Molecular docking using the molecular lipophilicity potential as hydrophobic descriptor: Impact on GOLD docking performance

Journal of Chemical Information and Modeling

Volumn 52, Issue 5, 2012, Pages 1319-1327

  Nurisso, Alessandra ^a   Bravo, Juan ^a   Carrupt, Pierre Alain ^a   Daina, Antoine ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; GOLD; LENNARD-JONES POTENTIAL; LIGANDS; MOLECULAR MODELING; PROTEINS;

EXPERIMENTAL PARTITION COEFFICIENT; HYDROPHOBIC MOIETIES; HYDROPHOBIC REGIONS; LIGAND-PROTEIN COMPLEXES; MOLECULAR DOCKING; MOLECULAR INTERACTION FIELDS; PROTEIN CAVITY; PROTEIN STRUCTURES;

HYDROPHOBICITY;

LIGAND; PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; DRUG DESIGN; HUMAN;

BINDING SITES; DRUG DESIGN; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIGANDS; MODELS, MOLECULAR; PROTEINS; SOFTWARE;

EID: 84861495307     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200515g     Document Type: Article

References (41)

1. Kroemer, R. T. Structure-based drug design: docking and scoring Curr. Protein Pept. Sci. 2007, 8, 312-328 (Pubitemid 47317039)
2. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. A review of protein-small molecule docking methods J. Comput.-Aided Mol. Des. 2002, 16, 151-166
3. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J. Protein-ligand docking: current status and future challenges Proteins: Struct., Funct., Bioinf. 2006, 65, 15-26 (Pubitemid 44320611)
4. Warren, G. L.; Peishoff, C. E.; Head, M. S. Docking algorithms and scoring functions;state of the art and current limitations. In Computational and structural approaches to drug discovery: ligand-protein interactions; Stroud, R.M.; J. Finer-Moore, Eds.; RSC Publishing: San Francisco, CA, 2008, pp 137-154.
5. Cummings, M. D.; Des Jarlais, R. L.; Gibbs, A. C.; Mohan, V.; Jaeger, E. P. Comparison of automated docking programs as virtual screening tools J. Med. Chem. 2005, 48, 962-976 (Pubitemid 40270442)
6. Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications Nat. Rev. Drug Discovery 2004, 3, 935-949 (Pubitemid 39529931)
7. Klebe, G. Virtual ligand screening: strategies, perspectives and limitations Drug Discovery Today 2006, 11, 580-594
8. Meyer, E. E.; Rosenberg, K. J.; Israelachvili, J. Recent progress in understanding hydrophobic interactions Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 15739-15746 (Pubitemid 44657537)
9. Heiden, W.; Moeckel, G.; Brickmann, J. A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces J. Comput.-Aided Mol. Des. 1993, 7, 503-514
10. Cao, J.; Pham, D. K.; Tonge, L.; Nicolau, D. V. Predicting surface properties of proteins on the Connolly molecular surface Smart Mater. Struct. 2002, 11, 772-777 (Pubitemid 35298475)
11. Cruciani, G.; Crivori, P.; Carrupt, P. A.; Testa, B. Molecular fields in quantitative structure-permeation relationships: the VolSurf approach J. Mol. Struct.: THEOCHEM 2000, 503, 17-30
12. Pratt, L. R. Molecular Theory of Hydrophobic Effects: She is too mean to have her name repeated Annu. Rev. Phys. Chem. 2002, 53, 409-436
13. Chandler, D. Interfaces and the driving force of hydrophobic assembly Nature 2005, 437, 640-647 (Pubitemid 41486526)
14. Sarkar, A.; Kellogg, G. E. Hydrophobicity: Shake Flasks, Protein Folding and Drug Discovery Curr. Top. Med. Chem. 2010, 10, 67-83
15. o/w more than the sum of its parts Eur. J. Med. Chem. 2000, 35, 651-661 (Pubitemid 30490272)
16. Carrupt, P. A.; Testa, B.; Gaillard, P. Computational approaches to lipophilicity: methods and applications, In Reviews in Computational Chemistry; Lipkowitz, K. B.; Boyd, D. B., Eds; Wiley-VCH: New York, 1997; vol. 1, pp 241-315. (Pubitemid 127463234)
17. Testa, B.; Carrupt, P. A.; Gaillard, P.; Billois, F.; Weber, P. Lipophilicity in molecular modeling Pharm. Res. 1996, 13, 335-343 (Pubitemid 26112258)
18. Audry, E.; Dubost, J. P.; Colleter, J. C.; Dallet, P. A new approach to structure-activity relations: the molecular lipophilicity potential Eur. J. Med. Chem. 1986, 21, 71-72 (Pubitemid 16114129)
19. Gaillard, P.; Carrupt, P. A.; Testa, B.; Boudon, A. Molecular lipophilicity potential, a tool in 3D QSAR: method and applications J. Comput.-Aided Mol. Des. 1994, 8, 83-96
20. Broto, P.; Moreau, G.; Vandycke, C. Molecular structures: perception, autocorrelation descriptor and SAR studies. Autocorrelation descriptor Eur. J. Med. Chem. 1984, 19, 66-70 (Pubitemid 14156801)
21. Fauchere, J. L.; Quarendon, P.; Kaetterer, L. Estimating and representing hydrophobicity potential J. Mol. Graphics Modell. 1988, 6, 203-206
22. Novaroli, L.; Daina, A.; Favre, E.; Bravo, J.; Carotti, A.; Leonetti, F.; Catto, M.; Carrupt, P. A.; Reist, M. Impact of species-dependent differences on screening, design, and development of MAO B inhibitors J. Med. Chem. 2006, 49, 6264-6272 (Pubitemid 44595203)
23. Gohier, A.; Espinosa, J. F.; Jimenez-Barbero, J.; Carrupt, P. A.; Perez, S.; Imberty, A. Knowledge-based modeling of a legume lectin and docking of the carbohydrate ligand: the Ulex europaeus lectin I and its interaction with fucose J. Mol. Graphics Modell. 1996, 14, 322-327 (Pubitemid 27302821)
24. Efremov, R. G.; Chugunov, A. O.; Pyrkov, T. V.; Priestle, J. P.; Arseniev, A. S.; Jacoby, E. Molecular lipophilicity in protein modeling and drug design Curr. Top. Med. Chem. 2007, 14, 393-415
25. Jones, G.; Willett, P. Docking small-molecule ligands into active sites Curr. Opin. Biotechnol. 1995, 6, 652-656
26. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 1997, 267, 727-748 (Pubitemid 27170693)
27. Hartshorn, M. J.; Verdonk, M. L.; Chessari, G.; Brewerton, S. C.; Mooij, W. T. M.; Mortenson, P. N.; Murray, C. W. Diverse, A performance of four molecular docking programs on a diverse set of protein ligand complexes J. Med. Chem. 2007, 50, 726-741
28. Li, X.; Li, Y.; Cheng, T.; Liu, Z.; Wang, R. Evaluation of the performance of four molecular docking programs on a diverse set of protein ligand complexes J. Comput. Chem. 2010, 31, 2109-2125
29. Clark, M.; Cramer, R. D.; Van Opdenbosch, N. Validation of the general purpose Tripos 5.2 force field J. Comput. Chem. 1989, 10, 982-1012
30. Verdonk, M. L.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Taylor, R. D. Improved protein-ligand docking using GOLD Proteins: Struct., Funct., Bioinf. 2003, 52, 609-623 (Pubitemid 37034158)
31. GOLD, version 4.1; Cambridge Crystallographic Data Center: Cambridge UK, 2008.
32. Hawkins, P. C. D.; Warren, G. L.; Skillman, A. G.; Nicholls, A. How to do an evaluation: pitfalls and traps J. Comput. Aided Mol. Des. 2008, 22, 179-190
33. Mannhold, R.; Van de Waterbeemd, H. Substructure and whole molecule approaches for calculating log P J. Comput. Aided Mol. Des. 2001, 15, 337-354 (Pubitemid 32366724)
34. Perola, E.; Walters, W. P.; Charifson, P. S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance Proteins: Struct. Funct. Bioinfo. 2004, 56, 235-249 (Pubitemid 38850158)
35. Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 1985, 28, 849-857 (Pubitemid 15012490)
36. GOLD, version 2.0; Cambridge Crystallographic Data Center: Cambridge, U.K., 2002.
37. Yamashita, M. M.; Wesson, L.; Eisenman, G.; Eisenberg, D. Where metal ions bind in proteins Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 5648-5652
38. Ye, L.; Li, Y. L.; Mellstrom, K.; Mellin, C.; Bladh, L. G.; Koehler, K.; Garg, N.; Collazo, A. M. G.; Litten, C.; Husman, B. Thyroid receptor ligands. 1. Agonist ligands selective for the thyroid receptor 1 J. Med. Chem. 2003, 46, 1580-1588 (Pubitemid 36452328)
39. Biswal, B. K.; Wang, M.; Cherney, M. M.; Chan, L.; Yannopoulos, C. G.; Bilimoria, D.; Bedard, J.; James, M. N. G. Non-nucleoside inhibitors binding to hepatitis C virus NS5B polymerase reveal a novel mechanism of inhibition J. Mol. Biol. 2006, 361, 33-45 (Pubitemid 44041453)
40. Jain, A. N. Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search J. Comput.-Aided Mol. Des. 2007, 21, 281-306 (Pubitemid 46630055)
41. Moustakas, D. T.; Lang, P. T.; Pegg, S.; Pettersen, E.; Kuntz, I. D.; Brooijmans, N.; Rizzo, R. C. Development and validation of a modular, extensible docking program: DOCK 5 J. Comput.-Aided Mol. Des. 2006, 20, 601-619 (Pubitemid 46023925)