Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery

Bioorganic and Medicinal Chemistry

Volumn 21, Issue 24, 2013, Pages 7898-7920

  Chen, I Jen ^a   Foloppe, Nicolas ^a  

^a Vernalis PLC   (United Kingdom)

Author keywords

Bioactive structures; Computational chemistry; Conformational sampling; Drug discovery; Flexible compounds; Global energy minimum; Low mode; Macrocycles

Indexed keywords

MACROCYCLIC COMPOUND; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CONFORMATIONAL TRANSITION; DRUG DEVELOPMENT; MOLECULAR MODEL; PHARMACOLOGY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

%BIOCONF_REP; %GLOBMIN_FOUND; 3D; BIOACTIVE STRUCTURES; COMPUTATIONAL CHEMISTRY; CONFORMATIONAL SAMPLING; DIEL; DISTANCE-DEPENDENT DIELECTRIC; DRUG DISCOVERY; FLEXIBLE COMPOUNDS; GB; GENERALIZED BORN; GLOBAL ENERGY MINIMUM; GRAPHICAL USER INTERFACE; GUI; LARGE-SCALE LOW-MODE; LLMOD; LMOD; LOW-MODE; LOWMODEMD; MACROCYCLES; MAX-ITERATION; MAXIMUM NUMBER OF SEARCH ITERATIONS PER COMPOUND; MD-BASED SIMULATED ANNEALING FOLLOWED BY LARGE-SCALE LOW-MODE; MD/LLMOD; MERCK MOLECULAR FORCE FIELD; MIXED TORSIONAL/LARGE-SCALE LOW-MODE; MIXED TORSIONAL/LOW-MODE; MMFF; MOE; MOLECULAR OPERATING ENVIRONMENT; MOLECULAR WEIGHT; MT/LLMOD; MT/LMOD; MW; NBCONFS; NROT; NUMBER OF CONFORMERS; NUMBER OF MOVES PER ROTATABLE BOND; NUMBER OF ROTATABLE BONDS; OPLS; OPREA NUMBER OF ROTATABLE BONDS; OPR_NROT; OPTIMIZED POTENTIALS FOR LIQUID SIMULATIONS FORCE FIELD; PDB; PERCENTAGE OF COMPOUNDS FOR WHICH THE BIOACTIVE STRUCTURE WAS REPRODUCED; PERCENTAGE OF COMPOUNDS FOR WHICH THE GLOBAL ENERGY MINIMUM WAS FOUND; PROTEIN DATA BANK; RADIUS OF GYRATION; RGYR; ROTSTEPS; SEARCH METHOD COMBINING LOW-MODE MOVES AND MOLECULAR DYNAMICS; THREE-DIMENSIONAL;

DRUG DISCOVERY; MACROCYCLIC COMPOUNDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE;

EID: 84888440984     PISSN: 09680896     EISSN: 14643391     Source Type: Journal    
DOI: 10.1016/j.bmc.2013.10.003     Document Type: Article

References (72)

1. K.A. Brameld, B. Kuhn, D.C. Reuter, and M. Stahl J. Chem. Inf. Model. 48 2008 1
2. R.J. Chein, and E.J. Corey Org. Lett. 12 2010 132
3. J.P. Terhorst, and W.L. Jorgensen J. Chem. Theory Comput. 6 2010 2762
4. R. Taylor J. Chem. Inf. Model. 51 2011 897
5. W.C. Still, and I. Galynker Tetrahedron 37 1981 3981
6. A.J. Cruz-Cabeza, J.W. Liebeschuetz, and F.H. Allen CrystEngComm 14 2012 6797
7. S. Wlodek, A.G. Skillman, and A. Nicholls Acta Cryst. D62 2006 741
8. J.A. Bell, K.L. Ho, and R. Farid Acta Crystallogr., Sect. D 68 2012 935
9. I. Kolossvary, and W.C. Guida J. Am. Chem. Soc. 118 1996 5011
10. H. Matter, L. Szilagyi, P. Forgo, Z. Marinic, and B. Klaic J. Am. Chem. Soc. 119 1997 2212
11. M.W. Lodewyk, M.R. Siebert, and D.J. Tantillo Chem. Rev. 112 2012 1839
12. C.D. Blundell, M.J. Packer, and A. Almond Bioorg. Med. Chem. 21 2013 4976
13. G. Jones, P. Willett, and R.C. Glen J. Comput.-Aided Mol. Des. 9 1995 532
14. P. Labute, and C. Williams J. Med. Chem. 44 2001 1483
15. A.R. Leach, V.J. Gillet, R.A. Lewis, and R. Taylor J. Med. Chem. 53 2010 539
16. N. Foloppe, K. Benwell, T.D. Brooks, G. Kennett, A.R. Knight, A. Misra, and N.J.T. Monck Bioorg. Med. Chem. Lett. 19 2009 4183
17. A. Nicholls, G.B. McGaughey, R.P. Sheridan, A.C. Good, G. Warren, M. Mathieu, S.W. Muchmore, S.P. Brown, J.A. Grant, J.A. Haigh, N. Nevins, A.N. Jain, and B. Kelley J. Med. Chem. 53 2010 3862
18. O. Trott, and A.J. Olson J. Comput. Chem. 31 2010 455
19. T. Cheeseright, M. Mackey, S. Rose, and A. Vinter J. Chem. Inf. Model. 46 2006 665
20. J. Bostrom, P.O. Norrby, and T. Liljefors J. Comput.-Aided Mol. Des. 12 1998 383
21. E. Perola, and P.S. Charifson J. Med. Chem. 47 2004 2499
22. I. Chen, and N. Foloppe J. Chem. Inf. Model. 48 2008 1773
23. M. Sitzmann, I.E. Weidlich, I.V. Filippov, C. Liao, M.L. Peach, W.-D. Ihlenfeldt, R.G. Karki, Y.V. Borodina, R.E. Cachau, and M.C. Nicklaus J. Chem. Inf. Model. 52 2012 739
24. D.K. Agrafiotis, A.C. Gibbs, F. Zhu, S. Izrailev, and E. Martin J. Chem. Inf. Model. 47 2007 1067
25. J. Li, T. Ehlers, J. Sutter, S. Varma-O'Brien, and J. Kirchmair J. Chem. Inf. Model. 47 2007 1923
26. O. Sperandio, M. Souaille, F. Delfaud, M.A. Miteva, and B.O. Villoutreix Eur. J. Med. Chem. 44 2009 1405
27. P. Bonnet, D.K. Agrafiotis, F. Zhu, and E. Martin J. Chem. Inf. Model. 49 2009 2242
28. X. Liu, F. Bai, S. Ouyang, X. Wang, H. Li, and H. Jiang BMC Bioinformatics 10 2009 101
29. K.S. Watts, P. Dalal, R.B. Murphy, W. Sherman, R.A. Friesner, and J.C. Shelley J. Chem. Inf. Model. 50 2010 534
30. I. Chen, and N. Foloppe J. Chem. Inf. Model. 50 2010 822
31. P.C.D. Hawkins, A.G. Skillman, G.L. Warren, B.A. Ellingson, and M.T. Stahl J. Chem. Inf. Model. 50 2010 572
32. A. Andronico, A. Randall, R.W. Benz, and P. Baldi J. Chem. Inf. Model. 51 2011 760
33. F. Bai, X. Liu, J. Li, H. Zhang, H. Jiang, X. Wang, and H. Li BMC Bioinformatics 11 2010 545
34. P. Labute J. Chem. Inf. Model. 50 2010 792
35. J.P. Ebejer, G.M. Morris, and C. Deane J. Chem. Inf. Model. 52 2012 1146
36. P.C.D. Hawkins, and A. Nicholls J. Chem. Inf. Model. 52 2012 2919
37. C. Schärfer, T. Schulz-Gasch, H.C. Ehrlich, W. Guba, M. Rarey, and M. Stahl J. Med. Chem. 56 2013 2016
38. N. Foloppe, and I. Chen Curr. Med. Chem. 16 2009 3381
39. J. Shim, and A.D.J. Mackerell MedChemComm 2 2011 356
40. G. Chang, W.C. Guida, and W.C. Still J. Am. Chem. Soc. 111 1989 4379
41. D.M. Ferguson, and D.J. Raber J. Am. Chem. Soc. 111 1989 4371
42. N. Foloppe, and L. Nilsson J. Phys. Chem. B 109 2005 9119
43. I. Kolossvary, and G.M. Keseru J. Comput. Chem. 22 2001 21
44. A. Smellie, S.L. Teig, and P. Towbin J. Comput. Chem. 16 1995 171
45. S. Izrailev, F. Zhu, and D.K. Agrafiotis J. Comput. Chem. 27 2006 1962
46. I. Chen, and N. Foloppe Drug Dev. Res. 72 2011 85
47. H. Ledford Nature 468 2010 608
48. A.M.S. Mayer, K.B. Glaser, C. Cuevas, R.S. Jacobs, W. Kem, R.D. Little, J.M. McIntosh, D.J. Newman, B.C. Potts, and D.E. Shuster Trends Pharmacol. Sci. 31 2010 255
49. N. Foloppe, N. Matassova, and F. Aboul-ela Drug Discovery Today 11 2006 1019
50. P. Vlieghe, V. Lisowski, J. Martinez, and M. Khrestchatisky Drug Discov. Today 15 2010 40
51. E.M. Driggers, S.P. Hale, J. Lee, and N.K. Terrett Nat. Rev. Drug Disc. 7 2008 608
52. J.A. Wells, and C.L. McClendon Nature 450 2007 1001
53. D.J. Diller, and K.M. Merz J. Comput.-Aided Mol. Des. 16 2002 105
54. I. Kolossvary, and W.C. Guida J. Comput. Chem. 20 1999 1671
55. C. Parish, R. Lombardi, K. Sinclair, E. Smith, A. Goldberg, M. Rappleye, and M. Dure J. Mol. Graphics Modell. 21 2002 129
56. http://www.chemcomp.com/.
57. F. Mohamadi, M.G.J. Richards, W.C. Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chang, T. Hendrickson, and W.C. Still J. Comp. Chem. 11 1990 440
58. http://www.schrodinger.com.
59. J. Bostrom J. Comput.-Aided Mol. Design 15 2001 1137
60. M.J. Loferer, I. Kolossvary, and A. Aszodi J. Mol. Graphics Modell. 25 2007 700
61. T. Halgren J. Comput. Chem. 17 1996 490
62. W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives J. Am. Chem. Soc. 118 1996 11225
63. D. Shivakumar, E. Harder, W. Damm, R.A. Friesner, and W. Sherman J. Chem. Theory Comput. 8 2012 2553
64. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne Nucleic Acids Res. 28 2000 235
65. T.I. Oprea J. Comput.-Aided Mol. Des. 14 2000 251
66. A. Onufriev, D. Bashford, and D.A. Case J. Phys. Chem. B 104 2000 3712
67. A. Smellie, S.D. Kahn, and S.L. Teig J. Chem. Inf. Comput. Sci. 35 1995 285
68. Y. Borodina, E. Bolton, F. Fontaine, and S.H. Bryant J. Chem. Inf. Model. 47 2007 1428
69. M. Saunders J. Am. Chem. Soc. 109 1987 3150
70. M.C. Nicklaus, W. Shaomeng, J.S. Driscoll, and W.A. Milne Biorg. Med. Chem. 3 1995 411
71. J. Kirchmair, C. Laggner, G. Wolber, and T. Langer J. Chem. Inf. Model. 45 2005 422
72. H. Ming-Hong, O. Haq, and I. Muegge J. Chem. Inf. Model. 47 2007 2242