Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation Analysis Reveal Insights into the Molecular Mechanism of Cordia myxa in the Treatment of Liver Cancer.

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On the other hand, bioactive phytochemicals employed in complementary alternative medicine have recently gained interest due to their ability to control a wide range of molecular pathways while being less harmful. As a result, we used a network pharmacology approach to study the possible regulatory mechanisms of active constituents of Cordia myxa for the treatment of liver cancer (LC). Active constituents were retrieved from the IMPPAT database and the literature review, and their targets were retrieved from the STITCH and Swiss Target Prediction databases. LC-related targets were retrieved from expression datasets (GSE39791, GSE76427, GSE22058, GSE87630, and GSE112790) through gene expression omnibus (GEO). The DAVID Gene Ontology (GO) database was used to annotate target proteins, while the Kyoto Encyclopedia and Genome Database (KEGG) was used to analyze signaling pathway enrichment. STRING and Cytoscape were used to create protein-protein interaction networks (PPI), while the degree scoring algorithm of CytoHubba was used to identify hub genes. The GEPIA2 server was used for survival analysis, and PyRx was used for molecular docking analysis. Survival and network analysis revealed that five genes named heat shot protein 90 AA1 (HSP90AA1), estrogen receptor 1 (ESR1), cytochrome P450 3A4 (CYP3A4), cyclin-dependent kinase 1 (CDK1), and matrix metalloproteinase-9 (MMP9) are linked with the survival of LC patients. Finally, we conclude that four extremely active ingredients, namely cosmosiin, rosmarinic acid, quercetin, and rubinin influence the expression of HSP90AA1, which may serve as a potential therapeutic target for LC. These results were further validated by molecular dynamics simulation analysis, which predicted the complexes with highly stable dynamics. The residues of the targeted protein showed a highly stable nature except for the N-terminal domain without affecting the drug binding. An integrated network pharmacology and docking study demonstrated that C. myxa had a promising preventative effect on LC by working on cancer-related signaling pathways.", "claims": [{"id": "claim-method", "statement": "A Kaplan–Meier survival plot was used to compare the two groups of LC patients who were classified into high- and low-expression groups [32]. Hazard ratios (HRs; 95% confidence intervals) and logrank p values were determined for survival, with logrank p < 0.05 serving as the statistical significance threshold [33].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38785796", "locator": "sections[7] \"2.5. Survival Analysis\" paragraph 2", "quote": "A Kaplan–Meier survival plot was used to compare the two groups of LC patients who were classified into high- and low-expression groups [32]. Hazard ratios (HRs; 95% confidence intervals) and logrank p values were determined for survival, with logrank p < 0.05 serving as the statistical significance threshold [33]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data are available publicly and within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38785796", "locator": "sections[29] \"notes\" paragraph 1", "quote": "All the data are available publicly and within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "From 10 hub genes, HSP90AA1, ESR1, CYP3A4, CDK1, and MMP9 were linked to overall survival in all LC patients (logrank p < 0.05), suggesting that they may prevent LC development.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "From 10 hub genes, HSP90AA1, ESR1, CYP3A4, CDK1, and MMP9 were linked to overall survival in all LC patients (logrank p < 0.05), suggesting that they may prevent LC development."}, "evidence": [{"asset": "source:pmid:38785796", "locator": "sections[17] \"3.6. 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