Fluorescent compounds that bind to histone deacetylase

1 . A compound represented by the following structural Formula

wherein A is aryl, heteroaryl or H, optionally substituted with halo, methyl, methoxy, amino, hydroxyl or halomethyl;

R 1 and R 2 are independently selected from H, OH, halo, NH 2 , C 1 -C 4 alkyl, or C 1 -C 4 alkoxy;

R 3 is independently selected from H, OH, NH 2 , nitro, CN, amide, carboxyl, C 1 -C 7 alkoxy, C 1 -C 7 alkyl, C 1 -C 7 haloalkyl, C 1 -C 7 haloalkyloxy, C 1 -C 7 hydroxyalkyl, C 1 -C 7 alkenyl, C 1 -C 7 alkyl-C(═O)O—, C 1 -C 7 alkyl-C(═O)—, C 1 -C 7 alkynyl, halo, hydroxyalkoxy, C 1 -C 7 alkyl-NHSO 2 —, C 1 -C 7 alkyl-SO 2 NH—, C 1 -C 7 alkylsulfonyl, C 1 -C 7 alkylamino or di(C 1 -C 7 )alkylamino;

R 4 is selected from —NR 6 R 7 ;

R 5 is independently selected from H, OH, NH 2 , nitro, CN, amide, carboxyl, C 1 -C 2 alkoxy, C 1 -C 2 alkyl, C 1 -C 2 haloalkyl, C 1 -C 2 haloalkyloxy, C 1 -C 2 hydroxyalkyl, C 1 -C 2 alkenyl, C 1 -C 2 alkyl-C(═O)O—, C 1 -C 2 alkyl-C(═O)—, C 1 -C 2 alkynyl, halo, hydroxyalkoxy, C 1 -C 2 alkyl-NHSO 2 —, C 1 -C 2 alkyl-SO 2 NH—, C 1 -C 2 alkylsulfonyl, C 1 -C 2 alkylamino or di(C 1 -C 2 )alkylamino;

R 6 is independently selected from H or C 1 -C 4 alkyl;

R 7 is selected from —(CR a 2 ) s C(O)(CR a 2 ) q R 12 , or —(CR a 2 )C(O)O(CR a 2 ) q R 12 ;

R 12 is selected from C 1 -C 4 alkyl, C 3 -C 6 cycloalkyl, heteroaryl, aryl or heterocyclic, wherein the alkyl, cycloalkyl, heteroaryl, heterocyclic or aryl is attached to a fluorophore through a linker, and optionally substituted OH, NH 2 , nitro, CN, amide, carboxyl, C 1 -C 7 alkoxy, C 1 -C 7 alkyl, C 1 -C 7 haloalkyl, C 1 -C 7 haloalkyloxy, C 1 -C 7 hydroxyalkyl, C 1 -C 7 alkenyl, C 1 -C 7 alkyl-C(═O)O—, C 1 -C 7 alkyl-C(═O)—, C 1 -C 7 alkynyl, halo, hydroxyalkoxy, C 1 -C 7 alkyl-NHSO 2 —, C 1 -C 7 alkyl-SO 2 NH—, C 1 -C 7 alkylsulfonyl, C 1 -C 7 alkylamino or di(C 1 -C 7 )alkylamino, aryl, heterocyclic or cycloalkyl;

R a is independently selected from H or C 1 -C 4 alkyl;

p is 1, 2, 3 or 4;

s and q are independently 0, 1, 2, 3, or 4;

L 1 is (CH 2 ) r , ethenyl or cyclopropyl, wherein r is 0, 1 or 2;

X is OH or NH 2 ;

Z is C or N;

or a stereoisomer or pharmaceutically acceptable salt thereof.

2 . The compound of claim 1 , wherein

A is

R 1 and R 2 are independently selected from H, OH, halo, NH 2 , C 1 -C 4 alkyl, or C 1 -C 4 alkoxy;

R 3 is H;

R 4 is —NR 6 R 7 ;

R 5 is H;

R 6 is selected from H or C 1 -C 4 alkyl;

R 7 is —C(O)O(CR a 2 ) q R 12 ;

R 12 is selected from aryl or heteroaryl; wherein the aryl or heteroaryl is attached to a fluorophore through a linker, and optionally substituted with OH, NH 2 , nitro, CN, amide, carboxyl, C 1 -C 7 alkoxy, C 1 -C 7 alkyl, C 1 -C 7 haloalkyl, C 1 -C 7 haloalkyloxy, C 1 -C 7 hydroxyalkyl, C 1 -C 7 alkenyl, C 1 -C 7 alkyl-C(═O)O—, C 1 -C 7 alkyl-C(═O)—, C 1 -C 7 alkynyl, halo, hydroxyalkoxy, C 1 -C 7 alkyl-NHSO 2 —, C 1 -C 7 alkyl-SO 2 NH—, C 1 -C 7 alkylsulfonyl, C 1 -C 7 alkylamino or di(C 1 -C 7 )alkylamino, aryl, heterocyclic or cycloalkyl;

R 17 and R 21 are independently selected from hydrogen or fluoro;

R 18 , R 19 or R 20 are independently selected from hydrogen, halo, methyl, methoxy or halomethyl;

R 22 , R 23 and R 24 are independently selected from hydrogen, methyl, amino, hydroxyl or halo;

R a is independently H or C 1 -C 4 alkyl;

Ring B is aryl or heteroaryl;

q is independently 0, 1 or 2;

L 1 is a bond;

X is NH 2 ;

or a stereoisomer or pharmaceutically acceptable salt thereof.

3 . The compound of claim 2 , wherein A is

4 . The compound of claim 2 , wherein R 1 and R 2 are H; R a is H; R 6 is H, and q is 1.

5 . The compound of claim 1 , wherein the fluorophore is selected from the fluorophore in fluorescein, BODIPY TMR dye, BODIPY TR dye, Cascade Blue, Cascade Yellow, Dapoxyl Dyes, Marina Blue, Lucifer yellow, Pacific Blue dyes, Oregon Green 488 dye, Oregon Green 514 dye, NODIPY FL dye, tetramethylrhodamine, rhodamine, X-Rhodamine, rhodamine 6G, rhodamine B, rhodamine 123, Rhodamine Red, Rhodamine Green, Rhodol Green, sulforhodamine 101, Texas Red, coumarin, hydroxycoumarin, aminocoumarin, methoxycoumarin, cyanine, Alexa Fluor dyes, DyLight 549 and DyLight 633.

6 . The compound of claim 1 , wherein the linker is

wherein R 31 is H or C 1 -C 4 alkyl;

m is 0, 1 or 2.

7 . A compound represented by the following structural Formula

Wherein,

R 25 is F-L-, where L is a linker, and F is a fluorophore;

R 26 to R 29 is independently selected from H, C 1 -C 4 alkyl, CN, azido, C 1 -C 4 cyanoalkyl, nitro, halo, C 1 -C 4 haloalkyl, amino, amide, carboxyl, C 1 -C 4 alkoxycarbonyl, C 1 -C 4 alkylaminocarbonyl, hydroxyl, C 1 -C 4 alkoxy, aryl-C 1 -C 4 -alkoxy, C 1 -C 4 haloalkyloxy, C 1 -C 4 hydroxyalkyl, C 1 -C 4 alkenyl, C 1 -C 4 alkyl-C(═O)O—, C 1 -C 4 alkyl-C(═O)—, C 1 -C 4 alkynyl, hydroxyalkoxy, C 1 -C 4 alkyl-NHSO 2 —, C 1 -C 4 alkyl-SO 2 NH—, C 1 -C 4 alkylsulfonyl, C 1 -C 4 alkylamino or di(C 1 -C 4 )alkylamino;

R 30 is selected from H or C 1 -C 4 alkyl;

n is 4, 5, 6, 7 or 8;

or a stereoisomer or pharmaceutically acceptable salt thereof.

8 . The compound of claim 7 , wherein the fluorophore is selected from the fluorophore in fluorescein, BODIPY TMR dye, BODIPY TR dye, Cascade Blue, Cascade Yellow, Dapoxyl Dyes, Marina Blue, Lucifer yellow, Pacific Blue dyes, Oregon Green 488 dye, Oregon Green 514 dye, NODIPY FL dye, tetramethylrhodamine, rhodamine, X-Rhodamine, rhodamine 6G, rhodamine B, rhodamine 123, Rhodamine Red, Rhodamine Green, Rhodol Green, sulforhodamine 101, Texas Red, coumarin, hydroxycoumarin, aminocoumamm, methoxycoumarin, cyanine, Alexa Fluor dyes, DyLight 549 and DyLight 633.

9 . The compound of claim 7 , wherein the linker is

wherein R 31 is H or C 1 -C 4 alkyl;

m is 0, 1 or 2.

10 . A compound selected from:

5-{[({4-[({[(4-{[(4-aminobiphenyl-3-yl)amino]carbonyl}benzyl)amino]carbonyl}oxy)methyl]benzyl}amino)carbonothioyl]amino}-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid;

5-({[(4-{[8-(hydroxyamino)-8-oxooctanoyl]amino}benzyl)amino]carbonothioyl}amino)-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid;

5-{[({4-[({[(4-{[(2-aminophenyl)amino]carbonyl}benzyl)amino]carbonyl}oxy)methyl]benzyl}amino)carbonothioyl]amino}-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid.

or a stereoisomer or pharmaceutically acceptable salt thereof.