Designing of new multi-targeted inhibitors of spleen tyrosine kinase (Syk) and zeta-associated protein of 70 kDa (ZAP-70) using hierarchical virtual screening protocol

Journal of Molecular Graphics and Modelling

Volumn 39, Issue , 2013, Pages 165-175

  Kaur, Maninder ^a   Kumari, Archna ^a   Bahia, Malkeet Singh ^a   Silakari, Om ^a  

^a PUNJABI UNIVERSITY   (India)

Author keywords

Hierarchical virtual screening; Multi pharmacophore protocol; Spleen tyrosine kinase (Syk); T cell signaling; Zeta associated protein of 70 kDa (ZAP 70)

Indexed keywords

3D-QSAR; AUTOIMMUNE DISEASE; BEST MODEL; DOCKING SIMULATIONS; INFLAMMATORY DISORDERS; INHIBITOR MOLECULES; INHIBITORY ACTIVITY; PHARMACOPHORE MODELS; PHARMACOPHORES; PROTEIN TYROSINE KINASE; SPLEEN TYROSINE KINASE; STRUCTURAL FEATURE; T-CELL SIGNALING; T-LYMPHOCYTES; THERAPEUTIC AGENTS; THERAPEUTIC TARGETS; VIRTUAL SCREENING; ZETA-ASSOCIATED PROTEIN OF 70 KDA (ZAP-70);

AMINO ACIDS; COMPUTATIONAL CHEMISTRY; DIAGNOSIS; ENZYMES; PHARMACODYNAMICS; PROTEINS;

COMPUTER SIMULATION;

PROTEIN KINASE SYK; PROTEIN KINASE SYK INHIBITOR; PROTEIN TYROSINE KINASE; PROTEIN TYROSINE KINASE INHIBITOR; UNCLASSIFIED DRUG; ZETA ASSOCIATED PROTEIN OF 70 KDA; ZETA ASSOCIATED PROTEIN OF 70 KDA INHIBITOR;

ARTICLE; COMPUTER PROGRAM; DRUG ABSORPTION; DRUG DESIGN; DRUG DISTRIBUTION; DRUG EXCRETION; DRUG METABOLISM; DRUG PROTEIN BINDING; DRUG SCREENING; MOLECULAR DOCKING; PHARMACOPHORE; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

COMPUTER SIMULATION; DRUG DESIGN; HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; PROTEIN KINASE INHIBITORS; PROTEIN-TYROSINE KINASES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REPRODUCIBILITY OF RESULTS; ZAP-70 PROTEIN-TYROSINE KINASE;

EID: 84871563714     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2012.11.011     Document Type: Article

References (31)

1. J. Schlessinger, and A. Ullrich Growth factor signaling by receptor tyrosine kinases Neuron 9 1992 383 391
2. P. Van der Geer, T. Hunter, and R.A. Lindberg Receptor protein-tyrosine kinases and their signal transduction pathways Annual Review of Cell Biology 10 1994 251 337
3. A. Levitzki, and A. Gazit Tyrosine kinase inhibition: an approach to drug development Science 267 1995 1782 1788
4. T. Taniguchi, T. Kobayashi, J. Kondo, K. Takahashi, H. Nakamura, J. Suzuki, K. Nagai, T. Yamada, S. Nakamura, and H. Yamamura Molecular cloning of a porcine gene syk that encodes a 72-kDa protein-tyrosine kinase showing high susceptibility to proteolysis Journal of Biological Chemistry 266 1991 15790 15796
5. A.C. Chan, M. Iwashima, C.W. Turck, and A. Weiss ZAP-70: a 70 kDa protein-tyrosine kinase that associates with the TCR zeta chain Cell 71 1992 649 662
6. B.R. Wong, E.B. Grossbard, D.G. Payan, and E.S. Masuda Targeting Syk as a treatment for allergic and autoimmune disorders Expert Opinion on Investigational Drugs 13 2004 743 762
7. R. Singh, and E.S. Masuda Spleen tyrosine kinase (Syk) biology, inhibitors and therapeutic applications Annual Reports in Medicinal Chemistry 42 2007 379 391
8. S. Faruki, R.L. Geahlen, and D.J. Asai Syk-dependent phosphorylation of microtubules in activated B-lymphocytes Journal of Cell Science 113 2000 2557 2565
9. A.K. Saxena, and K.K. Roy Hierarchical virtual screening: identification of potential high affinity and selective β3-adrenergic receptor agonists SAR and QSAR in Environmental Research 2012 10.1080/1062936X.2012.664824
10. C.L. Cywin, B.P. Zhao, D.W. McNeil, M. Hrapchak, A.S. Prokopowicz, D.R. Goldberg, T.M. Morwick, A. Gao, S. Jakes, M. Kashem, R.L. Magolda, R.M. Soll, M.R. Player, M.A. Bobko, J. Rinker, R.L. DesJarlaisb, and M.P. Winters Discovery and SAR of novel [1,6]naphthyridines as potent inhibitors of spleen tyrosine kinase (SYK) Bioorganic and Medicinal Chemistry Letters 13 2003 1415 1418
11. A. Hirabayashi, H. Mukaiyama, H. Kobayashi, H. Shiohara, S. Nakayama, M. Ozawa, E. Tsuji, K. Miyazawa, K. Misawa, H. Ohnota, and M. Isaji Structure activity relationship studies of imidazo[1,2-c]pyrimidine derivatives as potent and orally effective Syk family kinases inhibitors Bioorganic and Medicinal Chemistry 16 2008 9247 9260
12. H. Hisamichi, R. Naito, A. Toyoshima, N. Kawano, A. Ichikawa, A. Orita, M. Orita, N. Hamada, M. Takeuchi, M. Ohtaa, and S. Tsukamotoa Synthetic studies on novel Syk inhibitors. Part 1: synthesis and structure activity relationships of pyrimidine-5-carboxamide derivatives Bioorganic and Medicinal Chemistry 13 2005 4936 4951
13. A. Hirabayashi, H. Mukaiyama, H. Kobayashi, H. Shiohara, S. Nakayama, M. Ozawa, K. Miyazawa, K. Misawa, H. Ohnota, and M. Isaji A novel Syk family kinase inhibitor: design, synthesis, and structure activity relationship of 1,2,4-triazolo[4,3-c]pyrimidine and 1,2,4-triazolo[1,5-c]pyrimidine derivatives Bioorganic and Medicinal Chemistry 16 2008 7347 7357
14. J.Y.Q. Lai, P.J. Cox, R. Patel, S. Sadiq, D.J. Aldous, S. Thurairatnam, K. Smith, D. Wheeler, S. Jagpal, S. Parveen, G. Fenton, T.K.P. Harrison, C. McCarthy, and P. Bamborough Potent small molecule inhibitors of spleen tyrosine kinase (Syk) Bioorganic and Medicinal Chemistry Letters 13 2003 3111 3114
15. D. Moffat, P. Davis, M. Hutchings, J. Davis, D. Berg, M. Batchelor, J. Johnson, J. O'Connell, R. Martin, T. Crabbe, J. Delgado, and M. Perry 4-Pyridin-5-yl-2-(3,4,5-trimethoxyphenylamino)pyrimidines: potent and selective inhibitors of ZAP-70 Bioorganic and Medicinal Chemistry Letters 9 1999 3351 3356
16. A. Hirabayashi, H. Mukaiyama, H. Kobayashi, H. Shiohara, S. Nakayama, M. Ozawa, K. Miyazawa, K. Misawa, H. Ohnota, and M. Isaji Structure activity relationship studies of 5-benzylaminoimidazo[1, 2-c] pyrimidine-8-carboxamide derivatives as potent, highly selective ZAP-70 kinase inhibitors Bioorganic and Medicinal Chemistry 17 2009 284 294
17. Maestro, Version 9.2, User Manual, Schrödinger, LLC, New York, 2011.
18. Ligprep, Version 2.5, User Manual, Schrödinger, LLC, New York, 2011.
19. PHASE, Version 3.3, Schrödinger, LLC, New York, NY, 2011.
20. S.L. Dixon, A.M. Smondyrev, E.H. Knoll, S.N. Rao, D.E. Shaw, and R.A. Friesner PHASE: a new engine for pharmacophore perception. 3D QSAR model development, and 3D database screening. 1. Methodology and preliminary results Journal of Computer-Aided Molecular Design 20 2006 647 671
21. J. Verma, V.M. Khedkar, and E.C. Coutinho 3D-QSAR in drug design: a review Current Topics in Medicinal Chemistry 10 2010 95 115
22. A. Golbraikh, and A. Tropsha Beware of q2! Journal of Molecular Graphics and Modelling 20 2002 269 276
23. V.D. Mouchlis, G. Melagraki, T. Mavromoustakos, G. Kollias, and A. Afantitis Molecular modeling on pyrimidine-urea inhibitors of TNF-α production: an integrated approach using a combination of molecular docking, classification techniques, and 3D-QSAR CoMSIA Journal of Chemical Information and Modeling 52 2012 711 723
24. S. Zhang, A. Golbraikh, S. Oloff, H. Kohn, and A. Tropsha A novel automated lazy learning QSAR (ALL-QSAR) approach: method development, applications, and virtual screening of chemical databases using validated ALL-QSAR models Journal of Chemical Information and Modeling 46 2006 1984 1995
25. R.D. Cramer, J.D. Bunce, D.E. Patterson, and I.E. Frank Crossvalidation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies Quantitative Structure-Activity Relationship 7 1988 18 25
26. S. Atwell, J.M. Adams, J. Badger, M.D. Buchanan, I.K. Feil, K.J. Froning, X. Gao, J. Hendle, K. Keegan, B.C. Leon, H.J. Muller-Deickmann, V.L. Nienaber, B.W. Noland, K. Post, K.R. Rajashankar, A. Ramos, M. Russell, S.K. Burley, and S.G. Buchanan A novel mode of Gleevec binding is revealed by the structure of spleen tyrosine kinase Journal of Biological Chemistry 279 2004 55827 55832
27. L.J. Farmer, G. Bemis, S.D. Britt, J. Cochran, M. Connors, E.M. Harrington, T. Hoock, W. Markland, S. Nanthakumar, P. Taslimi, E.T. Haar, J. Wang, D. Zhaveri, and F.G. Salituro Discovery and SAR of novel 4-thiazolyl-2-phenylaminopyrimidines as potent inhibitors of spleen tyrosine kinase (SYK) Bioorganic and Medicinal Chemistry Letters 18 2008 6231 6235
28. A.G. Villasenor, R. Kondru, H. Ho, S. Wang, E. Papp, D. Shaw, J.W. Barnett, M.F. Browner, and A. Kuglstatter Structural insights for design of potent spleen tyrosine kinase inhibitors from crystallographic analysis of three inhibitor complexes Chemical Biology and Drug Design 73 2009 466 470
29. L. Jin, S. Pluskey, E.C. Petrella, S.M. Cantin, J.C. Gorga, M.J. Rynkiewicz, P. Pandey, J.E. Strickler, R.E. Babine, D.T. Weaver, and K.J. Seidl The three-dimensional structure of the ZAP-70 kinase domain in complex with staurosporine: implications for the design of selective inhibitors Journal of Biological Chemistry 279 2004 42818 42825
30. Glide, Version 5.6, User Manual, Schrödinger, LLC, New York, NY, 2010.
31. R.A. Friesner, J. Banks, R.B. Murphy, T.A. Halgren, J.J. Klicic, D.T. Mainz, M.P. Repasky, E.H. Knoll, D.E. Shaw, M. Shelley, J.K. Perry, P. Francis, and P.S. Shenkin Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy Journal of Medicinal Chemistry 47 2004 1739 1749