초록

The invention relates to the inhibition of histone deacetylase. The invention provides compounds and methods for inhibiting histone deacetylase enzymatic activity. The invention also provides compositions and methods for treating cell proliferative diseases and conditions.

대표청구항 ▼

The invention claimed is: 1. A histone deacetylase inhibitor of formula (3): or a pharmaceutically acceptable salt thereof, wherein Ar3 is arylene or heteroarylene, either of which is optionally substituted; Cy3 is optionally substituted, heteroaryl which is optionally fused to one or two aryl o

The invention claimed is: 1. A histone deacetylase inhibitor of formula (3): or a pharmaceutically acceptable salt thereof, wherein Ar3 is arylene or heteroarylene, either of which is optionally substituted; Cy3 is optionally substituted, heteroaryl which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings is optionally substituted; provided that when Cy3 has —C(O)—, —C(S)—, —S(O)—, or —S(O)2— in the ring, then Cy3 is not additionally substituted with a group comprising an aryl or heteroaryl ring; and X2 is selected from the group consisting of a chemical bond, L3 and W1-L3, wherein W1, at each occurrence, is S, O, or N(R9), where R9 is selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; and L3 is C1-C4 alkylene, C2-C4 alkenylene, or C2-C4 alkynylene; provided that X2 does not comprise a —C(O)— or —C(S)— group; and further provided that when Cy3 is pyridine, then X2 is L3 or W1-L3. 2. The compound according to claim 1 wherein Ar3 has the structure: wherein Q, at each occurrence, is independently N or C, and C is optionally substituted. 3. The compound according to claim 1 wherein when X2 is a chemical bond, then Ar3 is not and Cy3 is not the radical of a substituted or unsubstituted benzofuran, wherein Q, at each occurrence, is independently N or C, and C is optionally substituted. 4. The compound according to claim 2 wherein Q at each occurrence is C(R8), where R8 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, alkoxy, amino, nitro, halo, haloalkyl, and haloalkoxy. 5. The compound according to claim 2 wherein from one to about three Q are nitrogen. 6. The compound according to claim 1 wherein Ar3 is selected from the group consisting of phenylene, pyridylene, thiazolylene, and quinolylene. 7. The compound according to claim 1 wherein X2 is a chemical bond. 8. The compound according to claim 1 wherein X2 is C1-C4 alkylene, C2-C4 alkenylene, or C2-C4 alkynylene. 9. The compound according to claim 1 wherein X2 is C1C4 alkylene. 10. The compound according to claim 1 wherein X2 is methylene or ethylene. 11. The compound according to claim 1 wherein X2 is C2-C4 alkenylene or C2-C4 alkynylene. 12. A histone deacetylase inhibitor of formula (3): or a pharmaceutically acceptable salt thereof, wherein Ar3 is arylene or heteroarylene, either of which is optionally substituted; Cy3 is optionally substiuted heteroaryl which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings is optionally substituted; provided that when Cy3 has —C(O)—, —C(S)—, —S(O)—, or —S(O)2— in the ring, then Cy3 is not additionally substituted with a group comprising an aryl or heteroaryl ring; and X2 is C1-C4 alkylene, C2-C4 alkenylene or C2-C4 alkynylene, wherein the carbon in the C1-C4 alkylene adjacent to Cy3, or one saturated carbon in the C2-C4 alkenylene or C2-C4 alkynylene is replaced with —NH— or —S—, provided that X2 does not comprise a —C(O)— or —C(S)— group. 13. The compound according to claim 1 wherein Cy3 is heteroaryl which is optionally substituted and is optionally fused to one or two aryl rings. 14. The compound according to claim 1 wherein Cy3 is pyridyl, pyrimidinyl, imidazolyl, thiazolyl, oxadiazolyl, or quinolyl, each of which is optionally substituted and is optionally fused to one or two aryl rings. 15. The compound according to the claim 1 wherein Cy3 is fused to a benzene ring. 16. The compound according to claim 1 wherein Cy3 has from one to three substituents independently selected from the group consisting of alkyl, alkoxy, aryl, aralkyl, amino, halo, haloalkyl, and hydroxyalkyl. 17. The compound according to claim 16 wherein the substituents are selected from methyl, methoxy, fluoro, trifluoromethyl, amino, aminomethyl, hydroxymethyl, and phenyl. 18. The compound according to claim 1 wherein Cy3 has from one to three substituents of the formula —K1—N(H)(R10), wherein K1 is a chemical bond or C1-C4 alkylene; R10 is selected from the group consisting of Z′ and -Ak2-Z′, wherein Ak2 is C1-C4 alkylene; and Z′ is cycloalkyl, aryl, heteroaryl, or heterocyclyl, each of which is optionally substituted, and each of which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings. 19. The compound according to claim 18 wherein the substituent is selected from 20. The compound of claim 1 wherein when Ar3 is quinoxalinylene, then X2 is not —CH(OH)—. 21. The compound of claim 1 wherein Ar3 is wherein X is —CH2—, —NH—, O, or S. 22. The compound of claim 1 wherein Ar3 is wherein X is S or O. 23. A compound of formula or a pharmaceutically acceptable salt thereof, wherein Cy2 is heteroaryl, which is optionally substituted and each of which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings is optionally substituted; X1 is a chemical bond, M1-L2-M1 or L2-M2-L2 wherein L2 , at each occurrence, is independently selected from the group consisting of a chemical bond, C1-C4 alkylene, C2-C4 alkenylene, and C2-C4 alkynylene, provided that L2 is not a chemical bond when X1 is M1-L2-M1; M1, at each occurrence, is independently selected from the group consisting of —S(O)—, S(O)2—, —S(O)2N(R7)—, —N(R7)—S(O)2—, and —C(O)—, wherein R7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and M2 is selected from the group consisting of M1, heteroarylene, and heterocyclylene, either of which rings is optionally substituted; Ar2 is arylene or heteroarylene, each of which is optionally substituted; R5 and R6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; Ay2 is ortho-anilinyl; and q is 0. 24. A composition comprising a compound according to claim 1 and a pharmaceutically acceptable carrier. 25. A method of treating colon cancer, lung cancer or pancreatic cancer in a human, the method comprising administering to a human in need of such treatment a compound according to claim 1. 26. A composition comprising a compound according to claim 23 and a pharmaceutically acceptable carrier. 27. A method of treating colon cancer, lung cancer or pancreatic cancer in a human, the method comprising administering to a human in need of such treatment a compound according to claim 24. 28. A compound of formula or a pharmaceutically acceptable salt thereof wherein Cy2 is acridinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl, benzoxazolyl, benzthiazolyl, benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl, carbazolyl, carbolinyl, cinnolinyl, furanyl, fiarazanyl, imidazolyl, 1H-indazolyl, indolenyl, indolizinyl, indolyl, 3H-indolyl, isobenzofiaranyl, isoindazolyl, isoindolyl, isoguinolinyl, isothiazolyl, isoxazolyl, naphthyridinyl, 1,2,3-oxadiazolyl, 1,2,4-oxadiazolyl, 1,2,5 -oxadiazolyl, 1,3,4-oxadiazolyl, oxazolyl, phenanthridinyl, phenanthrolinyl, phenazinyl, phthalazinyl, pteridinyl, purinyl, pyrazinyl, pyrazolyl, pyridazinyl, pyridooxazolyl, pyridoimidazolyl, pyridothiazolyl, pyrimidinyl, 2H-pyrrolyl, pyrrolyl, quinazolinyl, quinolinyl, 4H-quinolizinyl, quinoxalinyl, tetrahydroisoquinolinyl, tetrahydroquinolinyl, tetrazolyl, 1,2,3-thiadiazolyl, 1,2,4-thiadiazolyl, 1,2,5-thiadiazolyl, 1,3,4-thiadiazolyl, thiazolyl, thienyl, thienothiazolyl, thienooxazolyl, thienoimidazolyl, triazinyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,2,5-triazolyl, or 1,3,4-triazolyl, each of which is optionally substituted and each of which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings is optionally substituted; X1 is M1-L2-M1 or L2-M2-L2 wherein L2 , at each occurrence, is independently selected from the group consisting of a chemical bond, C1-C4 alkylene, C2-C4 alkenylene, and C2-C4 alkynylene, provided that L2 is not a chemical bond when X1 is M1-L2-M1; M1, at each occurrence, is independently selected from the group consisting of —S(O)—, S(O)2—, —S(O)2N(R7)—, —N(R7)—SO2—, and —C(O)—, wherein R7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and M2 is selected from the group consisting of M1, heteroarylene, and heterocyclylene, either of which rings is optionally substituted; Ar2 is arylene or heteroarylene, each of which is optionally substituted; R5 and R6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; Ay2 is ortho-anilinyl; and q is 0. 29. A composition comprising a compound according to claim 28 and a pharmaceutically acceptable carrier. 30. A method of treating colon cancer, lung cancer or pancreatic cancer in a human, the method comprising administering to a human in need of such treatment a compound according to claim 28. 31. A histone deacetylase inhibitor selected from the group consisting of N-(2-Amino-phenyl)-4-{[4-amino-6-(4-phenyl-piperazin-1-yl)-[1,3,5]triazin-2-ylamino]-methyl}-benzamide; 4-{[4-amino-6-(2-pyridinyl-methyl-amino)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; N-(2-Amino-phenyl)-4-{[4-amino-6-(3,4,5-trimethoxy-phenylamino)-[1,3,5]triazin-2-ylamino]-methyl}-benzamide; 4-({4-Amino-6-[2-(2-methoxy-phenyl)-ethylamino][1,3,5]triazin-2-ylamino}-methyl)-N-(2-amino-phenyl)-benzamide; 4-{[6-(2-indanyl-amino)-4-(3-pyridinyl-methyl-amino)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; N-(2-Amino-phenyl)-4-{[2-piperidin-1-yl-6-(2-pyrrolidin-1-yl-ethylamino)-pyrimidin-4-ylamino]-methyl}-benzamide; N-(2-Amino-phenyl)-4-{[2-piperidin-1-yl-6-(2-pyrrolidin-1-yl-ethylamino)-pyrimidin-4-ylamino]-methyl}-benzamide; N-(2-amino-phenyl)-4-{[4-cyclopropyl-methylamino-6-(2-indanyl-amino)- [1,3,5]-triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-{[4-(2-methoxy-ethyl-1-amino)-6-phenethyl-amino-[1,3,5]-triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-{[6-cyclopropyl-amino-4-(4-methoxy-phenethyl-amino)-[1,3,5]triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-{[6-cyclopropyl-amino-4-(3,4-dimethoxy-phenethyl-amino)-[1,3,5]triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-{[6-cyclopropyl-amino-4-(3-methoxy-phenethyl-amino)-[1,3,5]triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-{[6-cyclopropyl-amino-4-(2-pyridin-2-yl-ethyl-1-amino)-[1,3,5]triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-{[6-cyclopropyl-amino-4-(3-pyridin-2-yl-ethyl-1-amino)-[1,3,5]triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-[(4-cyclopropyl-amino-6-phenethyl-oxy-[1,3,5]triazin-2-yl-amino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-{5-[(3,4,5-trimethoxy-phenylamino)-methyl]-thiophen-2-ylmethyl}-benzamide; N-(2-Amino-phenyl)-4-{6-[(pyridin-3-ylmethyl)-amino]-benzothiazol-2-ylsulfanylmethyl}-benzamide; N-(2-Amino-phenyl)-4-{6-[(pyridin-2-ylmethyl)-amino]-benzothiazol-2-ylsulfanylmethyl}-benzamide; N-(2-Amino-phenyl)-4-[4-cyano-3-methyl-5-(3-phenyl-ureido)-thiophen-2-ylmethyl]-benzamide; N-(2-Amino-phenyl)-4-({4-chloro-6-[(pyridin-3-ylmethyl)-amino]-pyrimidin-2-ylamino}-methyl)-benzamide; N-(2-Amino-phenyl)-4-{[4-chloro-6-(3,4,5-trimethoxy-benzylamino)-pyrimidin-2-ylamino]-methyl}-benzamide; N-(2-Amino-phenyl)-4-{[4-chloro-6-(3,4,5-trimethoxy-phenylamino)-pyrimidin-2-ylamino]-methyl}-benzamide; N-(2-Amino-phenyl)-4-{[4-(3,4-dimethoxy-phenylamino)-pyrimidin-2-ylamino]-methyl}-benzamide; N-(2-Amino-phenyl)-4-[5-(pyridin-2-ylaminomethyl)-thiophen-2-ylmethyl]-benzamide; N-(2-Amino-phenyl)-4-{[4-(6-methoxy-pyridin-3-yl)-pyrimidin-2-ylamino]-methyl}-benzamide; 4-((4-amino-6-(2-(4-(benzo[d][1,3]dioxol-5-ylmethyl)piperazin-1-yl)-2-oxoethyl)-1,3,5-triazin-2-ylamino)methyl)-N-(2-aminophenyl)benzamide; N-(2-aminophenyl)-4-((6-(2-morpholinoethylamino)benzo[d]thiazol-2-ylthio)methyl)benzamide; N-(2-aminophenyl)-4-((5-(2-morpholinoethoxy)-1H-benzo[d]imidazol-2-ylthio)methyl)benzamide; N-(2-aminophenyl)-4-((6-(2-morpholinoethoxy)benzo[d]thiazol-2-ylamino)methyl)benzamide; and pharmaceutically acceptable salts thereof. 32. A histone deacetylase inhibitor selected from the group consisting of 4-[(4-amino-6-morpholin-4-yl-[1,3,5]-triazin-2-ylamino)-methyl]-N-(2-amino-phenyl)-benzamide; 4-{[4-amino-6-(1-indanyl-amino)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; 4-{[4,6-bis-(2-indanyl-amino)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; 4-{[4-Amino-6-(9H-fluoren-9-ylamino)-[1,3,5]triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; N-(2-amino-phenyl)-4- [(4-amino-6-piperidin- l-yl-[l ,3 ,5 ]-triazin-2-ylamino)-methyl]-benzamide; 4-[(4-amino-6-cyclopentyl-amino-[1,3,5]-triazin-2-yl-amino)-methyl]-N-(2-amino-phenyl)-benzamide; (1R)-4-{[4-amino-6-(2-exo-fenchyl-amino)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; 4-{[4-allyl-amino-6-(2-indanyl-amino)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; 4-{[4-cyclopropyl-amino-6-(2-indanyl-amino)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; 4-[(4-Amino-6-phenethylamino-[1,3,5]triazin-2-ylamino)-methyl]-N-(2-amino-phenyl)-benzamide; 4-{[4-Amino-6-(2,3 -dihydro-indol-1-yl)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; 4-({4-Amino-6-[2-(2-fluoro-phenyl)-ethylamino]-[1,3,5]triazin-2-ylamino}-methyl)-N-(2-amino-phenyl)-benzamide; 4-{[4-benzyl-amino-6-(2-indanyl-amino)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; N-(2-Amino-phenyl)-4-[(4,6-di-piperidin-1-yl-[1,3,5]triazin-2-ylamino)-methyl]-benzamide; 4-{[6-(2-indanyl-amino)-4-phenethyl-amino-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; 4-{[4-benzyl-amino-6-(2-indanyl-amino)-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; 4-[(4-Amino-6-benzylamino-[1,3,5]triazin-2-ylamino)-methyl]-N-(2-amino-phenyl)-benzamide; N-(2-Amino-phenyl)-4-[(4-piperidin-1-yl-6-pyrrolidin-1-yl-[1,3,5]triazin-2-ylamino)-methyl]-benzamide; 4-{[6-(2-indanyl-amino)-4-morpholin-4-yl-[1,3,5]-triazin-2-ylamino]-methyl}-N-(2-amino-phenyl)-benzamide; 4-({4-Amino-6-[2-(1H-indol-3-yl)-ethylamino]-[1,3,5]triazin-2-ylamino}-methyl)-amino-phenyl)-benzamide; 4-{[4-amino-6-(3-phenyl-propyl-1-amino)-[1,3,5]triazin-2-yl-amino]-methyl}-N-(2-amino-phenyl)-benzamide; N-(2-amino-phenyl)-4-[(4-cyclopropyl-amino-6-phenethyl-amino-[1,3,5]triazin-2-yl-amino)-methyl]-benzamide; N-(2-amino-phenyl)-4-[(4-n-butyl-amino-6-phenethyl-amino-[1,3,5]triazin-2-yl-amino)-methyl]-benzamide; N-(2-amino-phenyl)-4-{[4-(4-chloro-phenethyl-amino)-6-cyclopropyl-amino-[1,3,5]triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-{[4-(3-chloro-phenethyl-amino)-6-cyclopropyl-amino-[1,3,5]triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-[(6-methyl-4-phenethylamino-[1,3,5 ]triazin-2-yl-amino)-methyl]-benzamide; N-(2-amino-phenyl)-4-{[4-amino-6-phenyl-[1,3,5]-triazin-2-yl-amino]-methyl}-benzamide; N-(2-amino-phenyl)-4-{[6-(2-indanyl-amino)-4-phenyl-[1,3,5]-triazin-2-yl-amino]-methyl}-benzamide; N-(2-Amino-phenyl)-4-[(4,6-dimethoxy-pyrimidin-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-(quinolin-2-ylsulfanylmethyl)-benzamide; N-(2-Amino-phenyl)-4-(benzothiazol-2-ylsulfanylmethyl]-benzamide; N-(2-Amino-phenyl)-4-(5-phenyl-[1,3,4]oxadiazol-2-ylsulfanylmethyl]-benzamide; N-(2-Amino-phenyl)-4-(4,6-dimethyl-pyrimidin-2-ylsulfanylmethyl)-benzamide; N-(2-Amino-phenyl)-4-(4-trifluoromethyl-pyrimidin-2-ylsulfanylmethyl)benzamide; N-(2-Amino-phenyl)-4-[(5 -chloro-benzooxazol-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-{[4-(4-chloro-phenyl)-thiazol-2-ylamino]-methyl}-benzamide; N-(2-Amino-phenyl)-4-[(5-bromo-benzothiazol-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-(1H-imidazol-2-ylsulfanylmethyl)-benzamide; 4-[(2-Amino-9-butyl-9H-purin-6-ylamino)-methyl]-N-(2-amino-phenyl)-benzamide; N-(2-Amino-phenyl)-4-[(2-amino-9H-purin-6-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(2-chloro-9H-purin-6-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(9-butyl-2-chloro-9H-purin-6-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(3-fluoro-2-pyridinyl-amino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(3,4,5-trifluoro-2-pyridinyl-amino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-(5-phenyl-[1,2,4]oxadiazol-3-yl)-benzamide; N-(2-Amino-phenyl)-4-(5-methyl-[1,2,4]oxadiazol-3-yl)-benzamide; N-(2-Amino-phenyl)-4-(5-piperidin-1-ylmethyl-[1 ,2,4]oxadiazol-3-yl)-benzamide; N-(2-Amino-phenyl)-4-(5-morpholin-4-ylmethyl-[1 ,2,4]oxadiazol-3-yl)-benzamide; N-(2-Amino-phenyl)-4-(5-propyl-[1,2,4]oxadiazol-3-ylmethyl)-benzamide; N-(2-Amino-phenyl)-4-(5-pyridin-3-yl-[1,2,4]oxadiazol-3-ylmethyl)-benzamide; N-(2-Amino-phenyl)-4-(5-pyridin-4-yl-[1,2,4]oxadiazol-3-ylmethyl)-benzamide; 4-(5-Acetylamino-4-cyano-thiophen-2-ylmethyl)-N-(2-amino-phenyl)-benzamide; 4-(5-Benzoylamino-4-cyano-3-methyl-thiophen-2-ylmethyl)-N-(2-amino-phenyl)-benzamide; N-(2-Amino-phenyl)-4-(pyrimidin-2-ylaminomethyl)-benzamide; N-(2-Amino-phenyl)-4-(4,6-dimethyl-pyrimidin-2-ylsulfanylmethyl)-benzamide; N-(2-Amino-phenyl)-4-(4-trifluoromethyl-pyrimidin-2-ylsulfanylmethyl)-benzamide; N-(2-Amino-phenyl)-4-(pyridin-2-ylsulfanylmethyl)-benzamide; N-(2-Amino-phenyl)-4-[(4,6-dimethyl-pyrimidin-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(4,6-dimethyl-pyridin-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-(4,6-dimethyl-pyrimidin-2-yloxymethyl)-benzamide; N-(2-Amino-phenyl)-4-[(6-methoxy-pyrimidin-4-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(4-chloro-6-methoxy-pyrimidin-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(2,6-dimethoxy-pyridin-3-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(1H-benzoimidazol-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(6-methoxy-pyridin-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(2,6-dimethoxy-pyrimidin-4-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-(quinolin-2-yloxymethyl)-benzamide; N-(2-Amino-phenyl)-4-(isoquinolin-1-ylaminomethyl)-benzamide; N-(2-Amino-phenyl)-4-[(4-chloro-6-morpholin-4-yl-pyrimidin-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(4-chloro-6-methyl-pyrimidin-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(4,6-dichloro-pyrimidin-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(6-methoxy-pyridin-3-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(4-morpholin-4-yl-pyrimidin-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-{[4-chloro-6-(3,4-dimethoxy-phenyl)-pyrimidin-2-ylamino]-methyl}-benzamide; N-(2-Amino-phenyl)-4-{[4-(3,4-dimethoxy-phenyl)-pyrimidin-2-ylamino]-methyl}-benzamide; N-(2-Amino-phenyl)-4-[5-(indan-2-ylaminomethyl)-thiophen-2-ylmethyl]-benzamide; N-(2-Amino-phenyl)-4-[(5-bromo-thiazol-2-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-[(5-phenyl-1H-pyrazol-3-ylamino)-methyl]-benzamide; N-(2-Amino-phenyl)-4-(3-cyano-6-methyl-pyridin-2-yloxymethyl)-benzamide; 2-Acetylamino-5-[4-(2-amino-phenylcarbamoyl)-benzyl]-thiophene-3-carboxamide; 5-(5-Methoxy-1H-benzoimidazol-2-ylsulfanylmethyl)-benzofuran-2-carboxylic acid (2-amino-phenyl)amide; 4-((4-amino-6-(2,3-dihydro-1H-inden-2-ylamino)-1,3,5-triazin-2-ylamino)methyl)-N-(2-aminophenyl)benzamide; 4-(4-amino-6-(2,3-dihydro-1H-inden-2-ylamino)-1,3,5-triazin-2-ylamino)-N-(2-aminophenyl)benzamide; 4-((4-amino-6-(2,3-dihydro-1H-inden-2-ylamino)-1,3,5-triazin-2-yloxy)methyl)-N-(2-aminophenyl)benzamide; N-(2-aminophenyl)-4-((4-(phenethylamino)-1,3,5-triazin-2-ylamino)methyl)benzamide; N-(2-aminophenyl)-4-((4,6-dimethoxy-1,3,5-triazin-2-ylamino)methyl)benzamide; N-(2-aminophenyl)-4-((4-(2,3-dihydro-1H-inden-2-ylamino)-6-methoxy-1,3,5-triazin-2-ylamino)methyl)benzamide; 4-(((4-amino-6-(2,3-dihydro-1H-inden-2-ylamino)-1,3,5-triazin-2-yl)(methyl)amino)methyl)-N-(2-aminophenyl)benzamide; N-(2-aminophenyl)-4-((4-(2,3-dihydro-1H-inden-2-ylamino)-6-methyl-1,3,5-triazin-2-ylamino)methyl)benzamide; (E)-N-(2-aminophenyl)-4-(2-(4,6-diamino-1,3,5-triazin-2-yl)vinyl)benzamide; (E)-4-(2-(4-amino-6-(piperidin-1-yl)-1,3,5-triazin-2-yl)vinyl)-N-(2-aminophenyl)benzamide; 4-(2-(4-amino-6-(piperidin-1-yl)-1,3,5-triazin-2-yl)ethyl)-N-(2-aminophenyl)benzamide; 4-((1H-benzo[d]imidazol-2-ylthio)methyl)-N-(2-aminophenyl)benzamide; N-(2-aminophenyl)-4-((quinolin-2-ylthio)methyl)benzamide; N-(2-aminophenyl)-4-((1-methyl-1H-imidazol-2-ylthio)methyl)benzamide; N-(2-aminophenyl)-6-(3-methoxyphenyl)nicotinamide; N-(2-aminophenyl)-4-((5-(3,4,5-trimethoxyphenyl)benzo[d]thiazol-2-ylamino)methyl)benzamide; N-(2-aminophenyl)-4-((6-methoxybenzo[d]thiazol-2-ylamino)methyl)benzamide; N-(2-aminophenyl)-4-((2-chloro-9-(2-methoxyethyl)-9H-purin-6-ylamino)methyl)benzamide; N-(2-aminophenyl)-4-(1H-imidazol-2-yl)benzamide; N-(2-aminophenyl)-4-((4-(morpholinomethyl)thiazol-2-yl)methyl)benzamide; N-(2-aminophenyl)-4-((3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)methyl)benzamide; 4-((5-acetamido-4-cyano-3-methylthiophen-2-yl)methyl)-N-(2-aminophenyl)benzamide; N-(2-aminophenyl)-4-((5-methyl-1,2,4-oxadiazol-3-yl)methyl)benzamide; N-(2-aminophenyl)-4-(3,5-dimethyl-1H-pyrazol-1-yl)benzamide; N-(2-aminophenyl)-6-(quinolin-2-ylthio)nicotinamide; N-(2-aminophenyl)-4-((5-methoxy-1H-benzo[d]imidazol-2-ylthio)methyl)benzamide; and pharmaceutically acceptable salts thereof. 33. A histone deacetylase inhibitor of formula (3): or a pharmaceutically acceptable salt thereof, wherein Ar3 is arylene or heteroarylene, either of which is optionally substituted; Cy3 is optionally substituted heteroaryl which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings is optionally substituted; provided that when Cy3 has —C(O)—, —C(S)—, —S(O)—, or —S(O)2— in the ring, then Cy3 is not additionally substituted with a group comprising an aryl or heteroaryl ring; and X2 is selected from the group consisting of L3-W1, L3-W1-L3 and W1-L3-W1, wherein W1, at each occurrence, is S, O, or N(R9), where R9 is selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; and L3 is C2-C4 alkenylene, or C2-C4 alkynylene; provided that X2 does not comprise a —C(O)— or —C(S) group; and further provided that when Cy3 is pyridine, then X2 is L3-W1. 34. A compound of formula or a pharmaceutically acceptable salt thereof, wherein Cy2 is heteroaryl, which is optionally substituted and each of which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings is optionally substituted; X1 is a chemical bond or M2-L2, wherein L2, at each occurrence, is independently selected from the group consisting of a chemical bond, C1-C4 alkylene, C2-C4 alkenylene, and C2-C4 alkynylene; M1, at each occurrence, is independently selected from the group consisting of —O—, —N(R7)— and —S—, wherein R7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and M2 is selected from the group consisting of M1, heteroarylene, and heterocyclylene, either of which rings is optionally substituted; Ar2 is arylene or heteroarylene, each of which is optionally substituted; R5 and R6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; Ay2 is ortho-anilinyl; and q is 0. 35. The compound according to claim 34 wherein Ar2 is aryl or heteroaryl; and Cy2-X1- is collectively selected from the group consisting of a) A1-L1-B1-, wherein A1 is an optionally substituted heteroaryl wherein L1 is NH(CH2)0-1— or —NHCH2—; and wherein B1 is phenyl or a covalent bond; b) A5-L5-B5-, wherein A5 is an optionally substituted heteroaryl wherein L5 is a covalent bond; and wherein B5 is —SCH2—; c) A6-L6-B6-, wherein A6 is an optionally substituted heteroaryl wherein L6 is a covalent bond; and wherein B6 is —NHCH2—; d) optionally substituted heteroaryl; p1 e) A11-L11-B11-, wherein A11 is an optionally substituted heteroaryl wherein L11 is a covalent bond; and wherein B11 is —OCH2—; and f) A16-L16-B16-, wherein A16 is an optionally substituted heteroaryl wherein L16 is a covalent bond; and wherein B16 is —N(optionally substituted alkyl)CH2. 36. The compound according to claim 24 wherein Cy2-X1- is collectively selected from the group consisting of a) D2-E2-F2-, wherein D2 is optionally substituted heteroaryl wherein E2 is —NH(CH2)0-2—; and wherein F2 is a covalent bond; and b) D4-E4-F4-, wherein D4 is an optionally substituted heteroaryl wherein E4 is —S(CH2)0-2—; and wherein F4 is a covalent bond. 37. A compound of formula or a pharmaceutically acceptable salt thereof, wherein Cy2 is heteroaryl, which is optionally substituted and each of which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings is optionally substituted; X1 is a chemical bond, M1-L2-M1 or L2-M2-L2 wherein L2, at each occurrence, is independently selected from the group consisting of a chemical bond, C2-C4 alkenylene, and C2-C4 alkynylene, provided that L2 is not a chemical bond when X1 is M1-L2-M1; M1, at each occurrence, is independently selected from the group consisting of —O—, —N(R7)— and —S—, wherein R7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and M2 is selected from the group consisting of M1, heteroarylene, and heterocyclylene, either of which rings is optionally substituted; Ar2 is arylene or heteroarylene, each of which is optionally substituted; R5 and R6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; Ay2 is ortho-anilinyl; and q is 0. 38. A compound of formula or a pharmaceutically acceptable salt thereof, wherein Cy2 is acridinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl, benzoxazolyl, benzthiazolyl, benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl, carbazolyl, carbolinyl, cinnolinyl, furanyl, furazanyl, imidazolyl, 1H-indazolyl, indolenyl, indolizinyl, indolyl, 3H-indolyl, isobenzofuranyl, isoindazolyl, isoindolyl, isoquinolinyl, isothiazolyl, isoxazolyl, naphthyridinyl, 1,2,3-oxadiazolyl, 1,2,4-oxadiazolyl, 1,2,5-oxadiazolyl, 1,3,4-oxadiazolyl, oxazolyl, phenanthridinyl, phenanthrolinyl, phenazinyl, phthalazinyl, pteridinyl, purinyl, pyrazinyl, pyrazolyl, pyridazinyl, pyridooxazolyl, pyridoimidazolyl, pyridothiazolyl, pyrimidinyl, 2H-pyrrolyl, pyrrolyl, quinazolinyl, quinolinyl, 4H-quinolizinyl, quinoxalinyl, tetrahydroisoquinolinyl, tetrahydroquinolinyl, tetrazolyl, 1,2,3-thiadiazolyl, 1,2,4-thiadiazolyl, 1,2,5-thiadiazolyl, 1,3,4-thiadiazolyl, thiazolyl, thienyl, thienothiazolyl, thienooxazolyl, thienoimidazolyl, triazinyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,2,5-triazolyl, or 1,3,4-triazolyl, each of which is optionally substituted and each of which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings is optionally substituted; X1 is M2-L2 wherein L2, at each occurrence, is independently selected from the group consisting of a chemical bond, C1-C4 alkylene, C2-C4 alkenylene, and C2-C4 alkynylene; M1, at each occurrence, is independently selected from the group consisting of —O—, —N(R7)— and —S—, wherein R7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and M2 is selected from the group consisting of M1, heteroarylene, and heterocyclylene, either of which rings is optionally substituted; Ar2 is arylene or heteroarylene, each of which is optionally substituted; R5 and R6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; Ay2 is ortho-anilinyl; and q is 0. 39. A compound of formula or a pharmaceutically acceptable salt thereof, wherein Cy2 is acridinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl, benzoxazolyl, benzthiazolyl, benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl, carbazolyl, carbolinyl, cinnolinyl, furanyl, furazanyl, imidazolyl, 1H-indazolyl, indolenyl, indolizinyl, indolyl, 3H-indolyl, isobenzofuranyl, isoindazolyl, isoindolyl, isoquinolinyl, isothiazolyl, isoxazolyl, naphthyridinyl, 1,2,3-oxadiazolyl, 1,2,4-oxadiazolyl, 1,2,5-oxadiazolyl, 1,3,4-oxadiazolyl, oxazolyl, phenanthridinyl, phenanthrolinyl, phenazinyl, phthalazinyl, pteridinyl, purinyl, pyrazinyl, pyrazolyl, pyridazinyl, pyridooxazolyl, pyridoimidazolyl, pyridothiazolyl, pyrimidinyl, 2H-pyrrolyl, pyrrolyl, quinazolinyl, quinolinyl, 4H-quinolizinyl, quinoxalinyl, tetrahydroisoquinolinyl, tetrahydroquinolinyl, tetrazolyl, 1,2,3-thiadiazolyl, 1,2,4-thiadiazolyl, 1,2,5-thiadiazolyl, 1,3,4-thiadiazolyl, thiazolyl, thienyl, thienothiazolyl, thienooxazolyl, thienoimidazolyl, triazinyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,2,5-triazolyl, or 1,3,4-triazolyl, each of which is optionally substituted and each of which is optionally fused to one or two aryl or heteroaryl rings, or to one or two saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings is optionally substituted; X1 is M1-L2-M1 or L2-M2-L2 wherein L2, at each occurrence, is independently selected from the group consisting of a chemical bond, C2-C4 alkenylene, and C2-C4 alkynylene, provided that L2 is not a chemical bond when X1 is M1-L2-M1; M1, at each occurrence, is independently selected from the group consisting of —O—, —N(R7)— and —S—, wherein R7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and M2 is selected from the group consisting of M1, heteroarylene, and heterocyclylene, either of which rings is optionally substituted; Ar2 is arylene or heteroarylene, each of which is optionally substituted; R5 and R6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; Ay2 is ortho-anilinyl; and q is 0. 40. A composition comprising a compound according to claim 33 and a pharmaceutically acceptable carrier. 41. A method of treating colon cancer, lung cancer or pancreatic cancer in a human, the method comprising administering to a human in need of such treatment a compound according to claim 33. 42. A composition comprising a compound according to claim 34 and a pharmaceutically acceptable carrier. 43. A method of treating colon cancer, lung cancer or pancreatic cancer in a human, the method comprising administering to a human in need of such treatment a compound according to claim 34. 44. A composition comprising a compound according to claim 37 and a pharmaceutically acceptable carrier. 45. A method of treating colon cancer, lung cancer or pancreatic cancer in a human, the method comprising administering to a human in need of such treatment a compound according to claim 37. 46. A composition comprising a compound according to claim 38 and a pharmaceutically acceptable carrier. 47. A method of treating colon cancer, lung cancer or pancreatic cancer in a human, the method comprising administering to a human in need of such treatment a compound according to claim 38. 48. A composition comprising a compound according to claim 39 and a pharmaceutically acceptable carrier. 49. A method of treating colon cancer, lung cancer or pancreatic cancer in a human, the method comprising administering to a human in need of such treatment a compound according to claim 39.