Antiviral inhibition of capsid proteins

Abstract

Methods for evaluating the antiviral activity of test compounds are provided. Further aspects of the methods involve the retroviral capsid protein of HIV-1. In another aspect, methods of reducing mortality associated with AIDS with a compound that binds to the apical cleft near the C-terminal end of the N-terminal domain of the HIV-1 capsid protein are provided. Derivatives of CAP-1, CAP-2, CAP-3, CAP-4, CAP-5, CAP-6 and CAP-7 are described that bind to the apical cleft of the N-terminal domain of the HIV-1 capsid protein and inhibit proper assembly of the core particle.

1 .- 8 . (canceled) 
     
     
         9 . A method of reducing mortality associated with AIDS comprising the step of administering a therapeutically effective amount of a compound that binds to the apical cleft near the C-terminal end of the N-terminal domain of the HIV capsid protein to a human suffering from AIDS. 
     
     
         10 . The method of  claim 9  wherein the capsid protein is an HIV-1 capsid protein. 
     
     
         11 . The method of  claim 9  wherein the compound is selected form the group consisting of N-(3-chloro-4-methylphenyl)-N′-[2-thioethyl-2′-[5-(dimethylaminomethyl)]-2-methylfuryl]urea (CAP-1), N-(4-N-acetamidophenyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-2), N-(2-propyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-3), N-(3-chloro-4-methyl phenyl)-N′-(4-cyanophenyl)urea (CAP-4), N-(3-chloro-4-methyl phenyl)-N′-[4-(1,1,1-trichloromethyl)phenyl]urea (CAP-5), N-(3-nitro-4-fluorophenyl)-N′-[3-(1,1,1-trifluoromethyl)phenyl]urea (CAP-6), N-[(3-chloro-4-methyl phenyl)-N′,N′-propyl]urea (CAP-7). 
     
     
         12 . The method of  claim 11  wherein the compound is N-(3-chloro-4-methylphenyl)-N′-[2-thioethyl-2′-[5-(dimethylaminomethyl)]-2-methylfuryl]urea (CAP-1). 
     
     
         13 . The method of  claim 11  wherein the compound is N-(4-N-acetamidophenyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-2). 
     
     
         14 . The method of  claim 11  wherein the compound is N-(2-propyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-3). 
     
     
         15 . The method of  claim 11  wherein the compound is N-(3-chloro-4-methyl phenyl)-N′-(4-cyanophenyl)urea (CAP-4). 
     
     
         16 . The method of  claim 11  wherein the compound is N-(3-chloro-4-methyl phenyl)-N′-[4-(1,1,1-trichloromethyl)phenyl]urea (CAP-5). 
     
     
         17 . The method of  claim 11  wherein the compound is N-(3-nitro-4-fluorophenyl)-N′-[3-(1,1,1-trifluoromethyl)phenyl]urea (CAP-6). 
     
     
         18 . The method of  claim 11  wherein the compound is N-[(3-chloro-4-methyl phenyl)-N′,N′-propyl]urea (CAP-7). 
     
     
         19 . A method of treating a human suffering from AIDS comprising the step of administering a compound that binds to the apical cleft near the C-terminal end of the N-terminal domain of the HIV capsid protein in an amount effective to reduce the number and severity of morbidities. 
     
     
         20 . The method of  claim 19  wherein the HIV capsid protein is an HIV-1 capsid protein. 
     
     
         21 . The method of  claim 19  wherein the compound is selected form the group consisting of N-(3-chloro-4-methylphenyl)-N′-[2-thioethyl-2′-[5-(dimethylaminomethyl)]-2-methylfuryl]urea (CAP-1), N-(4-N-acetamidophenyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-2), N-(2-propyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-3), N-(3-chloro-4-methyl phenyl)-N′-(4-cyanophenyl)urea (CAP-4), N-(3-chloro-4-methyl phenyl)-N′-[4-(1,1,1-trichloromethyl)phenyl]urea (CAP-5), N-(3-nitro-4-fluorophenyl)-N′-[3-(1,1,1-trifluoromethyl)phenyl]urea (CAP-6), N-[(3-chloro-4-methyl phenyl)-N′,N′-propyl]urea (CAP-7). 
     
     
         22 . The method of  claim 21  wherein the compound is N-(3-chloro-4-methylphenyl)-N′-[2-thioethyl-2′-[5-(dimethylaminomethyl)]-2-methylfuryl]urea (CAP-1). 
     
     
         23 . The method of  claim 21  wherein the compound is N-(4-N-acetamidophenyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-2). 
     
     
         24 . The method of  claim 21  wherein the compound is N-(2-propyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-3). 
     
     
         25 . The method of  claim 21  wherein the compound is N-(3-chloro-4-methyl phenyl)-N′-(4-cyanophenyl)urea (CAP-4). 
     
     
         26 . The method of  claim 21  wherein the compound is N-(3-chloro-4-methyl phenyl)-N′-[4-(1,1,1-trichloromethyl)phenyl]urea (CAP-5). 
     
     
         27 . The method of  claim 21  wherein the compound is N-(3-nitro-4-fluorophenyl)-N′-[3-(1,1,1-trifluoromethyl)phenyl]urea (CAP-6). 
     
     
         28 . The method of  claim 21  wherein the compound is), N-[(3-chloro-4-methyl phenyl)-N′,N′-propyl]urea (CAP-7). 
     
     
         29 . A method of evaluating a compound for the ability to inhibit β-hairpin formation of Gag comprising:
 a) contacting said compound with Gag 283  or a fragment thereof, and   b) determining the ability of said compound to interfere with β-hairpin formation of Gag 283 .   
     
     
         30 . A method of screening a candidate compound for the ability to inhibit β-hairpin formation of Gag 283  comprising:
 a) contacting said compound with Gag 283  or a fragment thereof, and   b) determining the ability of said compound to interfere with β-hairpin formation of Gag 283 .   
     
     
         31 . A method of identifying a compound for the ability to inhibit β-hairpin formation of Gag 283  comprising:
 a) generating a 3D computer model of Gag 283  using Gag 283  molecular coordinates, and   b) using said model to identify a compound that binds to Gag 283 .   
     
     
         32 . A method of identifying a compound that binds to the apical cleft near the C-terminal end of the N-terminal domain of a viral capsid protein comprising:
 a) generating a 3D computer model of Gag 283  using Gag 283  molecular coordinates, and   b) using said model to identify a compound that binds to said apical cleft.   
     
     
         33 . The method of  claim 32  wherein the capsid protein is an HIV-1 capsid protein. 
     
     
         34 . A method of inhibiting capsid assembly with a compound that binds to the apical cleft near the C-terminal end of the N-terminal domain of a capsid protein. 
     
     
         35 . The method of  claim 34  wherein the capsid protein is selected from the group consisting of viral capsid proteins and retroviral capsid proteins. 
     
     
         36 . The method of  claim 35  wherein the capsid protein is an HIV-1 capsid protein. 
     
     
         37 . The method of  claim 34  wherein said compound is selected from the group consisting of N-(3-chloro-4-methylphenyl)-N′-[2-thioethyl-2′-[5-(dimethylaminomethyl)]-2-methylfuryl]urea (CAP-1), N-(4-N-acetamidophenyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-2), N-(2-propyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-3), N-(3-chloro-4-methylphenyl)-N′-(4-cyanophenyl)urea (CAP-4), N-(3-chloro-4-methyl phenyl)-N′-[4-(1,1,1-trichloromethyl)phenyl]urea (CAP-5), N-(3-nitro-4-fluorophenyl)-N′-[3-(1,1,1-trifluoromethyl)phenyl]urea (CAP-6), N-[(3-chloro-4-methyl phenyl)-N′,N′-propyl]urea (CAP-7). 
     
     
         38 . The method of  claim 36  wherein said compound is selected from the group consisting of N-(3-chloro-4-methylphenyl)-N′-[2-thioethyl-2′-[5-(dimethylaminomethyl)]-2-methylfuryl]urea (CAP-1), N-(4-N-acetamidophenyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-2), N-(2-propyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-3), N-(3-chloro-4-methyl phenyl)-N′-(4-cyanophenyl)urea (CAP-4), N-(3-chloro-4-methyl phenyl)-N′-[4-(1,1,1-trichloromethyl)phenyl]urea (CAP-5), N-(3-nitro-4-fluorophenyl)-N′-[3-(1,1,1-trifluoromethyl)phenyl]urea (CAP-6), N-[(3-chloro-4-methyl phenyl)-N′,N′-propyl]urea (CAP-7). 
     
     
         39 . A method of inhibiting capsid disassembly during infectivity with a compound that binds to the apical cleft near the C-terminal end of the N-terminal domain of a capsid protein. 
     
     
         40 . The method of  claim 39  wherein the capsid protein is selected from the group consisting of viral capsid proteins and retroviral capsid proteins. 
     
     
         41 . The method of  claim 39  wherein the capsid protein is an HIV-1 capsid protein. 
     
     
         42 . The method of  claim 39  wherein said compound is selected from the group consisting of N-(3-chloro-4-methylphenyl)-N′-[2-thioethyl-2′-[5-(dimethylaminomethyl)]-2-methylfuryl]urea (CAP-1), N-(4-N-acetamidophenyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-2), N-(2-propyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-3), N-(3-chloro-4-methyl phenyl)-N′-(4-cyanophenyl)urea (CAP-4), N-(3-chloro-4-methyl phenyl)-N′-[4-(1,1,1-trichloromethyl)phenyl]urea (CAP-5), N-(3-nitro-4-fluorophenyl)-N′-[3-(1,1,1-trifluoromethyl)phenyl]urea (CAP-6), N-[(3-chloro-4-methyl phenyl)-N′,N′-propyl]urea (CAP-7). 
     
     
         43 . The method of claim  4 1 wherein said compound is selected from the group consisting of N-(3-chloro-4-methylphenyl)-N′-[2-thioethyl-2′-[5-(dimethylaminomethyl)]-2-methylfuryl]urea (CAP-1), N-(4-N-acetamidophenyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-2), N-(2-propyl)-N′-(3-nitro-4-methyl phenyl)urea (CAP-3), N-(3-chloro-4-methyl phenyl)-N′-(4-cyanophenyl)urea (CAP-4), N-(3-chloro-4-methyl phenyl)-N′-[4-(1,1,1-trichloromethyl)phenyl]urea (CAP-5), N-(3-nitro-4-fluorophenyl)-N′-[3-(1,1,1-trifluoromethyl)phenyl]urea (CAP-6), N-[(3-chloro-4-methyl phenyl)-N′,N′-propyl]urea (CAP-7). 
     
     
         44 . A compound or its pharmaceutically acceptable salt having the formula I: 
       
         
           
           
               
               
           
         
         wherein: 
         (a) R 1  represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NHCHR 8 COOH, —NHCR 8 R 9 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (b) R 2  represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NHCHR 8 COOH, —NHCR 8 R 9 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (c) R 3  represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NHCHR 8 COOH, —NHCR 8 R 9 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (d) R 4  represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NHCHR 8 COOH, —NHCR 8 R 9 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (e) R 5  represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NHCHR 8 COOH, —NHCR 8 R 9 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (f) Halogen is limited to fluoro, chloro, bromo, and iodo; 
         (g) R 8  and R 9  are independently methyl, ethyl, n-propyl, i-propyl, n-butyl, i-butyl, sec-butyl, t-butyl, pentyl, hexyl, neo-pentyl, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclopropylmethyl, cyclopropylethyl, cyclobutylmethyl, cyclobutylethyl, cyclopentylmethyl, cyclohexylmethyl, or cyclohexylethyl; 
         (h) The letters n, m, and p represent independently any integer from 1 to 6; 
         (i) R 6  and R 7  are independently selected from the group consisting of hydrogen or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 6 carbon atoms; 
         (j) X is selected from the group consisting of O or S; 
         (k) Y is heterocyclic, carbocyclic, or optionally substituted phenyl; 
         (l) Heterocyclic is selected from any stable 5, 6, or 7-membered monocyclic or bicyclic or 7, 8, 9, or 10-membered bicyclic heterocyclic ring which is saturated, partially unsaturated or unsaturated (aromatic), and which consists of carbon atoms and 1, 2, 3, or 4 heteroatoms independently selected from the group consisting of N, NH, O and S and including any bicyclic group in which any of the above-defined heterocyclic rings is fused to a benzene ring. The nitrogen and sulfur heteroatoms may optionally be oxidized. The heterocyclic ring may be attached to its pendant group at any heteroatom or carbon atom which results in a stable structure. The heterocyclic rings described herein may be substituted on carbon or on a nitrogen atom if the resulting compound is stable. If specifically noted, a nitrogen in the heterocycle may optionally be quaternized. It is preferred that when the total number of S and O atoms in the heterocycle exceeds 1, then these heteroatoms are not adjacent to one another. As used herein, the term “aromatic heterocyclic system” is intended to mean a stable 5- to 7-membered monocyclic or bicyclic or 7- to 10-membered bicyclic heterocyclic aromatic ring which consists of carbon atoms and from 1 to 4 heteroatoms independently selected from the group consisting of N, O and S. Examples of heterocycles include, but are not limited to, 1H-indazole, 2-pyrrolidonyl, 2H,6H-1,5,2-dithiazinyl, 2H-pyrrolyl, 3H-indolyl, 4-piperidonyl, 4aH-carbazole, 4H-quinolizinyl, 6H-1,2,5-thiadiazinyl, acridinyl, azocinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl, benzothiophenyl, benzoxazolyl, benzthiazolyl, benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl, benzimidazalonyl, carbazolyl, 4aH-carbazolyl, β-carbolinyl, chromanyl, chromenyl, cinnolinyl, decahydroquinolinyl, 2H,6H-1,5,2-dithiazinyl, dihydrofuro[2,3-b]tetrahydrofuran, furanyl, furazanyl, imidazolidinyl, imidazolinyl, imidazolyl, 1H-indazolyl, indolenyl, indolinyl, indolizinyl, indolyl, isobenzofuranyl, isochromanyl, isoindazolyl, isoindolinyl, isoindolyl, isoquinolinyl (benzimidazolyl), isothiazolyl, isoxazolyl, morpholinyl, naphthyridinyl, octahydroisoquinolinyl, oxadiazolyl, 1,2,3-oxadiazolyl, 1,2,4-oxadiazolyl, 1,2,5-oxadiazolyl, 1,3,4-oxadiazolyl, oxazolidinyl, oxazolyl, oxazolidinylperimidinyl, phenanthridinyl, phenanthrolinyl, phenarsazinyl, phenazinyl, phenothiazinyl, phenoxathiinyl, phenoxazinyl, phthalazinyl, piperazinyl, piperidinyl, pteridinyl, piperidonyl, 4-piperidonyl, pteridinyl, purinyl, pyranyl, pyrazinyl, pyrazolidinyl, pyrazolinyl, pyrazolyl, pyridazinyl, pyridooxazole, pyridoimidazole, pyridothiazole, pyridinyl, pyridyl, pyrimidinyl, pyrrolidinyl, pyrrolinyl, pyrrolyl, quinazolinyl, quinolinyl, 4H-quinolizinyl, quinoxalinyl, quinuclidinyl, carbolinyl, tetrahydrofuranyl, tetrahydroisoquinolinyl, tetrahydroquinolinyl, 6H-1,2,5-thiadiazinyl, 1,2,3-thiadiazolyl, 1,2,4-thiadiazolyl, 1,2,5-thiadiazolyl, 1,3,4-thiadiazolyl, thianthrenyl, thiazolyl, thienyl, thienothiazolyl, thienooxazolyl, thienoimidazolyl, thiophenyl, triazinyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,2,5-triazolyl, 1,3,4-triazolyl, tetrazolyl, and xanthenyl, Preferred heterocycles include, but are not limited to, pyridinyl, thiophenyl, furanyl, indazolyl, benzothiazolyl, benzimidazolyl, benzothiaphenyl, benzofuranyl, benzoxazolyl, benzisoxazolyl, quinolinyl, isoquinolinyl, imidazolyl, indolyl, isoidolyl, piperidinyl, piperidonyl, 4-piperidonyl, piperonyl, pyrrazolyl, 1,2,4-triazolyl, 1,2,3-triazolyl, tetrazolyl, thiazolyl, oxazolyl, pyrazinyl, and pyrimidinyl, and fused ring and spiro compounds containing the above heterocycles; 
         (m) carbocyclic is intended to mean any stable 3, 4, 5, 6, or 7-membered monocyclic or bicyclic or 7, 8, 9, 10, 11, 12, or 13-membered bicyclic or tricyclic, any of which may be saturated, partially unsaturated, or aromatic. Examples of such carbocycles include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, cyclooctyl, [3.3.0] bicyclooctane, [4.3.0]bicyclononane, [4.4.0]bicyclodecane (decalin), [2.2.2]bicyclooctane, fluorenyl, phenyl, naphthyl, indanyl, adamantyl, or tetrahydronaphthyl (tetralin); 
         (n) Substituted phenyl is defined by Structure II 
       
       
         
           
           
               
               
           
         
         wherein: 
         (o) R 10  represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (p) R 11  independently represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (q) R 12  independently represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (r) R 13  independently represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (s) R 14  independently represents hydrogen, halogen, cyano, trifluoromethyl, trichloromethyl, nitro, —OR 8 , —SR 8 , —NHR 8 , —NR 8 R 9 , —NHCOOH, —NHCH 2 COOH, —NR 8 COOR 9 , —COOR 8  or a hydrocarbon group comprising a straight chained, branched or cyclic group each containing up to 9 carbon atoms; 
         (t) R 8  and R 9  are independently methyl, ethyl, n-propyl, i-propyl, n-butyl, i-butyl, sec-butyl, t-butyl, pentyl, hexyl, neo-pentyl, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclopropylmethyl, cyclopropylethyl, cyclobutylmethyl, cyclobutylethyl, cyclopentylmethyl, cyclohexylmethyl, or cyclohexylethyl; 
         (u) Halogen is limited to fluoro, chloro, bromo, and iodo.