基于网络药理学和分子对接技术探讨四神煎治疗膝骨关节炎的作用机制

A study on the action mechanism of the Sishen decoction on knee osteoarthritis based on network pharmacology and molecular docking technology

目的:基于网络药理学及分子对接技术分析四神煎治疗膝骨关节炎活性成分及药物分子的作用机制。方法:通过中药系统药理学数据库与分析平台(TCMSP)及ETCM数据库筛选四神煎的有效药物成分及对应的靶点基因,使用GeneCards数据库获取膝骨关节炎的疾病靶点,使用R语言Limma包筛选差异表达的基因,接着对药物靶点与疾病靶点、差异表达基因取交集,并使用R语言ClusterProfiler包进行基因本体论(GO)/京都基因与基因组百科全书(KEGG)富集分析;利用Cytoscape软件绘制关键靶点-功能、关键靶点-通路的调控网络图;对交集基因、药物活性成分绘制中药药理调控网络;针对交集靶点绘制蛋白质-蛋白质相互作用网络图,并采用Cytoscape进行可视化;最后针对蛋白质-蛋白质相互作用网络中排名居前5位的基因及其对应的活性成分进行分子对接。结果:通过TCMSP及ETCM数据库筛选出药物靶点取并集,去重复后得到四神煎的药物靶点491个,膝骨关节炎的疾病靶点共1477个;在膝骨关节炎/正常样本之间共存在2988个差异表达的基因,其中1539个基因在膝骨关节炎样本中为上调表达,1449个基因为下调表达,利用差异表达基因、药物靶点和疾病靶点取交集获得交集靶点21个。共富集到44个KEGG通路和311个GO功能条目,蛋白质-蛋白质相互作用网络分析表明前列腺素氧化环化酶2(ProstaglandinEndoperoxide Synthase 2,PTGS2)、趋化因子CCL2(C-C Motif Chemokine Ligand 2,CCL2)、血管细胞附着分子1(Vascular Cell Adhesion Molecule 1,VCAM1)、白细胞介素(Interleukin,IL)-2及基质金属蛋白酶(Matrix Metallopeptidase,MMP)3等关键靶点处于蛋白质-蛋白质相互作用网络的中心,与其他蛋白具有更多的联系。分子对接表明四神煎中主要活性成分豆甾醇、槲皮素等与核心作用靶点(PTGS2、CCL2、VCAM1、IL-2、MMP3)可成功对接且具有较高的结合亲和力。结论:本研究运用网络药理学预测四神煎治疗膝骨关节炎可能的活性成分、关键靶点及其作用通路,旨在阐明四神煎治疗膝骨关节炎的分子机制,为其药效物质基础和作用机制研究提供理论依据和参考价值。

Objective:To analyze the action mechanism of the Sishen decoction(四神煎)on knee osteoarthritis based on network pharmacology and molecular docking technology.Methods:The effective drug components and corresponding target genes of the Sishen decoction were screened through TCMSP and ETCM database.The disease target of knee osteoarthritis were obtained through GeneCards database.Differentially expressed genes were screened by R language limma.The intersection of drug targets,disease targets and differentially expressed genes were selected.The GO/KEGG enrichment analysis were performed by R language ClusterProfiler.The regulatory networks of key target-function and key target-pathway were mapped by Cytoscape software.Pharmacological regulatory networks of TCM medicine were mapped in intersecting genes and drug active ingredients.The protein-protein interaction network diagram of the intersection target was drawn and visualized by Cytoscape.Among them,the top 5 genes and their corresponding active components were molecularly docked.Results:The drug targets were selected and collected by TCMSP and ETCM database.A total of 491 drug targets of the Sishen decoction and 1477 disease targets of knee osteoarthritis were obtained after deduplication.There were 2988 differentially expressed genes between knee osteoarthritis and normal samples,of which 1539 genes were up-regulated and 1449 genes were down-regulated.A total of 21 intersection targets were obtained by the intersection of differentially expressed genes,drug targets and disease targets.A total of 44 KEGG pathways and 311 GO functional entries were enriched.Protein-protein interaction network analysis showed that key targets such as PTGS2,CCL2,VCAM1,IL-2 and MMP3 were at the center of protein-protein interaction,and that they had more connection with other proteins.Molecular docking showed that the main active components of the Sishen decoction,such as stigmasterol and quercetin,could successfully dock with the core targets(PTGS2,CCL2,VCAM1,IL-2,MMP3),and had high binding affinities.Conclusion:In this study,network pharmacology was used to predict the possible active components,key targets and pathways of the Sishen decoction on knee osteoarthritis,in order to analyze the molecular mechanism and provide a theoretical basis for the pharmacodynamic material basis and action mechanism.