DFGmodel: Predicting protein kinase structures in inactive states for structure-based discovery of type-II inhibitors

ACS Chemical Biology

Volumn 10, Issue 1, 2015, Pages 269-278

  Ung, Peter Man Un ^a   Schlessinger, Avner ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN KINASE; PROTEIN KINASE INHIBITOR; SORAFENIB; DFG PEPTIDE; OLIGOPEPTIDE;

AMINO ACID COMPOSITION; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DRUG DESIGN; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME PHOSPHORYLATION; ENZYME STRUCTURE; POLYPHARMACOLOGY; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; BIOLOGY; CHEMICAL MODEL; CHEMISTRY; DRUG DEVELOPMENT; METABOLISM; MOLECULAR DOCKING; PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE; STRUCTURE ACTIVITY RELATION;

BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DRUG DISCOVERY; MODELS, CHEMICAL; MOLECULAR DOCKING SIMULATION; OLIGOPEPTIDES; PROTEIN CONFORMATION; PROTEIN KINASE INHIBITORS; PROTEIN KINASES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84921417609     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb500696t     Document Type: Article

References (54)

1. Manning, G., Whyte, D. B., Martinez, R., Hunter, T., and Sudarsanam, S. (2002) The protein kinase complement of the human genome Science 298, 1912-1934
2. Manning, G., Plowman, G. D., Hunter, T., and Sudarsanam, S. (2002) Evolution of protein kinase signaling from yeast to man Trends Biochem. Sci. 27, 514-520
3. Lahiry, P., Torkamani, A., Schork, N. J., and Hegele, R. A. (2010) Kinase mutations in human disease: interpreting genotype-phenotype relationships Nat. Rev. Genet. 11, 60-74
4. Chang, F., Steelman, L. S., Lee, J. T., Shelton, J. G., Navolanic, P. M., Blalock, W. L., Franklin, R. A., and McCubrey, J. A. (2003) Signal transduction mediated by the Ras/Raf/MEK/ERK pathway from cytokine receptors to transcription factors: potential targeting for therapeutic intervention Leukemia 17, 1263-1293
5. He, Y., Xu, H., Liang, L., Zhan, Z., Yang, X., Yu, X., Ye, Y., and Sun, L. (2008) Antiinflammatory effect of Rho kinase blockade via inhibition of NF-kappaB activation in rheumatoid arthritis Arthritis Rheum. 58, 3366-3376
6. Cohen, P. (2002) Protein kinasesthe major drug targets of the twenty-first century? Nat. Rev. Drug Discovery 1, 309-315
7. Roberts, P. J. and Der, C. J. (2007) Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer Oncogene 26, 3291-3310
8. Fabbro, D., Cowan-Jacob, S. W., Mobitz, H., and Martiny-Baron, G. (2012) Targeting cancer with small-molecular-weight kinase inhibitors Methods Mol. Biol. 795, 1-34
9. Zhao, Z., Wu, H., Wang, L., Liu, Y., Knapp, S., Liu, Q., and Gray, N. S. (2014) Exploration of type II binding mode: a privileged approach for kinase inhibitor focused drug discovery? ACS Chem. Biol. 9, 1230-1241
10. Hanks, S. K. and Hunter, T. (1995) Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification FASEB J. 9, 576-596
11. Masterson, L. R., Cheng, C., Yu, T., Tonelli, M., Kornev, A., Taylor, S. S., and Veglia, G. (2010) Dynamics connect substrate recognition to catalysis in protein kinase A Nat. Chem. Biol. 6, 821-828
12. Canagarajah, B. J., Khokhlatchev, A., Cobb, M. H., and Goldsmith, E. J. (1997) Activation mechanism of the MAP kinase ERK2 by dual phosphorylation Cell 90, 859-869
13. Stevenson, L. M., Deal, M. S., Hagopian, J. C., and Lew, J. (2002) Activation mechanism of CDK2: role of cyclin binding versus phosphorylation Biochemistry 41, 8528-8534
14. Frankel, M., Bishop, S. M., Ablooglu, A. J., Han, Y. P., and Kohanski, R. A. (1999) Conformational changes in the activation loop of the insulin receptors kinase domain Protein Sci. 8, 2158-2165
15. Huse, M. and Kuriyan, J. (2002) The conformational plasticity of protein kinases Cell 109, 275-282
16. Huang, H., Zhao, R., Dickson, B. M., Skeel, R. D., and Post, C. B. (2012) alphaC helix as a switch in the conformational transition of Src/CDK-like kinase domains J. Phys. Chem. B 116, 4465-4475
17. Martz, K. E., Dorn, A., Baur, B., Schattel, V., Goettert, M. I., Mayer-Wrangowski, S. C., Rauh, D., and Laufer, S. A. (2012) Targeting the hinge glycine flip and the activation loop: novel approach to potent p38alpha inhibitors J. Med. Chem. 55, 7862-7874
18. Gustafson, W. C., Meyerowitz, J. G., Nekritz, E. A., Chen, J., Benes, C., Charron, E., Simonds, E. F., Seeger, R., Matthay, K. K., Hertz, N. T., Eilers, M., Shokat, K. M., and Weiss, W. A. (2014) Drugging MYCN through an allosteric transition in Aurora kinase A Cancer Cell 26, 414-427
19. Kornev, A. P., Haste, N. M., Taylor, S. S., and Eyck, L. F. (2006) Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism Proc. Natl. Acad. Sci. U.S.A. 103, 17783-17788
20. Blanc, J., Geney, R., and Menet, C. (2013) Type II kinase inhibitors: an opportunity in cancer for rational design Anti-Cancer Agents Med. Chem. 13, 731-747
21. Kufareva, I. and Abagyan, R. (2008) Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states J. Med. Chem. 51, 7921-7932
22. Xu, M., Yu, L., Wan, B., Yu, L., and Huang, Q. (2011) Predicting inactive conformations of protein kinases using active structures: conformational selection of type-II inhibitors PLoS One 6, e22644
23. Zhao, S., Zhu, K., Li, J., and Friesner, R. A. (2011) Progress in super long loop prediction Proteins 79, 2920-2935
24. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank Nucleic Acids Res. 28, 235-242
25. Hari, S. B., Merritt, E. A., and Maly, D. J. (2013) Sequence determinants of a specific inactive protein kinase conformation Chem. Biol. 20, 806-815
26. Davis, M. I., Hunt, J. P., Herrgard, S., Ciceri, P., Wodicka, L. M., Pallares, G., Hocker, M., Treiber, D. K., and Zarrinkar, P. P. (2011) Comprehensive analysis of kinase inhibitor selectivity Nat. Biotechnol. 29, 1046-1051
27. Livingstone, C. D. and Barton, G. J. (1993) Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation Comput. Appl. Biosci. 9, 745-756
28. Brennan, D. F., Dar, A. C., Hertz, N. T., Chao, W. C., Burlingame, A. L., Shokat, K. M., and Barford, D. (2011) A Raf-induced allosteric transition of KSR stimulates phosphorylation of MEK Nature 472, 366-369
29. Larsson, P., Wallner, B., Lindahl, E., and Elofsson, A. (2008) Using multiple templates to improve quality of homology models in automated homology modeling Protein Sci. 17, 990-1002
30. Pieper, U., Eswar, N., Stuart, A. C., Ilyin, V. A., and Sali, A. (2002) MODBASE, a database of annotated comparative protein structure models Nucleic Acids Res. 30, 255-259
31. Shen, M. Y. and Sali, A. (2006) Statistical potential for assessment and prediction of protein structures Protein Sci. 15, 2507-2524
32. Zhang, Y. and Skolnick, J. (2004) Scoring function for automated assessment of protein structure template quality Proteins 57, 702-710
33. Eramian, D., Eswar, N., Shen, M. Y., and Sali, A. (2008) How well can the accuracy of comparative protein structure models be predicted? Protein Sci. 17, 1881-1893
34. Xu, J. and Zhang, Y. (2010) How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26, 889-895
35. Fan, H., Irwin, J. J., Webb, B. M., Klebe, G., Shoichet, B. K., and Sali, A. (2009) Molecular docking screens using comparative models of proteins J. Chem. Inf. Model. 49, 2512-2527
36. Kuntz, I. D. (1992) Structure-based strategies for drug design and discovery Science 257, 1078-1082
37. Shoichet, B. K. (2004) Virtual screening of chemical libraries Nature 432, 862-865
38. Schlessinger, A., Geier, E., Fan, H., Irwin, J. J., Shoichet, B. K., Giacomini, K. M., and Sali, A. (2011) Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET Proc. Natl. Acad. Sci. U.S.A. 108, 15810-15815
39. Baldwin, I., Bamborough, P., Haslam, C. G., Hunjan, S. S., Longstaff, T., Mooney, C. J., Patel, S., Quinn, J., and Somers, D. O. (2008) Kinase array design, back to front: biaryl amides Bioorg. Med. Chem. Lett. 18, 5285-5289
40. Wenglowsky, S., Moreno, D., Laird, E. R., Gloor, S. L., Ren, L., Risom, T., Rudolph, J., Sturgis, H. L., and Voegtli, W. C. (2012) Pyrazolopyridine inhibitors of B-Raf(V600E). Part 4: rational design and kinase selectivity profile of cell potent type II inhibitors Bioorg. Med. Chem. Lett. 22, 6237-6241
41. Dar, A. C., Das, T. K., Shokat, K. M., and Cagan, R. L. (2012) Chemical genetic discovery of targets and anti-targets for cancer polypharmacology Nature 486, 80-84
42. Dar, A. C., Lopez, M. S., and Shokat, K. M. (2008) Small molecule recognition of c-Src via the Imatinib-binding conformation Chem. Biol. 15, 1015-1022
43. Nazarenko, I., Hede, S. M., He, X., Hedren, A., Thompson, J., Lindstrom, M. S., and Nister, M. (2012) PDGF and PDGF receptors in glioma Upsala J. Med. Sci. 117, 99-112
44. Notredame, C., Higgins, D. G., and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment J. Mol. Biol. 302, 205-217
45. Armougom, F., Moretti, S., Poirot, O., Audic, S., Dumas, P., Schaeli, B., Keduas, V., and Notredame, C. (2006) Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee Nucleic Acids Res. 34, W604-608
46. Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M., and Barton, G. J. (2009) Jalview version 2a multiple sequence alignment editor and analysis workbench Bioinformatics 25, 1189-1191
47. Hamelryck, T. and Manderick, B. (2003) PDB file parser and structure class implemented in Python Bioinformatics 19, 2308-2310
48. Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., and de Hoon, M. J. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics Bioinformatics 25, 1422-1423
49. The PyMOL Molecular Graphics System, 1.6.0.0 ed., Schrodinger, LLC, New York.
50. Chartier, M., Chenard, T., Barker, J., and Najmanovich, R. (2013) Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree PeerJ 1, e126
51. Sali, A. and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234, 779-815
52. Durrant, J. D., de Oliveira, C. A., and McCammon, J. A. (2011) POVME: an algorithm for measuring binding-pocket volumes J. Mol. Graphics Modell. 29, 773-776
53. OEDocking, 3.0.1; OMEGA, 2.5.1.4, OpenEye Scientific Software, Santa Fe, NM.
54. Hawkins, P. C., Skillman, A. G., Warren, G. L., Ellingson, B. A., and Stahl, M. T. (2010) Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database J. Chem. Inf. Model. 50, 572-584