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Xu X, Yao Q. Scaffold Hopping Approach to a New Series of Pyridine Derivatives as Potent Inhibitors of CDK2. Arch Pharm (Weinheim) 2016; 349:224-31. [DOI: 10.1002/ardp.201500335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/14/2016] [Accepted: 01/20/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaojuan Xu
- School of Chemistry and Chemical Engineering; Yancheng Teachers University; Yancheng China
| | - Qizheng Yao
- Department of Medicinal Chemistry, School of Pharmacy; China Pharmaceutical University; Nanjing China
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Kokh DB, Wade RC, Wenzel W. Receptor flexibility in small‐molecule docking calculations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.29] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Daria B. Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany
| | - Wolfgang Wenzel
- Karlsruhe Institute of Technology, Institute of Nanotechnology, Karlsruhe, Germany
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Paulsen JL, Anderson AC. Scoring ensembles of docked protein:ligand interactions for virtual lead optimization. J Chem Inf Model 2010; 49:2813-9. [PMID: 19950979 DOI: 10.1021/ci9003078] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ensembles of protein structures to simulate protein flexibility are widely used throughout several applications including virtual lead optimization where they have been shown to improve ligand ranking. Yet, there is no established convention for weighting individual scores generated from ensemble members. To investigate the best method for weighting ensemble scores for proper ligand ranking, a series of dihydrofolate reductase inhibitors was docked to ensembles of Candida albicans dihydrofolate reductase (CaDHFR) structures created from a molecular dynamics (MD) simulation. From a single MD simulation, two ensemble collections were generated, one of which was subjected to a minimization procedure to create a group of structures of equal probability. As expected, ligand ranking accuracy was significantly improved when Boltzmann weighting was applied to the energies of the ensemble without structural minimization (60%), relative to that achieved with averaging (36%). However, accuracy was further improved (72%) by averaging docking scores across a minimized ensemble. To examine whether this accuracy results from structural variation in the single trajectory versus the possibility that error is minimized by averaging, a third collection of receptor structures was created in which each member was taken from an independent molecular dynamics simulation after minimization. Comparison of the docking accuracy results from the single trajectory (72%) to this third collection (61%) showed decreased accuracy, suggesting that ligands are more accurately oriented and assessed when docked to the minimized ensemble from a single MD trajectory, an effect that is more than simply error minimization. Averaging docking scores over a minimized ensemble of another target, influenza A neuraminidase, yielded a ligand ranking accuracy of 83%, representing a 24% improvement over other methods tested.
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Affiliation(s)
- Janet L Paulsen
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, Connecticut 06269, USA.
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Rossi KA, Nayeem A, Weigelt CA, Krystek SR. Closing the side-chain gap in protein loop modeling. J Comput Aided Mol Des 2009; 23:411-8. [PMID: 19459054 DOI: 10.1007/s10822-009-9274-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 04/18/2009] [Indexed: 11/25/2022]
Abstract
The success of structure-based drug design relies on accurate protein modeling where one of the key issues is the modeling and refinement of loops. This study takes a critical look at modeled loops, determining the effect of re-sampling side-chains after the loop conformation has been generated. The results are evaluated in terms of backbone and side-chain conformations with respect to the native loop. While models can contain loops with high quality backbone conformations, the side-chain orientations could be poor, and therefore unsuitable for ligand docking and structure-based design. In this study, we report on the ability to model loop side-chains accurately using a variety of commercially available algorithms that include rotamer libraries, systematic torsion scans and knowledge-based methods.
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Affiliation(s)
- Karen A Rossi
- Bristol-Myers Squibb Company, Research & Development, Computer-Assisted Drug Design, P.O. Box 5400, Princeton, NJ 08543, USA.
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Corbeil CR, Englebienne P, Yannopoulos CG, Chan L, Das SK, Bilimoria D, L’Heureux L, Moitessier N. Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of Fitted 1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors. J Chem Inf Model 2008; 48:902-9. [DOI: 10.1021/ci700398h] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Christopher R. Corbeil
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada H3A 2K6, and ViroChem Pharma Inc., 275 Armand-Frappier Blvd., Laval, QC, Canada H7V 4A7
| | - Pablo Englebienne
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada H3A 2K6, and ViroChem Pharma Inc., 275 Armand-Frappier Blvd., Laval, QC, Canada H7V 4A7
| | - Constantin G. Yannopoulos
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada H3A 2K6, and ViroChem Pharma Inc., 275 Armand-Frappier Blvd., Laval, QC, Canada H7V 4A7
| | - Laval Chan
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada H3A 2K6, and ViroChem Pharma Inc., 275 Armand-Frappier Blvd., Laval, QC, Canada H7V 4A7
| | - Sanjoy K. Das
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada H3A 2K6, and ViroChem Pharma Inc., 275 Armand-Frappier Blvd., Laval, QC, Canada H7V 4A7
| | - Darius Bilimoria
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada H3A 2K6, and ViroChem Pharma Inc., 275 Armand-Frappier Blvd., Laval, QC, Canada H7V 4A7
| | - Lucille L’Heureux
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada H3A 2K6, and ViroChem Pharma Inc., 275 Armand-Frappier Blvd., Laval, QC, Canada H7V 4A7
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada H3A 2K6, and ViroChem Pharma Inc., 275 Armand-Frappier Blvd., Laval, QC, Canada H7V 4A7
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