CROSS-REFERENCE TO RELATED APPLICATIONS

This is a non-provisional filing of U.S. Provisional Application No. 60/413,337, filed Sep. 24, 2002, the disclosure of which is incorporated herein by reference in its entirety for all purposes.

BACKGROUND OF THE INVENTION

RNA viral diseases are responsible for the vast majority of viral morbidity and mortality of viral diseases of mankind, including AIDS, hepatitis, rhinovirus infections of the respiratory tract, flu, measles, polio and others. There are a number of chronic persistent diseases caused by RNA or DNA viruses that replicate through an RNA intermediate which are difficult to treat, such as hepatitis B and C, and T-cell human leukemia. Many common human diseases are caused by RNA viruses that are replicated by a viral encoded RNA replicase. Included in this group are influenza (Zurcher, et al., J. Gen. Virol. 77:1745 (1996), dengue fever (Becker, Virus-Genes 9:33 (1994), and rhinovirus infections (Horsnell, et al., J. Gen. Virol., 76:2549 (1995). Important RNA viral diseases of animals include feline leukemia and immunodeficiency, Visna maedi of sheep, bovine viral diarrhea, bovine mucosal disease, and bovine leukemia. Although some vaccines are available for DNA viruses, diseases such as hepatitis B are still prevalent. Hepatitis B is caused by a DNA virus that replicates its genome through a RNA intermediate (Summers and Mason, Cell 29:4003 (1982). While an effective vaccine exists as a preventive, there is no efficacious treatment for chronic persistent HBV infection.

Chain terminating nucleoside analogs have been used extensively for the treatment of infections by DNA viruses and retroviruses. These analogs are incorporated into DNA by DNA polymerases or reverse transcriptases. Once incorporated, they cannot be further extended and thus terminate DNA synthesis. Unfortunately, there is immediate selective pressure for the development of resistance against such chain terminating analogs that results in development of mutations in the viral polymerase that prevent incorporation of the nucleoside analog.

An alternative strategy is to utilize mutagenic deoxyribonucleosides (MDRN) or mutagenic ribonucleosides (MRN) that are preferentially incorporated into a viral genome. MDRN are incorporated into DNA by viral reverse transcriptase or by a DNA polymerase enzyme. MRN are incorporated into viral RNAs by viral RNA replicases. As a result, the mutations in the viral genome are perpetuated and accumulated with each viral replication cycle. With each cycle of viral infection, there ensues a chain like increase in the number of mutations in the viral genome. Eventually the number of mutations in each viral genome is so large that no active virally encoded proteins are produced.

5-aza-2â€²-deoxycytidine (5-aza-dC) is an antineoplastic agent that has been tested in patients with leukemia and is thought to act predominantly by demethylating DNA. 5-aza-cytidine (5-aza-C) has also been used to treat patients with leukemia. Methylation is thought to silence tumor growth suppressor and differentiation genes. Interestingly deamination of 5-aza-dC to 5-aza-2â€²-deoxyuridine (5-aza-dU) has been shown to result in loss of antineoplastic activity (see e.g., Momparler, et al., Leukemia. 11:1-6 (1997)).

5-aza-cytidine (5-aza-C) has also been used to treat patients with leukemia. Both 5-aza-C and 5-aza-dC were shown to inhibit HIV replication in vitro, although the mechanism of action was not determined (see e.g., Bouchard et al, Antimicrob. Agents Chemother. 34: 206-209 (2000)). More recently, 5-aza-C has been shown to be mutagenic to foot-and-mouth disease virus (see e.g., Sierra et al., J. Virol. 74(18): 8316-8323 (2000)). Both 5-aza-C and 5-aza-dC are unstable compounds. 5-aza-dC is rapidly degraded upon reconstitution. At pH 7.0, a 10% degradation occurs at temperatures of 25Â° C. and 50Â° C. after 5 and 0.5 hours, respectively (see e.g., Van Groeningen et al., Cancer Res. 46:4831-4836 (1986)). Thus, therapeutic use of 5-aza-C and 5-aza-dC is limited for treatment of both viral diseases and cancer. The present invention solves this and other problems.

BRIEF SUMMARY OF THE INVENTION

The present invention provides a genus of nucleoside or nucleotide analogues and method of using the analogues as antiviral and anti-cancer chemotherapeutic agents.

Thus, in a first aspect, there is provided a compound according to Formula I: [Image Omitted]

In Formula I, the dashed circle indicates that the ring system may include one or more double bonds at any position, such that the valence of the intra-annular atoms is satisfied. The ring system may be aromatic (e.g., heteroaryl) or non-aromatic. The substituents R², R⁷, R⁸are present or absent as dictated by the application of the laws of valency to a selected ring structure.

The symbol Y represents C, CH or N, and the symbol Z represents C, CH or B. R¹is a member selected from H, acyl, OR⁹, SR⁹, NR⁹NHR¹⁰, NR⁹R¹⁰, â• O and â• NR⁹, in which R⁹and R¹⁰are members independently selected from H, substituted or unsubstituted alkyl, acyl, substituted or unsubstituted heteroalkyl and substituted or unsubstituted aryl.

The symbol R²represents a substituent that is a member selected from H, acyl, substituted or unsubstituted alkyl, OR¹¹, SR¹¹, NR^11a, NR^12a, halogen, and â• O. The symbol R¹¹represents a member selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heterocycloalkyl, or substituted or unsubstituted heteroaryl. R^11aand R^12aare members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl and substituted or unsubstituted heteroaryl.

R³is a member selected from H, acyl, substituted or unsubstituted alkyl, NR¹²R¹³, NR¹²OR¹³, SR¹², (â• O) and OR¹². The symbols R¹²and R¹³represent members independently selected from H, substituted or unsubstituted alkyl, acyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl or substituted or unsubstituted heteroaryl.

R⁴and R^4aare members independently selected from H, halogen, OMe and OH. In a preferred embodiment, the halogen is F.

R⁵and R⁶are members independently selected from H, and OR¹⁴. The symbol R¹⁴represents H, substituted or unsubstituted alkyl, acyl, substituted or unsubstituted heteroalkyl, or substituted or unsubstituted aryl and P(O)(R¹⁵)(R¹⁶). R¹⁵and R¹⁶are independently selected from OR¹⁷, NR¹⁷R¹⁸, substituted or unsubstituted alkyl and substituted or unsubstituted nucleosides. R¹⁷and R¹⁸are independently selected from H, CH₂CH CN, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl and substituted or unsubstituted heteroaryl.

A member selected from R⁵and R³; R⁶and R³; and R¹⁵and R¹⁶together with the atoms to which they are attached, are optionally joined to form a ring system selected from substituted or unsubstituted cycloalkyl and substituted or unsubstituted heterocycloalkyl. In an exemplary embodiment, the ring system is a 5 or 6 membered ring system.

R⁷and R⁸are independently selected from H, acyl, substituted or unsubstituted alkyl. R¹and R⁸, together with the atoms to which they are attached are optionally joined into a ring system selected from substituted or unsubstituted cycloalkyl and substituted or unsubstituted heterocycloalkyl.

In another aspect of the present invention, the nucleoside and nucleotide analogues (e.g., the compounds of Formula I) of the present invention are used for treating a viral disease by administering a therapeutically effective amount of a compound of Formula I to a patient with a viral disease. In some embodiments, the compounds are given orally. In other embodiments, the compound is given in an enteric formulation. In a further embodiment, the compound is delivered in an oral osmotic drug delivery device.

When the compounds are given orally, it is generally preferred that they have a bioavailability that is greater than about 15%, more preferably greater than about 20% of the administered dose. In an exemplary embodiment, the compound is formulated as an acid addition salt, e.g. a quaternary ammonium salt. The salt is generally formed by contacting the compound with a mineral or an organic acid. In a preferred embodiment, the acid is a carboxylic acid, such as palmitic acid.

The viral disease can be a viral disease caused by an RNA virus, a DNA virus, or a retrovirus. In some embodiments, the viral disease is caused by HIV. In a further embodiment, the HIV strain is resistant to nucleotide reverse transcriptase inhibitors or other treatments of HIV infection, including non-nucleoside reverse transcriptase inhibitors, or protease inhibitors. In other embodiments, the viral disease is caused by a virus of the Flaviviridae family. In a further embodiment the viral disease is hepatitis C. In other embodiments, the viral disease is caused by a virus of the Paramyxoviridae family. In a further aspect, the virus is hepatitis B virus or smallpox/vaccinia virus.

In another aspect of the present invention the compounds of Formula I are used to treat cancer, e.g., hematopoetic cancers.

Other aspects, objects and advantages of the present invention will be apparent from the detailed description that follows.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is an illustration of the hydrophobic-hydrophobic stacking interactions of selected compositions of the invention.

FIG. 2 is an illustration of the complexes of the invention formed between the pharmacophore modified with a hydrophobic modifying group and a poly-ion.

FIG. 3 is an illustration of the complexes of the invention formed between the pharmacophore modified with a hydrophobic modifying group and a dendrimeric poly-ion.

FIG. 4 depicts the EC₅₀values for 5-Aza-dC, DHAdC and 5-Me-DHAdC against wild-type HIV virus. The experiments were carried out in MT-2 cells infected with HIV strain LAI.

FIG. 5 is an illustration of compounds 1-4.

FIG. 6 is an exemplary synthetic scheme for compounds 7 and 8.

FIG. 7 is an exemplary synthetic scheme for compounds 9 and 10.

FIG. 8 is an exemplary synthetic scheme for compounds 9, and 11-14.

FIG. 9 is an exemplary synthetic scheme for compounds 14-18.

FIG. 10 is an exemplary synthetic scheme for compounds 20-21.

FIG. 11 is an exemplary synthetic scheme for compounds 20-21.

FIG. 12 is an exemplary synthetic scheme for a compound of the invention including a modified phosphodiester group.

FIG. 13 is an exemplary synthetic scheme for a compound of the invention including a modified phosphodiester group derivatized with a hydrophobic moiety.

FIG. 14 is a retrosynthetic scheme for preparing a compound of the invention.

FIG. 15 is an exemplary synthetic scheme for compounds 23, 24 and 26.

DETAILED DESCRIPTION OF THE INVENTION

Introduction

The present invention is directed to a method of inducing viral mutagenesis, using hydrolytically stable derivatives and formulations of 5-aza-cytidine, 5-aza-2â€²-deoxycytidine and derivatives and variants thereof, which is useful in cell culture as well as in therapy for animals and humans. This method is advantageous in that it is useful against DNA or RNA viruses (i.e., viruses that have DNA or RNA genomes). In one embodiment, the methods of the invention are advantageous when used to target RNA viruses (viruses with an RNA genome), and retroviruses or other viruses otherwise replicated by an RNA intermediate. In another embodiment, the methods of the invention are advantageous for targeting DNA viruses such as hepatitis B virus, herpes viruses, and papilloma viruses. Without being held to a mechanism of action, in one embodiment, the methods of the invention utilize miscoding nucleosides and nucleotides that are incorporated into both viral encoded and cellular encoded viral genomic nucleic acids, thereby causing miscoding in progeny copies of the genomic virus, e.g., by tautomerism, which promotes base mispairing (see, e.g., Moriyama et al., Nucleic Acids Symposium 42: 131-132 (1999); Robinson et al., Biochemistry 37: 10897-10905 (1998); Anensen et al., Mutation Res. 476: 99-107 (2001); Lutz et al., Bioorganic & Medicinal Chem. Letts. 8: 499-504 (1998); and Klungland et al., Toxicology Letts. 119: 71-78 (2001)).

The virus may be one in which the viral genomic nucleic acid is integrated into the cellular genome. Examples of viruses that integrate their cellular genome include, but are not limited to, retroviruses. In one particularly preferred embodiment, the virus is HIV. Other preferred viruses include HIV-1, HIV-2, HTLV-1, HTLV-II, and SIV. In another embodiment, the virus is a DNA virus such as hepatitis B virus, herpes viruses (e.g., HSV, CMV, EBV), smallpox virus, or papilloma virus (e.g., HPV). Alternatively, the viral genome can be episomal. These include many human and animal pathogens, e.g., flaviviruses such as dengue fever, West Nile virus, and yellow fever, pestiviruses (a genus of the Flaviviridae family) such as BVDV (bovine viral diarrhea virus), hepatitis C viruses (also a genus of the Flaviviridae family), filoviruses such as ebola virus, influenza viruses, parainfluenza viruses, including respiratory syncytial virus, measles, mumps, the picornaviruses, including the echoviruses, the coxsackieviruses, the polioviruses, the togaviruses, including encephalitis, coronoviruses, rubella, bunyaviruses, reoviruses, including rotaviruses, rhabdoviruses, arenaviruses such as lymphocytic choriomeningitis as well as other RNA viruses of man and animals.

Retroviruses that can be targeted include the human T-cell leukemia (HTLV) viruses such as HTLV-1 and HTLV-2, adult T-cell leukemia (ATL), the human immunodeficiency viruses such as HIV-1 and HIV-2 and simian immunodeficiency virus (SIV). In some embodiments, the HIV virus is resistant to non-nucleoside reverse transcriptase inhibitors. In certain embodiments, the virus is hepatitis A or hepatitis B. See, e.g., Fields Virology (3rd ed. 1996). Further information regarding viral diseases and their replication can be found in White and Fenner, Medical Virology 4th ed. Academic Press (1994) and in Principles and Practice of Clinical Virology, ed. Zuckerman, Banatvala and Pattison, John Wiley and Sons (1994). In addition, the compounds of the invention can be used to treat cancer.

Assays for detecting the mutagenic potential of a nucleoside or nucleotide analog are provided (see, e.g., Example 1). In the assays, the nucleoside or nucleotide analog is incorporated into a viral nucleic acid in the presence of a nucleic acid template, the nucleic acid synthesized by a cellular or viral polymerase, and a determination is made regarding whether the incorporation causes a mutation in a progeny virus. Optionally, naturally occurring (i.e., G, A, U, and/or C) nucleotides are also incorporated into the nucleic acid polymer. The method optionally comprises comparing the rate of incorporation of the nucleoside or nucleotide analog and any naturally occurring ribonucleoside in the assay into the nucleic acid. For additional examples of assays, see, e.g., U.S. Pat. Nos. 6,132,776, 6,130,036, 6,063,628, and 5,512,431 and patent applications U.S. Ser. No. 10/226,799 and 60/314,728, which are incorporated herein by reference in their entirety.

Exemplary compounds for use in the methods of the invention include 5-aza-cytidine, 5-aza-2â€²-deoxycytidine, and derivatives and variants thereof.

Definitions

Where substituent groups are specified by their conventional chemical formulae, written from left to right, they equally encompass the chemically identical substituents which would result from writing the structure from right to left, e.g., â€”CH₂Oâ€” is intended to also recite â€”OCH₂â€”; â€”NHS(O)₂â€” is also intended to represent â€”S(O)₂HNâ€”, etc.

As used herein, â€œlinking memberâ€ refers to an alkylene unit or a covalent chemical bond that includes at least one heteroatom. Exemplary linking members include â€”C(O)NHâ€”, â€”C(O)Oâ€”, â€”NHâ€”, â€”Sâ€”, â€”Oâ€”, and the like.

The term â€œtargeting groupâ€ is intended to mean a moiety that is (1) able to direct the entity to which it is attached (e.g., therapeutic agent or marker) to a target region, e.g. cell; or (2) is preferentially activated at a target region, for example a region of viral infection. The targeting group can be a small molecule, which is intended to include both non-peptides and peptides. The targeting group can also be a macromolecule, which includes saccharides, lectins, receptors, ligand for receptors, proteins such as BSA, antibodies, and so forth.

The term â€œalkyl,â€ by itself or as part of another substituent, means, unless otherwise stated, a straight or branched chain, or cyclic hydrocarbon radical, or combination thereof, which may be fully saturated, mono- or poly-unsaturated and can include di- and multivalent radicals, having the number of carbon atoms designated (i.e. C₁-C₁₀means one to ten carbons). Examples of saturated hydrocarbon radicals include, but are not limited to, groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl, sec-butyl, cyclohexyl, (cyclohexyl)methyl, cyclopropylmethyl, homologs and isomers of, for example, n-pentyl, n-hexyl, n-heptyl, n-octyl, and the like. An unsaturated alkyl group is one having one or more double bonds or triple bonds. Examples of unsaturated alkyl groups include, but are not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(1,4-pentadienyl), ethynyl, 1- and 3-propynyl, 3-butynyl, and the higher homologs and isomers. The term â€œalkyl,â€ unless otherwise noted, is also meant to include those derivatives of alkyl defined in more detail below, such as â€œheteroalkyl.â€ Alkyl groups, which are limited to hydrocarbon groups, are termed â€œhomoalkylâ€ .

The term â€œalkyleneâ€ by itself or as part of another substituent means a divalent radical derived from an alkane, as exemplified, but not limited, by â€”CH₂CH₂CH₂CH₂â€”, and further includes those groups described below as â€œheteroalkylene.â€ Typically, an alkyl (or alkylene) group will have from 1 to 24 carbon atoms, with those groups having 10 or fewer carbon atoms being preferred in the present invention. A â€œlower alkylâ€ or â€œlower alkyleneâ€ is a shorter chain alkyl or alkylene group, generally having eight or fewer carbon atoms.

The terms â€œalkoxy,â€ â€œalkylaminoâ€ and â€œalkylthioâ€ (or thioalkoxy) are used in their conventional sense, and refer to those alkyl groups attached to the remainder of the molecule via an oxygen atom, an amino group, or a sulfur atom, respectively.

â€œAcylâ€ refers to a moiety that is a residue of a carboxylic acid from which an oxygen atom is removed, i.e., â€”C(O)R, in which R is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl or substituted or unsubstituted heteroaryl.

The term â€œheteroalkyl,â€ by itself or in combination with another term, means, unless otherwise stated, a stable straight or branched chain, or cyclic hydrocarbon radical, or combinations thereof, consisting of the stated number of carbon atoms and at least one heteroatom selected from the group consisting of O, N, Si and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized and the nitrogen heteroatom may optionally be quaternized. The heteroatom(s) O, N and S and Si may be placed at any interior position of the heteroalkyl group or at the position at which the alkyl group is attached to the remainder of the molecule. Examples include, but are not limited to, â€”CH₂â€”CH₂â€”Oâ€”CH₃, â€”CH₂â€”CH₂â€”NHâ€”CH₃, â€”CH₂â€”CH₂â€”N(CH₃)â€”CH₃, â€”CH₂â€”Sâ€”CH₂â€”CH₃, â€”CH₂â€”CH₂, â€”S(O)â€”CH₃, â€”CH₂â€”CH₂â€”S(O)₂â€”CH₃, â€”CHâ• CHâ€”Oâ€”CH₃, â€”Si(CH₃)₃, â€”CH₂â€”CHâ• Nâ€”OCH₃, and â€”CHâ• CHâ€”N(CH₃)â€”CH₃. Up to two heteroatoms may be consecutive, such as, for example, â€”CH₂â€”NHâ€”OCH₃and â€”CH₂â€”Oâ€”Si(CH₃)₃. Similarly, the term â€œheteroalkyleneâ€ by itself or as part of another substituent means a divalent radical derived from heteroalkyl, as exemplified, but not limited by, â€”CH₂â€”CH₂â€”Sâ€”CH₂â€”CH₂â€” and â€”CH₂â€”Sâ€”CH₂â€”CH₂â€”NHâ€”CH₂â€”. For heteroalkylene groups, heteroatoms can also occupy either or both of the chain termini (e.g., alkyleneoxy, alkylenedioxy, alkyleneamino, alkylenediamino, and the like). Still further, for alkylene and heteroalkylene linking groups, no orientation of the linking group is implied by the direction in which the formula of the linking group is written. For example, the formula â€”C(O)₂Râ€²â€” represents both â€”C(O)₂Râ€²â€” and â€”Râ€²C(O)₂â€”.

The terms â€œcycloalkylâ€ and â€œheterocycloalkylâ€ , by themselves or in combination with other terms, represent, unless otherwise stated, cyclic versions of â€œalkylâ€ and â€œheteroalkylâ€ , respectively. Additionally, for heterocycloalkyl, a heteroatom can occupy the position at which the heterocycle is attached to the remainder of the molecule. Examples of cycloalkyl include, but are not limited to, cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl, and the like. Examples of heterocycloalkyl include, but are not limited to, 1-(1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl, tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-yl, 1-piperazinyl, 2-piperazinyl, and the like.

The term â€œarylâ€ means, unless otherwise stated, a polyunsaturated, typically aromatic, hydrocarbon substituent, which can be a single ring or multiple rings (up to three rings), which are fused together or linked covalently. The term â€œheteroarylâ€ refers to aryl groups (or rings) that contain from zero to four heteroatoms selected from N, O, and S, wherein the nitrogen and sulfur atoms are optionally oxidized, and the nitrogen atom(s) are optionally quaternized. A heteroaryl group can be attached to the remainder of the molecule through a heteroatom. Non-limiting examples of aryl and heteroaryl groups include phenyl, 1-naphthyl, 2-naphthyl, 4-biphenyl, 1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl, 1-isoquinolyl, 5-isoquinolyl, 2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and 6-quinolyl. Substituents for each of the above noted aryl and heteroaryl ring systems are selected from the group of acceptable substituents described below.

For brevity, the term â€œarylâ€ when used in combination with other terms (e.g., aryloxy, arylthioxy, arylalkyl) includes both aryl and heteroaryl rings as defined above. Thus, the term â€œarylalkylâ€ is meant to include those radicals in which an aryl group is attached to an alkyl group (e.g., benzyl, phenethyl, pyridylmethyl and the like) including those alkyl groups in which a carbon atom (e.g., a methylene group) has been replaced by, for example, an oxygen atom (e.g., phenoxymethyl, 2-pyridyloxymethyl, 3-(1-naphthyloxy)propyl, and the like).

The terms â€œhaloâ€ or â€œhalogen,â€ by themselves or as part of another substituent, mean, unless otherwise stated, a fluorine, chlorine, bromine, or iodine atom. Additionally, terms such as â€œhaloalkyl,â€ are meant to include monohaloalkyl and polyhaloalkyl. For example, the term â€œhalo(C₁-C₄)alkylâ€ is mean to include, but not be limited to, trifluoromethyl, 2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the like.

Substituents for the alkyl and heteroalkyl radicals (including those groups often referred to as alkylene, alkenyl, heteroalkylene, heteroalkenyl, alkynyl, cycloalkyl, heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl) can be one or more of a variety of groups selected from, but not limited to: â€”ORâ€², â• O, â• NRâ€², â• Nâ€”ORâ€², â€”NRâ€²Râ€³, â€”SRâ€², -halogen, â€”SiRâ€²Râ€³Râ€²â€³, â€”OC(O)Râ€², â€”C(O)Râ€², â€”CO₂Râ€², â€”CONRâ€²Râ€³, â€”OC(O)NRâ€²Râ€³, â€”NRâ€³C(O)Râ€², â€”NRâ€²â€”C(O)NRâ€³Râ€²â€³, â€”NRâ€³C(O)₂Râ€², â€”NRâ€”C(NRâ€²Râ€³Râ€²â€³)â• NRâ€³â€³, â€”NRâ€”C(NRâ€²Râ€³)â• NRâ€²â€³, â€”S(O)Râ€², â€”S(O)₂Râ€², â€”S(O)₂NRâ€²Râ€³, â€”NRSO₂Râ€², â€”CN and â€”NO₂in a number ranging from zero to (2mâ€²+1), where mâ€² is the total number of carbon atoms in such radical. Râ€², Râ€³, Râ€²â€³ and Râ€³â€³ each preferably independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, e.g., aryl substituted with 1-3 halogens, substituted or unsubstituted alkyl, alkoxy or thioalkoxy groups, or arylalkyl groups. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each Râ€², Râ€³, Râ€²â€³ and Râ€³â€³ groups when more than one of these groups is present. When Râ€² and Râ€³ are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 5-, 6-, or 7-membered ring. For example, â€”NRâ€²Râ€³ is meant to include, but not be limited to, 1-pyrrolidinyl and 4-morpholinyl. From the above discussion of substituents, one of skill in the art will understand that the term â€œalkylâ€ is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (e.g., â€”CF₃and â€”CH₂CF₃) and acyl (e.g., â€”C(O)CH₃, â€”C(O)CF₃, â€”C(O)CH₂OCH₃, and the like).

Similar to the substituents described for the alkyl radical, substituents for the aryl and heteroaryl groups are varied and are selected from, for example: halogen, â€”ORâ€², â• O, â• NRâ€², â• Nâ€”ORâ€², â€”NRâ€²Râ€³, â€”SRâ€², -halogen, â€”SiRâ€²Râ€³Râ€²â€³, â€”OC(O)Râ€², â€”C(O)Râ€², â€”CO₂Râ€², â€”CONRâ€²Râ€³, â€”OC(O)NRâ€²Râ€³, â€”NRâ€³C(O)Râ€², â€”NRâ€²â€”C(O)NRâ€³Râ€²â€³, â€”NRâ€³C(O)₂Râ€², â€”NRâ€”C(NRâ€²Râ€³)â• NRâ€²â€³, â€”S(O)Râ€², â€”S(O)₂Râ€², â€”S(O)₂NRâ€²Râ€³, â€”NRSO₂Râ€², â€”CN and â€”NO₂, â€”Râ€², â€”N₃, â€”CH(Ph)₂, fluoro(C₁-C₄)alkoxy, and fluoro(C₁-C₄)alkyl, in a number ranging from zero to the total number of open valences on the aromatic ring system. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each Râ€², Râ€³, Râ€²â€³ and Râ€³â€³ groups when more than one of these groups is present.

Two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -T-C(O)â€”(CRRâ€²)_qâ€”Uâ€”, wherein T and U are independently â€”NRâ€”, â€”Oâ€”, â€”CRRâ€²â€” or a single bond, and q is an integer of from 0 to 3. Alternatively, two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -A-(CH₂)_râ€”Bâ€”, wherein A and B are independently â€”CRRâ€²â€”, â€”Oâ€”, â€”NRâ€”, â€”Sâ€”, â€”S(O)â€”, â€”S(O)₂â€”, â€”S(O)₂NRâ€²â€” or a single bond, and r is an integer of from 1 to 4. One of the single bonds of the new ring so formed may optionally be replaced with a double bond. Alternatively, two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula â€”(CRRâ€²)_sâ€”Xâ€”(CRâ€³Râ€²â€³)_dâ€”, where s and d are independently integers of from 0 to 3, and X is â€”Oâ€”, â€”NRâ€²â€”, â€”Sâ€”, â€”S(O)â€”, â€”S(O)₂â€”, or â€”S(O)₂NRâ€²â€”. The substituents R, Râ€², Râ€³ and Râ€²â€³ are preferably independently selected from hydrogen or substituted or unsubstituted (C₁-C₆)alkyl.

As used herein, the term â€œheteroatomâ€ includes oxygen (O), nitrogen (N), sulfur (S) and silicon (Si).

â€œMoietyâ€ refers to the radical of a molecule that is attached to another moiety.

The symbol â€œRâ€ is a general abbreviation that represents a substituent group that is selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and substituted or unsubstituted heterocyclyl groups.

â€œReactive functional group,â€ as used herein refers to groups including, but not limited to, olefins, acetylenes, alcohols, phenols, ethers, oxides, halides, aldehydes, ketones, carboxylic acids, esters, amides, cyanates, isocyanates, thiocyanates, isothiocyanates, amines, hydrazines, hydrazones, hydrazides, diazo, diazonium, nitro, nitriles, mercaptans, sulfides, disulfides, sulfoxides, sulfones, sulfonic acids, sulfinic acids, acetals, ketals, anhydrides, sulfates, sulfenic acids, isonitriles, amidines, imides, imidates, nitrones, hydroxylamines, oximes, hydroxamic acids, thiohydroxamic acids, allenes, ortho esters, sulfites, enamines, ynamines, ureas, pseudoureas, semicarbazides, carbodiimides, carbamates, imines, azides, azo compounds, azoxy compounds, and nitroso compounds. Reactive functional groups also include those used to prepare bioconjugates, e.g., N-hydroxysuccinimide esters, maleimides and the like. Methods to prepare each of these functional groups are well known in the art and their application to or modification for a particular purpose is within the ability of one of skill in the art (see, for example, Sandler and Karo, eds. ORGANIC FUNCTIONAL GROUP PREPARATIONS, Academic Press, San Diego, 1989).

â€œProtecting group,â€ as used herein refers to a portion of a substrate that is substantially stable under a particular reaction condition, but which is cleaved from the substrate under a different reaction condition. A protecting group can also be selected such that it participates in the direct oxidation of the aromatic ring component of the compounds of the invention. For examples of useful protecting groups, see, for example, Greene et al., PROTECTIVE GROUPS IN ORGANIC SYNTHESIS, John Wiley & Sons, New York, 1991.

As used herein the term â€œnucleoside,â€ includes both the naturally occurring nucleosides and modifications thereof. Modifications include, but are not limited to, those providing chemical groups that incorporate additional charge, polarizability, hydrogen bonding, and electrostatic interaction to the nucleosides. Such modifications include, but are not limited to, peptide nucleic acids (PNAs), 2â€²-position sugar modifications, 5-position pyrimidine modifications, 8-position purine modifications, modifications at exocyclic amines, substitution of 4-thiouridine, substitution of 5-bromo or 5-iodo-uracil; backbone modifications, methylations, isobases, such as isocytidine and isoguanidine and the like. â€œNucleosidesâ€ can also include non-natural bases, such as, for example, nitroindole. Modifications can also include derivitization with a quencher, a fluorophore or another moiety. â€œNucleotidesâ€ are phosphate esters of nucleosides. Many modifications of nucleosides can be also be practiced on nucleotides.

The symbol [Image Omitted] , whether utilized as a bond or displayed perpendicular to a 0621bond indicates the point at which the displayed moiety is attached to the remainder of the molecule, solid support, etc.

The term â€œpharmaceutically acceptable saltsâ€ includes salts of the active compounds prepared with relatively nontoxic acids or bases, depending on the particular substituents found on the compounds described herein. When compounds of the present invention contain relatively acidic functionalities, base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt. When compounds of the present invention contain relatively basic functionalities, acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic, citric, tartaric, methanesulfonic, palmitic and the like. Also included are salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, for example, Berge et al., â€œPharmaceutical Saltsâ€ , Journal of Pharmaceutical Science, 1977, 66, 1-19). Certain specific compounds of the present invention contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts.

The neutral forms of the compounds are preferably regenerated by contacting the salt with a base or acid and isolating the parent compound in the conventional manner. The parent form of the compound differs from the various salt forms in certain physical properties, such as solubility in polar solvents, but otherwise the salts are equivalent to the parent form of the compound for the purposes of the present invention.

In addition to salt forms, the present invention provides compounds, which are in a prodrug form. Prodrugs of the compounds described herein are those compounds that readily undergo chemical changes under physiological conditions to provide the compounds of the present invention. Additionally, prodrugs can be converted to the compounds of the present invention by chemical or biochemical methods in an ex vivo environment. For example, prodrugs can be slowly converted to the compounds of the present invention when placed in a transdermal patch reservoir with a suitable enzyme or chemical reagent.

Certain compounds of the present invention can exist in unsolvated forms as well as solvated forms, including hydrated forms. In general, the solvated forms are equivalent to unsolvated forms and are encompassed within the scope of the present invention. Certain compounds of the present invention may exist in multiple crystalline or amorphous forms. In general, all physical forms are equivalent for the uses contemplated by the present invention and are intended to be within the scope of the present invention.

Certain compounds of the present invention possess asymmetric carbon atoms (optical centers) or double bonds; the racemates, diastereomers, geometric isomers and individual isomers are encompassed within the scope of the present invention.

The compounds of the invention may be prepared as a single isomer (e.g., enantiomer, cis-trans, positional, diastereomer) or as a mixture of isomers. In a preferred embodiment, the compounds are prepared as substantially a single isomer. Methods of preparing substantially isomerically pure compounds are known in the art. For example, enantiomerically enriched mixtures and pure enantiomeric compounds can be prepared by using synthetic intermediates that are enantiomerically pure in combination with reactions that either leave the stereochemistry at a chiral center unchanged or result in its complete inversion. Alternatively, the final product or intermediates along the synthetic route can be resolved into a single stereoisomer. Techniques for inverting or leaving unchanged a particular stereocenter, and those for resolving mixtures of stereoisomers are well known in the art and it is well within the ability of one of skill in the art to choose and appropriate method for a particular situation. See, generally, Furniss et al. (eds.), VOGEL'S ENCYCLOPEDIA OF PRACTICAL ORGANIC CHEMISTRY 5^THED., Longman Scientific and Technical Ltd., Essex, 1991, pp. 809-816; and Heller, Acc. Chem. Res. 23: 128 (1990).

The compounds of the present invention may also contain unnatural proportions of atomic isotopes at one or more of the atoms that constitute such compounds. For example, the compounds may be radiolabeled with radioactive isotopes, such as for example tritium (³H), iodine-125 (¹²⁵I) or carbon-14 (¹⁴C). All isotopic variations of the compounds of the present invention, whether radioactive or not, are intended to be encompassed within the scope of the present invention.

The term â€œviral diseaseâ€ refers to a condition caused by a virus. A viral disease can be caused by a DNA virus, an RNA virus, or by a retrovirus. In some embodiments, viral diseases include virus of the Flavaviridae family. The family Flaviviridae includes the three genera of the family, the flaviviruses, the pestiviruses (e.g., BVDV), and the hepatitis C viruses (e.g., HCV). The family Paramyxoviridae includes without limitation, parainfluenza virus, respiratory syncytial virus, Newcastle Disease virus, mumps virus and measles virus. DNA virus includes the family Poxyiridae. Poxyiridae family members include vaccinia virus and variola virus, which can cause small pox. DNA virus includes, but is not limited to, the Hepatitis B virus, which replicates its genome through an RNA intermediate. Retrovirus includes HIV-1, HIV-2, HTLV-1, HTLV-II, and SIV.

In a preferred embodiment, the compounds of the invention are used to treat an HIV strain that is resistant to nucleoside reverse transcriptase inhibitors (NRTI).

The four â€œnaturally occurring nucleotidesâ€ in RNA and DNA contain adenine, guanine, uracil, thymine or cytosine. Nucleotides which are complementary to one another are those that tend to form complementary hydrogen bonds between them and, specifically, the natural complement to A is U or T, the natural complement to U is A, the natural complement to T is A, the natural complement to C is G and the natural complement to G is C.

A â€œnucleic acidâ€ is a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise limited, encompasses analogs of natural nucleotides.

A â€œnucleoside analogâ€ as used herein is defined in more detail below and includes analogs of ribonucleosides and deoxyribonucleosides and the mono- di-, an triphosphates (nucleotides) thereof. As described above, they can be naturally occurring or non-naturally occurring, and derived from natural sources or synthesized. These monomeric units are nucleoside analogs (or â€œnucleotideâ€ analogs if the monomer is considered with reference to phosphorylation). For instance, structural groups are optionally added to the sugar or base of a nucleoside for incorporation into an oligonucleotide, such as a methyl or allyl group at the 2â€²-O position on the sugar, or a fluoro group which substitutes for the 2â€²-O group, or a bromo group on the nucleoside base. The phosphodiester linkage, or â€œsugar-phosphate backboneâ€ of the oligonucleotide analog is substituted or modified, for instance with methyl phosphonates or O-methyl phosphates.

A â€œgenomic nucleic acidâ€ is a nucleic acid polymer homologous to a nucleic acid which encodes a naturally occurring nucleic acid polymer (RNA or DNA) packaged by a viral particle. Typically, the packaged nucleic acid encodes some or all of the components necessary for viral replication. The genomic nucleic acid optionally includes nucleotide analogs. Nucleic acids are homologous when they are derived from a nucleic acid with a common sequence (an â€œancestralâ€ nucleic acid) by natural or artificial modification of the ancestral nucleic acid. Retroviral genomic nucleic acids optionally encode an RNA competent to be packaged by a retroviral particle. Such nucleic acids can be constructed by recombinantly combining a packaging site with a nucleic acid of choice.

A â€œvirally infected cellâ€ is a cell transduced with a viral nucleic acid. The nucleic acid is optionally incorporated into the cellular genome, or is optionally episomal.

The â€œmutation rateâ€ of a virus or nucleic acid refers to the number of changes occurring upon copying the nucleic acid, e.g., by a polymerase. Typically, this is measured over time, i.e., the number of alterations occurring during rounds of copying or generations of virus.

A â€œpolymeraseâ€ refers to an enzyme (DNA or RNA polymerase) that produces a polynucleotide sequence, complementary to a pre-existing template polynucleotide (DNA or RNA). For example, an RNA polymerase may be either an RNA viral polymerase or replicase or RNA cellular polymerase. A â€œcellular polymeraseâ€ is a polymerase derived from a cell. The cell may be prokaryotic or eukaryotic. The cellular RNA polymerase is typically an RNA polymerase such as Pol II or Pol III. Pol II enzymes are most preferred. A â€œmammalian RNA polymerase IIâ€ is an RNA polymerase II derived from a mammal. A â€œhuman RNA polymerase IIâ€ is an RNA polymerase II derived from a human. A â€œmurine RNA polymerase IIâ€ is an RNA polymerase II derived from a mouse. The polymerase is optionally naturally occurring, or artificially (e.g., recombinantly) produced.

A â€œcell cultureâ€ is a population of cells residing outside of an animal. These cells are optionally primary cells isolated from a cell bank, animal, or blood bank, or secondary cells cultured from one of these sources, or long-lived artificially maintained in vitro cultures that are widely available.

A â€œprogressive loss of viabilityâ€ refers to a measurable reduction in the replicative or infective ability of a population of viruses over time.

A â€œviral particleâ€ is a viral particle substantially encoded by an RNA virus or a virus with an RNA intermediate, such as BVDV, HCV, or HIV. The presence of non-viral or cellular components in the particle is a common result of the replication process of a virus, which typically includes budding from a cellular membrane.

An â€œHIV particleâ€ is a retroviral particle substantially encoded by HIV. The presence of non-HIV viral or cellular components in the particle is a common result of the replication process of HIV, typically including budding from a cellular membrane. In certain applications, retroviral particles are deliberately â€œpseudotypedâ€ by co-expressing viral proteins from more than one virus (often HIV and VSV) to expand the host range of the resulting retroviral particle. The presence or absence of non-HIV components in an HIV particle does not change the essential nature of the particle, i.e., the particle is still produced as a primary product of HIV replication.

Where the methods discussed below require sequence alignment, such methods of alignment of sequences for comparison are well known in the art. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2: 482; by the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48: 443; by the search for similarity method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85: 2444; by computerized implementations of these algorithms (including, but not limited to CLUSTAL in the PC/Gene program by Intelligenetics, Mountain View, Calif., GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis., USA); the CLUSTAL program is well described by Higgins and Sharp (1988) Gene, 73: 237-244 and Higgins and Sharp (1989) CABIOS 5: 151-153; Corpet, et al., (1988) Nucleic Acids Research 16, 10881-90; Huang, et al., (1992) Computer Applications in the Biosciences 8, 155-65, and Pearson, et al., (1994) Methods in Molecular Biology 24, 307-31. Typically, the alignments are visually inspected and refined manually after computer-aided adjustment.

A preferred example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. BLAST and BLAST 2.0 are used, with the default parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=âˆ’4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=âˆ’4, and a comparison of both strands.

As used herein, â€œcancerâ€ includes solid tumors and hematological malignancies. The former includes cancers such as breast, colon, and ovarian cancers. The latter include hematopoietic malignancies including leukemias, lymphomas and myelomas. This invention provides new effective methods, compositions, and kits for treatment and/or prevention of various types of cancer.

Hematological malignancies, such as leukemias and lymphomas, are conditions characterized by abnormal growth and maturation of hematopoietic cells.

Leukemias are generally neoplastic disorders of hematopoietic stem cells, and include adult and pediatric acute myeloid leukemias (AML), chronic myeloid leukemia (CML), acute lymphocytic leukemia (ALL), chronic lymphocytic leukemia (CLL), hairy cell leukemia and secondary leukemia. Myeloid leukemias are characterized by infiltration of the blood, bone marrow, and other tissues by neoplastic cells of the hematopoietic system. CLL is characterized by the accumulation of mature-appearing lymphocytes in the peripheral blood and is associated with infiltration of bone marrow, the spleen and lymph nodes.

Specific leukemias include acute nonlymphocytic leukemia, chronic lymphocytic leukemia, acute granulocytic leukemia, chronic granulocytic leukemia, acute promyelocytic leukemia, adult T-cell leukemia, aleukemic leukemia, a leukocythemic leukemia, basophylic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross' leukemia, hairy-cell leukemia, hemoblastic leukemia, hemocytoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenous leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, micromyeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myelocytic leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Naegeli leukemia, plasma cell leukemia, plasmacytic leukemia, promyelocytic leukemia, Rieder cell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia, and undifferentiated cell leukemia.

Lymphomas are generally neoplastic transformations of cells that reside primarily in lymphoid tissue. Among lymphomas, there are two major distinct groups: non-Hodgkin's lymphoma (NHL) and Hodgkin's disease. Lymphomas are tumors of the immune system and generally are present as both T cell- and as B cell-associated disease. Bone marrow, lymph nodes, spleen and circulating cells are all typically involved. Treatment protocols include removal of bone marrow from the patient and purging it of tumor cells, often using antibodies directed against antigens present on the tumor cell type, followed by storage. The patient is then given a toxic dose of radiation or chemotherapy and the purged bone marrow is then reinfused in order to repopulate the patient's hematopoietic system.

Other hematological malignancies include myelodysplastic syndromes (MDS), myeloproliferative syndromes (MPS) and myelomas, such as solitary myeloma and multiple myeloma. Multiple myeloma (also called plasma cell myeloma) involves the skeletal system and is characterized by multiple tumorous masses of neoplastic plasma cells scattered throughout that system. It may also spread to lymph nodes and other sites such as the skin. Solitary myeloma involves solitary lesions that tend to occur in the same locations as multiple myeloma.

Hematological malignancies are generally serious disorders, resulting in a variety of symptoms, including bone marrow failure and organ failure. Treatment for many hematological malignancies, including leukemias and lymphomas, remains difficult, and existing therapies are not universally effective. While treatments involving specific immunotherapy appear to have considerable potential, such treatments are limited by the small number of known malignancy-associated antigens. Moreover the ability to detect such hematological malignancies in their early stages can be quite difficult depending upon the particular malady. Accordingly, there remains a need in the art for improved methods for treatment of hematological malignancies such as B cell leukemias and lymphomas and multiple myelomas. The present invention fulfills these and other needs in the field.

Other cancers are also of concern, and represent similar difficulties insofar as effective treatment is concerned. Such cancers include those characterized by solid tumors. Examples of other cancers of concern are skin cancers, including melanomas, basal cell carcinomas, and squamous cell carcinomas. Epithelial carcinomas of the head and neck are also encompassed by the present invention. These cancers typically arise from mucosal surfaces of the head and neck and include salivary gland tumors.

The present invention also encompasses cancers of the lung. Lung cancers include squamous or epidermoid carcinoma, small cell carcinoma, adenocarcinoma, and large cell carcinoma. Breast cancer is also included, both invasive breast cancer and non-invasive breast cancer, e.g., ductal carcinoma in situ and lobular neoplasia.

The present invention also encompasses gastrointestinal tract cancers. Gastrointestinal tract cancers include esophageal cancers, gastric adenocarcinoma, primary gastric lymphoma, colorectal cancer, small bowel tumors and cancers of the anus. Pancreatic cancer and cancers that affect the liver are also of concern, including hepatocellular cancer. The present invention also includes treatment of bladder cancer and renal cell carcinoma.

The present invention also encompasses prostatic carcinoma and testicular cancer.

Gynecologic malignancies are also encompassed by the present invention including ovarian cancer, carcinoma of the fallopian tube, uterine cancer, and cervical cancer.

Treatment of sarcomas of the bone and soft tissue are encompassed by the present invention. Bone sarcomas include osteosarcoma, chondrosarcoma, and Ewing's sarcoma.

The present invention also encompasses malignant tumors of the thyroid, including papillary, follicular, and anaplastic carcinomas.

In some embodiments, a â€œsubject in need of treatmentâ€ is a mammal with a viral disease that is life-threatening, or that impairs health, or shortens the lifespan of the mammal. In other embodiments, a â€œsubject in need of treatmentâ€ is a mammal with cancer that is life-threatening or that impairs health or shortens the lifespan of the mammal.

A â€œpharmaceutically acceptableâ€ component is one that is suitable for use with humans and/or animals without undue adverse side effects (such as toxicity, irritation, and allergic response) commensurate with a reasonable benefit/risk ratio.

A â€œsafe and effective amountâ€ refers to the quantity of a component that is sufficient to yield a desired therapeutic response without undue adverse side effects (such as toxicity, irritation, or allergic response) commensurate with a reasonable benefit/risk ratio when used in the manner of this invention. In some embodiments â€œtherapeutically effective amountâ€ refers to an amount of a component effective to yield the desired therapeutic response, for example, an amount effective to enhance mutagenesis of a virus, or to diminish the ability of the virus to produce active proteins, or to inhibit replication of a virus, or to eliminate or diminish the ability of a virus to produce infectious particles, or to kill the virus or a virally infected cell. Other embodiments encompass other therapeutic responses, for example, an amount of a component effective to halt or to delay the growth of a cancer, or to cause a cancer to shrink, or not metastasize. The specific safe and effective amount or therapeutically effective amount will vary with such factors as the particular condition being treated, the physical condition of the patient, the type of mammal being treated, the duration of the treatment, the nature of concurrent therapy (if any), and the specific formulations employed and the structure of the compounds or its derivatives.

An â€œenteric formulationâ€ is a formulation of a compound wherein the compound is stable in the acidic environment of the stomach, and after passage through the stomach, an active form of the compound is available for absorbtion in the intestinal tract. An â€œoral osmotic drug deviceâ€ as used herein is a device that delivers a drug at a controlled rate in a region of the gastrointestinal tract having a pH less than 3.5, and then delivers all the drug in the immediately continuing region of the gastrointestinal tract having a pH greater than 3.5. Methods to make and use an oral osmotic drug device are found, for example, in U.S. Pat. No. 4,587,117, herein incorporated by reference.

The Compounds

The present invention provides compounds that display antiviral activity, in addition to salts and prodrugs of such compounds. The compounds are generally nucleosides, nucleotides, nucleoside analogues, nucleotide analogues, salts and prodrugs thereof. The inventors have recognized that antiviral pharamacophores comprising highly active, yet biologically unstable nucleosides or nucleotides and nucleoside or nucleotide analogues are converted to useful therapeutic agents by altering selected properties of the pharmacophore. In an exemplary embodiment, the pharmacophore is stabilized by the attachment of the active species containing the pharmacophore to a modifying group that increases the lipophilicity of the pharmacophore. The combination of the pharmacophore and the modifying group preferably provides the pharmacophore in a prodrug format.

Prodrugs comprise inactive forms of active drugs in which a chemical group is present on the prodrug, which renders it inactive and/or confers solubility or some other property to the drug. Prodrugs are generally inactive, or less active than the parent compound, but once the chemical group has been cleaved from the prodrug (e.g., by hydrolysis, heat, cavitation, pressure, and/or enzymes in the surrounding environment), the active drug is generated. Prodrugs may be designed as reversible drug derivatives and utilized as modifiers to enhance drug transport to site-specific tissues. Prodrugs are described in the art, for example, in Sinkula et al., J. Pharm. Sci 64: 181-210 (1975) and in U.S. Provisional Patent Application No. 60/480,037, filed Jun. 20, 2003, which is herein incorporated by reference for all purposes.

Thus, the present invention provides, inter alia, novel nucleoside and nucleotide analogues that are covalently attached to a group that modifies the properties of the nucleoside or nucleotide analogue. In exemplary embodiments, the â€œmodifying groupâ€ enhances the stability or bioavailability of nucleoside or nucleotide or its analogue. In the discussion that follows, the invention is exemplified by reference to lipophilic modifying groups. The focus of the discussion is for clarity of illustration, and those of skill in the art will appreciate that compounds including modifying groups other the lipophilic groups discussed herein are within the scope of the invention.