Inhibitors of protein arginine deiminases (pads) and methods of preparation and use thereof

Abstract

The invention provides novel inhibitors or inactivators of protein arginine deiminases, pharmaceutical compositions and methods of use thereof. The invention also relates to molecular probes based on such compounds and methods of use thereof.

1 - 37 . (canceled) 
     
     
         38 . A molecular imaging probe having the structural formula:
   A F -L F -W   (II)
   
       wherein
 A F  is a group comprising an optically detectable moiety; 
 L F  is a linking group; and 
 W is group comprising a benzimidazole moiety, or a derivative or analog thereof, capable of inhibiting or inactivating a biological function of a protein arginine deiminase. 
 
     
     
         39 . The molecular imaging probe of  claim 38 , wherein A F  is a group comprising a fluorophore. 
     
     
         40 . The molecular imaging probe of  claim 39 , wherein the fluorophore is selected from the group consisting of xanthene dyes, cyanine dyes, coumarin dyes and bodipy dyes. 
     
     
         41 . The molecular imaging probe of  claim 40 , wherein the fluorophore is a xanthene dye selected from the group consisting of fluorescein, eosins, and rhodamines. 
     
     
         42 . The molecular imaging probe of  claim 40  wherein the fluorophore is a cyanine dye. 
     
     
         43 . The molecular imaging probe of  claim 40 , wherein the fluorophore is a coumarin dye. 
     
     
         44 . The molecular imaging probe of  claim 40 , wherein the fluorophore is a bodipy dye. 
     
     
         45 . The molecular imaging probe of  claim 38 , wherein the protein arginine deiminase is selected from the group consisting of: PAD1, PAD2, PAD3 and PAD4. 
     
     
         46 . The molecular imaging probe of  claim 45 , wherein the protein arginine deiminase is PAD2. 
     
     
         47 . The molecular imaging probe of  claim 45 , wherein the protein arginine deiminase is PAD4. 
     
     
         48 . The molecular imaging probe of  claim 38 , wherein W is a monovalent radical derived from a compound having the structural formula: 
       
         
           
           
               
               
           
         
       
       wherein,
 each of R a  and R b  is independently selected from the group consisting of H, D and F; 
 L is a bivalent hydrocarbyl linker, optionally with one or more carbon atoms replaced by a heteroatom selected from the group consisting of O, S and N; 
 X is a halogen atom; 
 Y is N, O or S; provided that when Y is S or O, its bonding to the adjacent carbons are single bonds; 
 Z is N—R 1 , O or S; 
 R 1  is selected from the group consisting of: H, a C 1-6  alkyl, OH, a C 1-3  alkoxy, CF 3 , COCH 3 , and COCF 3  groups; 
 each of R 2 , R 3 , R 4  and R 5  is independently selected from the group consisting of: H, hydroxyl, halogen atom, C 1-6  alkyl, C 1-6  alkoxy, alkynyl, CF 2 R c  and OCF 2 R c  groups, where R c  is H, F or alkyl; and 
 R 6  is a group comprising a cyclic alkyl or aryl moiety. 
 
     
     
         49 . A method for identifying a protein arginine deiminase inhibitor or inactivator, comprising:
 performing a competitive assay wherein a test compound competes with a molecular imaging probe according to  claim 38  to bind to a protein arginine deiminase; and   measuring fluorescence to determine an amount of fluorescent protein arginine deiminase present in the test assay.   
     
     
         50 . The method of  claim 49 , further comprising:
 performing a control assay wherein the molecular imaging probe binds to the protein arginine deiminase; and   measuring fluorescence to determine an amount of fluorescent protein arginine deiminase present in the control assay.   
     
     
         51 . The method of  claim 50 , wherein a change in fluorescence in the assay greater than a pre-selected value when compared to the control assay is indicative that the test compound is an inhibitor to the protein arginine deiminase. 
     
     
         52 . The method of  claim 50 , wherein the change in fluorescence in the assay is a decrease in fluorescence in the assay.