WO2006026619A2 - Inhibition of viruses using rnase h inhibitors - Google Patents

Abstract

The present invention relates to methods and compositions for the treatment of viral infections including HIV using RNase H inhibitors. Compounds are e.g. 2-amino-5,6,7,8-tetrahydro-4H-cyclohepta (b) thiophene-3-carboxamide, N-(3-(aminocarbonyl)-4,5-dimehtyl-2-thienyl)-2-furamide, N-(3-(aminocarbonyl)-4,5-dimethyl-2-thienyl)-tetrahydro-2-furancarboxamide, etc.

Description

Methods And Compositions Related To The Inhibition Of Viruses Using

RNase H Inhibitors

Cross-reference to Related Applications

This application claims the benefit of U.S. provisional patent application serial no.

60/605,165, filed August 30, 2004, the contents of which are incorporated herein by reference in their entirety.

Field of the Invention:

The present invention relates to the discovery of a class of compounds that inhibit HIV RNase H, to methods of using these compounds for the treatment of HIV infections, and to pharmaceutical compositions of these compounds.

Statement of Governmental Interest:

This invention was funded by the National Cancer Institute at the National Institutes of Health. The United States Government has certain rights to this invention.

Background of the Invention :

Retroviral reverse transcription is a complex process carried out by the viral enzyme reverse transcriptase (RT). The complexity of reverse transcription requires RT to be multifunctional, with both RNA-dependent and DNA-dependent DNA polymerase activities and ribonuclease H (RNase H) activity, each of which is essential for HIV replication. RNase H specifically hydrolyzes the RNA strand of an RNA/DNA hybrid. This enzyme activity is found in virtually all organisms, including retroviruses such as HIV-I, where it is present as a specific subdomain of the viral RT. HIV-I RT-RNase H catalyzes a series of "sequence nonspecific" and "sequence-specific" cleavage reactions needed during reverse transcription. Nonspecific cleavages by RT-RNase H hydrolyze the retroviral (+) strand genomic RNA once this RNA has been used as template for (-) strand DNA synthesis. These cleavages free the newly synthesized DNA strand to participate in strand transfer reactions and to be used as a template in the synthesis of the second DNA strand ((+) strand DNA) to complete viral DNA synthesis. Specific cleavages by RT- RNase H generate and subsequently remove the polypurine tract RNA primer needed to initiate (+) strand DNA synthesis.

Mutations in the RNase H domain of HIV-I RT that reduce or eliminate RNase H activity result in noninfectious virions (Schatz et al. in Oncogensis and AIDS, pp. 293-303 (Papas, Ed. 1990); Tisdale et al., 1991, J. Gen. Virol. 72:59-66), demonstrating that retroviral RNase H is essential for virus replication and that cellular RNase H cannot substitute for the retroviral enzyme. HIV-I RT-associated RNase H thus represents a ^• potential target for anti-HIV therapies.

Many inhibitors of HIV-I RT-DNA polymerase activity have been described and a high proportion of clinically used anti-HIV drugs target this activity. In contrast, no drugs targeting RT-RNase H activity are presently in clinical use. Inhibition of reverse- transcriptase-associated RNase H activity has mostly been demonstrated in cell-free systems. RNase H activity may be inhibited by 3'-azido thymidylate 5 '-monophosphate (AZT-MP), a major intracellular metabolite of the NNRT inhibitor AZT, with an IC₅₀ in the 50 μM range (Tan et al., 1991, Biochemistry 30:4831-4835; Zhan et al., 1994, Biochemistry 33:1366-1372). However, the activity of AZT-MP is-dependent on the presence of a metal cation, with Mg²⁺ being the most effective co-activator. The metal chelator N~(4-tert- butylbenzoyl)-2-hydroxy-lnaphthaldehyde hydrazone (BBNH) has demonstrated potent RNase H inhibitory activity (IC₅o-3.5 μM) and is effective against mutant reverse transcriptase enzymes that have a high-level of resistance to other NNRTIs (Borkow et al., 1997, Biochemistry 36:3179-3185). However, BBNH also inhibits the DNA polymerase activity of reverse transcriptase, and thus may interact with more than one domain of reverse transcriptase. Illimaquinone, a natural product of marine origin, preferentially inhibits the RNase H activity of HIV-I reverse transcriptase. However, Illimaquinone is not specific to HIV-I RNase and also inhibits the RNase H function of murine leukemia virus reverse transcriptase and E. coli Rnase H (Loya, 1993, J. Biol. Chan. 268:9323-9328; Loya et al., 1990, Antimicrob. Agents Chemother. 34(10):2009-2012).

Although current therapies are initially very effective at controlling the course of HIV spread in an infected individual, thereby improving the quality of life and longevity of HlV-infected patients, their prolonged use has thus far invariably led to the rise of HIV strains that exhibit resistance to these drugs. Clinical appearance of drug-resistant HW imparts an unfavorable prognosis and poses a risk for the introduction of resistant strains of HIV into uninfected individuals.

Therefore, there is an urgent need to identify new inhibitors of HIV that act on viral targets not presently targeted by current therapies. One such target is RNase H and there is a need in the art for reverse transcriptase RNase H inhibitors that exhibit high inhibitory activity and that are specific for viral RNase H with minimal or no affinity for human ribonucleases. The invention described herein is directed to address this and other needs.

Summary of the Invention :

In one aspect, the invention relates to the recognition of a class of compounds that are useful for the inhibition of viral RNase H and thus are useful for the treatment of viral disease.

In one aspect, the invention relates to a method of treating a subject having a retroid virus infection or at risk of having a retroid virus infection. The method includes the step of administering a retroid virus RNase H inhibitor to the subject, in which the viral RNase H inhibitor includes a compound having the following structure (Formula I): T7US2005/030846

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. (Formula I)

In Formula I,

X is N(R') or oxygen; R₁, independently for each occurrence, is selected from the group consisting of a halogen atom, a hydroxyl group, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; y is O to 3;

R₂ is selected from the group consisting of -R₅, — C(O)-N(R')- R₆, and— C(O)-O-R₆;

R₅ is selected from the group consisting, of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group;

R₆ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; or

R₁ and R₂, together with the atoms to which they are attached, may form a ring structure; 2005/030846

R₃ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group;

R₄ is selected from the group consisting of -NR⁵R", -N(R')-C(O)-R₇, and -N=C-R₇; or

R₃ and R₄, together with the atoms to which they are attached, may form a ring structure;

R' and R" are each, independently for each occurrence, hydrogen or lower alkyl;

R₇ is selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; or or a pharmaceutically acceptable salt thereof.

In another aspect the invention relates to an anti-retroid virus composition comprising a pharmacologically acceptable excipient and a retroid virus RNase H inhibitor having Formula I above.

hi another aspect, the invention relates to a method of treating a subject having a retroid virus infection or at risk of having a retroid virus infection. The method includesthe step of administering a retroid virus RNase H inhibitor to the subject, wherein the RNase H inhibitor comprises a compound having the following structure: US2005/030846

Formula II

Wherein X is nitrogen or oxygen; wherein R₂ is selected from the group consisting of— C— R₅t, -C(O)-N-R₆, -C(O)-O-R₆; wherein R₁ and R₅ are each independently selected from the group consisting of a halogen atom, a hydroxyl group, a hydrocarbon group, a substituted hydrocarbon group; a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; wherein y is O to 3; wherein t is O to 3; wherein R₆ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; wherein R₄ is selected from the group consisting of -NH₂, -N-C(O)-R₇, and -N=C-R₇; wherein R₃ and R₇ are each independently selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; 30846

wherein z is 0 to 1; wherein R₁ and R₂ may cyclize to form a ring structure, and wherein R₃ and R₄ may cyclize to form a ring structure.

In another aspect the invention relates to an anti-retroid virus composition comprising a pharmacologically acceptable excipient and a retroid virus RNase H inhibitor having Formula II above.

Additional features, embodiments and advantages of the invention will be apparent to the skilled artisan in view of the specification and claims which follow.

Brief Description of the Figures: ■ Figure 1 depicts a comparison of the inhibitory effects of NSC 727447 on RNase H proteins derived from the following organisms: HIV-I, HIV-2, E. coli, moloney murine leukemia virus (MMLV) and humans. '

Figure 2 depicts a comparison of the inhibitory effects of NSC 727448 on RNase H proteins derived from the following organisms: HIV-I, HIV-2, E. coli, moloney murine leukemia virus (MMLV) and humans.

Figure 3 is a graph showing the effects of varying concentrations of NSC 727447 (Panel A) or NSC 727448 (Panel B) on HIV-I infection of the CΕM T4 lymphocyte cell line and on cell viability. Cell viability in both the infected and uninfected samples is measured by assaying the ability of the cells to convert a colorless tetrazolium salt (XTT) to a highly colored soluble formazan. Results are measured in a spectrophotometer and presented as a percentage of control values.

Figure 4 is a graph showing the effects of varying concentrations of NSC 727447 on HIV-I infection of the CΕM T4 lymphocyte cell line and on cell viability. Cell viability in both the infected and uninfected samples is measured by assaying the ability of the cells to convert a colorless tetrazolium salt (XTT) to a highly colored soluble formazan. Results are measured in a spectrophotometer and presented as a percentage of control values. 8

Figure 5 is a graph showing the effects of varying concentrations of NSC 731246 (Panel A) or NSC 731247 (Panel B) on HIV-I infection of the CEM T4 lymphocyte cell line and on cell viability. Cell viability in both the infected and uninfected samples is measured by assaying the ability of the cells to convert a colorless tetrazolium salt (XTT) to a highly colored soluble formazan. Results are measured in a spectrophotometer and presented as a percentage of control values.

Figure 6 is a graph showing the effects of varying concentrations of NSC 732532 (Panel A) or NSC 732533 (Panel B) on HIV-I infection of the CEM T4 lymphocyte cell line and on cell viability. Cell viability in both the infected and uninfected samples is measured by assaying the ability of the cells to convert a colorless tetrazolium salt (XTT) to a highly colored soluble formazan. Results are measured in a spectrophotometer and presented as a percentage of control values.

Figure 7 is a graph showing the effects of varying concentrations of NSC 732526 (Panel A) or NSC 732527 (Panel B) on HIV-I infection of the CEM T4 lymphocyte cell line and on cell viability. Cell viability in both the infected and uninfected samples is measured by assaying the ability of the cells to convert a colorless tetrazolium salt (XTT) to a highly colored soluble formazan. Results are measured in a spectrophotometer and presented as a percentage of control values.

Figure 8 is a graph showing the effects of varying concentrations of NSC 732520 (Panel A) or NSC 732521 (Panel B) on HIV-I infection of the CEM T4 lymphocyte cell line and on cell viability. Cell viability in both the infected and uninfected samples is measured by assaying the ability of the cells to convert a colorless tetrazolium salt (XTT) to a highly colored soluble formazan. Results are measured in a spectrophotometer and presented as a percentage of control values.

Description of the Preferred Embodiments:

In one aspect, the invention relates to the activity of a certain class of compounds that are effective in inhibiting RNase H activity of HIV-I and HIV-2, and that have been 5 030846

shown to reduce the cytopathic effect of HIV-I. Thus, the invention relates to the uses of a class of compounds that are useful for the treatment of human immunodeficiency virus infections, particularly HIV-I and HIV-2, and other retroid virus and retrovirus infections in humans and in non-human mammals and birds.

In one embodiment of the invention, preferred compounds of the invention have the following structure (Formula I):

. Formula I

In Formula I, X is N(R') or oxygen;

R₁, independently for each occurrence, is selected from the group consisting of a halogen atom, a hydroxyl group, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; y is 0 to 3;

R₂ is selected from the group consisting Of-R₅, — C(O)-N(R')- R₆, and— C(O)-O-R₆, R₅ is selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted T/US2005/030846

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heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group;

R₆ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; or

R₁ and R₂, together with the atoms to which they are attached, may form a ring structure;

R₃ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group;

R₄ is selected from the group consisting of-NR'R", -N(R')-C(O)-R₇, and -N=C-R₇; or R₃ and R₄, together with the atoms to which they are attached, may form a ring structure;

R' and R" are each, independently for each occurrence, hydrogen or lower alkyl;

R₇ is selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; or or a pharmaceutically acceptable salt thereof.

In preferred embodiments of the invention, y is equal to 0 or 1, and if y is 1, R₁ together with R₂ forms a ring structure, preferably a carbocyclic ring comprising 5-8 ring atoms, more preferably 6, 7, or 8 carbon ring atoms.

In certain preferred embodiments of Formula I, R₂ taken together with R₁ and the atoms to which they are attached, forms a ring structure. In other preferred embodiments, 2005/030846

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R₂ is methyl, phenyl, -C(0)-N(R')-R.6, Or-C(O)-O-R₆; in which R' is H and R₆ is alkyl or optionally substituted aromatic.

In preferred embodiments of the invention, in Formula I: R₄ is selected from the group consisting of NH₂ and -N-C(O)-R₇, wherein R₄ and R₃ are not cyclized in a ring structure. In a preferred embodiment, R₄ is NH₂. In another preferred embodiment, R₄ is — N-C(O)-R₇, and R₇ is an aromatic or heteroaromatic group or -CH₂-aromatic group or - CH₂-heteroaromatic group; in each case, the aromatic or heteroaromatic group may be substituted or unsubstituted. In a preferred aromatic, an aromatic group is a phenyl group. Li a preferred embodiment, a heteroaroamtic group is a furanyl group, more preferably a furan-2-yl group.

In preferred embodiments, in Formula I, when R₃ and R₄, together with the atoms to which they are attached, form a ring structure, the ring structure has from 5 to 8 atoms in ^■ the ring, including 1-2 heteroatoms. ' '

In another aspect, the invention relates to a method of treating a subject having a retroid virus infection or at risk of having a retroid virus infection. The method includes administering a retroid virus RNase H inhibitor to the subject, wherein the RNase H inhibitor comprises a compound having the following structure (Formula II):

Formula II

Wherein X is nitrogen or oxygen; wherein R₂ is selected from the group consisting of— C— Rs_t, -C(O)-N-R₆,

-C(O)-O-R_6; 2005/030846

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wherein R₁ and R₅ are each independently selected from the group consisting of a halogen atom, a hydroxyl group, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; wherein y is 0 to 3; wherein t is 0 to 3; wherein R₆ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; wherein R₄ is selected from the group consisting of -NH₂, -N-C(O)-R₇, and -N=C-R₇; wherein R₃ and R₇ are each independently selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; wherein z is O to 1; wherein R₁ and R₂ may cyclize to form a ring structure, and wherein R₃ and R₄ may cyclize to form a ring structure.

In preferred embodiments of Formula II: y is equal to 0 or 1, and if y is 1, R₁ cyclizes with R₂ to form a ring structure, preferably a carbocyclic ring comprising 6, 7, or 8 carbon ring atoms. 2005/030846

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In preferred embodiments of Formula II, R₄ is selected from the group consisting of NH₂, -N-C(O)-R₇, wherein R₄ and R₃ are not cyclized in a ring structure.

In preferred embodiments of of Formula II, when R₁ and R₂ are cyclized in a ring structure, R₃ and R₄ are not cyclized in a ring structure.

In another aspect the invention relates to an anti-retroid virus composition including a pharmacologically acceptable excipient and a retroid virus RNase H inhibitor having Formula II above.

In preferred embodiments of the invention, in Formulas I or II, when R₁ and R₂ are cyclized in a ring structure, R₃ and R₄ are not cyclized in a ring structure.

In a preferred embodiment of the invention, a compound of the formula:

2-Benzamido-3-Carboxy-4,5,6,7-Tetrahydrobenz[b]Thiophene (as described in United States Patent No.6,083,706 (herein incorporated by reference)) is excluded by proviso from the class of compounds described by Formula I or II herein.

As used herein, "hydrocarbon group" means a chain of 1 to 25 carbon atoms, preferably 1 to 12 carbon atoms, more preferably 1 to 10 carbon atoms, and most preferably

1 to 8 carbon atoms. Hydrocarbon groups may have a linear or branched chain structure.

Preferred hydrocarbon groups have one or two branches, preferably 1 branch. Preferred hydrocarbon groups are saturated (i.e., alkyl groups), more preferably lower alkyl groups.

Unsaturated hydrocarbon groups (including alkenyl and alkynyl groups) have one or more double bonds, one or more triple bonds, or combinations thereof. Preferred unsaturated hydrocarbon groups have one or two double bonds or one triple bond; more preferred unsaturated hydrocarbon groups have one double bond.

As used herein, "heterogeneous group" means a saturated or unsaturated chain of non-hydrogen member atoms comprising carbon atoms and at least one heteroatom. Heterogeneous groups typically have 1 to 25 member atoms. Preferably, the chain contains 2005/030846

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1 to 12 member atoms, more preferably 1 to 10, and most preferably 1 to 6. The chain may be linear or branched. Preferred branched heterogeneous groups have one or two branches, preferably one branch. Preferred heterogeneous groups are saturated. Unsaturated heterogeneous groups have one or more double bonds, one or more triple bonds, or both. Preferred unsaturated heterogeneous groups have one or two double bonds or one triple bond. More preferably, the unsaturated heterogeneous group has one double bond.

As used herein, "aromatic group" means an aromatic group having a monocyclic or polycyclic ring structure. Monocyclic aromatic groups contain 4 to 10 carbon atoms, preferably 4 to 7 carbon atoms, and more preferably 4 to 6 carbon atoms in the ring. Preferred polycyclic ring structures have two or three rings. Polycyclic structures having two rings typically have 8 to 12 carbon atoms, preferably 8 to 10 carbon atoms in the rings. Polycyclic aromatic groups include groups wherein at least one, but not all, of the rings are aromatic. • , ; • ,

As used herein, "heteroaromatic group" means an aromatic group containing carbon atoms and 1 to 4 heteroatoms in the ring. Monocyclic heteroaromatic groups contain 4 to 10 member atoms, preferably 4 to 7 member atoms, and more preferably 4 to 6 member atoms in the ring. Preferred polycyclic ring structures have two or three rings. Polycyclic structures having two rings typically have 8 to 12 member atoms, preferably 8 to 10 member atoms in the rings. Polycyclic heteroaromatic groups include groups wherein at least one, but not all, of the rings are heteroaromatic.

As used herein, "carbocyclic group" means a saturated or unsaturated carbocyclic hydrocarbon ring. Carbocyclic groups are not aromatic. Carbocyclic groups are monocyclic or polycyclic. Polycyclic carbocyclic groups can be fused, spiro, or bridged ring systems. Monocyclic carbocyclic groups contain 4 to 10 carbon atoms, preferably 4 to 7 carbon atoms, and more preferably 5 to 6 carbon atoms in the ring. Bicyclic carbocyclic groups preferably contain 8 to 12 carbon atoms, preferably 9 to 10 carbon atoms in the rings. As used herein, "heterocyclic group" means a saturated or unsaturated ring structure containing carbon atoms and 1 or more heteroatoms in the ring. Heterocyclic groups are not aromatic. Heterocyclic groups are monocyclic or polycyclic. Polycyclic heteroaromatic groups can be fused, spiro, or bridged ring systems. Monocyclic heterocyclic groups contain 4 to 10 member atoms (i.e., including both carbon atoms and at least 1 heteroatom), preferably 4 to 7, and more preferably 5 to 6 in the ring. Bicyclic heterocyclic groups preferably contain 8 to 18 member atoms, preferably 9 or 10 in the rings.

As used herein, "heteroatom" means an atom other than carbon or hydrogen, e.g., in the ring of a heterocyclic group or the chain of a heterogeneous group. Preferably, heteroatoms are selected from the group consisting of sulfur, phosphorous, nitrogen and oxygen atoms. Groups containing more than one heteroatom may contain different heteroatoms.

As used herein, "substituted hydrocarbon group" means a hydrocarbon group wherein 1 or more of the hydrogen atoms bonded to carbon atoms in the chain have been replaced with other substituents. Preferred substituents include halogen atoms (e.g., fluorine, chlorine, bromine, iodine), monovalent aromatic groups, monovalent substituted aromatic groups, monovalent hydrocarbon groups including alkyl groups (e.g. methyl groups), monovalent substituted hydrocarbon groups such as benzyl, and monovalent heterogeneous groups including alkoxy groups (e.g. methoxy). Additional preferred substituents include hydroxy, nitro, cyano, and trifluoromethyl.

As used herein, "substituted heterogeneous group" means a heterogeneous group, wherein 1 or more of the hydrogen atoms bonded to carbon atoms in the chain have been replaced with other substituents. Preferred substituents include monovalent hydrocarbon groups including alkyl groups (e.g. methyl groups) and monovalent heterogeneous groups including alkoxy groups (e.g. methoxy groups). Additional preferred substituents include hydroxy, nitro, cyano, and trifluoromethyl groups. As used herein, "substituted aromatic group" means an aromatic group wherein 1 or more of the hydrogen atoms bonded to carbon atoms in the ring have been replaced with other substituents. Preferred substituents include halogen atoms, nitro groups, hydrocarbon groups (e.g. methyl groups) and heterogeneous groups including alkoxy groups (e.g. methoxy groups). Additional preferred substituents include hydroxy, cyano, and trifluoromethyl groups. The substituents maybe substituted at the ortho, meta, or para position on the ring, or any combination thereof.

As used herein, "substituted heteroaromatic group" means a heteroaromatic group wherein 1 or more hydrogen atoms bonded to carbon atoms in the ring have been replaced with other substituents. Preferred substituents include monovalent hydrocarbon groups including alkyl groups (e.g. methyl groups) such as methyl groups and monovalent ^••: : ^■ heterogeneous groups including alkoxy groups (e.g. methoxy groups). Additional preferred substituents include halogen atoms, hydroxy, nitro, cyano, and trifluoromethyl groups:- The substituents may be substituted at the ortho, meta, or para position on the ring, or any*" ^■ combination thereof.

As used herein, "substituted carbocyclic group" means a carbocyclic group wherein 1 or more hydrogen atoms bonded to carbon atoms in the ring have been replaced with other substituents. Preferred substituents include hydrocarbon groups such as alkyl groups (e.g., methyl groups) and heterogeneous groups such as alkoxy groups (e.g., methoxy groups). Additional preferred substituents include halogen atoms, hydroxy, nitro, cyano, and trifluoromethyl groups.

As used herein, "substituted heterocyclic group" means a heterocyclic group wherein 1 or more hydrogen atoms bonded to carbon atoms in the ring have been replaced with other substituents. Preferred substituents include monovalent hydrocarbon groups including alkyl groups such as methyl groups and monovalent heterogeneous groups including alkoxy groups such as methoxy groups. Additional preferred substituents include halogen atoms, hydroxy, nitro, cyano, and trifluoromethyl groups. Substituted heterocyclic groups are not aromatic. The invention also relates to the optically active forms (stereoisomers), the enantiomers, the racemates, the diastereomers and the clathrates, hydrates and solvates of compounds of Formula I. The term solvates of the compounds is taken to mean adductions of inert solvent molecules onto the compounds which form owing to their mutual attractive force. Solvates are, for example, monohydrates or dihydrates or alkoxides.

Combinations of substituents and variables envisioned by this invention are only those that result in the formation of stable compounds. The term "stable", as used herein, refers to compounds which possess stability sufficient to allow manufacture and which maintains the integrity of the compound for a sufficient period of time to be useful for the purposes detailed herein (e.g., formulation into therapeutic products, intermediates for use in production of therapeutic compounds, isolatable or storable intermediate compounds). The compounds delineated herein are commercially available or readily synthesized by one of ordinary skill in the art using methodology known in the art.

As used herein, the term "pharmaceutically acceptable salt," is a salt formed from, for example, an acid and a basic group of a compound of any one of the formulae disclosed herein. Illustrative salts include, but are not limited, to sulfate, citrate, acetate, oxalate, chloride, bromide, iodide, nitrate, bisulfate, phosphate, acid phosphate, isonicotinate, lactate, salicylate, acid citrate, tartrate, oleate, tannate, pantothenate, bitartrate, ascorbate, succinate, maleate, besylate, gentisinate, fumarate, gluconate, glucaronate, saccharate, formate, benzoate, glutamate, methanesulfonate, ethanesulfonate, benzenesulfonate, p- toluenesulfonate, and pamoate {i.e., l,l'-methylene-bis-(2-hydroxy-3-naphthoate)) salts. The term "pharmaceutically acceptable salt" also refers to a salt prepared from a compound of any one of the formulae disclosed herein having an acidic functional group, such as a carboxylic acid functional group, and a pharmaceutically acceptable inorganic or organic base. Suitable bases include, but are not limited to, hydroxides of alkali metals such as sodium, potassium, and lithium; hydroxides of alkaline earth metal such as calcium and magnesium; hydroxides of other metals, such as aluminum and zinc; ammonia, and organic amines, such as unsubstituted or hydroxy-substituted mono-, di-, or trialkylamines; dicyclohexylamine; tributyl amine; pyridine; N-methyl,N-ethylamine; diethylamine; triethylamine; mono-, bis-, or tris-(2-hydroxy-lower alkyl amines), such as mono-, bis-, or tris-(2-hydroxyethyl)amine, 2-hydroxy-tert-butylamine, or tris- (hydroxymethyl)methylamine, N, N,-di-lower alkyl-N-(hydroxy lower alkyl)-amines, such as N₅N-dimethyl-N-(2-hydroxyethyl)amine, or tri-(2-hydroxyethyl)amine; N-methyl-D- glucamine; and amino acids such as arginine, lysine, and the like. The term "pharmaceutically acceptable salt" also refers to a salt prepared from a compound of any one of the formulae disclosed herein having a basic functional group, such as an amino functional group, and a pharmaceutically acceptable inorganic or organic acid. Suitable acids include hydrogen sulfate, citric acid, acetic acid, oxalic acid, hydrochloric acid.(HCl), hydrogen bromide (HBr), hydrogen iodide (HI), nitric acid, phosphoric acid, lactic acid, salicylic acid, tartaric acid, bitartratic acid, ascorbic acid, succinic acid, maleic acid, besylic acid, fumaric acid, gluconic acid, glucaronic acid, formic acid, benzoic acid, glutamic acid, methanesulfonic acid, ethanesulfonic acid, benzenesulfonic acid, and/>-toluenesulfonic acid.

Certain compounds of the invention are shown in Table 1 below.

Table 1 Exemplified Compounds of the Invention

NSC 732801 NSC 732802 NSC 732803

In light of the present invention and the above-disclosed structures, compounds of the invention may be readily synthesized by one of skill in the art. Additional compounds of the invention, and specific details on methods of chemical synthesis of these compounds, may be obtained from ChemBridge Corporation (San Diego, California) (see also U.S. Pat. No. 6,414,013 and US2004/0082602, both herein incorporated by reference). The exemplified compounds of Table 1 above are listed in Table 2 below, along with their ChemBridge Corporation identification number and certain physical data.

Table 2 Additional Data for Exemplified Compounds

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Preferred compounds of the invention show a greater than 10%, preferably greater than 20%, more preferably greater than 30% and most preferably greater than 40% inhibition of HIV-I RT associated RNaseH at a concentration of 10 μM. Inhibition of HIV- 1 RT associated RNase H can be assessed, for example, using the fluorescence resonance energy transfer (FRET) quenching assay described in Example 1 herein. Preferred compounds of the invention show inhibition of the cytopathic effect of an HIV virus at concentrations that do not significantly inhibit cell growth. For example, preferred compounds of the invention are NSC 727447, NSC 731247, NSC 732520, NSC 732526, and NSC 732533, as shown in the Tables, supra. Cytopathic effect may be measured, for example, using an isolated HW strain and the CD4+ lymphoblast cell line, CEM (ATCC Number: CCL-119), and using the procedures described by Weislow et al. (1989, J. Natl. Cancer Inst. 81:577-586). The EC₅₀ represents the concentration of agent which reduces an HIV cytopathic effects 50% relative to untreated control. The TC₅0 represents the concentration of the agent which inhibits 50% of the viability of uninfected cells. For preferred compositions of the invention, the EC₅₀ is less than about 75% of the TC₅₀, more preferably less than about 50% of the TC_5O, and most preferably less than about 25% of the TC₅₀.

Compounds and pharmaceutical compositions provided herein are useful in preventing or treating retroid virus infections via decreasing or inhibiting the proliferation or replication of a retroid virus, particularly retrovirus infections, particularly lentivirus infections, most preferably human immunodeficiency virus infections in humans or non- human mammals. Exemplary retroid viruses include, but are not limited to, Hepadnaviruses (e.g., Arctic ground squirrel hepatitis B virus, Duck hepatitis B virus, Ground squirrel hepatitis virus, Hepatitis B virus, Heron hepatitis B virus, Orangutan hepadnavirus, Stork hepatitis B virus, Woodchuck hepatitis B virus, Woolly monkey hepatitis B Virus) and retroviruses (e.g., Abelson murine leukemia virus, Avian leukosis virus, Avian myelocytomatosis virus, Avian sarcoma virus, Avian sarcoma virus Y73, Bovine foamy virus, Bovine immunodeficiency virus, Bovine leukemia virus, Caprine arthritis-encephalitis virus, Caprine nasal tumor virus, Equine foamy virus, Equine infectious anemia virus, Feline foamy virus, Feline immunodeficiency virus, Feline leukemia virus, Friend murine leukemia virus, Fujinami sarcoma virus, Gibbon ape leukemia virus, Human foamy virus, Human immunodeficiency virus 1, Human immunodeficiency virus 2, Human spumaretrovirus, Human T-lymphotropic virus 1, Human T-lymphotropic virus 2, Jembrana disease virus, Mason-Pfizer monkey virus, Moloney murine sarcoma virus, Mouse mammary tumor virus, Murine leukemia virus, Murine osteosarcoma virus, Murine sarcoma virus, Murine type C retrovirus, Ovine lentivirus, Ovine pulmonary adenocarcinoma virus, Porcine endogenous retrovirus, Primate T-lymphotropic virus 3, Rauscher murine leukemia virus, Rous sarcoma virus, Simian foamy virus, Simian immunodeficiency virus, Simian immunodeficiency virus 2, Simian T- lymphotropic virus 1, Simian T-lymphotropic virus 2, Simian-Human immunodeficiency virus, Snakehead retrovirus, Spleen focus-forming virus, Visna virus, Walleye dermal sarcoma virus, Woolly monkey sarcoma virus).

Accordingly, the present invention provides a method of preventing or treating a retroid virus infection by administering to a subject having or at risk of having a retroid virus infection an effective amount of an inhibitory agent of Formula I or II or pharmaceutical composition containing an inhibitory agent of Formula I or II.

An effective amount of an inhibitory agent of Formula I or II is an amount which inhibits, reduces, or stabilizes at least one sign or symptom associated with a retroid virus infection. Signs or symptoms which may be evaluated to determine the effectiveness of a compound or composition of the invention include, but are not limited to, viral load as determined by well-known methods such as quantitative RT-PCR, northern blot analysis, determining RNase H activity, measuring cell-associated viral capsid protein, and the like. Additionally, with HIV infections, CD4⁺ T cell responses are generally related to the degree of viral load/viral load suppression, and these responses may also be measured. Individuals who have benefited from a compound or composition of the present invention may exhibit a low baseline viremia, a high baseline CD4+ T cell count, or a rapid decline of viremia.

Administration

Compounds of the invention may be administered therapeutically, so as to lessen the severity of an existing infection, or they may be administered prophylactically to prevent or lessen the likelihood of a future infection. An effective amount of one or more of the RNase H inhibitors of the present invention maybe determined by one of ordinary skill in the art, and includes exemplary dosage amounts for a human of from about 0.05 to about 200 mg/kg/day. This dosage is typically administered in a single dose, but can be given in multiple doses. The compound(s) may be administered in a frequent regimen, e.g., daily, every two days for five doses, etc. or intermittently, e.g., every four days for three doses or every eight days for three doses. It will be understood that the specific dose level and frequency of administration for a given subject may be varied and will depend upon a variety of factors including, for example, the subject's age, body weight, general health, sex, diet and the like, and the mode of administration, the stage and type of disease associated with HIV infection, and the other types of anti-HIV compounds that are being simultaneously administered.

The RNase inhibitor compounds are administered in pharmaceutical compositions containing an amount thereof effective for anti-HIV therapy, and a pharmaceutically acceptable carrier. Such compositions may contain other therapeutic agents as described below, and may be formulated, for example, by employing conventional solid or liquid vehicles or diluents, as well as pharmaceutical additives of a type appropriate to the mode of desired administration (for example, excipients, binders, preservatives, stabilizers, flavors, etc.) according to techniques such as those well known in the art of pharmaceutical formulation and/or called for by accepted pharmaceutical practice.

The RNase inhibitor compounds may be administered by any suitable means, for example, orally, such as in the form of tablets, capsules, granules or powders; sublingually; bucally; parenterally, such as by subcutaneous, intravenous, intramuscular, intracissternal, or intrathecal injection or infusion techniques (e.g., as sterile injectable aqueous or non¬ aqueous solutions or suspensions); nasally, such as by inhalation spray; topically, such as in the form of a cream or ointment; or rectally such as in the form of suppositories; in dosage unit formulations containing non-toxic, pharmaceutically acceptable vehicles or diluents. The subject compounds may, for example, be administered in a form suitable for immediate release or extended release. Immediate release or extended release may be achieved by the 46

28

use of suitable pharmaceutical compositions comprising the present compounds, or, particularly in the case of extended release, by the use of devices such as subcutaneous implants or osmotic pumps. The subject compounds may also be administered liposomally.

Suitable dosage forms for the RNase H inhibitor compounds include, without intended limitation, an orally effective composition such as a tablet, capsule, solution or suspension containing about 0.1 to about 500 mg per unit dosage of a compound of the invention. They may be compounded in a conventional manner with a physiologically acceptable vehicle or carrier, excipient, binder, preservative, stabilizer, flavor, etc. The RNase H inhibitor compounds can also be formulated in compositions such as sterile solutions or suspensions for parenteral administration. About 0.1 mg to about 500 mg of a compound of the invention may be compounded with a physiologically acceptable vehicle, carrier, excipient, binder preservative, stabilizer, etc., in a unit dosage form as called for by accepted pharmaceutical practice. The amount of active substance in these compositions or preparations is preferably such that a suitable dosage in the range indicated is obtained.

Exemplary compositions for oral administration include suspensions which may contain, for example, microcrystalline cellulose for imparting bulk, alginic acid or sodium alginate as a suspending agent, methylcellulose as a viscosity enhancer, and sweeteners or flavoring agents such as those known in the art; and immediate release tablets which may contain, for example, microcrystalline cellulose, dicalcium phosphate, starch, magnesium stearate and/or lactose and/or other excipients, binders, extenders, disintegrants, diluents and lubricants such as those known in the art. Molded tablets, compressed tablets or freeze- dried tablets are exemplary forms that may be used. Exemplary compositions include those formulating the present compound(s) with fast dissolving diluents such as mannitol, lactose, sucrose and/or cyclodextrins. Also included in such formulations may be high molecular weight excipients such as celluloses (Avicel) or polyethylene glycols (PEG). Such formulations may also include an excipient to aid mucosal adhesion such as hydroxy propyl cellulose (HPC), hydroxy propyl methyl cellulose (HPMC), sodium carboxy methyl cellulose (SCMC), maleic anhydride copolymer (e.g. Gantrez), and agents to control release such as polyacrylic acid copolymer (e.g. Carbopol 934). Lubricants, glidants, flavors, coloring agents and stabilizers may also be added for ease of fabrication and use.

Exemplary compositions for nasal aerosol or inhalation administration include solutions in saline, which may contain, for example, benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, and/or other solubilizing or dispersing agents such as those known in the art.

Exemplary compositions for parenteral administration include injectable solutions or suspensions which may contain, for example, suitable non-toxic, parentally acceptable diluents or solvents, such as Cremophor (polyoxyethylated caster oil surfactant), mannitol, 1,3-butanediol, water, Ringer's solution, Lactated Ringer's solution, an isotonic sodium chloride solution, or other suitable dispersing or wetting and suspending agents, including synthetic mono- or diglycerides, and fatty acids, including oleic acid. Exemplary compositions for rectal administration include suppositories, which may contain, for example, a suitable non-irritating excipient, such as cocoa butter, synthetic glyceride esters or polyethylene glycols, which are solid at ordinary temperature, but liquefy and/or dissolve in the rectal cavity to release the drug.

The RNase H inhibitors may be administered either alone or in combination with other anti-HIV drugs. Preferably, the RNase inhibitors will be administered in combination with other anti-HIV drugs. Such anti-HIV drugs may include (but are not limited to), for example, the following: nonnucleoside reverse transcriptase inhibitors, nucleoside analog reverse transcriptase inhibitors, nucleotide reverse transcriptase inhibitor, protease inhibitors, and fusion inhibitors. Nonnucleoside reverse transcriptase inhibitors include, for example, Delaviridine, Efavirenz, and Nevirapine. Nucleoside reverse transcriptase inhibitors include, for example, Abacavir, Lamivudine, Zidovudine, Didanosine, Emtricitabine, Stavudine, Tenofovir DF, and Zalcitabine. Nucleotide reverse transcriptase inhibitors include tenofovir disoproxil fumarate (sold under the trade name Viread) Protease inhibitors include, for example, Amprenavir, Atazanavir, Fosamprenavir, 46

30

Indinavir, Lopinavir, Ritonavir, Nelfinavir, and Saquinavir. Enfuvirtide maybe used as a fusion inhibitor.

In one embodiment of the invention, the RNase H inhibitors are administered prophylactically to prevent or lessen the likelihood of the transfer of an HIV virus from an infected individual, or a potentially infected individual, to second individual. For example, the RNase H inhibitors may be administered as a composition (e.g. a foam or gel) that is applied, for example, vaginally, rectally, or to the penis prior to sexual contact. Compositions of the invention may also be formulated or packaged with condoms or gloves, or other physical barrier devices, for prophylactic use.

Having now generally described the invention, the same will be more readily understood through reference to the following examples, which are provided by way of . illustration and are not intended to be limiting of the present invention unless specified. • ■

Example 1

Initial Identification of RNase H Inhibitory Compounds Using a Fluorescence Based High-Throughput Screen

A homogeneous fluorescence resonance energy transfer (FRET) quenching assay designed for high through-put screening of inhibitors of HIV-I (Parniak et al, 2003, Anal. Bioch. 322:33-39) is used for screening small molecule libraries. The FRET assay uses an 18- nucleotide-3'-FAM-labeled heteropolymeric RNA annealed to a complementary 5'- dabcyl-labeled DNA. RT-associated RNase H cleaves the RNA strand four nucleotides from the 3 'end. The labeled tetranucleotide dissociates from the DNA and a fluorescent signal is detected by a conventional fluorescence plate reader.

The oligonucleotides 5'-GAU CUG AGC CUG GGA GCU-fluorescein-3' (SEQ ID NO:1) and 5'-Dabcyl-AGC TCC CAG GCT CAG ATC-3' (SEQ ID NO:2) are synthesized and provided as the annealed RNA/DNA hybrid by TriLink Biotechnologies (San Diego, CA). Recombinant wild-type p66/p51 HIV-I RT is over-expressed and purified as described in Miller et al., 2001, Methods MoI. Biol. 160:335-354. The oligonucleotides and the purified HIV RT is used in a high-throughput screen of a non¬ exclusive library purchased from ChemBridge Corporation (San Diego, California).

RNA/DNA hybrid substrate is stored frozen at -2O⁰C as a 0.1 mM stock solution. After thawing, 400 μl is added to 100 ml of assay buffer immediately prior to assay. Then 22 μl of duplex in assay buffer is added to individual wells of the microplate (Cliniplate 384 black, round-well, low profile plates; Thermo Labsystems, Boston, MA; total volume 56 μl) using a 96-channel robotic liquid handler (Biomek FX; Beckman Coulter, Fullerton, CA). HIV-I RT is stored at -2O⁰C as a stock solution at 2.7 mg/rnl in 50% glycerol. Sixty-seven microliters of stock solution is diluted immediately prior to assay in 100ml of 50 mM Tris, pH 8.0,. containing 60 mM KCl and 10 mM MgCl₂. Reactions are started by the addition of 23 μl of enzyme to each well of the microplate, providing a level of 42 ng/well of HIV-I RT (7.5nM p66/p51 RT). Samples are mixed and the plates are incubated at room ' temperature for 30, min. The reactions are quenched by the addition of 5 μl of 0.5 M EDTA, pH 8.0. Fluorescence intensity in each well is assessed using standard fluorescein filter settings. To detect inhibitors, 3 μl of inhibitor in DMSO is added to the microplate well prior to the addition of the RT solution, with the stock concentration based on the average molecular weight of library compounds, to give a nominal final test concentration of lO μM.

Compounds are identified as hits if they show >40% inhibition at a 10 μM concentration after replicate (n=3) testing. Twenty-seven compounds, all of which are listed in Table 1 and Table 2 above, are identified as RNase H inhibitors.

Example 2 Confirmation of Hits Using Capillary Electrophoresis Assay

The RNase H inhibiting activity of the twenty-seven compounds identified in Example 1 above is confirmed using capillary-electrophoresis (CE)-based assay that allows for quantitative and qualitative analyses in a moderate through-put format (Chan et al., 2004, A capillary electrophoresis assay for ribonuclease activity, Anal. Biochem. 331(2): 296-302). The CE assay is an extension of the FRET assay described in Example 1 above, wherein the substrate lacks a dabcyl quencher and its cleavage product is separated by CE. In comparison to the FRET assay, the CE assay allows for the separation of fluorescent or fluorescence quenching sample compounds from the assay components, thereby yielding a more reliable measurement of enzyme inhibition.

The oligonucleotides 5'-GAU CUG AGC CUG GGA GCU-fluorescein-3' (SEQ ID NO: 1) and 5'-AGC TCC CAG GCT CAG ATC-3' (SEQ ID NO:2) are synthesized and provided as the annealed RNA/DNA hybrid by TriLink Biotechnologies (San Diego, CA). Recombinant wild-type p66/p51 HIV-I RT is expressed and purified as described in Miller et al., 2001, Methods MoI. Biol. 160:335-354.

Samples for assay are prepared in 96-well black polystyrene plates in a total volume of 100 μl. Stock solutions of the substrate and HIV-I RT are diluted to the appropriate concentration immediately before use, since extended dilution reduced enzymatic activity. Fifty microliters of a 0.4 μM solution of RNA/DNA hybrid in 5OmM Tris, pH 8.0, containing 6OmM KCl and 1OmM MgCl₂ is added to individual wells of the microplate using a Beckman BioMek FX. Reactions are initiated by addition of 50 μl of 13.6 nM HIV- 1 RT in 5OmM Tris, pH 8.0, containing 6OmM KCl and 1OmM MgCl₂ and allowed to proceed at room temperature for 30 minutes. Reactions are quenched by the addition of 10 μl of 0.5M EDTA, pH 8.0. To assess the effect of inhibitors, 6 μl of inhibitor in dimethyl sulfoxide was added to the microplate well after addition of substrate but prior to RT addition. Completed assay plates are stored frozen at -20 ⁰C before CE analysis.

A Beckman MDQ CE system equipped with a 488 nm laser-induced fluorescence module is used to analyze the samples. Separations are performed with either a 30- or 50- μm i.d.x30-cm capillary (Polymicro) at 20 °C. A new capillary was treated by washing it with IN sodium hydroxide overnight. The capillary was rinsed with IN NaOH and running buffer for lmin each between runs. All samples were diluted fivefold with distilled water before injection. Samples were injected by vacuum (0.5 psi at 5 s) or voltage (5 kV at 5 s) and typically separated by applying a voltage of 15 kV. MALDI-TOF mass spectroscopy was performed on an Axima-CFR MALDI mass spectrometer (Shimadzu) in reflectron mode. Substrate and product spectra were obtained by drying the reaction mixtures described above after incubation with or without enzyme. The enzyme concentration is doubled to increase the extent of substrate cleavage. The resulting samples are processed through C-18 ZipTips (Millipore) according to the manufacturer's specifications, and their spectra are obtained, without additional purification, using 3- hydroxypicolinic acid (Fluka) or 6-aza-2-thiothymine (Aldrich) as a matrix.

All of the twenty-seven compounds identified in the FRET assay of Example 1 as RNase H inhibitors are confirmed to be RNase H inhibitors by the CE-assay.

Example 3 Selectivity of the Identified RNase H Inhibitors

The twenty-seven identified RNase H inhibitors are assessed for their selectivity in inhibiting HIV RNase H versus E. coli, moloney murine leukemia virus, or human RNase H. Selectivity is assessed using the FRET assay described in Example 1 on a smaller scale and in a dose response format. HIV 1 and HIV-2 RT are prepared as described in Miller et al., 2001, Methods MoI. Biol. 160:335-354. E. coli RNase HI is prepared as described in Ma et al., 1994, Bioorg. Med. Chem. 2:169-179. Human RNase Hl is prepared as described in Pileur et al., 2003, Nucleic Acids Res. 31 -.5776-5788. Enzyme levels were adjusted to give equivalent levels of cleavage using the FRET quenching assay. All of the identified twenty seven HW-I RNase H inhibitors showed selectivity for inhibiting HIV-I and HIV-2 RNase H versus human, moloney murine leukemia virus, or E. coli RNase H. For two of the compounds, NSC 727447 and NSC 727448, results from the selectivity analysis are shown in Figure 1 and Figure 2, respectively. 05/030846

34

Example 4 Assessments of Inhibitory Effects on HIV Cytopathicity

Compounds identified as inhibitors of isolated HIV RNase H are assessed for activity in inhibiting the cytopathicity HIV-I . Using the method described by Weislow et al. (1989, J. Natl. Cancer Inst. 81:577-586), compounds are assessed for activity in inhibiting the cytopathicity of HIV-I (RF strain) in the CEM cell line of CD4⁺ lymphoblast cells (ATCC Number: CCL-119). Briefly, samples containing lymphoblast cells, the HIV-I virus, and appropriate dilutions of the test compounds are incubated at 37⁰C for six days. Cell viability is measured by the ability of cells to convert a colorless tetrazolium salt (XTT) to a highly colored soluble formazan, and the intensity of the color is read using a spectrophotometer using an automated system. Samples are also examined microscopically to confirm the protective activity of the compounds. The EC₅₀ represents the concentration of agent which reduces HIV-I cytopathic effects 50% relative to untreated control. Cellular toxicity of the agents is estimated from the TG₅₀, which represents the concentration of the agent which inhibits 50% of the viability of uninfected cells. Results from the cytopathicity inhibition assays are presented in Table 3 and Table 4 below. Table 3 shows a summary of the results of the cytopathicity inhibition assays for twenty-seven compounds that were identified as specific RNase H inhibitors in the assays described in Examples 1 and 2 above. Table 4 shows the specific results for certain of these compounds, and the results presented in Table 4 are also shown in graphs in Figures 3 through 8. This data shows that five compounds out of the twenty-seven identified RNase H inhibitors were able to block the cytopathic effect of the HIV-I virus at concentrations which did not inhibit cell growth.

Table 3 Inhibition of HIV-I Cytopathicity - Summary of Results

2005/030846

35

Table 4

Assays for Activity in Inhibiting HIV-I Cytopathicity

NSC 727447 EC₅O = 4.36 TC₅₀ = 19.9

Infected Uninfected fμMl O.D. % Control O.D. % Control

0.032 0.33 23 1.53 105

0.100 0.27 18 1.55 107

0.317 0.30 21 1.51 103

1.003 0.34 23 1.52 104

3.169 0.53 37 1.47 101

10.014 1.24 85 1.82 125

31.646 0.00 0 -0.01 0

100.000 0.04 3 -0.12 0

Controls: Virus = 0.31 Cell = 1.46 %Survival = 21.07

NSC 727448 EC50 - XX TC₅₀ = 62.6

Infected Uninfected

FμMl O.D. % Control O.D. % Control 005/030846

36

NSC 731246 EC50 — XX TC₅₀ = 12.3

Infected Uninfected fμMl O.D. % Control O.D. % Control

0.064 0.42 31 1.25 92

0.201 0.39 28 1.32 96

0.635 0.35 25 1.24 90

2.006 0.40 29 1.25 91

6.338 0.66 49 1.19 87

20.029 0.33 24 0.31 22

63.291 -1.00 0 -1.00 0

200.000 0.01 0 0.02 1

Controls: Virus = 0.43 Cell = 1.37 %Survival = 31.50

NSC 731247 EC50- 10.43 TC₅₀ = 40.3

Infected Uninfected

FμMl O.D. % Control O.D. % Control

0.064 0.45 33 1.37 100

0.201 0.44 32 1.27 93

0.635 0.37 27 1.27 93

2.006 0.32 24 1.29 95 46

37

6

38

Controls: Virus = 0.26 Cell = 1.65 %Survival = 15.72

NSC 732527 EC₅₀ = XX TC₅₀ = 37.3

Infected Uninfected fμMl O.D. % Control O.D. % Control

0.064 0.15 9 1.59 97

0.201 0.16 10 1.63 99

0.635 0.17 10 1.63 99

2.006 0.17 10 1.66 101

6.338 0.22 13 1.73 105

20.029 0.23 14 1.77 107

63.291 -0.03 0 0.02 1

200.000 -0.08 0 -0.04 0

Controls: Virus = 0.26 Cell = 1.65 %Survival = 15.72 ,

NSC 732521 EC50 — XX TC₅₀ = 34.6

Infected Uninfected

FμMl O.D. % Control O.D. % Control

0.064 0.35 20 1.60 93

0.201 0.27 16 1.59 92

0.635 0.25 15 1.62 94

2.006 0.16 9 1.64 96

6.338 0.19 11 1.76 102

20.029 0.42 25 1.63 95

63.291 0.03 2 0.01 1

200.000 0.05 3 0.02 1

Controls: Virus = 0.29 Cell = 1.72 %Survival = 17. 10 AU publications and patents mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth. Other embodiments are within the following claims.

Claims

2005/03084640What Is Claimed Is:

1. A method of treating a subject having a retroid virus infection or at risk of having a retroid virus infection comprising administering a retroid virus RNase H inhibitor to the subject, wherein the viral RNase H inhibitor comprises a compound having the following structure:

wherein

X is N(R' ) or oxygen;

R₁, independently for each occurrence, is selected from the group consisting of a halogen atom, a hydroxyl group, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; y is O to 3;

R₂ is selected from the group consisting of -R₅, — C(O)-N(R')- R₆, and— C(O)- O— R_6;

R₅ is selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group;

R₆ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; or

R₁ and R₂, together with the atoms to which they are attached, may form a ring structure; R₃ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; R₄ is selected from the group consisting of -NR'R' ' , -N(R')-C(O)-R₇, and -N=C-R₇; or

R₃ and R₄, together with the atoms to which they are attached, may form a ring structure; ;

R' and R" are each, independently for each occurrence, hydrogen or lower alkyl; . ^'< ■ ..< ^'

R₇ is selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; or or a pharmaceutically acceptable salt thereof.

2. A method according to claim 1, wherein the viral infection is a human immunodeficiency virus infection.

3. A method according to claim 1, wherein the viral infection is an HIV-I infection.

4. A method according to claim 1, wherein the viral infection is an HIV-2 infection.

5. A method according to claim 1 , wherein the subject is a human subject.

6. A method according to claim 1 , wherein y is equal to 0 or 1 , and if y is 1 , Ri together with R₂ and the atoms to which they are attached,forms a ring structure.

7. A method according to claim 1, wherein R₄ is selected from the group consisting of NH₂ and -N-C(O)-R_?, wherein R₄ and R₃ are not cyclized in a ring structure.

8. A method according to claim 6, wherein R₄ is selected from the group consisting of NH₂ and -N-C(O)-R₇, wherein R₄ and R₃ are not cyclized in a ring structure.

9. A pharmaceutical composition comprising a pharmacologically acceptable excipient and a compound having the following structure:

wherein

X is N(R') or oxygen; R₁, independently for each occurrence, is selected from the group consisting of a halogen atom, a hydroxyl group, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; y is O to 3;

R₂ is selected from the group consisting of -R₅, -C(O)-N(R')-R₆, and -C(O)-O-R₆;

R₅ is selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; 46

43

R₆ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; or

R₁ and R₂, together with the atoms to which they are attached, may form a ring structure;

R₃ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group;

R₄ is selected from the group consisting of-NR'R", -N(R')-C(O)-R₇, and -N=C-R₇; or

R₃ and R₄, together with the atoms to which they are attached, may form a ring structure;

R' and R' ' are each, independently for each occurrence, hydrogen or lower alkyl; R₇ is selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; or or a pharmaceutically acceptable salt thereof.

10. A composition according to claim 9, wherein the compound is a retroid virus RNase H inhibitor, and the RNase H inhibitor inhibits HIV RNase H.

11. A composition according to claim 9, wherein the compound is a retroid virus RNase H inhibitor, and the RNase H inhibitor inhibits inhibits HIV-I RNase H.

12. A composition according to claim 9, wherein the compound is a retroid virus RNase H inhibitor, and the RNase H inhibitor inhibits HIV-2 RNase H.

13. A composition according to claim 9, wherein y is equal to 0 or 1, and if y is 1, R₁ together with R₂ and the atoms to which they are attached,forms a ring structure.

14. A composition according to claim 9, wherein R₄ is selected from the group consisting of NH₂ and -N-C(O)-R₇, wherein R₄ and R₃ are not cyclized in a ring structure.

15. A method of treating a subject having a retroid virus infection or at risk of having a retroid virus infection comprising administering a retroid virus RNase H inhibitor to the subject, wherein the RNase H inhibitor comprises a compound having the following structure (Formula II):

Formula π

wherein X is nitrogen or oxygen; wherein R₂ is selected from the group consisting of— C— R_5t, -C(O)-N-R₆, -C(O)-O-R₆; wherein R₁ and R₅ are each independently selected from the group consisting of a halogen atom, a hydroxyl group, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; wherein y is 0 to 3; wherein t is 0 to 3; wherein R₆ is selected from the group consisting of hydrogen, a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; wherein R₄ is selected from the group consisting of -NH₂, -N-C(O)-R₇, and -N=C-R₇; wherein R₃ and R₇ are each independently selected from the group consisting of a hydrocarbon group, a substituted hydrocarbon group, a heterogeneous group, a substituted heterogeneous group, a carbocyclic group, a substituted carbocyclic group, a heterocyclic group, a substituted heterocyclic group, an aromatic group, a substituted aromatic group, a heteroaromatic group, and a substituted heteroaromatic group; wherein z is 0 to 1 ; ' _. wherein R₁ and R₂ may cyclize to form a ring structure, and wherein R₃ and R₄ may cyclize to form a ring structure.

16. An pharmaceutical composition comprising a pharmacologically acceptable excipient and a retroid virus RNase H inhibitor represented by Formula II.