Immunoregulatory mechanism studies of ginseng leaves on lung cancer based on network pharmacology and molecular docking

Li, Zao-Hui; Yu, Dan; Huang, Nannan; Wu, Jinshan; Du, Xiaomei; Wang, Xijun

doi:10.1038/s41598-021-97115-8

Cited by 11 publications

(7 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The data concerning the lowest binding energy resulting from molecular docking was obtained. The lower the binding energy, the stronger the binding force between the active ingredient and the target protein: a drug molecule with binding energy ≤ −5.0 kJ/mol is considered to have a good binding activity to the target ( Li et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Pharmacological effects and target analysis of Guipi wan in the treatment of cerebral ischemia-reperfusion injury

Zhang,

Luo,

Guo

et al. 2024

Front. Pharmacol.

View full text Add to dashboard Cite

Guipi wan (GPW) is a traditional Chinese medicine commonly used in clinical practice, typically to treat neurological diseases such as neurasthenia and traumatic brain injury. It may have positive effects on cerebral ischemia‒reperfusion injury (cI/R). This study aimed to assess the effects of GPW in a mouse model of cI/R and find its possible targets. C57BL/6J mice were used to establish the cI/R model, and the laser speckle doppler was used to determine the success of the model. GPW was administered intragastrically for 7 days, brain tissue sections were stained with TTC, HE, and TUNEL, Western blot assay was performed to detect the effect of apoptosis-related proteins. Furthermore, we screened active ingredients from the TCM Database and constructed a compound‒target network using the Cytoscape 3.8.0 software. Moreover, we employed protein‒protein interaction and component‒target‒pathway network analyses to determine the potential components of GPW and its target genes, the key target was verified through molecular docking. Finally, we detected the influence of the downstream signaling pathway of the target through Western blot. The results showed that GPW decreased the cerebral infarction area, neurological function scores, and neuronal apoptosis in mice by regulating PI3K/AKT signaling pathway. Network analysis indicated that gamma-aminobutyric acid B receptor 1 (GABBR1) might be a potential target for the treatment of cI/R. Molecular docking indicated that 9 active components in GPW could bind to GABBR1 with desirable binding energy. This study represented the demonstratable effect of GPW in the treatment of cI/R injury and suggested GABBR1 as a potential target using network analysis.

show abstract

Section: Methodsmentioning

confidence: 99%

Pharmacological effects and target analysis of Guipi wan in the treatment of cerebral ischemia-reperfusion injury

Zhang,

Luo,

Guo

et al. 2024

Front. Pharmacol.

View full text Add to dashboard Cite

show abstract

“…Therefore, for ginsenosides with too many targets, we only selected the top 20 targets associated with DM for subsequent analysis. The UniProt database ( https://www.uniprot.org/ ) was used to convert target protein names into target gene names to standardize gene names 17 , 18 .…”

Section: Methods and Analysismentioning

confidence: 99%

“…Next, the GeneCards (GeneCards, https://www.genecards.org/ ), the Online Mendelian Inheritance of Human Beings (OMIM, https://www.omim.org/ ), the Pharmacogenetics and Pharmacogenomics Database (PharmGkb, https://www.pharmgkb.org ), the Therapeutic Targets Database (TTD, http://db.idrblab.net/ttd/ ), and the Drugs and Drug Target Information Databases DM-related disease target genes (Drug Bank, https://go.drug/bank.com/ ) were integrated 18 . Finally, we used BioLadder ( https://www.bioladder.cn/web/#/pro/index ) to identify and visualise the intersecting targets of both ginsenosides and disease targets.…”

Section: Methods and Analysismentioning

confidence: 99%

“…All intersecting targets were analyzed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment by the Bioconductor cluster analyzer of R 4.0.2 ( https://www.r-project.org/ ). The results were ranked according to the number of molecules in pathways with a cut-off value ( P < 0.05) 18 . Plotting histograms of GO and KEGG analysis using R. We collected some significant and DM related targets.…”

Section: Methods and Analysismentioning

confidence: 99%

See 1 more Smart Citation

Exploring the mechanism of active components from ginseng to manage diabetes mellitus based on network pharmacology and molecular docking

Jin

et al. 2023

Sci Rep

View full text Add to dashboard Cite

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.

show abstract

“…For the treatment of tumors, traditional Chinese medicine schemes have the advantages of low risk, high safety, and low price, and have been widely verified both theoretically and experimentally. It has been found that saffron, ginseng, and other traditional Chinese medicines have anti-tumor effects ( 12 , 13 ). The present study regarding the relationship between traditional Chinese medicine and GBM will assist in guiding the development of new drugs and improving the prognosis of patients.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the key prognostic genes and potential traditional Chinese medicine therapeutic targets in glioblastoma based on bioinformatics and network pharmacology methods

Xia

Gao

Chen

et al. 2022

Transl Cancer Res TCR

View full text Add to dashboard Cite

Background To analyze the key prognostic genes and potential traditional Chinese medicine targets in glioblastoma (GBM) by bioinformatics and network pharmacology. Methods GBM datasets were obtained from the Gene Expression Omnibus (GEO) database to clarify the differentially-expressed genes (DEGs) in the carcinoma and paracancerous tissues. The molecular functions (MF) and signaling pathways of enriched DEGs were analyzed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The STRING database and Cytoscape software were used to construct the protein-protein interaction (PPI) network and screen hub genes to focus on genes with greater clinical significance. The transcription expression and prognosis of hub genes were analyzed using the Gene Expression Profiling Interactive Analysis 2 (GEPIA 2) database. The important compounds and target molecules were obtained via the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) database. We identified the active ingredients by setting the property values of pharmacokinetic attribute values. We constructed the network of “Chinese medicine ingredients-DEGs target” and screened out the target genes and active ingredients with high correlation scores. Finally, molecular docking verification was carried out using AutoDock Tools and PyMOL. Results We obtained 271 DEGs, including 212 up-regulated genes and 59 down-regulated genes and screened ten hub genes. GO and KEGG analyses suggested that the hub genes were mainly involved in the following biological processes: the cell cycle, cell division, and cell adhesion, as well as extracellular matrix adhesion-related pathways, the p53 signaling pathways, and cadherin binding involved in cell-cell adhesion. We established the interaction network between the components and DEGs to screen out the traditional Chinese medicine active component (luteolin) and target genes (BIRC5 and CCNB1) for the treatment of GBM. The molecular docking results showed that the bindings of protein receptors, BIRC5 and CCNB1, with the compound ligand, luteolin, were stable and formed by hydrogen bonding interaction. Conclusions In this study, we determined that luteolin potentially inhibits glioblastoma proliferation and migration through key target genes, BIRC5 and CCNB1, via bioinformatics and network pharmacology analysis, and affects the prognosis of GBM patients, providing new ideas for clinical targeted therapy and new drug development.

show abstract

Immunoregulatory mechanism studies of ginseng leaves on lung cancer based on network pharmacology and molecular docking

Cited by 11 publications

References 79 publications

Pharmacological effects and target analysis of Guipi wan in the treatment of cerebral ischemia-reperfusion injury

Pharmacological effects and target analysis of Guipi wan in the treatment of cerebral ischemia-reperfusion injury

Exploring the mechanism of active components from ginseng to manage diabetes mellitus based on network pharmacology and molecular docking

Analysis of the key prognostic genes and potential traditional Chinese medicine therapeutic targets in glioblastoma based on bioinformatics and network pharmacology methods

Contact Info

Product

Resources

About