Prediction of the mechanisms of action of Shenkang in chronic kidney disease: A network pharmacology study and experimental validation

Qin, Tianyu; Wu, Lili; Hua, Qian; Song, Zilin; Pan, Yajing; Liu, Tonghua

doi:10.1016/j.jep.2019.112128

Cited by 70 publications

(41 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To investigate the pharmacological mechanisms of FA at the system level, compound-target-pathway-disease networks were separately constructed and visualized using Cytoscape 3.6.1 software to comprehensively clarify the complicated relationships among the compounds, targets, diseases, and related pathways [ 23 ]. This software allowed for data integration to analyze and visualize complex interaction networks.…”

Section: Methodsmentioning

confidence: 99%

Systematically Deciphering the Pharmacological Mechanism of Fructus Aurantii via Network Pharmacology

Jin

Gao

et al. 2021

Evidence-Based Complementary and Alternative Medicine

View full text Add to dashboard Cite

Fructus Aurantii (FA) is a traditional herbal medicine that has been widely used for thousands of years in China and possesses a variety of pharmacological effects. However, the active ingredients in FA and the potential mechanisms of its therapeutic effects have not been fully explored. Here, we applied a network pharmacology approach to explore the potential mechanisms of FA. We identified 5 active compounds from FA and a total of 209 potential targets to construct a protein-protein interaction (PPI) network. Prostaglandin G/H synthase 2 (PTGS2), heat shock protein 90 (HSP90), cell division protein kinase 6 (CDK6), caspase 3 (CASP3), apoptosis regulator Bcl-2 (Bcl-2), and matrix metalloproteinase-9 (MMP9) were identified as key targets of FA in the treatment of multiple diseases. Gene ontology (GO) enrichment demonstrated that FA was highly related to transcription initiation from RNA polymerase II promoter, DNA-templated transcription, positive regulation of transcription, regulation of apoptosis process, and regulation of cell proliferation. Various signaling pathways involved in the treatment of FA were identified, including pathways in cancer and pathways specifically related to prostate cancer, colorectal cancer, PI3K-Akt, apoptosis, and non-small-cell lung cancer. TP53, AKT1, caspase 3, MAPK3, PTGS2, and BAX/BCL2 were related key targets in the identified enriched pathways and the PPI network. In addition, our molecular docking results showed that the bioactive compounds in FA can tightly bind to most target proteins. This article reveals via network pharmacology research the possible mechanism(s) by which FA exerts its activities in the treatment of various diseases and lays a foundation for further experiments and the development of a rational clinical application of FA.

show abstract

Section: Methodsmentioning

confidence: 99%

Systematically Deciphering the Pharmacological Mechanism of Fructus Aurantii via Network Pharmacology

Jin

Gao

et al. 2021

Evidence-Based Complementary and Alternative Medicine

View full text Add to dashboard Cite

show abstract

“…Compounds were screened based on absorption, distribution, metabolism, and excretion (ADME), and pharmacokinetic information retrieval filters were used to obtain bioactive compounds for further analysis using the thresholds OB ≥ 30% and DL ≥ 0.18 [ 19 , 20 ]. A network was generated using Cytoscape to visualize the complex relationships between active compounds and potential targets [ 21 ]. Nodes represent compounds and targets, and edges indicate the intermolecular interactions.…”

Section: Methodsmentioning

confidence: 99%

Molecular Targets and Pathways Contributing to the Effects of Wenxin Keli on Atrial Fibrillation Based on a Network Pharmacology Approach

Zhang

Zhang²,

Zhang³

et al. 2020

Evidence-Based Complementary and Alternative Medicine

View full text Add to dashboard Cite

Background. Atrial fibrillation (AF) is the most common sustained arrhythmia and is associated with high rates of mortality and morbidity. The traditional Chinese medicine Wenxin Keli (WXKL) can effectively improve clinical symptoms and is safe for the treatment of AF. However, the active substances in WXKL and the molecular mechanisms underlying its effects on AF remain unclear. In this study, the bioactive compounds in WXKL, as well as their molecular targets and associated pathways, were evaluated by systems pharmacology. Materials and Methods. Chemical constituents and potential targets of WXKL were obtained via the Traditional Chinese Medicine Systems Pharmacology (TCMSP). The TTD, DrugBank, DisGeNET, and GeneCards databases were used to collect AF-related target genes. Based on common targets related to both AF and WXKL, a protein interaction network was generated using the STRING database. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGGs) pathway enrichment analyses were performed. Network diagrams of the active component-target and protein-protein interactions (PPIs) were constructed using Cytoscape. Results. A total of 30 active ingredients in WXKL and 219 putative target genes were screened, including 83 genes identified as therapeutic targets in AF; these overlapping genes were considered candidate targets for subsequent analyses. The effect of treating AF was mainly correlated with the regulation of target proteins, such as IL-6, TNF, AKT1, VEGFA, CXCL8, TP53, CCL2, MMP9, CASP3, and NOS3. GO and KEGG analyses revealed that these targets are associated with the inflammatory response, oxidative stress reaction, immune regulation, cardiac energy metabolism, serotonergic synapse, and other pathways. Conclusions. This study demonstrated the multicomponent, multitarget, and multichannel characteristics of WXKL, providing a basis for further studies of the mechanism underlying the beneficial effects of WXKL in AF.

show abstract

“…Visual component-target network was established based on aforementioned data sets through Cytoscape 3.7.2 (http://www.cytoscape.org/) to reflect the complex relationships between active compounds and their potential targets [25]. Cytoscape 3.7.2 is an open-source software platform which is used to visualize complicated networks and integrate different types of attribute data [26].…”

Section: Construction Of Component-target Gene Networkmentioning

confidence: 99%

Network pharmacology and molecular docking analysis on molecular targets and mechanisms of Huashi Baidu formula in the treatment of COVID-19

Tao

et al. 2020

Drug Development and Industrial Pharmacy

178

143

View full text Add to dashboard Cite

Purpose: Huashi Baidu formula (HSBDF) was developed to treat the patients with severe COVID-19 in China. The purpose of this study was to explore its active compounds and demonstrate its mechanisms against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through network pharmacology and molecular docking. Methods: All the components of HSBDF were retrieved from the pharmacology database of TCM system. The genes corresponding to the targets were retrieved using UniProt and GeneCards database. The herb-compound-target network was constructed by Cytoscape. The target protein-protein interaction network was built using STRING database. The core targets of HSBDF were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The main active compounds of HSBDF were docked with SARS-CoV-2 and angiotensin converting enzyme II (ACE2). Results: Compound-target network mainly contained 178 compounds and 272 corresponding targets. Key targets contained MAPK3, MAPK8, TP53, CASP3, IL6, TNF, MAPK1, CCL2, PTGS2, etc. There were 522 GO items in GO enrichment analysis (p < .05) and 168 signaling pathways (p < .05) in KEGG, mainly including TNF signaling pathway, PI3K-Akt signaling pathway, NOD-like receptor signaling pathway, MAPK signaling pathway, and HIF-1 signaling pathway. The results of molecular docking showed that baicalein and quercetin were the top two compounds of HSBDF, which had high affinity with ACE2. Conclusion: Baicalein and quercetin in HSBDF may regulate multiple signaling pathways through ACE2, which might play a therapeutic role on COVID-19.

show abstract

Prediction of the mechanisms of action of Shenkang in chronic kidney disease: A network pharmacology study and experimental validation

Cited by 70 publications

References 80 publications

Systematically Deciphering the Pharmacological Mechanism of Fructus Aurantii via Network Pharmacology

Systematically Deciphering the Pharmacological Mechanism of Fructus Aurantii via Network Pharmacology

Molecular Targets and Pathways Contributing to the Effects of Wenxin Keli on Atrial Fibrillation Based on a Network Pharmacology Approach

Network pharmacology and molecular docking analysis on molecular targets and mechanisms of Huashi Baidu formula in the treatment of COVID-19

Contact Info

Product

Resources

About