QSAR models for predicting the similarity in binding profiles for pairs of protein kinases and the variation of models between experimental data sets

Journal of Chemical Information and Modeling

Volumn 49, Issue 8, 2009, Pages 1974-1985

  Sheridan, Robert P ^a   Nam, Kiyean ^a   Maiorov, Vladimir N ^a   McMasters, Daniel R ^a   Cornell, Wendy D ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DECISION TREES; ENZYMES; FORECASTING; MOLECULAR GRAPHICS; PREDICTIVE ANALYTICS;

ACTIVE SITE; ATP-BINDING SITE; BINDING PROFILES; CROSS VALIDATION; HUMAN GENOMES; INDIVIDUAL MODELS; PROTEIN KINASE; RANDOM FOREST MODELING;

COMPUTATIONAL CHEMISTRY;

PROTEIN KINASE; PROTEIN KINASE INHIBITOR;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; METABOLISM; PROTEIN BINDING; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

BINDING SITES; HUMANS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN KINASE INHIBITORS; PROTEIN KINASES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 69549121940     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900176y     Document Type: Article

References (40)

1. Manning, G.; Whyte, D. B.; Martinez, R.; Hunter, T.; Sudarsanam, S. The protein kinase complement of the human. Science 2002, 298, 1912-1934.
2. Bain, J.; Cummings, L.; Elliot, M; Shpiro, N.; Hastie, J.; McLauchian, H.; Klevernic, L; Arthur, S.; Alessi, D.; Cohen, P. The selectivity of protein kinase inhibitors; a further update. Biochem. J. 2007,48, 297-315.
3. Bamborough, P.; Drewry, D.; Harper, G.; Smith, G. K.; Schneider, K. Assessment of chemical coverage of kinome space and its implications for kinase drug discovery. J. Med. Chem. 2008, 57, 7998-17914
4. Federov, O.; Marsden, B.; Pogacic, V.; Rellos, P.; Muller, S.; Bullock, A. N.; Schwaller, J.; Sundstrom, M.; Knapp, S. A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases. Proc. Natl. Acad. Sci. U S. A. 2007, 104, 20523-20528.
5. Karaman, M. W.; Herrgard, S.; Treiber, D. K.; Gallant, P.; Atteridge, C. E.; Campbell, B. T.; Chan, K. W.; Cicerci, P.; Davis, M. I.; Edeen, P. T.; Faraóni, R.; Floyd, M.; Hunt, J. P.; Lockhart, D. J.; Milanov, Z. V.; Morrison, M. J.; Pallares, G.; Patel, H. K.; Pritchard, S.; Wodicka, L. M.; Zarrinkar, P. P. A quantitative analysis of kinase inhibitor selectivity. Nat. Biotechnol. 2008, 26, 127-132.
6. Melnick, J. S.; Janes, J.; Kim, S.; Chang, J. Y.; Sipes, D. G.; Gunderson, D.; Jarnes, L.; Matzen, J. T.; Garcia, M. E.; Hood, T. L.; Beigi, R.; Xia, G.; Harig, R. A.; Asatryan, H.; Yan, S. F.; Zhou, Y.; Gu, X.-J.; Saadat, A.; Zhou, V.; King, F. J.; Shaw, C. M.; Su, A. I.; Downs, R.; Gray, N. S.; Schultz, P. G.; Warmuth, M.; Caldwell, J. S. An efficient rapid system for profiling the cellular activities of molecular libraries. Proc. Natl. Acad. U. S. A. 2006, 103, 3153-3158.
7. (7) Bonn, S.; Herrero, S; Breitenlechner, C. B.; Erlbruch, A.; Lehmann, W.; Engh, R. A.; Gassel, M.; Bossemeyer, D. Structural analysis of protein kinase A mutants with rho-kinase inhibitor specificity. Biol. Chem. 2006, 287, 24818-24830. (Pubitemid 44274255)
8. Cheney, I. W.; Yan, S.; Appleby, T.; Walker, H.; Vo, T.; Yao, N.; Hamatake, R.; Hong, Z.; Wu, J. Z. Identification and structure-activity relationships of substituted pyridones as inhibitors of Pim-1 kinase. Bioorg. Med. Chem. Lett. 2007, 77, 1679-1683.
9. Cherry, M.; Williams, D. H. Recent kinase and kinase inhibitor X-ray structures: Mechanisms of inhibition and selectivity insights. Curr. Med. Chem. 2004, 77, 663-673.
10. (10) Cohen, M. S.; Zhang, C.; Shokat, K. M.; Taunton, J. Structural bioinformatics-based design of selective, irreversible kinase inhibitors. Science 2005, 308, 1318-1321. (Pubitemid 40746129)
11. (11) Debreczeni, J. E.; Bullock, A. N.; Atilla, G. E.; Williams, D. S.; Bregman, H.; Knapp, S.; Meggers, E. Ruthenium half-sandwich complexes bound to protein kinase Pim-1. Angew. Chem., Int. Ed. 2006, 45, 1580-1585. (Pubitemid 44109229)
12. Emrick, M. A.; Lee, T.; Starkey, P. J.; Mumby, M. C.; Resing, K. A.; Ahn, N. G. The gatekeeper residue controls autoactivation of ERK2 via a pathway of intramolecular connectivity. Proc. Natl. Acad. SCi U. S. A 2006, 103, 18101-18106.
13. (13) Fitzgerald, C. E.; Patel, S. B.; Becker, J. W.; Cameron, P. M.; Zaller, D.; Pikounis, V. B.; O'Keefe, S. J.; Scapin, G. Structural basis for p38a MAP kinase quinazolinone and pyridol-pyrimidine inhibitor specificity. Nat. Struct. Biol. 2003, 70, 764-769. (Pubitemid 37052417)
14. Goldberg, D. R.; Hao, M.-H.; Qian, K. C.; Swinamer, A. D.; Gao, D. A.; Xiong, Z.; Sarko, C.; Berry, A.; Lord, J.; Magolda, R. L.; Fadra, T.; Kroe, R. R.; Kukula, A.; Madwed, J. B.; Martin, L.; Pargellis, C.; Skow, D.; Song, J. J.; Tan, Z.; Torcelli, C. A.; Zimmitti, C. S.; Yee, N. K.; Moss, N. Discovery and optimization of p38 inhibitors via computer-assisted drug design. J. Med. Chem. 2007, 50, 4016-4026.
15. Hamdouchi, C.; Zhong, B.; Mendoza, J.; Collins, E.; Jaramillo, C.; De Diego, J. E.; Robertson, D.; Spencer, C. D.; Anderson, B. D.; Watkins, S. A.; Zhang, F.; Brooks, H. B. Structure-based design of a new class of highly selective aminoimiazo[l,2-a]pyridine-based inhibitors of cyclin dependent kinases. Bioorg. Med Chem. Lett. 2005, 75, 1943-1947.
16. Kothe, M.; Kohls, D.; Low, S.; Coli, R.; Rennie, G. R.; Feru, F.; Kuhn, C.; Ding, Y.-H. Selectivity-determining residues in Plkl. Chem. Biol. Drug Des. 2007, 70, 540-546.
17. (17) Myrianthopoulos, V.; Magiatis, P.; Ferandin, Y.; Skalt Sounis, A. J.; Meijer, L.; Mikros, E. A integrated computational approach to the phenomenon of potent and selective inhibition of Aurora kinases B and C by a series of 7-substituted indirubins. J. Med. Chem. 2007, 50, 4027-4037. (Pubitemid 47301735)
18. Pande, V.; Ramos, M. J. Structural basis for the GSK-3b binding affinity and selectivity against CDK-2 of l-(4-aminofurazan-3yl)-5dialkylaminomethyl-l-H- [l,2,3] triazole-4-carboxylic acid derivatives. Biorg. Med. Chem. Lett. 2005, 15, 5129-5135.
19. Azam, M.; Seeliger, M. A.; Gray, N. S.; Kuriyan, J.; Daley, G. Q. Activation of tyrosine kinases by mutation of the gatekeeper threonine. Nat. Struct. Mol. Biol. 2008, 75, 1109-1118.
20. Aronov, A. M.; Murcko, M. A. Toward a pharmacophore for kinase frequent hitters. J. Med Chem. 2004, 47, 5616-5619.
21. Aronov, A. M.; McClain, B.; Moody, C. S.; Murcko, M. A. Kinaselikeness and kinase-privileged fragments: Toward a virtual polypharmacology. J. Med. Chem. 2008, 57, 1214-1222.
22. Sprous, D. G.; Zhang, J.; Zhang, L.; Wang, Z.; Tepper, M. A. Kinase inhibitor recognition by use of a multivariable QSAR model. J. Mol. Graph. Model. 2006, 24, 278-295.
23. (23) Sutherland, J. J.; Higgs, R. E.; Watson, I.; Vieth, M. Chemical fragments as foundations for understanding target space and activity prediction. J. Med. Chem. 2008, 57, 2689-2700. (Pubitemid 351620791)
24. Gozalbes, R.; Simon, L.; Froloff, N.; Sartori, E.; Monteils, C.; Baudelle, R. Development and experimental validation of a docking strategy for the generation of kinase-targeted libraries. J. Med. Chem. 2008, 57, 3124-3132.
25. Muegge, I.; Enyedy, I. J. Virtual screening for kinase targets. Curr. Med. Chem. 2004, 11, 693-707.
26. Rockey, W. M.; Elcock, A. H. Rapid computational identification of the targets of protein kinase inhibitors. J. Med. Chem. 2005,48, 4138-4152.
27. (27) Zahler, S.; Tietze, S.; Totzke, F.; Kubbutat, M.; Meijer, L; Vollmar, A. M.; Apostolakis, J. Inverse in silico screening for identification of kinase inhibitor targets. Chem. Biol. 2007, 14, 1207-1214. (Pubitemid 350102244)
28. Heady, L.; Fernandez-Serra, M.; Mancera, R. L.; Joyce, S.; Venkitaraman, A. R.; Artacho, E.; Skylarkis, C.-K.; Ciacchi, L. C.; Payne, M. C. Novel structural features of CDK inhibition revealed by ab initio computational method combined with dynamic simulations. J. Med. Chem. 2006, 49, 5141-5153.
29. (29) Sheinerman, F. B.; Giraud, E.; Laoui, A. High affinity targets of protein kinase inhibitors have similar residues at the positions energetically important for binding. J. Mol. Biol. 2005, 352, 1134-1156. (Pubitemid 41316721)
30. (30) Chen, J.; Zhang, X.; Fernandez, A. Molecular basis for specificity in the druggable kinome: Sequence-based analysis. Bioinformatics 2007, 23, 563-572. (Pubitemid 46522589)
31. Kinnings, S. L.; Jackson, R. M. Binding site similarity analysis for the functional classification of the protein kinase family. J. Chem. Inf. Model. 2009, 49, 318-329.
32. Sciabola, S.; Stanton, R. V.; Wittkopp, S.; Wildman, S.; Moshinsky, D.; Potluri, S; Xi, H. Predicting kinase selectivity profiles using FreeWilson QSAR analysis. J. Chem. Inf. Model. 2008, 48, 1851-1867.
33. Graczyk, P. P. A Gini coefficient: a new way to express selectivity of kinase inhibitors against a family of kinases. J. Med. Chem. 2007, 50, 5773-5779.
34. Fabian, M. A.; Biggs, W. H., III; Trieber, D. K.; Atteridge, C. E.; Azimioara, M. D.; Benedetti, M. G.; Carter, T. A.; Ciceri, P.; Edeen, P. T.; Floyd, M.; Ford, J. M.; Gal vin, M.; Gerlach, J. L.; Grotzfeld, R. M.; Herrgard, S.; Insko, D. E.; Insko, M. A.; Lai, A. G.; Lelias, J.-M.; Mehta, S. A.; Milanov, Z. V.; Velasco, A. M.; Wodicka, L. M.; Patel, H. K.; Zarrinkar, P. P.; Lockhart, D. J. A small molecule-kinase interaction map for clinical kinase inhibitors. Nat. Biotechnol. 2005, 23, 329-336.
35. Vieth, M.; Sutherland, J. J.; Robertson, D. H.; Cambell, R. M. Kinomics: Characterizing the therapeutically validated kinase space. Drug Discovery Today 2005, 10, 839-846.
36. RCSB Protein Data Bank, www.rscb.org. (accessed July 2009).
37. Abagayan, R. A.; Totrov, M. M.; Kuznetsov, D. N. ICM-A new method for protein modeling and design. Applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 1994, 15, 488-506.
38. Svetnik, V.; Liaw, A.; Tong, C.; Culberson, J. C.; Sheridan, R. P.; Feuston, B. P. Random forest: A classification and regression tool for compound classification and QSAR modeling. J. Chem. Inf. Comput. Sci. 2003, 43, 1947-1958.
39. (39) Schneider, T. D.; Stephens, R. M. Sequence Logos: A new way to display consensus sequences. Nucleic Acids Res. 1990, 18, 6097-6100. (Pubitemid 20364672)
40. Crooks, G. E.; Hon, G.; Chandonia, J.-M.; Brenner, S. E. WebLogo: A sequence logo generator. Genome Res. 2004, 14, 1188-1190.