基于网络药理学与分子对接方法探讨羌活胜湿汤治疗类风湿关节炎的作用机制

Mechanism of Qianghuo Shengshi Decoction in the Treatment of Rheumatoid Arthritis Based on Network Pharmacology and Molecular Docking

目的:基于网络药理学和分子对接方法,探讨羌活胜湿汤治疗类风湿关节炎(RA)的作用机制。方法:通过查阅文献结合中药系统药理学数据库与分析平台,得到羌活胜湿汤中7味中药的主要活性成分及其靶点基因;在GeneCards和人类孟德尔遗传综合数据库中进行检索,查找RA相关靶点基因,基于R语言,获得羌活胜湿汤-RA共同作用的靶点基因。运用STRING数据库构建蛋白质-蛋白质相互作用网络图,利用R语言计算各节点的度值得到柱形图并获得度值排序居前5位的靶点蛋白;运用Cytoscape 3.8.2软件,构建中药相关成分与RA靶点相互作用的网络图,使用Analyze Network插件进行分析,得到度值排序居前5位的活性物质。运用R语言和Bioconductor生物信息软件包对获得的基因进行基因本体(GO)功能富集分析和京都基因与基因组百科全书(KEGG)通路富集分析。运用Cytoscape 3.8.2软件构建信号-靶点通路网络图。运用Pymol和Auto Dock Tools软件处理得到的蛋白、配体及小分子,利用Vina计算结合自由能并绘制分子对接图。结果:筛选得到羌活胜湿汤活性成分141个,靶点基因2497个。获得RA相关靶点633个,去除重复后得到羌活胜湿汤-RA共同靶点基因70个,主要通过信号转导及转录激活因子3、JUN原癌基因、相关因子A(RELA)、丝裂原激活的蛋白激酶(MAPK)1和MAPK14等靶点发挥作用。GO功能及KEGG通路分析显示,主要作用途径为通过对脂多糖的反应、对细菌源性分子的反应、细胞对化学应激的反应、对氧化应激的反应及炎症反应的调节等信号通路发挥作用。分子对接显示,有效成分与靶点基因具有较好的结合效果。结论:羌活胜湿汤治疗RA具有多成分、多靶点、多通路的特点,本研究可为其临床应用与进一步实验研究提供科学依据。

OBJECTIVE:To explore the mechanism of Qianghuo Shengshi decoction in the treatment of rheumatoid arthritis(RA)based on network pharmacology and molecular docking.METHODS:After reviewing the literature and exploring the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform,the key active components and target genes of seven traditional Chinese medicines in Qianghuo Shengshi decoction were obtained.RA-related target genes in GeneCards and on-line Mendelian Inheritance in Man database were retrieved.Based on R language,the target gene of Qianghuo Shengshi decoction-RA interaction was obtained.STRING database was used to construct the protein-protein interaction network diagram.R language was used to calculate the degree value of each node to the histogram and obtain the top 5 target proteins of the degree value.Cytoscape 3.8.2 software was used to construct the network diagram of interaction between traditional Chinese medicine related components and RA targets.The top 5 active components in terms of degree value were analyzed by using the Analyze Network plug-in.The obtained genes were analyzed for Gene Ontology(GO)functional enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment by using R language and Bioconductor bioinformatics software package.The signal-target pathway network diagram was constructed by using Cytoscape 3.8.2 software.Pymol and AutoDockTools software were adopted to process proteins,ligands and small molecules for molecular docking analysis,Vina was used to calculate the binding free energy and generate molecular docking diagrams.RESULTS:A total of 141 active components and 2497 target genes were screened for Qianghuo Shengshi decoction.A total of 633 RA-related targets were obtained,and 70 common target genes of Qianghuo Shengshi decoction-RA were obtained after removing duplicates,mainly for signal transduction and transcriptional activator 3,JUN,RELA,mitogen activated protein kinase(MAPK)1 and MAPK14.GO function and KEGG analysis revealed that the main pathways of action were the response to lipopolysaccharides,the response to bacterial derived molecules,the response of cells to chemical stress,the response to oxidative stress,and the regulation of inflammatory responses.Notably,molecular docking analysis indicated a strong binding effect between the active components and target genes.CONCLUSIONS:Qianghuo Shengshi decoction in the treatment of RA is characterized by multi-components,multi-targets and multi-pathways,which provides scientific basis for its clinical application and further experimental research.