Berberine ameliorates thioacetamide-induced liver injury in zebrafish through PPARγ signaling and restores bile acid homeostasis

Ethnopharmacological Relevance Coptis chinensis Franch. (Huanglian), a traditional Chinese medicinal herb used for “heat” and “dampness” syndromes, is clinically associated with metabolic disorders such as NAFLD. Berberine (BBR), its major bioactive alkaloid, has shown metabolic benefits, though its mechanistic basis in NAFLD remains unclear. Aim of the Study To identify candidate pathways underlying the effects of BBR in NAFLD, a computational target prediction approach was employed, followed by in vivo experimental validation in a zebrafish model. Materials and Methods A thioacetamide (TAA)-induced liver injury zebrafish model was established. Hepatic lipid accumulation and histopathology were assessed by Oil Red O staining, H&E staining, and qPCR. A computational target prediction approach was employed to identify potential BBR-NAFLD overlapping targets, followed by pathway enrichment analysis and molecular docking simulations to prioritize candidate pathways. Bile acid profiles were analyzed using UHPLC-MS/MS metabolomics. The predicted PPARγ pathway was experimentally validated using the specific antagonist GW9662 and the agonist rosiglitazone. Results BBR significantly reduced hepatic steatosis and restored liver morphology. A total of 104 overlapping targets were identified, with PPAR signaling emerging as a key pathway. BBR showed stable binding to PPARγ (−7.92 kcal/mol). In vivo, BBR restored the expression of pparg, rxra, cyp7a1, cyp27a1, and cyp8b1, all of which were suppressed by TAA; these effects were reversed by GW9662, confirming PPARγ dependence. Metabolomics revealed reduced levels of 6-ketoLCA and UDCA-3S, which were partially reversed by PPARγ inhibition. Conclusion BBR alleviates TAA-induced liver injury by regulating PPARγ and bile acid homeostasis, integrating systems pharmacology and experimental validation to support the ethnopharmacological use of C. chinensis in metabolic liver disease.