Exploration of Berberine Against Ulcerative Colitis via TLR4/NF-κB/HIF-1α Pathway by Bioinformatics and Experimental Validation

Abstract

Purpose

This study aimed to delineate the molecular processes underlying the therapeutic effects of berberine on UC by employing network pharmacology tactics, molecular docking, and dynamic simulations supported by empirical validations both in vivo and in vitro.

Patients and Methods

We systematically screened potential targets and relevant pathways affected by berberine for UC treatment from comprehensive databases, including GeneCards, DisGeNET, and GEO. Molecular docking and simulation protocols were used to assess the interaction stability between berberine and its principal targets. The predictions were validated using both a DSS-induced UC mouse model and a lipopolysaccharide (LPS)-stimulated NCM460 cellular inflammation model.

Results

Network pharmacology analysis revealed the regulatory effect of the TLR4/NF-κB/HIF-1α pathway in the ameliorative action of berberine in UC. Docking and simulation studies predicted the high-affinity interactions of berberine with pivotal targets: TLR4, NF-κB, HIF-1α, and the HIF inhibitor KC7F2. Moreover, in vivo analyses demonstrated that berberine attenuates clinical severity, as reflected by decreased disease activity index (DAI) scores, reduced weight loss, and mitigated intestinal inflammation in DSS-challenged mice. These outcomes include suppression of the proinflammatory cytokines IL-6 and TNF-α and downregulation of TLR4/NF-κB/HIF-1α mRNA and protein levels. Correspondingly, in vitro findings indicate that berberine decreases cellular inflammatory injury and suppresses TLR4/NF-κB/HIF-1α signaling, with notable effectiveness similar to that of the HIF-1α inhibitor KC7F2.

Conclusion

Through network pharmacology analysis and experimental substantiation, this study confirmed that berberine enhances UC treatment outcomes by inhibiting the TLR4/NF-κB/HIF-1α axis, thereby mitigating inflammatory reactions and improving colonic pathology.

Graphical Abstract

Keywords:

• berberine
• ulcerative colitis
• TLR4/NF-κB/HIF-1α
• network pharmacology
• molecular docking
• experimental validation
• inhibitor

Abbreviations

UC, ulcerative colitis; BBR, berberine; IBD, inflammatory bowel disease; DAI, disease activity index TNF-α, tumor necrosis factor alpha; IL-6, interleukin 6; IL-1β, interleukin 1β; IL-10, interleukin 10; qRT‒PCR, Quantitative Real-Time PCR; 5-ASA,5-Amino salicylic acid; MPO, Manufacturing Production Order; MD Molecular docking; MDS, Molecular dynamics simulations; GO, Gene Ontology; NF-κB, RMSD, Root Mean Square Displacement; RMSF, Root Mean Square Fluctuation; LPS, Lipopolysaccharide; BP, Biological Process; CCK-8, Cell Counting Kit-8; IκB, Inhibitor of NF-κB; C/EBPβ, CCAAT-enhancer-binding protein β; Th17, T helper cell 17; IFN-γ, Interferon-gamma; CC, Cell Component.

Ethics Statement

This study involves the use of the GEO database, as it is a public database for human data. Ethical approval for the research was granted by the Ethics Committee of the Beijing Institute of Traditional Chinese Medicine (approval number: BJTCM-M-2023-10-17). Ethical approval for animal experimentation was also granted (approval number: BJTCM-M-2023-11-07). GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open source data, so there are no ethical issues.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work. Jilei Li and Wenchao Dan are the co-first authors, Shengsheng Zhang are the corresponding author.

Disclosure

The authors declare that there are no conflicts of interest in this work.

Additional information

Funding

This study was supported by National Natural Science Foundation of China (82174304).