Multi-Omics-Driven Network Pharmacology and Experimental Validation Reveal the Molecular Mechanism of Bupi Yichang Pill in Treating Ulcerative Colitis Through Regulation of the PI3K/Akt/IKK/NF-κB Pathway.
ETHNOPHARMACOLOGICAL RELEVANCE Bupi Yichang Pill (BYP) is a traditional Chinese medicine (TCM) formula with an established clinical history in managing chronic intestinal disorders and has shown promising protective effects against ulcerative colitis (UC). However, its pharmacodynamic basis and underlying molecular mechanisms remain poorly characterized. AIM OF THE STUDY This study systematically investigated the pharmacological basis and mechanistic underpinnings of BYP in UC through an integrated strategy combining network pharmacology, multi-omics profiling, and experimental validation. MATERIALS AND METHODS A dextran sulfate sodium (DSS)-induced murine UC model was used to evaluate BYP's protective effects, with disease severity assessed by body weight, disease activity index (DAI), colon length, and histopathology, and inflammatory responses quantified by ELISA and RT-qPCR. Chemical constituents were characterized by UPLC-HRMS, and bioactive compounds, targets, and pathways were identified through network pharmacology and molecular docking. Gut microbiota composition, metabolic profiles, and transcriptomic changes were interrogated by 16S rRNA sequencing, untargeted metabolomics, and RNA-seq, respectively. The PI3K/Akt/IKK/NF-κB axis was validated by Western blotting and immunofluorescence in colonic tissues and LPS-stimulated RAW264.7 macrophages. RESULTS BYP significantly attenuated DSS-induced colitis, as evidenced by reduced body weight loss, lower DAI scores, preserved colon length, and alleviated mucosal injury. BYP markedly decreased TNF-α, IL-1β, and IL-6 levels while upregulating IL-10. UHPLC-HRMS identified 115 constituents, of which eight-including kaempferol, liquiritin, quercetin, berberine, paeoniflorin, cryptopine, perlolyrine, and glabrone-were prioritized as overlapping bioactive compounds. Network pharmacology implicated key targets including IL6, TNF, AKT1, and PTGS2, and molecular docking confirmed favorable binding affinities. KEGG enrichment highlighted the PI3K/Akt and NF-κB pathways as principal regulatory axes. Multi-omics analysis revealed that BYP restored gut microbiota dysbiosis, ameliorated bile acid and amino acid metabolism, and modulated the expression of inflammation- and barrier-related genes. Western blotting confirmed suppression of PI3K, Akt, IKK, and NF-κB p65 phosphorylation, corroborated by immunofluorescence in both colonic tissue and macrophages. CONCLUSION BYP confers protection against DSS-induced ulcerative colitis through a multi-component, multi-target, and multi-level regulatory mechanism. Kaempferol and liquiritin emerge as principal bioactive contributors, acting through UC-associated molecular targets and inflammatory signaling cascades. Integrated multi-omics analyses and experimental validation collectively demonstrate that BYP ameliorates gut microbial and metabolic dysregulation while suppressing PI3K/Akt/IKK/NF-κB pathway activation, providing both a mechanistic basis and pharmacological rationale for its traditional clinical use in UC management.