LC–MS/MS-based metabolomic profiling of Syzygium cumini (L.) Skeels: Identifying key phytochemicals driving α-amylase inhibition and antioxidant activity

Indian blackberry ( Syzygium cumini (L.) Skeels) possesses immense pharmacological potential, yet unlocking the mechanisms behind these health benefits requires a precise elucidation of the fruit’s complex metabolic architecture. This study provides a comprehensive LC–MS/MS-based profiling of bioactive compounds and sugars in three contrasting genotypes (PCJ-9, 15, 17) across pulp and seed tissues. We quantified 49 metabolites, identifying distinct tissue-specific fingerprints via OPLS-DA (Q² = 0.756–0.988). Seeds were enriched with phenolics (rutin, gallic acid), while pulp dominated in anthocyanins and soluble sugars. Correlation analysis revealed that total flavonoid content (TFC), specifically catechin and protocatechuic acid, rather than total phenolics, is the primary driver of antioxidant and α-amylase inhibitory activities (r = 0.95–0.97). The small-seeded PCJ-15 genotype emerged as the most potent therapeutic candidate. KEGG pathway analysis revealed a metabolic "hub" in flavonoid biosynthesis and identified a significant inverse correlation between primary sugar accumulation and secondary metabolite synthesis (r < − 0.70). This suggests that S. cumini operates as a naturally optimized delivery system, providing high-density phytochemicals with minimal glycemic impact. These findings establish a mechanistic foundation for the clinical application of jamun-derived bioactives in managing metabolic disorders, aligning with the therapeutic goals of functional food development.