Comparative Metabolomics and Network Pharmacology Study Reveals Chemopreventive Potential of Wild Soybean (Glycine soja)

Wild soybean (Glycine soja), as the wild ancestor of cultivated soybean, serves as a rich reservoir of phytochemicals with significant potential in functional food applications and chemoprevention. However, its metabolic characteristics and health benefits remain to be systematically elucidated. In this study, non-targeted metabolomics technology was employed, in conjunction with network pharmacology and molecular docking analysis, to systematically investigate the metabolic differences between wild soybean seeds from three distinct ecological regions and cultivated soybean seeds. Metabolomic profiling revealed the unique metabolic characteristics of wild soybean, identifying 124 significantly upregulated metabolites and 7 unique compounds, with the most notable enrichment in flavonoids and prunolides. Network pharmacology analysis indicated that 22 key metabolites in wild soybeans were associated with 503 pan-cancer targets (covering breast, lung, and colorectal cancers), primarily regulating pathways related to “cancer” and “lipids and atherosclerosis.” Molecular docking experiments further confirmed the stable binding affinity of key bioactive components, including quercetin and L-arginine, with core targets such as TP53, TNF, EGFR, IL1B, and JUN. These findings elucidate the unique phytochemical profile of wild soybean and its potential multi-target chemopreventive mechanisms, providing theoretical support for developing it as a natural chemopreventive agent.