物理化学学报2012，Vol.28Issue(9)：2191-2201,11.DOI:10.3866/PKU.WHXB201207063
葡萄糖苷酶抑制剂作用机理的分子动力学模拟和自由能计算
Interaction Mechanisms of Inhibitors of Glucoamylase by Molecular Dynamics Simulations and Free Energy Calculations
摘要
Abstract
Sulfonium ion glucosidase inhibitors such as kotalanol (SK) and de-O-sulfonated kotalanol (DSK) are potential drug candidates for the treatment of type Ⅱ diabetes,with no serious toxicity or side effects.Experimental binding assays against glucosidase show that the activity of DSK is slightly higher than that of SK,while the activity of the nitrogen analogue of de-O-sulfonated kotalanol (DSN) is ～1500-fold higher than that of the nitrogen analog of kotalanol (SN).Here,the binding mechanisms of four representative inhibitors of glucoamylase,SK,DSK,and their two nitrogen analogues,were explored in an integrated modeling study combining molecular dynamics (MD) simulations,binding free energy calculations,and binding free energy decomposition analysis.Our simulations highlight the significant impact of the combination of nitrogen substitution and sulfate anion group.Nitrogen substitution in the five-membered ring leads to the overturning of the polyhydroxylated chain,originating from the shorter bond length of N — C compared with S — C,while the sulfate anion group restrains the freedom of the polyhydroxylated chain.These cumulative effects are able to significantly change the binding conformation of the inhibitor and substantially impair interactions between the inhibitor and glucosidase.The structural insights obtained in this study are expected to be valuable for increased understanding of the binding mechanism of sulfonium ion glucosidase inhibitors and future design of more potent glucosidase inhibitors.关键词
锍离子/葡萄糖苷酶抑制剂/分子动力学模拟/自由能计算/自由能分解Key words
Sulfonium ion/ Glucoamylase inhibitor/ Molecular dynamic simulation/ Free energy calculation/ Free energy decomposition分类
化学化工引用本文复制引用
罗芳,高剑,成元华,崔巍,计明娟..葡萄糖苷酶抑制剂作用机理的分子动力学模拟和自由能计算[J].物理化学学报,2012,28(9):2191-2201,11.基金项目
国家自然科学基金(21173264),科技部重大专项(2009ZX09501-011)和中国科学院知识创新工程基金(ZNWH-2011-011)资助项目 （21173264）
The project was supported by the National Natural Science Foundation of China (21173264),National Science and Technology Major Special Project of China (2009ZX09501-011),and Foundation of Knowledge Innovative Engineering of Chinese Academy of Sciences (ZNWH-2011-011). （21173264）
