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Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors worldwide. Both experimental and clinical studies confirm the anti-HCC effects of Yiguanjian (YGJ), though its material basis and pharmacological mechanisms remain unclear. This study integrated UHPLC-Q-TOF-MS with network pharmacology, molecular docking, and MDS to explore YGJ's potential anti-HCC mechanisms and active ingredients. In vitro analysis identified 96 chemical constituents in the YGJ extract, while network pharmacology revealed 57 potential targets and 51 bioactive compounds related to HCC treatment. The top nine key targets were AKT1, CTNNB1, EGFR, IL6, STAT3, BCL2, CASP3, MMP9, and TNF-α; the top seven active compounds included kaempferol, quercetin, luteolin, senkyunolide O, jasmolone, azaron, and dihydroartemisinin. These components may regulate HCC cell processes like gene expression, signal transduction, proliferation, apoptosis, and angiogenesis through pathways such as PI3K-Akt, TNF signaling pathway, and HIF-1 signaling pathway. Molecular docking and MDS showed that kaempferol, quercetin, luteolin, and dihydroartemisinin bind favorably to TNF-α, MMP9, BCL2, and IL6 proteins. Therefore, these proteins may serve as YGJ's therapeutic targets, while the compounds contribute to its pharmacological effects.