Computational modeling of kinase inhibitor selectivity

ACS Medicinal Chemistry Letters

Volumn 1, Issue 8, 2010, Pages 395-399

  Subramanian, Govindan ^a   Sud, Manish ^b  

^a SANOFI   (France)

^b MayaChemTools   (United States)

Author keywords

binding hot spots; binding site signature; computational prediction; kinase conformation; kinase inhibitors; Kinase selectivity

Indexed keywords

PHOSPHOTRANSFERASE INHIBITOR; SORAFENIB; SUNITINIB;

ARTICLE; CONFORMATION; DRUG SELECTIVITY; DRUG TARGETING; PRIORITY JOURNAL; STATISTICAL MODEL;

EID: 78649231963     PISSN: None     EISSN: 19485875     Source Type: Journal    
DOI: 10.1021/ml1001097     Document Type: Article

References (34)

1. Sawa, M. Strategies for the design of selective protein kinase inhibitors Mini Rev. Med. Chem. 2008, 8, 1291-1297
2. Morphy, R. Selectively nonselective kinase inhibition: Striking the right balance J. Med. Chem. 2010, 53, 1413-1437
3. Manning, G.; Whyte, D. B.; Martinez, R.; Hunter, T.; Sudarsanam, S. The protein kinase complement of the human genome Science 2002, 298, 1912-1934
4. 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. Sci. U.S.A. 2006, 103, 3153-3158
5. Bain, J.; Cummings, L.; Elliot, M; Shapiro, N.; Hastie, J.; McLauchian, H.; Klevernic, I.; Arthur, S.; Alessi, D.; Cohen, P. The selectivity of protein kinase inhibitors; a further update Biochem. J. 2007, 48, 297-315
6. 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
7. Bamborough, P.; Drewry, D.; Harper, G.; Smith, G. K.; Schneider, K. Assessment of chemical coverage of kinome space and its implication for kinase drug discovery J. Med. Chem. 2008, 51, 7998-7914
8. Goldstein, D. M.; Gray, N. S.; Zarrinkar, P. P. High-throughput kinase profiling as a platform for drug discovery Nature Rev. Drug Discovery 2008, 7, 391-397
9. Graczyk, P. P. Gini coefficient: A new way to express selectivity of kinase inhibitors against a family of kinases J. Med. Chem. 2007, 50, 5773-5779
10. Chen, Z.; Zhang, X.; Fernandez, A. Molecular basis for specificity in the druggable kinome: sequence-based analysis Bioinformatics 2007, 23, 563-572
11. 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
12. Kuhn, D.; Weskamp, N.; Hullermeier, E.; Klebe, G. Functional classification of protein kinase binding sites using Cavbase ChemMedChem 2007, 2, 1432-1447
13. Sciabola, S.; Stanton, R. V.; Wittkopp, S.; Wildman, S.; Moshinsky, D.; Potluri, S.; Xi, H. Predicting kinase selectivity profiles using Free-Wilson QSAR analysis J. Chem. Inf. Model. 2008, 48, 1851-1867
14. 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, 51, 2689-2700
15. Caffrey, D. R.; Lunney, E. A.; Moshinsky, D. Prediction of specificity-determining residues for small-molecule kinase inhibitors BMC Bioinf. 2008, 9, 491
16. 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
17. Brandt, P.; Jensen, A. J.; Nilsson, J. Small kinase assay panels can provide a measure of selectivity Bioorg. Med. Chem. Lett. 2009, 19, 5861-5863
18. 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 and references therein
19. Huang, D.; Zhou, T.; Lafleur, K.; Nevado, C.; Caflisch, A. Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis Bioinformatics 2010, 26, 198-204
20. 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
21. 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, 243-257
22. 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.; 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, 329-336
23. Vieth, M.; Sutherland, J. J.; Robertson, D. H.; Cambell, R. M. Characterizing the therapeutically validated kinase space Drug Discovery Today 2005, 10, 839-846
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, 1974-1985
25. 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.; 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, 127-132
26. 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
27. Ghose, A. K.; Herbertz, T.; Pippin, D. A.; Salvino, J. M.; Mallamo, J. P. Knowledge based prediction of ligand binding modes and rational inhibitor design for kinase drug discovery J. Med. Chem. 2008, 51, 5149-5171
28. Zuccotto, F.; Ardini, E.; Casale, E.; Angiolini, M. Through the "gatekeeper door": Exploiting the active kinase conformation J. Med. Chem. 2010, 53, 2681-2694
29. Zarrinkar, P. P.; Gunawardane, R. N.; Cramer, M. D.; Gardner, M. F.; Bringham, D.; Belli, B.; Karaman, M. W.; Pratz, K. W.; Pallares, G.; Chao, Q.; Sprankle, K. G.; Patel, H. K.; Levis, M.; Armstrong, R. C.; James, J.; Bhagwat, S. S. AC220 is a uniquely potent and selective inhibitor of FLT3 for the treatment of acute myeloid leukemia (AML) Blood 2009, 114, 2984-2992
30. Li, J.; Rix, U.; Fang, B.; Bai, Y.; Edwards, A.; Colinge, J.; Bennett, K. L.; Gao, J.; Song, L.; Eschrich, S.; Superti-Furga, G.; Koomen, J.; Haura, E. B. A chemical and phosphoproteomic characterization of dasatinib action in lung cancer Nat. Chem. Biol. 2010, 6, 291-299
31. Fedorov, O.; Mueller, S.; Knapp, S. The (un)targeted cancer kinome Nat. Chem. Biol. 2010, 6, 166-169
32. LoRusso, P. M.; Eder, J. P. Therapeutic potential of novel selective-spectrum kinase inhibitors in oncology Expert Opin. Invest. Drugs 2008, 17, 1013-1028
33. Knight, Z. A.; Lin, H.; Shokat, K. M. Targeting the cancer kinome through polypharmacology Nat. Rev. Cancer 2010, 10, 130-137 and references therein
34. Westhouse, R. A. Safety assessment considerations and strategies for targeted small molecule cancer therapeutics in drug discovery Toxicol. Pathol. 2010, 38, 165-168