Analyzing the molecular mechanism of xuefuzhuyu decoction in the treatment of pulmonary hypertension with network pharmacology and bioinformatics and verifying molecular docking

Yu, Xiaoming; Qin, Wenxiang; Cai, Haijian; Ren, Chufan; Huang, Shengjing; Lin, Xiao; Tang, Lin; Shan, Zhuohan; AL-Ameer, Wail Hussein Ahmed; Wang, Liangxing; Yan, Hanhan; Chen, Mayun

doi:10.1016/j.compbiomed.2023.107863

Cited by 14 publications

(2 citation statements)

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“…To gain insights into the biological significance of the identified genes, functional enrichment analyses were performed incorporating GO terms ( http://GeneOntology .org/) and KEGG pathways ( https://www .kegg.jp/eg/) ( Yu et al, 2023 ). R packages ( Yu et al, 2023 ), including “clusterProfiler,” “org.Hs.eg.db,” “enrichplot,” “ggplot2,” and “DOSE,” were used with specified filter conditions: “ p -value cutoff = 0.05” and “q value cutoff = 0.05.” GO enrichment analysis encompassing CC, BP, and MF outcomes were presented in a visually informative bubble chart. Similarly, the KEGG pathway enrichment analysis outcomes were depicted in a column chart.…”

Section: Methodsmentioning

confidence: 99%

Section: Functional Enrichment Analysismentioning

confidence: 99%

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Elucidation of the mechanism of action of ailanthone in the treatment of colorectal cancer: integration of network pharmacology, bioinformatics analysis and experimental validation

Ma,

Guo,

Han

et al. 2024

Front. Pharmacol.

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Background: Ailanthone, a small compound derived from the bark of Ailanthus altissima (Mill.) Swingle, has several anti-tumour properties. However, the activity and mechanism of ailanthone in colorectal cancer (CRC) remain to be investigated. This study aims to comprehensively investigate the mechanism of ailanthone in the treatment of CRC by employing a combination of network pharmacology, bioinformatics analysis, and molecular biological technique.Methods: The druggability of ailanthone was examined, and its targets were identified using relevant databases. The RNA sequencing data of individuals with CRC obtained from the Cancer Genome Atlas (TCGA) database were analyzed. Utilizing the R programming language, an in-depth investigation of differentially expressed genes was carried out, and the potential target of ailanthone for anti-CRC was found. Through the integration of protein-protein interaction (PPI) network analysis, GO and KEGG enrichment studies to search for the key pathway of the action of Ailanthone. Then, by employing molecular docking verification, flow cytometry, Transwell assays, and Immunofluorescence to corroborate these discoveries.Results: Data regarding pharmacokinetic parameters and 137 target genes for ailanthone were obtained. Leveraging The Cancer Genome Atlas database, information regarding 2,551 differentially expressed genes was extracted. Subsequent analyses, encompassing protein–protein interaction network analysis, survival analysis, functional enrichment analysis, and molecular docking verification, revealed the PI3K/AKT signaling pathway as pivotal mediators of ailanthone against CRC. Additionally, the in vitro experiments indicated that ailanthone substantially affects the cell cycle, induces apoptosis in CRC cells (HCT116 and SW620 cells), and impedes the migration and invasion capabilities of these cells. Immunofluorescence staining showed that ailanthone significantly inhibited the phosphorylation of AKT protein and suppressed the activation of the PI3K/AKT signaling pathway, thereby inhibiting the proliferation and metastasis of CRC cells.Conclusion: Therefore, our findings indicate that Ailanthone exerts anti-CRC effects primarily by inhibiting the activation of the PI3K/AKT pathway. Additionally, we propose that Ailanthone holds potential as a therapeutic agent for the treatment of human CRC.

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Section: Methodsmentioning

confidence: 99%

Section: Functional Enrichment Analysismentioning

confidence: 99%