Novel Kinase Inhibition Models and Their Uses

Abstract

The present invention provides a c-Met inhibition model. The invention further provides a method to derive inhibition models for other kinases. The kinase inhibition models of the present invention can be used to design or screen for inhibitors for kinases.

1 . A method for generating a kinase inhibition model, comprising:
 a) performing sequence alignment between the amino acid sequences of the kinase and the c-Met kinase domain of SEQ ID NO: 2;   b) identifying non-conserved amino acids between the kinase and the c-Met kinase domain;   c) replacing in the crystal structure of the c-Met kinase domain the amino acids corresponding to the non-conserved amino acids with the amino acids of the kinase corresponding to the non-conserved amino acids; and   d) refining the crystal structure with the amino acids of the kinase corresponding to the non-conserved amino acids.   
     
     
         2 . The method of  claim 1 , wherein the kinase is a tyrosine kinase. 
     
     
         3 . The method of  claim 2 , wherein the tyrosine kinase is a receptor tyrosine kinase. 
     
     
         4 . The method of  claim 3 , wherein the receptor tyrosine kinase is selected from the group consisting of EGFR, VEGFR, FGFR, PDGFR, HER2, Kit, IRK, RET, AXL, FLT-3, EphB4, c-Met homologs and c-Met mutants. 
     
     
         5 . The method of  claim 3 , wherein the receptor tyrosine kinase is FGFR-2. 
     
     
         6 . The method of  claim 2 , wherein the tyrosine kinase is a non-receptor tyrosine kinase. 
     
     
         7 . The method of  claim 6 , wherein the non-receptor tyrosine kinase is selected from the group consisting of c-Abl, Src, Fyn, Lyn and Yes. 
     
     
         8 . The method of  claim 6 , wherein the non-receptor tyrosine kinase is c-Abl. 
     
     
         9 . The method of  claim 1 , wherein the kinase is a serine/threonine kinase. 
     
     
         10 . The method of  claim 9 , wherein the serine/threonine kinase is selected from the group consisting of B-Raf, PIM, PAK, MEK, MAPK, AKT and Aurora. 
     
     
         11 . A kinase inhibition model generated according to the method of  claim 1 . 
     
     
         12 . The kinase inhibition model of  claim 11 , wherein the kinase inhibition model is a c-Abl inhibition model, comprising the crystallography coordinates of c-Abl amino acids L — 266, G — 267, Y — 271, V — 274, A — 287, V — 288, K — 289, V — 317, I — 331, T — 333, E — 334, F — 335, M — 336, T — 337, Y — 338, G — 339, N — 340, L — 388, A — 398, D — 399, F — 400, S — 403 and R — 404, wherein the crystallography coordinates are within about a root mean square deviation of not more than about 1.5 Å from the backbone atoms of the amino acids according to Table 5. 
     
     
         13 . The kinase inhibition model of  claim 11 , wherein the kinase inhibition model is a FGFR-2 inhibition model, comprising the crystallography coordinates of FGFR-2 amino acids L — 487, G — 488, F — 492, V — 495, A — 515, V — 516, K — 517, I — 548, V 562, V 564, E — 565, Y 566, A 567, S 568, K 569, G — 570, N — 571, L — 633, A — 643, D — 644, F — 645, A 648 and R — 649, wherein the crystallography coordinates are within about a root mean square deviation of not more than about 1.5 Å from the backbone atoms of the amino acids according to Table 7. 
     
     
         14 . A method comprising comparing the inhibition models of kinases generated according to the method of  claim 1 . 
     
     
         15 . The method of  claim 14 , comprising applying a weighting system. 
     
     
         16 . The method of  claim 15 , wherein the weighting system comprises positive scores for conserved residue substitutions, residues critical for ligand binding, residues with side chain lining the inhibition model, and residues which are part of backbone of the inhibition model; and negative scores for additions, deletions and changes in backbone flexibility, lack of residue alignment, dramatic changes in size and/or polarity inside the inhibition model, and lack of alignment of critical residues. 
     
     
         17 . The method of  claim 16 , wherein the positive score for residues critical for ligand binding is 2, the positive score for residues with side chain lining the inhibition model is 1, and the positive score for residues which are part of backbone of the inhibition model is 1; and the negative score for additions, deletions and changes in backbone flexibility or lack of residue alignment is −1, and the negative score for dramatic changes in size and/or polarity inside the inhibition model or lack of alignment of critical residues is −2. 
     
     
         18 . The method of  claim 16 , wherein the positive score for conserved residue substitutions is 1. 
     
     
         19 . A c-Abl inhibition model comprising the crystallography coordinates of c-Abl amino acids L — 266, G — 267, Y — 271, V — 274, A — 287, V — 288, K — 289, V — 317, I — 331, T — 333, E — 334, F — 335, M — 336, T — 337, Y — 338, G — 339, N — 340, L — 388, A — 398, D — 399, F — 400, S — 403, and R — 404 which are within about a root mean square deviation of not more than about 1.5 Å from the backbone atoms of said amino acids according to Table 5. 
     
     
         20 . An FGFR-2 inhibition model comprising the crystallography coordinates of FGFR-2 amino acids L — 487, G — 488, F — 492, V — 495, A — 515, V — 516, K — 517, I — 548, V 562, V 564, E — 565, Y 566, A 567, S 568, K 569, G — 570, N — 571, L — 633, A — 643, D — 644, F — 645, A 648, and R — 649 which are within about a root mean square deviation of not more than about 1.5 Å from the backbone atoms of said amino acids according to Table 7.