Ulcerative colitis (UC) is a chronic inflammatory bowel disease with limited therapeutic options. Clerodendranthus spicatus, a traditional medicinal plant, has demonstrated anti-inflammatory properties, yet its bioactive compounds and mechanisms in UC remain unclear. Five polymethoxylated flavonoids (compounds 1-5) were isolated from Clerodendranthus spicatus, with three reported for the first time of this plant. An integrative approach combining network pharmacology, transcriptomics (GSE243625, GSE66407, GSE206171), weighted gene co-expression network analysis (WGCNA), machine learning (LASSO and SVM-RFE), gene set enrichment analysis (GSEA), and molecular docking was employed to elucidate therapeutic mechanisms. Network pharmacology revealed that the five compounds converged on the IL-17 and TNF-α signaling pathways. Machine learning identified five core inflammation-related genes (NPTX2, SIGLEC12, SPINK4, SOX12, ZNF575), which were validated across independent cohorts (combined AUC > 0.81). GSEA confirmed that all five genes were embedded in cytokine/JAK-STAT, TLR/NF-κB, and TNF signaling networks. Molecular docking demonstrated favorable binding affinities (−8.0 to −4.8 kcal/mol) between the flavonoids and core targets. The five Clerodendranthus spicatus flavonoids exertanti-UC effects through dual mechanisms: modulating IL-17 and TNF-α pathways at the systems level and targeting core inflammatory genes at the molecular level, providing a scientific basis for developing natural product-derived UC therapeutics.
