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Objective To investigate the material basis and antitumor mechanism of Marsdenia tenacissima (MT) on hepatocellular carcinoma (HCC) by bioinformatics, network pharmacology and molecular docking technology. Methods Active ingredients of MT were collected by literature search and screened by Swiss ADME website, which targets were predicted by Swiss Target Prediction. The chip data of HCC (GSE147888) were downloaded from the NCBI Gene Expression Omnibus (GEO) database. Differentially expressed genes were screened by R software. HCC-related targets were collected from the Genecards and OMIM databases. The Venny online tool was used to obtain the intersection of the herbal medicine targets and the disease targets. Subsequently, drug-target network and protein–protein interaction (PPI) network were constructed by Cytoscape software and String platform. GO enrichment analysis and KEGG pathway analysis were performed to analysis the functions and pathways enriched by key genes. The expression of key genes in HCC and its effect on survival were analyzed by the GEPIA database. The Human Protein Atlas (HPA) was used to analyze the immunohistochemical expression of key genes in HCC. Finally, molecular docking was carried out to investigate interactions between the top five targets and their related active compounds. Results A total of 50 active components were screened and 12 common targets were identified related to MT and HCC. Scutellarein-4-Methylether, Tenasogenin, Sinapic Acid, Dresgenin and Kaempferol were considered as the critical components. JUN, MMP9 and PTGS2 were recognized as key therapeutic targets. The GO analyses demonstrated that key targets mainly involved in the process of gene silencing and inflammatory response. KEGG analysis suggested that key targets were enriched in TNF signaling pathway and IL-17 signaling pathway. Survival analysis by the GEPIA showed significant differences in the expression of ESR1, MMP1, MMP9, JUN, and PPARG between high and low risk groups. Immunohistochemical results showed that ESR1 and MMP9 were differentially expressed in normal and hepatocellular carcinoma tissues. The molecular docking results verified that the drug active ingredient could be stably bound to the target protein. Conclusion This study reflected the multi-component, multi-target and multi-pathway characteristics of the MT in the treatment of HCC, which could provide a scientific basis for the clinical application of MT in HCC.
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ObjectiveTo explore the mechanism of Cordyceps in treating bronchial asthma and chronic renal failure with the concept of "same treatment for different diseases" in traditional Chinese medicine （TCM） by network pharmacology and molecular docking technology. MethodThe active components and potential targets of Cordyceps were collected from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform （TCMSP） and SwissTargetPrediction. The disease targets were obtained from Therapeutic Target Database （TTD）， DrugBank， GeneCards and other databases. The common targets were obtained from the intersection of potential targets and disease targets. The protein-protein interaction （PPI） network was constructed by STRING11.5， and the ''component-target-diseas'' network of Cordyceps was established by Cytoscape 3.9.0. Gene Ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） enrichment analyses were carried out by Metascape， and molecular docking was performed by Autodock 4.2. ResultSixty common targets of disease and drug were screened out. The core targets mainly involved protein kinase B1 （Akt1）， non-receptor tyrosine kinase， sarcoma virus protein （SRC）， TP53， matrix metalloproteinase-9 （MMP-9）， and prostaglandin endoperoxide synthase 2 （PTGS2）. The potential targets were mainly enriched in the signaling pathways of renin-angiotensin system （RAS）， RAP1， phosphoinositide 3 kinase/protein kinase B （PI3K/Akt）， mitogen-activated protein kinase （MAPK）， etc. ConclusionThe active components of Cordyceps inhibited inflammatory response and reduced fibrosis and cell apoptosis in a multi-target and multi-pathway manner. The findings of this study preliminarily revealed the potential targets and modern biological mechanism of Cordyceps in treating bronchial asthma and chronic renal failure with the concept of ''same treatment for different diseases''， and provided references for in-depth experimental verification and clinical application.
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Possible mechanisms by which Polygonati rhizoma opposes atherosclerosis (AS) were identified by network pharmacology and molecular docking analyses. The Traditional Chinese Medicine Database (TCMD) and the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) were utilized to identify the likely active components of Polygonati rhizoma. The potential targets set of Polygonati rhizoma were predicted with the PharmaDB database and the Swiss TargetPrediction database. The targets set for AS was retrieved by OMIM, DisGeNET and NCBI Gene database. We used the STRING platform to construct a protein-protein interaction network of the intersectional targets and performed visual analysis in Cytoscape. The key targets of Polygonati rhizoma in AS were searched by network topology and the resulting GO and KEGG enrichment was analyzed by Clue GO. In addition, the key targets were verified by molecular docking in Discovery Studio 4.0. A total of 45 active ingredients and 51 potential targets were obtained in the treatment of AS. The results of the topology analysis included five key targets: serum albumin, mitogen-activated protein kinase 3, mitogen-activated protein kinase 1, proto-oncogene tyrosine-protein kinase Src and matrix metalloproteinase-9. The 131 GO items showed that the biological process mainly involved the steroid receptor, cell response to steroid stimulation, the phosphatidylinositol-3 kinase signal pathway, and others. The KEGG pathway analysis included 37 pathways, which were closely related to peroxisome proliferation activated receptor signaling pathway, platelet activation pathway, vascular endothelial growth factor pathway, hypoxia inducible factor pathway and adhesion connection pathway. The results of molecular docking proved that the combined activity of the components with potential key targets is excellent. This study proposes mechanisms by which Polygonati rhizoma might act to reverse or minimize AS and provides a scientific basis for clinical research on Polygonati rhizoma.
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Traditional Chinese medicine (TCM) network pharmacology and molecular docking technology were applied to explore the mechanism of anti-coronavirus pneumonia (coronavirus disease 2019, COVID-19) of Qingfei Paidu decoction. The Chinese Pharmacopoeia (2015 edition) and Traditional Chinese Medicine Systems Pharmacology (TCMSP), OMIM (Online Mendelian Inheritance in Man), GeneCard, STRING, and others online databases are used for building a series of network, and selecting the core target and analyzing the signal pathway. Finally, we make molecular docking predictions for the important compounds. The results showed that the Qingfei Paidu decoction compound-pneumonia target network contained 292 compounds and 214 corresponding targets, and the core targets involved AKT1 (AKT serine/threonine kinase 1), IL6 (interleukin 6), MAPK8 (mitogen-activated protein kinase 8), MAPK1 (mitogen-activated protein kinase 1), and JUN (jun proto-oncogene). GO (Gene Ontology) function enrichment analysis yielded 858 GO entries, and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment screening yielded 122 related pathways, including hypoxia inducible factor-1 (HIF-1) and Toll-like receptor (TLRs) signaling pathways related to pneumonia, as well as T-cell receptor (TCR) signaling pathway related to lung injury protection. The molecular docking results showed that some core compounds of the Chinese herbal medicine of Qingfei Paidu decoction have a certain degree of affinity for 2019-novel coronavirus (2019-nCoV) main protease (3C-like protease, 3CLpro) and angiotensin-converting enzyme 2 (ACE2). In this paper, we preliminarily explored the potential therapeutic mechanism for Qingfei Paidu decoction to against COVID-19 and predicted the active ingredients. We hope that the results will help to the further study on the active ingredients and mechanism of Qingfei Paidu decoction to COVID-19.
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Objective::Based on LC-MS and molecular docking strategy, to study the pharmacodynamic material basis of Jinqi Jiangtang tablets in the treatment of type 2 diabetes mellitus(T2DM). Method::UPLC-Q-TOF-MS was used to identify the chemical constituents of Jinqi Jiangtang tablets. On this basis, the disease targets were screened based on the online disease target database and protein-protein interaction(PPI). The molecular docking technology was used to verify the relationship between the chemical constituents and disease targets in Jinqi Jiangtang tablets, so as to find out the potential pharmacodynamic basis of Jinqi Jiangtang tablets in the treatment of T2DM. Result::Based on UPLC-Q-TOF-MS, 51 chemical constituents were identified in Jinqi Jiangtang tablets, including 31 astragalus, 16 coptis and 4 honeysuckle. The key targets of catalase from micrococcus lysodeiktic(CAT) receptor, peroxisome proliferative actived receptor(PPARG) receptor and insulin(INS) receptor were identified by CTD database, topological analysis and related literature. Based on LC-MS and molecular docking technology, we found that magnoflorine, coptisine, epiberberine, astragaloside Ⅳ, caffeic acid, palmatine, berberine, jateorhizine, berberubine, berberastine, groenlandne, lycoranine B, demethyleneberberine, isomucrontolula-7-O-glucoside and calycosin-7-O-glucoside were used to treat type 2 diabetes potential pharmacodynamic material basis of urinary diseases. Conclusion::Protein interaction and network topology analysis are helpful for the rapid localization of core targets. In addition, molecular docking technology can realize large-scale virtual screening of potential candidate compounds. The integration of LC-MS and molecular docking technology can facilitate and quickly find the potential pharmacodynamic substance basis in traditional Chinese medicine prescriptions, and provide a reference for subsequent drug activity screening experiments.
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OBJECTIVE:To screen the agonist active ingredients of peroxisome proliferator-activated receptor-γ (PPAR-γ) in flavonoids from Artemisia ordosica,and provide reference for finding antidiabetic agents in A.ordosica.METHODS:Using known PPAR-γagonist rosiglitazone as positive control,molecular docking technology was conducted for docking one by one for 18 flavonoids and PPAR-7 targets obtained from A.ordosica.It was compared with binding affinities and binding modes of compounds and PPAR-7 targets,and the possible PPAR-γ agonist ingredients in A.ordosica were screened.RESULTS:5 flavonoids showed good docking affinities,in which,compound 3 (5,3',4'-trihydroxy-7-methoxyflavone) showed the highest (-8.3 kcal/mol).Docking mode analysis showed that the phenol oxygen on ring A and ring B of the flavonoids with LBD active site of PPAR-γ formed one (Tyr327) or two hydrogen bonding (Tyr327,Arg288),which played an important role in the binding of flavonoids and PPAR-γ and the stability of PPAR-γ conformation.CONCLUSIONS:Results of virtual screening in molecular docking technology indicate that flavonoids (mostly containing multiple free phenolic hydroxyl groups) in can easily form good docking mode and high affinity with PPAR-γ,showing potential antidiabetic activity.The study can provide reference for further research of chemical ingredients for the treatment of type 2 diabetes.
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objective To explore the role of Xanthatin in the targets of epithelial-mesenchymal transition (EMT) process using molecular docking method,and the effect on the target protein expression of HepG2 cells was detected by Western assay.Method Dhs,Vimentin,Snail and VEGFR3 are critical targets in EMT process,the spatial binding ability of Xanthium was evaluated by molecular docking method,compared with the corresponding endogenous substances:nicotinarnide adenine dinucleotide,Acetate ion,flavin adenine dinucleotide,and N-Acetyl-D-glucosamine.HepG2 cells were cultured,and the effects of Xanthatin of 1,5 and 20 mol/L concentrations on Dhs,Vimentin,Snail and VEGFR3 protein expression were detected by Western Blotting assay.Rusult Molecular docking show that Xanthatin has obvious affinity to key factors of EMT process such as Dhs,Vimentin,and VEGF-R3,higher than that of endogenous substance;and the affinity with Vimentin was less than that of endogenous substance;Western Blotting experiments proved the virtual results.The expression of Vimentin,Snail,VEGFR3 protein was significantly lowered,and the expression of e-cadherin was significantly raised.Conclusion The influence of Xanthatin to key factor e-cadherin,Vimentin,Snail,VEGFR3 are obvious,Which is likely to be a potential target.The results of computer virtual experiment and Western Blotting have certain similarity.Molecular virtual docking can pre hint the potential target factor.