化湿败毒方抗COVID-19和MERS、SARS作用机制分析:基于网络药理学和分子对接技术

Mechanism of Huashi Baidu Decoction for Treatment of COVID-19 and MERS,SARS Basedon Network Pharmacology and Molecular Docking

目的:采用网络药理学和分子对接技术探讨化湿败毒方发挥对新型冠状病毒感染(COVID-19)和中东呼吸综合征(MERS)、严重急性呼吸综合征(SARS)治疗作用的主要成分、作用靶点和信号通路,阐释其共性作用机制。方法:采用TCMSP数据库和UniProt数据库筛选化湿败毒方的主要成分及其作用靶点,使用Cytoscape 3.8.2构建“化合物-靶点(基因)”网络图;在GeneCards数据库中搜集“COVID-19”和“MERS”“SARS”相关靶点,通过Venny 2.1.0数据库映射筛选出COVID-19和MERS、SARS的共有靶点;将上述共有靶点与化湿败毒方中的化合物靶点取交集筛选出共同靶点作为研究靶点;将共同靶点导入STRING数据库获取数据后,使用Cytoscape 3.8.2构建蛋白质-蛋白质相互作用(PPI)网络;采用R语言进行GO生物学功能富集分析及KEGG信号通路富集分析,绘制柱状图及气泡图进行可视化分析,并构建“药物-成分-靶点-通路”网络图;选取“药物-成分-靶点-通路”网络中的关键化合物及阳性对照药分别与新型冠状病毒(SARS-CoV-2)3CL水解酶、血管紧张素转化酶II(ACE2)进行分子对接。结果:通过对化湿败毒方进行筛选得到120个活性化合物,125个作用靶点;COVID-19相关靶点4585个,MERS相关靶点2145个,SARS相关靶点4556个,三者共有靶点1210个,与化湿败毒方的共同靶点27个,其中10个核心靶点为AKT1、VEGFA、HIF1A、STAT3、CASP8、JUN、TP53、CASP3、AR、IL1B。GO功能富集分析得到生物进程(BP)1864个,分子功能(MF)113种,细胞组分(CC)32种;KEGG富集分析共得到137条信号通路(P<0.05),主要有甲型流感(Influenza A)、人巨细胞病毒感染(Human cytomegalovirus infection)、卡波西肉瘤相关疱疹病毒感染(Kaposi sarcoma-associated herpesvirus infection)等病毒感染通路以及核苷酸寡聚结构域样受体(NOD-like receptor signaling pathway)、白介素-17(IL-17 signaling pathway)、肿瘤坏死因子(TNF signaling pathway)等炎症信号通路。分子对接结果显示化湿败毒方中β-谷固醇、黄芩素、汉黄芩素、芒柄花黄素4种核心活性化合物与SARS-CoV-23CL水解酶及ACE2具有较好的结合活性,并且结合体构象稳定。结论:化湿败毒方对SARS、MERS和COVID-19具有潜在共性作用,该作用可能与活性化合物β-谷固醇、黄芩素、汉黄芩素、芒柄花黄素等作用于AKT1、CASP8、JUN、TP53、CASP3、IL1B等靶点,调节AGE-RAGE、IL-17、TNF、NOD-样受体等多种信号通路发挥抑制炎症风暴、调节免疫功能、抗病毒等作用。

Objective:To explore the effective components,target and signal pathway of Huashi Baidu Decoction in treatment of COVID-19 and MERS,SARS,and to explain its mechanism of action.Methods:The TCMSP database was used to retrieve the chemical components and targets of Huashi Baidu Decoction.The gene corresponding to the target was searched by UniProt database,and Cytoscape 3.8.2 was used to build a“compound-target(gene)”network.Three coronavirus-related targets were collected in the GeneCards database with the key words of“SARS”“MERS”and“COVID-19”,and common targets of COVID-19 and MERS,SARS were screened out through Venny 2.1.0 database.The common targets of COVID-19 and MERS,SARS were intersected with the targets of Huashi Baidu Decoction,and the common targets were selected as research targets.Protein-protein interaction(PPI)network map was constructed by Cytoscape 3.8.2 software after importing the common targets into the STRING database to obtain data;R language was used to carry out GO biological function enrichment analysis and KEGG signaling pathway enrichment analysis,draw histograms and bubble charts,and construct“drug-component-target-pathway”network diagrams;The key compounds in“drug-component-target-pathway”network were selected for molecular docking with novel coronavirus(SARS-CoV-2)3CL hydrolase,and angiotensin-converting enzyme II(ACE2).Results:120 active compounds and 125 corresponding targets were obtained from Huashi Baidu Decoction.4585 COVID-19-related targets,2145 MERS-related targets,4556 SARS-related targets,and 1210 targets for the three diseases.27 common targets with Huashi Baidu Decoction,the 10 core targets were:AKT1,VEGFA,HIF1A,STAT3,CASP8,JUN,TP53,CASP3,AR,IL1B.GO function enrichment analysis revealed 1864 biological processes(BP),113 molecular functions(MF),and 32 cellular components(CC).KEGG pathway enrichment analysis screened 137 signal pathways(P<0.05),mainly related to Human cytomegalovirus infection,Kaposi sarcoma-associated herpesvirus infection,Influenza A,as well as inflammatory signaling pathways such as IL-17 signaling pathway,TNF signaling pathway,NOD-like receptor signaling pathway.The molecular docking results showed that the four core active flavonoids ofβ-Sitosterol,baicalein,wogonin,formononetin in Huashi Baidu Decoction had good affinity with SARS-CoV-23CL hydrolase and ACE2,and the binding body was conformationally stable.Conclusion:Huashi Baidu Decoction has potential common effects on the three diseases of COVID-19 and MERS,SARS.This effect may be related to those active compounds such as beta-Sitosterol,baicalein,wogonin,formononetin acting on targets such as AKT1,CASP8,JUN,TP53,CASP3,IL1B to regulate IL-17,TNF,NOD-like receptor signaling pathway and exerting anti-virus,suppression of inflammatory storm,and regulation of immune function.