期刊
BULLETIN OF THE KOREAN CHEMICAL SOCIETY
卷 38, 期 7, 页码 728-734出版社
WILEY-V C H VERLAG GMBH
DOI: 10.1002/bkcs.11162
关键词
Quorum sensing; In silico development; Molecular docking; Molecular dynamics
资金
- Korea Healthcare Technology R&D, Ministry of Health and Welfare, Republic of Korea [HI12C0675]
Quorum sensing (QS) is a chemical communication between bacteria, with which bacteria sense the population of their own species. Autoinducer-2 (AI-2) is a class of universal quorum-sensing molecules, which is used by both Gram-negative and Gram-positive bacteria. The inhibition of AI-2-mediated QS has various practical applications, including the prevention of the formation of biofilm in dental gums. In this work, we develop a computational protocol for developing AI-2 inhibitors. A challenging aspect of such an endeavor is that the receptor undergoes a large conformational change upon ligand binding. We combine several methods such as molecular docking with multiple conformations, molecular dynamics simulations, and molecular mechanics Poisson-Boltzmann computation, in order to estimate binding affinity of candidate molecules to a quorum-sensing receptor. We apply our method to rank the substances in a chemical library. We indeed find a molecule that has a higher affinity than previously known ligands, thus showing the feasibility of the protocol for the development of quorum-sensing inhibitors.
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