Inhibitors of histone deacetylase

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

or a pharmaceutically acceptable salt thereof, wherein

Ar 2 is a saturated or mono- or poly- unsaturated C 5 -C 14 -mono- or fused poly-cyclic hydrocarbyl, optionally containing one, two, three, or four annular heteroatoms per ring optionally substituted with one or more groups selected from C 1 -C 7 -alkyl, hydroxy, C 1 -C 7 -alkoxy, halo, and amino, provided that an annular O or S is not adjacent to another annular O or S;

R 5 and R 6 are independently selected from the group consisting of hydrogen, C 1 -C 7 -alkyl, aryl, and aralkyl;

R 2 , R 3 and R 4 are independently selected from the group consisting of hydrogen, halogen, —NH 2 , nitro, hydroxy, aryl, heterocyclyl, C 3 -C 8 -cycloalkyl, heteroaryl, C 1 -C 7 -alkyl, haloalkyl, C 1 -C 7 -alkenyl, C 1 -C 7 -alkynyl, C 1 -C 7 -acyl, C 1 -C 7 -alkyl-aryloxy, C 1 -C 7 -alkyl-arylsulfanyl, C 1 -C 7 -alkyl-arylsulfinyl, C 1 -C 7 -alkyl-arylsulfonyl, C 1 -C 7 -alkyl-arylaminosulfonyl, C 1 -C 7 -alkyl-arylamine, C 1 -C 7 -alkynyl-C(O)-amine, C 1 -C 7 -alkenyl-C(O)-amine, C 1 -C 7 -alkynyl-R 9 , C 1 -C 7 -alkenyl-R 9 wherein R 9 is hydrogen, hydroxy, amino, C 1 -C 7 -alkyl or C 1 -C 7 -alkoxy;

q is 0 or 1;

R 1 is a mono-, bi-, or tri-cyclic aryl or heteroaryl, each of which is optionally substituted;

Y is Cy 2 -X 1 - and

Cy 2 is hydrogen, 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, and wherein any of the aforementioned rings are optionally substituted; and

X 1 is selected from the group consisting of a covalent bond, M 1 -L 2 -M 1 , and L 2 -M 2 -L 2 wherein

L 2 , at each occurrence, is independently selected from the group consisting of a chemical bond, C 0 -C 4 -hydrocarbyl, C 0 -C 4 -hydrocarbyl-(NH)—C 0 -C 4 -hydrocarbyl, C 0 -C 4 -hydrocarbyl-(S)—C 0 -C 4 -hydrocarbyl, and C 0 -C 4 -hydrocarbyl-(O)—C 0 -C 4 -hydrocarbyl, 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 )—, —S—, —S(O)—, —S(O) 2 —, —S(O) 2 N(R 7 )—, —N(R 7 )—S(O) 2 —, —C(O)—, —C(O)—NH—, —NH—C(O)—, —NH—C(O)—O— and —O—C(O)—NH—, —NH—C(O)—NH—,

R 7 is selected from the group consisting of hydrogen, C 1 -C 6 -hydrocarbyl, aryl, aralkyl, acyl, C 0 -C 6 -hydrocarbyl-heterocyclyl, and C 0 -C 6 -hydrocarbyl-heteroaryl, wherein the hydrocarbyl moieties are optionally substituted with —OH, —NH 2 , —N(H)CH 3 , —N(CH 3 ) 2 , or halo; and

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

provided that

when R 1 is N-imidazolyl, R 2 -R 4 are H, q is 0, and Ar 2 is pyridine, Y is not Cl; and

when R 1 is p-aminophenyl, R 2 -R 4 are H, q is 0, and Ar 2 is phenyl, Y is not H.

2. The compound according to claim 1 wherein R 1 is phenyl, naphthyl, anthracenyl, or fluorenyl.

3. The compound according to claim 1 wherein R 1 is furanyl or thienyl.

4. The compound according to claim 2 wherein R 2 , R 3 , and R 4 are all —H.

5. The compound according to claim 3 wherein R 2 , R 3 , and R 4 are all —H.

6. The compound according to claim 1 , wherein X 1 is selected from the group consisting of a —N(Z)-C 0 -C 7 -alkyl-, —O—C 0 -C 7 -alkyl-, —C(H)═CH—C 0 -C 7 -alkyl-, —S—C 0 -C 7 -alkyl-, or —C 1 -C 7 -alkyl-, wherein Z is —H or —C 1 -C 7 -alkyl- optionally substituted with —OH, —NH 2 , or halo.

7. The compound according to claim 1 , wherein X 1 is selected from methylene, aminomethyl, and thiomethyl.

8. The compound according to claim 1 , wherein Cy 2 is selected from

each of which optionally is substituted and optionally is fused to one or more aryl rings.

9. The compound according to claim 1 wherein Cy 2 is aryl or heteroaryl, each optionally substituted.

10. The compound according to claim 1 wherein Cy 2 is phenyl, pyrimidinyl, benzoimidazolyl or benzothiazolyl, each of which is optionally substituted.

11. The compound according to claim 10 wherein Cy 2 has from one and three substituents independently selected from the group consisting of C 1 -C 7 -alkoxy, halo, di-C 1 -C 7 -alkylamino-C 1 -C 7 -alkoxy and heteroaryl.

12. The compound according to claim 11 wherein the substituents are selected from methoxy, fluoro, chloro, pyridinyl and dimethylamino-cthoxy.

13. The compound according to claim 12 wherein Cy 2 is phenyl substituted with one to three CH 3 O—.

14. The compound according to claim 1 wherein Y is (V′-L 4 ) t -V-L 3 -, and

L 3 is a direct bond, —C 1 -C 6 -hydrocarbyl, —(C 1 -C 3 -hydrocarbyl) m1 -X′—(C 1 -C 3 -hydrocarbyl) m2 , —NH—(C 0 -C 3 -hydrocarbyl), (C 1 -C 3 -hydrocarbyl)-NH—, or —NH—(C 1 -C 3 -hydrocarbyl)-NH—;

m1 and m2 are independently 0 or 1;

X′ is —N(R 21 )—, —C(O)N(R 21 )—, N(R 21 )C(O)—, —O—, or —S—;

R 21 is —H, V″-(C 1 -C 6 -hydrocarbyl) a ;

L 4 is (C 1 -C 6 -hydrocarbyl) a -M-(C 1 -C 6 -hydrocarbyl) b ;

a and b are independently 0 or 1;

M is —NH—, —NHC(O)—, —C(O)NH—, —C(O)—, —SO 2 —, —NHSO 2 —, or —S0 2 NH—

V, V′, and V″ are independently selected from cycloalkyl, heterocyclyl, aryl, and heteroaryl;

t is 0 or 1.

15. The compound according to claim 14 wherein Y is V-L 3 and

L 3 is —NH—CH— or —CH—NH—;

V is phenyl optionally substituted with from 1 to 3 moieties independently selected from halo, hydroxy, C 1 -C 6 -hydrocarbyl, C 1 -C 6 -hydrocarbyl-oxy or -thio (particularly methoxy or methylthio), wherein each of the hydrocarbyl moieties are optionally substituted with one or more moieties independently selected from halo, nitroso, amino, sulfonamido, and cyano.

16. The compound according to claim 15 wherein V is an optionally substituted ring moiety selected from:

17. The compound according to claim 1 wherein

Cy 2 is cycloalkyl, aryl, heteroaryl, or heterocyclyl, each of which optionally is substituted, and each of which optionally is fused to one or more aryl or heteroaryl rings, or to one or more saturated or partially unsaturated cycloalkyl or heterocyclic rings, each of which rings optionally is substituted, provided that when Cy 2 is a cyclic moiety having —C(O)—, —C(S)—, —S(O)—, or —S(O) 2 — in the ring, then Cy 2 is not additionally substituted with a group comprising an aryl or heteroaryl ring; and

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

18. The compound according to claim 1 wherein Y is selected from:

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

b) A 2 -L 2 -B 2 —, wherein A 2 is CH 3 (C═CH 2 )—; optionally substituted cycloalkyl, optionally substituted alkyl, or optionally substituted aryl; wherein L 2 is —C≡C—; and wherein B 2 is a covalent bond;

c) A 3 -L 3 -B 3 —, wherein A 3 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 3 is a covalent bond; and wherein B 3 is —CH 2 NH—;

d) A 4 -L 4 -B 4 —, wherein A 4 is an optionally substituted aryl; wherein L 4 is —NHCH 2 —; and wherein B 4 is a thienyl group;

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

f) morpholinyl-CH 2 —

g) optionally substituted aryl;

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

i) A 7 -L 7 -B 7 —, wherein A 7 is an optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 7 is a covalent bond; and wherein B 7 is —CH 2 —;

j) optionally substituted heteroaryl or optionally substituted heterocyclyl;

k) A 8 -L 8 -B 8 —, wherein A 8 is optionally substituted phenyl; wherein L 8 is a covalent bond; and wherein B 8 is —O—;

l) A 9 -L 9 -B 9 —; wherein A 9 is an optionally substituted aryl; wherein L 9 is a covalent bond; and wherein B 9 is a furan group;

m) A 10 -L 10 -B 10 —, wherein A 10 is an optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 10 is —CH(CH 2 CH 3 )—; and wherein B 10 is —NHCH 2 —;

n) A 11 -L 11 -B 11 —, wherein A 11 is an optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 11 is a covalent bond; and wherein B 11 is —OCH 2 —;

o) A 12 -L 12 -B 12 —, wherein A 12 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 12 is —NHC(O)—; and wherein B 12 is —N(optionally substituted aryl)CH 2 —;

P) A 13 -L 13 -B 13 —, wherein A 13 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 13 is a covalent bond; and wherein B 13 is —NHC(O)—;

q) A 14 -L 14 -B 14 —, wherein A 14 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 14 is —NHC(O) (optionally substituted heteroaryl); and wherein B 14 is —S—S—;

r) F 3 CC(O)NH—;

s) A 15 -L 15 -B 15 —, wherein A 15 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 15 is —(CH 2 ) 0-1 NH (optionally substituted heteroaryl)-; and wherein B 15 is —NHCH 2 —;

t) A 16 -L 15 -B 16 —, wherein A 16 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 16 is a covalent bond; and wherein B 16 is —N(optionally substituted alkyl)CH 2 —; and

u) A 17 -L 17 -B 17 —, wherein A 17 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein L 17 is a covalent bond; and wherein B 17 is -(optionally substituted aryl-CH 2 ) 2 —N—.

19. The compound according to claim 1 wherein Y is selected from:

a) D 1 -E 1 -F 1 —, wherein D 1 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein E 1 is —CH 2 — or a covalent bond; and wherein F 1 is a covalent bond;

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

c) D 3 -E 3 -F 3 —, wherein D 3 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein E 3 is —(CH 2 ) 0-2 NH—; and wherein F 3 is a covalent bond;

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

e) D 5 -E 5 -F 5 —, wherein D 5 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein E 5 is —(CH 2 ) 0-2 S—; and wherein F 5 is a covalent bond; and

f) D 6 -E 6 -F 6 —, wherein D 6 is an optionally substituted aryl, optionally substituted heteroaryl or optionally substituted heterocyclyl; wherein E 6 is —NH(CH 2 ) 0-2 NH—; and wherein F 6 is a covalent bond.

20. The compound according to claim 2 wherein R 2 to R 4 are independently hydrogen, —NH 2 , nitro, furanyl, chloro, fluoro, butyl, trifluoromethyl, bromo, thienyl, phenyl, —CHCHC(O)—NH 2 , —C≡CCH 2 —R 9 wherein R 9 is hydrogen, C 1 -C 7 -alkyl, hydroxy, amino, or C 1 -C 7 -alkoxy.

21. The compound according to claim 3 wherein R 2 to R 4 are independently hydrogen, —NH 2 , nitro, furanyl, chloro, fluoro, butyl, trifluoromethyl, bromo, thienyl, phenyl, —CHCHC(O)—NH 2 , —C≡CCH 2 —R 9 wherein R 9 is hydrogen, C 1 -C 7 -alkyl, hydroxy, amino, or C 1 -C 7 -alkoxy.

22. The compound according to claim 1 wherein q is 0 and X 1 is independently selected from the group consisting of a —NH—CH 2 —, —S—CH 2 — and —CH 2 —.

23. The compound according to claim 1 wherein Ar 2 has the formula

and wherein G, at each occurrence, is independently N or C, and C is optionally substituted.

24. The compound according to claim 23 wherein Ar 2 has the formula

25. The compound according to claim 23 wherein Ar 2 is selected from the group consisting of phenylene, benzofuranylene and indolinylene.

26. The compound according to claim 1 wherein the moiety formed by Cy 2 -X 1 is selected from:

27. The compound of claim 1 of formula (2):

or a pharmaceutically acceptable salt thereof, wherein

R 2 and R 3 are independently selected from the group consisting of hydrogen, trifluoromethyl, butyl, —(CH 2 ) 3 —OH, chloro, fluoro, amino, phenyl, thienyl, furanyl, —CHCCHC(O)NH 2 , —C≡CCH 2 —OH, —C≡CCH 2 —OCH 3 ; and

the A ring is optionally further substituted with from 1 to 3 substituents independently selected from methyl, hydroxy, methoxy, halo, and amino.

28. The compound according to claim 27 wherein Cy 2 is selected from:

29. The compound according to claim 27 wherein the A ring is not further substituted.

30. The compound according to claim 27 wherein R 2 and R 3 are —H.

31. A compound according to claim 1 selected from:

N-[2-amino-5-(2-thienyl)phenyl]-4-{[(3,4-dimethoxyphenyl)amino]methyl}benzamide;

N-[2-amino-5-(2-thienyl)phenyl]-4-{[(4-pyridin-3-ylpyrimidin-2-yl)amino]methyl}benzamide;

N-[2-amino-5-(2-thienyl)phenyl]-4-[({6-[2-(dimethylamino)ethoxy]-1H-benzimidazol-2-yl}thio)methyl]benzamide;

N-[2-amino-5-(2-thienyl)phenyl]-4-{[(5-chloro-6-fluoro-1H-benzimidazol-2-yl)amino]methyl}benzamide;

N-[2-amino-5-(2-thienyl)phenyl]-5-{[(3,4,5-trimethoxyphenyl)amino]methyl}-1-benzofuran-2-carboxamide;

N-[2-amino-5-(2-thienyl)phenyl]-1-(3,4,5-trimethoxybenzyl)indoline-6-carboxamide;

trans-N-[2-amino-5-(2-thienyl)phenyl]-3-(4-{[(3,4,5-trimethoxyphenyl)amino]methyl}phenyl)acrylamide;

N-[2-amino-5-(2-thienyl)phenyl]-4-{[(3-fluoro-4-methoxyphenyl)amino]methyl}benzamide;

N-[2-amino-5-(2-thienyl)phenyl]-4-{[(6-chloro-5-fluoro-1H-benzimidazol-2-yl)thio]methyl}benzamide;

and a pharmaceutically acceptable salt of any one or more of the foregoing.

32. A pharmaceutical composition comprising a compound according to claims 1 and a pharmaceutically acceptable carrier, diluent, or excipient.