Metabolomics and network pharmacology identify three key bioactive organic acid metabolites in Amomum tsao-ko.

Amomum tsao-ko is a medicinal spice whose organic acids determine flavor and bioactivity, yet systematic profiling is lacking. We performed metabolomics across three accessions and two processing states, network pharmacology on differential metabolites, and transcriptomics on fresh fruits of three accessions. Metabolomics resolved accession-specific and drying-responsive profiles. Network pharmacology identified core targets converging on steroid hormone biosynthesis and inflammatory pathways, and molecular docking prioritized three organic acids, including jasmonic acid, abscisic acid, and 1-(2-amino-3-methylpentanoyl)pyrrolidine-2-carboxylic acid, with strong binding to PTGS2, AKR1C3, and CYP19A1. Transcriptomics revealed that key biosynthetic genes for jasmonic acid and abscisic acid, including LOX2S, AOS, NCED, and ABA2, were differentially expressed across accessions in patterns consistent with the corresponding metabolite accumulation levels. These cross-validated findings link organic acid composition to genotype and processing, highlight candidate bioactives for inflammation and endocrine modulation, and provide a foundation for germplasm evaluation and medicinal development of A. tsao-ko.