Isolation and identification of the components in Cybister chinensis Motschulsky against inflammation and their mechanisms of action based on network pharmacology and molecular docking

Che, Yi-Hao; Xu, Zhongren; Ni, Lian-Li; Dong, Xinxin; Yang, Zizhong; Ye, Zhibin

doi:10.1016/j.jep.2021.114851

Cited by 10 publications

(8 citation statements)

References 35 publications

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“…Based on the network pharmacology, Che et al. (2022) found that the ethyl acetate extract of Cybister Chinensis , including nine compounds (benzoic acid, protocatechualdehyde, and 3‐phenylpropionic acid), could relieve the inflammation through multi‐compounds and multi‐pathways. Our results showed that the anti‐inflammatory targets of key compounds in different fractions of coffee leaves were more related to cancer.…”

Section: Resultsmentioning

confidence: 99%

Combination of HPLC–orbitrap‐MS/MS and network pharmacology to identify the anti‐inflammatory phytochemicals in the coffee leaf extracts

Mei

Chen

2023

Food Frontiers

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In this study, we investigated the phytochemical compositions and the associated anti‐inflammatory activity of coffee leaf fractions prepared by sequential solvent extraction using high‐performance liquid chromatography–orbitrap‐tandem mass spectrometry (HPLC–orbitrap‐MS/MS) combined with network pharmacology. The results showed that the ethyl acetate fraction (EAC‐L) had the highest nitric oxide (NO), ABTS, and DPPH free radical scavenging abilities due to the higher concentrations of mangiferin, rutin, 3,5‐dicaffeoylquinic acid (3,5‐diCQA), and 4,5‐diCQA. The extraction solvents had the greatest impact on the anti‐inflammatory activity of coffee leaf fractions, whereas the processing method had the most significant effect on the antioxidant activity of these fractions. Untargeted metabolomics analysis using HPLC–orbitrap‐MS/MS indicated that palmitic acid, 3,4‐dihydroxybenzaldehyde, and caffeic acid may be involved in the anti‐inflammatory activity of EAC‐L fraction obtained from fresh coffee leaves. On the other hand, processed coffee leaf fraction exhibited anti‐inflammatory activity that was attributed to the presence of 9S,13R‐12‐oxophytodienoic acid, pinocembrin, and quercetin, which have high degree values associated with the inflammation network. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment of network pharmacology analysis showed that these 35 differential compounds in the coffee leaf fractions affect cell transcription, apoptosis, phosphorylation, NO synthesis, phosphatidylinositide 3‐kinases‐protein kinase B (PI3K‐Akt) signaling pathway, focal adhesion, hypoxia‐inducible factor‐1, hepatitis, cancer, and so on. This result indicated that coffee leaf extract may also function as an inhibitor for inflammation‐related cancers. The findings of our research are valuable in guiding the extraction of anti‐inflammatory components from coffee leaves.

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Section: Resultsmentioning

confidence: 99%

Combination of HPLC–orbitrap‐MS/MS and network pharmacology to identify the anti‐inflammatory phytochemicals in the coffee leaf extracts

Mei

Chen

2023

Food Frontiers

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“…Considering the evidence for angiogenesis, the target genes associated with "Coronary artery disease" (CAD) were collected using the DisGeNET (http://www.disgenet.org/) and GeneCards (https://www.genecards.org/) databases. The candidate targets were inputted to String 11.5 (https://string-db.org/) to obtain the relevant information on protein interactions [39]. Furthermore, a compound-target network was constructed by employing Cytoscape 3.6.1. to study the therapeutic mechanism of CAD.…”

Section: Target Database Construction and Bioinformatics Analysismentioning

confidence: 99%

LC-MS Analysis of Ginsenosides in Different Parts of Panax quinquefolius and Their Potential for Coronary Disease Improvement

et al. 2023

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Seven main ginsenosides, including ginsenoside Re, ginsenoside Rb1, pseudoginsenoside F11, ginsenoside Rb2, ginsenoside Rb3, ginsenoside Rd and ginsenoside F2, were identified by LC-QTOF MS/MS from root, leaf and flower extracts of Panax quinquefolius. These extracts promoted intersegmental vessel growth in a zebrafish model, indicating their potential cardiovascular health benefits. Network pharmacology analysis was then conducted to reveal the potential mechanisms of ginsenoside activity in the treatment of coronary artery disease. GO and KEGG enrichment analyses elucidated that G protein-coupled receptors played a critical role in VEGF-mediated signal transduction and that the molecular pathways associated with ginsenoside activity are involved in neuroactive ligand-receptor interaction, cholesterol metabolism and the cGMP–PKG signaling pathway, etc. Moreover, VEGF, FGF2, and STAT3 were confirmed as the major targets inducing proliferation of endothelial cells and driving the pro-angiogenic process. Overall, ginsenosides could be potent nutraceutical agents that act to reduce the risks of cardiovascular disease. Our findings will provide a basis to utilize the whole P. quinquefolius plant in drugs and functional foods.

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“…Finally, save the results as pdbqt files. (3) Docking parameter settings: Referring to the original ligand binding site in the file, get the molecular docking coordinates and the size of the docking box, [39,40] set num_ modes to 20, exhaustiveness to 10, and other parameters to their default settings. (4) Docking and result processing: The best affinity conformation was chosen as the final docking conformation using Autodockvina 1.1.2, [41,42] and the picture of the best conformation was created using Pymol 2.6.0 free source software.…”

Section: Molecular Dockingmentioning

confidence: 99%

Exploring the potential mechanism of Taohong Siwu decoction in the treatment of avascular necrosis of the femoral head based on network pharmacology and molecular docking

Chen,

Song,

Qiu

et al. 2023

Medicine

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Based on network pharmacology and molecular docking, this study seeks to investigate the mechanism of Taohong Siwu decoction (THSWD) in the treatment of avascular necrosis of the femoral head (AVNFH). The Traditional Chinese Medicine Systems Pharmacology database was used in this investigation to obtain the active ingredients and related targets for each pharmaceutical constituent in THSWD. To find disease-related targets, the terms “avascular necrosis of the femoral head,” “necrosis of the femoral head,” “steroid-induced necrosis of the femoral head,” “osteonecrosis,” and “avascular necrosis of the bone” were searched in the databases DisGeNET, GeneCards, Comparative Toxicogenomics Database, and MalaCards. Following the identification of the overlap targets of THSWD and AVNFH, enrichment analysis using gene ontology, Kyoto Encyclopedia of Genes and Genomes, Reactome, and WikiPathways was conducted. The “THSWD-drug-active compound-intersection gene-hub gene-AVNFH” network and protein-protein interaction network were built using Cytoscape 3.9.1 and string, and CytoHubba was used to screen hub genes. The binding activities of hub gene targets and key components were confirmed by molecular docking. 152 prospective therapeutic gene targets were found in the bioinformatics study of ONFH treated with THSWD, including 38 major gene targets and 10 hub gene targets. The enrichment analysis of 38 key therapeutic targets showed that the biological process of gene ontology analysis mainly involved cytokine-mediated signaling pathway, angiogenesis, cellular response to reactive oxygen species, death-inducing signaling complex. The Kyoto Encyclopedia of Genes and Genomes signaling pathway mainly involves TNF signaling pathway, IL-17 signaling pathway, and the Recactome pathway mainly involves Signaling by Interleukins, Apoptosis, and Intrinsic Pathway for Apoptosis. WikiPathways signaling pathway mainly involves TNF-related weak inducer of apoptosis signaling pathway, IL-18 signaling pathway. According to the findings of enrichment analysis, THSWD cured AVNFH by regulating angiogenesis, cellular hypoxia, inflammation, senescence, apoptosis, cytokines, and cellular proliferation through the aforementioned targets and signaling pathways. The primary component of THSWD exhibits a strong binding force with the key protein of AVNFH. This study sheds new light on the biological mechanism of THSWD in treating AVNFH by revealing the multi-component, multi-target, and multi-pathway features and molecular docking mechanism of THSWD.

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Isolation and identification of the components in Cybister chinensis Motschulsky against inflammation and their mechanisms of action based on network pharmacology and molecular docking

Cited by 10 publications

References 35 publications

Combination of HPLC–orbitrap‐MS/MS and network pharmacology to identify the anti‐inflammatory phytochemicals in the coffee leaf extracts

Combination of HPLC–orbitrap‐MS/MS and network pharmacology to identify the anti‐inflammatory phytochemicals in the coffee leaf extracts

LC-MS Analysis of Ginsenosides in Different Parts of Panax quinquefolius and Their Potential for Coronary Disease Improvement

Exploring the potential mechanism of Taohong Siwu decoction in the treatment of avascular necrosis of the femoral head based on network pharmacology and molecular docking

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