基于基因芯片技术和分子对接探索扶肾颗粒治疗腹膜纤维化的药理学潜在机制

Exploring the Potential Pharmacological Mechanism of Fushen Granule in the Treatment of Peritoneal Fibrosis Based on Gene Chip Technology and Molecular Docking

目的:基于GEO基因芯片技术和分子对接探索扶肾颗粒治疗腹膜纤维化(peritoneal fibrosis,PF)的潜在作用机制。方法:借助中药系统药理学分析平台(traditional chinese medicine systems pharmacology database and analysis platform,TCMSP)检索扶肾颗粒所含化学成分的相关信息,通过生物利用度和类药性筛选潜在药效成分和对应靶标;根据UniProt数据库确定与扶肾颗粒相关调控的靶蛋白;再从疾病入手,根据genecard、OMIM疾病数据库,检索与PF相关的已知靶点;通过可视化工具绘制潜在药效成分-靶基因、靶蛋白-疾病的网络示意图,并以R4.0.0语言进行基因本体论(gene ontology,GO)、京都基因和基因组的百科全书(kyoto encyclopedia of genes and genomes,KEGG)通路富集分析,根据GEO数据库中的GSE62928基因芯片进行相关基因的验证,最后行分子对接,探索蛋白与分子间的亲和力。结果:扶肾颗粒共有110个有效成分,共267个相关靶点。腹膜纤维化共有408个相关基因,共有84个交集基因,String互作用蛋白显示共84个靶点,排名前5位的靶点分别是肿瘤坏死因子(tumor necrosis factor,TNF)、白细胞介素-6(interleukin-6,IL-6)、RAC-α丝氨酸/苏氨酸蛋白激酶(RAC-alpha serine/threonine protein kinase,AKT1)、血管内皮生长因子A(vascular endothelial growth factor A,VEGFA)、促分裂原活化蛋白激酶3(promote the split the original activated protein kinase 3,MAPK3)。GO功能富集分析得到条目118个(P<0.05),主要与细胞因子活性相关,KEGG通路富集分析的相关通路有163个(P<0.05),包括糖基化终产物受体配体通路、液体剪切应力和动脉粥样硬化通路、肿瘤坏死因子信号通路、丝裂原活化蛋白激酶信号通路、癌症蛋白聚糖信号通路等。根据GEO数据库药物-疾病交集基因进行测试,共有6条基因相交,均为上调基因,说明扶肾颗粒治疗腹膜纤维化的作用机制可能和抑制CCL2、F3、HIF1A、HSPB1、IL-6、TIMP1这6条基因有关。分子对接显示2ZOQ与3L0V对接良好,可能是扶肾颗粒治疗腹膜纤维化的靶点。结论:扶肾颗粒治疗腹膜纤维化可能通过调节TNF、IL-6、AKT1、VEGFA、MAPK3等靶点,调节糖基化终产物受体配体通路、液体剪切应力和动脉粥样硬化通路、肿瘤坏死因子信号通路、丝裂原活化蛋白激酶信号通路、癌症蛋白聚糖信号通路等发挥治疗作用。

Objective:To explore the potential mechanism of Fushen Granule in network pharmacology in the treatment of peritoneal fibrosis(PF)based on GEO gene chip technology and molecular docking.Methods:With the help of traditional Chinese medicine systems pharmacology database and analysis platform(TCMSP),the relevant information of chemical components contained in Fushen Granules was retrieved,and the potential pharmacodynamic components and corresponding targets were screened through bioavailability and drug class;The target proteins related to Fushen Granule were determined according to UniProt database;Then,starting from the disease,the known targets related to PF were retrieved according to genecard and OMIM disease databases;through visualization tools,the network diagrams of potential pharmacodynamic components-target genes and target proteins-diseases were drawn,and gene ontology(GO)and kyoto encyclopedia of genes and genomes(KEGG)pathway enrichment analysis were carried out in R4.0.0 language.Relevant genes were verified according to GSE62928 gene chip in geo database.Finally,molecular docking was performed to explore the affinity between proteins and molecules.Results:There were 110 active components and 267 related targets in Fushen Granule.There were 408 related genes and 84 intersection genes in peritoneal fibrosis.String interaction protein showed a total of 84 targets.The top five targets were tumor necrosis factor(TNF),interleukin-6(IL-6)and RAC-alpha serine/threonine protein kinase(AKT1),vascular endothelial growth factor A(VEGFA),promote the split the original activated protein kinase 3(MAPK3).118 items were obtained by GO functional enrichment analysis(P<0.05),which were mainly related to cytokine activity.There were 163 related pathways in KEGG pathway enrichment analysis(P<0.05),including AGE-RAGE,Fluid shear stress and atherosclerosis,TNF signaling pathway,MAPK signaling pathway,proteoglycans in cancer and other related pathways.According to the test of drug disease intersection gene in GEO database,there were 6 genes intersecting,all of which were up-regulated genes,indicating that the mechanism of Fushen Granule in the treatment of peritoneal fibrosis may be related to the inhibition of CCL2,F3,HIF1 A,HSPB1,IL-6 and TIMP1.Molecular docking shows that 2 ZOQ was well connected with 3 L0 V,which may be the target of Fushen Granule in the treatment of peritoneal fibrosis.Conclusion:Fushen Granule may treat peritoneal fibrosis by regulating targets such as TNF,IL-6,AKT1,VEGFA and MAPK3,AGE-RAGE,fluid shear stress and atherosclerosis,TNF signaling pathway and MAPK signaling pathway and proteoglycans in cancer.