Conformational sampling for large-scale virtual screening: accuracy versus ensemble size

Journal of Chemical Information and Modeling

Volumn 49, Issue 10, 2009, Pages 2303-2311

  Griewel, Axel ^a   Kayser, Ole ^a   Schlosser, Jochen ^a   Rarey, Matthias ^a  

^a UNIVERSITY OF HAMBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ECONOMIC AND SOCIAL EFFECTS; EXPONENTIAL FUNCTIONS; MOLECULES; TREES (MATHEMATICS);

COMPUTER AIDED DRUG DESIGN; CONFORMATIONAL ENERGIES; CONFORMATIONAL ENSEMBLE; CONFORMATIONAL SAMPLINGS; CRUCIAL PARAMETERS; ENERGY CONFORMERS; FLEXIBLE MOLECULES; TREE DATA STRUCTURES;

CONFORMATIONS;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; COMPUTER INTERFACE; CONFORMATION; DRUG SCREENING; FACTUAL DATABASE; METHODOLOGY; TIME;

ALGORITHMS; DATABASES, FACTUAL; DRUG EVALUATION, PRECLINICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; TIME FACTORS; USER-COMPUTER INTERFACE;

EID: 70350501158     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9002415     Document Type: Article

References (42)

1. Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A critical assessment of docking programs and scoring functions. J. Med. Chem. 2006, 49 (20), 5912-5931.
2. Moitessier, N.; Englebienne, P.; Lee, D.; Lawandi, J.; Corbeil, C. R. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br. J. Pharmacol. 2008, 153 (1), S7-26.
3. Mobley, D. L.; Dill, K. A. Binding of small-molecule ligands to proteins: "'what you see"' is not always "'what you get"' Structure 2009, 17 (4), 489-498.
4. (4) Bostrom, J.; Norrby, P. O.; Liljefors, T. Conformational energy penalties of protein-bound ligands. J. Comput.-Aided Mol. Des. 1998, 12 (4), 383-396. (Pubitemid 128513201)
5. Nicklaus, M. C.; Wang, S.; Driscoll, J. S.; Milne, G. W. Conformational changes of small molecules binding to proteins, Bioorg. Med. Chem. 1995, 3 (4), 411-428.
6. (6) Günther, S.; Senger, C.; Michalsky, E.; Goede, A.; Preissner, R. Representation of target-bound drugs by computed conformers: implications for conformational libraries. BMC Bioinf. 2006, 7, 293. (Pubitemid 44144647)
7. Perola, E.; Charifson, P. S. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J. Med. Chem. 2004, 47 (10), 2499-2510.
8. Wang, Q.; Pang, Y. P. Preference of small molecules for local minimum conformations when binding to proteins. PLoS One 2007, 2 (9), e820.
9. Gund, P. Pharmacophoric Pattern. Searching and Receptor Matching. Annu. Rep. Med. Chem. 1979, 14, 299-308.
10. Gund, P.; Wipke, W. T.; Langridge, R. In Computer searching of a molecular structure file for pharmacophoric patterns, International Conference on Computers in Chemistry Research and Education, Ljubljana, 1974, 1973; Hadzi, D., Zupan, J., Eds.; Elsevier: Amsterdam, Ljubljana, 1973; pp 5/33-5/38.
11. Pearlman, R. S. Rapid generation, of high quality approximate 3D molecular structures. Chem. Des. Autom. News 1987, 2 (1), 5-7.
12. Gasteiger, J.; Rudolph, C.; Sadowski, J. Automatic generation of 3Datomic coordinates for organic molecules. Tetrahedron Comput. Methodol. 1990, 3 (6, Part 3), 537-547.
13. Kearsley, S. K.; Smith, G. M. An alternative method for the alignment of molecular structures:Maximizing electrostatic and steric overlap. Tetrahedron Comput. Methodol. 1990, 3 (6), 615-633.
14. Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 1982, 161 (2), 269-288.
15. Van Drie, J. H.; Weininger, D.; Martin, Y. C. ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of threedimensional molecular structures. J. Comout.-Aided Mol. Des. 1989, 3 (3), 225-251.
16. Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P.; Miller, M. D. Flexibases: a way to enhance the use of molecular docking methods. J. Comput.-Aided Mol, Des. 1994, 8 (5), 565-582.
17. Miller, M. D.; Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P. FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8 (2), 153-174.
18. ROTATE; Molecular Networks: Erlangen, Germany, 2009.
19. OMEGA; OpenEye Scientific Software, Inc.: Santa Fe, NM, U.S.A., 2009.
20. Catalyst; Accelrys: San Diego, CA, U.S.A. 2009.
21. Leach, A. R.; Smellie, A. S. A combined model-building and distancegeometry approach to automated conformational analysis and search. J. Chem. Inf. Model. 1992, 32 (4), 379-385.
22. Smellie, A.; Kahn, S. D.; Teig, S. L. Analysis of Conformational Coverage. 2. Applications of Conformational Models. J. Chem. Inf. Madel. 1995, 35 (2), 295-304.
23. Smellie, A.; Kahn, S. D.; Teig, S. L. Analysis of Conformational Coverage. 1. Validation and Estimation of Coverage, J. Chem. Inf. Madel. 1995, 35 (2), 285-294.
24. Smellie, A.; Teig, L. T.; Towbin, P. Poling: Promoting Conformational Variation, J. Comput. Chem. 1995, 16 (2), 171-187.
25. FRED; OpenEye Scientific Software, Inc.: Santa Fe, NM, U.S.A., 2009.
26. Sauton, N.; Lagorce, D.; Villoutreix, B. O.; Miteva, M. A. MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMC Bioinf. 2008, 9, 184.
27. ROCS; OpenEye Scientific Software, Inc.: Santa Fe, NM, U.S.A., 2009.
28. Schlosser, J.; Rarey, M. Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds. J. Chem. Inf. Madel. 2009, 49 (4), 800-809.
29. (29) Kirchmair, J.; Wolber, G.; Laggner, C.; Langer, T. Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations, J. Chem. Inf. Model. 2006, 46 (4), 1848-1861. (Pubitemid 44185709)
30. (30) Rarey, M.; Wefing, S.; Lengauer, T. Placement of medium-sized molecular fragments into active sites of proteins. J. Comput.-Aided Mol. Des. 1996, 10 (1), 41-54. (Pubitemid 126712801)
31. Klebe, G.; Mietzner, T. A fast and efficient method to generate biologically relevant conformations. J. Comput.-Aided Mol. Des. 1994, 8 (5), 583-606.
32. Leach, A. R.; Prout, K. Automated conformational analysis: Directed conformational search using the A* algorithm. J. Comput. Chem. 1990, 11 (10), 1193-1205.
33. Clark, M.; Cramer III, R. D.; van Opdenbosch, N. Validation of the General Purpose Tripos 5.2 Force Field, J. Comput. Chem. 1989, 10 (8), 982-1012.
34. Stockwell, G. R.; Thornton, J. M. Conformational diversity of ligands bound to proteins. J. Mol. Biol. 2006, 356 (4), 928-944.
35. Diller, D. J.; Merz, K. M. J. Can we separate active from inactive conformations. J. Comput.-Aided Mol. Des. 2002, 16 (2), 105-112.
36. Allen, F. H.; Davies, J. E.; Galloy, J. J.; Johnson, O.; Kennard, O.; Macrae, C. F.; Mitchell, E. M.; Mitchell, G. F.; Smith, J. M.; Watson, D. G. The development of versions 3 and 4 of the Cambridge Structural Database System. J. Chem. Inf. Comput. Sei. 2002, 31 (2), 187-204.
37. Maass, P.; Schulz-Gasch, T.; Stahl, M.; Rarey, M. Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformations, J. Chem. Inf. Model. 2007, 47 (2), 390-399.
38. (38) Oprea, T. I.; Davis, A. M.; Teague, S. J.; Leeson, P. D. Is there a difference between leads and drugs? A historical perspective. J. Chem. Inf. Comput. Sei. 2001, 41 (5), 1308-1315. (Pubitemid 33663896)
39. Feng, Z.; Chen, L.; Maddula, H.; Akcan, O.; Oughtred, R.; Berman, H. M.; Westbrook, J. Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics 2004, 20 (13), 2153-2155.
40. Wang, L.; Zuercher, W. J.; Consler, T. G.; Lambert, M. H.; Miller, A. B.; Orband-Miller, L. A.; McKee, D. D.; Willson, T. M.; Nolte, R. T. X-ray crystal structures of the estrogen-related receptor-gamma ligand binding domain in three functional states reveal the molecular basis of small molecule regulation. J. Biol. Chem. 2006, 281 (49), 37773-37781.
41. Wu, Y. H.; Ko, T. P.; Guo, R. T.; Hu, S. M.; Chuang, L. M.; Wang, A. H. Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2. Structure 2008,16 (11), 1714-1723.
42. Mol, C. D.; Dougan, D. R.; Schneider, T. R.; Skene, R. J.; Kraus, M. L.; Scheibe, D. N.; Snell, G. P.; Zou, H.; Sang, B. C.; Wilson, K. P. Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase. J. Mol. Chem. 2004, 279 (30), 31655-31663.