Small Molecule Choline Kinase Inhibitors, Screening Assays, and Methods for Safe and Effective Treatment of Neoplastic Disorders

Abstract

Small molecule choline kinase inhibitors, pharmaceutical compositions thereof, and screening methods for identifying and evaluating choline kinase inhibitors are provided. Safe and effective methods for treating subjects suffering from a disorder or disease characterized by neoplastic cell proliferation employing the choline kinase inhibitors are also provided.

1 . A method of treating a subject suffering from a disorder or disease characterized by neoplastic cell proliferation, the method comprising administering to the subject a therapeutically effective amount of a selective choline kinase (ChoK) inhibitor, wherein the ChoK inhibitor is selected from compounds having the following structural formula: 
       
         
           
           
               
               
           
         
         wherein Het can be a substituted or unsubstituted bivalent heterocyclic group, L 1  can be a bond, or substituted or unsubstituted bivalent C 1 -C 2  alkane, L 1  can be straight-chained or branched-chain, L 2  can be a substituted or unsubstituted bivalent C 3 -C 5  alkane, where one or more of the carbons of the bivalent C 3 -C 5  alkane can be replaced with one or more heteroatoms, such as N, S, O, or P; L 2  can be straight-chained or branched-chain; A 1  and A 2  can be the same or different and can be substituted or unsubstituted aryl groups or substituted or unsubstituted aromatic heterocyclic groups; or 
       
       
         
           
           
               
               
           
         
         wherein L 3  can be a substituted or unsubstituted bivalent C 1 -C 3  alkane, where one or more of the carbons of the bivalent C 1 -C 3  alkane can be replaced with one or more heteroatoms, such as N, S, O, or P, and L 3  can be straight-chained or branched-chained; L 4  can be a substituted or unsubstituted bivalent C 1 -C 4  alkane, where one or more of the carbons of the bivalent C 1 -C 4  alkane can be replaced with one or more heteroatoms, such as N, S, O, or P; L 4  can be straight-chained or branched-chained; A 3  and A 4  can be the same or different and can be substituted or unsubstituted aryl groups or substituted or unsubstituted aromatic heterocycle groups (e.g., univalent radicals of indole, benzofuran, benzothiophene, naphthalene, quinoline, pyridine, or thiophene); L 5  can be the substituted or unsubstituted bivalent 
       
       
         
           
           
               
               
           
         
       
       where X 1  can be C, or N, S, O, or P; and X 2  can be N, S, O, P, or C; and X 1  can be the same as or different from X 2 . 
     
     
         2 . The method according to  claim 1 , wherein the disease comprises tumor cell proliferation. 
     
     
         3 . The method according to  claim 2 , wherein the tumor is a lung, breast, colorectal, pancreatic, cervical or ovarian tumor. 
     
     
         4 . The method according to  claim 1 , wherein the compound directly inhibits ChoK by interacting with a phosphocholine binding pocket of ChoK. 
     
     
         5 . The method according to  claim 1 , wherein Formula (I) is: 
       
         
           
           
               
               
           
         
         including the 1H, 2H, and 4H (1, 2, 4-triazole) tautomers thereof. 
       
     
     
         6 . The method according to  claim 5 , wherein Formula (I) is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
       and mixtures thereof. 
     
     
         7 . The method according to  claim 1 , wherein Formula (II) is 
       
         
           
           
               
               
           
         
       
     
     
         8 . The method according to  claim 1 , wherein Formula (II) is 
       
         
           
           
               
               
           
         
       
     
     
         9 . The method according  claim 1 , wherein the selective ChoK inhibitor is a compound selected from Table 1, or an isomer, tautomer, pharmaceutically acceptable salt or prodrug thereof. 
     
     
         10 . A ChoK inhibitor selected from the compounds set forth in Table 3. 
     
     
         11 . The method according to  claim 1 , wherein the selective ChoK inhibitor is a compound selected from Table 2 or Table 3, or an isomer, tautomer, pharmaceutically acceptable salt or prodrug thereof. 
     
     
         12 . A pharmaceutical composition comprising a compound selected from Table 1, or an isomer, tautomer, pharmaceutically acceptable salt or prodrug thereof, together with a pharmaceutically acceptable carrier. 
     
     
         13 . A pharmaceutical composition comprising a compound selected from Table 2, or an isomer, tautomer, pharmaceutically acceptable salt or prodrug thereof, together with a pharmaceutically acceptable carrier. 
     
     
         14 . A pharmaceutical composition comprising a compound selected from Table 3, or an isomer, tautomer, pharmaceutically acceptable salt or prodrug thereof, together with a pharmaceuctially acceptable carrier. 
     
     
         15 . A method of treating a subject suffering from a disorder or disease benefited by suppressing cellular apoptosis, the method comprising administering to the subject an amount of a choline kinase inhibitor effective to suppress cellular apoptosis. 
     
     
         16 . A method for identifying a compound that directly modulates ChoK activity, the method comprising: a) obtaining a crystal structure of ChoK or obtaining information relating to a crystal structure of ChoK, and b) modeling a test compound into or on the crystal structure coordinates to determine whether the compound binds to ChoK, wherein modeling comprises determining the ability of the compound to bind to or associate with a choline (Cho) binding pocket of ChoK defined by structural coordinates of one or more ChoK amino acid residues forming the Cho binding pocket. 
     
     
         17 . The method according to  claim 16 , wherein the crystal structure is of a splice isoform of choline kinase-a and the amino acid residues forming the Cho binding pocket include amino acid residues 116-124, 146, 256, 305-306, 308, 310-311, 323, 330, 332, 333, 345, 348-349, 354, 416, 420, 422-423, 427, 440, and 444 of the amino acid sequence set forth as SEQ ID NO: 1. 
     
     
         18 . A method for identifying a compound that directly modulates ChoK activity, the method comprising using atomic coordinates of one or more of ChoK amino acid residues to generate a three-dimensional structure of a molecule comprising a Cho binding pocket of ChoK, and employing the three-dimensional structure to identify a compound that directly modulates the activity of ChoK. 
     
     
         19 . The method according to  claim 1 , wherein administering comprises employing a drug delivery technology capable of delivering the ChoK inhibitor to the tumor. 
     
     
         20 . The method according to  claim 1 , wherein the ChoK inhibitor is administered in a dose effective to suppress cell proliferation in the substantial absence of toxic side effects. 
     
     
         21 . The method according to  claim 20 , wherein the ChoK inhibitor is selected from N-(3,5-dimethylphenyl)-2-[[5-(4-ethylphenyl)-1H-1,2,4-triazol-3-yl]sulfanyl]acetamide, N-(3,5-dimethylphenyl)-2-[[5-(4-ethylphenyl)-2H-1,2,4-triazol-3-yl]sulfanyl]acetamide, N-(3,5-dimethylphenyl)-2-[[5-(4-ethylphenyl)-4H-1,2,4-triazol-3-yl]sulfanyl]acetamide, mixtures thereof, and [(2R)-1-(naphthalen-1-ylamino)-1-oxopropan-2-yl]2-(4-methoxyphenoxy)acetate.