.2 g, 5.7 mmol) in a mixture of dimethylformamide (40 mL), triethylamine (2.0 mL, 14 mmol) and 3-butyn-l-ol (1.5 mL, 20 mmol). The reaction mixture was shaken at 80 °C for 3 h, then the resin 50b was filtered from the hot solution. The resin was washed with dimethylformamide (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin 50b was dried under high vacuum at 40 °C. Mass: 4.5 g.

Triphenylphosphine (505 mg, 1.9 mmol), cupric iodide (370 mg, 1.9 mmol) and palladium(II) acetate (190 mg, 0.80 mmol) were added to a suspension of resin 49 (5.5 g, 5.5 mmol) in a mixture of dimethylformamide (20 mL) and 2-(tributylstannyl)furan (6.0 mL, 19 mmol). The reaction mixture was shaken at 70 °C for 16 h, then the resin was filtered from the hot solution. The resin 50c was washed with dimethylformamide (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). The resin 50c was dried under high vacuum at 40 °C. Mass: 5.0 g.

3-Nitro-l,2,4-triazole (3.4 g, 30 mmol) was added to a suspension of resin 50 (5.0 mmol) in a mixture of pyridine (40 mL) and diphenylchlorophosphate (4.1 mL, 20 mmol). The reaction mixture was shaken at room temperature for 48 h, then the resin 51 was filtered and washed with pyridine (3 x 10 mL), methanol (3 x 10 mL) and methylene chloride (3 x 10 mL). Resin 51 was dried under high vacuum at 40°C.

Cyclopropylamine (2 M in DMF, 0.25 mL) was added to a suspension of resin 51 (50 mg, 0.04 mmol) in DMF (0.75 mL). The reaction mixture was shaken at 95 °C for 24 h, then filtered. The resin 52 was washed with DMF (3 x 1 mL), methanol (3 x 1 mL) and methylene chloride (3 x 1 mL).

A methylamine solution (1.0 M in methanol, 1 mL) was added to resin 52 (50 mg, 0.04 mmol) and the reaction mixture was shaken at room temperature for 16 h, then filtered. The resin 53 was washed with methanol (3 x 1 mL), and methylene chloride (3 x 1 mL). A 1.5% solution of TFA in dichloroethane (1 mL) was added to the resin 53 and the reaction mixture was shaken for 2 min, then methanol (1 mL) was added and the resin was filtered. The resin was washed with methanol (3 x 0.25 mL). The filtrate was evaporated under high vacuum at room temperature to give the desired nucleoside 54.

Anhydro-Nucleoside Libraries and Compounds (Scheme 2J)

Synthesis of anhydronucleoside libraries 58. A mixture of 4'-thio-3'-azido-5-aza- arobinocytidine (55, 2 equiv) and MMTC1 resin (1 equiv) in pyridine was shaken for 24 hours. The resin was filtered and washed with DMF, pyridine and dichloromethane. A mixture of the above dried resin and t-butyldimethylsilylchloride (2 equiv) in pyridine was shaken for 24 hours in the presence of DMAP and imidazole. The resin 56 was filtered and washed with DMF, pyridine and dichloromethane. The resulted resin was treated with alkyl carboxylic acid chloride ROC1 (first set of substrates, 3 equiv) in DMF for 24 hours and washed with DMF, pyridine and dichloromethane. The resin was further treated with tetrabutylammonium fluoride (1 M) in THF and DMF overnight. After washing as above, the resin 57 was treated with triphenylphosphine to reduce the azido group to the corresponding amino group. After thoroughly washing, the resin was treated with trifluoroacetic acid for 10 minutes. The mixture was filtered and the filtrate was concentrated to give the corresponding final libraries 58. Triazine C-Nucleoside Libraries (Scheme 2K)

A mixture of 1 '-aldehyde sugar 59 (2 equiv) and resin (1 equiv) in pyridine was shaken for 24 hours. The resin was filtered and washed with DMF, pyridine and methylenedichloride, and then heated with methanol. After washing as above, the resin 60 was treated with compound 61 for 2 days. The resin was treated with primary amines (5 equiv) in DMF and pyridine for 24 hours. The mixture was filtered and the filtrate was concentrated to provide the library 63.

Exemplary Amino Building blocks (R-NH₂ or RNHR) used for the libraries

l-(Benzyl)benzylamine, 2-phenyl-n-propylamine, m-trifluorobenzylamine, 2,2-diphenylethylamine, cyclobutylamine, methylcyclohexylamine, 2-methylpropylamine, allylcyclopentanylamine, N-methyl-4-piperidinylmethylamine, 4-hydroxypiperidine, 3-hydroxypiperidine, 1 -benzylpiperazine, p-methoxybenzylamine, N,N- bis(isopropyl)aminoethylamine, 2-ethylhexylamine, 5-methyl-2-furanosylmethylamine, N,N- dimethylaminopropylamine, 3-(N,N-dimethylamino)-2,2-dimethylpropylamine, 2- methylbutylamine, o-ethoxybenzylamine, 3-(2-methyl-N-piperidinylpropylamine, l-(2- aminoethyl)pyrrolidine, 2-morpholinylethylamine, N4-hydroxyethylpiperazine, N- methylethylenediamine, 3-morpholinylpropylamine, pyridinyl-2-ethylamine, butylamine, hexylamine, methylamine, 2-hydroxyethylamine, N,N-dimethylethylenediamine, 3-methoxypropylamine, 2-methoxylethylamine, ethylamine, 2-isopropylamine, methylethylamine, 2-methylthioethylamine, di-n-butylamine, dimethylamine, allylamine, cyclopantylamine, 2-(N-methyl-pyrrolidin-2-yl)ethylamine, tetrahydrofuranosyl-2- methylamine, piperidine, N-benzyl-4-aminopiperidine, aminomethylcyclopropane, cyclopropylamine, 3-methylpiperizine, 4-piperidin-l-ylpiperidine, cyclohexylamine, piperazine, 4-pyridin-2-ylpiperazine, 1-methylpiperazine, N-(2-methoxyphenyl)piperazine, N-pyrimidin-2-ylpiperazine, cycloheptylamine, p-trifluorobenzylamine, benzylamine, 3 -imidazol- 1 -ylpropylamine, exo-2-aminonorborane, N-phenylethylenediamine, 1-methylbenzylamine, 3,4-(l,3-dioxolanyl)benzylamine, pyridin-2-ylmethylamine, pyridin- 3-ylmethylamine, pyridin-4-ylmethylamine, thiophen-2-ylmethylamine, 3,3- dimethylbutylamine, o-methoxybenzylamine, l-(3-aminopropyl)pyrrolidin-2-one, N- methylethylenediamine, m-methylbenzylamine, 3-methylbutylamine, 2-methylbutylamine, heptylamine, 3-butoxypropyamine, 3-isopropoxypropylamine, 2-morpholin-4-ylpropylamine, N 1 ,N 1 -diethylethylenediamime, 2-ethylthioethylamine, 4-(2-aminoethyl)phenol, furfurylamine, 4-aminomethylpiperidine, 2-(2-aminoethyl)pyridine, 2-phenoxyethylamine, 2-aminoethylthiophene, p-methoxybenzylamine, 2-(N,N-dimethylamino)ethylamine, l-amino-2-propanol, 5-methylfurfurylamine, 3-(dimethylamino)propylamine, o- methoxybenzylamine, l-(3-aminopropyl)-2-pipecoline, hydrazine, 4-hydroxypiperidine, ethylenediamine, 1,4-diaminobutane, N-methylpropylamine, trans- 1,4-diaminocyclohexane, 2,2,2-trifluoroethylamine, 3-chloropropylamine, 3-ethoxypropylamine, aminoacetaldehyde dimethyl acetal, 3-amino-l,2-propanediol, l,3-diamino-2-hydroxypropane, 1- aminopyrrolidine, 2-(2-aminoethyl)-l-methylpyrrolidine, 3-methylpiperidine, 2-piperidine methanol, 3-piperidine methanol, 1 -aminohomopiperidine, homopiperazine, 4- aminomo holine, 3-bromobenzylamine, piperonylamine, 1,2,3,4-tetrahydroisoquinoline, L-proline methyl ester, l-(2-pyridyl)piperazine, 4-(2-aminoethyl)morpholine, l-(2- aminoethyl)piperidine, 3-aminopropipnitrile, 3-(aminomethyl)pyridine, 2- (aminomethyl)pyridine, thiomorpholine, l,4-dioxa-8-azaspiro(4,5)-decane, 2- hydroxylethylamine, 1 -(2-aminoethyl)pyrrolidine, aminomethylcyclohexane, 2- hydroxymethylpyrrolidine, 3-amino-l,2-propanediol acetone ketal, N-(2- hydroxyethyl)piperazine, N-phenylethylenediamine, 4-amino-2,2,6,6-tetramethylpiperidine, N-(4-nitrophenyl)ethylenediamine, 1 ,2-diphenylethylamine, 1 -(N,N-dimethylamino)-2- propylamine, 2-phenylpropylamine, 2-methylcyclopropylamine, 2-methylaziridine, aminomethylcyclopropane, l-aminomethyl-2-methylcyclopropane, butten-3-ylamine, 3- methyl-buten-2-ylamine, 3-methyl-buten-3-ylamine, 4-aminomethyl-l-cyclohexene, 3- phenylallylamine, 2,2-dimethylethylenediamine, 3-ethylhexylamine, 3-(N,N-dimethylamino)- 2,2-dimethylpropylamine, 2-methyl-N-aminopropylpiperidine, as well as other related aliphatic and aromatic primary and secondary amines that are good nucleophiles to react with leaving groups on the scaffolds.

Exemplary Building Blocks for 5-Position used for the libraries

2-Ethynylpyridine, 5-Phenyl- 1 -pentyne, 4-(tert-Butyl)phenylacetylene, Phenylacetylene, 3-Dibutylamino-l-propyne, Phenyl propargyl ether, 5-Chloro-l -pentyne, 3- Diethylamino-1-propyne, 4-Phenyl-l-butyne, 1-Heptyne, l-Dimethylamino-2-propyne, 1- Pentyne, 2-Methyl-l-hexene, (Triethylsilyl)acetylene, 3 -Phenyl- 1-propyne, Methyl propargyl ether, 3 -Cyclopentyl- 1-propyne, 1-Ethynylcyclohexene, 3-Butyn-l-ol, Styrene, Vinylcyclohexane, 2-(Tributylstannyl)furan, 2-(Tributylstannyl)thiophene, Tetraphenyltin, 3-Cyclohexyl- 1 -propyne, 4-methoxyphenylacetylene, 4-(trifluoromethyl)phenyleneacetylene, 4-fluorophenylacetylene, 4-pentayn-l-ol, 4-methylphenylacetylene, 1-ethynylcyclopentanol, tetraethyltin, 2-(tributylstannyl)pyridine, 3 -methyl- 1-propyne, 5 -cyano-1 -pentyne, tributylstannyl-4-t-butylbenzene, and other related alkenes, alkynes as well as organic tin reagents.

For Heck Reaction: 4-n-pentylphenylacetylene, 1-ethynyl-l-cyclohexanol, 1- ethynylcyclohexene, N,N-dimethylpropenoamide, 2-ethynylpyridine, 5-phenyl-l -pentyne, 4-(tert-butyl)phenylacetylene, phenylacetylene, 3-dibutylamino- 1-propyne, phenyl propargyl ether, 5-chloro-l -pentyne, 3-diethylamino- 1-propyne, 4-phenyl-l-butyne, 1-heptyne, 1- dimethylamino-2-propyne, 1 -pentyne, 2-methyl-l-hexene, (triethylsilyl)acetylene, 3 -phenyl- 1- propyne, methyl propargyl ether, 3 -cyclopentyl- 1-propyne, 1-ethynylcyclohexene, 3-butyn-l- ol, styrene, vinylcyclohexane, 2-(tributylstannyl)furan, 2-(tributylstannyl)thiophene, tetraphenyltin, 3 -cyclohexyl- 1-propyne, 4-methoxyphenylacetylene, 4- (trifluoromethyl)phenyleneacetylene, 4-fluorophenylacetylene, 4-pentayn-l-ol, 4- methylphenylacetylene, 1-ethynylcyclopentanol, 3 -methyl- 1-propyne, 5-cyano-l -pentyne, cyclohexylethyne, 1-ethynylcyclohexene, 5-cyano-l -pentyne, 1 -dimethylamino-2 -propyne, N-methyl-N-propargylbenzylamine, 2-methyl-l-buten-3-yne, cyclopentylethyne, 4- nitrophenylacetylene, phenyl propargylsulfide, 4-methyl-l -pentyne, propargyl ethylsulfide, 2-prop-2-ynyloxybenzothiazole, 4-ethoxy-l-prop-2-ynyl-l,5-dihydro-2H-pyrrol-2-one, 6- methyl-5-(2-propynyl)-2-thioxo-2,3-dihydro-4(lH)-pyrimidinone and related end-alkenes and alkynes.

For Stille Reaction: tetraethyltin, 2-(tributylstannyl)pyridine, tributylstannyl-4-t- butylbenzene, ethynyltri-n-butyltin, vinyltri-n-butyltin, allyltri-n-butyltin, phenylethynyltri-n- butyltin, phenyltri-n-butyltin, (2-methoxy-2-cyclohexen-l-yl)tributyltin, 5,6-dihydro-2- (tributylstannyl)-4H-pyran, tri-n-butyl(2-furanyl)tin, tri-n-butyl(2-thienyl)tin, tributyl(phenylethenyl)tin, 4-fluoro-(tri-n-butylstannyl)benzene, 5-fluoro-2-methoxy(tri-n- butylstannyl)benzene, 1 -methyl-2-(tributylstannyl)-lH-pyrrole, 5-methyl-2- tributylstannylthiophene, 2-tributylstannylthiazole, 2-trybutylstannylpyrrazine, tributyl[3- (trifluoromethyl)phenyl]stannane and other related organic tin reagents. For Suzuki Reaction: phenylboronic acid, 4-tolylboronic acid, 2-thiopheneboronic acid, thiophene-3-boronic acid, furan-2-boronic acid, cyclopentylboronic acid, 4-methylfuran- 2-boronic acid, 3-hydroxyphenyl)boronic acid, 5-methylfuran-2-boronic acid, 3- cyanophenylboronic acid, 4-cyanophenylboronic acid, (5-formyl-3-furanyl)boronic acid, furan-3-boronic acid and other related organic boronic acids.

Exemplary Building Blocks for 4 -Position used for the libraries

Phenyl disulfide, benzoyl chloride, p-toluoyl chloride, 4-biphenylcarbonyl chloride, 4-entylbenzoyl chloride, 2-naphtoyl chloride, 3-(trifluoromethyl)benzoyl chloride, 4- hexyloxy)benzoyl chloride and other related carboxylic acid chlorides.

Thus, specific embodiments and applications of substituted cytidine libraries and compounds have been disclosed. It should be apparent, however, to those skilled in the art that many more modifications besides those already described are possible without departing from the inventive concepts herein. The inventive subject matter, therefore, is not to be restricted except in the spirit of the appended claims. Moreover, in interpreting both the specification and the claims, all terms should be interpreted in the broadest possible manner consistent with the context. In particular, the terms "comprises" and "comprising" should be interpreted as referring to elements, components, or steps in a non-exclusive manner, indicating that the referenced elements, components, or steps may be present, or utilized, or combined with other elements, components, or steps that are not expressly referenced.

Claims

What is claimed is:

1. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 1 A with a first set of substituents A, X, Ri, and R₂, wherein another one of the at least two library compounds has a structure according to Formula 1A with a second set of substituents A, X, Ri, and R₂

Formula 1A

wherein A is a protected sugar bound to a solid phase or an unprotected sugar bound to a solid phase;

X is NH, NR, S, or O; Y is C=O, CONH, CSNH, or SO₂;

R', Ri and R₂ are independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl; and

wherein not all of the substituents A, X, Y, Ri, and R₂ in the first set are the same as the substituents A, X, Y, Ri, and R2 in the second set.

The library of claim 1 wherein the sugar is selected from the group consisting of a ribofuranose, a substituted ribofuranose, a carbocyclic ring system, and an arabinose, wherein the sugar is in a D-configuration or in an L-configuration, and wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atom, with R being Cι_ι₀ alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CCI₃, CC1₂H, CH₂OH, CN, COOR, and CONHR, and with R' being C ₀ alkyl, alkenyl, alkynyl, aryl.

The library of claim 2 wherein X is NH.

4. The library of claim 3 wherein the sugar is a ribofuranose.

5. A compound according to formula 1A

Formula 1A

wherein A is a protected or unprotected sugar, X is NH, NR, S, or O, and Y is C=O, CONH, CSNH, or SO₂; and

wherein R', Ri and R₂ are independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl.

6. The compound of claim 5 wherein the sugar is selected from the group consisting of a ribofuranose, a substituted ribofuranose, a carbocyclic ring system, and an arabinose, wherein the sugar is in a D-configuration or in an L-configuration, and wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atom, with R being C_MO alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CCI₃, CC1₂H, CH₂OH, CN, COOR', and CONHR, and with R being C ₀ alkyl, alkenyl, alkynyl, aryl.

7. The compound of claim 6 wherein X is NH.

8. The compound of claim 7 wherein the sugar is a ribofuranose.

9. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula IB with a first set of substituents Z, X,

and R2, wherein another one of the at least two library compounds has a structure according to Formula IB with a second set of substituents

Formula IB'

wherein X is NH, S, or O;

Z is hydrogen, N₃, NH₂, OH, SH, or NHR, wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl;

wherein R_\ and R₂ are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl; and

wherein • comprises a solid phase, and wherein not all of the substituents Z, X, Ri, and R₂ in the first set are the same as the substituents Z, X, Ri, and R₂ in the second set.

10. The library of claim 9 wherein the sugar is selected from the group consisting of a ribofuranose, a substituted ribofuranose, a carbocyclic ring system, and an arabinose, wherein the sugar is in a D-configuration or in an L-configuration, and wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atom, with R being C_MO alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CCI₃, CC1₂H, CH₂OH, CN, COOR, and CONHR', and with R* being C..ι₀ alkyl, alkenyl, alkynyl, aryl.

11. The library of claim 10 wherein X is NH and wherein Z is hydrogen, N₃, NH₂, SH, or NHR, wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl.

12. A compound according to formula IB Formula IB

wherein X is NH, S, or O;

Z is hydrogen, N₃, NH₂, OH, SH, or NHR wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl; and

wherein Ri and R₂ are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl.

13. The compound of claim 12 wherein the sugar is selected from the group consisting of a ribofuranose, a substituted ribofuranose, a carbocyclic ring system, and an arabinose, wherein the sugar is in a D-configuration or in an L-configuration, and wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atom, with R being Cι.ι₀ alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CCI₃, CC1₂H, CH₂OH, CN, COOR, and CONHR, and with R being C_MO alkyl, alkenyl, alkynyl, aryl.

14. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2A with a first set of substituents X, Ri, R₂, and R₃, and wherein another one of the at least two library compounds has a structure according to Formula 2 A with a second set of substituents

HO R₃

wherein X is NH, NHO, NHNH, or ONH;

Ri is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl;

R₂ is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, and a heterocyclic base;

R₃ is selected from the group consisting of hydrogen, methyl, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, O-alkynyl; and

wherein • comprises a solid phase, and wherein not all of the substituents X, Ri, R₂, and R₃ in the first set are the same as the substituents X, Ri, R₂, and R₃ in the second set.

15. The library of claim 14 wherein the sugar is selected from the group consisting of a ribofuranose, a substituted ribofuranose, a carbocyclic ring system, and an arabinose, wherein the sugar is in a D-configuration or in an L-configuration, and wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atom, with R being Ci-io alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CCI₃, CC1₂H, CH₂OH, CN, COOR, and CONHR', and with R being C_MO alkyl, alkenyl, alkynyl, aryl.

16. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2B with a first set of substituents X, Y, Ri, R₂, and R₃, and wherein another one of the at least two library compounds has a structure according to Formula 2B with a second set of substituents

wherein X is NH, NHO, NHNH, or ONH;

Y is CO, CS, SO₂, CONH, CSNH;

Ri is selected from the group consisting of hydrogen an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl;

wherein • comprises a solid phase, and wherein not all of the substituents X, Y, Ri, R₂, and R₃ in the first set are the same as the substituents X, Y, Ri, R₂, and R₃ in the second set.

17. The library of claim 6 wherein the sugar is selected from the group consisting of a ribofuranose, a substituted ribofuranose, a carbocyclic ring system, and an arabinose, wherein the sugar is in a D-configuration or in an L-configuration, and wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atom, with R being C_MO alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CC1₃, CC1₂H, CH₂OH, CN, COOR, and CONHR, and with R being C ₀ alkyl, alkenyl, alkynyl, aryl..

18. A compound according to Formula 2C or 2D

wherein X is NH, NHO, NHNH, or ONH;

Y is CO, CS, SO₂, CONH, CSNH;

R_\ is selected from the group consisting of hydrogen an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl;

with the proviso that Ri is not H or CH₃, when X-R₂ is NH₂.

19. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 3 A with a first set of substituents X, R, Ri, R₂, and R₃, and wherein another one of the at least two library compounds has a structure according to Formula 3 A with a second set of substituents

HO R₃

wherein X is NH, NHO, NHNH, ONH, or NHSO₂;

R and Ri are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl;

R₃ is selected from the group consisting of hydrogen, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, O-alkynyl; and

wherein • comprises a solid phase, and wherein not all of the substituents X, R, Ri, R₂, and R₃ in the first set are the same as the substituents X, R, Ri, R₂, and R₃ in the second set.

20. A compound according to Formula 3A'

Formula 3A'

HO R₃

wherein X is NH, NHO, NHNH, ONH, or NHSO₂; R and Ri are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl;

R₂ is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an aryl, a substituted aryl, and a heterocyclic base; and

R₃ is selected from the group consisting of hydrogen, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, O-alkynyl, with the proviso that R and R_\ is not H at the same time.

21. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2E with a first substituent R, and wherein another one of the at least two library compounds has a structure according to Formula 2E with a second substituent R

Formula 2E

wherein O _\PG is a protected hydroxyl, and wherein • comprises a solid phase;

wherein R is an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, or a substituted aryl; and

wherein R in the first library compound is not the same R in the second library compound.

22. A compound according to Formula 2F

23. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2G with a first substituent R, and wherein another one of the at least two library compounds has a structure according to Formula 2G with a second substituent R

Formula 2G

wherein R is an alkynyl or a substituted alkynyl, and wherein the first substituent is not the same as the second substituent.

24. A nucleoside according to Formula 2G

Formula 2G

wherein R is an alkynyl or a substituted alkynyl.

25. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2H with a first set of substituents Ri and R₂, and wherein another one of the at least two library compounds has a structure according to Formula 2H with a second set of substituents

Formula 2H

wherein R_\ is an alkynyl or a substituted alkynyl, and wherein R₂ is NRR' with R and R independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl; and

wherein not all of the substituents Ri and R₂ in the first set are the same as the substituents Ri and R2 in the second set.

26. A nucleoside according to Formula 2H

Formula 2H

wherein Ri is an alkynyl or a substituted alkynyl, and wherein R₂ is NRR' with R and R independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, and a substituted aryl.

27. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 21 with a first set of substituents A, Ri, R₂, and R₃, and wherein another one of the at least two library compounds has a structure according to Formula 21 with a second set of substituents A, R,, R₂, and R₃

wherein A is a protected or unprotected sugar bound to a solid phase;

Ri is RS, RC(O), or ROC(O); R₂ is R, and R₃ is RNH, RR'N, RNHNH, or RS;

wherein R and R' are independently hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl; and

wherein not all of the substituents A, Ri, R₂, and R₃ in the first set are the same as the substituents A, Ri, R₂, and R₃ in the second set.

28. The nucleoside library of claim 27 wherein the sugar comprises a moiety selected from the group consisting of a ribofuranose, a substituted ribofuranose, an arabinose, and a xylofuranose, and wherein the substituent on the substituted ribofuranose is a - CR substituent on at least at one of the 2' and 3' carbon atom, with R being Ci-io alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CC1₃, CC1₂H, CH₂OH, CN, COOR, and CONHR, and with R being C_MO alkyl, alkenyl, alkynyl, aryl.

29. A nucleoside according to Formula 2J Formula 2J

wherein A is a protected or unprotected sugar;

Ri is RS, RC(O), or ROC(O); R₂ is R, and R₃ is RNH, RR'N, RNHNH, or RS; and

wherein R and R' are independently hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl.

30. The nucleoside of claim 29 wherein the sugar comprises a moiety selected from the group consisting of a ribofuranose, a substituted ribofuranose, an arabinose, and a xylofuranose, and wherein the substituent on the substituted ribofuranose is a -CR substituent on at least at one of the 2' and 3' carbon atom, with R being d.ι₀ alkyl, alkenyl, alkynyl, aryl, heterocycle, CF₃, CF₂H, CC1₃, CC1₂H, CH₂OH, CN, COOR, and CONHR, and with R' being C_MO alkyl, alkenyl, alkynyl, aryl..

31. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2K with a first set of substituents A, Ri, and R₂, and wherein another one of the at least two library compounds has a structure according to Formula 2K with a second set of substituents

Formula 2K

wherein A is a protected or unprotected sugar bound to a solid phase; Ri is RS, RC(O), or ROC(O), and R₂ is R, wherein R may be hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, or a substituted alkaryl; and

wherein not all of the first set of substituents A, Ri, and R2, are the same as the second set of substituents A, Ri, and R₂.

32. A nucleoside according to Formula 2L

Formula 2L

wherein A is a protected or unprotected sugar; and

wherein R_\ is RS, RC(O), or ROC(O), and R₂ is R, wherein R is selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, and a substituted alkaryl.

33. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 2M with a first set of substituents A, Ri, and R₂, and wherein another one of the at least two library compounds has a structure according to Formula 2M with a second set of substituents

wherein A is a protected or unprotected sugar bound to a solid phase; Ri is RS, RC(O), or ROC(O), and R₂ is RNH, RR'N, RNHNH, or RS, wherein R and R are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, and a substituted alkaryl; and

wherein not all of the first set of substituents A, Ri, and R₂, are the same as the second set of substituents A, Ri, and R₂.

34. A nucleoside according to Formula 2N

la 2N

wherein A is a protected or unprotected sugar; and

wherein R, is RS, RC(O), or ROC(O), and R₂ is RNH, RR'N, RNHNH, or RS, wherein R and R are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, and a substituted alkaryl.

35. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 20 with a first set of substituents A, Ri, and R₂, and wherein another one of the at least two library compounds has a structure according to Formula 20 with a second set of substituents

Formula 20

wherein A is a protected or unprotected sugar bound to a solid phase; Ri is R, and R₂ is RNH, RR'N, RNHNH, or RS, wherein R and R' are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, and a substituted alkaryl; and

wherein not all of the first set of substituents A, Ri, and R₂, are the same as the second set of substituents A, Ri, and R2.

36. A nucleoside according to Formula 2P

Formula 2P

wherein A is a protected or unprotected sugar; and

wherein R, is R, and R₂ is RNH, RR'N, RNHNH, or RS, wherein R and R are independently selected from the group consisting of an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, a substituted alkynyl, an aryl, a substituted aryl, an alkaryl, and a substituted alkaryl.

37. A nucleoside library comprising at least two library compounds, wherein one of the at least two library compounds has a structure according to Formula 3B with a first set of substituents X, R, Ri, R₂, R₃, Rt, R₅, and Re, and wherein another one of the at least two library compounds has a structure according to Formula 3B with a second set of substituents X, R, Ri, R2, R3, Rt, R5, and R$

wherein X is NH, NHO, NHNH, or ONH, NHSO₂;

Y is C(O), CONH, CSNH, or SO₂;

Ri, R₂, R_t, R₅, and R<$ are independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl;

R₃ is in alpha or beta orientation and is selected from the group consisting of hydrogen, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, and O-alkynyl; and

wherein not all of the substituents X, Y, Ri, R₂, R₃, R_t, R₅, and R,s in the first set are the same as the substituents X, Y, Ri, R₂, R₃, R_t, R₅, and R_ό in the second set.

38. A nucleoside according to Formula 3B'

wherein X is NH, NHO, NHNH, ONH, or NHSO₂; Y is C(O), CONH, CSNH, or SO₂;

Ri, R₂, R», R₅, and R_ are independently selected from the group consisting of hydrogen, an alkyl, a substituted alkyl, an alkenyl, a substituted alkenyl, an alkynyl, and a substituted alkynyl, an aryl and a substituted aryl; and

wherein R₃ is in alpha or beta orientation and is selected from the group consisting of hydrogen, OH, OCH₃, SH, SCH₃, O-alkyl, O-alkenyl, and O-alkynyl.

39. A nucleoside according to Formula 2V

cture 2V

wherein X is H, OH, SH, N₃, CN, NH₂, NHR, NHCOR, NHSO₂R, COOH, COOR, CH₂NO₂, Cl, F, Br, alkyl, alkenyl, or alkynyl;

R is independently alkyl, aryl, RCO, R^*SO₂, R'NHCO, R'NHCS, RNH, SH, OH, N₃, R'O, H; and

wherein R is substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or aralkyl.

40. A nucleoside according to Formula 2U

wherein R, is H, N₃, NH₂, R'CO, or R'CONH;

R₂ is H, CH₃, CF₃, CH=CH₂, or alkynyl; R₃ is H, R, COR, SO₂R, or OCOR;

R₄ is NH₂, NHR, R, halogen, or CH=CHR; and

41. A nucleoside according to Formula 2W

Structure 2W

wherein X is H, OH, SH, N₃, CN, NH₂, NHR, NHCOR', NHSO₂R, COOH, COOR, CH₂NO₂, Cl, F, Br, alkyl, alkenyl, or alkynyl;

Y is O, S, NH, CH₂, CHR;

Z is N or CH; and

R is independently alkyl, aryl, R'CO, RSO₂, R'NHCO, R'NHCS, RNH, SH, OH, N₃, R'O, H, and wherein R is substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or aralkyl.

42. A nucleoside according to Formula 2Z

Structure 2Z

wherein R is hydrogen, a substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, or alkaryl.