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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Antolin, Albert A. Carotti, Andrea Nuti, Roberto Hakkaya, Aydie Camaioni, Emidio Mestres, Jordi Pellicciari, Roberto Macchiarulo, Antonio |
| Description | Country affiliation: Spain Author Affiliation: Antolin AA ( Chemogenomics Laboratory, Research Program in Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain.) |
| Abstract | Poly(ADP-ribose)polymerase-1 (PARP-1) is an enzyme belonging to the ADP-ribosyltransferase family. A large body of works has validated PARP-1 as an attractive drug target for different therapeutic areas, including cancers and ischemia. Accordingly, sampling the conformational space of the enzyme is pivotal to understand its functions and improve structure-based drug discovery approaches. In the first part of this study we apply replica exchange molecular dynamic (REMD) simulations to sample the conformational space of the catalytic domain of PARP-1 in the ligand-bound and unbound forms. In the second part, we assess how and to what extend the emerging enzyme flexibility affects the performance of docking experiments of a library of PARP-1 inhibitors. This study pinpoints a putative key role of conformational shifts of Leu324, Tyr325 and Lys242 in opening an additional binding site pocket that affects the binding of ligands to the catalytic cleft of PARP-1. Furthermore, it highlights the improvement of the enrichment factor of active ligands obtained in docking experiments when using conformations generated with REMD simulations of ligand-bound PARP-1. |
| File Format | HTM / HTML |
| ISSN | 10933263 |
| Volume Number | 45 |
| e-ISSN | 18734243 |
| Journal | Journal of Molecular Graphics and Modelling |
| Language | English |
| Publisher | Elsevier |
| Publisher Date | 2013-09-01 |
| Publisher Place | United States |
| Access Restriction | One Nation One Subscription (ONOS) |
| Subject Keyword | Discipline Molecular Biology Models, Molecular Poly(adp-ribose) Polymerases Chemistry Protein Conformation Binding Sites Catalytic Domain Enzyme Inhibitors Metabolism Humans Hydrogen Bonding Ligands Molecular Docking Simulation Molecular Dynamics Simulation Protein Binding Solvents Temperature Journal Article Research Support, Non-u.s. Gov't |
| Content Type | Text |
| Resource Type | Article |
| Subject | Computer Graphics and Computer-Aided Design Spectroscopy Materials Chemistry Physical and Theoretical Chemistry |
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