期刊
CHEMICAL BIOLOGY & DRUG DESIGN
卷 79, 期 4, 页码 530-534出版社
WILEY
DOI: 10.1111/j.1747-0285.2011.01313.x
关键词
aa residue flexibility; docking; drug design; VEGFR-2; virtual screening
资金
- Foundation for Science and Technology (Portugal)
- COMPETE/QREN/EU [PTDC/QUI-QUI/111060/2009]
- [SFRH/PROTEC/49450/2009]
Selective side-chain residue flexibility is an option available on AutoDock Vina docking software. This approach is promising as it attempts to provide a more realistic ligandprotein interaction environment without an unmanageable increase in computer processing time. However, studies validating this approach are still scarce. VEGFR-2 (vascular endothelial growth factor receptor 2), a known protein target for anti-angiogenic agents, was used in this study. Four residues located in the VEGFR-2 kinase site were selected and made flexible: Lys868, Glu885, Cys919, and Asp1046. The docking scores for all possible combinations of flexible residues were compared to the docking scores using a rigid conformation. The best overall docking scores were obtained using the Glu885 flexible conformation, with Pearson and Spearman rank correlation values of 0.568 and 0.543, respectively, and a 51% increase in processing time. Using different VEGFR-2 crystal structures, a similar trend was observed with the Glu885 flexible conformation presenting best scores. This study demonstrates that careful use of selective side-chain residue flexibility can improve AutoDock Vina docking score accuracy, without a significant increase in processing time. This methodology can be a valuable tool in drug design projects using VEGFR-2 but will also probably be useful if applied to other protein targets.
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