Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations

European Journal of Medicinal Chemistry

Volumn 58, Issue , 2012, Pages 431-440

  Sgobba, Miriam ^a   Caporuscio, Fabiana ^a   Anighoro, Andrew ^a   Portioli, Corinne ^a   Rastelli, Giulio ^a  

^a UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

Author keywords

Drug design; Enrichment factor; MM GBSA; MM PBSA; Post docking refinement; Virtual screening

Indexed keywords

(2) (3' AMIDINO 3 BIPHENYL) 5 (4 PYRIDYLAMINO) PENTANOIC ACID; ADENOSINE DEAMINASE; ALDEHYDE REDUCTASE; BLOOD CLOTTING FACTOR 10A; ENOYL ACP REDUCTASE; ESTROGEN RECEPTOR; FIDARESTAT; FR 221647; GANCICLOVIR; GENZ 10850; IDD 552; LIGAND; N (4 METHYLBENZOYL) 4 BENZYLPIPERIDINE; OXIDOREDUCTASE; PIPERIDINE; RALOXIFENE; RPR 208815; TAMOXIFEN; THYMIDINE; THYMIDINE KINASE; TRICLOSAN; UNCLASSIFIED DRUG; VALERIC ACID;

ARTICLE; BINDING AFFINITY; CRYSTALLOGRAPHY; DATA BASE; DRUG TARGETING; MATHEMATICAL MODEL; MOLECULAR DOCKING; MOLECULAR MECHANICS; MOLECULAR MECHANICS GENERALIZED BORN SURFACE; MOLECULAR MECHANICS POISSONEBOLTZMANN SURFACE AREA; PROTEIN CONFORMATION;

ALGORITHMS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS; SURFACE PROPERTIES;

EID: 84868699636     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2012.10.024     Document Type: Article

References (43)

1. F. Caporuscio, G. Rastelli, C. Imbriano, and A. Del Rio J. Med. Chem. 54 2011 4006 4017
2. K.P. Ravindranathan, V. Mandiyan, A.R. Ekkati, J.H. Bae, J. Schlessinger, and W.L. Jorgensen J. Med. Chem. 53 2010 1662 1672
3. M.L. Teodoro, and L.E. Kavraki Curr. Pharm. Des. 9 2003 1635 1648
4. S. Huang, and X. Zou Proteins 66 2007 399 421
5. M. Totrov, and R. Abagyan Curr. Opin. Struct. Biol. 18 2008 178 184
6. J. Lin Curr. Top. Med. Chem. 11 2011 171 178
7. P. Kollman Chem. Rev. 93 1993 2395 2417
8. T.P. Lybrand, J.A. McCammon, and G. Wipff Proc. Natl. Acad. Sci. U.S.A. 83 1986 833 835
9. J. Aqvist, C. Medina, and J.E. Samuelsson Protein Eng. 7 1994 385 391
10. P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, and T.E. Cheatham III Acc. Chem. Res. 33 2000 889 897
11. J. Wang, P. Morin, W. Wang, and P.A. Kollman J. Am. Chem. Soc. 123 2001 5221 5230
12. A. Lindström, L. Edvinsson, A. Johansson, C.D. Andersson, I.E. Andersson, F. Raubacher, and A. Linusson J. Chem. Inf. Model. 51 2011 267 282
13. T. Hou, J. Wang, Y. Li, and W. Wang J. Comput. Chem. 32 2011 866 877
14. A.P. Graves, D.M. Shivakumar, S.E. Boyce, M.P. Jacobson, D.A. Case, and B.K. Shoichet J. Mol. Biol. 377 2008 914 934
15. D.C. Thompson, C. Humblet, and D. Joseph-McCarthy J. Chem. Inf. Model. 48 2008 1081 1091
16. N. Huang, C. Kalyanaraman, J.J. Irwin, and M.P. Jacobson J. Chem. Inf. Model. 46 2006 243 253
17. B. Kuhn, P. Gerber, T. Schulz-Gasch, and M. Stahl J. Med. Chem. 48 2005 4040 4048
18. G. Degliesposti, V. Kasam, A. Da Costa, H.-K. Kang, N. Kim, D.-W. Kim, V. Breton, D. Kim, and G. Rastelli ChemMedChem 4 2009 1164 1173
19. N. Huang, C. Kalyanaraman, K. Bernacki, and M.P. Jacobson Phys. Chem. Chem. Phys. 8 2006 5166 5177
20. A.M. Ferrari, G. Degliesposti, M. Sgobba, and G. Rastelli Bioorg. Med. Chem. 15 2007 7865 7877
21. G. Rastelli, G. Degliesposti, A. Del Rio, and M. Sgobba Chem. Biol. Drug Des. 73 2009 283 286
22. G. Rastelli, A. Del Rio, G. Degliesposti, and M. Sgobba J. Comput. Chem. 31 2010 797 810
23. G. Degliesposti, C. Portioli, M.D. Parenti, and G. Rastelli J. Biomol. Screen. 16 2011 129 133
24. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson J. Comput. Chem. 19 1998 1639 1662
25. G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, and A.J. Olson J. Comput. Chem. 30 2009 2785 2791
26. D.J. Diller, and K.M. Merz Jr. Proteins 43 2001 113 124
27. N. Huang, B.K. Shoichet, and J.J. Irwin J. Med. Chem. 49 2006 6789 6801
28. T. Kinoshita, I. Nakanishi, T. Terasaka, M. Kuno, N. Seki, M. Warizaya, H. Matsumura, T. Inoue, K. Takano, H. Adachi, Y. Mori, and T. Fujii Biochemistry 44 2005 10562 10569
29. V. Limongelli, L. Marinelli, S. Cosconati, C. La Motta, S. Sartini, L. Mugnaini, F. Da Settimo, E. Novellino, and M. Parrinello Proc. Natl. Acad. Sci. U.S.A. 109 2012 1467 1472
30. A. Onufriev, D. Bashford, and D.A. Case Proteins 55 2004 383 394
31. G.D. Hawkins, C.J. Cramer, and D.G. Truhlar Chem. Phys. Lett. 246 1995 122 129
32. G.D. Hawkins, C.J. Cramer, and D.G. Truhlar J. Phys. Chem. 100 1996 19824 19839
33. G. Bottegoni, W. Rocchia, M. Rueda, R. Abagyan, and A. Cavalli Plos One 6 2011 e18845
34. T.A. Halgren, R.B. Murphy, R.A. Friesner, H.S. Beard, L.L. Frye, W.T. Pollard, and J.L. Banks J. Med. Chem. 47 2004 1750 1759
35. C. Bissantz, G. Folkers, and D. Rognan J. Med. Chem. 43 2000 4759 4767
36. P.S. Charifson, J.J. Corkery, M.A. Murcko, and W.P. Walters J. Med. Chem. 42 1999 5100 5109
37. D.A. Case, T.A. Darden, T.E. Cheatham III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, M. Crowley, R.C. Walker, W. Zhang, K.M. Merz, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, and P.A. Kollman AMBER 10 2008 University of California San Francisco
38. http://mgltools.scripps.edu/.
39. X. Hu, and W.H. Shelver J. Mol. Graph. Model. 22 2003 115 126
40. M.S. Armstrong, G.M. Morris, P.W. Finn, R. Sharma, L. Moretti, R.I. Cooper, and W.G. Richards J. Comput.-Aided Mol. Des. 24 2010 789 801
41. C.A. Lipinski, C.E. Aldinger, T.A. Beyer, J. Bordner, D.F. Burdi, D.L. Bussolotti, P.B. Inskeep, and T.W. Siegel J. Med. Chem. 35 1992 2169 2177
42. Accelrys Software Inc., San Diego, CA, USA.
43. A. Coi, M. Tonelli, M.L. Ganadu, and A.M. Bianucci Bioorg. Med. Chem. 14 2006 2636 2641