Docking and molecular dynamics studies on triclosan derivatives binding to FabI
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- 作者：Xuyun Yang ; Junrui Lu ; Ming Ying ; Jiangbei Mu ; Peichun Li…
- 关键词：Enoyl ; ACP reductase ; MM ; PBSA ; Molecular dynamics simulation ; Triclosan
- 刊名：Journal of Molecular Modeling
- 出版年：2017
- 出版时间：January 2017
- 年：2017
- 卷：23
- 期：1
- 全文大小：
- 刊物类别：Chemistry and Materials Science
- 刊物主题：Computer Applications in Chemistry; Molecular Medicine; Computer Appl. in Life Sciences; Characterization and Evaluation of Materials; Theoretical and Computational Chemistry;
- 出版者：Springer Berlin Heidelberg
- ISSN：0948-5023
- 卷排序：23
文摘
FabI, enoyl-ACP reductase (ENR), is the rate-limiting enzyme in the last step for fatty acids biosynthesis in many bacteria. Triclosan (TCL) is a commercial bactericide, and as a FabI inhibitor, it can depress the substrate (trans-2-enoyl-ACP) binding with FabI to hinder the fatty acid synthesis. The structure-activity relationship between TCL derivatives and FabI protein has already been acknowledged, however, their combination at the molecular level has never been investigated. This paper uses the computer-aided approaches, such as molecular docking, molecular dynamics simulation, and binding free energy calculation based on the molecular mechanics/Poisson-Bolzmann surface area (MM/PBSA) method to illustrate the interaction rules of TCL derivatives with FabI and guide the development of new derivatives. The consistent data of the experiment and corresponding activity demonstrates that electron-withdrawing groups on side chain are better than electron-donating groups. 2-Hydroxyl group on A ring, promoting the formation of hydrogen bond, is vital for bactericidal effect; and the substituents at 4-position of A ring, 2′-position and 4′-position of B ring benefit antibacterial activity due to forming a hydrogen bond or stabilizing the conformation of active pocket residues of receptor. While the substituents at 3′-position and 5′-position of B ring destroy the π-π stacking interaction of A ring and NAD+ which depresses the antibacterial activity. This study provides a new sight for designing novel TCL derivatives with superior antibacterial activity.