Stage-specific harvest of Akebia trifoliata flowers: An integrated multi-omics strategy for optimizing natural colorants, antioxidants and bioactive ingredients

The underutilized flowers of Akebia trifoliata represent a promising source of high-value plant-based ingredients. To unlock their potential, we applied an integrated multi-omics approach combining dynamic metabolomics, bioactivity assays, and network pharmacology to analyze metabolic profiles across three developmental stages: bud (S1), partially open (S2), and fully open (S3). We identified 2738 metabolites, with 893 exhibiting differential accumulation. A clear stage-specific allocation was observed: S3 flowers were rich in cyanidin-based anthocyanins (e.g., cyanidin-3-O-glucoside), identifying this stage as optimal for natural colorants. In contrast, S1 buds were enriched with defense-related alkaloids (e.g., dhurrin), antimicrobial organic acids, triterpenoids. A diverse array of bioactive oligopeptides, potentially beneficial for managing type 2 diabetes and hypertension, were also identified, predominantly accumulating in S1 or S3. Nine key antioxidant compounds were systematically screened, and network pharmacology elucidated their synergistic mechanisms, identifying six core targets—confirmed by molecular docking to exhibit strong binding affinity. This study deciphers the developmental metabolome of A. trifoliata flowers and establishes a precision, stage-specific harvest strategy to facilitate sustainable production of natural colorants, antioxidants, and multifunctional bioactive ingredients for food, pharmaceutical, and cosmetic applications. • Metabolite profiling shows stage-specific accumulation of bioactive compounds in Akebia trifoliata flowers. • Fully open flowers are optimal for natural colorant due to high cyanidin-based anthocyanin content. • Bud flowers are enriched in defense compounds and exhibit the highest antioxidant capacity. • Bioactive oligopeptides with anti-diabetic/hypertension potential show stage-specific accumulation. • Nine key antioxidants act synergistically via six core targets, validated by molecular docking.