Analysis of c-Met kinase domain complexes: A new specific catalytic site receptor model for defining binding modes of atp-competitive ligands

Chemical Biology and Drug Design

Volumn 74, Issue 6, 2009, Pages 560-570

  Asses, Yasmine ^a   Leroux, Vincent ^a   Tairi Kellou, Safia ^b   Dono, Rosanna ^c   Maina, Flavio ^c   Maigret, Bernard ^a  

^a UNIVERSITÉ DE LORRAINE   (France)

^b UNIVERSITY OF SCIENCES AND TECHNOLOGY HOUARI BOUMEDIENE   (Algeria)

^c AIX MARSEILLE UNIVERSITÉ   (France)

Author keywords

Allosteric interactions; ATP binding site; C Met; Kinase inhibitors; Ligand binding modes; Molecular modeling; Protein receptor model; Protein ligand complexes; Structure based drug design

Indexed keywords

IMATINIB; SCATTER FACTOR RECEPTOR;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; DRUG BINDING; DRUG DESIGN; LIGAND BINDING; MOLECULAR MECHANICS; MOLECULAR MODEL; PRIORITY JOURNAL;

ADENOSINE TRIPHOSPHATE; ALLOSTERIC REGULATION; AMINO ACID SEQUENCE; ANTINEOPLASTIC AGENTS; CATALYTIC DOMAIN; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; LIGANDS; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN KINASE INHIBITORS; PROTEIN STRUCTURE, SECONDARY; PROTO-ONCOGENE PROTEINS C-MET;

EID: 70350544043     PISSN: 17470277     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2009.00895.x     Document Type: Article

References (50)

1. Birchmeier B., Birchmeier W., Gherardi E., Vande Woude G.F. (2003) MET, metastasis, motility and more. Nat Rev Mol Cell Biol 4 : 915 925.
2. Ma P.C., Maulik G., Christensen J., Salgia R. (2003) c-Met: structure, functions and potential for therapeutic intervention. Cancer Met Rev 22 : 309 325.
3. Michalopoulos G.K., DeFrances M.C. (1997) Liver regeneration. Science 276 : 60 66.
4. Birchmeier C., Gherardi E. (1998) Developmental roles of HGF/SF and its receptor, the c-Met tyrosine kinase. Trends Cell Biol 8 : 404 410.
5. Maina F., Panté G., Helmbacher F., Andres R., Porthin A., Davies A.M., Ponzetto C., Klein R. (2001) Coupling Met to specific pathways results in distinct developmental outcomes. Mol Cell 7 : 1293 1306.
6. Chmielowiec J., Borowiak M., Morkel M., Stradal T., Munz B., Werner S., Wehland J., Birchmeier C., Birchmeier W. (2007) c-Met is essential for would healing in the skin. J Cell Biol 177 : 151 162.
7. Maulik G., Shrikhande A., Kijima T., Ma P.C., Morrison P.T., Salgia R. (2002) Role of the hepatocyte growth factor receptor, c-Met, in oncogenesis and potential for therapeutic inhibition. Cytokine Growth Factor Rev 13 : 41 59.
8. Christensen J.G., Burrows J., Salgia R. (2005) c-Met as a target for human cancer and characterization of inhibitors for therapeutic intervention. Cancer Lett 225 : 1 26.
9. Zhang Y.-W., Vande Woude G.F. (2003) HGF/SF-Met signaling in the control of branching morphogenesis and invasion. J Cell Biochem 88 : 408 417.
10. Mazzone M., Comoglio P.M. (2006) The Met pathway: master switch and drug target in cancer progression. FASEB J 20 : 1611 1621.
11. Gentile A., Trusolino L., Comoglio P.M. (2008) The Met tyrosine kinase receptor in development and cancer. Cancer Met Rev 27 : 85 94.
12. Engelman J.A., Zejnullahu K., Mitsudomi T., Song Y., Hyland C., Park J.O., Lindeman N. et al. (2007) MET amplification leads to Gefitinib resistance in lung cancer by activating ERBB3 signaling. Science 316 : 1039 1043.
13. Shattuck D.L., Miller J.K., Carraway K.L., Sweeney C. (2008) Met receptor contributes to trastuzumab resistance of Her2-overexpressing breast cancer cells. Cancer Res 68 : 1471 1477.
14. Guo A., Villén J., Kornhauser J., Lee K.A., Stokes M.P., Rikova K., Possemato A. et al. (2008) Signaling networks assembled by oncogenic EGFR and c-Met. PNAS 105 : 692 697.
15. Shen Y., Naujokas M., Park M., Ireton K. (2000) InlB-dependent internalization of listeria is mediated by the Met receptor tyrosine kinase. Cell 103 : 501 510.
16. Cunha-Rodrigues M., Prudêncio M., Mota M.M., Haas W. (2006) Antimalarial drugs - host targets (re)visited. Biotechnol J 1 : 321 332.
17. Knudsen B.S., Vande Woude G.F. (2008) Showering c-MET-dependent cancers with drugs. Curr Opin Genet Dev 18 : 87 96.
18. Cui J.J. (2007) Inhibitors targeting hepatocyte growth factor receptor and their potential therapeutic applications. Expert Opin Ther Pat 17 : 1035 1045.
19. Druker B.J., Talpaz M., Resta D.J., Peng B., Buchdunger E., Ford J.M., Lydon N.B., Kantarjian H., Capdeville R., Ohno-Jones S., Sawyers C.L. (2001) Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. N Engl J Med 344 : 1031 1037.
20. Capdeville R., Buchdunger E., Zimmermann J., Matter A. (2002) Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug. Nat Rev Drug Discov 1 : 493 502.
21. Brehmer D., Greff Z., Godl K., Blencke S., Kurtenbach A., Weber M., Müller S., Klebl B., Cotten M., Kéri G., Wissing J., Daub H. (2005) Cellular targets of Gefitinib. Cancer Res 65 : 379 382.
22. Koshland D.E. (1994) The key-lock theory and the induced fit theory. Angew Chem 33 : 2375 2378.
23. Dussault I., Bellon S.F. (2008) c-Met inhibitors with different binding modes. Two is better than one. Cell Cycle 7 : 1157 1160.
24. Miller J.R., Dunham S., Mochalkin I., Banotai C., Bowman M., Buist S., Dunkle B. et al. (2009) A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore. PNAS 106 : 1737 1742.
25. Knighton D.R., Zheng J.H., Ten Eyck L.F., Ashford V.A., Xuong N.H., Taylor S.S., Sowadski J.M. (1991) Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science 253 : 407 414.
26. Knighton D.R., Zheng J.H., Ten Eyck L.F., Xuong N.H., Taylor S.S., Sowadski J.M. (1991) Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science 253 : 414 420.
27. Furet P., Caravatti G., Lydon N., Priestle J.P., Sowadski J.M., Trinks U., Traxler P. (1995) Modelling study of protein kinase inhibitors: binding mode of staurosporine and origin of the selectivity of CGP 52411. J Comput Aided Mol Des 9 : 465 472.
28. Traxler P., Furet P. (1999) Strategies toward the design of novel and selective protein tyrosine kinase inhibitors. Pharmacol Ther 82 : 195 206.
29. Schindler T., Bornmann W., Pellicena P., Miller W.T., Clarkson B., Kuriyan J. (2000) Structural mechanism for STI-571 inhibition of Abelson tyrosine kinase. Science 289 : 1938 1942.
30. Cowan-Jacob S.W., Fendrich G., Floersheimer A., Furet P., Liebetanz J., Rummel G., Rheinberger P., Centeleghe M., Fabbro D., Manley P.W. (2007) Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia. Acta Crystallogr 63 : 80 93.
31. Liu Y., Gray N.S. (2006) Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol 2 : 358 364.
32. Kinnings S.L., Jackson R.M. (2009) Binding site similarity analysis for the functional classification of the protein kinase family. J Chem Inf Model 49 : 318 329.
33. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. (2000) The Protein Data Bank. Nucleic Acids Res 28 : 235 242.
34. Kabsch W., Sander C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 : 2577 2637.
35. Frishman D., Argos P. (1995) Knowledge-based protein secondary structure assignment. Proteins 23 : 566 579.
36. Humphrey W., Dalke A., Schulten K. (1996) VMD: visual molecular dynamics. J Mol Graph 14 : 33 38.
37. Ghose A.K., Herbertz T., Pippin D.A., Salvino J.M., Mallamo J.P. (2008) Knowledge based prediction of ligand binding modes and rational inhibitor design for kinase drug discovery. J Med Chem 51 : 5149 5171.
38. Sánchez R., Sali A. (1997) Advances in comparative protein-structure modelling. Curr Opin Struc Biol 7 : 206 214.
39. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kalé L., Schulten K. (2005) Scalable molecular dynamics with NAMD. J Comp Chem 26 : 1781 1802.
40. MacKerell A.D. Jr., Bashford D., Bellott M., Dunbrack R.L., Evanseck J.D., Field M.J., Fischer S. et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102 : 3586 3616.
41. Momany F.A., Rone R. (1992) Validation of the general purpose QUANTA 3.2/CHARMm force field. J Comp Chem 13 : 888 900.
42. Leroux V., Gresh N., Liu W.-Q., Garbay C., Maigret B. (2007) Role of water molecules for binding inhibitors in the SH2 domain of Grb2: a molecular dynamics study. J Mol Struc-Theochem 806 : 51 66.
43. Patané S., Pietrancosta N., Hassani H., Leroux V., Maigret M., Kraus J.-L., Dono R., Maina F. (2008) A new Met inhibitory-scaffold identified by a focused forward chemical biological screen. Biochem Biophys Res Comm 375 : 184 189.
44. Déliot N., Chavent M., Nourry C., Lécine P., Arnaud C., Hermant A., Maigret B., Borg J.-P. (2009) Biochemical studies and molecular dynamics simulations of Smad3-Erbin interaction identify a non-classical Erbin PDZ binding. Biochem Biophys Res Comm 378 : 360 365.
45. Hanks S.K., Quinn A.M., Hunter T. (1988) The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science 241 : 42 52.
46. Hanks S.K., Hunter T. (1995) The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J 9 : 576 596.
47. Hanks S.K. (2003) Genomic analysis of the eukaryotic protein kinase superfamily: a perspective. Genome Biol 4 : 111.
48. Moretti L. (2007) Exploring Structure and Plasticity of Tyrosine Kinase Domains for Drug Discovery. PhD thesis. Université de Genève.
49. Jacobs M.D., Caron P.R., Hare B.J. (2008) Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: structure of lck/imatinib complex. Proteins 70 : 1451 1460.
50. Vieth M., Higgs R.E., Robertson D.H., Shapiro M., Gragg E.A., Hemmerle H. (2004) Kinomics - structural biology and chemogenomics of kinase inhibitors and targets. Biochim Biophys Acta 1697 : 243 257.