Inhibitors of histone deacetylase

1. A histone deacetylase inhibitor of formula (3):

or a pharmaceutically acceptable salt thereof, wherein

Ar 3 is arylene or heteroarylene, either of which is optionally substituted;

Cy 3 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 Cy 3 has —C(O)—, —C(S)—, —S(O)—, or —S(O) 2 — in the ring, then Cy 3 is not additionally substituted with a group comprising an aryl or heteroaryl ring; and

X 2 is selected from the group consisting of a chemical bond, L 3 and W 1 -L 3 , wherein

W 1 , at each occurrence, is S, O, or N(R 9 ), where R 9 is selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; and

L 3 is C 1 -C 4 alkylene, C 2 -C 4 alkenylene, or C 2 -C 4 alkynylene;

provided that X 2 does not comprise a —C(O)— or —C(S)— group;

and further provided that when Cy 3 is pyridine, then X 2 is L 3 or W 1 -L 3 .

2. The compound according to claim 1 wherein Ar 3 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 X 2 is a chemical bond, then Ar 3 is not

and Cy 3 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(R 8 ), where R 8 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 Ar 3 is selected from the group consisting of phenylene, pyridylene, thiazolylene, and quinolylene.

7. The compound according to claim 1 wherein X 2 is a chemical bond.

8. The compound according to claim 1 wherein X 2 is C 1 -C 4 alkylene, C 2 -C 4 alkenylene, or C 2 -C 4 alkynylene.

9. The compound according to claim 1 wherein X 2 is C 1 C 4 alkylene.

10. The compound according to claim 1 wherein X 2 is methylene or ethylene.

11. The compound according to claim 1 wherein X 2 is C 2 -C 4 alkenylene or C 2 -C 4 alkynylene.

12. A histone deacetylase inhibitor of formula (3):

or a pharmaceutically acceptable salt thereof, wherein

Ar 3 is arylene or heteroarylene, either of which is optionally substituted;

Cy 3 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 Cy 3 has —C(O)—, —C(S)—, —S(O)—, or —S(O) 2 — in the ring, then Cy 3 is not additionally substituted with a group comprising an aryl or heteroaryl ring; and

X 2 is C 1 -C 4 alkylene, C 2 -C 4 alkenylene or C 2 -C 4 alkynylene, wherein the carbon in the C 1 -C 4 alkylene adjacent to Cy 3 , or one saturated carbon in the C 2 -C 4 alkenylene or C 2 -C 4 alkynylene is replaced with —NH— or —S—, provided that X 2 does not comprise a —C(O)— or —C(S)— group.

13. The compound according to claim 1 wherein Cy 3 is heteroaryl which is optionally substituted and is optionally fused to one or two aryl rings.

14. The compound according to claim 1 wherein Cy 3 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 Cy 3 is fused to a benzene ring.

16. The compound according to claim 1 wherein Cy 3 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 Cy 3 has from one to three substituents of the formula —K 1 —N(H)(R 10 ), wherein

K 1 is a chemical bond or C 1 -C 4 alkylene;

R 10 is selected from the group consisting of Z′ and -Ak 2 -Z′, wherein

Ak 2 is C 1 -C 4 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 Ar 3 is quinoxalinylene, then X 2 is not —CH(OH)—.

21. The compound of claim 1 wherein Ar 3 is

wherein X is —CH 2 —, —NH—, O, or S.

22. The compound of claim 1 wherein Ar 3 is

wherein X is S or O.

23. A compound of formula

or a pharmaceutically acceptable salt thereof, wherein

Cy 2 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;

X 1 is a chemical bond, M 1 -L 2 -M 1 or L 2 -M 2 -L 2 wherein

L 2 , at each occurrence, is independently selected from the group consisting of a chemical bond, C 1 -C 4 alkylene, C 2 -C 4 alkenylene, and C 2 -C 4 alkynylene, provided that L 2 is not a chemical bond when X 1 is M 1 -L 2 -M 1 ;

M 1 , at each occurrence, is independently selected from the group consisting of —S(O)—, S(O) 2 —, —S(O) 2 N(R 7 )—, —N(R 7 )—S(O) 2 —, and —C(O)—, wherein R 7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and

M 2 is selected from the group consisting of M 1 , heteroarylene, and heterocyclylene, either of which rings is optionally substituted;

Ar 2 is arylene or heteroarylene, each of which is optionally substituted;

R 5 and R 6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl;

Ay 2 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

Cy 2 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;

X 1 is M 1 -L 2 -M 1 or L 2 -M 2 -L 2 wherein

L 2 , at each occurrence, is independently selected from the group consisting of a chemical bond, C 1 -C 4 alkylene, C 2 -C 4 alkenylene, and C 2 -C 4 alkynylene, provided that L 2 is not a chemical bond when X 1 is M 1 -L 2 -M 1 ;

M 1 , at each occurrence, is independently selected from the group consisting of —S(O)—, S(O) 2 —, —S(O) 2 N(R 7 )—, —N(R 7 )—SO 2 —, and —C(O)—, wherein R 7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and

M 2 is selected from the group consisting of M 1 , heteroarylene, and heterocyclylene, either of which rings is optionally substituted;

Ar 2 is arylene or heteroarylene, each of which is optionally substituted;

R 5 and R 6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl;

Ay 2 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

Ar 3 is arylene or heteroarylene, either of which is optionally substituted;

Cy 3 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 Cy 3 has —C(O)—, —C(S)—, —S(O)—, or —S(O) 2 — in the ring, then Cy 3 is not additionally substituted with a group comprising an aryl or heteroaryl ring; and

X 2 is selected from the group consisting of L 3 -W 1 , L 3 -W 1 -L 3 and W 1 -L 3 -W 1 , wherein

W 1 , at each occurrence, is S, O, or N(R 9 ), where R 9 is selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl; and

L 3 is C 2 -C 4 alkenylene, or C 2 -C 4 alkynylene;

provided that X 2 does not comprise a —C(O)— or —C(S) group;

and further provided that when Cy 3 is pyridine, then X 2 is L 3 -W 1 .

34. A compound of formula

or a pharmaceutically acceptable salt thereof, wherein

Cy 2 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;

X 1 is a chemical bond or M 2 -L 2 , wherein

L 2 , at each occurrence, is independently selected from the group consisting of a chemical bond, C 1 -C 4 alkylene, C 2 -C 4 alkenylene, and C 2 -C 4 alkynylene;

M 1 , at each occurrence, is independently selected from the group consisting of —O—, —N(R 7 )— and —S—, wherein R 7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and

M 2 is selected from the group consisting of M 1 , heteroarylene, and heterocyclylene, either of which rings is optionally substituted;

Ar 2 is arylene or heteroarylene, each of which is optionally substituted;

R 5 and R 6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl;

Ay 2 is ortho-anilinyl; and

q is 0.

35. The compound according to claim 34 wherein Ar 2 is aryl or heteroaryl; and Cy 2 -X 1 - is collectively selected from the group consisting of

a) A 1 -L 1 -B 1 -, wherein A 1 is an optionally substituted heteroaryl wherein L 1 is NH(CH 2 ) 0-1 — or —NHCH 2 —; and wherein B 1 is phenyl or a covalent bond;

b) A 5 -L 5 -B 5 -, wherein A 5 is an optionally substituted heteroaryl wherein L 5 is a covalent bond; and wherein B 5 is —SCH 2 —;

c) A 6 -L 6 -B 6 -, wherein A 6 is an optionally substituted heteroaryl wherein L 6 is a covalent bond; and wherein B 6 is —NHCH 2 —;

d) optionally substituted heteroaryl; p 1 e) A 11 -L 11 -B 11 -, wherein A 11 is an optionally substituted heteroaryl wherein L 11 is a covalent bond; and wherein B 11 is —OCH 2 —; and

f) A 16 -L 16 -B 16 -, wherein A 16 is an optionally substituted heteroaryl wherein L 16 is a covalent bond; and wherein B 16 is —N(optionally substituted alkyl)CH 2 .

36. The compound according to claim 24 wherein Cy 2 -X 1 - is collectively selected from the group consisting of

a) D 2 -E 2 -F 2 -, wherein D 2 is optionally substituted heteroaryl wherein E 2 is —NH(CH 2 ) 0-2 —; and wherein F 2 is a covalent bond; and

b) D 4 -E 4 -F 4 -, wherein D 4 is an optionally substituted heteroaryl wherein E 4 is —S(CH 2 ) 0-2 —; and wherein F 4 is a covalent bond.

37. A compound of formula

or a pharmaceutically acceptable salt thereof, wherein

Cy 2 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;

X 1 is a chemical bond, M 1 -L 2 -M 1 or L 2 -M 2 -L 2 wherein

L 2 , at each occurrence, is independently selected from the group consisting of a chemical bond, C 2 -C 4 alkenylene, and C 2 -C 4 alkynylene, provided that L 2 is not a chemical bond when X 1 is M 1 -L 2 -M 1 ;

M 1 , at each occurrence, is independently selected from the group consisting of —O—, —N(R 7 )— and —S—, wherein R 7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and

M 2 is selected from the group consisting of M 1 , heteroarylene, and heterocyclylene, either of which rings is optionally substituted;

Ar 2 is arylene or heteroarylene, each of which is optionally substituted;

R 5 and R 6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl;

Ay 2 is ortho-anilinyl; and

q is 0.

38. A compound of formula

or a pharmaceutically acceptable salt thereof, wherein

Cy 2 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;

X 1 is M 2 -L 2 wherein

L 2 , at each occurrence, is independently selected from the group consisting of a chemical bond, C 1 -C 4 alkylene, C 2 -C 4 alkenylene, and C 2 -C 4 alkynylene;

M 1 , at each occurrence, is independently selected from the group consisting of —O—, —N(R 7 )— and —S—, wherein R 7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and

M 2 is selected from the group consisting of M 1 , heteroarylene, and heterocyclylene, either of which rings is optionally substituted;

Ar 2 is arylene or heteroarylene, each of which is optionally substituted;

R 5 and R 6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl;

Ay 2 is ortho-anilinyl; and

q is 0.

39. A compound of formula

or a pharmaceutically acceptable salt thereof, wherein

Cy 2 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;

X 1 is M 1 -L 2 -M 1 or L 2 -M 2 -L 2 wherein

L 2 , at each occurrence, is independently selected from the group consisting of a chemical bond, C 2 -C 4 alkenylene, and C 2 -C 4 alkynylene, provided that L 2 is not a chemical bond when X 1 is M 1 -L 2 -M 1 ;

M 1 , at each occurrence, is independently selected from the group consisting of —O—, —N(R 7 )— and —S—, wherein R 7 is selected from the group consisting of hydrogen, alkyl, aryl, aralkyl, acyl, heterocyclyl, and heteroaryl; and

M 2 is selected from the group consisting of M 1 , heteroarylene, and heterocyclylene, either of which rings is optionally substituted;

Ar 2 is arylene or heteroarylene, each of which is optionally substituted;

R 5 and R 6 are independently selected from the group consisting of hydrogen, alkyl, aryl, and aralkyl;

Ay 2 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 .