3D-QSAR studies of checkpoint kinase 1 inhibitors based on molecular docking and CoMFA

Molecular Simulation

Volumn 36, Issue 2, 2010, Pages 87-110

  Wang, Rong Wei ^a   Zhou, Lu ^a   Zuo, Zhili ^b,c   Ma, Xiang ^a   Yang, Min ^a  

^a SICHUAN UNIVERSITY   (China)

^b SINGAPORE POLYTECHNIC   (Singapore)

^c CURTIN UNIVERSITY   (Australia)

Author keywords

3D QSAR; Checkpoint kinase 1 (CHK1); CoMFA; Molecular docking; Substituted 1,4 dihydroindeno 1,2 c pyrazoles

Indexed keywords

3D-QSAR; COMPARATIVE MOLECULAR FIELD ANALYSIS; INHIBITORY ACTIVITY; KEY FEATURE; MOLECULAR DOCKING; PARTIAL LEAST SQUARES; PREDICTIVE ABILITIES; PYRAZOLES; THREE-DIMENSIONAL QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

ABILITY TESTING; ALIGNMENT; DOCKING; MOLECULAR GRAPHICS; MOLECULAR MODELING; SULFUR COMPOUNDS;

THREE DIMENSIONAL;

EID: 77049096519     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020903115260     Document Type: Article

References (32)

1. L.H. Hurley, DNA and its associated processes as targets for cancer therapy, Nat. Rev. Cancer 2 (2002), pp. 188-200.
2. Z.F. Tao, G.Q. Li, Y.S. Tong, K.D. Stewart, Z. Chen, M.H. Bui, P. Merta, C. Park, P. Kovar, H.Y. Zhang, H.L. Sham, S.H. Rosenberg, T.J. Sowin, and N.H. Lin, Discovery of 40-(1,4- dihydro-indeno[1,2-c]pyrazol-3-yl)-benzonitriles and 40-(1,4-dihydro- indeno[1,2-c]pyrazol-3-yl)-pyridine-20-carbonitriles as potent checkpoint kinase 1 (Chk1) inhibitors, Bioorg. Med. Chem. Lett. 17 (2007), pp. 5944-5951.
3. A. Sancar, L.A. Lindsey-Boltz, K. Unsal-Kacmaz, and S. Linn, Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints, Annu. Rev. Biochem. 73 (2004), pp. 39-85.
4. B.B. Zhou and J. Bartek, Targeting the checkpoint kinases: chemosensitization versus chemoprotection, Nat. Rev. Cancer 4 (2004), pp. 216-225.
5. M.B. Kastan and J. Bartek, Cell-cycle checkpoints and cancer, Nature 432 (2004), pp. 316-323.
6. Z.F. Tao, L. Wang, K.D. Stewart, Z. Chen, W. Gu, M. Bui, P. Merta, H. Zhang, P. Kovar, E. Johnson, C. Park, R. Judge, S. Rosenberg, T. Sowin, and N.H. Lin, Structure-based design, synthesis, and biological evaluation of potent and selective macrocyclic checkpoint kinase 1 inhibitors, J. Med. Chem. 50 (2007), pp. 1514-1527. (Pubitemid 46564373)
7. N. Walworth, S. Davey, and D. Beach, Fission yeast Chk1 protein kinase links the rad checkpoint pathway to cdc2, Nature 363 (1993), pp. 368-371.
8. Y. Chen and Y. Sanchez, Chk1 in the DNA damage response: conserved roles from yeasts to mammals, DNA Repair 3 (2004), pp. 1025-1032.
9. Q. Liu, S. Guntuku, X.S. Cui, S. Matsuoka, D. Cortez, K. Tamain, G.B. Luo, S.C. Rivera, F. Demya, A. Bradley, L.A. Donehower, and S.J. Elledge, Chk1 is an essential kinase that is regulated by Atr and required for the G2/M DNA damage checkpoint, Genes Dev. 14 (2000), pp. 1448-1459.
10. R.T. Abraham, Cell cycle checkpoint signaling through the ATM and ATR kinases, Genes Dev. 15 (2001), pp. 2177-2196.
11. Y. Tong, A. Claiborne, M. Pyzytulinska, Z.F. Tao, K.D. Stewart, P. Park, P. Kovar, Z. Chen, R.B. Credo, R. Guan, P.L. Merta, H. Zhang, J. Bouska, E.A. Everitt, B.P. Murry, D. Hickman, T.J. Stratton, J. Wu, S.H. Rosenberg, H.L. Sham, T.J. Sowin, and N.H. Lin, 1,4-Dihydroindeno[1,2-c]pyrazoles as potent checkpoint kinase 1 inhibitors: Extended exploration on phenyl ring substitutions and preliminary ADME/PK studies, Bioorg. Med. Chem. Lett. 17 (2007), pp. 3618-3623.
12. P.R. Graves, L. Yu, J.K. Schwarz, J. Gales, E.A. Sausville, P.M. O'Connor, and H. Piwnica-Worms, The chk1 protein kinase and the Cdc25C regulatory pathways are targets of the anticancer agent UCN-01, J. Biol. Chem. 275 (2000), pp. 5600-5605.
13. X. Jiang, B. Zhao, R. Britton, L.Y. Lim, D. Leong, J.S. Sanghera, B.B.S. Zhou, S. Piers, R.J. Andersen, and M. Roberge, Inhibition of Chk1 by the G2 DNA damage checkpoint inhibitor isogranulatimide, Mol. Cancer Ther. 3 (2004), pp. 1221-1227.
14. D. Curman, B. Cinel, D.E. Williams, N. Rundle, W.D. Block, A.A. Goodarzi, J.R. Hutchins, P.R. Clarke, B.B.S. Zhou, S.P. Lees- Miller, R.J. Andersen, and M. Roberge, Inhibition of the G2 DNA damage checkpoint and of protein kinases Chk1 and Chk2 by the marine sponge alkaloid debromohymenialdisine, J. Biol. Chem. 276 (2001), p. 17914.
15. P.D. Lyne, P.W. Kenny, D.A. Cosgrove, C. Deng, S. Zabludoff, S. Ashwell, and J.J. Wendoloski, Identification of compounds with nanomolar binding affinity for checkpoint kinase-1 using knowledge- based virtual screening, J. Med. Chem. 47 (2004), pp. 1962-1968.
16. N. Foloppe, L.M. Fisher, R. Howes, P. Kierstan, A. Potter, A.G.S. Robertson, and A.E. Surgenor, Structure-based design of novel Chk1 inhibitors: Insights into hydrogen bonding and protein-ligand affinity, J. Med. Chem. 48 (2005), pp. 4332-4345.
17. M.E. Fraley, J.T. Steen, E.J. Brnardic, K.L. Arrington, K.L. Spencer, B.A. Hanney, Y. Kim, G.D. Hartman, S.M. Stirdivant, B.A. Drakas, K. Rickert, E.S. Walsh, K. Hamilton, C.A. Buser, J. Hardwick, W. Tao, S.C. Beck, X. Mao, R.B. Lobell, L. Sepp- Lorenzino, Y. Yan, M. Ikuta, S.K. Munshi, L.C. Kuo, and C. Kreatsoulas, 3-(Indol-2-yl)indazoles as Chek1 kinase inhibitors: Optimization of potency and selectivity via substitution at C6, Bioorg. Med. Chem. Lett. 16 (2006), pp. 6049-6053.
18. Z.J. Ni, P. Barsanti, N. Brammeier, A. Diebes, D.J. Poon, S. Ng, S. Pecchi, K. Pfister, P.A. Renhowe, S. Ramurthy, A.S. Wagman, D.E. Bussiere, V. Le, Y. Zhou, J.M. Jansen, S. Ma, and T.G. Gesner, 4-(Aminoalkylamino)-3- benzimidazole-quinolinones as potent CHK-1 inhibitors, Bioorg. Med. Chem. Lett. 16 (2006), pp. 3121-3124.
19. Y. Tong, A. Claiborne, K.D. Stewart, P. Park, P. Kovar, Z. Chen, R.B. Credo, W.Z. Gu, S.L. Gwaltney, R.A. Judge, H. Zhang, S.H. Rosenberg, H.L. Sham, T.J. Sowin, and N.H. Lin, Discovery of 1,4-dihydroindeno[1,2-c]pyrazoles as a novel class of potent and selective checkpoint kinase 1 inhibitors, Bioorg. Med. Chem. Lett 15 (2007), pp. 2759-2767. (Pubitemid 46367696)
20. Z.F. Tao, G. Li, Y. Tong, Z. Chen, P. Merta, H. Zhang, P. Kovar, S. Rosenberg, H.L. Sham, T.J. Sowin, and N.H. Lin, Synthesis and biological evaluation of 40-(6,7-disubstituted-2,4-dihydro-indenol] 1,2-c]pyrazol-3-yl)- biphenyl-4-ol as potent Chk1 inhibitors, Bioorg. Med. Chem. Lett. 15 (2007), pp. 4308-4315. (Pubitemid 47021390)
21. M.D.M. AbdulHameed, A. Hamza, J. Liu, and C.G. Zhan, Combined 3D-QSAR modeling and molecular docking study on indolinone derivatives as inhibitors of 3-phosphoinositide-dependent protein kinase-1, J. Chem. Inf. Model. 48 (2008), pp. 1760-1772.
22. G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor, Development and validation of a genetic algorithm for flexible docking, J. Mol. Biol. 267 (1997), pp. 727-748.
23. X. Ma, L. Zhou, Z.L. Zuo, J. Liu, M. Yang, and R.W. Wang, Molecular docking and 3D QSAR studies of substituted 2,2-bisarylbicycloheptanes as human 5-lipoxygenase-activating protein (FLAP) inhibitors, QSAR Comb. Sci. 27 (2008), pp. 1083-1091.
24. M.D. Eldridge, C.W. Murray, T.R. Auton, G.V. Paolini, and R.P. Mee, Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes, J. Comput.-Aided Mol. Des. 11 (1997), pp. 425-445.
25. C.A. Baxter, C.W. Murray, D.E. Clark, D.R. Westhead, and M.D. Eldridge, Flexible docking using tabu search and an empirical estimate of binding affinity, Proteins 33 (1998), pp. 367-382.
26. M.L. Verdonk, J.C. Cole, M.J. Hartshorn, C.W. Murray, and R.D. Taylor, Improved protein-ligand docking using GOLD, Proteins 52 (2003), pp. 609-623.
27. P. Yi, X. Fang, and M. Qiu, 3D-QSAR studies of checkpoint kinase weel inhibitors based on molecular docking, CoMFA and CoMSIA, Eur. J. Med. Chem. 43 (2008), pp. 925-938.
28. P. Yi and M. Qiu, 3D-QSAR and docking studies of aminopyridine carboxamide inhibitors of c-Jun N-terminal kinase-1, Eur. J. Med. Chem. 43 (2008), pp. 604-613.
29. S.J. Teague, Implications of protein flexibility for drug discovery, Nat. Rev. Drug Discov. 2 (2003), pp. 527-541.
30. K. Gunasekaran and R. Nussinov, How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding, J. Mol. Biol. 365 (2007), pp. 257-273.
31. T.A. Halgren, Maximally diagonal force constants in dependent angle-bending coordinates. II. Implications for the design of empirical force fields, Am. J. Chem. Soc. 112 (1990), pp. 4710-4723.
32. B.L. Podlogar and D.M. Ferguson, QSAR and CoMFA: a perspective on the practical application to drug discovery, Drug Des. Discov. 17 (2000), pp. 4-12.