Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes

Journal of Chemical Information and Modeling

Volumn 56, Issue 3, 2016, Pages 580-587

  Anighoro, Andrew ^a   Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; MOLECULAR MODELING;

ACTIVE COMPOUNDS; COCRYSTAL STRUCTURE; MOLECULAR DOCKING; SCORING FUNCTIONS; SCREENING METHODS; SIMILARITY CALCULATION; STRUCTURE-BASED; VIRTUAL SCREENING;

LIGANDS;

LIGAND;

DRUG DESIGN; MOLECULAR DYNAMICS; UNCERTAINTY; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; LIGANDS; MOLECULAR DYNAMICS SIMULATION; UNCERTAINTY;

EID: 84962339121     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00745     Document Type: Article

References (43)

1. Lavecchia, A.; Di Giovanni, C. Virtual Screening Strategies in Drug Discovery: A Critical Review Curr. Med. Chem. 2013, 20, 2839-2860 10.2174/09298673113209990001
2. Heikamp, K.; Bajorath, J. The Future of Virtual Compound Screening Chem. Biol. Drug Des. 2013, 81, 33-40 10.1111/cbdd.12054
3. Cheng, T.; Li, Q.; Zhou, Z.; Wang, Y.; Bryant, S. H. Structure-Based Virtual Screening for Drug Discovery: A Problem-Centric Review AAPS J. 2012, 14, 133-141 10.1208/s12248-012-9322-0
4. Ripphausen, P.; Nisius, B.; Bajorath, J. State-of-the-Art in Ligand-Based Virtual Screening Drug Discovery Today 2011, 16, 372-376 10.1016/j.drudis.2011.02.011
5. Pappalardo, M.; Shachaf, N.; Basile, L.; Milardi, D.; Zeidan, M.; Raiyn, J.; Guccione, S.; Rayan, A. Sequential Application of Ligand and Structure Based Modeling Approaches to Index Chemicals for Their hH4R Antagonism PLoS One 2014, 9, e109340 10.1371/journal.pone.0109340
6. Wiggers, H. J.; Rocha, J. R.; Cheleski, J.; Montanari, C. A. Integration of Ligand- and Target-Based Virtual Screening for the Discovery of Cruzain Inhibitors Mol. Inf. 2011, 30, 565-578 10.1002/minf.201000146
7. Sastry, G. M.; Inakollu, V. S. S.; Sherman, W. Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking J. Chem. Inf. Model. 2013, 53, 1531-1542 10.1021/ci300463g
8. Postigo, M. P.; Guido, R. V. C.; Oliva, G.; Castilho, M. S.; da R. Pitta, I.; de Albuquerque, J. F. C.; Andricopulo, A. D. Discovery of New Inhibitors of Schistosoma Mansoni PNP by Pharmacophore-Based Virtual Screening J. Chem. Inf. Model. 2010, 50, 1693-1705 10.1021/ci100128k
9. Chen, Z.; Tian, G.; Wang, Z.; Jiang, H.; Shen, J.; Zhu, W. Multiple Pharmacophore Models Combined with Molecular Docking: A Reliable Way for Efficiently Identifying Novel PDE4 Inhibitors with High Structural Diversity J. Chem. Inf. Model. 2010, 50, 615-625 10.1021/ci9004173
10. Perryman, A. L.; Santiago, D. N.; Forli, S.; Santos-Martins, D.; Olson, A. J. Virtual Screening with AutoDock Vina and the Common Pharmacophore Engine of a Low Diversity Library of Fragments and Hits against the Three Allosteric Sites of HIV Integrase: Participation in the SAMPL4 Protein-ligand Binding Challenge J. Comput.-Aided Mol. Des. 2014, 28, 429-441 10.1007/s10822-014-9709-3
11. Jiang, L.; Rizzo, R. C. Pharmacophore-Based Similarity Scoring for DOCK J. Phys. Chem. B 2015, 119, 1083-1102 10.1021/jp506555w
12. Kumar, A.; Zhang, K. Y. J. Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise J. Chem. Inf. Model. 2015, 10.1021/acs.jcim.5b00279
13. Broccatelli, F.; Brown, N. Best of Both Worlds: On the Complementarity of Ligand-Based and Structure-Based Virtual Screening J. Chem. Inf. Model. 2014, 54, 1634-1641 10.1021/ci5001604
14. Drwal, M. N.; Griffith, R. Combination of Ligand- and Structure-Based Methods in Virtual Screening Drug Discovery Today: Technol. 2013, 10, e395-e401 10.1016/j.ddtec.2013.02.002
15. Hawkins, P. C. D.; Skillman, A. G.; Nicholls, A. Comparison of Shape-Matching and Docking as Virtual Screening Tools J. Med. Chem. 2007, 50, 74-82 10.1021/jm0603365
16. Peltason, L.; Bajorath, J. Molecular Similarity Analysis Uncovers Heterogeneous Structure-Activity Relationships and Variable Activity Landscapes Chem. Biol. 2007, 14, 489-497 10.1016/j.chembiol.2007.03.011
17. Hu, Y.; Furtmann, N.; Gütschow, M.; Bajorath, J. Systematic Identification and Classification of Three-Dimensional Activity Cliffs J. Chem. Inf. Model. 2012, 52, 1490-1498 10.1021/ci300158v
18. Kramer, B.; Rarey, M.; Lengauer, T. Evaluation of the FLEXX Incremental Construction Algorithm for Protein-Ligand Docking Proteins: Struct., Funct., Genet. 1999, 37, 228-241 10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8
19. McGann, M. FRED and HYBRID Docking Performance on Standardized Datasets J. Comput.-Aided Mol. Des. 2012, 26, 897-906 10.1007/s10822-012-9584-8
20. Huang, S.-Y.; Li, M.; Wang, J.; Pan, Y. HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches J. Chem. Inf. Model. 2015, 10.1021/acs.jcim.5b00275
21. Klon, A. E.; Héroux, A.; Ross, L. J.; Pathak, V.; Johnson, C. A.; Piper, J. R.; Borhani, D. W. Atomic Structures of Human Dihydrofolate Reductase Complexed with NADPH and Two Lipophilic Antifolates at 1.09 Å and 1.05 Å Resolution J. Mol. Biol. 2002, 320, 677-693 10.1016/S0022-2836(02)00469-2
22. Kauppi, B.; Jakob, C.; Färnegårdh, M.; Yang, J.; Ahola, H.; Alarcon, M.; Calles, K.; Engström, O.; Harlan, J.; Muchmore, S.; Ramqvist, A.-K.; Thorell, S.; Öhman, L.; Greer, J.; Gustafsson, J.-Å.; Carlstedt-Duke, J.; Carlquist, M. The Three-Dimensional Structures of Antagonistic and Agonistic Forms of the Glucocorticoid Receptor Ligand-Binding Domain RU-486 Induces a Trans Conformation that Leads to Active Antagonism J. Biol. Chem. 2003, 278, 22748-22754 10.1074/jbc.M212711200
23. Shen, C.-H.; Wang, Y.-F.; Kovalevsky, A. Y.; Harrison, R. W.; Weber, I. T. Amprenavir Complexes with HIV-1 Protease and Its Drug-Resistant Mutants Altering Hydrophobic Clusters FEBS J. 2010, 277, 3699-3714 10.1111/j.1742-4658.2010.07771.x
24. Miyamoto, N.; Sakai, N.; Hirayama, T.; Miwa, K.; Oguro, Y.; Oki, H.; Okada, K.; Takagi, T.; Iwata, H.; Awazu, Y.; Yamasaki, S.; Takeuchi, T.; Miki, H.; Hori, A.; Imamura, S. Discovery of N-[5-({2-[(cyclopropylcarbonyl)amino]imidazo[1,2-B]pyridazin-6-Yl}oxy)-2-Methylphenyl]-1,3-Dimethyl-1H-Pyrazole-5-Carboxamide (TAK-593), a Highly Potent VEGFR2 Kinase Inhibitor Bioorg. Med. Chem. 2013, 21, 2333-2345 10.1016/j.bmc.2013.01.074
25. Chemical Computing Group, Inc. Molecular Operating Environment, version 2014.09.
26. Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility J. Comput. Chem. 2009, 30, 2785-2791 10.1002/jcc.21256
27. Sanner, M. F. Python: A Programming Language for Software Integration and Development J. Mol. Graph. Model. 1999, 17, 57-61
28. Kempf, D. J.; Marsh, K. C.; Denissen, J. F.; McDonald, E.; Vasavanonda, S.; Flentge, C. A.; Green, B. E.; Fino, L.; Park, C. H.; Kong, X. P. ABT-538 Is a Potent Inhibitor of Human Immunodeficiency Virus Protease and Has High Oral Bioavailability in Humans Proc. Natl. Acad. Sci. U. S. A. 1995, 92, 2484-2488 10.1073/pnas.92.7.2484
29. Munshi, S.; Chen, Z.; Li, Y.; Olsen, D. B.; Fraley, M. E.; Hungate, R. W.; Kuo, L. C. Rapid X-Ray Diffraction Analysis of HIV-1 Protease-Inhibitor Complexes: Inhibitor Exchange in Single Crystals of the Bound Enzyme Acta Crystallogr., Sect. D: Biol. Crystallogr. 1998, 54, 1053-1060 10.1107/S0907444998003588
30. Reddy, G. S.; Ali, A.; Nalam, M. N.; Anjum, S. G.; Cao, H.; Nathans, R. S.; Schiffer, C. A.; Rana, T. M. Design and Synthesis of HIV-1 Protease Inhibitors Incorporating Oxazolidinones as P2/P2′ Ligands in Pseudosymmetric Dipeptide Isosteres J. Med. Chem. 2007, 50, 4316-4328 10.1021/jm070284z
31. Tie, Y.; Wang, Y.-F.; Kovalevsky, A. Y.; Weber, I. T. Atomic Resolution Crystal Structures of HIV-1 Protease and Mutants V82A and I84V with Saquinavir Proteins: Struct., Funct., Genet. 2007, 67, 232-242 10.1002/prot.21304
32. Bauer, M. R.; Ibrahim, T. M.; Vogel, S. M.; Boeckler, F. M. Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0-A Public Library of Challenging Docking Benchmark Sets J. Chem. Inf. Model. 2013, 53, 1447-1462 10.1021/ci400115b
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, D198-D201 10.1093/nar/gkl999
34. Irwin, J. J.; Shoichet, B. K. ZINC-A Free Database of Commercially Available Compounds for Virtual Screening J. Chem. Inf. Model. 2005, 45, 177-182 10.1021/ci049714+
35. OpenEye Scientific Software, Inc. ROCS, version 3.2.1.4.
36. King, N. M.; Prabu-Jeyabalan, M.; Bandaranayake, R. M.; Nalam, M. N.; Nalivaika, E. A.; Ozen, A.; Yilmaz, N. K.; Schiffer, C. A. Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease ACS Chem. Biol. 2012, 7, 1536-1546 10.1021/cb300191k
37. Mittal, S.; Cai, Y.; Nalam, M. N.; Bolon, D. N.; Schiffer, C. A. Hydrophobic Core Flexibility Modulates Enzyme Activity in HIV-1 Protease J. Am. Chem. Soc. 2012, 134, 4163-4168 10.1021/ja2095766
38. Munshi, S.; Chen, Z.; Li, Y.; Olsen, D. B.; Fraley, M. E.; Hungate, R. W.; Kuo, L. C. Rapid X-Ray Diffraction Analysis of HIV-1 Protease-Inhibitor Complexes: Inhibitor Exchange in Single Crystals of the Bound Enzyme Acta Crystallogr., Sect. D: Biol. Crystallogr. 1998, 54, 1053-1060 10.1107/S0907444998003588
39. Reddy, G. S.; Ali, A.; Nalam, M. N.; Anjum, S. G.; Cao, H.; Nathans, R. S.; Schiffer, C. A.; Rana, T. M. Design and Synthesis of HIV-1 Protease Inhibitors Incorporating Oxazolidinones as P2/P2′ Ligands in Pseudosymmetric Dipeptide Isosteres J. Med. Chem. 2007, 50, 4316-4328 10.1021/jm070284z
40. Muzammil, S.; Armstrong, A. A.; Kang, L. W.; Jakalian, A.; Bonneau, P. R.; Schmelmer, V.; Amzel, L. M.; Freire, E. Unique Thermodynamic Response of Tipranavir to Human Immunodeficiency Virus Type 1 Protease Drug Resistance Mutations J. Virol. 2007, 81, 5144-5154 10.1128/JVI.02706-06
41. Yuriev, E.; Ramsland, P. A. Latest Developments in Molecular Docking: 2010-2011 in Review J. Mol. Recognit. 2013, 26, 215-239 10.1002/jmr.2266
42. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching J. Chem. Inf. Model. 1998, 38, 983-996 10.1021/ci9800211
43. Accelrys, Inc. MACCS Structural Keys, 2011.