基于生物信息学与分子动力学的仙方活命饮治疗猴痘作用机制与分子靶点预测

Mechanism and molecular target prediction of Xianfang Huoming Drink in treatment of monkeypox based on bioinformatics and molecular dynamics

目的 利用生物信息学、分子对接与分子动力学的方法,识别仙方活命饮的生物活性成分和靶点,寻找仙方活命饮治疗猴痘的靶点与通路,以期对相关治疗药物与治疗策略的开发提供帮助。方法 使用中药系统药理学数据库与分析平台(Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform,TCMSP)筛选仙方活命饮的活性成分和相关靶点,利用高通量基因表达数据库(Gene Expression Omnibus,GEO)获取猴痘病毒感染相关靶点。构建蛋白质相互作用(proteinprotein interaction,PPI)网络,通过基因本体论(gene ontology,GO)功能富集分析和京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)通路富集分析分析,获得关键的靶点和信号通路。将预测的活性化合物与核心靶点进行分子对接验证。使用GROMACS对对接的部分结果进行分子动力学分析,通过不同指标判断其结合的稳定程度与作用效果。结果 通过TCMSP共筛选出仙方活命饮191种活性成分,296种相关蛋白,259个相关基因。通过GEO数据库获得321个猴痘差异基因。二者交集靶点基因共有9个。GO富集分析获得502条有意义条目,KEGG富集分析获得73条有意义通路。有520组活性成分-靶点对接成功,其中前列腺素过氧化物内合酶1(prostaglandin-endoperoxide synthase 1,PTGS1)-甘草异黄烷酮、PTGS1-3′-甲氧基光甘草定、PTGS1-shinpterocarpin、PTGS1-4′-甲氧基光甘草定作为有继续研究意义的构象进一步进行分子动力学模拟分析,结合自由能分别为(-86.380±1.257)、(-61.168±1.088)、(-103.463±1.371)、(-96.986±1.236)k J/mol,均可以稳定结合。结论 仙方活命饮治疗猴痘的作用机制可能为甘草异黄烷酮、3′-甲氧基光甘草定、shinpterocarpin、4′-甲氧基光甘草定分别与PTGS1结合,通过抗炎、抗氧化作用降低猴痘引发的炎症反应,减轻炎症损伤。其中,shinpterocarpin的结合能最优,可能发挥了主要作用效果。所得结果为猴痘后续的治疗方案与相关治疗药物的开发提供新的研究方向。

Objective Bioinformatics,molecular docking and molecular dynamics methods were used to identify the bioactive ingredients and targets of Xianfang Huoming Drink(仙方活命饮),and to find the targets and pathways of Xianfang Huoming Drink in the treatment of monkeypox,in order to provide help for the development of related therapeutic drugs and strategies.Methods Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)was used to identify the active ingredients and related targets of Xianfang Huoming Drink,and the Gene Expression Omnibus(GEO)was used to obtain the targets related to monkeypox virus infection.The protein-protein interaction(PPI)network was constructed.The key potential targets and signaling pathways related to monkeypox virus infection through gene ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)analyses.Subsequently,molecular docking was performed to predict the combination of active compounds with core targets.Afterwards,the results of the docking performed were subjected to molecular dynamics calculations using GROMACS to determine the stability and effect of the binding by calculating different indicators.Results A total of 191 active ingredients,296 related proteins,and 259 related genes of Xianfang Huoming Drink were screened.A total of 321 monkeypox differential genes were obtained through the GEO database.There were nine intersecting target genes between the two.GO enrichment analysis yielded 502 meaningful entries,and KEGG enrichment analysis yielded 73 meaningful pathways.A total of 520 groups of active ingredient-target docked successfully,among which prostaglandin-endoperoxide synthase 1(PTGS1)-licoisoflavanone,PTGS1-3'-methoxyglabridin,PTGS1-shinpterocarpin,and PTGS1-4'-methoxyglabridin were further analyzed for molecular dynamics simulations as conformations of further research significance,and the binding free energies(−86.380±1.257),(−61.168±1.088),(−103.463±1.371),and(−96.986±1.236)kJ/mol,respectively,could be stably bound.Conclusion The mechanism of Xianfang Huoming Drink in the treatment of monkeypox may be that licoisoflavanone,3'-methoxyglabridin,shinpterocarpin and 4'-methoxyglabridin are combined with PTGS1,respectively,to reduce the inflammatory response caused by monkeypox and reduce the inflammatory damage through anti-inflammatory and anti-oxidant effects Among them,shinpterocarpin had the best binding energy,which may have played the main role.The results provide a new research direction for the follow-up treatment of monkeypox and the development of related therapeutic drugs.