[关键词]
[摘要]
目的 基于网络药理学与分子对接探讨清肺达原颗粒治疗新型冠状病毒肺炎(COVID-19)的主要活性成分、靶标及通路,以期阐述其作用机制。方法 通过TCMSP、ETCM、YATCM数据库检索清肺达原颗粒的中药化学成分,以口服生物利用度(OB)≥30%和类药性(DL)≥0.18为阈值筛选潜在的活性化合物。通过SIB、STITCH数据库查询活性化合物对应的靶标,利用STRING数据库获取蛋白-蛋白相互作用(PPI)网络和网络拓扑参数,导入Cytoscape 3.6.0对网络进行分析,筛选关键靶标。通过DAVID进行基因本体(GO)功能富集分析、京都基因与基因组百科全书(KEGG)通路富集分析和组织富集(tissue enrichment)预测其作用机制。利用AutoDock将化合物与新型冠状病毒(SARS-CoV-2)S蛋白受体结合结构域与血管紧张素转化酶II(ACE2)蛋白酶结构域复合物(SARS-CoV-2-S-RBD-ACE2)进行分子对接。结果 筛选得到清肺达原颗粒活性化合物251个,对应靶点共1 037个;筛选出关键靶标107个,对应化合物185个,关键靶点涉及ESR1、AR、EGFR、KDR、MMP2等,与ACE2共表达基因52个。GO功能富集分析结果显示清肺达原颗粒主要对细胞表面信号转导、分子功能、磷酸化和转录等生物学过程起调节作用,KEGG通路富集主要涉及趋化因子信号通路、T细胞受体信号通路、B细胞受体信号通路、自然杀伤细胞介导的细胞毒性和Toll样受体信号通路等。组织富集显示关键基因表达部位主要分布在肺及上皮细胞,涉及多种免疫细胞,如T细胞、B细胞、淋巴细胞等。分子对接结果显示与SARS-CoV-2-S-RBD-ACE2复合物亲和力较好的化合物主要来源于柴胡、党参、知母、甘草,其中柴胡皂苷、甘草酸、知母皂苷与SARS-CoV-2- S-RBD-ACE2复合物结合力较强,可能为抗SARS-CoV-2的潜在活性成分。结论 清肺达原颗粒具有多成分、多靶点、多途径的整体调控特点。其中柴胡皂苷、甘草酸、知母皂苷可能为抗SARS-CoV-2的潜在活性成分,治疗COVID-19的作用机制可能与调控ACE2共表达的基因、调节炎症和免疫相关的信号通路、影响SARS-CoV-2-S-RBD-ACE2复合物的稳定有关。
[Key word]
[Abstract]
Objective To explore the main active components, key targets and signaling pathways of Qingfei Dayuan Granules in treating of COVID-19 based on network pharmacology and molecular docking. Methods TCMSP, ETCM and YATCM databases were used to search the chemical constituents of Qingfei Dayuan Granules, and the threshold values of OB ≥ 30% and DL ≥ 0.18 were used to screen the potential active compounds. SIB and STITCH databases were used to query the targets corresponding to the active compounds, and the PPI network and network topology parameters were obtained by using STRING database. Cytoscape 3.6.0 was used to screen the hub targets. The key targets were analyzed by Gene Ontology (GO), the Kyoto Encyclopedia of genes and genomes (KEGG) pathway enrichment and tissue enrichment using DAVID 6.8 software. The molecular docking was performed by AutoDock Tools 1.5.6 software. Results A total of 251 active compounds and 1 037 targets were obtained, 107 key targets and 185 corresponding compounds were screened. The key targets involved ESR1, AR, EGFR, KDR, MMP2, and 52 genes were coexpressed with ACE2. The results of GO function enrichment analysis showed that Qingfei Dayuan Granules mainly regulated the biological processes of cell surface signaling transduction, molecular function, phosphorylation and transcription. KEGG pathway enrichment mainly involved chemokine signaling pathway, T cell receptor signaling pathway, B cell receptor signaling pathway, natural killer cell mediated cytotoxicity and Toll like receptor signaling pathway. The results of tissue enrichment showed that the key gene expression sites were mainly in lung and epithelial cells, involving a variety of immune cells, such as T cells, B cells, lymphocytes, etc. Molecular docking showed that the compounds with good binding power to SARS-CoV-2-RBD-ACE2 complex in Qingfei Dayuan granules were mainly come from Bupleuri Radix, Codonopsis Radix, Anemarrhenae Rhizoma, and Glycyrrhizae Radix et Rhizoma. Saikosaponin, glycyrrhizic acid, anemarsaponin had good binding power with SARS-CoV-2-S-RBD-ACE2, which may be potential active components against SARS-CoV-2. Conclusion Qingfei Dayuan Granules has the characteristics of multi-components, multi-targets and multi-pathway regulation. Saikosaponin, glycyrrhizic acid, and anemarsaponin may be the potential active components against SARS-CoV-2. The mechanisms of its treatment against COVID-19 may be related to the regulation of the co-expressed genes with ACE2, inhibition of inflammation and immune related signaling pathways, and the destruction of the complex structure of SARS-CoV-2-S-RBD-ACE2.
[中图分类号]
R285.5
[基金项目]
湖北省科技厅新型肺炎应急科技攻关项目:基于肺炎1号为主的中医药治疗新型冠状病毒肺炎的临床研究(2020FCA007)