High-performance drug discovery: Computational screening by combining docking and molecular dynamics simulations

PLoS Computational Biology

Volumn 5, Issue 10, 2009, Pages

  Okimoto, Noriaki ^a,b   Futatsugi, Noriyuki ^a,b   Fuji, Hideyoshi ^a,c   Suenaga, Atsushi ^a   Morimoto, Gentaro ^a,b   Yanai, Ryoko ^a   Ohno, Yousuke ^b   Narumi, Tetsu ^a,d   Taiji, Makoto ^a,b  

^a Advanced Science Institute   (Japan)

^b RIKEN   (Japan)

^c CHIBA UNIVERSITY   (Japan)

^d UNIVERSITY OF ELECTRO COMMUNICATIONS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPUTATIONAL CHEMISTRY; LEAD COMPOUNDS; MOLECULAR MODELING; PROTEINS;

COMPOUND SCREENINGS; DRUG DESIGN; DRUG DISCOVERY; DYNAMICS SIMULATION; LIGAND CONFORMATIONS; MOLECULAR DOCKING; PERFORMANCE; PROTEIN LIGANDS; SCREENING APPROACHES; TARGET PROTEINS;

MOLECULAR DYNAMICS;

LIGAND; WATER; ACETYLCHOLINESTERASE; CYCLIN DEPENDENT KINASE 2; P16 PROTEASE, HUMAN IMMUNODEFICIENCY VIRUS 1; PROTEINASE; TRYPSIN;

ARTICLE; BINDING AFFINITY; MATHEMATICAL COMPUTING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PROTEIN CONFORMATION; PROTEIN TARGETING; SCREENING; SIMULATION; AREA UNDER THE CURVE; BINDING SITE; BIOLOGY; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DRUG DEVELOPMENT; METABOLISM; METHODOLOGY; PHARMACOKINETICS; RECEIVER OPERATING CHARACTERISTIC; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ACETYLCHOLINESTERASE; AREA UNDER CURVE; BINDING SITES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; CYCLIN-DEPENDENT KINASE 2; DRUG DISCOVERY; HIV PROTEASE; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; PHARMACOKINETICS; ROC CURVE; THERMODYNAMICS; TRYPSIN;

EID: 73349093728     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000528     Document Type: Article

References (74)

1. Young K, Lin S, Sun L, Lee E, Modi M, et al. (1998) Identification of a calcium channel modulator using a high throughput yeast two-hybrid screen. Nat Biotechnol 16: 946-950.
2. Hamasaki K, Rando RR (1998) A high-throughput fluorescence screen to monitor the specific binding of antagonists to RNA targets. Anal Biochem 261: 183-190.
3. Moore KJ, Turconi S, Miles-Williams A, Djaballah H, Hurskainen P, et al. (1999) A Homogenous 384-Well High Throughput Screen for Novel Tumor Necrosis Factor Receptor: Ligand Interactions Using Time Resolved Energy Transfer. J Biomol Screen 4: 205-214.
4. Dunn D, Orlowski M, McCoy P, Gastgeb F, Appell K, et al. (2000) Ultra-high throughput screen of two-million-member combinatorial compound collection in a miniaturized, 1536-well assay format. J Biomol Screen 5: 177-188.
5. Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, et al. (2002) Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 45: 2213-2221.
6. Chen J, Zhang Z, Stebbins JL, Zhang X, Hoffman R, et al. (2007) A fragmentbased approach for the discovery of isoform-specific p38alpha inhibitors. ACS Chem Biol 2: 329-336.
7. Carr RA, Congreve M, Murray CW, Rees DC (2005) Fragment-based lead discovery: leads by design. Drug Discov Today 10: 987-992.
8. Hann MM, Leach AR, Harper G (2001) Molecular complexity and its impact on the probability of finding leads for drug discovery. J Chem Inf Comput Sci 41: 856-864.
9. Jones G, Willett P, Glen RC (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245: 43-53.
10. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267: 727-748.
11. Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15: 411-428.
12. Goodsell DS, Morris GM, Olson AJ (1996) Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 9: 1-5.
13. Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47: 1750-1759.
14. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47: 1739-1749.
15. Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261: 470-489.
16. Bursulaya BD, Totrov M, Abagyan R, Brooks CL (2003) Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des 17: 755-763.
17. Stahl M, Rarey M (2001) Detailed analysis of scoring functions for virtual screening. J Med Chem 44: 1035-1042.
18. Wyss PC, Gerber P, Hartman PG, Hubschwerlen C, Locher H, et al. (2003) Novel dihydrofolate reductase inhibitors. Structure-based versus diversity-based library design and high-throughput synthesis and screening. J Med Chem 46: 2304-2312.
19. Pearlman DA, Charifson PS (2001) Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system. J Med Chem 44: 3417-3423.
20. Kollman P (1993) Free-Energy Calculations - Applications to Chemical and Biochemical Phenomena. Chemical Reviews 93: 2395-2417.
21. Aqvist J, Luzhkov VB, Brandsdal BO (2002) Ligand binding affinities from MD simulations. Acc Chem Res 35: 358-365.
22. Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, et al. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research 33: 889-897.
23. Huo S, Wang J, Cieplak P, Kollman PA, Kuntz ID (2002) Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J Med Chem 45: 1412-1419.
24. Masukawa KM, Kollman PA, Kuntz ID (2003) Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. J Med Chem 46: 5628-5637.
25. Kuhn B, Gerber P, Schulz-Gasch T, Stahl M (2005) Validation and use of the MM-PBSA approach for drug discovery. J Med Chem 48: 4040-4048.
26. Ferrara P, Curioni A, Vangrevelinghe E, Meyer T, Mordasini T, et al. (2006) New scoring functions for virtual screening from molecular dynamics simulations with a quantum-refined force-field (QRFF-MD). Application to cyclin-dependent kinase 2. J Chem Inf Model 46: 254-263.
27. Narumi T, Ohno Y, Okimoto N, Koishi T, Suenaga A, et al. (2006) A 185 Tflops simulation of amyloid-forming peptides from Yeast Prion Sup35 with the special-purpose computer System MD-GRAPE3. Proc Supercomputing 2006, in CD-ROM.
28. Taiji M (2004) MDGRAPE-3 chip: a 165 Gflops application specific LSI for molecular dynamics simulations.; 2004. IEEE Computer Society. pp. in CDROM.
29. Thomas MP, McInnes C, Fischer PM (2006) Protein structures in virtual screening: A case study with CDK2. J Med Chem 49: 92-104.
30. Kontoyianni M, McClellan LM, Sokol GS (2004) Evaluation of docking performance: comparative data on docking algorithms. J Med Chem 47: 558-565.
31. Wang R, Lu Y, Wang S (2003) Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 46: 2287-2303.
32. Cho AE, Wendel JA, Vaidehi N, Kekenes-Huskey PM, Floriano WB, et al. (2005) The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals. J Comput Chem 26: 48-71.
33. Erickson JA, Jalaie M, Robertson DH, Lewis RA, Vieth M (2004) Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J Med Chem 47: 45-55.
34. Kua J, Zhang Y, McCammon JA (2002) Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. J Am Chem Soc 124: 8260-8267.
35. Witten IH, Frank E (1999) Data mining: practical machine learning tools and techniques with java implementations. New York: Morgan Kaufmann.
36. Habe H, Morii K, Fushinobu S, Nam JW, Ayabe Y, et al. (2003) Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme). Biochem Biophys Res Commun 303: 631-639.
37. Dorfman DD, Berbaum KS, Metz CE (1992) Receiver operating characteristic rating analysis. Generalization to the population of readers and patients with the jackknife method. Invest Radiol 27: 723-731.
38. Hillis SL, Berbaum KS (2005) Monte Carlo validation of the Dorfman-Berbaum-Metz method using normalized pseudovalues and less data-based model simplification. Acad Radiol 12: 1534-1541.
39. Hillis SL, Obuchowski NA, Schartz KM, Berbaum KS (2005) A comparison of the Dorfman-Berbaum-Metz and Obuchowski-Rockette methods for receiver operating characteristic (ROC) data. Stat Med 24: 1579-1607.
40. Roe CA, Metz CE (1997) Variance-component modeling in the analysis of receiver operating characteristic index estimates. Acad Radiol 4: 587-600.
41. Roe CA, Metz CE (1997) Dorfman-Berbaum-Metz method for statistical analysis of multireader, multimodality receiver operating characteristic data: validation with computer simulation. Acad Radiol 4: 298-303.
42. Gohlke H, Case DA (2004) Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. Journal of Computational Chemistry 25: 238-250.
43. Numata J, Wan M, Knapp EW (2007) Conformational entropy of biomolecules: beyond the quasi-harmonic approximation. Genome Inform 18: 192-205.
44. Chang CE, Chen W, Gilson MK (2005) Evaluating the accuracy of the quasiharmonic approximation. Journal of Chemical Theory and Computation 1: 1017-1028.
45. Davies TG, Bentley J, Arris CE, Boyle FT, Curtin NJ, et al. (2002) Structurebased design of a potent purine-based cyclin-dependent kinase inhibitor. Nat Struct Biol 9: 745-749.
46. Davis ST, Benson BG, Bramson HN, Chapman DE, Dickerson SH, et al. (2001) Prevention of chemotherapy-induced alopecia in rats by CDK inhibitors. Science 291: 134-137.
47. Lamb ML, Jorgensen WL (1997) Computational approaches to molecular recognition. Curr Opin Chem Biol 1: 449-457.
48. Zhou Z, Madura JD (2004) Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS. Proteins 57: 493-503.
49. Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49: 6789-6801.
50. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, et al. (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33: 889-897.
51. Katz BA, Mackman R, Luong C, Radika K, Martelli A, et al. (2000) Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator. Chem Biol 7: 299-312.
52. Ala PJ, DeLoskey RJ, Huston EE, Jadhav PK, Lam PY, et al. (1998) Molecular recognition of cyclic urea HIV-1 protease inhibitors. J Biol Chem 273: 12325-12331.
53. Dvir H, Wong DM, Harel M, Barril X, Orozco M, et al. (2002) 3D structure of Torpedo californica acetylcholinesterase complexed with huprine X at 2.1 A resolution: kinetic and molecular dynamic correlates. Biochemistry 41: 2970-2981.
54. MOE. Montreal: Chemical Computing Group Inc.
55. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46: 3-26.
56. Wang R, Fang X, Lu Y, Yang CY, Wang S (2005) The PDBbind database: methodologies and updates. J Med Chem 48: 4111-4119.
57. Wang R, Fang X, Lu Y, Wang S (2004) The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J Med Chem 47: 2977-2980.
58. Gray NS, Wodicka L, Thunnissen AMWH, Norman TC, Kwon SJ, et al. (1998) Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Science 281: 533-538.
59. Schrödinger Inc. PortlandOR).
60. Sørenson T (1948) A method of establishing groups of equal amplitude in a plant based on similarity of species content and its applications to analysis of vegetation on Danish commons. Biologiske Skrifter 5: 1-34.
61. Hoffmann D, Kramer B, Washio T, Steinmetzer T, Rarey M, et al. (1999) Two-stage method for protein-ligand docking. J Med Chem 42: 4422-4433.
62. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of Simple Potential Functions for Simulating Liquid Water. Journal of Chemical Physics 79: 926-935.
63. Case DA, Darden TA, Cheatham TEr, Simmerling CL, Wang J, et al. (2004) AMBER 8 University of California San Francisco.
64. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24: 1999-2012.
65. Berendsen HJC, Postma JMP, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Comput Phys 81: 3684-3690.
66. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25: 1157-1174.
67. Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23: 1623-1641.
68. Jakalian A, Bush BL, Jack DB, Bayly CI (2000) Fast, efficient generation of high-quality atomic Charges. AM1-BCC model: I. Method. Journal of Computational Chemistry 21: 132-146.
69. Rocchia W, Alexov E, Honig B (2001) Extending the applicability of the nonlinear poisson-boltzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem B 105: 6507-6514.
70. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, et al. (2002) Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem 23: 128-137.
71. Sitkoff D, Sharp KA, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98: 1978-1988.
72. Swanson JMJ, Adcock SA, McCammon JA (2005) Optimized radii for Poisson-Boltzmann calculations with the AMBER force field. Journal of Chemical Theory and Computation 1: 484-493.
73. Sanner MF, Olson AJ, Spehner JC (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38: 305-320.
74. Levy RM, Karplus M, Kushick J, Perahia D (1984) Evaluation of the Configurational Entropy for Proteins - Application to Molecular-Dynamics Simulations of an Alpha-Helix. Macromolecules 17: 1370-1374.