# Patent

## Title
Nucleoside compounds for treating viral infections

## Abstract

Disclosed are compounds, compositions and methods for treating viral infections caused by a flaviviridae family virus, such as hepatitis C virus. Such compounds are represented by Formula I as follows:




wherein, R, Y, W, W1 and W2 are as defined herein.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit under 35 U.S.C. 119(e) of U.S. Provisional Patent Application Ser. No. 60/515,153 filed Oct. 27, 2003 which application is incorporated herein by reference in its entirety.


FIELD OF THE INVENTION
The invention relates to the field of pharmaceutical chemistry, in particular to compounds, compositions and methods for treating viral infections in mammals mediated, at least in part, by a virus in the flaviviridae family of viruses.
REFERENCES
The following publications are cited in this application as superscript numbers:

    1. Giangaspero, et al., Arch. Virol. Suppl., 7: 53–62 (1993);
    2. Giangaspero, et al., Int. J. STD. AIDS, 4(5): 300–302 (1993);
    3. Yolken, et al., Lancet, 1(8637): 517–20 (1989);
    4. Wilks, et al., Lancet, 1(8629): 107 (1989);
    5. Giangaspero, et al., Lancet, 2: 110 (1988);
    6. Potts, et al., Lancet, 1(8539): 972–973 (1987);
    7. Cornberg, et al., “Hepatitis C: therapeutic perspectives.” Forum (Genova), 11(2):154–62 (2001);
    8. Dymock, et al., Antivir. Chem. Chemother. 11(2):79–96 (2000);
    9. Devos, et al., International Patent Application Publication No. WO 02/18404 A2, published 7 Mar. 2002;
    10. Sommadossi, et al., International Patent Application Publication No. WO 01/90121, published 23 May 2001;
    11. Carroll, S. S., et al., International Patent Application Publication No. WO 02057287, published 25 Jul. 2002;
    12. Carroll, S. S., et al., International Patent Application Publication No. WO 02057425, published 25 Jul. 2002;
    13. Herr, J. R., Bioorg. Med. Chem., 10: 3379–3393 (2002);
    14. Andersen, K. E. et al., Eur. J. Med. Chem, 31: 417–425 (1996);
    15. Thornber, C. W. Chem. Soc. Rev. 8: 563–580 (1979);
    16. Lipinski, C. A. Annual Reports in Med. Chem. 21: 283–297 (1986);
    17. Wissner, A. et al., J. Med. Chem. 23: 715–717 (1980);
    18. Patani, G. A. et al., Chem. Rev. 96: 3147–3176 (1996).


All of the above publications and applications are herein incorporated by reference in their entirety to the same extent as if each individual publication or application was specifically and individually indicated to be incorporated by reference in its entirety.
STATE OF THE ART
The Flaviviridae family of viruses is composed of three genera: pestivirus, flavivirus and hepacivirus (hepatitis C virus). Of these genera, flaviviruses and hepaciviruses represent important pathogens of man and are prevalent throughout the world. There are 38 flaviviruses associated with human disease, including the dengue fever viruses, yellow fever virus and Japanese encephalitis virus. Flaviviruses cause a range of acute febrile illnesses and encephalitic and hemorrhagic diseases. Hepaciviruses currently infect approximately 2 to 3% of the world population and cause persistent infections leading to chronic liver disease, cirrhosis, hepatocellular carcinoma and liver failure. Human pestiviruses have not been as extensively characterized as the animal pestiviruses. However, serological surreys indicate considerable pestivirus exposure in humans. Pestivirus infections in man have been implicated in several diseases including, but not likely limited to, congenital brain injury, infantile gastroenteritis and chronic diarrhea in human immunodeficiency virus (HIV) positive patients.1-6 
Currently, there are no antiviral pharmaceutical drugs to prevent or treat pestivirus or flavivirus infections. For hepacivirus, i.e, hepatitis C virus (HCV) infections, interferon alpha (IFN) is currently the only approved drug in the United States. HCV is a major causative agent for post-transfusion and for sporadic non-A, non-B hepatitis. Infection by HCV is insidious in a high proportion of chronically infected (and infectious) carriers who may not experience clinical symptoms for many years.
At present, the only acceptable treatment for chronic HCV is interferon (IFN-alpha) and this requires at least six (6) months of treatment and/or ribavarin, which can inhibit viral replication in infected cells and also improve liver function in some people.
SUMMARY OF THE INVENTION
This invention is directed to novel compounds that are useful in the viral infections in mammals, mediated at least in part by a virus in the flaviviridae family of viruses. Specifically, the compounds of this invention are represented by Formula I below:




wherein

    Y is a bond, CH2, or —O—;
    each of W, W1, and W2 is independently selected from the group consisting of hydrogen and a pharmaceutically acceptable prodrug;
    R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and —CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
    or pharmaceutically acceptable salts or partial salts thereof.


Preferrably, each W, W1 and W2 is independently hydrogen or a pharmaceutically acceptable prodrug selected from the group consisting of acyl, oxyacyl, phosphonate, phosphate esters, phosphate, phospho, diphospho, triphospho, phosphonamidate, phosphorodiamidate, phosphoramidate monoester, cyclic phosphoramidate, cyclic phosphorodiamidate, phosphoramidate diester, and —C(O)CHR4NH2 where R4 is a sidechain of an amino acid; or where W and W1 may optionally join together to form a cyclic phosphonamidate.
In a particularly preferred embodiment, the compounds of this invention are represented by Formula II below:




wherein:

    each W, W1, and W2 is independently selected from the group consisting of hydrogen and a pharmaceutically acceptable prodrug;
    R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and —CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
    or pharmaceutically acceptable salts or partial salts thereof.


In a still further preferred embodiment, the compounds of this invention are represented by Formula III–IX as follows:







where R, W, W1 and W2 are as defined above.
In the compounds of formulas I–IV and VIII, preferably W is hydrogen, phospho, diphospho, or triphospho.
R is preferably, formyl, carbaldehyde oxime, —B(OH)2, —CH═NNHR1, or —CH(OEt)2.
Particularly preferred compounds of this invention include those set forth in the following Table I (including pharmaceutically acceptable salts or partial salts thereof):









TABLE I





#
Structure
Name

















100




7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(diisopropoxymethyl)pyrrolo[2,3-d]pyrimidine


 


101




7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine


 


102




7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(carbaldehyde oxime)-pyrrolo[2,3-d]pyrimidine


 


103




7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(boronic acid)-pyrrolo[2,3-d]pyrimidine


 


104




7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(diethoxymethyl)-pyrrolo[2,3-d]pyrimidine


 


 


105




7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine


 


106




7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(carbaldehydeoxime)-pyrrolo[2,3-d]pyrimidine


 


107




7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(boronic acid)-pyrrolo[2,3-d]pyrimidine


 


108




7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(diethoxymethyl)-pyrrolo[2,3-d]pyrimidine


 


109




7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine


 


110




7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine


 


111




7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(boronicacid)-pyrrolo[2,3-d]pyrimidine


 


112




7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(diethoxymethyl)-pyrrolo[2,3-d]pyrimidine


 


113




7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine


 


114




7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine


 


115




7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(boronicacid)-pyrrolo[2,3-d]pyrimidine


 


 


116




7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(diethoxymethyl)-pyrrolo[2,3-d]pyrimidine


 


117




7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(hydrazono)-pyrrolo[2,3-d]pyrimidine


 


118




7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(hydrazono)-pyrrolo[2,3-d]pyrimidine


 


119




7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(hydrazono)-pyrrolo[2,3-d]pyrimidine


 


120




7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(hydrazono)-pyrrolo[2,3-d]pyrimidine


 


121




7-(2′-C-methyl-5′-monophospho-β-D-ribofuranosyl)-4-amino-5-(diisopropoxymethyl)-pyrrolo[2,3-d]pyrimidine


 


122




7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(diisopropoxymethyl)-pyrrolo[2,3-d]pyrimidine


 


123




7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(diisopropoxymethyl)-pyrrolo[2,3-d]pyrimidine









Compounds of this invention are active as antiviral agents or useful as intermediates in the preparation of antiviral agents of Formula I–IX.
This invention is also directed to pharmaceutical compositions comprising a pharmaceutically acceptable diluent and a therapeutically effective amount of a compound of Formula I–IX or mixtures of one or more of such compounds.
This invention is still further directed to methods for treating a viral infection mediated at least in part by a virus in the flaviviridae family of viruses, such as HCV, in mammals which methods comprise administering to a mammal, that has been diagnosed with said viral infection or is at risk of developing said viral infection, a pharmaceutical composition comprising a pharmaceutically acceptable diluent and a therapeutically effective amount of a compound of Formula I–IX or mixtures of one or more of such compounds.
In yet another embodiment of the invention, methods of treating or preventing viral infections in mammals are provided where in the compounds of this invention are administered in combination with the administration of a therapeutically effective amount of one or more agents active against HCV. Active agents against HCV include ribavirin, levovirin, thymosin alpha-1, an inhibitor of NS3 serine protease, and inhibitor of inosine monophosphate dehydrogenase, interferon-alpha, pegylated interferon-alpha, alone or in combination with ribavirin or levovirin. Prefereably the additional agent active against HCV is interferon-alpha or pegylated interferon-alpha alone or in combination with ribavirin or levovirin.


DETAILED DESCRIPTION OF THE INVENTION
The invention is directed to compounds, compositions and methods for treating flaviviridae viruses, such as hepatitis C virus infections. However, prior to describing this invention in detail, the following terms will first be defined:
Definitions
As used herein, “alkyl” refers to alkyl groups having from 1 to 6 carbon atoms and more preferably 1 to 3 carbon atoms. This term is exemplified by groups such as methyl, ethyl, n-propyl, iso-propyl, n-butyl, t-butyl, n-pentyl and the like.
“Substituted alkyl” refers to an alkyl group having from 1 to 3, and preferably 1 to 2, substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, oxyacyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclic, and substituted heterocyclic.
“Alkoxy” refers to the group “alkyl-O—” which includes, by way of example, methoxy, ethoxy, n-propoxy, iso-propoxy, n-butoxy, t-butoxy, sec-butoxy, n-pentoxy and the like.
“Substituted alkoxy” refers to the group “substituted alkyl-O—”.
“Acyl” refers to the groups H—C(O)—, alkyl-C(O)—, substituted alkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—, substituted alkynyl-C(O)— cycloalkyl-C(O)—, substituted cycloalkyl-C(O)—, aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substituted heteroaryl-C(O), heterocyclic-C(O)—, and substituted heterocyclic-C(O)—.
“Acylamino” refers to the group —C(O)NR2R2 where each R2 is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclic, substituted heterocyclic and where each R2 is joined to form together with the nitrogen atom a heterocyclic or substituted heterocyclic ring.
“Acyloxy” refers to the groups alkyl-C(O)O—, substituted alkyl-C(O)O—, alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substituted alkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—, heterocyclic-C(O)O—, and substituted heterocyclic-C(O)O—.
“Oxyacyl” refers to the groups alkyl-OC(O)—, substituted alkyl-OC(O)—, alkenyl-OC(O)—, substituted alkenyl-OC(O)—, alkynyl-OC(O)—, substituted alkynyl-OC(O)—, aryl-OC(O)—, substituted aryl-OC(O)—, cycloalkyl-OC(O)—, substituted cycloalkyl-OC(O)—, heteroaryl-OC(O)—, substituted heteroaryl-OC(O)—, heterocyclic-OC(O)—, and substituted heterocyclic-OC(O)—.
“Alkenyl” refers to alkenyl group preferably having from 2 to 6 carbon atoms and more preferably 2 to 4 carbon atoms and having at least 1 and preferably from 1–2 sites of alkenyl unsaturation. Such groups are exemplified by vinyl (ethen-1-yl), allyl, but-3-en-1-yl, and the like.
“Substituted alkenyl” refers to alkenyl groups having from 1 to 3 substituents, and preferably 1 to 2 substituents, selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl esters, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclic, and substituted heterocyclic with the proviso that any hydroxyl substitution is not attached to a vinyl (unsaturated) carbon atom. Preferred substituted alkenyl groups are selected from, but not limit to, 2,2-difluoroethen-1-yl, 2-methoxyethen-1-yl, and the like.
It is understood that the term “substituted alkenyl” includes both E (cis) and Z (trans) isomers as appropriate. The isomers can be pure isomeric compounds or mixtures of E and Z components.
“Alkynyl” refers to an unsaturated hydrocarbon having at least 1 site of alkynyl unsaturation and having from 2 to 6 carbon atoms and more preferably 2 to 4 carbon atoms. Preferred alkynyl groups are selected from but not limit to ethyn-1-yl, propyn-1-yl, propyn-2-yl, butyn-1-yl, and the like.
“Substituted alkynyl” refers to alkynyl groups having from 1 to 3 substituents, and preferably 1 to 2 substituents, selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclic, and substituted heterocyclic. Preferred substituted alkynyl groups are selected from but not limit to 2-fluoroethyn-1-yl, 3,3,3-trifluoropropyn-1-yl, 3-aminopropyn-1-yl, 3-hydroxypropyn-1-yl, and the like.
“Amino” refers to the group —NH2.
“Substituted amino” refers to the group —NR′R′′ where R′ and R′′ are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclic, substituted heterocyclic and where R′ and R′′ are joined, together with the nitrogen bound thereto to form a heterocyclic or substituted heterocyclic group provided that R′ and R′′ are both not hydrogen. When R′ is hydrogen and R′′ is alkyl, the substituted amino group is sometimes referred to herein as alkylamino. When R′ and R′′ are alkyl, the substituted amino group is sometimes referred to herein as dialkylamino.
“Aminoacyl” refers to the groups —NR3C(O)alkyl, —NR3C(O)substituted alkyl, —NR3C(O)cycloalkyl, —NR3C(O)substituted cycloalkyl, —NR3C(O)alkenyl, —NR3C(O)substituted alkenyl, —NR3C(O)alkynyl, —NR3C(O)substituted alkynyl, —NR3C(O)aryl, —NR3C(O)substituted aryl, —NR3C(O)heteroaryl, —NR3C(O)substituted heteroaryl, —NR3C(O)heterocyclic, and —NR3C(O)substituted heterocyclic where R3 is hydrogen or alkyl.
“Aryl” or “Ar” refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring (e.g., phenyl) or multiple condensed rings (e.g., naphthyl or anthryl) which condensed rings may or may not be aromatic (e.g., 2-benzoxazolinone, 2H-1,4-benzoxazin-3(4H)-one-7-yl, and the like) provided that the point of attachment is at an aromatic carbon atom. Preferred aryls include phenyl and naphthyl.
“Substituted aryl” refers to aryl groups which are substituted with from 1 to 3 substituents, and preferably 1 to 2 substituents, selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclic, substituted thioheterocyclic, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclic, substituted heterocyclic, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy.
“Aryloxy” refers to the group aryl-O— that includes, by way of example, phenoxy, naphthoxy, and the like.
“Substituted aryloxy” refers to substituted aryl-O— groups.
“Carboxyl” refers to —COOH or salts thereof.
“Carboxyl ester” refers to the groups —C(O)O-alkyl, —C(O)O-substituted alkyl, —C(O)Oaryl, and —C(O)O-substituted aryl wherein alkyl, substituted alkyl, aryl and substituted aryl are as defined herein.
“Cycloalkyl” refers to cyclic alkyl groups of from 3 to 10 carbon atoms having single or multiple cyclic rings including, by way of example, adamantyl, cyclopropyl, cyclobutyl, cyclopentyl, cyclooctyl and the like.
“Cycloalkenyl” refers to cyclic alkenyl groups of from 4 to 10 carbon atoms having single or multiple cyclic rings and further having at least 1 and preferably from 1 to 2 internal sites of ethylenic or vinyl (>C═C<) unsaturation.
“Substituted cycloalkyl” and “substituted cycloalkenyl” refers to an cycloalkyl or cycloalkenyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl esters, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclic, and substituted heterocyclic.
“Cycloalkoxy” refers to —O-cycloalkyl groups.
“Substituted cycloalkoxy” refers to —O-substituted cycloalkyl groups.
“Halo” or “halogen” refers to fluoro, chloro, bromo or iodo and preferably is fluoro or chloro.
“Heteroaryl” refers to an aromatic group of from 1 to 10 carbon atoms and 1 to 4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur within the ring. Such heteroaryl groups can have a single ring (e.g., pyridyl or furyl) or multiple condensed rings (e.g., indolizinyl or benzothienyl) wherein the condensed rings may or may not be aromatic and/or contain a heteroatom provided that the point of attachment is through an atom of the aromatic heteroaryl group. Preferred heteroaryls include pyridyl, pyrrolyl, indolyl, thiophenyl, and furyl.
“Substituted heteroaryl” refers to heteroaryl groups that are substituted with from 1 to 3 substituents selected from the same group of substituents defined for substituted aryl.
“Heteroaryloxy” refers to the group —O-heteroaryl and “substituted heteroaryloxy” refers to the group —O-substituted heteroaryl.
“Heterocycle” or “heterocyclic” or “heterocycloalkyl” refers to a saturated or unsaturated group having a single ring or multiple condensed rings, from 1 to 10 carbon atoms and from 1 to 4 heteroatoms selected from the group consisting of nitrogen, sulfur or oxygen within the ring wherein, in fused ring systems, one or more the rings can be cycloalkyl, aryl or heteroaryl provided that the point of attachment is through the heterocyclic ring.
“Substituted heterocyclic” or “substituted heterocycloalkyl” refers to heterocycle groups that are substituted with from 1 to 3 of the same substituents as defined for substituted cycloalkyl.
Examples of heterocycles and heteroaryls include, but are not limited to, azetidine, pyrrole, imidazole, pyrazole, pyridine, pyrazine, pyrimidine, pyridazine, indolizine, isoindole, indole, dihydroindole, indazole, purine, quinolizine, isoquinoline, quinoline, phthalazine, naphthylpyridine, quinoxaline, quinazoline, cinnoline, pteridine, carbazole, carboline, phenanthridine, acridine, phenanthroline, isothiazole, phenazine, isoxazole, phenoxazine, phenothiazine, imidazolidine, imidazoline, piperidine, piperazine, indoline, phthalimide, 1,2,3,4-tetrahydro-isoquinoline, 4,5,6,7-tetrahydrobenzo[b]thiophene, thiazole, thiazolidine, thiophene, benzo[b]thiophene, morpholinyl, thiomorpholinyl (also referred to as thiamorpholinyl), piperidinyl, pyrrolidine, tetrahydrofuranyl, and the like.
“Heterocyclyloxy” refers to the group —O-heterocyclic and “substituted heterocyclyloxy” refers to the group —O-substituted heterocyclic.
“Phosphate” refers to the groups —OP(O)(OH)2 (monophosphate or sometimes phospho), —OP(O)(OH)OP(O)(OH)2 (diphosphate or sometimes diphospho) and —OP(O)(OH)OP(O)(OH)OP(O)(OH)2 (triphosphate or sometimes triphospho) or salts thereof including partial salts thereof.
“Phosphate esters” refers to the mono-, di- and tri-phosphate groups described above wherein one or more of the hydroxyl groups is replaced by an alkoxy group.
“Phosphonate” refers to the groups —OP(O)(R)(OH) or —OP(O)(R)(OR) or salts thereof including partial salts thereof, wherein each R is independently selected from hydrogen, alkyl, substituted alkyl, carboxyl, and carboxyl ester.
“Phosphorodiamidate” refers to the group below, where each R* may be the same or different and each is preferably H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.




“Phosphoramidate monoester” refers to the group below, where R′′ is preferably H or alkyl and R* may be the same or is preferably H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.




“Phosphoramidate diester” refers to the group below, where R′′ is preferably H or alkyl, R′ is preferably aryl, substituted aryl, alkyl, or substutituted alkyl, and R* is preferably H, alkyl, substituted alkyl, cycloalkyl, and substituted cycloalkyl.




“Cyclic phosphoramidate” refers to the group below, where n is 1 to 3, more preferably n is 1 to 2.




“Phosphonamidate” refers to the group below, where R* is preferably H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.




“Thiol” refers to the group —SH.
“Thioalkyl” or “alkylthioether” or “thioalkoxy” refers to the group —S-alkyl.
“Substituted thioalkyl” or “substituted alkylthioether” or “substituted thioalkoxy” refers to the group —S-substituted alkyl.
“Thiocycloalkyl” refers to the groups —S-cycloalkyl and “substituted thiocycloalkyl” refers to the group —S-substituted cycloalkyl.
“Thioaryl” refers to the group —S-aryl and “substituted thioaryl” refers to the group —S-substituted aryl.
“Thioheteroaryl” refers to the group —S-heteroaryl and “substituted thioheteroaryl” refers to the group —S-substituted heteroaryl.
“Thioheterocyclic” refers to the group —S-heterocyclic and “substituted thioheterocyclic” refers to the group —S-substituted heterocyclic.
The term “amino acid sidechain” refers to the R4 substituent of α-amino acids of the formula R5NHCH(R4)COOH where R4 is selected from the group consisting of hydrogen, alkyl, substituted alkyl and aryl and R5 is hydrogen or together with R4 and the nitrogen and carbon atoms bound thereto respectively form a heterocyclic ring. Preferably, the α-amino acid sidechain is the sidechain one of the twenty naturally occurring L amino acids.
The term “pharmaceutically acceptable prodrugs” refers to art recognized modifications to one or more functional groups which functional groups are metabolized in vivo to provide a compound of this invention or an active metabolite thereof. Such functional groups are well known in the art including acyl groups for hydroxyl and/or amino substitution, esters of mono-, di- and tri-phosphates wherein one or more of the pendent hydroxyl groups have been converted to an alkoxy, a substituted alkoxy, an aryloxy or a substituted aryloxy group, and the like.
“Pharmaceutically acceptable salt” refers to pharmaceutically acceptable salts of a compound, which salts are derived from a variety of organic and inorganic counter ions well known in the art and include, by way of example only, sodium, potassium, calcium, magnesium, ammonium, tetraalkylammonium, and the like; and when the molecule contains a basic functionality, salts of organic or inorganic acids, such as hydrochloride, hydrobromide, tartrate, mesylate, acetate, maleate, oxalate and the like.
The term “pharmaceutically acceptable partial salts” refers to compounds having a substituent capable of having more than one group form a salt but less than the maximum amount of such groups actually form a salt. For example, a diphospho group can form a plurality of salts and, if only partially ionized, the resulting group is sometimes referred to herein as a partial salt.
It is understood that in all substituted groups defined above, polymers arrived at by defining substituents with further substituents to themselves (e.g., substituted aryl having a substituted aryl group as a substituent which is itself substituted with a substituted aryl group, etc.) are not intended for inclusion herein. In such cases, the maximum number of such substituents is three. That is to say that each of the above definitions is constrained by a limitation that, for example, substituted aryl groups are limited to —substituted aryl-(substituted aryl)-substituted aryl.
Similarly, it is understood that the above definitions are not intended to include impermissible substitution patterns (e.g., methyl substituted with 5 fluoro groups or a hydroxyl group alpha to ethenylic or acetylenic unsaturation). Such impermissible substitution patterns are well known to the skilled artisan.
General Synthetic Methods
The compounds of this invention can be prepared from readily available starting materials using the following general methods and procedures. It will be appreciated that where typical or preferred process conditions (i.e., reaction temperatures, times, mole ratios of reactants, solvents, pressures, etc.) are given, other process conditions can also be used unless otherwise stated. Optimum reaction conditions may vary with the particular reactants or solvent used, but such conditions can be determined by one skilled in the art by routine optimization procedures.
Additionally, as will be apparent to those skilled in the art, conventional protecting groups may be necessary to prevent certain functional groups from undergoing undesired reactions. Suitable protecting groups for various functional groups as well as suitable conditions for protecting and deprotecting particular functional groups are well known in the art. For example, numerous protecting groups are described in T. W. Greene and G. M. Wuts, Protecting Groups in Organic Synthesis, Third Edition, Wiley, New York, 1999, and references cited therein.
Furthermore, the compounds of this invention contain one or more chiral centers. Accordingly, if desired, such compounds can be prepared or isolated as pure stereoisomers, i.e., as individual enantiomers or diastereomers, or as stereoisomer-enriched mixtures. All such stereoisomers (and enriched mixtures) are included within the scope of this invention, unless otherwise indicated. Pure stereoisomers (or enriched mixtures) may be prepared using, for example, optically active starting materials or stereoselective reagents well-known in the art. Alternatively, racemic mixtures of such compounds can be separated using, for example, chiral column chromatography, chiral resolving agents and the like.
The starting materials for the following reactions are generally known compounds or can be prepared by known procedures or obvious modifications thereof. For example, many of the starting materials are available from commercial suppliers such as Aldrich Chemical Co. (Milwaukee, Wis., USA), Bachem (Torrance, Calif., USA), Emka-Chemce or Sigma (St. Louis, Mo., USA). Others may be prepared by procedures, or obvious modifications thereof, described in standard reference texts such as Fieser and Fieser's Reagents for Organic Synthesis, Volumes 1–15 (John Wiley and Sons, 1991), Rodd's Chemistry of Carbon Compounds, Volumes 1–5 and Supplementals (Elsevier Science Publishers, 1989), Organic Reactions, Volumes 1–40 (John Wiley and Sons, 1991), March's Advanced Organic Chemistry, (John Wiley and Sons, 4th Edition), and Larock's Comprehensive Organic Transformations (VCH Publishers Inc., 1989). Specifically, the compounds of this invention may be prepared by various methods known in the art of organic chemistry in general and nucleoside and nucleotide analogue synthesis in particular. General reviews of the preparation of nucleoside and nucleotide analogues include 1) Michelson A. M. “The Chemistry of Nucleosides and Nucleotides,” Academic Press, New York, 1963; 2) Goodman L. “Basic Principles in Nucleic Acid Chemistry,” Academic Press, New York, 1974, vol. 1, Ch. 2; and 3) “Synthetic Procedures in Nucleic Acid Chemistry,” Eds. Zorbach W. & Tipson R., Wiley, New York, 1973, vol. 1 & 2.
The synthesis of the compounds of this invention generally follows either a convergent or linear synthetic pathway as described below.
The strategies available for synthesis of compounds of this invention include for example:
General Synthesis of 2′-C-Branched Nucleosides
2′-C-Branched ribonucleosides of Formula I:




where R, W, W1, and W2 are as defined above, can be prepared by one of the following general methods.

Convergent Approach: Glycosylation of Nucleobase with Appropriately Modified Sugar

The key starting material of this process is an appropriately substituted sugar with 2′-OH and 2′-H with the appropriate leaving group, for example, an acyl group or a chloro, bromo, fluoro or iodo group. The sugar can be purchased or can be prepared by any known means including standard epimerization, substitution, oxidation and/or reduction techniques. For example, commercially available 1,3,5-tri-ο-benzoyl-α-D-ribofuranose (Pfanstiel Laboratories, Inc.) can be used. The substituted sugar can then be oxidized with the appropriate oxidizing agent in a compatible solvent at a suitable temperature to yield the 2′-modified sugar. Possible oxidizing agents are, for example, Dess-Martin periodine reagent, Ac2O+ DCC in DMSO, Swern oxidation (DMSO, oxalyl chloride, triethylamine), Jones reagent (a mixture of chromic acid and sulfuric acid), Collins's reagent (dipyridine Cr(VI) oxide, Corey's reagent (pyridinium chlorochromate), pyridinium dichromate, acid dichromate, potassium permanganate, MnO2, ruthenium tetraoxide, phase transfer catalysts such as chromic acid or permanganate supported on a polymer, Cl2-pyridine, H2O2-ammonium molybdate, NaBrO2—CAN, NaOCl in HOAc, copper chromite, copper oxide, Raney nickel, palladium acetate, Meerwin-Pondorf-Verley reagent (aluminum t-butoxide with another ketone) and N-bromosuccinimide.
Coupling of an organometallic carbon nucleophile, such as a Grignard reagent, an organolithium, lithium dialkylcopper or R2—SiMe3 in TBAF with the ketone with the appropriate non-protic solvent at a suitable temperature, yields the 2′-methyl sugar. For example, CH3MgBr/TiCl4 or CH3MgBr/CeCl3 can be used as described in Wolfe et al. 1997. J. Org. Chem. 62: 1754–1759. The methylated sugar can be optionally protected with a suitable protecting group, preferably with an acyl, substituted alkyl or silyl group, by methods well known to those skilled in the art, as taught by Greene et al. Protective Groups in Organic Synthesis, John Wiley and Sons, Second Edition, 1991.
The optionally protected sugar can then be coupled to the purine base by methods well known to those skilled in the art, as taught by Townsend Chemistry of Nucleosides and Nucleotides, Plenum Press, 1994. For example, an acylated sugar can be coupled to a silylated base with a Lewis acid, such as tin tetrachloride, titanium tetrachloride or trimethylsilyltriflate in the appropriate solvent at a suitable temperature. Alternatively, a halo-sugar can be coupled to a silylated base with the presence of trimethylsilyltriflate.
In addition to the above, the 2′-C-substituted sugars used in the synthetic methods described herein are well known in the art and are described, for example, by Sommadossi, et al.5 and by Carrol, et al.6 both of which are incorporated herein by reference in their entirety.
Scheme 1 below describes the alternative synthesis of a protected sugar that is useful for coupling to the bases described herein.




where Ph is a phenyl and X is a suitable leaving group such as halo.

Formation of sugar a in Scheme 1, above, is accomplished as described by Mandal, S. B., et al., Synth. Commun., 1993, 9, page 1239, starting from commercial D-ribose. Protection of the hydroxyl groups to form sugar b is described in Witty, D. R., et al., Tet. Lett., 1990, 31, page 4787. Sugar c and d are prepared using the method of Ning, J. et al., Carbohydr. Res., 2001, 330, page 165, and methods described herein. Sugar e is prepared by using a modification of the Grignard reaction with CH3MgBr or other appropriate organometallic as described herein (with no titanium/cerium needed). Finally the halogenated sugar (X=halo) used in the subsequent coupling reaction is prepared using the same protection method as used in to make sugar b above. The halogenation is described in Seela.7 
Subsequently, any of the described nucleosides can be deprotected by methods well known to those skilled in the art, as taught by Greene et al. Protective Groups in Organic Synthesis, Jon Wiley and Sons, Second Edition, 1991.
An alternative approach to making protected sugars useful for coupling to heterocyclic bases is detailed in Scheme 2 below.




In Scheme 2, methylation of the hydroxyl group of compound 1 proceeds via conventional methodology to provide for compound 2. The 2, 3 and 5 hydroxyl groups of the compound 2 are each protected with 2,4-dichlorobenzyl groups to provide for compound 3. Selective deprotection of the 2-(2′,4′-dichlorobenzyl) group on compound 3 proceeds via contact with stannous chloride in a suitable solvent such as methylene chloride, chloroform, and the like at reduced temperatures, e.g.,  ̃0 to 5° C., until reaction completion, e.g., 24–72 hours. Oxidation of the 2-hydroxyl group proceeds as described herein to provide for compound 7. Methylation also proceeds as described herein to provide for compound 8.
Linear Approach: Modification of a Pre-Formed Nucleoside
The key starting material for this process is an appropriately substituted nucleoside with a 2′-OH and 2′-H. The nucleoside can be purchased or can be prepared by any known means including standard coupling techniques. The nucleoside can be optionally protected with suitable protecting groups, preferably with acyl, substituted alkyl or silyl groups, by methods well known to those skilled in the art, as taught by Greene et al. Protective Groups in Organic Synthesis, John Wiley and Sons, Second Edition, 1991.
The appropriately protected nucleoside can then be oxidized with the appropriate oxidizing agent in a compatible solvent at a suitable temperature to yield the 2′-modified sugar. Possible oxidizing agents are, for example, Dess-Martin periodine reagent, Ac2O+ DCC in DMSO, Swern oxidation (DMSO, oxalyl chloride, triethylamine), Jones reagent (a mixture of chromic acid and sulfuric acid), Collins's reagent (dipyridine Cr(VI) oxide, Corey's reagent (pyridinium chlorochromate), pyridinium dichromate, acid dichromate, potassium permanganate, MnO2 ruthenium tetroxide, phase transfer catalysts such as chromic acid or permanganate supported on a polymer, Cl2-pyridine, H2O2-ammonium molybdate, NaBrO2—CAN, NaOCl in HOAc, copper chromite, copper oxide, Raney nickel, palladium acetate, Meerwin-Pondorf-Verley reagent (aluminum t-butoxide with another ketone) and N-bromosuccinimide.
Coupling of an organometallic carbon nucleophile, such as a Grignard reagent, an organolithium, lithium dialkylcopper or CH3SiMe3 in TBAF with the ketone with the appropriate non-protic solvent at a suitable temperature, yields the alkyl substituted nucleoside. Isolation of the appropriate isomer is conducted as needed.
Subsequently, the nucleoside can be deprotected by methods well known to those skilled in the art, as taught by Greene et al. Protective Groups in Organic Synthesis, John Wiley and Sons, Second Edition, 1991.
In one embodiment of the invention, the D-enantiomers are preferred. However, L-enantiomers are also contemplated to be useful herein. The L-enantiomers corresponding to the compounds of the invention can be prepared following the same foregoing general methods, beginning with the corresponding L-sugar or nucleoside as starting material. In a particular embodiment, the 2′-C-branched ribonucleoside is desired.
The compounds of this invention may be prepared by various methods known in the art of organic chemistry in general and nucleoside and nucleotide analogue synthesis in particular. The starting materials for the syntheses are either readily available from commercial sources or are known or may be prepared by techniques known in the art. General reviews of the preparation of nucleoside and nucleotide analogues are included in the following:

    Michelson A. M. “The Chemistry of Nucleosides and Nucleotides,” Academic Press, New York, 1963.
    Goodman L. “Basic Principles in Nucleic Acid Chemistry,” Academic Press, New York, 1974, vol. 1, Ch. 2.
    “Synthetic Procedures in Nucleic Acid Chemistry,” Eds. Zorbach W. & Tipson R., Wiley, New York, 1973, vol. 1 & 2.


The pyrrolo[2,3-d]pyrimidinyl nucleoside derivatives of the present invention can be synthesized using the methods depicted in Scheme 3 below.
A divergent approach for preparing the pyrrolo[2,3-d]pyrimidinyl nucleosides is shown in Scheme 3 below. First commercially available 4-chloropyrrolo[2,3-d]pyrimidine 11 is halogenated at the 5-position (compound 12) using well known methods, for example, the halogenation method described in A. Gangjee et al., J. Med. Chem. (2003) 46, 591. Intermediate compound 12 may be isolated and purified using standard techniques such as chromatography, precipitation, crystallization, filtration, and the like. Alternatively, compound 12 may be isolated and used in the next step without further purification.
Compound 12 is coupled to protected 2-methyl substituted sugar 8 (the synthesis of which is described above and by Carrol, et al.,11,12) using conditions well known in the art. For example, 1-ο-methyl-3,5-bis-ο-(2,4-dichlorophenylmethyl)-2′-C-methyl-β-D-ribofuranoside 8 is dissolved in a dry inert solvent, such as dichloromethane, chloroform, carbon tetrachloride and the like, and then the solution is cooled to about 0° C. Afterwards, an excess of HBr or other appropriate reagent, in acetic acid, is added drop wise. This reaction is run for typically at about 0° C. for about 1 hour or at ambient temperature for about 2.5 hours or until substantially complete as determined by conventional techniques such as tlc. The resulting brominated sugar mixture is isolated and purified using standard techniques such as chromatography, precipitation, crystallization, filtration, and the like. Alternatively this intermediate may be isolated and used in the next step without further purification. The resulting brominated sugar mixture is co-evaporated, preferably with dry toluene, dissolved in a suitable inert diluent such as dry acetonitrile and stirred with the sodium salt of compound 12 at room temperature over night. The sodium salt of compound 12 is prepared in an inert atmosphere by suspending compound 12 in a dry inert solvent such as, acetonitrile and the like, with NaH dispersed in oil. The reaction is run for about 2 to about 24 hours at a temperature of about 0 to about 40° C. Finally compound 19 is isolated and purified using standard techniques such as chromatography, precipitation, crystallization, filtration, and the like. Alternatively, this intermediate may be isolated and used in the next step without further purification.
Deprotection of compound 19 using standard methods affords compound 20, which is converted to the 4-amino derivative (compound 21) using methods well known in the art. For example, compound 20 is added to liquid ammonia at about −80° C. and is warmed to about 80° C. for about 24 to about 48 hours. Compound 21 is isolated and purified using standard techniques such as chromatography, precipitation, crystallization, filtration, and the like. Compound 21 is reacted with carbon monoxide in the presence of a slight excess of tributyltin hydride and a catalytic amount of tetrakis (triphenyl-phosphine)palladium(0) in an inert solvent such at THF to provide for compound 23. This reaction is typically conducted at elevated temperatures of from about 30° to about 70° C. for a period of about 6 to 48 hours. Compound 25 can be prepared from 23 by heating in an alcoholic solution with acid catalyst. Alternately compound 23 can be converted to compound 24 by reaction with various substituted amine reagents (preferably hydroxyl amine or hydrazine). Compound 22 can be made from 21 using diboron reagents in the presence of palladium catalyst according to the procedure in J. Org. Chem. 1995, 60, 7508–7510. For example, compound 21 is reacted with bis(neopentyl glycolato)diboron, P(Ph3)2PdCl2, and KOAc in DMSO at 80° C. for 4 hours to provide for compound 22.




Preparation of compounds where W, W1 or W2 is other than hydrogen, using the compounds prepared in Scheme 3 above as the starting materials, can be accomplished using the methods described in the following reviews of prodrug preparation:

    1) Cooperwood, J. S. et al., “Nucleoside and Nucleotide prodrugs,” in Ed(s) Chu, C. K. Recent Advances in Nucleosides (2002), 92–147.
    2) Zemlicka, J. et al., Biochimica et Biophysica Acta (2002), 158(2–3), 276–286.
    3) Wagner, C. et al., Medicinal Research Reviews (2002), 20(6), 417–451.
    4) Meier, C. et al., Synlett (1998), (3), 233–242.


[JLH*** For example, conversion of the 5′-hydroxyl group of the 1-[5-(substituted)-4-amino-pyrrolo[2,3-d]pyrimidine]-2′-C-methyl-β-D-ribofuranoside compounds to a phospho, diphospho or triphospho-analog can prepared using the methods describe in D. W. Hutchinson, (Ed. Leroy b. Townsend) “The Synthesis, reaction and Properties of Nucleoside Mono-, Di-, Tri-, and tertaphosphate and Nucleosides with Changes in the Phosphoryl Residue,” Chemistry of Nucleosides and Nucleotides, Plenum Press, (1991) 2.]
Utility, Testing, and Administration
Utility
The present invention provides novel compounds possessing antiviral activity, including hepatitis C virus. The compounds of this invention inhibit viral replication by inhibiting the enzymes involved in replication, including RNA dependent RNA polymerase. They may also inhibit other enzymes utilized in the activity or proliferation of viruses in the flaviviridae family, such as HCV.
The compounds of the present invention can also be used as prodrug nucleosides. As such they are taken up into the cells and can be intracellularly phosphorylated by kinases to the triphosphate and are then inhibitors of the polymerase (NS5b) and/or act as chain-terminators.
Compounds of this invention may be used alone or in combination with other compounds to treat viruses.
Administration and Pharmaceutical Composition
In general, the compounds of this invention will be administered in a therapeutically effective amount by any of the accepted modes of administration for agents that serve similar utilities. The actual amount of the compound of this invention, i.e., the active ingredient, will depend upon numerous factors such as the severity of the disease to be treated, the age and relative health of the subject, the potency of the compound used, the route and form of administration, and other factors. The drug can be administered more than once a day, preferably once or twice a day.
Therapeutically effective amounts of compounds of Formula I may range from approximately 0.05 to 50 mg per kilogram body weight of the recipient per day; preferably about 0.01–25 mg/kg/day, more preferably from about 0.5 to 10 mg/kg/day. Thus, for administration to a 70 kg person, the dosage range would most preferably be about 35–70 mg per day.
In general, compounds of this invention will be administered as pharmaceutical compositions by any one of the following routes: oral, systemic (e.g., transdermal, intranasal or by suppository), or parenteral (e.g., intramuscular, intravenous or subcutaneous) administration. The preferred manner of administration is oral using a convenient daily dosage regimen that can be adjusted according to the degree of affliction. Compositions can take the form of tablets, pills, capsules, semisolids, powders, sustained release formulations, solutions, suspensions, elixirs, aerosols, or any other appropriate compositions. Another preferred manner for administering compounds of this invention is inhalation. This is an effective method for delivering a therapeutic agent directly to the respiratory tract, in particular for the treatment of diseases such as asthma and similar or related respiratory tract disorders (see U.S. Pat. No. 5,607,915).
The choice of formulation depends on various factors such as the mode of drug administration and bioavailability of the drug substance. For delivery via inhalation the compound can be formulated as liquid solution, suspensions, aerosol propellants or dry powder and loaded into a suitable dispenser for administration. There are several types of pharmaceutical inhalation devices-nebulizer inhalers, metered dose inhalers (MDI) and dry powder inhalers (DPI). Nebulizer devices produce a stream of high velocity air that causes the therapeutic agents (which are formulated in a liquid form) to spray as a mist that is carried into the patient's respiratory tract. MDI's typically are formulation packaged with a compressed gas. Upon actuation, the device discharges a measured amount of therapeutic agent by compressed gas, thus affording a reliable method of administering a set amount of agent. DPI dispenses therapeutic agents in the form of a free flowing powder that can be dispersed in the patient's inspiratory air-stream during breathing by the device. In order to achieve a free flowing powder, the therapeutic agent is formulated with an excipient such as lactose. A measured amount of the therapeutic agent is stored in a capsule form and is dispensed with each actuation.
Recently, pharmaceutical formulations have been developed especially for drugs that show poor bioavailability based upon the principle that bioavailability can be increased by increasing the surface area i.e., decreasing particle size. For example, U.S. Pat. No. 4,107,288 describes a pharmaceutical formulation having particles in the size range from 10 to 1,000 nm in which the active material is supported on a crosslinked matrix of macromolecules. U.S. Pat. No. 5,145,684 describes the production of a pharmaceutical formulation in which the drug substance is pulverized to nanoparticles (average particle size of 400 nm) in the presence of a surface modifier and then dispersed in a liquid medium to give a pharmaceutical formulation that exhibits remarkably high bioavailability.
The compositions are comprised of in general, a compound of Formula I in combination with at least one pharmaceutically acceptable excipient. Acceptable excipients are non-toxic, aid administration, and do not adversely affect the therapeutic benefit of the compound of Formula I. Such excipient may be any solid, liquid, semi-solid or, in the case of an aerosol composition, gaseous excipient that is generally available to one of skill in the art.
Solid pharmaceutical excipients include starch, cellulose, talc, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, magnesium stearate, sodium stearate, glycerol monostearate, sodium chloride, dried skim milk and the like. Liquid and semisolid excipients may be selected from glycerol, propylene glycol, water, ethanol and various oils, including those of petroleum, animal, vegetable or synthetic origin, e.g., peanut oil, soybean oil, mineral oil, sesame oil, etc. Preferred liquid carriers, particularly for injectable solutions, include water, saline, aqueous dextrose, and glycols.
Compressed gases may be used to disperse a compound of this invention in aerosol form. Inert gases suitable for this purpose are nitrogen, carbon dioxide, etc. Other suitable pharmaceutical excipients and their formulations are described in Remington's Pharmaceutical Sciences, edited by E. W. Martin (Mack Publishing Company, 18th ed., 1990).
The amount of the compound in a formulation can vary within the full range employed by those skilled in the art. Typically, the formulation will contain, on a weight percent (wt %) basis, from about 0.01–99.99 wt % of a compound of Formula I based on the total formulation, with the balance being one or more suitable pharmaceutical excipients. Preferably, the compound is present at a level of about 1–80 wt %. Representative pharmaceutical formulations containing a compound of Formula I are described below.
EXAMPLES
The examples below as well as throughout the application, the following abbreviations have the following meanings. If not defined, the terms have their generally accepted meanings.

    AcOH or HOAc=acetic acid
    atm=atmosphere
    d=doublet
    dd=doublet of doublets
    dt=doublet of triplets
    DBU=1,8-diazabicyclo[5.4.0]undec-7-ene
    DCB=dichlorobenzyl
    DMEM=Delbecco's minimum eagles medium
    DMSO=dimethylsulfoxide
    DTT=dithiothreitol
    EDTA=ethylene diamine tetraacetic acid
    eq. or eq=equivalents
    g=gram
    h=hour
    HCV=hepatitis C virus
    HPLC=high performance liquid chromatography
    IPTG=Isopropyl β-D-1-thiogalactopyranoside
    IU=international units
    KOAc=potassium acetate
    kb=kilobase
    kg=kilogram
    m=multiplet
    M=molar
    Me=methyl
    MeOH=methanol
    mg=milligram
    mL=milliliter
    mm=millimeters
    mM=millimolar
    mmol=millimol
    MS=mass spectrum
    ng=nanograms
    nm=nanometers
    nM=nanomolar
    NMR=nuclear magnetic resonance
    NTA=nitrilotriacetic acid
    NTP=nucleotide triphosphate
    RP HPLC=reverse phase high performance liquid chromatography
    s=singlet
    t=triplet
    THF=tetrahydrofuran\
    Tm=melting temperature
    UTP=uridine triphosphate
    μL=microliters
    v/v=volume to volume
    w/w=weight to weight
    wt %=weight percent


In addition, all reaction temperatures are in degrees Celsius unless reported otherwise and all percentages are molar percents again unless indicated otherwise.
In the examples below as well as elsewhere throughout this application, the claimed compounds employ the following numbering system:




Example 1
Preparation of the Intermediate 1-ο-methyl-2-methyl-3,5-bis-ο-(2,4-dichlorobenzyl)-β-D-ribofuranose




Step 1: Preparation of 1-ο-methyl-2,3,5-tris-ο-(2,4-dichlorobenzyl)-β-D-ribofuranose

The title compound is synthesized using the methods described in Marin, P.; Helv. Chim. Acta, 1995, 78, 486 starting with commercially available D-ribose.
Step 2: Preparation of 1-ο-methyl-3,5-bis-ο-(2,4-dichlorobenzyl)-β-D-ribofuranose
To a solution of the product of Step 1 (171.60 g, 0.2676 mol) in 1.8 L of methylene chloride that was cooled to 0° C., was added dropwise a solution of stannous chloride (31.522 mL, 0.2676 mol) in 134 mL of methylene chloride while stirring. After maintaining the solution at about 3° C. for approximately 27 hours, another 5.031 mL of stannous chloride (SnCl4) (0.04282 mol) was added and the solution was kept at about 3° C. overnight. After a total reaction time of approximately 43 hours, the reaction was quenched by carefully adding the solution to 1.9 L of a saturated NaHCO3 solution. Tin salts were removed via filtration through Celite after which the organic phase was isolated, dried with MgSO4 and evaporated in vacuo. The yield of raw, dark yellow oil was 173.6 g. The crude oil was used directly in the next step without further purification.
Step 3: Preparation of 1-ο-methyl-2-oxo-3,5-bis-ο-(2,4-dichlorobenzyl)-β-D-ribofuranose
To an ice cold solution of Dess-Martin periodinane (106.75 g, 0.2517 mol) in 740 mL anhydrous methylene chloride, under argon, was added a solution of the product of Step 2 above in 662 mL anhydrous methylene chloride over 0.5 hours. The reaction mixture was stirred at 0° C. for 0.5 hours and then at room temperature for 6 days. The mixture was diluted with 1.26 L of anhydrous diethyl ether and then poured into an ice-cold mixture of Na2S3O3·5H2O (241.2 g, 1.5258 mol) in 4.7 L of saturated aqueous sodium bicarbonate. The layers were separated, and the organic layer was washed with 1.3 L of saturated aqueous sodium bicarbonate, 1.7 L water and 1.3 L brine, dried with MgSO4, filtered and evaporated to give the target compound. The compound (72.38 g, 0.1507 mol) was used without further purification in the next step.
Step 4: Preparation of the Title Compound
A solution of MeMgBr in 500 mL anhydrous diethyl ether maintained at −55° C. was added dropwise to a solution of the product of step 3 above (72.38 g, 0.1507 mol) also in 502 mL of anhydrous diethyl ether. The reaction mixture was allowed to warm to −30° C. and stirred mechanically for 4 hours at from −30° C. to −15° C., then poured into 2 L ice cold water. After stirring vigorously at ambient temperature for 0.5 hours, the mixture was filtered through a Celite pad (14×5 cm), which was thoroughly washed with diethyl ether. The organic layer was dried with MgSO4, filtered and concentrated in vacuo. The residue was dissolved in hexanes ( ̃1 mL per gram crude), applied to a silica gel column (1.5 L silica gel in hexanes) and eluted with hexanes and 4:1 hexanes:ethyl acetate (v/v) to give 53.58 g (0.1080 mol) of the final purified product. The morphology of the title compound was that of an off-yellow, viscous oil.
MS: m/z 514.06 (M+NH4+).
Example 2
Preparation of 7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine




Step 1. 4-Chloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine

4-Chloro-7H-pyrrolo[2,3-d]pyrimidine 10.75 g (70 mmol) and N-iodosuccinimide (16.8 g, 75 mmol) were dissolved in 400 mL of dry DMF and left at ambient temperature in the darkness over night. The solvent was evaporated. The yiellow residue was suspended in hot 10% solution of Na2SO3, filtered, washed twice with hot water and crystallized from ethanol to yield 14.6 g (74.6%) of the title compound as off-white crystals. The mother liquid was evaporated up to 1⁄3 volume and crystallize again from ethanol to give 2.47 g (12.3%) of the title product.
Total yield is close to 100%.
Tm 212–214 (decompose)
UV λmax: 307, 266, 230, 227 nm (methanol)
MS: 277.93 (M−H), 313 (M+Cl)
1H-NMR (DMSO-d6): δ 12.94 (s, 1H), 8.58 (s, 1H), 7.94 (s, 1H)
Step 2. 7-(2′-methyl-3′,5′-bis-ο-(2,4-dichlorobenzyl)-β-D-ribofuranosyl)-4-chloro-5-iodo-pyrrolo[2,3-d]pyrimidine
The base, obtained as described above (11.2 g, 40 mmol) was suspended in 500 mL of CH3CN, NaH was added (1.6 g, 40 mmol 60% in oil) and the reaction mixture was stirred at room temperature until NaH was dissolved (about 2 hour). 1-ο-Methyl-2-methyl-3,5-bis-ο-(2,4-dichlorobenzyl)-β-D-ribofuranose (10 g, 20 mmol) was dissolved in 500 mL of DCM and cooled down to 4° C. in ice/water bath. HBr—gas was bubled through DMC solution about 30 min. Reaction was controlled by TLC by disappearance of the starting sugar (ether/hexane 1:9 v/v). Upon the reaction was completed the solvent was evaporated at the temperature not higher that 20° C. and kept for 20 min in deep vacuum to remove the traces of HBr. Solution of Na-salt of the base was fast filtrated and the filtrate was added to the sugar component. The reaction was kept overnight at ambient temperature, neutralized with 0.1 N H2SO4 and evaporated. The residue was distributed between 700 mL of ethyl acetate and 700 mL of water. Organic fraction was washed with water (150 mL), brine (150 mL), dried over Na2SO4 and evaporated to give semi crystalline mixture. Toluene (500 mL) was added to form light tan precipitate of nonreacted heterocyclic base 2.5 g (25%). Filtrate was concentrated up to the volume of 50 mL and loaded on the glass filter with silica gel (10×10 cm). The filter was washed with 10% ethyl acetate in toluene collecting 500 mL fractions. Fraction 2–4 contained the title compound; fractions 6–7 contained the heterocyclic base.
Fractions 2–4 were evaporated, ether was added to the colorless oil and the mixture was sonicated for 5 min. The off-white precipitate was formed, yield 7.4 g (50%), mother liquid was evaporated and the described procedure was repeated to yield 0.7 g more of the title nucleoside. Total yield is 8.1 g (54.4%).
Tm 67–70° C.
1H-NMR (DMSO-d6): δ 8.66 (s, 1H), 8.07 (s, 1H), 7.62–7.34 (m, 6H), 6.22 (s, 1H), 5.64 (s, 1H), 4.78–4.55 (m, 4H), 4.20 (s, 2H), 3.97–3.93 and 3.78–3.75 (dd, 1H), 0.92 (s, 3H)
MS: 743.99 (M+H),
Recovered base (total): 4 g as off-white crystals, Tm 228–230° C.
Step 3. 7-(2′-methyl-β-D-ribofuranosyl)-4-chloro-5-iodo-pyrrolo[2,3-d]pyrimidine
To the solution of the compound from the previous step (8 g, 10.7 mmol) in DCM (200 mL) at −78° C. was added boron trichloride (1M in DCM, 88 mL, 88 mmol) dropwise. The mixture was stirred at −78° C. for 2.5 hours and additionally overnight at −20° C. The reaction was quenched by addition of methanol/DCM (90 mL, 1:1) and the resulting mixture stirred at −20° C. for 30 min, then neutralized by aqueous ammonia at the same temperature. The solid was filtered and washed with methanol/DCM (250 mL, 1:1). The filtrates were combined with 50 mL of silica gel and evaporated up to dryness. Dry silica was loaded on the glass filter with silica gel (10×10 cm). The filter was washed with ethyl acetate collecting 500 mL fractions. Fraction 2–4 contained the title compound. The solvent was evaporated and the residue crystallized from acetone/hexane to give 3.3 g (72%) of title nucleoside.
1H-NMR (DMSO-d6): δ 8.84 (s, 1H), 8.20 (s, 1H), 6.21 (s, 1H), 4.00–3.60 (m, sugar), 0.84 (s, 3H)
MS: 426.26 (M+H)
Tm 182–185° C.
Step 4. 7-(2′-methyl-β-D-ribofuranosyl)-4-amino-5-iodo-pyrrolo[2,3-d]pyrimidine
Nucleoside (1.5 g, 3.5 mmol) prepared above was treated with liquid ammonia at 85° C. for 24 hours in the metal pressure reactor. After evaporation of ammonia the residue was dissolved in methanol and co-evaporated with silica gel (about 20 mL). Silica gel bearing the product was on the column (5×10 cm) with silica gel in acetone collecting 50 mL fractions. Fractions 2–8 contained the titled compound. Aceton was evaporated and the residue crystallized from methanol/acetonitrile to give 1.2 g (84%) of the titled nucleoside
Tm 220–222° C. (decompose)
1H-NMR (DMSO-d6): δ 8.20 (s, 1H), 7.80 (s, 1H), 6.80–6.50 (bs, 1H), 6.09 (s, 1H), 5.19 (t, 1H), 5.13–5.11 (m, 2H), 4.00–3.70 (m, 3H), 3.60–3.20 (m, 1H), 0.84 (s, 3H).
MS 407.32 (M+H).
Step 5: Preparation of the Title Compound
A solution was made of the compound prepared in Step 3 above (50.0 mg, 0.1231 mmol) in 5 mL dry tetrahydrofuran, which was then purged of air by slowly bubbling with carbon monoxide. To this solution was added tetrakis (triphenyl-phosphine)palladium(0) (2.8 mg, 0.0025 mmol). The reaction was stirred for 10 minutes, and then heated to 50° C. Next, tributyltin hydride in THF (35.9 μL, 0.1354 mmol) was slowly added over 2.5 hours—CO gas being continually bubbled through during this time. Upon completion, the mixture was concentrated in vacuo. The reaction crude was dissolved in 1 mL dimethylformamide, diluted to 50 mL with deionized water, and then washed through a celite pad. The solution was again concentrated down to dryness then redissolved in 1.0 mL dimethylformamide and 3.5 mL water. Purification was via HPLC.
1H-NMR (DMSO-d6): δ 9.64 (s, 1H), 8.60 (s, 1H), 8.18 (s, 1H), 7.62 (m, 2H), 6.14 (s, 1H), 5.28–5.19 (m, 3H), 3.94–3.71 (m, 4H), 0.75 (s, 3H).
MS: 309.11 (m/z).
Example 3
Preparation of 7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(carbaldehyde oxime)-pyrrolo[2,3-d]pyrimidine




To a solution of the title compound (0.1 g, 0.325 mmol) from Example 2 in 10 mL 50% ethanol was added hydroxylamine hydrochloride (0.073 g, 1.05 mmol) and KOAc (0.103 g, 1.05 mmol) and heated to 60° C. for 2.5 hours. The crude mixture was concentrated, diluted with water and purified by reverse phase HPLC on Phenominex column (250×20 mm) using gradient of acetonitrile in water from 0 to 30% over 30 min at 10 mL/min to yield 10 mg of the title compound.
1H-NMR (CD3OD): δ 0.86 (s, 3H), 3.8–4.2 (m, 4H), 6.21 (s, 1H), 7.78, 8.06, 8.08 (s, 1H). MS: 324.15 (M+H).
Example 4
Preparation of 7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(boronic acid)-pyrrolo[2,3-d]pyrimidine




To a solution of the compound from Step 4, Example 2 (60 mg, 0.148 mmol) in 1 mL DMSO was added KOAc (44 mg, 0.449 mmol), bis(neopentyl glycoloto)diboron (40 mg, 0.177 mmol). The mixture was degassed with argon and P(Ph3)2PdCl2 (3.1 mg, 0.004 mmol) was added and the reaction was heated to 80° C. for 4 hours. The mixture was diluted with water and purified by RP HPLC on Phenominex column (250×20 mm) using gradient of acetonitrile in water (with from 0 to 50% over 30 min at 10 mL/min to yield 16 mg (33%) of the title compound.
1H-NMR (D2O): δ 8.12 (s, 1H), 7.75 (s, 1H), 6.12 (s, 1H), 4.2–3.8 (m, 4H), 0.70 (s, 3H).
MS 325.13 (M+H).
Example 5
Preparation of 7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(diethoxymethyl)-pyrrolo[2,3-d]pyrimidine




To a solution of the compound from Step 5, Example 2 in anhydrous ethanol is placed activated molecular sieves and the solution is acidified with HCL. The solution is heated between 50–80° C. until starting material has been consumed. The resulting diacetal is purified on RP HPLC on Phenominex column (250×20 mm) using gradient of acetonitrile in water (with from 0 to 50% over 30 min at 10 mL/min.
Example 6
Preparation of 7-(2′-methyl-β-D-ribofuranosyl)-4-amino-5-(hydrazono)-pyrrolo[2,3-d]pyrimidine




To a solution of the compound from Step 5, Example 2 (20 mg, 0.05 mmol) in DMF was added hydrazine (2 μl, 0.060 mmol) and the reaction stirred at 50° C. for 2.5 hours. The crude reaction was purified directly on RP HPLC on PHenominex column (250×20 mm) using gradient of acetonitrile in water (with from 0 to 50% over 30 min at 10 mL/min to yield 12 mg (75%) of the title compound.
1H-NMR (CD3OD): δ 8.03 (s, 1H), 7.85 (s, 1H), 7.68 (s, 1H), 6.21 (s, 1H), 4.115–3.8 (m, 4H, sugar), 0.85 (s, 3H).
MS 323.14 (M+H).
Biological Examples
Example 1
Anti-Hepatitis C Activity
Compounds can exhibit anti-hepatitis C activity by inhibiting HCV polymerase, by inhibiting other enzymes needed in the replication cycle, or by other pathways. A number of assays have been published to assess these activities. A general method that assesses the gross increase of HCV virus in culture is disclosed in U.S. Pat. No. 5,738,985 to Miles et al. In vitro assays have been reported in Ferrari et al. Jnl. of Vir., 73:1649–1654, 1999; Ishii et al., Hepatology, 29:1227–1235, 1999; Lohmann et al., Jnl of Bio. Chem., 274:10807–10815, 1999; and Yamashita et al., Jnl. of Bio. Chem., 273:15479–15486, 1998.
WO 97/12033, filed on Sep. 27, 1996, by Emory University, listing C. Hagedorn and A. Reinoldus as inventors, which claims priority to U.S. Ser. No. 60/004,383, filed on September 1995, describes an HCV polymerase assay that can be used to evaluate the activity of the of the compounds described herein. Another HCV polymerase assay has been reported by Bartholomeusz, et al., Hepatitis C Virus (HCV) RNA polymerase assay using cloned HCV non-structural proteins; Antiviral Therapy 1996:1 (Supp 4) 18–24.
Screens that measure reductions in kinase activity from HCV drugs are disclosed in U.S. Pat. No. 6,030,785, to Katze et al., U.S. Patent No. Delvecchio et al., and U.S. Pat. No. 5,759,795 to Jubin et al. Screens that measure the protease inhibiting activity of proposed HCV drugs are disclosed in U.S. Pat. No. 5,861,267 to Su et al., U.S. Pat. No. 5,739,002 to De Francesco et al., and U.S. Pat. No. 5,597,691 to Houghton et al.
Example 2
Replicon Assay
A cell line, ET (Huh-lucubineo-ET) is used for screening of compounds of the present invention for HCV RNA dependent RNA polymerase. The ET cell line is stably transfected with RNA transcripts harboring a I389luc-ubi-neo/NS3-3′/ET; replicon with firefly luciferase-ubiquitin-neomycin phosphotransferase fusion protein and EMCV-IRES driven NS3-5B polyprotein containing the cell culture adaptive mutations (E1202G; T1280I; K1846T) (Krieger at al, 2001 and unpublished). The ET cells are grown in DMEM, supplemented with 10% fetal calf serum, 2 mM Glutamine, Penicillin (100 IU/mL)/Streptomycin (100 μg/mL), 1× nonessential amino acids, and 250 μg/mL G418 (“Geneticin”). They are all available through Life Technologies (Bethesda, Md.). The cells are plated at 0.5–1.0×104 cells/well in the 96 well plates and incubated for 24 hrs before adding nucleoside analogs. Then the compounds each at 5 and 50 μM will be added to the cells. Luciferase activity will be measured 48–72 hours later by adding a lysis buffer and the substrate (Catalog number Glo-lysis buffer E2661 and Bright-Glo leuciferase system E2620 Promega, Madison, Wis.). Cells should not be too confluent during the assay. Percent inhibition of replication will be plotted relative to no compound control. Under the same condition, cytotoxicity of the compounds will be determined using cell proliferation reagent, WST-1 (Roche, Germany). The compounds showing antiviral activities, but no significant cytotoxicities will be chosen to determine IC50 and TC50.
Example 3
Cloning and Expression of Recombinant HCV-NS5b
The coding sequence of NS5b protein is cloned by PCR from pFKI389luc/NS3-3′/ET as described by Lohmann, V., et al. (1999) Science 285, 110–113 using the following primers:

    aggacatggatccgcggggtcgggcacgagacag (SEQ. ID. NO. 1)
    aaggctggcatgcactcaatgtcctacacatggac (SEQ. ID. NO. 2)


The cloned fragment is missing the C terminus 21 amino acid residues. The cloned fragment is inserted into an IPTG-inducible expression plasmid that provides an epitope tag (His)6 at the carboxy terminus of the protein.
The recombinant enzyme is expressed in XL-1 cells and after induction of expression, the protein is purified using affinity chromatography on a nickel-NTA column. Storage condition is 10 mM Tris-HCl pH 7.5, 50 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 20% glycerol at −20° C.
Example 4
HCV-NS5b Enzyme Assay
The polymerase activity is assayed by measuring incorporation of radiolabeled UTP into a RNA product using a biotinylated, heteropolymeric template, which includes a portion of the HCV genome. Typically, the assay mixture (50 uL) contains 10 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 0.2 mM EDTA, 10 mM KCl, 1 unit/uL RNAsin, 1 mM DTT, 10 uM each of NTP, including [3H]-UTP, and 10 ng/uL heteropolymeric template. Test compounds are initially dissolved in 100% DMSO and further diluted in aqueous buffer containing 5% DMSO. Typically, compounds are tested at concentrations between 1 nM and 100 uM. Reactions are started with addition of enzyme and allowed to continue at 37° C. for 2 hours. Reactions are quenched with 8 uL of 100 mM EDTA and reaction mixtures (30 uL) are transferred to streptavidin-coated scintillation proximity microtiter plates (FlashPlates) and incubated at 4° C. overnight. Incorporation of radioactivity is determined by scintillation counting.
Formulation Examples
The following are representative pharmaceutical formulations containing a compound of the present invention.
Example 1
Tablet Formulation
The following ingredients are mixed intimately and pressed into single scored tablets.















Quantity per



Ingredient
tablet, mg



















compound of this invention
400



cornstarch
50



croscarmellose sodium
25



lactose
120



magnesium stearate
5










Example 2
Capsule Formulation
The following ingredients are mixed intimately and loaded into a hard-shell gelatin capsule.















Quantity per



Ingredient
capsule, mg



















compound of this invention
200



lactose, spray-dried
148



magnesium stearate
2










Example 3
Suspension Formulation
The following ingredients are mixed to form a suspension for oral administration.














Ingredient
Amount




















compound of this invention
1.0
g



fumaric acid
0.5
g



sodium chloride
2.0
g



methyl paraben
0.15
g



propyl paraben
0.05
g



granulated sugar
25.0
g



sorbitol (70% solution)
13.00
g



Veegum K (Vanderbilt Co.)
1.0
g



flavoring
0.035
mL



colorings
0.5
mg



distilled water
q.s. to 100
mL










Example 4
Injectable Formulation
The following ingredients are mixed to form an injectable formulation.














Ingredient
Amount









compound of this invention
0.2 mg–20 mg



sodium acetate buffer solution, 0.4 M
2.0 mL



HCl (1 N) or NaOH (1 N)
q.s. to suitable pH



water (distilled, sterile)
q.s. to 20 mL










Example 5
Suppository Formulation
A suppository of total weight 2.5 g is prepared by mixing the compound of the invention with Witepsol® H-15 (triglycerides of saturated vegetable fatty acid; Riches-Nelson, Inc., New York), and has the following composition:














Ingredient
Amount









compound of the invention
500 mg



Witepsol ® H-15
balance

## Claims

1. A compound of Formula I:




wherein
Y is selected from the group consisting of a bond, —CH2— or —O—;
each of W, W1 and W2 is independently selected from the group consisting of hydrogen, acyl, oxyacyl, phosphonate, phosphate, phosphate ester, phosphonamidate, phosphorodiamidate, phosphoramidate monoester, cyclic phosphoramidate, cyclic phosphorodiamidate, phosphoramidate diester, and —C(O)CHR2NH2 where R2 is selected from the group consisiting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, and a sidechain of an amino acid; and
R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and —CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
or pharmaceutically acceptable salts or partial salts thereof,

wherein
substituted alkyl refers to an alkyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, oxyacyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
alkoxy refers to alkyl-O—;
substituted alkoxy refers to (substituted alkyl)-O—;
acyl refers to a moiety selected from the group consisting of H—C(O)—, alkyl-C(O)—, substituted alkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—, substituted alkynyl-C(O)-cycloalkyl-C(O)—, substituted cycloalkyl-C(O)—, aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substituted heteroaryl-C(O), heterocyclyl-C(O)—, and substituted heterocyclyl-C(O)—;
acylamino refers to —C(O)NR2R2 where each R2 is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where each R2 is joined to form together with the nitrogen atom a heterocyclyl or substituted heterocyclyl ring;
acyloxy refers to a moiety selected from the group consisting of alkyl-C(O)O—, substituted alkyl-C(O)O—, alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substituted alkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—, heterocyclyl-C(O)O—, and substituted heterocyclyl-C(O)O—;
oxyacyl refers to a moiety selected from the group consisting of alkyl-OC(O)—, substituted alkyl-OC(O)—, alkenyl-OC(O)—, substituted alkenyl-OC(O)—, alkynyl-OC(O)—, substituted alkynyl-OC(O)—, aryl-OC(O)—, substituted aryl-OC(O)—, cycloalkyl-OC(O)—, substituted cycloalkyl-OC(O)—, heteroaryl-OC(O)—, substituted heteroaryl-OC(O)—, heterocyclyl-OC(O)—, and substituted heterocyclyl-OC(O)—;
substituted alkenyl refers to an alkenyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl with the proviso that any hydroxyl substitution is not attached to an unsaturated carbon atom;
substituted alkynyl refers to an alkynyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
amino refers to —NH2;
substituted amino refers to NR′R′′ where R′ and R′′ are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where R′ and R′′ are joined, together with the nitrogen bound thereto to form a heterocyclyl or substituted heterocyclyl group provided that R′ and R′′ are both not hydrogen;
aminoacyl refers to a moiety selected from the group consisting of —NR3C(O)alkyl, —NR3C(O)substituted alkyl, —NR3C(O)cycloalkyl, —NR3C(O)substituted cycloalkyl, —NR3C(O)alkenyl, —NR3C(O)substituted alkenyl, —NR3C(O)alkynyl, —NR3C(O)substituted alkynyl, —NR3C(O)aryl, —NR3C(O)substituted aryl, —NR3C(O)heteroaryl, —NR3C(O)substituted heteroaryl, —NR3C(O)heterocyclyl, and —NR3C(O)substituted heterocyclyl where R3 is hydrogen or alkyl;
aryl refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring or multiple condensed rings, which condensed rings may or may not be aromatic provided that the point of attachment is at an aromatic carbon atom;
substituted aryl refers to an aryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
aryloxy refers to aryl-O—;
substituted aryloxy refers to (substituted aryl)-O—;
carboxyl refers to —COOH or salts thereof;
carboxyl ester refers to a moiety selected from the group consisting of —C(O)O-alkyl, —C(O)O-substituted alkyl, —C(O)Oaryl, and —C(O)O-substituted aryl;
cycloalkyl refers to cyclic alkyl groups of from 3 to 10 carbon atoms having single or multiple cyclic rings;
cycloalkenyl refers to cyclic alkenyl groups of from 4 to 10 carbon atoms having single or multiple cyclic rings and further having at least 1 internal site of ethylenic or vinyl (>C═C<) unsaturation;
substituted cycloalkyl refers to a cycloalkyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl substituted cycloalkenyl refers to a cycloalkenyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
cycloalkoxy refers to —O-cycloalkyl;
substituted cycloalkoxy refers to —O-substituted cycloalkyl;
halogen refers to fluoro, chloro, bromo or iodo;
heteroaryl refers to an aromatic group of from 1 to 10 carbon atoms and 1 to 4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur within a single ring or multiple condensed rings wherein the condensed rings may or may not be aromatic and/or contain a heteroatom provided that the point of attachment is through an atom of the aromatic heteroaryl group;
substituted heteroaryl refers to a heteroaryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
heteroaryloxy refers to —O-heteroaryl;
substituted heteroaryloxy refers to —O-(substituted heteroaryl);
heterocyclyl refers to a saturated or unsaturated group having a single ring or multiple condensed rings, from 1 to 10 carbon atoms and from 1 to 4 heteroatoms selected from the group consisting of nitrogen, sulfur or oxygen within the ring wherein, in fused ring systems, one or more the rings can be cycloalkyl, aryl or heteroaryl provided that the point of attachment is through the heterocyclyl ring;
substituted heterocyclyl refers to a heterocyclyl group substituted with from 1 to 3 of the same substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
heterocyclyloxy refers to the group —O-heterocyclyl;
substituted heterocyclyloxy refers to the group —O-(substituted heterocyclyl);
phosphate refers to a moiety selected from the group consisting of —OP(O)(OH)2 (monophosphate), —OP(O)(OH)OP(O)(OH)2 (diphosphate) and —OP(O)(OH)OP(O)(OH)OP(O)(OH)2 (triphosphate) or salts thereof, including partial salts thereof;
phosphate ester refers to a mono-, di- and tri-phosphate group, wherein one or more of the hydroxyl groups is replaced by an alkoxy group;
phosphonate refers to a moiety selected from the group consisting of —OP(O)(R)(OH) and —OP(O)(R)(OR) or salts thereof including partial salts thereof, wherein each R is independently selected from hydrogen, alkyl, substituted alkyl, carboxyl, and carboxyl ester;
phosphorodiamidate refers to the group




 where each R* may be the same or different and each is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate monoester refers to the group




 where R′′ is H or alkyl and R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate diester refers to the group below




 where R′′ is H or alkyl, R′ is aryl, substituted aryl, alkyl, or substutituted alkyl, and R* is H, alkyl, substituted alkyl, cycloalkyl, and substituted cycloalkyl;
cyclic phosphoramidate refers to the group




 where n is 1 to 3;
phosphonamidate refers to the group




 where R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
thiol refers to —SH;
thioalkyl refers to —S-alkyl;
substituted thioalkyl refers to —S-(substituted alkyl);
thiocycloalkyl refers to —S-cycloalkyl;
substituted thiocycloalkyl refers to —S-(substituted cycloalkyl);
thioaryl refers to —S-aryl;
substituted thioaryl refers to —S-(substituted aryl);
thioheteroaryl refers to —S-heteroaryl;
substituted thioheteroaryl refers to —S-(substituted heteroaryl);
thioheterocyclyl refers to —S-heterocyclyl; and
substituted thioheterocyclyl refers to —S-(substituted heterocyclyl).

2. A compound of Formula II:




wherein
each of W, W1 and W2 is independently selected from the group consisting of hydrogen, acyl, oxyacyl, phosphonate, phosphate, phosphate ester, phosphonamidate, phosphorodiamidate, phosphoramidate monoester, cyclic phosphoramidate, cyclic phosphorodiamidate, phosphoramidate diester, and —C(O)CHR2NH2 where R2 is selected from the group consisiting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, and a sidechain of an amino acid; and
R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
or pharmaceutically acceptable salts or partial salts thereof,
wherein
substituted alkyl refers to an alkyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, oxyacyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
alkoxy refers to alkyl-O—;
substituted alkoxy refers to (substituted alkyl)-O—;
acyl refers to a moiety selected from the group consisting of H—C(O)—, alkyl-C(O)—, substituted alkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—, substituted alkynyl-C(O)—cycloalkyl-C(O)—, substituted cycloalkyl-C(O)—, aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substituted heteroaryl-C(O), heterocyclyl-C(O)—, and substituted heterocyclyl-C(O)—;
acylamino refers to —C(O)NR2R2 where each R2 is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where each R2 is joined to form together with the nitrogen atom a heterocyclyl or substituted heterocyclyl ring;
acyloxy refers to a moiety selected from the group consisting of alkyl-C(O)O—, substituted alkyl-C(O)O—, alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substituted alkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—, heterocyclyl-C(O)O—, and substituted heterocyclyl-C(O)O—;
oxyacyl refers to a moiety selected from the group consisting of alkyl-OC(O)—, substituted alkyl-OC(O)—, alkenyl-OC(O)—, substituted alkenyl-OC(O)—, alkynyl-OC(O)—, substituted alkynyl-OC(O)—, aryl-OC(O)—, substituted aryl-OC(O)—, cycloalkyl-OC(O)—, substituted cycloalkyl-OC(O)—, heteroaryl-OC(O)—, substituted heteroaryl-OC(O)—, heterocyclyl-OC(O)—, and substituted heterocyclyl-OC(O)—;
substituted alkenyl refers to an alkenyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl with the proviso that any hydroxyl substitution is not attached to an unsaturated carbon atom;
substituted alkynyl refers to an alkynyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
amino refers to —H2;
substituted amino refers to —R′R′′ where R′ and R′′ are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where R′ and R′′ are joined, together with the nitrogen bound thereto to form a heterocyclyl or substituted heterocyclyl group provided that R′ and R′′ are both not hydrogen;
aminoacyl refers to a moiety selected from the group consisting of —NR3C(O)alkyl, —NR3C(O)substituted alkyl, —NR3C(O)cycloalkyl, —NR3C(O)substituted cycloalkyl, —NR3C(O)alkenyl, —NR3C(O)substituted alkenyl, —NR3C(O)alkynyl, —NR3C(O)substituted alkynyl, —NR3C(O)aryl, —NR3C(O)substituted aryl, —NR3C(O)heteroaryl, —NR3C(O)substituted heteroaryl, —NR3C(O)heterocyclyl, and —NR3C(O)substituted heterocyclyl where R3 is hydrogen or alkyl;
aryl refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring or multiple condensed rings, which condensed rings may or may not be aromatic provided that the point of attachment is at an aromatic carbon atom;
substituted aryl refers to an aryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
aryloxy refers to aryl-O—;
substituted aryloxy refers to (substituted aryl)-O—;
carboxyl refers to —COOH or salts thereof;
carboxyl ester refers to a moiety selected from the group consisting of —C(O)O-alkyl, —C(O)O-substituted alkyl, —C(O)Oaryl, and —C(O)O-substituted aryl;
cycloalkyl refers to cyclic alkyl groups of from 3 to 10 carbon atoms having single or multiple cyclic rings;
cycloalkenyl refers to cyclic alkenyl groups of from 4 to 10 carbon atoms having single or multiple cyclic rings and further having at least 1 internal site of ethylenic or vinyl (>C═C<) unsaturation;
substituted cycloalkyl refers to a cycloalkyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
substituted cycloalkenyl refers to a cycloalkenyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
cycloalkoxy refers to —O-cycloalkyl;
substituted cycloalkoxy refers to —O-substituted cycloalkyl;
halogen refers to fluoro, chloro, bromo or iodo;
heteroaryl refers to an aromatic group of from 1 to 10 carbon atoms and 1 to 4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur within a single ring or multiple condensed rings wherein the condensed rings may or may not be aromatic and/or contain a heteroatom provided that the point of attachment is through an atom of the aromatic heteroaryl group;
substituted heteroaryl refers to a heteroaryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
heteroaryloxy refers to —O-heteroaryl;
substituted heteroaryloxy refers to —O-(substituted heteroaryl);
heterocyclyl refers to a saturated or unsaturated group having a single ring or multiple condensed rings, from 1 to 10 carbon atoms and from 1 to 4 heteroatoms selected from the group consisting of nitrogen, sulfur and oxygen within the ring wherein, in fused ring systems, one or more the rings can be cycloalkyl, aryl or heteroaryl provided that the point of attachment is through the heterocyclyl ring;
substituted heterocyclyl refers to a heterocyclyl group substituted with from 1 to 3 of the same substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
heterocyclyloxy refers to the group —O-heterocyclyl;
substituted heterocyclyloxy refers to the group —O-(substituted heterocyclyl);
phosphate refers to a moiety selected from the group consisting of —OP(O)(OH)2 (monophosphate), —OP(O)(OH)OP(O)(OH)2 (diphosphate) and —OP(O)(OH)OP(O)(OH)OP(O)(OH)2 (triphosphate) or salts thereof, including partial salts thereof;
phosphate ester refers to a mono-, di- and tri-phosphate group, wherein one or more of the hydroxyl groups is replaced by an alkoxy group;
phosphonate refers to a moiety selected from the group consisting of —OP(O)(R)(OH) and —OP(O)(R)(OR) or salts thereof including partial salts thereof, wherein each R is independently selected from hydrogen, alkyl, substituted alkyl, carboxyl, and carboxyl ester;
phosphorodiamidate refers to the group




 where each R* may be the same or different and each is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate monoester refers to the group




 where R′′ is H or alkyl and R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate diester refers to the group below




 where R′′ is H or alkyl, R′ is aryl, substituted aryl, alkyl, or substutituted alkyl, and R* is H, alkyl, substituted alkyl, cycloalkyl, and substituted cycloalkyl;
cyclic phosphoramidate refers to the group




 where n is 1 to 3;
phosphonamidate refers to the group




 where R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
thiol refers to —SH;
thioalkyl refers to —S-alkyl;
substituted thioalkyl refers to —S-(substituted alkyl);
thiocycloalkyl refers to —S-cycloalkyl;
substituted thiocycloalkyl refers to —S-(substituted cycloalkyl);
thioaryl refers to —S-aryl;
substituted thioaryl refers to —S-(substituted aryl);
thioheteroaryl refers to —S-heteroaryl;
substituted thioheteroaryl refers to —S-(substituted heteroaryl);
thioheterocyclyl refers to —S-heterocyclyl; and
substituted thioheterocyclyl refers to —S-(substituted heterocyclyl).

3. A compound of Formula III;




wherein
each of W and W1 is independently selected from the group consisting of hydrogen, acyl, oxyacyl, phosphonate, phosphate, phosphate ester, phosphonamidate, phosphorodiamidate, phosphoramidate monoester, cyclic phosphoramidate, cyclic phosphorodiamidate, phosphoramidate diester, and —C(O)CHR2NH2 where R2 is selected from the group consisiting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heteroaryl, and a sidechain of an amino acid; and
R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and —CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
or pharmaceutically acceptable salts or partial salts thereof,
wherein
substituted alkyl refers to an alkyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, oxyacyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
alkoxy refers to alkyl-O—;
substituted alkoxy refers to (substituted alkyl)-O—;
acyl refers to a moiety selected from the group consisting of H—C(O)—, alkyl-C(O)—, substituted alkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—, substituted alkynyl-C(O)-cycloalkyl-C(O)—, substituted cycloalkyl-C(O)—, aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substituted heteroaryl-C(O), heterocyclyl-C(O)—, and substituted heterocyclyl-C(O)—;
acylamino refers to —C(O)NR2R2 where each R2 is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where each R2 is joined to form together with the nitrogen atom a heterocyclyl or substituted heterocyclyl ring;
acyloxy refers to a moiety selected from the group consisting of alkyl-C(O)O—, substituted alkyl-C(O)O—, alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substituted alkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—, heterocyclyl-C(O)O—, and substituted heterocyclyl-C(O)O—;
oxyacyl refers to a moiety selected from the group consisting of alkyl-OC(O)—, substituted alkyl-OC(O)—, alkenyl-OC(O)—, substituted alkenyl-OC(O)—, alkynyl-OC(O)—, substituted alkynyl-OC(O)—, aryl-OC(O)—, substituted aryl-OC(O)—, cycloalkyl-OC(O)—, substituted cycloalkyl-OC(O)—, heteroaryl-OC(O)—, substituted heteroaryl-OC(O)—, heterocyclyl-OC(O)—, and substituted heterocyclyl-OC(O)—;
substituted alkenyl refers to an alkenyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl with the proviso that any hydroxyl substitution is not attached to an unsaturated carbon atom;
substituted alkynyl refers to an alkynyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
amino refers to —NH2;
substituted amino refers to —NR′R′′ where R′ and R′′ are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where R′ and R′′ are joined, together with the nitrogen bound thereto to form a heterocyclyl or substituted heterocyclyl group provided that R′ and R′′ are both not hydrogen;
aminoacyl refers to a moiety selected from the group consisting of —NR3C(O)alkyl, —NR3C(O)substituted alkyl, —NR3C(O)cycloalkyl, —NR3C(O)substituted cycloalkyl, —NR3C(O)alkenyl, —NR3C(O)substituted alkenyl, —NR3C(O)alkynyl, —NR3C(O)substituted alkynyl, —NR3C(O)aryl, —NR3C(O)substituted aryl, —NR3C(O)heteroaryl, —NR3C(O)substituted heteroaryl, —NR3C(O)heterocyclyl, and —NR3C(O)substituted heterocyclyl where R3 is hydrogen or alkyl;
aryl refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring or multiple condensed rings, which condensed rings may or may not be aromatic provided that the point of attachment is at an aromatic carbon atom;
substituted aryl refers to an aryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
aryloxy refers to aryl-O—;
substituted aryloxy refers to (substituted aryl)-O—;
carboxyl refers to —COOH or salts thereof;
carboxyl ester refers to a moiety selected from the group consisting of —C(O)O-alkyl, —C(O)O-substituted alkyl, —C(O)Oaryl, and —C(O)O-substituted aryl;
cycloalkyl refers to cyclic alkyl groups of from 3 to 10 carbon atoms having single or multiple cyclic rings;
cycloalkenyl refers to cyclic alkenyl groups of from 4 to 10 carbon atoms having single or multiple cyclic rings and further having at least 1 internal site of ethylenic or vinyl (>C═C<) unsaturation;
substituted cycloalkyl refers to a cycloalkyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl substituted cycloalkenyl refers to a cycloalkenyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
cycloalkoxy refers to —O-cycloalkyl;
substituted cycloalkoxy refers to —O-substituted cycloalkyl;
halogen refers to fluoro, chloro, bromo or iodo;
heteroaryl refers to an aromatic group of from 1 to 10 carbon atoms and 1 to 4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur within a single ring or multiple condensed rings wherein the condensed rings may or may not be aromatic and/or contain a heteroatom provided that the point of attachment is through an atom of the aromatic heteroaryl group;
substituted heteroaryl refers to a heteroaryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
heteroaryloxy refers to —O-heteroaryl;
substituted heteroaryloxy refers to —O-(substituted heteroaryl);
heterocyclyl refers to a saturated or unsaturated group having a single ring or multiple condensed rings, from 1 to 10 carbon atoms and from 1 to 4 heteroatoms selected from the group consisting of nitrogen, sulfur and oxygen within the ring wherein, in fused ring systems, one or more the rings can be cycloalkyl, aryl or heteroaryl provided that the point of attachment is through the heterocyclyl ring;
substituted heterocyclyl refers to a heterocyclyl group substituted with from 1 to 3 of the same substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
heterocyclyloxy refers to the group —O-heterocyclyl;
substituted heterocyclyloxy refers to the group —O-(substituted heterocyclyl);
phosphate refers to a moiety selected from the group consisting of —OP(O)(OH)2 (monophosphate), —OP(O)(OH)OP(O)(OH)2 (diphosphate) and —OP(O)(OH)OP(O)(OH)OP(O)(OH)2 (triphosphate) or salts thereof, including partial salts thereof;
phosphate ester refers to a mono-, di- and tri-phosphate group, wherein one or more of the hydroxyl groups is replaced by an alkoxy group;
phosphonate refers to a moiety selected from the group consisting of —OP(O)(R)(OH) and —OP(O)(R)(OR) or salts thereof including partial salts thereof, wherein each R is independently selected from hydrogen, alkyl, substituted alkyl, carboxyl, and carboxyl ester;
phosphorodiamidate refers to the group




 where each R* may be the same or different and each is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate monoester refers to the group




 where R′′ is H or alkyl and R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate diester refers to the group below




 where R′′ is H or alkyl, R′ is aryl, substituted aryl, alkyl, or substutituted alkyl, and R* is H, alkyl, substituted alkyl, cycloalkyl, and substituted cycloalkyl;
cyclic phosphoramidate refers to the group




 where n is 1 to 3;
phosphonamidate refers to the group




 where R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
thiol refers to —SH;
thioalkyl refers to —S-alkyl;
substituted thioalkyl refers to —S-(substituted alkyl);
thiocycloalkyl refers to —S-cycloalkyl;
substituted thiocycloalkyl refers to —S-(substituted cycloalkyl);
thioaryl refers to —S-aryl;
substituted thioaryl refers to —S-(substituted aryl);
thioheteroaryl refers to —S-heteroaryl;
substituted thioheteroaryl refers to —S-(substituted heteroaryl);
thioheterocyclyl refers to —S-heterocyclyl; and
substituted thioheterocyclyl refers to —S-(substituted heterocyclyl).

4. A compound of Formula IV:




wherein
each of W and W2 is independently selected from the group consisting of hydrogen, acyl, oxyacyl, phosphonate, phosphate, phosphate ester, phosphonamidate, phosphorodiamidate, phosphoramidate monoester, cyclic phosphoramidate, cyclic phosphorodiamidate, phosphoramidate diester, and —C(O)CHR2NH2 where R2 is selected from the group consisiting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, and a sidechain of an amino acid; and
R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and —CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
or pharmaceutically acceptable salts or partial salts thereof;
wherein
substituted alkyl refers to an alkyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, oxyacyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
alkoxy refers to alkyl-O—;
substituted alkoxy refers to (substituted alkyl)-O—;
acyl refers to a moiety selected from the group consisting of H—C(O)—, alkyl-C(O)—, substituted alkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—, substituted alkynyl-C(O)-cycloalkyl-C(O)—, substituted cycloalkyl-C(O)—, aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substituted heteroaryl-C(O), heterocyclyl-C(O)—, and substituted heterocyclyl-C(O)—;
acylamino refers to —C(O)NR2R2 where each R2 is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where each R2 is joined to form together with the nitrogen atom a heterocyclyl or substituted heterocyclyl ring;
acyloxy refers to a moiety selected from the group consisting of alkyl-C(O)O—, substituted alkyl-C(O)O—, alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substituted alkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—, heterocyclyl-C(O)O—, and substituted heterocyclyl-C(O)O—;
oxyacyl refers to a moiety selected from the group consisting of alkyl-OC(O)—, substituted alkyl-OC(O)—, alkenyl-OC(O)—, substituted alkenyl-OC(O)—, alkynyl-OC(O)—, substituted alkynyl-OC(O)—, aryl-OC(O)—, substituted aryl-OC(O)—, cycloalkyl-OC(O)—, substituted cycloalkyl-OC(O)—, heteroaryl-OC(O)—, substituted heteroaryl-OC(O)—, heterocyclyl-OC(O)—, and substituted heterocyclyl-OC(O)—;
substituted alkenyl refers to an alkenyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl with the proviso that any hydroxyl substitution is not attached to an unsaturated carbon atom;
substituted alkynyl refers to an alkynyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
amino refers to —NH2;
substituted amino refers to —NR′ R′′ where R′ and R′′ are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where R′ and R′′ are joined, together with the nitrogen bound thereto to form a heterocyclyl or substituted heterocyclyl group provided that R′ and R′′ are both not hydrogen;
aminoacyl refers to a moiety selected from the group consisting of —NR3C(O)alkyl, —NR3C(O)substituted alkyl, —NR3C(O)cycloalkyl, —NR3C(O)substituted cycloalkyl, —NR3C(O)alkenyl, —NR3C(O)substituted alkenyl, —NR3C(O)alkynyl, —NR3C(O)substituted alkynyl, —NR3C(O)aryl, —NR3C(O)substituted aryl, —NR3C(O)heteroaryl, —NR3C(O)substituted heteroaryl, —NR3C(O)heterocyclyl, and —NR3C(O)substituted heterocyclyl where R3 is hydrogen or alkyl;
aryl refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring or multiple condensed rings, which condensed rings may or may not be aromatic provided that the point of attachment is at an aromatic carbon atom;
substituted aryl refers to an aryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, and, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
aryloxy refers to aryl-O—;
substituted aryloxy refers to (substituted aryl)—O—;
carboxyl refers to —COOH or salts thereof;
carboxyl ester refers to a moiety selected from the group consisting of —C(O)O-alkyl, —C(O)O-substituted alkyl, —C(O)Oaryl, and —C(O)O-substituted aryl;
cycloalkyl refers to cyclic alkyl groups of from 3 to 10 carbon atoms having single or multiple cyclic rings;
cycloalkenyl refers to cyclic alkenyl groups of from 4 to 10 carbon atoms having single or multiple cyclic rings and further having at least 1 internal site of ethylenic or vinyl (>C═C<) unsaturation;
substituted cycloalkyl refers to a cycloalkyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
substituted cycloalkenyl refers to a cycloalkenyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
cycloalkoxy refers to —O-cycloalkyl;
substituted cycloalkoxy refers to —O-substituted cycloalkyl;
halogen refers to fluoro, chloro, bromo or iodo;
heteroaryl refers to an aromatic group of from 1 to 10 carbon atoms and 1 to 4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur within a single ring or multiple condensed rings wherein the condensed rings may or may not be aromatic and/or contain a heteroatom provided that the point of attachment is through an atom of the aromatic heteroaryl group;
substituted heteroaryl refers to a heteroaryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
heteroaryloxy refers to —O-heteroaryl;
substituted heteroaryloxy refers to —O-(substituted heteroaryl);
heterocyclyl refers to a saturated or unsaturated group having a single ring or multiple condensed rings, from 1 to 10 carbon atoms and from 1 to 4 heteroatoms selected from the group consisting of nitrogen, sulfur and oxygen within the ring wherein, in fused ring systems, one or more the rings can be cycloalkyl, aryl or heteroaryl provided that the point of attachment is through the heterocyclyl ring;
substituted heterocyclyl refers to a heterocyclyl group substituted with from 1 to 3 of the same substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
heterocyclyloxy refers to the group —O-heterocyclyl;
substituted heterocyclyloxy refers to the group —O-(substituted heterocyclyl);
phosphate refers to a moiety selected from the group consisting of —OP(O)(OH)2 (monophosphate), —OP(O)(OH)OP(O)(OH)2 (diphosphate) and —OP(O)(OH)OP(O)(OH)OP(O)(OH)2 (triphosphate) or salts thereof, including partial salts thereof;
phosphate ester refers to a mono-, di- and tri-phosphate group, wherein one or more of the hydroxyl groups is replaced by an alkoxy group;
phosphonate refers to a moiety selected from the group consisting of —OP(O)(R)(OH) and —OP(O)(R)(OR) or salts thereof including partial salts thereof, wherein each R is independently selected from hydrogen, alkyl, substituted alkyl, carboxyl, and carboxyl ester;
phosphorodiamidate refers to the group




 where each R* may be the same or different and each is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate monoester refers to the group




substituted thiocycloalkyl refers to —S-(substituted cycloalkyl);
thioaryl refers to —S-aryl;
substituted thioaryl refers to —S-(substituted aryl);
thioheteroaryl refers to —S-heteroaryl;
substituted thioheteroaryl refers to —S-(substituted heteroaryl);
thioheterocyclyl refers to —S-heterocyclyl; and
substituted thioheterocyclyl refers to —S-(substituted heterocyclyl).

5. A compound of Formula V:




wherein
each of W1 and W2 is independently selected from the group consisting of hydrogen, acyl, oxyacyl, phosphonate, phosphate, phosphate ester, phosphonamidate, phosphorodiamidate, phosphoramidate monoester, cyclic phosphoramidate, cyclic phosphorodiamidate, phosphoramidate diester, and —C(O)CHR2NH2 where R2 is selected from the group consisiting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, and a sidechain of an amino acid; and
R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and —CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
or pharmaceutically acceptable salts or partial salts thereof,
wherein
substituted alkyl refers to an alkyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, oxyacyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
alkoxy refers to alkyl-O—;
substituted alkoxy refers to (substituted alkyl)-O—;
acyl refers to a moiety selected from the group consisting of H—C(O)—, alkyl-C(O)—, substituted alkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—, substituted alkynyl-C(O)-cycloalkyl-C(O)—, substituted cycloalkyl-C(O)—, aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substituted heteroaryl-C(O), heterocyclyl-C(O)—, and substituted heterocyclyl-C(O)—;
acylamino refers to —C(O)NR2R2 where each R2 is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where each R2 is joined to form together with the nitrogen atom a heterocyclyl or substituted heterocyclyl ring;
acyloxy refers to a moiety selected from the group consisting of alkyl-C(O)O—, substituted alkyl-C(O)O—, alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substituted alkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—, heterocyclyl-C(O)O—, and substituted heterocyclyl-C(O)O—;
oxyacyl refers to a moiety selected from the group consisting of alkyl-OC(O)—, substituted alkyl-OC(O)—, alkenyl-OC(O)—, substituted alkenyl-OC(O)—, alkynyl-OC(O)—, substituted alkynyl-OC(O)—, aryl-OC(O)—, substituted aryl-OC(O)—, cycloalkyl-OC(O)—, substituted cycloalkyl-OC(O)—, heteroaryl-OC(O)—, substituted heteroaryl-OC(O)—, heterocyclyl-OC(O)—, and substituted heterocyclyl-OC(O)—;
substituted alkenyl refers to an alkenyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl with the proviso that any hydroxyl substitution is not attached to an unsaturated carbon atom;
substituted alkynyl refers to an alkynyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
amino refers to —NH2;
substituted amino refers to NR′R′′ where R′ and R′′ are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where R′ and R′′ are joined, together with the nitrogen bound thereto to form a heterocyclyl or substituted heterocyclyl group provided that R′ and R′′ are both not hydrogen;
aminoacyl refers to a moiety selected from the group consisting of —NR3C(O)alkyl, —NR3C(O)substituted alkyl, —NR3C(O)cycloalkyl, —NR3C(O)substituted cycloalkyl, —NR3C(O)alkenyl, —NR3C(O)substituted alkenyl, —NR3C(O)alkynyl, —NR3C(O)substituted alkynyl, —NR3C(O)aryl, —NR3C(O)substituted aryl, —NR3C(O)heteroaryl, —NR3C(O)substituted heteroaryl, —NR3C(O)heterocyclyl, and —NR3C(O)substituted heterocyclyl where R3 is hydrogen or alkyl;
aryl refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring or multiple condensed rings, which condensed rings may or may not be aromatic provided that the point of attachment is at an aromatic carbon atom;
substituted aryl refers to an aryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
aryloxy refers to aryl-O—;
substituted aryloxy refers to (substituted aryl)-O—;
carboxyl refers to —COOH or salts thereof;
carboxyl ester refers to a moiety selected from the group consisting of —C(O)O-alkyl, —C(O)O-substituted alkyl, —C(O)Oaryl, and —C(O)O-substituted aryl;
cycloalkyl refers to cyclic alkyl groups of from 3 to 10 carbon atoms having single or multiple cyclic rings;
cycloalkenyl refers to cyclic alkenyl groups of from 4 to 10 carbon atoms having single or multiple cyclic rings and further having at least 1 internal site of ethylenic or vinyl (>C═C<) unsaturation;
substituted cycloalkyl refers to a cycloalkyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
substituted cycloalkenyl refers to a cycloalkenyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
cycloalkoxy refers to —O-cycloalkyl;
substituted cycloalkoxy refers to —O-substituted cycloalkyl;
halogen refers to fluoro, chloro, bromo or iodo;
heteroaryl refers to an aromatic group of from 1 to 10 carbon atoms and 1 to 4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur within a single ring or multiple condensed rings wherein the condensed rings may or may not be aromatic and/or contain a heteroatom provided that the point of attachment is through an atom of the aromatic heteroaryl group;
substituted heteroaryl refers to a heteroaryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
heteroaryloxy refers to —O-heteroaryl;
substituted heteroaryloxy refers to —O-(substituted heteroaryl);
heterocyclyl refers to a saturated or unsaturated group having a single ring or multiple condensed rings, from 1 to 10 carbon atoms and from 1 to 4 heteroatoms selected from the group consisting of nitrogen, sulfur and oxygen within the ring wherein, in fused ring systems, one or more the rings can be cycloalkyl, aryl or heteroaryl provided that the point of attachment is through the heterocyclyl ring;
substituted heterocyclyl refers to a heterocyclyl group substituted with from 1 to 3 of the same substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
heterocyclyloxy refers to the group —O-heterocyclyl;
substituted heterocyclyloxy refers to the group —O-(substituted heterocyclyl);
phosphate refers to a moiety selected from the group consisting of —OP(O)(OH)2 (monophosphate), —OP(O)(OH)OP(O)(OH)2 (diphosphate) and —OP(O)(OH)OP(O)(OH)OP(O)(OH)2 (triphosphate) or salts thereof, including partial salts thereof;
phosphate ester refers to a mono-, di- and tri-phosphate group, wherein one or more of the hydroxyl groups is replaced by an alkoxy group;
phosphonate refers to a moiety selected from the group consisting of —OP(O)(R)(OH) and —OP(O)(R)(OR) or salts thereof including partial salts thereof, wherein each R is independently selected from hydrogen, alkyl, substituted alkyl, carboxyl, and carboxyl ester;
phosphorodiamidate refers to the group




 where each R* may be the same or different and each is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate monoester refers to the group




 where R′′ is H or alkyl and R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate diester refers to the group below




 where R′′ is H or alkyl, R′ is aryl, substituted aryl, alkyl, or substutituted alkyl, and R* is H, alkyl, substituted alkyl, cycloalkyl, and substituted cycloalkyl;
cyclic phosphoramidate refers to the group




 where n is 1 to 3;
phosphonamidate refers to the group




 where R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
thiol refers to —SH;
thioalkyl refers to —S-alkyl;
substituted thioalkyl refers to —S-(substituted alkyl);
thiocycloalkyl refers to —S-cycloalkyl;
substituted thiocycloalkyl refers to —S-(substituted cycloalkyl);
thioaryl refers to —S-aryl;
substituted thioaryl refers to —S-(substituted aryl);
thioheteroaryl refers to —S-heteroaryl;
substituted thioheteroaryl refers to —S-(substituted heteroaryl);
thioheterocyclyl refers to —S-heterocyclyl; and
substituted thioheterocyclyl refers to —S-(substituted heterocyclyl).

6. A compound of Formula VI:




wherein
W1 is selected from the group consisting of hydrogen, acyl, oxyacyl, phosphonate, phosphate, phosphate ester, phosphonamidate, phosphorodiamidate, phosphoramidate monoester, cyclic phosphoramidate, cyclic phosphorodiamidate, phosphoramidate diester, and —C(O)CHR2NH2 where R2 is selected from the group consisiting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, and a sidechain of an amino acid; and
R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and —CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
or pharmaceutically acceptable salts or partial salts thereof,
wherein
substituted alkyl refers to an alkyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, oxyacyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
alkoxy refers to alkyl-O—;
substituted alkoxy refers to (substituted alkyl)-O—;
acyl refers to a moiety selected from the group consisting of H—C(O)—, alkyl-C(O)—, substituted alkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—, substituted alkynyl-C(O)-cycloalkyl-C(O)—, substituted cycloalkyl-C(O)—, aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substituted heteroaryl-C(O), heterocyclyl-C(O)—, and substituted heterocyclyl-C(O)—;
acylamino refers to —C(O)NR2R2 where each R2 is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where each R2 is joined to form together with the nitrogen atom a heterocyclyl or substituted heterocyclyl ring;
acyloxy refers to a moiety selected from the group consisting of alkyl-C(O)O—, substituted alkyl-C(O)O—, alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substituted alkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—, heterocyclyl-C(O)O—, and substituted heterocyclyl-C(O)O—;
oxyacyl refers to a moiety selected from the group consisting of alkyl-OC(O)—, substituted alkyl-OC(O)—, alkenyl-OC(O)—, substituted alkenyl-OC(O)—, alkynyl-OC(O)—, substituted alkynyl-OC(O)—, aryl-OC(O)—, substituted aryl-OC(O)—, cycloalkyl-OC(O)—, substituted cycloalkyl-OC(O)—, heteroaryl-OC(O)—, substituted heteroaryl-OC(O)—, heterocyclyl-OC(O)—, and substituted heterocyclyl-OC(O)—;
substituted alkenyl refers to an alkenyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl with the proviso that any hydroxyl substitution is not attached to an unsaturated carbon atom;
substituted alkynyl refers to an alkynyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
amino refers to —NH2;
substituted amino refers to NR′R′′ where R′ and R′′ are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where R′ and R′′ are joined, together with the nitrogen bound thereto to form a heterocyclyl or substituted heterocyclyl group provided that R′ and R′′ are both not hydrogen;
aminoacyl refers to a moiety selected from the group consisting of —NR3C(O)alkyl, —NR3C(O)substituted alkyl, —NR3C(O)cycloalkyl, —NR3C(O)substituted cycloalkyl, —NR3C(O)alkenyl, —NR3C(O)substituted alkenyl, —NR3C(O)alkynyl, —NR3C(O)substituted alkynyl, —NR3C(O)aryl, —NR3C(O)substituted aryl, —NR3C(O)heteroaryl, —NR3C(O)substituted heteroaryl, —NR3C(O)heterocyclyl, and —NR3C(O)substituted heterocyclyl where R3 is hydrogen or alkyl;
aryl refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring or multiple condensed rings, which condensed rings may or may not be aromatic provided that the point of attachment is at an aromatic carbon atom;
substituted aryl refers to an aryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
aryloxy refers to aryl-O—;
substituted aryloxy refers to (substituted aryl)-O—;
carboxyl refers to —COOH or salts thereof;
carboxyl ester refers to a moiety selected from the group consisting of —C(O)O-alkyl, —C(O)O-substituted alkyl, —C(O)Oaryl, and —C(O)O-substituted aryl;
cycloalkyl refers to cyclic alkyl groups of from 3 to 10 carbon atoms having single or multiple cyclic rings;
cycloalkenyl refers to cyclic alkenyl groups of from 4 to 10 carbon atoms having single or multiple cyclic rings and further having at least 1 internal site of ethylenic or vinyl (>C═C<) unsaturation;
substituted cycloalkyl refers to a cycloalkyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
substituted cycloalkenyl refers to a cycloalkenyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
cycloalkoxy refers to —O-cycloalkyl;
substituted cycloalkoxy refers to —O-substituted cycloalkyl;
halogen refers to fluoro, chloro, bromo or iodo;
heteroaryl refers to an aromatic group of from 1 to 10 carbon atoms and 1 to 4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur within a single ring or multiple condensed rings wherein the condensed rings may or may not be aromatic and/or contain a heteroatom provided that the point of attachment is through an atom of the aromatic heteroaryl group;
substituted heteroaryl refers to a heteroaryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
heteroaryloxy refers to —O-heteroaryl;
substituted heteroaryloxy refers to —O-(substituted heteroaryl);
heterocyclyl refers to a saturated or unsaturated group having a single ring or multiple condensed rings, from 1 to 10 carbon atoms and from 1 to 4 heteroatoms selected from the group consisting of nitrogen, sulfur and oxygen within the ring wherein, in fused ring systems, one or more the rings can be cycloalkyl, aryl or heteroaryl provided that the point of attachment is through the heterocyclyl ring;
substituted heterocyclyl refers to a heterocyclyl group substituted with from 1 to 3 of the same substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
heterocyclyloxy refers to the group —O-heterocyclyl;
substituted heterocyclyloxy refers to the group —O-(substituted heterocyclyl);
phosphate refers to a moiety selected from the group consisting of —OP(O)(OH)2 (monophosphate), —OP(O)(OH)OP(O)(OH)2 (diphosphate) and —OP(O)(OH)OP(O)(OH)OP(O)(OH)2 (triphosphate) or salts thereof, including partial salts thereof;
phosphate ester refers to a mono-, di- and tri-phosphate group, wherein one or more of the hydroxyl groups is replaced by an alkoxy group;
phosphonate refers to a moiety selected from the group consisting of —OP(O)(R)(OH) and —OP(O)(R)(OR) or salts thereof including partial salts thereof, wherein each R is independently selected from hydrogen, alkyl, substituted alkyl, carboxyl, and carboxyl ester;
phosphorodiamidate refers to the group




 where each R* may be the same or different and each is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate monoester refers to the group




 where R′′ is H or alkyl and R* and each is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate diester refers to the group below




 where R′′ is H or alkyl, R′ is aryl, substituted aryl, alkyl, or substutituted alkyl, and R* is H, alkyl, substituted alkyl, cycloalkyl, and substituted cycloalkyl;
cyclic phosphoramidate refers to the group




 where n is 1 to 3;
phosphonamidate refers to the group




 where R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
thiol refers to —SH;
thioalkyl refers to —S-alkyl;
substituted thioalkyl refers to —S-(substituted alkyl);
thiocycloalkyl refers to —S-cycloalkyl;
substituted thiocycloalkyl refers to —S-(substituted cycloalkyl);
thioaryl refers to —S-aryl;
substituted thioaryl refers to —S-(substituted aryl);
thioheteroaryl refers to —S-heteroaryl;
substituted thioheteroaryl refers to —S-(substituted heteroaryl);
thioheterocyclyl refers to —S-heterocyclyl; and
substituted thioheterocyclyl refers to —S-(substituted heterocyclyl).

7. A compound of Formula VII:




wherein
W2 is selected group consisting of hydrogen, acyl, oxyacyl, phosphonate, phosphate, phosphate ester, phosphonamidate, phosphorodiamidate, phosphoramidate monoester, cyclic phosphoramidate, cyclic phosphorodiamidate, phosphoramidate diester, and —C(O)CHR2NH2 where R2 is selected from the group consisiting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, and a sidechain of an amino acid; and
R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
or pharmaceutically acceptable salts or partial salts thereof,
wherein
substituted alkyl refers to an alkyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, oxyacyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
alkoxy refers to alkyl-O—;
substituted alkoxy refers to (substituted alkyl)-O—;
acyl refers to a moiety selected from the group consisting of H—C(O)—, alkyl-C(O)—, substituted alkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—, substituted alkynyl-C(O)-cycloalkyl-C(O)—, substituted cycloalkyl-C(O)—, aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substituted heteroaryl-C(O), heterocyclyl-C(O)—, and substituted heterocyclyl-C(O)—;
acylamino refers to —C(O)NR2R2 where each R2 is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where each R2 is joined to form together with the nitrogen atom a heterocyclyl or substituted heterocyclyl ring;
acyloxy refers to a moiety selected from the group consisting of alkyl-C(O)O—, substituted alkyl-C(O)O—, alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substituted alkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—, heterocyclyl-C(O)O—, and substituted heterocyclyl-C(O)O—;
oxyacyl refers to a moiety selected from the group consisting of alkyl-OC(O)—, substituted alkyl-OC(O)—, alkenyl-OC(O)—, substituted alkenyl-OC(O)—, alkynyl-OC(O)—, substituted alkynyl-OC(O)—, aryl-OC(O)—, substituted aryl-OC(O)—, cycloalkyl-OC(O)—, substituted cycloalkyl-OC(O)—, heteroaryl-OC(O)—, substituted heteroaryl-OC(O)—, heterocyclyl-OC(O)—, and substituted heterocyclyl-OC(O)—;
substituted alkenyl refers to an alkenyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl with the proviso that any hydroxyl substitution is not attached to an unsaturated carbon atom;
substituted alkynyl refers to an alkynyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
amino refers to —NH2;
substituted amino refers to —NR′R′′ where R′ and R′′ are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where R′ and R′′ are joined, together with the nitrogen bound thereto to form a heterocyclyl or substituted heterocyclyl group provided that R′ and R′′ are both not hydrogen;
aminoacyl refers to a moiety selected from the group consisting of —NR3C(O)alkyl, —NR3C(O)substituted alkyl, —NR3C(O)cycloalkyl, —NR3C(O)substituted cycloalkyl, —NR3C(O)alkenyl, —NR3C(O)substituted alkenyl, —NR3C(O)alkynyl, —NR3C(O)substituted alkynyl, —NR3C(O)aryl, —NR3C(O)substituted aryl, —NR3C(O)heteroaryl, —NR3C(O)substituted heteroaryl, —NR3C(O)heterocyclyl, and —NR3C(O)substituted heterocyclyl where R3 is hydrogen or alkyl;
aryl refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring or multiple condensed rings, which condensed rings may or may not be aromatic provided that the point of attachment is at an aromatic carbon atom;
substituted aryl refers to an aryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
aryloxy refers to aryl-O—;
substituted aryloxy refers to (substituted aryl)-O—;
carboxyl refers to —COOH or salts thereof;
carboxyl ester refers to a moiety selected from the group consisting of —C(O)O-alkyl, —C(O)O-substituted alkyl, —C(O)Oaryl, and —C(O)O-substituted aryl;
cycloalkyl refers to cyclic alkyl groups of from 3 to 10 carbon atoms having single or multiple cyclic rings;
cycloalkenyl refers to cyclic alkenyl groups of from 4 to 10 carbon atoms having single or multiple cyclic rings and further having at least 1 internal site of ethylenic or vinyl (>C═C<) unsaturation;
substituted cycloalkyl refers to a cycloalkyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
substituted cycloalkenyl refers to a cycloalkenyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
cycloalkoxy refers to —O-cycloalkyl;
substituted cycloalkoxy refers to —O-substituted cycloalkyl;
halogen refers to fluoro, chloro, bromo or iodo;
heteroaryl refers to an aromatic group of from 1 to 10 carbon atoms and 1 to 4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur within a single ring or multiple condensed rings wherein the condensed rings may or may not be aromatic and/or contain a heteroatom provided that the point of attachment is through an atom of the aromatic heteroaryl group;
substituted heteroaryl refers to a heteroaryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
heteroaryloxy refers to —O-heteroaryl;
substituted heteroaryloxy refers to —O-(substituted heteroaryl);
heterocyclyl refers to a saturated or unsaturated group having a single ring or multiple condensed rings, from 1 to 10 carbon atoms and from 1 to 4 heteroatoms selected from the group consisting of nitrogen, sulfur or oxygen within the ring wherein, in fused ring systems, one or more the rings can be cycloalkyl, aryl or heteroaryl provided that the point of attachment is through the heterocyclyl ring;
substituted heterocyclyl refers to a heterocyclyl group substituted with from 1 to 3 of the same substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
heterocyclyloxy refers to the group —O-heterocyclyl;
substituted heterocyclyloxy refers to the group —O-(substituted heterocyclyl);
phosphate refers to a moiety selected from the group consisting of —OP(O)(OH)2 (monophosphate), —OP(O)(OH)OP(O)(OH)2 (diphosphate) and —OP(O)(OH)OP(O)(OH)OP(O)(OH)2 (triphosphate) or salts thereof, including partial salts thereof;
phosphate ester refers to a mono-, di- and tri-phosphate group, wherein one or more of the hydroxyl groups is replaced by an alkoxy group;
phosphonate refers to a moiety selected from the group consisting of —OP(O)(R)(OH) and —OP(O)(R)(OR) or salts thereof including partial salts thereof, wherein each R is independently selected from hydrogen, alkyl, substituted alkyl, carboxyl, and carboxyl ester;
phosphorodiamidate refers to the group




 where each R* may be the same or different and each is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate monoester refers to the group




 where R′′ is H or alkyl and R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate diester refers to the group below




 where R′′ is H or alkyl, R′ is aryl, substituted aryl, alkyl, or substutituted alkyl, and R* is H, alkyl, substituted alkyl, cycloalkyl, and substituted cycloalkyl;
cyclic phosphoramidate refers to the group




 where n is 1 to 3;
phosphonamidate refers to the group




 where R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
thiol refers to —SH;
thioalkyl refers to —S-alkyl;
substituted thioalkyl refers to —S-(substituted alkyl);
thiocycloalkyl refers to —S-cycloalkyl;
substituted thiocycloalkyl refers to —S-(substituted cycloalkyl);
thioaryl refers to —S-aryl;
substituted thioaryl refers to —S-(substituted aryl);
thioheteroaryl refers to —S-heteroaryl;
substituted thioheteroaryl refers to —S-(substituted heteroaryl);
thioheterocyclyl refers to —S-heterocyclyl; and
substituted thioheterocyclyl refers to —S-(substituted heterocyclyl).

8. A compound of Formula VIII:




wherein
W is selected from the group consisting of hydrogen, acyl, oxyacyl, phosphonate, phosphate, phosphate ester, phosphonamidate, phosphorodiamidate, phosphoramidate monoester, cyclic phosphoramidate, cyclic phosphorodiamidate, phosphoramidate diester, and —C(O)CHR2NH2 where R2 is selected from the group consisiting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, and a sidechain of an amino acid; and
R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and —CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
or pharmaceutically acceptable salts or partial salts thereof,
wherein
substituted alkyl refers to an alkyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, oxyacyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
alkoxy refers to alkyl-O—;
substituted alkoxy refers to (substituted alkyl)-O—;
acyl refers to a moiety selected from the group consisting of H—C(O)—, alkyl-C(O)—, substituted alkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—, substituted alkynyl-C(O)-cycloalkyl-C(O)—, substituted cycloalkyl-C(O)—, aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substituted heteroaryl-C(O), heterocyclyl-C(O)—, and substituted heterocyclyl-C(O)—;
acylamino refers to —C(O)NR2R2 where each R2 is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where each R2 is joined to form together with the nitrogen atom a heterocyclyl or substituted heterocyclyl ring;
acyloxy refers to a moiety selected from the group consisting of alkyl-C(O)O—, substituted alkyl-C(O)O—, alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substituted alkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—, substituted cycloalkyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—, heterocyclyl-C(O)O—, and substituted heterocyclyl-C(O)O—;
oxyacyl refers to a moiety selected from the group consisting of alkyl-OC(O)—, substituted alkyl-OC(O)—, alkenyl-OC(O)—, substituted alkenyl-OC(O)—, alkynyl-OC(O)—, substituted alkynyl-OC(O)—, aryl-OC(O)—, substituted aryl-OC(O)—, cycloalkyl-OC(O)—, substituted cycloalkyl-OC(O)—, heteroaryl-OC(O)—, substituted heteroaryl-OC(O)—, heterocyclyl-OC(O)—, and substituted heterocyclyl-OC(O)—;
substituted alkenyl refers to an alkenyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl with the proviso that any hydroxyl substitution is not attached to an unsaturated carbon atom;
substituted alkynyl refers to an alkynyl group having from 1 to 3 substituents selected from the group consisting of alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
amino refers to —NH2;
substituted amino refers to NR′R′′ where R′ and R′′ are independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl and where R′ and R′′ are joined, together with the nitrogen bound thereto to form a heterocyclyl or substituted heterocyclyl group provided that R′ and R′′ are both not hydrogen;
aminoacyl refers to a moiety selected from the group consisting of —NR3C(O)alkyl, —NR3C(O)substituted alkyl, —NR3C(O)cycloalkyl, —NR3C(O)substituted cycloalkyl, —NR3C(O)alkenyl, —NR3C(O)substituted alkenyl, —NR3C(O)alkynyl, —NR3C(O)substituted alkynyl, —NR3C(O)aryl, —NR3C(O)substituted aryl, —NR3C(O)heteroaryl, —NR3C(O)substituted heteroaryl, —NR3C(O)heterocyclyl, and —NR3C(O)substituted heterocyclyl where R3 is hydrogen or alkyl;
aryl refers to a monovalent aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring or multiple condensed rings, which condensed rings may or may not be aromatic provided that the point of attachment is at an aromatic carbon atom;
substituted aryl refers to an aryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
aryloxy refers to aryl-O—;
substituted aryloxy refers to (substituted aryl)-O—;
carboxyl refers to —COOH or salts thereof;
carboxyl ester refers to a moiety selected from the group consisting of —C(O)O-alkyl, —C(O)O-substituted alkyl, —C(O)Oaryl, and —C(O)O-substituted aryl;
cycloalkyl refers to cyclic alkyl groups of from 3 to 10 carbon atoms having single or multiple cyclic rings;
cycloalkenyl refers to cyclic alkenyl groups of from 4 to 10 carbon atoms having single or multiple cyclic rings and further having at least 1 internal site of ethylenic or vinyl (>C═C<) unsaturation;
substituted cycloalkyl refers to a cycloalkyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
substituted cycloalkenyl refers to a cycloalkenyl group, having from 1 to 5 substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
cycloalkoxy refers to —O-cycloalkyl;
substituted cycloalkoxy refers to —O-substituted cycloalkyl;
halogen refers to fluoro, chloro, bromo or iodo;
heteroaryl refers to an aromatic group of from 1 to 10 carbon atoms and 1 to 4 heteroatoms selected from the group consisting of oxygen, nitrogen and sulfur within a single ring or multiple condensed rings wherein the condensed rings may or may not be aromatic and/or contain a heteroatom provided that the point of attachment is through an atom of the aromatic heteroaryl group;
substituted heteroaryl refers to a heteroaryl group substituted with from 1 to 3 substituents selected from the group consisting of hydroxyl, acyl, acylamino, acyloxy, alkyl, substituted alkyl, alkoxy, substituted alkoxy, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cycloalkoxy, substituted cycloalkoxy, carboxyl, carboxyl ester, cyano, thiol, thioalkyl, substituted thioalkyl, thioaryl, substituted thioaryl, thioheteroaryl, substituted thioheteroaryl, thiocycloalkyl, substituted thiocycloalkyl, thioheterocyclyl, substituted thioheterocyclyl, cycloalkyl, substituted cycloalkyl, halo, nitro, heteroaryl, substituted heteroaryl, heterocyclyl, substituted heterocyclyl, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, and substituted heterocyclyloxy;
heteroaryloxy refers to —O-heteroaryl;
substituted heteroaryloxy refers to —O-(substituted heteroaryl);
heterocyclyl refers to a saturated or unsaturated group having a single ring or multiple condensed rings, from 1 to 10 carbon atoms and from 1 to 4 heteroatoms selected from the group consisting of nitrogen, sulfur and oxygen within the ring wherein, in fused ring systems, one or more the rings can be cycloalkyl, aryl or heteroaryl provided that the point of attachment is through the heterocyclyl ring;
substituted heterocyclyl refers to a heterocyclyl group substituted with from 1 to 3 of the same substituents selected from the group consisting of oxo (═O), thioxo (═S), alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted amino, aminoacyl, aryl, substituted aryl, aryloxy, substituted aryloxy, cyano, halogen, hydroxyl, nitro, carboxyl, carboxyl ester, cycloalkyl, substituted cycloalkyl, heteroaryl, substituted heteroaryl, heterocyclyl, and substituted heterocyclyl;
heterocyclyloxy refers to the group —O-heterocyclyl;
substituted heterocyclyloxy refers to the group —O-(substituted heterocyclyl);
phosphate refers to a moiety selected from the group consisting of —OP(O)(OH)2 (monophosphate), —OP(O)(OH)OP(O)(OH)2 (diphosphate) and —OP(O)(OH)OP(O)(OH)OP(O)(OH)2 (triphosphate) or salts thereof, including partial salts thereof;
phosphate ester refers to a mono-, di- and tri-phosphate group, wherein one or more of the hydroxyl groups is replaced by an alkoxy group;
phosphonate refers to a moiety selected from the group consisting of —OP(O)(R)(OH) and —OP(O)(R)(OR) or salts thereof including partial salts thereof, wherein each R is independently selected from hydrogen, alkyl, substituted alkyl, carboxyl, and carboxyl ester;
phosphorodiamidate refers to the group




 where each R* may be the same or different and each is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate monoester refers to the group




 where R′′ is H or alkyl and R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
phosphoramidate diester refers to the group below




 where R′′ is H or alkyl, R′ is aryl, substituted aryl, alkyl, or substutituted alkyl, and R* is H, alkyl, substituted alkyl, cycloalkyl, and substituted cycloalkyl;
cyclic phosphoramidate refers to the group




 where n is 1 to 3;
phosphonamidate refers to the group




 where R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
thiol refers to —SH;
thioalkyl refers to —S-alkyl;
substituted thioalkyl refers to —S-(substituted alkyl);
thiocycloalkyl refers to —S-cycloalkyl;
substituted thiocycloalkyl refers to —S-(substituted cycloalkyl);
thioaryl refers to —S-aryl;
substituted thioaryl refers to —S-(substituted aryl);
thioheteroaryl refers to —S-heteroaryl;
substituted thioheteroaryl refers to —S-(substituted heteroaryl);
thioheterocyclyl refers to —S-heterocyclyl; and
substituted thioheterocyclyl refers to —S-(substituted heterocyclyl).

9. A compound of Formula IX:




wherein
R is selected from the group consisting of —C(═O)H, —CH═NNHR1, —CH═N(OR1), —B(OR1)2 and —CH(OR2)2 where each R1 is independently selected from the group consisting of hydrogen and C1 to C6 alkyl and each R2 is independently C2 to C6 alkyl;
or pharmaceutically acceptable salts or partial salts thereof.

10. A compound selected from the group consisting of;
7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(diisopropoxymethyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(carbaldehyde oxime)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(boronic acid)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-β-D-ribofuranosyl)-4-amino-5-(diethoxymethyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(carbaldehyde oxime)-pyrrolo{2,3-d]pyrimidine;
7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(boronic acid)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(diethoxymethyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(boronic acid)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(diethoxymethyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(formyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(boronic acid)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(diethoxymethyl)-pyrolo [2,3-d]pyrimidine;
7-(2′-methyl-β-D-ribofuranosyl)-4-amino-5-(hydrazono)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-phospho-β-D-ribofuranosyl)-4-amino-5-(hydrazono)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(hydrazono)pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(hydrazono)pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-monophospho-β-D-ribofuranosyl)-4-amino-5-(diisopropoxymethyl)-pyrrolo[2,3-d]pyrimidine;
7-(2′-C-methyl-5′-diphospho-β-D-ribofuranosyl)-4-amino-5-(diisopropoxymethyl)-pyrrolo[2,3-d]pyrimidine; and
7-(2′-C-methyl-5′-triphospho-β-D-ribofuranosyl)-4-amino-5-(diisopropoxymethyl)-pyrrolo[2,3-d]pyrimidine;
or pharmaceutically acceptable salts or partial salts thereof.

11. A pharmaceutical composition comprising a pharmaceutically acceptable diluent and a therapeutically effective amount of a compound of any one of claims 1, 2, 3, 4, 5, 6, 7, 8, 9, 10.

12. A method for treating a viral infection in a mammal in need of mediated at least in part by hepatitis C virus which method comprise administering to said mammal, that has been diagnosed with said viral infection or is at risk of developing said viral infection, a pharmaceutical composition according to claim 11.