Docking and scoring with ICM: the benchmarking results and strategies for improvement

Marco A. C. Neves1,2, Maxim Totrov3, Ruben Abagyan3,4
1Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, USA
2Lab. Química Farmacêutica, Centro de Neurociências, Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Coimbra, Portugal
3Molsoft L.L.C., San Diego, USA
4Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Andricopulo AD, Salum LB, Abraham DJ (2009) Structure-based drug design strategies in medicinal chemistry. Curr Top Med Chem 9:771–790

Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil CR (2008) Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol 153:S7–S26

Kroemer RT (2007) Structure-based drug design: docking and scoring. Curr Protein Peptide Sci 8:312–328

Morra G, Genoni A, Neves MAC, Merz KM, Colombo G (2010) Molecular recognition and drug-lead identification: what can molecular simulations tell us? Curr Med Chem 17:25–41

Zou XQ, Sun YX, Kuntz ID (1999) Inclusion of solvation in ligand binding free energy calculations using the generalized-born model. J Am Chem Soc 121:8033–8043

Ruvinsky AM (2007) Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions. J Comput Chem 28:1364–1372

Scharer K, Morgenthaler M, Paulini R, Obst-Sander U, Banner DW, Schlatter D, Benz J, Stihle M, Diederich F (2005) Quantification of cation-π interactions in protein-ligand complexes: crystal-structure analysis of factor Xa bound to a quaternary ammonium ion ligand. Angew Chem Int Edit 44:4400–4404

Bartlett GJ, Choudhary A, Raines RT, Woolfson DN (2010) n- > π* interactions in proteins. Nat Chem Biol 6:615–620

Takahashi O, Kohno Y, Nishio M (2010) Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 110:6049–6076

Milletti F, Vulpetti A (2010) Tautomer preference in PDB complexes and its impact on structure-based drug discovery. J Chem Inf Model 50:1062–1074

Robeits BC, Mancera RL (2008) Ligand-protein docking with water molecules. J Chem Inf Model 48:397–408

Kirton SB, Murray CW, Verdonk ML, Taylor RD (2005) Prediction of binding modes for ligands in the cytochromes p450 and other heme-containing proteins. Proteins 58:836–844

Irwin JJ, Raushel FM, Shoichet BK (2005) Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry 44:12316–12328

ten Brink T, Exner TE (2010) pKa based protonation states and microspecies for protein-ligand docking. J Comput Aided Mol Des 24:935–942

Rose PW, Beran B, Bi CX, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE (2011) The RCSB protein data bank: redesigned web site and web services. Nucleic Acids Res 39:D392–D401

Truchon JF, Bayly CI (2007) Evaluating virtual screening methods: good and bad metrics for the “early recognition” problem. J Chem Inf Model 47:488–508

Kufareva I, Abagyan R (2008) Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem 51:7921–7932

Monceaux CJ, Hirata-Fukae C, Lam PCH, Totrov MM, Matsuoka Y, Carlier PR (2011) Triazole-linked reduced amide isosteres: an approach for the fragment-based drug discovery of anti-Alzheimer’s BACE1 inhibitors. Bioorg Med Chem Lett 21:3992–3996

Bowers EM, Yan G, Mukherjee C, Orry A, Wang L, Holbert MA, Crump NT, Hazzalin CA, Liszczak G, Yuan H, Larocca C, Saldanha SA, Abagyan R, Sun Y, Meyers DJ, Marmorstein R, Mahadevan LC, Alani RM, Cole PA (2010) Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol 17:471–482

Endo S, Matsunaga T, Kuwata K, Zhao HT, El-Kabbani O, Kitade Y, Hara A (2010) Chromene-3-carboxamide derivatives discovered from virtual screening as potent inhibitors of the tumour maker, AKR1B10. Bioorg Med Chem 18:2485–2490

Odell LR, Howan D, Gordon CP, Robertson MJ, Chau N, Mariana A, Whiting AE, Abagyan R, Daniel JA, Gorgani NN, Robinson PJ, McCluskey A (2010) The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening. J Med Chem 53:5267–5280

Khan MTH, Fuskevag OM, Sylte I (2009) Discovery of potent thermolysin inhibitors using structure based virtual screening and binding assays. J Med Chem 52:48–61

Wu SD, Bottini M, Rickert RC, Mustelin T, Tautz L (2009) In silico screening for PTPN22 inhibitors: active hits from an inactive phosphatase conformation. Chemmedchem 4:440–444

An JH, Lee DCW, Law AHY, Yang CLH, Poon LLM, Lau ASY, Jones SJM (2009) A novel small-molecule inhibitor of the avian influenza H5N1 virus determined through computational screening against the neuraminidase. J Med Chem 52:2667–2672

Bisson WH, Cheltsov AV, Bruey-Sedano N, Lin B, Chen J, Goldberger N, May LT, Christopoulos A, Dalton JT, Sexton PM, Zhang XK, Abagyan R (2007) Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs. Proc Natl Acad Sci USA 104:11927–11932

Cavasotto CN, Orry AJ W, Murgolo NJ, Czarniecki MF, Kocsi SA, Hawes BE, O’Neill KA, Hine H, Burton MS, Voigt JH, Abagyan RA, Bayne ML, Monsma FJ (2008) Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. J Med Chem 51:581–588

Katritch V, Jaakola VP, Lane JR, Lin J, IJzerman AP, Yeager M, Kufareva I, Stevens RC, Abagyan R (2010) Structure-based discovery of novel chemotypes for adenosine A2A receptor antagonists. J Med Chem 53:1799–1809

Schapira M, Abagyan R, Totrov M (2003) Nuclear hormone receptor targeted virtual screening. J Med Chem 46:3045–3059

Schapira M, Raaka BM, Das S, Fan L, Totrov M, Zhou ZG, Wilson S, Abagyan R, Samuels HH (2003) Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proc Natl Acad Sci USA 100:7354–7359

Schapira M, Raaka BM, Samuels HH, Abagyan R (2001) In silico discovery of novel Retinoic Acid Receptor agonist structures. BMC Struct Biol 1:1–7

Dey R, Chen L (2011) In search of allosteric modulators of alpha 7-nAChR by solvent density guided virtual screening. J Biomol Struct Dyn 28:695–715

Schapira M, Abagyan R, Totrov M (2002) Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Struct Biol 2:1–8

Ravna AW, Sylte I, Sager G (2009) Binding site of ABC transporter homology models confirmed by ABCB1 crystal structure. Theor Biol Med Model 6

Ravna AW, Sylte I, Dahl SG (2003) Molecular mechanism of citalopram and cocaine interactions with neurotransmitter transporters. J Pharmacol Exp Ther 307:34–41

Ravna AW, Sylte I, Dahl SG (2003) Molecular model of the neural dopamine transporter. J Comput Aided Mol Des 17:367–382

Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortenson PN, Murray CW (2007) Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem 50:726–741

Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49:6789–6801

Good AC, Oprea TI (2008) Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? J Comput Aided Mol Des 22:169–178

Abagyan R, Totrov M, Kuznetsov D (1994) ICM—a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15:488–506

Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1092

Schapira M, Totrov M, Abagyan R (1999) Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recognit 12:177–190

Totrov M, Abagyan R (1997) Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 29 (suppl 1):215–220

Halgren TA (1996) Merck molecular force field.1. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem 17:490–519

Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R (2011) Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 19:1108–1126

Rueda M, Katritch V, Raush E, Abagyan R (2010) SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts. Bioinformatics 26:2784–2785

McGann M (2011) FRED pose prediction and virtual screening accuracy. J Chem Inf Model 51:578–596

Davis IW, Baker D (2009) ROSETTALIGAND docking with full ligand and receptor flexibility. J Mol Biol 385:381–392

Olsen L, Pettersson I, Hemmingsen L, Adolph HW, Jorgensen FS (2004) Docking and scoring of metallo-β-lactamases inhibitors. J Comput Aided Mol Des 18:287–302

Korb O, Stutzle T, Exner TE (2009) Empirical scoring functions for advanced protein-ligand docking with PLANTS. J Chem Inf Model 49:84–96

Donnecke D, Schweinitz A, Sturzebecher A, Steinmetzer P, Schuster M, Sturzebecher U, Nicklisch S, Sturzebecher J, Steinmetzer T (2007) From selective substrate analogue factor Xa inhibitors to dual inhibitors of thrombin and factor Xa. Part 3. Bioorga Medicinal Chem Lett 17:3322–3329

Nar H, Bauer M, Schmid A, Stassen JM, Wienen W, Priepke HW M, Kauffmann IK, Ries UJ, Hauel NH (2001) Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors. Structure 9:29–37

Kufareva I, Ilatovskiy AV, Abagyan R (2011) Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res

Bottegoni G, Kufareva I, Totrov M, Abagyan R (2009) Four-dimensional docking: A fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem 52:397–406

Neves MAC, Simoes S, Melo MLSE (2010) Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach. J Comput Aided Mol Des 24:1023–1033

Park SJ, Kufareva I, Abagyan R (2010) Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput Aided Mol Des 24:459–471