Four-dimensional docking: A fast and accurate account of discrete receptor flexibility in ligand docking

Journal of Medicinal Chemistry

Volumn 52, Issue 2, 2009, Pages 397-406

  Bottegoni, Giovanni ^a   Kufareva, Irina ^a   Totrov, Maxim ^b   Abagyan, Ruben ^a,b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b MOLSOFT LLC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; RECEPTOR; PROTEIN;

ACCURACY; ARTICLE; CONFORMATIONAL TRANSITION; FOUR DIMENSIONAL DOCKING; LIGAND BINDING; MOLECULAR DOCKING; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN STRUCTURE; RECEPTOR BINDING; SIMULATION; BINDING SITE; CHEMISTRY; MONTE CARLO METHOD;

BINDING SITES; LIGANDS; MONTE CARLO METHOD; PROTEINS;

EID: 60549086155     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm8009958     Document Type: Article

References (53)

1. Teague, S. J. Implications of protein flexibility for drug discovery. Nat. Rev. Drug Discovery 2003, 2, 527-541.
2. Bottegoni, G.; Kufareva, I.; Totrov, M.; Abagyan, R. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J. Comvut.-Aided Mol. Des. 2008, 22, 311-325.
3. Cavasotto, C. N.; Abagyan, R. A. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 2004, 337, 209-225.
4. Osterberg, F.; Morris, G. M.; Sanner, M. F.; Olson, A. J.; Goodsell, D. S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002, 46, 34-40.
5. Teodoro, M. L.; Kavraki, L. E. Conformational flexibility models for the receptor in structure based drug design. Curr. Pharm. Des. 2003, 9, 1635-1648.
6. Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr. Opin. Struct. Biol. 2008, 18, 178-184.
7. Damm, K. L.; Carlson, H. A. Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design. J. Am. Chem. Soc. 2007, 129, 8225-8235.
8. Carlson, H. A. Protein flexibility and drug design: how to hit a moving target. Curr. Opin. Chem. Biol. 2002, 6, 447-452.
9. Carlson, H. A.; McCammon, J. A. Accommodating protein flexibility in computational drug design. Mol. Pharmacol. 2000, 57, 213-218.
10. Knegtel, R. M. A.; Kuntz, I. D.; Oshiro, C. M. Molecular docking to ensembles of protein structures. J. Mol. Biol. 1997, 266, 424-440.
11. Shoichet, K. D.; Kuntz, I. D.; Bodian, D. L. Molecular docking using shape descriptors. J. Comput. Chem. 1992, 13, 380-397.
12. Garrett, M.; Goodsell, D.; Halliday, R.; Huey, R.; Hart, W.; Belew, R.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662.
13. Sotriffer, C. A.; Dramburg, I. "In situ cross-docking" to simultaneously address multiple targets. J. Med. Chem. 2005, 48, 3122-3125.
14. Zentgraf, M.; Fokkens, J.; Sotriffer, C. A. Addressing protein flexibility and ligand selectivity by "in situ cross-docking. ChemMedChem 2006, 1, 1355-1359.
15. Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. FlexE: efficient molecular docking considering protein structure variations. J. Mol. Biol. 2001, 308, 377-395.
16. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A Fast Flexible Docking Method using an Incremental Construction Algorithm. J. Mol. Biol. 1996, 261, 470-489.
17. Huang, S. Y.; Zou, X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 2007, 66, 399-421.
18. Ewing, T. J. A.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput.-Aided Mol. Des. 2001, 15, 411-428.
19. Barril, X.; Morley, S. D. Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures. J. Med. Chem. 2005, 48, 4432-4443.
20. Corbeil, C. R.; Englebienne, P.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J. Chem. Inf. Model. 2007, 47, 435-449.
21. Cheng, L. S.; Amaro, R. E.; Xu, D.; Li, W. W.; Arzberger, P. W.; McCammon, J. A. Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase. J. Med. Chem. 2008, 51, 3878-3894.
22. Wei, B. Q.; Weaver, L. H.; Ferrari, A. M.; Matthews, B. W.; Shoichet, B. K. Testing a Flexible-Receptor Docking Algorithm in a Model Binding Site. J. Mol. Biol. 2004, 337, 1161-1182.
23. Grünberg, R.; Leckner, J.; Nilges, M. Complementarity of Structure Ensembles in Protein-Protein Binding. Structure 2004, 12, 2125-2136.
24. Eisenstein, M. Introducing a 4th Dimension to Protein- Protein Docking. Structure 2004, 12, 2095-2096.
25. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
26. Bairoch, A.; Apweiler, R.; Wu, C. H.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M. J.; Natale, D. A.; O'Donovan, C.; Redaschi, N.; Yeh, L.- S. L. The Universal Protein Resource (UniProt). Nucleic Acids Res. 2005, 33, D154-D159.
27. Boeckmann, B.; Blatter, M.-C.; Famiglietti, L.; Hinz, U.; Lane, L.; Roechert, B.; Bairoch, A. Protein variety and functional diversity: Swiss-Prot annotation in its biological context. C. R. Biol. 2005, 328, 882-899.
28. Abagyan, R.; Orry, A.; Raush, E.; Budagyan, L.; Totrov, M. ICM Manual 3.5; Molsoft LCC: La Jolla, CA, 2007.
29. Kleywegt, G. J.; Harris, M. R.; Zou, J.-y.; Taylor, T. C.; Wahlby, A.; Jones, T. A. The Uppsala Electron-Density Server. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 2240-2249.
30. An, J.; Totrov, M.; Abagyan, R. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics 2005, 4, 752-761.
31. Hartshorn, M. J.; Verdonk, M. L.; Chessari, G.; Brewerton, S. C.; Mooij, W. T.; Mortenson, P. N.; Murray, C. W. Diverse, high-quality test set for the validation of protein- ligand docking performance. J. Med. Chem. 2007, 50, 726-741.
32. Matthieu Schapira, M. T. R. A. Prediction of the binding energy for small molecules, peptides and proteins. J. Mol. Recognit. 1999, 12, 177-190.
33. Totrov, M.; Abagyan, R. The contour-buildup algorithm to calculate the analytical molecular surface. J. Struct. Biol. 1996, 116, 138-143.
34. Abagyan, R.; Frishman, D.; Argos, P. Recognition of distantly related proteins through energy calculations. Proteins 1994, 19, 132-140.
35. Abagyan, R.; Totrov, M. Biased probability Monte Carlo conforma- tional searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 1994, 235, 983-1002.
36. Totrov, M.; Abagyan, R. Protein-ligand docking as an energy optimization problem. In Drug- Receptor Thermodynamics: Introduction and Applications; Raffa, R. B., Ed.; Wiley: New York, 2001; pp 603-624.
37. Nemethy, G.; Gibson, K. D.; Palmer, K. A.; Yoon, C. N.; Paterlini, G.; Zagari, A.; Rumsey, S.; Scheraga, H. A. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 1992, 96, 6472-6484.
38. Schapira, M.; Abagyan, R.; Totrov, M. Nuclear hormone receptor targeted virtual screening. J. Med. Chem. 2003, 46, 3045-3059.
39. Totrov, M.; Abagyan, R. In Derivation of Sensitive Discrimination Potential for Virtual Screening, RECOMB '99. Proceedings of the Third Annual International Conference on Computational Molecular Biology, Lyon, France, 1999; ACM Press: New York, 1999; pp 37-38.
40. Tremblay, A. M.; Giguere, V. The NR3B subgroup: an ovERRview. Nucl. Recept. Signaling 2007, 5, e009.
41. Greschik, H.; Flaig, R.; Renaud, J.-P.; Moras, D. Structural Basis for the Deactivation of the Estrogen-related Receptor {gamma} by Diethylstilbestrol or 4-Hydroxytamoxifen and Determinants of Selectivity. J. Biol. Chem. 2004, 279, 33639-33646.
42. Zuercher, W. J.; Gaillard, S.; Orband-Miller, L. A.; Chao, E. Y. H.; Shearer, B. G.; Jones, D. G.; Miller, A. B.; Collins, J. L.; McDonnell, D. P.; Willson, T. M. Identification and Structure-Activity Relationship of Phenolic Acyl Hydrazones as Selective Agonists for the Estrogen-Related Orphan Nuclear Receptors ERRβ and ERRγ. J. Med. Chem. 2005, 48, 3107-3109.
43. Jordan, V. C.; Collins, M. M.; Rowsby, L.; Prestwich, G. A monohydroxylated metabolite of tamoxifen with potent antioestrogenic activity. J. Endocrinol. 1977, 75, 305-316.
44. Chao, E. Y.; Collins, J. L.; Gaillard, S.; Miller, A. B.; Wang, L.; Orband-Miller, L. A.; Nolte, R. T.; McDonnell, D. P.; Willson, T. M.; Zuercher, W. J. Structure-guided synthesis of tamoxifen analogs with improved selectivity for the orphan ERRgamma. Bioorg. Med. Chem. Lett. 2006, 16, 821-824.
45. Savona, M.; Talpaz, M. Getting to the stem of chronic myeloid leukaemia. Nat. Rev. Cancer 2008, 8, 341-350.
46. Cowan-Jacob, S. W.; Fendrich, G.; Floersheimer, A.; Furet, P.; Liebetanz, J.; Rummel, G.; Rheinberger, P.; Centeleghe, M.; Fabbro, D.; Manley, P. W. Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2007, 63, 80-93.
47. Wishart, D. S.; Knox, C.; Guo, A. C.; Cheng, D.; Shrivastava, S.; Tzur, D.; Gautam, B.; Hassanali, M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2008, 36, D901-D906.
48. Cole, J.; Murray, C. W.; Willem, J.; Nissink, M.; Taylor, R. D.; Taylor, R. Comparing protein-ligand docking programs is difficult. Proteins: Struct., Funct., Bioinf. 2005, 60, 325-332.
49. Cavasotto, C. N.; Orry, A. J. W.; Abagyan, R. A. The Challenge of Considering Receptor Flexibility in Ligand Docking and Virtual Screening. Curr. Comput.-Aided Drug Des. 2005, 1, 423-440.
50. 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, S7-S26.
51. 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.
52. Bisson, W. H.; Cheltsov, A. V.; Bruey-Sedano, N.; Lin, B.; Chen, J.; Goldberger, N.; May, L. T.; Christopoulos, A.; Dalton, J. T.; Sexton, P. M.; Zhang, X. K.; Abagyan, R. Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 11927-11932.
53. Rao, S.; Sanschagrin, P. C.; Greenwood, J. R.; Repasky, M. P.; Sherman, W.; Farid, R. Improving database enrichment through ensemble docking. J. Comput.-Aided Mol. Des. 2008, 22, 621-627.