Crystal structure of liganded cFMS kinase domain

Abstract

A crystal structure of the cfms kinase domain, co-crystal structure with a bound small molecule, as well as methods of using the same in the discovery of cfms inhibitors and in the treatment of diseases mediated by inappropriate cfms activity.

We claim:  
     
         1 . A cFMS kinase domain in liganded crystalline form, comprising the amino acid sequence of SEQ ID NO: 1 or 2 and having the structural coordinates of Table 2.  
     
     
         2 . A cFMS kinase domain as claimed in  claim 1 , wherein the amino acid sequence is SEQ ID NO 1.  
     
     
         3 . A cFMS kinase domain as claimed in  claim 1 , wherein the amino acid sequence is SEQ ID NO 2.  
     
     
         4 . A cFMS kinase domain as claimed in  claim 1 , wherein the liganded cFMS kinase domain in crystalline form has lattice constants of a=80 A, b=80 A, and c=78 A, α=90°, β=90°, and γ=90°.  
     
     
         5 . A cFMS kinase domain as claimed in  claim 1 , wherein said liganded cFMS kinase in crystalline form has a spacegroup of R3.  
     
     
         6 . A cFMS kinase domain as claimed in  claim 1 , wherein said liganded cFMS kinase in crystalline form has an entire NT region which is ordered.  
     
     
         7 . A method of cFMS inhibitor design, comprising: 
 generating a three dimensional computer model which represents a cFMS kinase domain in liganded form, said kinase domain described by the amino acid sequence of SEQ ID NO: 1 or 2 and having the structural coordinates of Table 2;    evaluating compounds as potential cFMS inhibitors using said model; and    selecting compounds for further testing based on said evaluation.    
     
     
         8 . A method of cfms inhibitor design, comprising: 
 generating a three dimensional computer model which represents a cfms kinase domain in liganded form, said kinase domain described by the amino acid sequence of SEQ ID NO: 1 or 2 and having the structural coordinates of Table 2;    evaluating compounds as potential cFMS inhibitors using said model; wherein said evaluation comprises identifying compounds capable of at least one of the following cFMS kinase domain/compound interactions: 
 (i) one or more interactions with amino acid residues of the cFMS kinase domain hinge region;  
 (ii) one or more interactions with amino acid residues of the cFMS kinase domain adenine pocket,  
 (iii) one or more interactions with amino acid residues of the cFMS kinase sugar pocket and phosphate region,  
 (iv) one or more interactions with amino acid residues of the cFMS kinase domain back pocket, and  
 (v) one or more interactions with amino acid residues of the cFMS kinase domain solvent interface; and  
   selecting compounds for further testing based on said evaluation.    
     
     
         9 . A method of cfms inhibitor design, comprising: 
 generating a three dimensional computer model which represents a cfms kinase domain in liganded form, said kinase domain described by the amino acid sequence of SEQ ID NO: 1 or 2 and having the structural coordinates of Table 2;    evaluating compounds as potential cFMS inhibitors using said model; wherein said evaluation comprises identifying compounds capable of at least one of the following cFMS kinase domain/compound interactions: 
 (i) one or more interactions with amino acid residues 663, 664, 665, 666, 667, 668, and 669;  
 (ii) one or more interactions with amino acid residues 588, 614, 647, and 785,  
 (iii) one or more interactions with amino acid residues 596 and 797 and/or one or more hydrogen bonding interactions with amino acid residue residue 796,  
 (iv) one or more interactions with amino acid residues 550, 640, 646, 769, and 776, and  
 (v) one or more interactions with residues 668 and 672; and  
   selecting compounds for further testing based on said evaluation.    
     
     
         10 . A method of treating a disorder characterized by inappropriate cfms activity in a mammal, comprising: administering to said mammal a therapeutically effective amount of a compound that can form a complex with a cfms kinase domain thereby resulting in a cfms kinase domain in liganded form, said kinase domain in liganded form being described by the amino acid sequence of SEQ ID NO: 1 or 2 and the structural coordinates of Table 2, wherein said complex is characterized by at least one of the following cfms kinase domain/compound interactions: 
 (i) one or more interactions with amino acid residues of the cFMS kinase domain hinge region;    (ii) one or more interactions with amino acid residues of the cFMS kinase domain adenine pocket,    (iii) one or more interactions with amino acid residues of the cFMS kinase sugar pocket and phosphate region,    (iv) one or more interactions with amino acid residues of the cFMS kinase domain back pocket, and    (v) one or more interactions with amino acid residues of the cFMS kinase domain solvent interface.    
     
     
         11 . A method of inhibiting cfms in a mammal, comprising: administering to said mammal a therapeutically effective amount of a compound that can form a complex with a cfms kinase domain thereby resulting in a cfms kinase domain in liganded form, said kinase domain in liganded form being described by the amino acid sequence of SEQ ID NO: 1 or 2 and the structural coordinates of Table 2, wherein said complex is characterized by at least one of the following cfms kinase domain/compound interactions: 
 (i) one or more interactions with amino acid residues of the cFMS kinase domain hinge region;    (ii) one or more interactions with amino acid residues of the cFMS kinase domain adenine pocket,    (iii) one or more interactions with amino acid residues of the cFMS kinase sugar pocket and phosphate region,    (iv) one or more interactions with amino acid residues of the cFMS kinase domain back pocket, and    (v) one or more interactions with amino acid residues of the cFMS kinase domain solvent interface.    
     
     
         12 . A cFMS kinase domain/inhibitor complex which includes a cFMS liganded kinase domain described by the amino acid sequence of SEQ ID NO: 1 or 2 and the structural coordinates of Table 2 and a compound capable of at least one of the following interactions with the cFMS kinase domain: 
 (i) one or more interactions with amino acid residues of the cFMS kinase domain hinge region;    (ii) one or more interactions with amino acid residues of the cFMS kinase domain adenine pocket,    (iii) one or more interactions with amino acid residues of the cFMS kinase sugar pocket and phosphate region,    (iv) one or more interactions with amino acid residues of the cFMS kinase domain back pocket, and    (vii) one or more interactions with amino acid residues of the cFMS kinase domain solvent interface.    
     
     
         13 . A compound of formula (I):  
       
         
           
           
               
               
           
         
       
       or a salt, solvate, or physiologically functional derivative thereof:  
       wherein 
 R 1  is —H or C 1 -C 6  alkyl;  
 R 2  is —H, C 1 -C 6  alkyl, C 3 -C 7  cycloalkyl, aryl, heterocyclyl, heteroaryl, or —(CH 2 ) p R 6 ;  
 n is 1 or 2;  
 p is 1, 2, or 3;  
 R 3  is —H or C 1 -C 6  alkoxy;  
 R 4  is C 1 -C 6  alkyl, C 1 -C 6  alkenyl, C 1 -C 6  alkoxy, -halo, C 1 -C 6  haloalkyl, C 1 -C 6  haloalkoxy, aryl, —SR 5 , or n is 2 and each R 4  together with the phenyl ring to which they are attached form the group  
                     
 R 5  is C 1 -C 6  alkyl; and  
 R 6  is NR 5 R 5 , heterocyclyl, aryl, or heteroaryl.  
 
     
     
         14 . A pharmaceutical composition, comprising a a therapeutically effective amount of a compound as claimed in  claim 13 , or a salt, solvate, or a physiologically functional derivative thereof and one or more of pharmaceutically acceptable carriers, diluents and excipients.