Kdm4 inhibitors

Abstract

The present disclosure relates generally to compounds and methods for inhibiting the enzymatic activity of lysine demethylase 4 (KDM4) and treating cancer. Provided herein are substituted pyridine derivative compounds and pharmaceutical compositions comprising said compounds. The subject compounds and compositions are useful for inhibiting lysine demethylase 4. Furthermore, the subject compounds and compositions are useful for the treatment of breast cancer and the like.

We claim: 
     
         1 . A compound having the structure of Formula I: 
       
         
           
           
               
               
           
         
         wherein said compound includes stereoisomers and pharmaceutically acceptable salts thereof, and wherein 
         X is O or CH 2 , and 
         R 6  is N(R 1 )(R 2 ) or O(R 2 ), in which
 R 1  is H or C 1 -C 6  alkyl, and 
 R 2  is optionally substituted aryl, heteroaryl, cyclyl, or heterocyclyl. 
 
       
     
     
         2 . The compound of  claim 1  is R stereoisomer. 
     
     
         3 . The compound of  claim 1 , wherein R 1  is methyl or ethyl. 
     
     
         4 . The compound of  claim 1 , wherein R 2  is pyridine optionally substituted with alkyl selected from methyl, ethyl, and cyclopropyl. 
     
     
         5 . The compound of  claim 1 , wherein R 2  is phenyl optionally substituted with halo selected from fluoro and choloro; phenyl optionally substituted with alkyl selected from methyl, propanyl, and cyclopropyl; phenyl optionally substituted with amino; phenyl optionally substituted with a N-containing group selected from dimethylamino and azetidinyl; phenyl optionally substituted with alkoxy selected from ethoxy, cyclopropylmethoxy, methoxymethyl, difluoromethoxy, and trifluoromethoxy; or phenyl optionally substituted with heterocyclyl selected from azetidinyl and oxanyl. 
     
     
         6 . The compound of  claim 1 , wherein R 2  is an indane moiety. 
     
     
         7 . The compound of  claim 6 , wherein R 2  is 2,3-dihydro-1H-indenyl. 
     
     
         8 . The compound of  claim 1 , wherein X is CH 2  and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl or pyridinyl. 
     
     
         9 . The compound of  claim 1 , wherein X is CH 2  and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl substituted with methyl. 
     
     
         10 . The compound of  claim 1 , wherein X is CH 2  and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl substituted with dimethylamino. 
     
     
         11 . The compound of  claim 1 , wherein X is CH 2  and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl substituted with methoxymethyl, ethoxy, or difluoromethoxy. 
     
     
         12 . The compound of  claim 1 , wherein X is CH 2  and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is pyridinyl substituted with methyl. 
     
     
         13 . The compound of  claim 1 , wherein X is O and R 6  is N(R 1 )(R 2 ), in which R 1  is ethyl, and R 2  is phenyl. 
     
     
         14 . The compound of  claim 1 , wherein X is O and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl substituted with chloro or fluoro. 
     
     
         15 . The compound of  claim 1 , wherein X is O and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl substituted with methyl, ethyl, propyl, or cyclopropyl. 
     
     
         16 . The compound of  claim 1 , wherein X is O and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is pyridinyl substituted with methyl, ethyl, or cyclopropyl. 
     
     
         17 . The compound of  claim 1 , wherein X is O and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl substituted with trifluoroethyl. 
     
     
         18 . The compound of  claim 1 , wherein X is O and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl substituted with trifluoromethoxy, difluoroethoxy, or cyclopropylmethoxy. 
     
     
         19 . The compound of  claim 1 , wherein X is O and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl substituted with azetidinyl. 
     
     
         20 . The compound of  claim 1 , wherein X is O and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is phenyl substituted with oxanyl. 
     
     
         21 . The compound of  claim 1 , wherein X is O and R 6  is N(R 1 )(R 2 ), in which R 1  is methyl, and R 2  is 2,3-dihydro-1H-indenyl. 
     
     
         22 . The compound of  claim 1 , wherein X is CH 2  and R 6  is O(R 2 ), in which R 2  is phenyl substituted with fluoro and methyl. 
     
     
         23 . A compound selected from:
 3-([[(1R)-6-[methyl(phenyl) amino]-1,2,3,4-tetrahydronaphthalen-1-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(1R)-6-[methyl(pyridin-2-yl)amino]-1,2,3,4-tetrahydro-naphthalen-1-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(1R)-6-[methyl(4-methylphenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(1R)-6-[[4-(dimethylamino)phenyl](methyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(1R)-6-[[4-(methoxymethyl)phenyl](methyl)amino]-1,2,3,4-tetrahydro-naphthalen-1-yl]methyl]amino) pyridine-4-carboxylic acid;   3-([[(1R)-6-[[4-(difluoromethoxy)phenyl](methyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl]-methyl]amino) pyridine-4-carboxylic acid;   3 ([[(1R)-6-[(4-ethoxyphenyl)(methyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl]methyl]amino) pyridine-4-carboxylic acid;   3-([[(1R)-6-[methyl-[5-methylpyridin-2-yl) amino]-1,2,3,4-tetrahydronaphthalen-1-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(1R)-6-[methyl[6-methylpyridin-2-yl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[ethyl(phenyl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[3-fluorophenyl)(methyl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[4-fluorophenyl)(methyl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]-methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[4-chlorophenyl)(methyl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino) pyridine-4-carboxylic acid;   3-([[(4R)-7-[methyl(4-methylphenyl) amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[methyl(4-ethylphenyl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[methyl[4-propan-2-yl)phenyl]amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[methyl(5-methylpyridin-2-yl)amino]-2,3-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[methyl (5-methylpyridin-2-yl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[(5-cyclopropylpyridin-2-yl) (methyl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino) pyridine-4-carboxylic acid;   3-([[(4R)-7-[(4-cyclopropylphenyl)(methyl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid;   3-({[(1R)-6-{[4-(1H-imidazol-1-yl)phenyl](methyl)amino}-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid;   3-([[(1R)-6-[[4-(tri-fluoromethoxy) phenyl](methyl)amino 3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[[4-(difluoromethoxy)phenyl] (methyl)-amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl] amino)pyridine-4-carboxylic acid;   3-({[(1R)-6-{[4-(cyclo-propylmethoxy)phenyl](methyl)amino}-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[[4-azetidin-1-yl)phenyl] (methyl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl] amino)pyridine-4-carboxylic acid;   3-({[(4R)-7-{methyl[4-(oxan-4-yl)phenyl] amino}-3,4-dihydro-2H-1-benzopyran-4-yl]methyl}amino)pyridine-4-carboxylic acid;   3-([[(4R)-7-[2,3-dihydro-1H-inden-5-yl)(methyl)amino]-3,4-dihydro-2H-1-benzopyran-4-yl]methyl]amino)pyridine-4-carboxylic acid; and   3-([[(1R)-6-[2-fluoro-4-methyl-phenoxy)-1,2,3,4-tetrahydronaphthalen-1-yl]methyl] amino)pyridine-4-carboxylic acid.   
     
     
         24 . A pharmaceutical composition comprising a compound of Formula I as described in  claim 1 , or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. 
     
     
         25 . A pharmaceutical composition comprising a compound as described in  claim 23 , or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. 
     
     
         26 . A method of inhibiting a cancer associated with lysine demethylase 4 (KDM4) activity (a KDM4-associated cancer) comprising administering to a patient in need thereof a pharmaceutical composition as described in  claim 24 . 
     
     
         27 . A method of inhibiting a cancer associated with KDM4 activity (a KDM4-associated cancer) comprising administering to a patient in need thereof a pharmaceutical composition as described in  claim 25 . 
     
     
         28 . The method of  claim 26 , wherein the KDM4-associated cancer is triple-negative breast cancer. 
     
     
         29 . The method of  claim 27 , wherein the KDM4-associated cancer is triple-negative breast cancer. 
     
     
         30 . A method of selectively inhibiting lysine demethylase (KDM) activity in a cell comprising contacting the cell with a compound of Formula I as described in  claim 1 . 
     
     
         31 . A method of selectively inhibiting KDM activity in a cell comprising contacting the cell with a compound as described in  claim 23 . 
     
     
         32 . A formulation comprising a tablet containing 48% by weigh of a compound as described in  claim 23 , 45% by weight of microcrystalline cellulose, 5% by weight of low-substituted hydroxypropyl cellulose, and 2% by weight of magnesium stearate. 
     
     
         33 . A method of screening KDM4 inhibitory activity of a KDM4 inhibitory compound, in primary breast cancer stem cells comprising the steps of
 obtaining breast tumor material;   mechanically dissociating the tumor material;   treating the tumor material with at least one DNAse, dispase, or thermolysin;   diluting the tumor material in buffer;   straining the dissociated treated tumor material to obtain tumor cells;   optionally removing red blood cells with lysis buffer;   washing the tumor cells in cell culture media;   culturing the washed tumor cells in a stem cell enrichment medium comprising a 1:1 ratio of (a) liquid medium and (b) solid matrix, wherein (a) comprises:
 mammary epithelial basal medium, serum-free supplement, amphotericin, penicillin-streptomycin, epidermal growth factor, fibroblast growth factor, heparin, gentamicin, and Rho kinase inhibitor; 
   incubating the stem cell enrichment culture at 37° C. under low oxygen until the enriched cells proliferate as spheres;   expanding the population of cells that proliferated as spheres in an expansion medium comprising (a) and (b) at a 98:2 ratio, to obtain expanded breast cancer stem cells;   reculturing expanded breast cancer stem cells in stem cell enrichment medium comprising the KDM4 inhibitory compound;   wherein the KDM4 inhibitory compound inhibits the ability of breast cancer stem cells to proliferate as spheres in comparison with breast cancer stem cells recultured without a KDM4 inhibitor.   
     
     
         34 . The method of  claim 33 , wherein the KDM4 inhibitory compound having the structure of Formula I of  claim 1 .