ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Leis, Simon ^a   Zacharias, Martin ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME BINDING; ENZYME CONFORMATION; HUMAN IMMUNODEFICIENCY VIRUS 1; INTERMETHOD COMPARISON; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PHYSICAL CHEMISTRY; PREDICTION; RECEPTOR BINDING; RECEPTOR FLEXIBILITY BY INTERPOLATION; VALIDATION PROCESS;

BINDING, COMPETITIVE; COMPUTATIONAL BIOLOGY; HIV PROTEASE; HUMANS; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; ORGANIC CHEMICALS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REPRODUCIBILITY OF RESULTS; STRUCTURE-ACTIVITY RELATIONSHIP;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84868117557     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048008     Document Type: Article

References (41)

1. Lesk AM, Chothia C, (1984) Mechanisms of domain closure in proteins. J Mol Biol 174: 175-191.
2. Gerstein M, Chothia C, (1991) Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase. J Mol Biol 220: 133-149.
3. Gerstein M, Lesk AM, Chothia C, (1994) Structural mechanisms for domain movements in proteins. Biochemistry 33: 6739-6749.
4. Najmanovich R, Kuttner J, Sobolev V, Edelman M, (2000) Side-chain flexibility in proteins upon ligand binding. Proteins 39: 261-268.
5. Gutteridge A, Thornton J, (2005) Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding. Journal of Molecular Biology 346: 21-28.
6. Gunasekaran K, Nussinov R, (2007) How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding. Journal of Molecular Biology 365: 257-273.
7. Spyrakis F, BidonChanal A, Barril X, Luque FJ, (2011) Protein flexibility and ligand recognition: challenges for molecular modeling. Curr Top Med Chem 11: 192-210.
8. Teodoro ML, Kavraki LE, (2003) Conformational flexibility models for the receptor in structure based drug design. Curr Pharm Des 9: 1635-1648.
9. Teague SJ, (2003) Implications of protein flexibility for drug discovery. Nature Reviews Drug Discovery 2: 527-541.
10. May A, Sieker F, Zacharias M, (2008) How to efficiently include receptor flexibility during computational docking. Current Computer-Aided Drug Design 4: 143-153.
11. Cozzini P, Kellogg GE, Spyrakis F, Abraham DJ, Costantino G, et al. (2008) Target Flexibility: An Emerging Consideration in Drug Discovery and Design. Journal of Medicinal Chemistry 51: 6237-6255.
12. B-Rao C, Subramanian J, Sharma SD, (2009) Managing protein flexibility in docking and its applications. Drug Discov Today 14: 394-400.
13. Beier C, Zacharias M, (2010) Tackling the challenges posed by target flexibility in drug design. Expert Opinion on Drug Discovery 5: 347-359.
14. Durrant JD, McCammon JA, (2010) Computer-aided drug-discovery techniques that account for receptor flexibility. Current Opinion in Pharmacology 10: 770-774.
15. Halperin I, Ma B, Wolfson H, Nussinov R, (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47: 409-443.
16. Kitchen DB, Decornez H, Furr JR, Bajorath J, (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3: 935-949.
17. Pang YP, Kozikowski AP, (1994) Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies. J Comput Aided Mol Des 8: 669-681.
18. Barril X, Morley SD, (2005) Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J Med Chem 48: 4432-4443.
19. Totrov M, Abagyan R, (2008) Flexible ligand docking to multiple receptor conformations: a practical alternative. Current Opinion in Structural Biology 18: 178-184.
20. Craig IR, Essex JW, Spiegel K, (2010) Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments. Journal of Chemical Information and Modeling 50: 511-524.
21. Novoa EM, Pouplana LRd, Barril X, Orozco M, (2010) Ensemble Docking from Homology Models. Journal of Chemical Theory and Computation 6: 2547-2557.
22. Huang SY, Zou X, (2007) Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 66: 399-421.
23. Leis S, Zacharias M, (2011) Efficient inclusion of receptor flexibility in grid-based protein-ligand docking. J Comput Chem 32: 3433-3439.
24. Kohl NE, Emini EA, Schleif WA, Davis LJ, Heimbach JC, et al. (1988) Active human immunodeficiency virus protease is required for viral infectivity. Proceedings of the National Academy of Sciences 85: 4686-4690.
25. Wlodawer A, Vondrasek J, (1998) Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu Rev Biophys Biomol Struct 27: 249-284.
26. Freedberg DI, Ishima R, Jacob J, Wang YX, Kustanovich I, et al. (2002) Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations. Protein Sci 11: 221-232.
27. Ishima R, Freedberg DI, Wang YX, Louis JM, Torchia DA, (1999) Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Structure 7: 1047-1055.
28. Miller M, Jaskolski M, Rao JKM, Leis J, Wlodawer A, (1989) Crystal structure of a retroviral protease proves relationship to aspartic protease family. Nature 337: 576-579.
29. Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DR, et al. (1995) Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chemistry & Biology 2: 317-324.
30. Schaffer L, Verkhivker GM, (1998) Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins 33: 295-310.
31. Budin N, Majeux N, Caflisch A, (2001) Fragment-Based flexible ligand docking by evolutionary optimization. Biol Chem 382: 1365-1372.
32. de Magalhães CS, Barbosa HJC, Dardenne LE, (2004) A genetic algorithm for the ligand-protein docking problem. Genetics and Molecular Biology 27: 605-610.
33. Chang MW, Ayeni C, Breuer S, Torbett BE, (2010) Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina. PLoS ONE 5: e11955.
34. Jenwitheesuk E, Samudrala R, (2003) Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations. BMC Struct Biol 3: 2.
35. Huang SY, Zou X, (2007) Efficient molecular docking of NMR structures: application to HIV-1 protease. Protein Sci 16: 43-51.
36. Osguthorpe DJ, Sherman W, Hagler AT, (2012) Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols. Journal of Physical Chemistry B 116: 6952-6959.
37. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, et al. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry 19: 1639-1662.
38. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, et al. (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry 30: 2785-2791.
39. Fanfrlík J, Bronowska AK, R?eza?c? J, Pr?enosil O, Konvalinka J, et al. (2010) A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands. Journal of Physical Chemistry B 114: 12666-12678.
40. Erickson JA, Jalaie M, Robertson DH, Lewis RA, Vieth M, (2003) Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy. Journal of Medicinal Chemistry 47: 45-55.
41. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera- A visualization system for exploratory research and analysis. Journal of Computational Chemistry 25: 1605-1612.