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Computation-Directed Molecular Design, Synthesis, and Fungicidal Activity of Succinate Dehydrogenase Inhibitors

文献类型： 外文期刊

作者： Li, Kun 1 ; Hong, Shuang 1 ; Yu, Zhenwu 1 ; Hong, Zeyu 1 ; Sun, Yaru 1 ; Cheng, Jiagao 3 ; Tang, Liangfu 1 ; Wang, Yong 4 ; Qi, Xin 4 ; Fan, Zhijin 1 ;

作者机构： 1.Nankai Univ, Coll Chem, State Key Lab Elementoorgan Chem, Tianjin 300071, Peoples R China

2.Nankai Univ, Coll Chem, Frontiers Sci Ctr New Organ Matter, Tianjin 300071, Peoples R China

3.East China Univ Sci & Technol, Sch Pharm, Shanghai Key Lab Chem Biol, Shanghai 200237, Peoples R China

4.Tianjin Acad Agr Sci, Inst Germplasm Resources & Biotechnol, Tianjin 300112, Peoples R China

关键词： SDH; molecular docking; 3D-QSAR; moleculardynamics simulations; MM-GBSA; design and synthesize

期刊名称：JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY （ 影响因子：6.1； 五年影响因子：6.3 ）

ISSN： 0021-8561

年卷期： 2023 年 71 卷 49 期

页码：

收录情况： SCI

摘要： Succinate dehydrogenase inhibitors (SDHIs) are a class of fungicides targeting the pathogenic fungi mitochondrial SDH. Here, molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR), and molecular dynamics (MD) simulations were used to guide SDHI innovation. Molecular docking was performed to explore the binding modes of SDH and its inhibitors. 3D-QSAR models were carried out on 33 compounds with activity against Rhizoctonia cerealis (R. cerealis); their structure-activity relationships were analyzed using comparative molecular field analysis and comparative molecular similarity indices analysis. MD simulations were used to assess the stability of the complexes under physiological conditions, and the results were consistent with molecular docking. Binding free energy was calculated through the molecular mechanics generalized born surface area method, and the binding free energy was decomposed. The results are consistent with the activity of bioassay and indicate that van der Waals and lipophilic interactions contribute the most in the molecular binding process. Afterward, we designed and synthesized 12 compounds under the guidance of the above-mentioned analyses, bioassay found that F9 was active against R. cerealis with the EC50 value of 9.43 mu g/mL, and F4, F5, and F9 were active against Botrytis cinerea with an EC50 values of 5.80, 3.17, and 1.63 mu g/mL, respectively. They all showed good activity between positive controls of pydiflumetofen and thifluzamide. Our study provides new considerations for effective SDHIs discovery.

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