Citation: Di RAO, Jun-Bo HE, Jiang-Tao FENG, Wei-Nong ZHANG, Meng CAI, Hong-Wu HE. Homology Modeling, Molecular Docking, and Molecular Dynamic Simulation of the Binding Mode of PA-1 and Botrytis cinerea PDHc-E1[J]. Chinese Journal of Structural Chemistry, ;2022, 41(3): 220322. doi: 10.14102/j.cnki.0254-5861.2011-3335 shu

Homology Modeling, Molecular Docking, and Molecular Dynamic Simulation of the Binding Mode of PA-1 and Botrytis cinerea PDHc-E1

Di RAO ^a ,
Jun-Bo HE ^a,, ,
Jiang-Tao FENG ^a ,
Wei-Nong ZHANG ^a ,
Meng CAI ^b ,
Hong-Wu HE ^b,,

a.
Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, College of Food Science & Engineering, Wuhan Polytechnic University, Wuhan 430023, China
b.
Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China

Corresponding author: Jun-Bo HE, junb112he@whpu.edu.cn Hong-Wu HE, he1208@mail.ccnu.edu.cn
Received Date: 19 August 2021
Accepted Date: 17 November 2021

Fund Project: the National Natural Science Foundation of China 21807084

Figures(7)

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-E1. Molecular dynamic simulation and MM-PBSA calculation both demonstrate that two intermolecular 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 Ser181 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.
- 5-iodo-1,2,3-triazole,
- Botrytis cinerea,
- PDHc-E1 inhibitor,
- homology modeling,
- molecular dynamic simulation
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