基于网络药理学、分子对接及分子动力学研究巴马汀抗菌作用机制

Exploration of antibacterial mechanism of palmatine based on network pharmacology,molecular docking,and molecular dynamics

目的基于网络药理学、分子对接及分子动力学研究巴马汀的抗菌作用机制。方法通过Swiss Target Prediction网站预测巴马汀的药物靶点,并与GeneCards和OMIM数据库检索的抗菌靶点相映射得到巴马汀抗菌潜在作用靶点;利用STRING数据库和Cytoscape软件构建蛋白质-蛋白质相互作用网络并筛选关键靶点;使用DAVID数据库对潜在作用靶点进行基因本体(GO)功能分析和京都基因与基因组百科全书(KEGG)通路富集分析并做可视化处理,构建出巴马汀“成分-靶点-通路”网络;经分子对接和分子动力学模拟对巴马汀与关键靶点的结合进行验证;体外抑菌实验验证巴马汀的抗菌活性。结果共筛选出28个巴马汀关键抗菌靶点,富集到199个GO条目和105条相关通路,“成分-靶点-通路”网络分析表明MAPK8、RAC1、STAT3为巴马汀关键抗菌靶点;分子对接结果表明,巴马汀与关键靶点MAPK8和RAC1有很好的结合作用;分子动力学研究发现巴马汀与蛋白之间存在氢键及疏水作用,使巴马汀能够稳定地与靶点蛋白结合;体外抑菌实验证明巴马汀对金黄色葡萄球菌和白色念珠菌均有较强的抑制活性,且与阳性药联用有协同作用。结论巴马汀可能通过内分泌抵抗和PI3K-Akt、FoxO等信号通路抑制MAPK8和RAC1的基因表达发挥抗菌作用。

AIM To study the antibacterial mechanism of palmatine based on network pharmacology,molecular docking,and molecular dynamics.METHODS The drug targets of palmatine were predicted through the Swiss Target Prediction website,and the potential antibacterial targets of palmatine were obtained by mapping them with the antibacterial targets retrieved from GeneCards and OMIM databases.Protein-protein interaction network was constructed using STRING database and Cytoscape software and key targets were screened.The DAVID database was used to carry out Gene Ontology(GO)functional analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis of potential targets,and visual processing was performed to build the“Component-Target-Pathway”network of palmatine.The binding of palmatine to key targets was validated through molecular docking and molecular dynamics simulations.In vitro antibacterial experiments were conducted to verify the antibacterial activity of palmatine.RESULTS A total of 28 critical anti-bacterial targets of palmatine were screened and enriched to 199 GO entries and 105 related pathways.“Ingredients-Target-Pathway”network showed that MAPK8,RAC1,and STAT3 were key anti-bacterial targets.The molecular docking results indicated that palmatine had an excellent binding effect with key targets MAPK8 and RAC1.Molecular dynamics studies found that there were hydrogen bonds and hydrophobic interactions between palmatine and proteins,enabling stable binding of palmatine to target proteins.In vitro antibacterial experiments showed that palmatine had strong inhibitory activity against Staphylococcus aureus and Candida albicans,and it had synergistic effects when combined with positive drugs.CONCLUSION Palmatine may exert its antibacterial effects by inhibiting the gene expression of MAPK8 and RAC1 through endocrine resistance and signaling pathways such as PI3K-Akt and FoxO.