Ensemble-based docking using biased molecular dynamics

Journal of Chemical Information and Modeling

Volumn 54, Issue 7, 2014, Pages 2127-2138

  Campbell, Arthur J ^a   Lamb, Michelle L ^a   Joseph McCarthy, Diane ^a,b  

^a ASTRAZENECA   (United Kingdom)

^b EnBiotix Inc ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CONFORMATIONS; DRUG PRODUCTS; LIGANDS; MOLECULAR DYNAMICS;

COMPUTATIONAL COSTS; COMPUTER AIDED DRUG DESIGN; CONFORMATIONAL SPACE; CYCLIN-DEPENDENT KINASE; MOLECULAR DYNAMICS SIMULATIONS; PROTEIN CONFORMATION; PROTEIN FLEXIBILITY; PROTEIN-LIGAND INTERACTIONS;

PROTEINS;

BLOOD CLOTTING FACTOR 10A; CYCLIN DEPENDENT KINASE 2; LIGAND;

CHEMISTRY; DRUG DEVELOPMENT; METABOLISM; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; TEMPERATURE;

CYCLIN-DEPENDENT KINASE 2; DRUG DISCOVERY; FACTOR XA; LIGANDS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; TEMPERATURE;

EID: 84904976112     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400729j     Document Type: Article

References (51)

1. Munos, B. Lessons from 60 years of pharmaceutical innovation Nat. Rev. Drug Discovery 2009, 8, 959-968
2. Nichols, S. E.; Baron, R.; Ivetac, A.; McCammon, J. A. Predictive power of molecular dynamics receptor structures in virtual screening J. Chem. Inf. Model. 2011, 51, 1439-1446
3. McCammon, J. A.; Gelin, B. R.; Karplus, M. Dynamics of folded proteins Nature 1977, 267, 585-590
4. Adcock, S. A.; McCammon, J. A. Molecular dynamics: survey of methods for simulating the activity of proteins Chem. Rev. 2006, 106, 1589-1615
5. McMartin, C.; Bohacek, R. S. QXP: powerful, rapid computer algorithms for structure-based drug design J. Comput.-Aided Mol. Des. 1997, 11, 333-344
6. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 2006, 65, 712-725
7. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B. P.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M. -.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 11; University of California, San Francisco: San Francisco, CA, 2010.
8. Bowers, K. J.; Chow, E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossváry, I.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Shan, Y.; Shaw, D. E. In Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. Proceedings from the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11-17, 2006; IEEE: New York, 2006.
9. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable molecular dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
10. Shaw, D. E.; Deneroff, M. M.; Dror, R. O.; Kuskin, J. S.; Larson, R. H.; Salmon, J. K.; Young, C.; Batson, B.; Bowers, K. J.; Chao, J. C.; Eastwood, M. P.; Gagliardo, J.; Grossman, J. P.; Ho, C. R.; Ierardi, D. J.; Kolossváry, I.; Klepeis, J. L.; Layman, T.; McLeavey, C.; Moraes, M. A.; Mueller, R.; Priest, E. C.; Shan, Y.; Spengler, J.; Theobald, M.; Towles, B.; Wang, S. C. Anton, a special-purpose machine for molecular dynamics simulation Commun. ACM 2008, 51, 91-97
11. Shan, Y.; Kim, E. T.; Eastwood, M. P.; Dror, R. O.; Seeliger, M. A.; Shaw, D. E. How does a drug molecule find its target binding site? J. Am. Chem. Soc. 2011, 133, 9181-9183
12. Amaro, R. E.; Li, W. W. Emerging methods for ensemble-based virtual screening Curr. Top. Med. Chem. 2010, 10, 3-13
13. Nichols, S. E.; Baron, R.; McCammon, J. A. On the use of molecular dynamics receptor conformations for virtual screening Methods Mol. Biol. 2012, 819, 93-103
14. Craig, I. R.; Essex, J. W.; Spiegel, K. Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments J. Chem. Inf. Model. 2010, 50, 511-524
15. Rueda, M.; Bottegoni, G.; Abagyan, R. Recipes for the selection of experimental protein conformations for virtual screening J. Chem. Inf. Model. 2010, 50, 186-193
16. Bottegoni, G.; Rocchia, W.; Rueda, M.; Abagyan, R.; Cavalli, A. Systematic exploitation of multiple receptor conformations for virtual ligand screening PLoS One 2011, 6, e18845
17. Sherman, W.; Day, T.; Jacobson, M. P.; Friesner, R. A.; Farid, R. Novel procedure for modeling ligand/receptor induced fit effects J. Med. Chem. 2006, 49, 534-553
18. Amaro, R. E.; Baron, R.; McCammon, J. A. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design J. Comput.-Aided Mol. Des. 2008, 22, 693-705
19. Schames, J. R.; Henchman, R. H.; Siegel, J. S.; Sotriffer, C. A.; Ni, H.; McCammon, J. A. Discovery of a novel binding trench in HIV integrase J. Med. Chem. 2004, 47, 1879-1881
20. Cavasotto, C. N.; Abagyan, R. A. Protein flexibility in ligand docking and virtual screening to protein kinases J. Mol. Biol. 2004, 337, 209-225
21. Carlson, H. A.; Masukawa, K. M.; Rubins, K.; Bushman, F. D.; Jorgensen, W. L.; Lins, R. D.; Briggs, J. M.; McCammon, J. A. Developing a dynamic pharmacophore model for HIV-1 integrase J. Med. Chem. 2000, 43, 2100-2114
22. Robustelli, P.; Kohlhoff, K.; Cavalli, A.; Vendruscolo, M. Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins Structure 2010, 18, 923-933
23. Isin, B.; Schulten, K.; Tajkhorshid, E.; Bahar, I. Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes Biophys. J. 2008, 95, 789-803
24. Gerek, Z. N.; Ozkan, S. B. A flexible docking scheme to explore the binding selectivity of PDZ domains Protein Sci. 2010, 19, 914-928
25. Cavasotto, C. N.; Kovacs, J. A.; Abagyan, R. A. Representing receptor flexibility in ligand docking through relevant normal modes J. Am. Chem. Soc. 2005, 127, 9632-9640
26. Rueda, M.; Totrov, M.; Abagyan, R. ALiBERO: evolving a team of complementary pocket conformations rather than a single leader J. Chem. Inf. Model. 2012, 52, 2705-2714
27. Venkatraman, V.; Ritchie, D. W. Flexible protein docking refinement using pose-dependent normal mode analysis Proteins 2012, 80, 2262-2274
28. Schulze-Gahmen, U.; De Bondt, H. L.; Kim, S. H. High-resolution crystal structures of human cyclin-dependent kinase 2 with and without ATP: bound waters and natural ligand as guides for inhibitor design J. Med. Chem. 1996, 39, 4540-4546
29. Davie, E. W.; Fujikawa, K.; Kisiel, W. The coagulation cascade: initiation, maintenance, and regulation Biochemistry 1991, 30, 10363-10370
30. Borensztajn, K.; Spek, C. A. Blood coagulation factor Xa as an emerging drug target Expert Opin. Ther. Targets 2011, 15, 341-349
31. Kamata, K.; Kawamoto, H.; Honma, T.; Iwama, T.; Kim, S. H. Structural basis for chemical inhibition of human blood coagulation factor Xa Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 6630-6635
32. Guertin, K. R.; Gardner, C. J.; Klein, S. I.; Zulli, A. L.; Czekaj, M.; Gong, Y.; Spada, A. P.; Cheney, D. L.; Maignan, S.; Guilloteau, J. P.; Brown, K. D.; Colussi, D. J.; Chu, V.; Heran, C. L.; Morgan, S. R.; Bentley, R. G.; Dunwiddie, C. T.; Leadley, R. J.; Pauls, H. W. Optimization of the beta-aminoester class of factor Xa inhibitors. Part 2: Identification of FXV673 as a potent and selective inhibitor with excellent In vivo anticoagulant activity Bioorg. Med. Chem. Lett. 2002, 12, 1671-1674
33. Hamdouchi, C.; Zhong, B.; Mendoza, J.; Collins, E.; Jaramillo, C.; De Diego, J. E.; Robertson, D.; Spencer, C. D.; Anderson, B. D.; Watkins, S. A.; Zhang, F.; Brooks, H. B. Structure-based design of a new class of highly selective aminoimidazo[1,2-a]pyridine-based inhibitors of cyclin dependent kinases Bioorg. Med. Chem. Lett. 2005, 15, 1943-1947
34. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method J. Comput. Chem. 2000, 21, 132-146
35. Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation J. Comput. Chem. 2002, 23, 1623-1641
36. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174
37. Bradbrook, G. M.; Gleichmann, T.; Harrop, S. J.; Habash, J.; Raftery, J.; Kalb, J.; Yariv, J.; Hillier, I. H.; Helliwell, J. R. X-Ray and molecular dynamics studies of concanavalin-A glucoside and mannoside complexes Relating structure to thermodynamics of binding J. Chem. Soc., Faraday Trans. 1998, 1603-1611
38. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
39. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
40. Cheatham, T. E., III; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins J. Am. Chem. Soc. 1995, 4193-4194
41. Ryckaert, J.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
42. Shao, J.; Tanner, S. W.; Thompson, N.; Cheatham, T. E. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms J. Chem. Theory Comput. 2007, 3, 2312-2334
43. Verdonk, M. L.; Mortenson, P. N.; Hall, R. J.; Hartshorn, M. J.; Murray, C. W. Protein-ligand docking against non-native protein conformers J. Chem. Inf. Model. 2008, 48, 2214-2225
44. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy J. Med. Chem. 2004, 47, 1739-1749
45. Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening J. Med. Chem. 2004, 47, 1750-1759
46. Koska, J.; Spassov, V. Z.; Maynard, A. J.; Yan, L.; Austin, N.; Flook, P. K.; Venkatachalam, C. M. Fully automated molecular mechanics based induced fit protein-ligand docking method J. Chem. Inf. Model. 2008, 48, 1965-1973
47. Warren, G. M.; McGaughey, G. B.; Nevins, N. Editorial J. Comput.-Aided Mol. Des. 2012, 26, 674
48. Repasky, M. P.; Murphy, R. B.; Banks, J. L.; Greenwood, J. R.; Tubert-Brohman, I.; Bhat, S.; Friesner, R. A. Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide J. Comput.-Aided Mol. Des. 2012, 26, 787-799
49. Cheng, T.; Li, X.; Li, Y.; Liu, Z.; Wang, R. Comparative assessment of scoring functions on a diverse test set J. Chem. Inf. Model. 2009, 49, 1079-1093
50. 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, 5912-5931
51. Wang, R.; Lu, Y.; Wang, S. Comparative evaluation of 11 scoring functions for molecular docking J. Med. Chem. 2003, 46, 2287-2303