Characterization of small molecule binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening

Journal of Chemical Information and Modeling

Volumn 53, Issue 1, 2013, Pages 114-122

  Ding, Bo ^a   Wang, Jian ^a   Li, Nan ^a   Wang, Wei ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMISTRY;

COMPLEX STRUCTURE; COMPUTER AIDED DRUG DESIGN; INTEGRATED APPROACH; SCORING FUNCTIONS; SMALL-MOLECULE BINDINGS; STATISTICAL LEARNING; STRUCTURE MODELING; VIRTUAL SCREENING;

CHEMICAL ENGINEERING;

HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE INHIBITOR; LIGAND; SOLVENT;

ARTICLE; CHEMICAL PHENOMENA; CHEMISTRY; COMPUTER INTERFACE; DRUG SCREENING; ENZYMOLOGY; HUMAN IMMUNODEFICIENCY VIRUS 1; METABOLISM; MOLECULAR DOCKING; MOLECULAR LIBRARY; PROTEIN CONFORMATION; SUPPORT VECTOR MACHINE; THERMODYNAMICS;

DRUG EVALUATION, PRECLINICAL; HIV PROTEASE; HIV PROTEASE INHIBITORS; HIV-1; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIGANDS; MOLECULAR DOCKING SIMULATION; PROTEIN CONFORMATION; SMALL MOLECULE LIBRARIES; SOLVENTS; SUPPORT VECTOR MACHINES; THERMODYNAMICS; USER-COMPUTER INTERFACE;

MLCS; MLOWN;

EID: 84873041650     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300508m     Document Type: Article

References (46)

1. Knegtel, R. M.; Wagener, M. Efficacy and selectivity in flexible database docking Proteins 1999, 37 (3) 334-45
2. Pauli, I.; Timmers, L. F. S. M.; Caceres, R. A.; Soares, M. B. P.; de Azevedo, W. F. In silico and in vitro: identifying new drugs Curr Drug Targets 2008, 9 (12) 1054-1061
3. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 1996, 261 (3) 470-89
4. Rarey, M.; Kramer, B.; Lengauer, T. The particle concept: placing discrete water molecules during protein-ligand docking predictions Proteins 1999, 34 (1) 17-28
5. Morris, G. M.; G., D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; O., A. J Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function J. Comput. Chem. 1998, 19, 1639-1662
6. Morris, G. M.; Goodsell, D. S.; Huey, R.; Olson, A. J. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4 J. Comput. Aided Mol. Des. 1996, 10 (4) 293-304
7. Goodsell, D. S.; Olson, A. J. Automated docking of substrates to proteins by simulated annealing Proteins 1990, 8 (3) 195-202
8. Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening J. Med. Chem. 2004, 47 (7) 1750-9
9. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy J. Med. Chem. 2004, 47 (7) 1739-49
10. Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes J. Med. Chem. 2006, 49 (21) 6177-96
11. 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 (3) 727-48
12. Jones, G.; Willett, P.; Glen, R. C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation J. Mol. Biol. 1995, 245 (1) 43-53
13. Kim, R.; Skolnick, J. Assessment of programs for ligand binding affinity prediction J. Comput. Chem. 2008, 29 (8) 1316-31
14. Cheng, T.; Li, X.; Li, Y.; Liu, Z.; Wang, R. Comparative assessment of scoring functions on a diverse test set J. Chem. Inf. Model. 2009, 49 (4) 1079-1093
15. Altman, M. D.; Ali, A.; Reddy, G. S. K. K.; Nalam, M. N. L.; Anjum, S. G.; Cao, H.; Chellappan, S.; Kairys, V.; Fernandes, M. X.; Gilson, M. K.; Schiffer, C. A.; Rana, T. M.; Tidor, B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants J. Am. Chem. Soc. 2008, 130 (19) 6099-6113
16. Jorissen, R. N.; Reddy, G. S. K. K.; Ali, A.; Altman, M. D.; Chellappan, S.; Anjum, S. G.; Tidor, B.; Schiffer, C. A.; Rana, T. M.; Gilson, M. K. Additivity in the analysis and design of HIV protease inhibitors J. Med. Chem. 2009, 52 (3) 737-754
17. Nalam, M. N. L.; Ali, A.; Altman, M. D.; Reddy, G. S. K. K.; Chellappan, S.; Kairys, V.; Ozen, A.; Cao, H.; Gilson, M. K.; Tidor, B.; Rana, T. M.; Schiffer, C. A. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance J. Virol. 2010, 84 (10) 5368-5378
18. Fabry-Asztalos, L.; Andonie, R.; Collar, C. J.; Abdul-Wahid, S.; Salim, N. A genetic algorithm optimized fuzzy neural network analysis of the affinity of inhibitors for HIV-1 protease Bioorg. Med. Chem. 2008, 16 (6) 2903-2911
19. Geppert, H.; Horváth, T.; Gärtner, T.; Wrobel, S.; Bajorath, J. Support-vector-machine-based ranking significantly improves the effectiveness of similarity searching using 2D fingerprints and multiple reference compounds J. Chem. Inf. Model. 2008, 48 (4) 742-746
20. Agarwal, S.; Dugar, D.; Sengupta, S. Ranking chemical structures for drug discovery: a new machine learning approach J. Chem. Inf. Model. 2010, 50 (5) 716-731
21. Ballester, P. J.; Mitchell, J. B. O. A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking Bioinformatics 2010, 26 (9) 1169-1175
22. Marcou, G.; Rognan, D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints J. Chem. Inf. Model. 2007, 47 (1) 195-207
23. Deng, Z.; Chuaqui, C.; Singh, J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions J. Med. Chem. 2004, 47 (2) 337-44
24. Perez-Nueno, V. I.; Rabal, O.; Borrell, J. I.; Teixido, J. APIF: a new interaction fingerprint based on atom pairs and its application to virtual screening J. Chem. Inf. Model. 2009, 49 (5) 1245-60
25. Brewerton, S. C. The use of protein-ligand interaction fingerprints in docking Curr. Opin. Drug Discov. Devel. 2008, 11 (3) 356-64
26. Sato, T.; Honma, T.; Yokoyama, S. Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening J. Chem. Inf. Model. 2010, 50 (1) 170-185
27. Hou, T.; Zhang, W.; Case, D. A.; Wang, W. Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain J. Mol. Biol. 2008, 376 (4) 1201-14
28. Hou, T.; Zhang, W.; Wang, J.; Wang, W. Predicting drug resistance of the HIV-1 protease using molecular interaction energy components Proteins 2009, 74 (4) 837-46
29. Hou, T.; Xu, Z.; Zhang, W.; McLaughlin, W. A.; Case, D. A.; Xu, Y.; Wang, W. Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains Mol. Cell Proteom. 2009, 8 (4) 639-49
30. Li, N.; Hou, T.; Ding, B.; Wang, W. Characterization of PDZ domain-peptide interaction interface based on energetic patterns Proteins 2011, 79 (11) 3208-3220
31. Hou, T.; Li, N.; Li, Y.; Wang, W. Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models J. Proteome Res. 2012, 11 (5) 2982-95
32. Xu, Z.; Hou, T.; Li, N.; Xu, Y.; Wang, W. Proteome-wide detection of Abl1 SH3-binding peptides by integrating computational prediction and peptide microarray Mol. Cell Proteom. 2012, 11 (1) O111 010389
33. Liu, T.; Lin, Y.; Wen, X.; Jorissen, R. N.; Gilson, M. K. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities Nucleic Acids Res. 2007, 35 (Database issue) D198-201
34. Irwin, J. J.; Shoichet, B. K. ZINC - a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 2005, 45 (1) 177-82
35. Kim, E. E.; Baker, C. T.; Dwyer, M. D.; Murcko, M. A.; Rao, B. G.; Tung, R. D.; Navia, M. A. Crystal-Structure of Hiv-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme J. Am. Chem. Soc. 1995, 117 (3) 1181-1182
36. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Deliv. Rev. 2001, 46 (1-3) 3-26
37. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118 (45) 11225-11236
38. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 2001, 105 (28) 6474-6487
39. Chothia, C. Structural invariants in protein folding Nature 1975, 254 (5498) 304-8
40. Street, A. G.; Mayo, S. L. Pairwise calculation of protein solvent-accessible surface areas Fold Des. 1998, 3 (4) 253-8
41. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J. M.; Kollman, P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 2003, 24 (16) 1999-2012
42. Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25 (9) 1157-1174
43. Szekely, G. J.; Rizzo, M. L. Hierarchical clustering via joint between-within distances: Extending Ward's minimum variance method J. Classificat. 2005, 22 (2) 151-183
44. O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An open chemical toolbox J. Cheminf. 2011, 3, 33
45. Chang, C. C.; Lin, L. C. LIBSVM: a library for support vector machine. available at http://www.csie.ntu.edu.tw/∼cjlin/libsvm, 2001.
46. Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction J. Comput. Aided Mol. Des. 2002, 16 (1) 11-26