Isolation of polymethoxylated flavonoids from Clerodendranthus spicatus and an integrative network pharmacology study on their effect against ulcerative colitis

Abstract

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 exert anti-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.

Keywords

Ulcerative colitis / Clerodendranthus spicatus / Network pharmacology / Machine learning

References

[1] Calvez V, Puca P, Di Vincenzo F, et al. Novel Insights into the Pathogenesis of Inflammatory Bowel Diseases. Biomedicines, 2025, 13 (2): 305.

[2] Katsanos KH, Papadakis KA. Inflammatory Bowel Disease: Updates on Molecular Targets for Biologics. Gut Liver, 2017, 11 (4): 455-63.

[3] Paula Sanchez Zanotti M, Cataldi de Alcântara C, Junko Inoue C, et al. Involvement of IL17A and IL17RA variants in interleukin-17A levels and disease activity in ulcerative colitis. Cytokine, 2024, 182: 156716.

[4] Soldera J. Navigating treatment resistance: Janus kinase inhibitors for ulcerative colitis. World J Clin Cases, 2024, 12 (24): 5468-72.

[5] Wetwittayakhlang P, Lakatos PL. Advanced combination therapy: is it the best way to break the therapeutic ceiling? Therap Adv Gastroenterol, 2024, 17: 17562848241272995.

[6] Jiao X, Jin Q, Zhu P, et al. Clerodendranthus spicatus: a comprehensive review of the chemical constituents, pharmacology, quality control and clinical applications. Front Pharmacol, 2025, 16: 1452797.

[7] Li KW, Raza F, Jiang LD, et al. Clerodendranthus Spicatus: A review of its active compounds, mechanisms of action, and clinical studies in urinary diseases. Fitoterapia, 2024, 177: 106082.

[8] Ma GX, Zhang XP, Li PF, et al. Four new phenolic acid with unusual bicycle [2.2.2] octane moiety from Clerodendranthus spicatus and their anti-inflammatory activity. Fitoterapia, 2015, 105: 61-65.

[9] Ren D, Dong Z, Wang M, et al. Novel insight into the gene etiology of ulcerative colitis gained from transcriptome association study and single-cell sequence analysis. Medicine (Baltimore), 2025, 104 (51): e46678.

[10] Yan JW, Nie M, Zhang H, et al. Strengths, weaknesses, opportunities, and threats analysis of combination therapy for inflammatory bowel disease. World J Gastroenterol, 2025, 31 (9): 100607.

[11] Lundekvam JA, Høivik ML, Anisdahl K, et al. Tumour necrosis factor inhibitors in Ulcerative colitis: real-world data on Therapeutic drug monitoring and evaluation of current treatment targets (STRIDE II). Ann Med, 2025, 57 (1): 2424447.

[12] Magisetty J, Gadiraju B, Kondreddy V. Genomic analysis in the colon tissues of omega-3 fatty acid-treated rats identifies novel gene signatures implicated in ulcerative colitis. Int J Biol Macromol, 2024, 258 (Pt 1): 128867.

[13] Noh H, Hashem Z, Boms E, et al. SIGLEC12 mediates plasma membrane rupture during necroptotic cell death. Nature, 2026, 649 (8096): 460-66.

[14] Wang Y, Han J, Yang G, et al. Therapeutic potential of the secreted Kazal-type serine protease inhibitor SPINK4 in colitis. Nat Commun, 2024, 15 (1): 5874.

[15] Tanaka S, Suto A, Iwamoto T, et al. Sox12 promotes T reg differentiation in the periphery during colitis. J Exp Med, 2018, 215 (10): 2509-19.