Kinase-kernel models: Accurate in silico screening of 4 million compounds across the entire human kinome

Journal of Chemical Information and Modeling

Volumn 52, Issue 1, 2012, Pages 156-170

  Martin, Eric ^a   Mukherjee, Prasenjit ^a  

^a NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; COMPUTATIONAL CHEMISTRY; FORECASTING; GENETIC ALGORITHMS; MOLECULAR GRAPHICS; SCREENING;

ACTIVITY PREDICTIONS; CHEMICAL SIMILARITY; GENETIC-ALGORITHM OPTIMIZATIONS; HIGH-THROUGHPUT SCREENING; IN-SILICO SCREENING; KERNEL INTERPOLATIONS; OPTIMIZATION STUDIES; QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP;

ENZYMES;

PHOSPHOTRANSFERASE; PROTEIN KINASE INHIBITOR;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; DRUG ANTAGONISM; HUMAN; IC 50; PROTEIN BINDING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REPRODUCIBILITY; SEQUENCE HOMOLOGY;

BINDING SITES; HUMANS; INHIBITORY CONCENTRATION 50; MODELS, MOLECULAR; PHOSPHOTRANSFERASES; PROTEIN BINDING; PROTEIN KINASE INHIBITORS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REPRODUCIBILITY OF RESULTS; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 84858014049     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200314j     Document Type: Article

References (29)

1. Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions. J. Med. Chem. 2006, 49, 5912-5931. (Pubitemid 44484938)
2. Martin, E. J.; Mukherjee, P.; Sullivan, D. C.; Jansen, H. Profile-QSAR: A Novel Meta-QSAR Method that Combines Activities Across the Kinase Family to Accurately Predict Affinity, Selectivity and Cellular Activity. J. Chem. Inf. Model. 2011, 51, 1942-1956.
3. Martin, E. J.; Sullivan, D. C. Surrogate AutoShim: Predocking into a Universal Ensemble Kinase Receptor for Three Dimensional Activity Prediction, Very Quickly, without a Crystal Structure. J. Chem. Inf. Model. 2008, 48, 873-881. (Pubitemid 351757752)
4. Martin, E. J.; Sullivan, D. C. AutoShim: Empirically correctedsScoring functions for quantitative docking with a crystal structure and IC50 training data. J. Chem. Inf. Model. 2008, 48, 861-872. (Pubitemid 351757751)
5. Vieth, M.; Erickson, J.; Wang, J.; Webster, Y.; Mader, M.; Higgs, R.; Watson, I. Kinase Inhibitor Data Modeling and de Novo Inhibitor Design with Fragment Approaches. J. Med. Chem. 2009, 52, 6456-6466.
6. Vieth, M.; Sutherland, J. J.; Robertson, D. H.; Campbell, R. M. Kinomics: Characterizing the therapeutically validated kinase space. Drug Discovery Today 2005, 10, 839-846. (Pubitemid 40824738)
7. Cheng, A. C.; Eksterowicz, J.; Geuns-Meyer, S.; Sun, Y. Analysis of Kinase Inhibitor Selectivity using a Thermodynamics-Based Partition Index. J. Med. Chem. 2010, 53, 4502-4510.
8. Keiser, M. J.; Irwin, J. J.; Shoichet, B. K. The Chemical Basis of Pharmacology. Biochemistry 2010, 49, 10267-10276.
9. Brylinski, M.; Skolnick, J. Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach. Mol. Pharmaceutics 2010, 7, 2324-2333.
10. Kinnings, S. L.; Liu, N.; Buchmeier, N.; Tonge, P. J.; Xie, L.; Bourne, P. E. Drug discovery using chemical systems biology: Repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput. Biol. 2009, 5, No.
11. Tatonetti, N. P.; Liu, T.; Altman, R. B. Predicting drug sideeffects by chemical systems biology. Genome Biol 2009, 10, 238.
12. Kernel methods; http://en.wikipedia.org/wiki/Kernel-methods (accessed April 29, 2011).
13. Cristianini, N.; Shawe-Taylor, J. Kernel Methods for Pattern Analysis; Cambridge University Press: Cambridge, U.K., 2004.
14. Liu, W.; Principle, J.; Haykin, S. Kernel Adaptive Filtering: A Comprehensive Introduction. Wiley: Hoboken, NJ, 2010.
15. Nearest neighbor interpolation; http://en.wikipedia.org/wiki/ Nearest-neighbor-interpolation (accessed April 29, 2011).
16. Pyevolve genetic alogrithms; http://pyevolve.sourceforge.net/ (accessed April 29, 2011).
17. NumPy; http://numpy.scipy.org/ (accessed April 29, 2011).
18. Mead, R. Response surface exploration. In The Design of Experiments, Statistical principles for practical applications 1988.
19. Goldberg, D. E. Genetic Algorithms in Search, Optimization and Machine Learning; Addison-Wesley Professional: Boston, MA, 1989.
20. Schindler, T.; Sicheri, F.; Pico, A.; Gazit, A.; Levitzki, A.; Kuriyan, J. Crystal structure of HcK in complex with a Src familyselective tyrosine kinase inhibitor. Mol. Cell 1999, 3, 639-648. (Pubitemid 29268447)
21. Wang, Z.; Canagarajah, B. J.; Boehm, J. C.; Kassisa, S.; Cobb, M. H.; Young, P. R.; Abdel-Meguid, S.; Adams, J. L.; Goldsmith, E. J. Structural basis of inhibitor selectivity in MAP kinases. Structure (London) 1998, 6, 1117-1128. (Pubitemid 28434115)
22. Stamos, J.; Sliwkowski, M. X.; Eigenbrot, C. Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor. J. Biol. Chem. 2002, 277, 46265-46272. (Pubitemid 35417619)
23. Jacobs, M.; Hayakawa, K.; Swenson, L.; Bellon, S.; Fleming, M.; Taslimi, P.; Doran, J. The Structure of Dimeric ROCK I Reveals the Mechanism for Ligand Selectivity. J. Biol. Chem. 2006, 281, 260-268. (Pubitemid 43671185)
24. Shudler, M.;Niv,M. Y. BlockMaster: Partitioning Protein Kinase Structures Using Normal-Mode Analysis. J. Phys. Chem. A 2009, 113, 7528-7534.
25. Huse, M.; Kuriyan, J. The conformational plasticity of protein kinases. Cell (Cambridge, MA, U. S.) 2002, 109, 275-282. (Pubitemid 34606870)
26. Stevens, K. L.; Reno, M. J.; Alberti, J. B.; Price, D. J.; Kane-Carson, L. S.; Knick, V. B.; Shewchuk, L. M.; Hassell, A. M.; Veal, J. M.; Davis, S. T.; Griffin, R. J.; Peel, M. R. Synthesis and evaluation of pyrazolo[1,5-b] pyridazines as selective cyclin dependent kinase inhibitors. Bioorg. Med. Chem. Lett. 2008, 18, 5758-5762.
27. Kornev, A. P.; Haste, N. M.; Taylor, S. S.; Ten Eyck, L. F. Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 17783-17788. (Pubitemid 44852237)
28. Shokat, K. M. Tyrosine kinases: Modular signaling enzymes with tunable specificities. Chem. Biol. 1995, 2, 509-514.
29. Martin, E. J.; Mukherjee, P.; Sullivan, D. C.; Kinnings, S. L. Profile-QSAR: A Novel Meta-QSAR Method that Combines Activities Across the Kinase Family to Accurately Predict Affinity, Selectivity and Cellular Activity. J. Chem. Inf. Model. 2011, 51 (8), 1942-1956.