Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping

Future Medicinal Chemistry

Volumn 6, Issue 16, 2014, Pages 1741-1755

  Chen, Yu Chen ^a   Totrov, Max ^b   Abagyan, Ruben ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MOLSOFT LLC   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; MOLECULAR SCAFFOLD;

AREA UNDER THE CURVE; ARTICLE; BIOLOGICAL ACTIVITY; CRYSTAL STRUCTURE; CRYSTALLIZATION; CRYSTALLOGRAPHY; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR RECOGNITION; MULTICONFORMATIONAL DOCKING; NUCLEOTIDE SEQUENCE; PH; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN TARGETING; RECEIVER OPERATING CHARACTERISTIC; ANIMAL; DRUG SCREENING; HUMAN; MEDICINAL CHEMISTRY; PROCEDURES;

ANIMALS; CHEMISTRY, PHARMACEUTICAL; DRUG EVALUATION, PRECLINICAL; HUMANS; LIGANDS; MOLECULAR DOCKING SIMULATION;

EID: 84911914091     PISSN: 17568919     EISSN: 17568927     Source Type: Journal    
DOI: 10.4155/fmc.14.113     Document Type: Article

References (44)

1. McRobb FM, Sahagun V, Kufareva I, Abagyan R. In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environ. Sci. Technol. 48(3), 1964-1972 (2014
2. Ma DL, Chan DSH, Leung CH. Molecular docking for virtual screening of natural product databases. Chem. Sci. 2(9), 1656-1665 (2011
3. Leung CH, Chan DS, Yang H, et al. A natural product-like inhibitor of NEDD8-Activating enzyme. Chem. Commun. 47(9), 2511-2513 (2011
4. Chan DS, Lee HM, Yang F, et al. Structure-based discovery of natural-product-like TNF-Alpha inhibitors. Angew. Chem. Int. Ed. Engl. 49(16), 2860-2864 (2010
5. Lee HM, Chan DSH, Yang F, et al. Identification of natural product Fonsecin B as a stabilizing ligand of c-myc G-quadruplex DNA by high-Throughput virtual screening. Chem. Commun. 46(26), 4680-4682 (2010
6. Pollastri MP, Campbell RK. Target repurposing for neglected diseases. Future Med. Chem. 3(10), 1307-1315 (2011
7. Ma DL, Chan DS, Leung CH. Drug repositioning by structure-based virtual screening. Chem. Soc. Rev. 42(5), 2130-2141 (2013
8. Kharkar PS, Warrier S, Gaud RS. Reverse docking: a powerful tool for drug repositioning and drug rescue. Future Med. Chem. 6(3), 333-342 (2014
9. Tropsha A. Best practices for QSAR model development, validation, and exploitation. Mol. Informatics 29(6-7), 476-488 (2010
10. Totrov M. Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. Chem. Biol. Drug Des. 71(1), 15-27 (2008
11. Totrov M, Abagyan R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins (Suppl. 1), 215-220 (1997
12. Park SJ, Kufareva I, Abagyan R. Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J. Comput. Aided Mol. Des. 24(5), 459-471 (2010
13. Bottegoni G, Kufareva I, Totrov M, Abagyan R. Fourdimensional docking. a fast and accurate account of discrete receptor flexibility in ligand docking. J. Med. Chem. 52(2), 397-406 (2009
14. Kufareva I, Ilatovskiy AV, Abagyan R Pocketome: An Encyclopedia of Small-molecule Binding Sites in 4D. Nucleic Acids Res. 40, D535-D540 (2011
15. Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28(7), 849-857 (1985
16. Giganti D, Guillemain H, Spadoni JL, Nilges M, Zagury JF, Montes M. Comparative evaluation of 3D virtual ligand screening methods: impact of the molecular alignment on enrichment. J. Chem. Inf. Model. 50(6), 992-1004 (2010
17. Grigoryan AV, Kufareva I, Totrov M, Abagyan RA. Spatial chemical distance based on atomic property fields. J. Comput. Aided Mol. Des. 24(3), 173-182 (2010
18. Kufareva I, Chen YC, Ilatovskiy AV, Abagyan R. Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr. Top. Med. Chem. 12(17), 1869-1882 (2012
19. Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J. Med. Chem. 49(23), 6789-6801 (2006
20. Swann SL, Brown SP, Muchmore SW, et al. A unified, probabilistic framework for structure-And ligand-based virtual screening. J. Med. Chem. 54(5), 1223-1232 (2011
21. Neves MA, Totrov M, Abagyan R. Docking and scoring with ICM: the benchmarking results and strategies for improvement. J. Comput. Aided Mol. Des. 26(6), 675-686 (2012
22. Li R, Bajorath J. Systematic assessment of scaffold distances in ChEMBL: prioritization of compound data sets for scaffold hopping analysis in virtual screening. J. Comput. Aided Mol. Des. 26(10), 1101-1109 (2012
23. Rueda M, Bottegoni G, Abagyan R. Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J. Chem. Inf. Model. 49(3), 716-725 (2009
24. Gaulton A, Bellis LJ, Bento AP, et al. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 40(Database issue), D1100-D1107 (2012
25. Papadatos G, Overington JP. The ChEMBL database: a taster for medicinal chemists. Future Med. Chem. 6(4), 361-364 (2014
26. Cheng Y, Prusoff WH Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes per cent inhibition (I50) of an enzymatic reaction. Biochem. Pharmacol. 22(23), 3099-3108 (1973
27. Abagyan R, Totrov M, Kuznetsov D. ICM-A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 15(5), 488-506 (1994
28. Halgren TA. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem. 17(5-6), 490-519 (1996
29. Halgren TA. MMFF VI. MMFF94s option for energy minimization studies. J. Comput. Chem. 20(7), 720-729 (1999
30. Rose PW, Beran B, Bi C, et al. The RCSB Protein Data Bank. redesigned web site and web services. Nucleic Acids Res. 39, D392-D401 (2011
31. Abagyan R, Kufareva I. The flexible pocketome engine for structural chemogenomics. Methods Mol. Biol. 575, 249-279 (2009
32. Feng Z, Chen L, Maddula H, et al. Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics 20(13), 2153-2155 (2004
33. Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235(3), 983-1002 (1994
34. Totrov M, Abagyan R. Derivation of sensitive discrimination potential for virtual ligand screening. Presented at: RECOMB99 3rd International Conference on Computational Molecular Biology, Lyon, France, 312-320, 11-14 April (1999
35. Katritch V, Kufareva I, Abagyan R. Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology 60(1), 108-115 (2011
36. Schapira M, Totrov M, Abagyan R. Prediction of the binding energy for small molecules, peptides and proteins. J. Mol. Recognit. 12(3), 177-190 (1999
37. Bursulaya BD, Totrov M, Abagyan R, Brooks CL. 3rd: comparative study of several algorithms for flexible ligand docking. J. Comput. Aided Mol. Des. 17(11), 755-763 (2003
38. Truchon JF, Bayly CI. Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem. J. Chem. Inf. Model. 47(2), 488-508 (2007
39. Katritch V, Rueda M, Abagyan R. Ligand-guided receptor optimization. Methods Mol. Biol. 857, 189-205 (2012
40. Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R. GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins 78(1), 197-211 (2010
41. Bissantz C, Folkers G, Rognan D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 43(25), 4759-4767 (2000
42. Irwin JJ. Community benchmarks for virtual screening. J. Comput. Aided Mol. Des. 22(3-4), 193-199 (2008
43. Pham TA, Jain AN. Parameter estimation for scoring protein-ligand interactions using negative training data. J. Med. Chem. 49(20), 5856-5868 (2006
44. Verdonk ML, Berdini V, Hartshorn MJ, et al. Virtual screening using protein-ligand docking: avoiding artificial enrichment. J. Chem. Inf. Comput. Sci. 44(3), 793-806 (2004