Homology Modeling,Molecular Docking,and Molecular Dynamic Simulation of the Binding Mode of PA-1 and Botrytis cinerea PDHc-El

• 作者: RAO Di HE Jun-Bo FENG Jiang-Tao ZHANG Wei-Nong CAI Meng HE Hong-Wu
• 来源期刊: 结构化学
• 年，卷（期）: 2022,（3）
• 页码范围: 227-234
• 页数: 8页
• 语种: 英文
• DOI: 10.14102/j.cnki.0254-5861.2011-3335

摘要

To reveal the potential fungicidal mechanism of 5-((4-((4-chlorophenoxy)methyl)-5-iodo-1H-1,2,3-triazole-1-yl)methyl)-2-methylpyrimidin-4-amine(PA-1)against Botrytis cinerea(B.cinerea),the three-dimensional structure of B.cinerea pyruvate dehydrogenase complex E1 component(PDHc-E1)is homology modeled,as the PA-1 shows potent E.coli PDHc-E1 and B.cinerea inhibition.Subsequent molecular docking indicates the PA-1 can tightly bind to B.cinerea PDHc-El.Molecular dynamic simulation and MM-PBSA calculation both demonstrate that two in-termolecular interactions,π-π stacking and hydrophobic forces,provide the most contributions to the binding of PA-1 and B.cinerea PDHc-E1.Furthermore,the halogen bonding interaction between the iodine atom in PA-1 and OH in Ser1 81 is also crucial.The present study provides a valuable attempt to homology model the structure of B.cinerea PDHc-E1 and some key factors for the rational structure optimization of PA-1.