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Analysis of the active components and mechanism of Shufeng Jiedu capsule against COVID-19 based on network pharmacology and molecular docking.

ABSTRACT:

Abstract

This study investigates the active components and mechanism of Shufeng Jiedu Capsules (SFJDC) against novel coronavirus through network pharmacology and molecular docking.The TCMSP, TCMID, and BATMAN-TCM databases were used to retrieve the components of SFJDC. The active components were screened by ADME (absorption, distribution, metabolism, and excretion) parameters, and identified by Pubchem, Chemical Book, and ChemDraw softwares. The molecular docking ligands were constructed. SARS Coronavirus-2 Major Protease (SARS-CoV-2-Mpro) and angiotension converting enzyme 2 (ACE2) were used as molecular docking receptors. AutoDock software was used for molecular docking. Cytoscape 3.7.1 software was used to generate an herbs-active components-targets network. Gene Ontology gene function and Kyoto Encyclopedia of Genes and Genomes signal pathway analysis were performed by DAVID data.A total of 1244 components were identified from SFJDC, and 210 active components were obtained. Among them, 97 active components were used as docking ligands to dock with SARS-CoV-2-Mpro and ACE2. There were 48 components with good binding activity to SARS-CoV-2-Mpro. Ten active components (including 7-Acetoxy-2-methylisoflavone, Kaempferol, Quercetin, Baicalein, Glabrene, Glucobrassicin, Isoglycyrol, Wogonin, Petunidin, and Luteolin) combined with SARS-CoV-2-Mpro and ACE2 simultaneously. Among them, Kaempferol, Wogonin, and Baicalein showed higher binding activity. The herbs-active components-targets network contained 7 herbs, 10 active components, and 225 targets. The 225 target targets were involved in 653 biological processes of Gene Ontology analysis and 130 signal pathways (false discovery rate ≤ 0.01) of Kyoto Encyclopedia of Genes and Genomes analysis.The active components of SFJDC (such as Kaempferol, Wogonin, and Baicalein) may combine with ACE2 and act on multiple signaling pathways and targets to exert therapeutic effect on novel coronavirus.

SUBMITTER: Simayi J

PROVIDER: S-EPMC8735807 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:IntroductionThe novel coronavirus pneumonia that broke out in 2019 has become a global epidemic. According to the diagnosis and treatment plan issued in China and the existing clinical data, Shufeng Jiedu (SFJD) Capsule can be effectively used in the treatment of COVID-19 patients. This study aimed to explore its mechanism of action by network pharmacology and molecular docking technology.MethodsThe Chinese Medicine System Pharmacology Analysis Platform (TCMSP), a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine (BATMAN-TCM), the Encyclopedia of Traditional Chinese Medicine (ETCM) and related literature records were used to search the composition and main active compounds of SFJD, and to screen out the targets of drug components. Disease-associated genes were obtained by the Human Gene Database (GeneCards), the Human Online Mendelian Inheritance Platform (OMIM) and the DisGeNET database, and the co-targeted genes/proteins as targets of both SFJD and COVID-19 were selected by the Comparative Toxicogenomics Database (CTD). Co-targeted genes/proteins were analyzed by STRING, the Database for Annotation, Visualization and Integrated Discovery (DAVID) and Reactome for proteins to protein interaction (PPI), pathway and GO (gene ontology) enrichment, and predicted by AutoDock for their high-precision docking simulation. In addition, the therapeutic effect for SFJD treatment on COVID-19 was validated by the Chinese medicine anti-novel coronavirus pneumonia drug effect prediction and analysis platform (TCMCOVID).ResultsScreening resulted in 163 compounds and 463 targeted genes. The PPI core network contains 76 co-targeted proteins. The Reactome pathways were enriched in signaling by interleukins, immune system, etc. Finally, 6 key proteins of TNF, IL-10, IL-2, IL-6, STAT1 and CCL2 were selected and successfully docked with 4 active ingredients of quercetin, luteolin, wogonin and kaempferol.ConclusionSFJD may play a role in the prevention and treatment of COVID-19 through multiple active compounds acting on multiple targets and then multiple pathways.

Project description:BackgroundMicrovascular angina (MVA) substantially threatens human health, and the Shenzhi Tongxin (SZTX) capsule demonstrates a remarkable cardioprotective effect, making it a potential treatment option for MVA. However, the precise mechanism of action for this medication remains unclear. This study utilized network pharmacology and molecular docking technology to investigate the active components and potential mechanisms underlying the efficacy of the SZTX capsule in alleviating MVA.MethodsThe main ingredients of the SZTX capsule, along with their targets proteins and potential disease targets associated with MVA, were extracted from public available databases. This study utilized the STRING database and Cytoscape 3.7.2 software to establish a protein-protein interaction network and determine key signaling pathway targets. Subsequently, the DAVID database was utilized to conduct Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes analyses on the intersection targets. To further investigate the molecular interactions, Autodock and PyMOL software were employed to perform molecular docking and visualize the resulting outcomes.ResultsA total of 130 and 142 bioactive ingredients and intersection targets were identified respectively. Six core targets were obtained through protein-protein interaction network analysis. Gene Ontology enrichment analysis showed that 610 biological processes, 75 cellular components, and 92 molecular functions were involved. The results of Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that SZTX capsule molecular mechanism in the treatment of MVA may be related to several pathways, including mitogen-activated protein kinases, PI3K-Akt, HIF-1, and others. The results of molecular docking showed that the 7 key active ingredients of SZTX capsule had good binding ability to 6 core proteins.ConclusionSZTX capsule potentially exerts its effects by targeting multiple signaling pathways, including the mitogen-activated protein kinases signaling pathway, PI3K-Akt signaling pathway, and HIF-1 signaling pathway. This multi-target approach enables SZTX capsule to inhibit inflammation, alleviate oxidative stress, regulate angiogenesis, and enhance endothelial function.

Project description:BackgroundXianlinggubao formula (XLGB), a Chinese State Food and Drug Administration-permitted traditional Chinese herbal medicine, has been extensively used to treat osteoporosis. Although XLGB was shown to improve bone mass in ovariectomized rats and clinically alleviate osteoporosis symptoms, its pharmacological mechanisms remain unclear.MethodsIn this study, we used a network pharmacological approach to explore the potential mechanism of XLGB in treating osteoporosis. We obtained XLGB compounds from the TCMSP and TCMID databases and identified potential targets of these compounds through target fishing based on the TCMSP and Swiss Target Prediction databases. Next, we identified the osteoporosis targets by using the CTD, TTD, GeneCards, OMIM and PharmGKB databases. Then, the overlapping genes between the XLGB potential targets and the osteoporosis targets were used to establish a protein-protein interaction (PPI) network and to analyze their interactions and identify the major hub genes in this network. Subsequently, the Metascape database was utilized to conduct the enrichment of Gene Ontology biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.ResultsThere were 104 active compounds and 295 related targets identified overall. After the Metascape enrichment analysis, we identified the top 25 cellular biological processes and top 15 pathways based on the logP value and found that the XLGB-mediated anti-osteoporosis effect was mainly associated with reactive oxygen species, organonitrogen compound response and cell migration. Furthermore, 36 hub genes of XLGB, such as EGF, EGFR, MTOR, MAPK14 and NFKB1, were considered potential therapeutic targets, suggesting the underlying mechanisms of XLGB acting on osteoporosis.ConclusionWe investigated the possible therapeutic mechanisms of XLGB from a systemic perspective. These key targets and pathways provide promising directions for future research to reveal the exact regulatory mechanisms of XLGB.

Project description:A large body of literature has shown that ginseng had a role in diabetes mellitus management. Ginsenosides are the main active components of ginseng. But what ginsenosides can manage in diabetic are not systematic. The targets of these ginsenosides are still incomplete. Our aim was to identify which ginsenosides can manage diabetes mellitus through network pharmacology and molecular docking. To identify the targets of these ginsenosides. In this work, we retrieved and screened ginsenosides and corresponding diabetes mellitus targets across multiple databases. PPI networks of the genes were constructed using STRING, and the core targets were screened out through topological analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed by using the R language. Finally, molecular docking was performed after bioinformatics analysis for verification. Our research results showed that 28 ginsenosides in ginseng might be against diabetes mellitus by modulating related proteins such as VEGFA, Caspase 3, and TNF-α. Among the 28 ginsenosides, 20(R)-Protopanaxatriol, 20(R)-Protopanaxadiol, and Ginsenoside Rg1 might play a significant role. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analysis showed that the management of diabetes mellitus by ginsenosides may be related to the positive regulation of reactive oxygen metabolic processes, associated with the insulin signaling pathway, TNF signaling pathway, and AMPK signaling pathway. Molecular docking results and molecular dynamics simulation showed that most ginsenosides could stably bind to the core target, mainly hydrogen bonding and hydrophobic bond. This study suggests the management of ginseng on diabetes mellitus. We believe that our results can contribute to the systematic study of the mechanism of ginsenosides for the management of diabetes mellitus. At the same time, it can provide a theoretical basis for subsequent studies on the management of ginsenosides in diabetes mellitus.

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Analysis of the active components and mechanism of Shufeng Jiedu capsule against COVID-19 based on network pharmacology and molecular docking.

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