FReDoWS: A method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection

BMC Genomics

Volumn 12, Issue SUPPL. 4, 2011, Pages

  Machado, Karina S ^a   Schroeder, Evelyn K ^a   Ruiz, Duncan D ^a   Cohen, Elisângela M L ^a   Norberto de Souza, Osmar ^a  

^a PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; LIGAND; MUTANT PROTEIN; BACTERIAL PROTEIN; INHA PROTEIN, MYCOBACTERIUM; OXIDOREDUCTASE;

ARTICLE; AUTOMATION; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DRUG DESIGN; EXPLICIT RECEPTOR FLEXIBILITY; FULLY FLEXIBLE RECEPTOR MODEL; LIGAND BINDING; METHODOLOGY; MODEL; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MYCOBACTERIUM TUBERCULOSIS; PROTEIN CONFORMATION; RATIONAL DRUG DESIGN; SCREENING; SIMULATION; VIRTUAL REALITY; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; MUTATION;

AUTOMATION; BACTERIAL PROTEINS; DRUG DESIGN; LIGANDS; MOLECULAR DYNAMICS SIMULATION; MUTATION; MYCOBACTERIUM TUBERCULOSIS; OXIDOREDUCTASES; SOFTWARE;

EID: 84255209045     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-S4-S6     Document Type: Article

References (50)

1. Caskey CT. The Drug Development Crisis: Efficiency and Safety. Annu Rev Med 2007, 58:1-16. 10.1146/annurev.med.58.042705.124037, 17059362.
2. Diago LA, Morell P, Aguilera L, Moreno E. Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms. BMC Bioinformatics 2007, 8:310. 10.1186/1471-2105-8-310, 2008766, 17718923.
3. Drews J. Drug Discovery: A Historical Perspective. Science 2000, 287:1960-1964. 10.1126/science.287.5460.1960, 10720314.
4. Kuntz ID. Structure-based strategies for drug design and discovery. Science 1992, 257:1078-1082. 10.1126/science.257.5073.1078, 1509259.
5. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. PDB - Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
6. Irwin JJ, Shoichet B. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. J Chem Inf Model 2005, 45(1):177-82. 10.1021/ci049714+, 1360656, 15667143.
7. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J Comput Chem 1998, 19:1639-1662.
8. Ewing TJA, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: Search Strategies for Automated Molecular Docking of Flexible Molecule Database. J Comput Aided Mol Des 2001, 15:411-428. 10.1023/A:1011115820450, 11394736.
9. Claussen H, Buning C, Rarey M, Lengauer T. FlexE: Efficient molecular docking considering protein structure variations. J Mol Biol 2001, 308:377-395. 10.1006/jmbi.2001.4551, 11327774.
10. Lybrand TP. Ligand-protein docking and rational drug design. Curr Opin Struct Biol 1995, 5:224-228. 10.1016/0959-440X(95)80080-8, 7648325.
11. Wang R, Lu Y, Wang S. Comparative Evaluation of 11 Scoring Functions for Molecular Docking. J Med Chem 2003, 46:2287-2303. 10.1021/jm0203783, 12773034.
12. Totrov M, Abagyan R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol 2008, 18:178-184. 10.1016/j.sbi.2008.01.004, 2396190, 18302984.
13. Cozzini P, Kellogg GE, Spyrakis F, Abraham DJ, Constantino G, Emerson A, Fanelli F, Gohlke H, Kuhn LA, Morris GM, Orozco M, Pertinhez TA, Rizzi M, Sotriffer CA. Target Flexibility: An Emerging Consideration in Drug Discovery and Design. J Med Chem 2008, 51(20):6237-6255. 10.1021/jm800562d, 2701403, 18785728.
14. Cavasotto CN, Abagyan RA. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol 2004, 337:209-225. 10.1016/j.jmb.2004.01.003, 15001363.
15. Huang S, Zou X. Ensemble Docking of Multiple Protein Structures: Considering Protein Structural Variations in Molecular Docking. Proteins 2007, 66:399-421.
16. Wong CF. Flexible ligand-flexible protein in protein kinase systems. Biochim Biophys Acta 2008, 1784:244-251.
17. Alonso H, Bliznyuk AA, Gready JE. Combining Docking and Molecular Dynamic Simulations in Drug Design. Med Res Rev 2006, 26:531-568. 10.1002/med.20067, 16758486.
18. Teodoro ML, Kavraki LE. Conformational flexibility models for the receptor in structure based drug design. Curr Pharm Des 2003, 9:1635-1648. 10.2174/1381612033454685, 12871062.
19. Chandrika B, Subramanian J, Sharma SD. Managing protein flexibility in docking and its applications. Drug Discov Today 2009, 14:394-400. 10.1016/j.drudis.2009.01.003, 19185058.
20. Sali A. 100.000 Protein Structures for the Biologist. Nat Struct Biol 1998, 5:1029-1032. 10.1038/4136, 9846869.
21. van Gunsteren WF, Berendsen HJC. Computer Simulation of Molecular Dynamics Methodology, Applications and Perspectives in Chemistry. Angew Chem Int Ed Engl 1990, 29:992-1023.
22. Karplus M. Molecular Dynamics Simulations of Biomolecules. Acc Chem Res 2002, 35:321-323. 10.1021/ar020082r, 12069615.
23. Pang Y-P, Kozikowski AP. Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies. J Comput Aided Mol Des 1994, 8:669-681. 10.1007/BF00124014, 7738603.
24. Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA. Developing a dynamic pharmacophore model for HIV-1 Integrase. J Med Chem 2000, 43:2100-2114. 10.1021/jm990322h, 10841789.
25. Lin J-H, Perryman AL, Schames JR, McCammon JA. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc 2002, 124:5632-5633. 10.1021/ja0260162, 12010024.
26. Lin J-H, Perryman AL, Schames JR, McCammon JA. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003, 68(1):47-62. 10.1002/bip.10218, 12579579.
27. Amaro RE, Baron R, McCammon JA. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des 2008, 22:693-705. 10.1007/s10822-007-9159-2, 2516539, 18196463.
28. Machado KS, Schroeder EK, Ruiz DD, Norberto de Souza O. Automating Molecular Docking with Explicit Receptor Flexibility Using Scientific Workflows. Lect Notes Comput Sc 2007, 4643:1-11.
29. Workflow Management Coalition - Terminology & Glossary. Document Status- Issue 3.0 1999, Document number WFMC-TC-1011. http://www.wfmc.org/standards/docs/TC-1011_term_glossary_v3.pdf.
30. Ludäscher B, Altintas I, Berkley C, Higgins D, Jaeger E, Jones M, Lee EA, Tao J, Zhao Y. Scientific Workflow Management and the Kepler System. Concurr Comp-Pract E 2005, 18:1039-1065.
31. Oinn T, Greenwood M, Addis M, Alpdemir MN, Ferris J, Glover K, Goble C, Goderis A, Hull D, Marvin D, Li P, Lord P, Pocock MR, Senger M, Stevens R, Wipat A, Wroe C. Taverna: lessons in creating a workflow environment for the life sciences. Concurr Comp-Pract E 2005, 18(10):1067-1100.
32. Kawas E, Senger M, Wilkinson MD. BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinformatics 2006, 7:523. 10.1186/1471-2105-7-523, 1693925, 17137515.
33. Bartocci E, Corradini F, Merelli E, Scortichini L. BIOWMS: a web-based Workflow Management System for bioinformatics. BMC Bioinformatics 2007, 8:S2. 2230503, 18269696.
34. Ludäscher B, Altintas I, Bowers S, Cummings J, Critchlow T, Deelman E, Roure DD, Freire J, Goble C, Jones M, Klasky S, McPhillips T, Podhorszki N, Silva C, Taylor I, Vouk M. Scientific process automation and workflow management. Scientific Data Management, Computational Science Series 2009, 1-28. Chapman & Hall, Shoshani A, Rotem D.
35. Mehta N, Barter RH. Design document for jawe2openflow project. Technical Report UCRL-TR-206044 2004, Lawrence Livermore National Laboratory (LLNL), University of California., http://www.llnl.gov/tid/lof/documents/pdf/310223.pdf
36. Enhydra Shark Homepage. , http://www.enhydra.org/workflow/shark/index.html
37. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: An Environment for Comparative Protein Modeling. Electrophoresis 1997, 18:2714-2723. 10.1002/elps.1150181505, 9504803.
38. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods R. The AMBER Biomolecular Simulation Programs. J Comput Chem 2005, 26:1668-1688. 10.1002/jcc.20290, 1989667, 16200636.
39. Dessen A, Quémard A, Blanchard JS, Jacobs WR, Sacchettini JC. Crystal structure and function of the isoniazid target of Mycobacterium tuberculosis. Science 1995, 267:1638-1641. 10.1126/science.7886450, 7886450.
40. Schroeder EK, Basso LA, Santos DS, Norberto de Souza O. Molecular Dynamics Simulation Studies of the Wild-Type, I21V, and I16T Mutants of Isoniazid-Resistant Mycobacterium tuberculosis Enoyl Reductase (InhA) in Complex with NADH: Toward the Understanding of NADH-InhA Different Affinities. Biophys J 2005, 89:876-884. 10.1529/biophysj.104.053512, 1366637, 15908576.
41. Oliveira JS, Moreira IS, Santos DS, Basso LA. Enoyl reductases as targets for the development of anti-tubercular and anti-malarial agents. Curr Drug Targets 2007, 8(3):399-411. 10.2174/138945007780058942, 17348833.
42. Schroeder EK, Norberto de Souza O, Santos DS, Blanchard JS, Basso LA. Drugs that inhibit mycolic acid biosynthesis in Mycobacterium tuberculosis. Curr Pharm Biotechnol 2002, 3(3):197-225. 10.2174/1389201023378328, 12164478.
43. Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL. Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov 2008, 7:900-907. 10.1038/nrd2684, 3184002, 18927591.
44. Banerjee A, Dubnau E, Quemard A, Balasubramanian V, Um KS, Wilson T, Collins D, de Lisle G, Jacobs WR. inhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis. Science 1994, 263:227-30. 10.1126/science.8284673, 8284673.
45. Kuo MR, Morbidoni HR, Alland D, Sneddon SF, Gourlie BB, Staveski MM, Leonard M, Gregory JS, Janjigian AD, Yee C, Musser JM, Kreiswirth B, Iwamoto H, Perozzo R, Jacobs WR, Sacchettini JC, Fodock DA. Targeting tuberculosis and malaria through inhibition of enoyl reductase: compound activity and structural data. J Biol Chem 2003, 278:20851-20859. 10.1074/jbc.M211968200, 12606558.
46. Oliveira JS, Sousa EHS, Basso LA, Palaci M, Dietze R, Santos DS, Moreira IS. An inorganic iron complex that inhibits wild-type and an isoniazid-resistant mutant 2-trans-enoyl-ACP (CoA) reductase from Mycobacterium tuberculosis. Chem Comm 2004, 3:312-313.
47. Oliveira JS, de Sousa EH, de Souza ON, Moreira IS, Santos DS, Basso LA. Slow-onset inhibition of 2-trans-enoyl-ACP (CoA) reductase from Mycobacterium tuberculosis by an inorganic complex. Curr Pharm Des 2006, 12(19):2409-2424. 10.2174/138161206777698927, 16842188.
48. Baulard AR, Betts JC, Engohang-Ndong J, Quan S, McAdam RA, Brennan PJ, Locht C, Besra GS. Activation of the pro-drug ethionamide is regulated in mycobacteria. J Biol Chem 2000, 275(36):28326-31.
49. Vasconcelos IB, Meyer E, Sales FAM, Moreira IS, Basso LA, Santos DS. The mode of inhibition of Mycobacterium tuberculosis wild-type and isoniazid-resistant 2-trans-enoyl-ACP(CoA) reductase enzymes by an inorganic complex. Anti-Infect Agent Med Chem 2008, 7:50-62.
50. Wang F, Langley R, Gulten G, Dover LG, Besra GS, Jacobs WR, Sacchettini JC. Mechanism of thioamide drug action against tuberculosis and leprosy. J Exp Med 2007, 204:73-78. 10.1084/jem.20062100, 2118422, 17227913.