Emergence of hydrogen bonds from molecular dynamics simulation of substituted N-phenylthiourea–catechol oxidase complex

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• 作者：Kyung-Lae Park
• 关键词：Molecular mechanics ; Catechol oxidase ; Molecular dynamics ; Hydrogen bond
• 刊名：Archives of Pharmacal Research
• 出版年：2017
• 出版时间：January 2017
• 年：2017
• 卷：40
• 期：1
• 页码：57-68
• 全文大小：
• 刊物主题：Pharmacy; Pharmacology/Toxicology;
• 出版者：Pharmaceutical Society of Korea
• ISSN：1976-3786
• 卷排序：40

文摘

A series of N-phenylthiourea derivatives was built starting from the X-ray structure in the molecular mechanics framework and the interaction profile in the complex with the catechol oxidase was traced using molecular dynamics simulation. The results showed that the geometry and interactions between ligand and receptor were highly related to the position of the substituted side chains of phenyl moiety. At the end of molecular dynamics run, a concentrated multicenter hydrogen bond was created between the substituted ligand and receptor. The conformation of the ligand itself were also restricted in the receptor pocket. Furthermore, the simulation time of 50 ns were found to be long enough to explore the relevant conformational space and the stationary behavior of the molecular dynamic could be observed.