数字农科院2.0

Discovery of potential anti- Staphylococcus aureus natural products and their mechanistic studies using machine learning and molecular dynamic simulations

文献类型： 外文期刊

作者： Zinan Wang;Fei Pan;Min Zhang;Shan Liang;Wenli Tian

作者机构：

关键词： 2-HTPA;Anti-S. aureus;Hesperetic acid;Molecular dynamic simulation;QSAR

期刊名称： Heliyon

ISSN： 2405-8440

年卷期： 2024 年 10 卷 9 期

页码：

收录情况： SCIE（2024版）

摘要： The structure-activity analysis (SAR) and machine learning were used to investigate potential anti-S. aureus agents in a faster method. In this study, 24 oxygenated benzene ring components with S. aureus inhibition capacity were confirmed by literature exploring and in-house experiments, and the SAR analysis suggested that the hydroxyl group position may affect the anti-S. aureus activity. The 2D-MLR-QSAR model with 9 descriptors was further evaluated as the best model among the 21 models. After that, hesperetic acid and 2-HTPA were further explored and evaluated as the potential anti-S. aureus agents screening in the natural product clustering library through the best QSAR model calculation. The antibacterial capacities of hesperetic acid and 2-HTPA had been investigated and proved the similar predictive pMIC value resulting from the QSAR model. Besides, the two novel components were able to inhibit the growth of S. aureus by disrupting the cell membrane through the molecular dynamics simulation (MD), which further evidenced by scanning electron microscopy (SEM) test and PI dye results. Overall, these results are highly suggested that QSAR can be used to predict the antibacterial agents targeting S. aureus, which provides a new paradigm to research the molecular structure-antibacterial capacity relationship.

分类号：

  • 相关文献

[1]Experimental and Molecular Dynamic Simulation of Droplet Deposition on Superhydrophobic Plant Leaf Surfaces. Cao C.,Zhang P.,Cao L.,Liu M.,Song Y.,Chen P.,Huang Q.,Han B.. 2022

[2]Inhibitory effects of nobiletin-mediated interfacial instability of bile salt emulsified oil droplets on lipid digestion. Xingran Kou,Min Hong,Fei Pan,Xin Huang,Qingran Meng,Yunchong Zhang,Qinfei Ke. 2024

[3]Understanding the mechanism of saccharides type and concentration affecting texture of freeze-dried pectin-CMC cryogels through experiment and molecular dynamic simulation. Youchuan Ma,Jinfeng Bi,Zhonghua Wu,Jianyong Yi. 2025

[4]Novel strategy for screening aptamers of Staphylococcus aureus enterotoxin A based on active fragments and fusion design. Shujing Ge,Mengyao Guan,Fei Pan,Yanli Wang,Daodong Pan,Chaoying Zhang,Xinchang Gao,Yali Dang. 2025

[5]Synthesis and biological activities of 2-oxocycloalkylsulfonamides. Yang, Xinling,Liang, Xiaomei,Kai, Zhenpeng,Yuan, Dekai,Zhang, Jianjun,Ling, Yun,Chen, Fuheng,Wang, Daoquan,Yuan, Huizu,Qi, Shuhua,Wang, Ruiqing,Ran, Fuxiang. 2008

[6]Quantitative structure-toxicity relationship study of lethal concentration to tadpole (Bufo vulgaris formosus) for organophosphorous pesticides. Yan, Dongyun,Xu, Shaohui,Yan, Dongyun,Jiang, Xin,Bian, Yongrong,Yu, Guifen,Wang, Ligang.

[7]N '-Nitro-2-hydrocarbylidenehydrazinecarboximidamides: Design, Synthesis, Crystal Structure, Insecticidal Activity, and Structure-Activity Relationships. Zhou, Yihui,Ma, Yongqiang,Wang, Lei,Zhang, Zheng,Duan, Hongxia,Qin, Zhaohai,Rui, Changhui. 2012

[8]Virtual screening strategy for anti-DPP-IV natural flavonoid derivatives based on machine learning. Lu, Gen,Pan, Fei,Li, Xiaotong,Zhu, Zehui,Zhao, Lei,Wu, Ya,Tian, Wenli,Peng, Wenjun,Liu, Jinling. 2023

[9]Development of QSAR models for evaluating pesticide toxicity against Skeletonema costatum. Lu Yang,Cuihong Sang,Yinghuan Wang,Wentao Liu,Weiyu Hao,Jing Chang,Jianzhong Li. 2021

[10]Data driven toxicity assessment of organic chemicals against Gammarus species using QSAR approach. Lu Yang,Ruya Tian,Zhoujing Li,Xiaomin Ma,Hongyan Wang,Wei Sun. 2023

[11]Design and Synthesis of Pleuromutilin Derivatives as Antibacterial Agents Using Quantitative Structure-Activity Relationship Model. Jiaming Zhang,Qinqin Liu,Haoxia Zhao,Guiyu Li,Yunpeng Yi,Ruofeng Shang. 2024

[12]QSAR model of pancreatic lipase inhibition by phenolic acids and their derivatives based on machine learning and multi-descriptor strategy. Yaqi Liu,Fei Pan,Ou Wang,Zehui Zhu,Qing Li,Zicheng Yang,Wenli Tian,Liang Zhao,Lei Zhao. 2023

[13]Identification and mechanistic study of piceatannol as a natural xanthine oxidase inhibitor. Xinxu Yan,Baolong Feng,Hongjie Song,Lili Wang,Yehui Wang,Yulin Sun,Xiaoshuang Cai,Yating Rong,Xibo Wang,Yutang Wang. 2025

作者其他论文 更多>>