基于网络药理学与分子对接技术探讨复方仙草颗粒治疗足细胞损伤的作用机制

Mechanism of Compound Xiancao Granules in the treatment of podocyte injury:an exploration based on network pharmacology and molecular docking technique

目的通过网络药理学结合分子对接的方式,分析复方仙草颗粒治疗足细胞损伤的可能作用机制。方法在中药系统药理学数据库与分析平台筛选复方仙草颗粒组方中各味中药的有效活性成分及对应作用靶点。在GeneCards®、OMIM®、PHARMGKB数据库检索足细胞损伤相关靶点。对有效活性成分的作用靶点及足细胞损伤的相关靶点取交集以获得交集靶点。针对有效活性成分与交集靶点,利用Cytoscape 3.9.1软件制作成分-靶点网络并获得关键有效活性成分。通过STRING数据库及Cytoscape 3.9.1软件构建交集靶点的蛋白-蛋白互相作用网络,再利用Cytoscape 3.9.1软件的CytoNCA插件筛选核心靶点。通过R 4.0.5软件对交集靶点进行基因本体论(GO)功能富集分析,通过Metascape数据库对交集靶点进行京都基因与基因组百科全书(KEGG)通路富集分析。应用SYBYL-X软件2.0的Surflex模块对关键有效活性成分和与足细胞损伤关联最大的核心靶点进行分子对接。结果共收集到133种有效活性成分、234个有效活性成分的作用靶点、1733个足细胞损伤相关靶点,取交集后获得102个交集靶点。最终筛选得到3个关键有效活性成分(槲皮素、山柰酚、柚皮素)及17个核心靶点,其中表皮生长因子受体(EGFR)、基质金属蛋白酶9(MMP9)、信号转导及转录激活子3(STAT3)、血管内皮生长因子(VEGF)A、前列腺素内过氧化物合酶2(PTGS2)是与足细胞损伤关联最大的核心靶点。GO功能富集分析提示交集靶点主要涉及氧化应激等生物过程,囊泡等细胞组分,以及酶结合、抗氧化活性等分子功能;KEGG通路富集分析提示交集靶点涉及的主要信号通路包括糖尿病并发症中的终末期糖基化终产物(AGE)-AGE受体信号通路、核因子κB信号通路、VEGF信号通路、叉头框O蛋白信号通路、AMP依赖的蛋白激酶信号通路、坏死性凋亡等。EGFR、MMP9、PTGS2与槲皮素、山柰酚之间,以及EGFR、MMP9与柚皮素之间均有一定的结合活性。结论复方仙草颗粒治疗足细胞损伤具有多成分、多靶点、多通路协同作用的特点,复方仙草颗粒的多个有效活性成分可能通过EGFR、MMP9、PTGS2、STAT3、VEGFA等主要靶点作用于多个信号通路,来发挥抗氧化应激、抗炎及抗细胞凋亡等作用,从而减轻足细胞损伤。

Objective To analyze the possible mechanism of Compound Xiancao Granules in the treatment of podocyte injury through the methods of network pharmacology combined with molecular docking.Methods The effective active components and corresponding effect targets of various flavors of Traditional Chinese Medicine in the compositions of Compound Xiancao Granules were screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform.The targets related to podocyte injury were retrieved from the GeneCards,OMIM,and PHARMGKB databases.The intersection targets were obtained by acquiring intersection between effect targets of effective active components and targets related to podocyte injury.For the effective active components and intersection targets,the Cytoscape 3.9.1 software was used to make components-targets network for obtaining key effective active components.The protein-protein interaction network of intersection targets was established by the STRING database and Cytoscape 3.9.1 software,and then the core targets were screened by using the CytoNCA plugin of Cytoscape 3.9.1 software.The Gene Ontology(GO)functional enrichment analysis was performed on the intersection targets through the R 4.0.5 software,and the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis was performed on the intersection targets through Metascape database.The Surflex module of SYBYL-X 2.0 software was employed to performed molecular docking on key effective active components and the core targets most associated with podocyte injury.Results A total of 133 effective active components,234 effect targets of effective active components,1733 targets related to podocyte injury were collected,after obtaining intersection,102 intersection targets were acquired.Finally,3 key effective active components(quercetin,kaempferol,and naringenin),and 17 core targets were screened,therein epidermal growth factor receptor(EGFR),matrix metalloproteinase 9(MMP9),signal transducer and activator of transcription 3(STAT3),vascular endothelial growth factor(VEGF)A,prostaglandin-endoperoxide synthase 2(PTGS2)were the core targets most associated with podocyte injury.The results of GO functional enrichment analysis indicated that the intersection targets mainly involved biological processes of oxidative stress,etc.,cellular compositions of vesicles,etc.,and molecular functions of enzyme binding and antioxidant activity,etc.The results of KEGG pathway enrichment analysis suggested that the main signaling pathways involved in the intersection targets included advanced glycation end products(AGE)-receptor of AGE signaling pathway in diabetic complications,nuclear factor kappa B signaling pathway,VEGF signaling pathway,forkhead box O protein signaling pathway,AMP-activated protein kinase signaling pathway,necroptosis,etc.There were binding activities between EGFR,MMP9,PTGS2 and quercetin,kaempferol,as well as between EGFR,MMP9 and naringenin to a certain extent.Conclusion Compound Xiancao Granules has characteristics of multi-component,multi-target and multi-pathway synergistic effect in the treatment of podocyte injury.The multiple effective active components of Compound Xiancao Granules may act on multiple signaling pathways,exert effects of anti-oxidant stress,anti-inflammation,and anti-cell apoptosis,so as to relieve podocyte injury through EGFR,MMP9,PTGS2,STAT3,VEGFA,and other main targets.