Molecular Mechanisms of Panax japonicus var. major Against Gastric Cancer: Metabolite Analysis, Signaling Pathways, and Protein Targets

<b>Background/Objectives:</b> Ginseng (<i>Panax japonicus</i> var. <i>major</i>) is a traditional medicinal plant with anticancer properties. We aimed to assess the biological activity, potential targets, and molecular mechanisms of <i>P. japonicus</i> var. <i>major</i> in resisting gastric cancer. <b>Methods:</b> We developed a model that combines network pharmacology, molecular docking, untargeted metabolomics, and molecular dynamics simulations to predict which compounds from <i>P. japonicus</i> var. <i>major</i> might be active in the treatment of gastric cancer. We conducted in vitro experiments and immunoblot validation to test these predictions. <b>Results:</b> We identified 44 main active compounds from <i>P. japonicus</i> var. <i>major</i> and 29 core targets. These compounds showed anti-gastric cancer activity against the HGC-27 cell line by acting on TNF and T-cell receptor signaling pathways to diminish inflammatory factor production and promote apoptosis of gastric cancer cells. Clinical survival analysis identified four core proteins (CASP3, TNF, AKT1, and EGFR) whose abundance was associated with survival status in gastric cancer patients. Molecular docking, along with molecular dynamics simulations, revealed that these core proteins could be stably bound by the identified active compounds. The anti-gastric cancer effects of <i>P. japonicus</i> var. <i>major</i> compounds involved a lower Bcl-2/Bax ratio and upregulation of CASP3 and CASP9 levels, highlighting significant differences in anti-gastric cancer activity between extracts prepared from fresh versus dried <i>P. japonicus</i> var. <i>major</i>. <b>Conclusions:</b> Our results provide background for the indigenous medicinal use of <i>P. japonicus</i> var. <i>major</i> to treat gastric cancer and lay the foundation for further pharmacological experiments and clinical tests.