Cross-reactivity virtual profiling of the human kinome by X-React KIN: A chemical systems biology approach

Molecular Pharmaceutics

Volumn 7, Issue 6, 2010, Pages 2324-2333

  Brylinski, Michal ^a   Skolnick, Jeffrey ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; DASATINIB; ERLOTINIB; GEFITINIB; HUMAN KINOME; IMATINIB; PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE INHIBITOR; PROTEOME; SORAFENIB; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CROSS REACTION; DRUG SELECTIVITY; FALSE POSITIVE RESULT; MACHINE LEARNING; PRIORITY JOURNAL; PROTEIN FAMILY; SENSITIVITY AND SPECIFICITY; TECHNIQUE; VIRTUAL REALITY;

ADENOSINE TRIPHOSPHATE; ARTIFICIAL INTELLIGENCE; BINDING SITES; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; INTERNET; MODELS, STATISTICAL; PROTEIN KINASE INHIBITORS; PROTEIN KINASES; PROTEOMICS; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; SYSTEMS BIOLOGY;

EID: 78649946365     PISSN: 15438384     EISSN: 15438392     Source Type: Journal    
DOI: 10.1021/mp1002976     Document Type: Article

References (65)

1. Manning, G.; Whyte, D. B.; Martinez, R.; Hunter, T.; Sudarsanam, S. The protein kinase complement of the human genome Science 2002, 298 (5600) 1912-34
2. Hanks, S. K.; Hunter, T. Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification FASEB J. 1995, 9 (8) 576-96
3. Kennelly, P. J. Protein kinases and protein phosphatases in prokaryotes: a genomic perspective FEMS Microbiol. Lett. 2002, 206 (1) 1-8
4. Blume-Jensen, P.; Hunter, T. Oncogenic kinase signalling Nature 2001, 411 (6835) 355-65
5. Sasase, T. PKC-a target for treating diabetic complications Drugs Future 2006, 31 (6) 503-11
6. Müller, S.; Knapp, S. Targeting kinases for the treatment of inflammatory diseases Expert Opin. Drug Discovery 2010, 5 (9) 867-81
7. Saarela, J.; Kallio, S. P.; Chen, D.; Montpetit, A.; Jokiaho, A.; Choi, E.; Asselta, R.; Bronnikov, D.; Lincoln, M. R.; Sadovnick, A. D.; Tienari, P. J.; Koivisto, K.; Palotie, A.; Ebers, G. C.; Hudson, T. J.; Peltonen, L. PRKCA and multiple sclerosis: association in two independent populations PLoS Genet. 2006, 2 (3 e42
8. Bynagari-Settipalli, Y. S.; Chari, R.; Kilpatrick, L.; Kunapuli, S. P. Protein Kinase C-Possible Therapeutic Target to Treat Cardiovascular Diseases. Cardiovasc. Hematol. Disord. Drug Targets 2010. DOI: 10.2174/87121020678065529X.
9. Mueller, B. K.; Mack, H.; Teusch, N. Rho kinase, a promising drug target for neurological disorders Nat. Rev. Drug Discovery 2005, 4 (5) 387-98
10. Cohen, P. The development and therapeutic potential of protein kinase inhibitors Curr. Opin. Chem. Biol. 1999, 3 (4) 459-65
11. Johnson, L. Protein kinases and their therapeutic exploitation Biochem. Soc. Trans. 2007, 35 (Part 1) 7-11
12. Weinmann, H.; Metternich, R. Drug discovery process for kinase inhibitors ChemBioChem 2005, 6 (3) 455-9
13. Noble, M. E.; Endicott, J. A.; Johnson, L. N. Protein kinase inhibitors: insights into drug design from structure Science 2004, 303 (5665) 1800-5
14. McInnes, C.; Fischer, P. M. Strategies for the design of potent and selective kinase inhibitors Curr. Pharm. Des. 2005, 11 (14) 1845-63
15. Sawa, M. Strategies for the design of selective protein kinase inhibitors Mini-Rev. Med. Chem. 2008, 8 (12) 1291-7
16. Liao, J. J. Molecular recognition of protein kinase binding pockets for design of potent and selective kinase inhibitors J. Med. Chem. 2007, 50 (3) 409-24
17. Stout, T. J.; Foster, P. G.; Matthews, D. J. High-throughput structural biology in drug discovery: protein kinases Curr. Pharm. Des. 2004, 10 (10) 1069-82
18. Cheek, S.; Zhang, H.; Grishin, N. V. Sequence and structure classification of kinases J. Mol. Biol. 2002, 320 (4) 855-81
19. Vieth, M.; Higgs, R. E.; Robertson, D. H.; Shapiro, M.; Gragg, E. A.; Hemmerle, H. Kinomics-structural biology and chemogenomics of kinase inhibitors and targets Biochim. Biophys. Acta 2004, 1697 (1-2) 243-57
20. Vieth, M.; Sutherland, J. J.; Robertson, D. H.; Campbell, R. M. Kinomics: characterizing the therapeutically validated kinase space Drug Discovery Today 2005, 10 (12) 839-46
21. 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, 51 (24) 7898-914
22. Frye, S. V. Structure-activity relationship homology (SARAH): a conceptual framework for drug discovery in the genomic era Chem. Biol. 1999, 6 (1) R3-7
23. Zhang, X.; Fernandez, A. In silico drug profiling of the human kinome based on a molecular marker for cross reactivity Mol. Pharmaceutics 2008, 5 (5) 728-38
24. Sheridan, R. P.; Nam, K.; Maiorov, V. N.; McMasters, D. R.; Cornell, W. D. QSAR models for predicting the similarity in binding profiles for pairs of protein kinases and the variation of models between experimental data sets J. Chem. Inf. Model. 2009, 49 (8) 1974-85
25. Naumann, T.; Matter, H. Structural classification of protein kinases using 3D molecular interaction field analysis of their ligand binding sites: target family landscapes J. Med. Chem. 2002, 45 (12) 2366-78
26. Kuhn, D.; Weskamp, N.; Hullermeier, E.; Klebe, G. Functional classification of protein kinase binding sites using Cavbase ChemMedChem 2007, 2 (10) 1432-47
27. 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 (2) 318-29
28. Subramanian, G.; Sud, M. Computational Modeling of Kinase Inhibitor Selectivity. ACS Med. Chem. Lett. 2010. DOI: 10.1021/ml1001097.
29. Cozzetto, D.; Kryshtafovych, A.; Fidelis, K.; Moult, J.; Rost, B.; Tramontano, A. Evaluation of template-based models in CASP8 with standard measures Proteins 2009, 77 (Suppl. 9) 18-28
30. Ginalski, K. Comparative modeling for protein structure prediction Curr. Opin. Struct. Biol. 2006, 16 (2) 172-7
31. Moult, J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction Curr. Opin. Struct. Biol. 2005, 15 (3) 285-9
32. DeWeese-Scott, C.; Moult, J. Molecular modeling of protein function regions Proteins 2004, 55 (4) 942-61
33. Piedra, D.; Lois, S.; de la Cruz, X. Preservation of protein clefts in comparative models BMC Struct. Biol. 2008, 8, 2
34. Brylinski, M.; Skolnick, J. Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening J. Chem. Inf. Model. 2010, 50 (10) 1839-54
35. Zhang, Y.; Skolnick, J. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins Biophys. J. 2004, 87 (4) 2647-55
36. Skolnick, J.; Kihara, D.; Zhang, Y. Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm Proteins 2004, 56 (3) 502-18
37. Brylinski, M.; Skolnick, J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (1) 129-34
38. Brylinski, M.; Skolnick, J. FINDSITE(LHM): a threading-based approach to ligand homology modeling PLoS Comput. Biol. 2009, 5 (6 e1000405
39. Brylinski, M.; Skolnick, J. Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling J. Comput. Chem. 2010, 31 (5) 1093-105
40. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28 (1) 235-42
41. Zhang, Y.; Skolnick, J. TM-align: a protein structure alignment algorithm based on the TM-score Nucleic Acids Res. 2005, 33 (7) 2302-9
42. Yeturu, K.; Chandra, N. PocketMatch: a new algorithm to compare binding sites in protein structures BMC Bioinformatics 2008, 9, 543
43. Kendall, M. G. A new measure of rank correlation Biometrika 1938, 30 (Part 1-2) 81-9
44. Irwin, J. J.; Shoichet, B. K. ZINC-a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 2005, 45 (1) 177-82
45. Brylinski, M.; Skolnick, J. Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints J. Comput. Chem. 2008, 29 (10) 1574-88
46. Davies, S. P.; Reddy, H.; Caivano, M.; Cohen, P. Specificity and mechanism of action of some commonly used protein kinase inhibitors Biochem. J. 2000, 351 (Pt 1) 95-105
47. Karaman, M. W.; Herrgard, S.; Treiber, D. K.; Gallant, P.; Atteridge, C. E.; Campbell, B. T.; Chan, K. W.; Ciceri, P.; Davis, M. I.; Edeen, P. T.; Faraoni, 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 (1) 127-32
48. Fabian, M. A.; Biggs, W. H., 3rd; Treiber, D. K.; Atteridge, C. E.; Azimioara, M. D.; Benedetti, M. G.; Carter, T. A.; Ciceri, P.; Edeen, P. T.; Floyd, M.; Ford, J. M.; Galvin, 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 (3) 329-36
49. Witten, I. H.; Frank, E. Data Mining: Practical Machine Learning Tools and Techniques, 2nd ed.; Morgan Kaufmann Publishers: San Francisco, 2005.
50. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching J. Chem. Inf. Comput. Sci. 1998, 38 (6) 983-96
51. Kestler, H. A. ROC with confidence-a Perl program for receiver operator characteristic curves Comput. Methods Programs Biomed. 2001, 64 (2) 133-136
52. Dagpunar, J. S. An Easily Implemented Generalised Inverse Gaussian Generator Commun. Stat.-Simul. Comput. 1989, 18 (2) 703-10
53. The R Development Core Team R: A language and environment for statistical computing; R Foundation for Statistical Computing: Vienna, Austria, 2008.
54. Pavlidis, P.; Noble, W. S. Matrix2png: a utility for visualizing matrix data Bioinformatics 2003, 19 (2) 295-6
55. Karypis, G. CLUTO: A Clustering Toolkit, version 2.1.1; 2003.
56. Martin, M. W.; Newcomb, J.; Nunes, J. J.; McGowan, D. C.; Armistead, D. M.; Boucher, C.; Buchanan, J. L.; Buckner, W.; Chai, L.; Elbaum, D.; Epstein, L. F.; Faust, T.; Flynn, S.; Gallant, P.; Gore, A.; Gu, Y.; Hsieh, F.; Huang, X.; Lee, J. H.; Metz, D.; Middleton, S.; Mohn, D.; Morgenstern, K.; Morrison, M. J.; Novak, P. M.; Oliveira-dos-Santos, A.; Powers, D.; Rose, P.; Schneider, S.; Sell, S.; Tudor, Y.; Turci, S. M.; Welcher, A. A.; White, R. D.; Zack, D.; Zhao, H.; Zhu, L.; Zhu, X.; Ghiron, C.; Amouzegh, P.; Ermann, M.; Jenkins, J.; Johnston, D.; Napier, S.; Power, E. Novel 2-aminopyrimidine carbamates as potent and orally active inhibitors of Lck: synthesis, SAR, and in vivo antiinflammatory activity J. Med. Chem. 2006, 49 (16) 4981-91
57. Patel, K.; Fattaey, A.; Burd, A. ACTB-1003: An oral kinase inhibitor targeting cancer mutations (FGFR), angiogenesis (VEGFR2, TEK), and induction of apoptosis (RSK and p70S6K) J. Clin. Oncol. (Meeting Abstr.) 2010, 28 (15-suppl e13665
58. Okram, B.; Nagle, A.; Adrian, F. J.; Lee, C.; Ren, P.; Wang, X.; Sim, T.; Xie, Y.; Xia, G.; Spraggon, G.; Warmuth, M.; Liu, Y.; Gray, N. S. A general strategy for creating "inactive-conformation" abl inhibitors Chem. Biol. 2006, 13 (7) 779-86
59. Scapin, G.; Patel, S. B.; Lisnock, J.; Becker, J. W.; LoGrasso, P. V. The structure of JNK3 in complex with small molecule inhibitors: structural basis for potency and selectivity Chem. Biol. 2003, 10 (8) 705-12
60. Deuse, T.; Velotta, J. B.; Hoyt, G.; Govaert, J. A.; Taylor, V.; Masuda, E.; Herlaar, E.; Park, G.; Carroll, D.; Pelletier, M. P.; Robbins, R. C.; Schrepfer, S. Novel immunosuppression: R348, a JAK3- and Syk-inhibitor attenuates acute cardiac allograft rejection Transplantation 2008, 85 (6) 885-92
61. Bleicher, K. H.; Bohm, H. J.; Muller, K.; Alanine, A. I. Hit and lead generation: beyond high-throughput screening Nat. Rev. Drug Discovery 2003, 2 (5) 369-78
62. Petrelli, A.; Giordano, S. From single- to multi-target drugs in cancer therapy: when aspecificity becomes an advantage Curr. Med. Chem. 2008, 15 (5) 422-32
63. Morphy, R. Selectively nonselective kinase inhibition: striking the right balance J. Med. Chem. 2010, 53 (4) 1413-37
64. Marsden, B. D.; Knapp, S. Doing more than just the structure-structural genomics in kinase drug discovery Curr. Opin. Chem. Biol. 2008, 12 (1) 40-5
65. Verdonk, M. L.; Mortenson, P. N.; Hall, R. J.; Hartshorn, M. J.; Murray, C. W. Protein-Ligand Docking against Non-Native Protein Conformers J. Chem. Inf. Model. 2008, 48 (11) 2214-25