A study published in Nature Microbiology describes a structure-guided strategy to inhibit Clostridioides difficile toxin B (TcdB), the primary virulence factor responsible for infectious diarrhea and colitis, leading to the development of a synthetic bile acid that protected mice from toxin-induced disease pathology.
C difficile remains the leading cause of health care–associated infectious diarrhoea, with disease severity driven largely by TcdB-mediated epithelial injury and inflammation. Although intestinal bile acids—host- and microbiota-derived metabolites, have previously been shown to inhibit TcdB activity, the molecular mechanism underlying this inhibition had not been fully defined.
Using cryogenic electron microscopy, investigators resolved high-resolution structures of TcdB bound to two inhibitory bile acids: cholic acid (methyl ester) at 2.9 Å resolution and taurochenodeoxycholic acid at 3.3 Å resolution. Structural analysis revealed that bile acids bind the toxin’s C-terminal combined repetitive oligopeptide (CROP) domain, stabilizing it in a closed conformation that allosterically masks both receptor-binding sites. This conformational locking prevents TcdB from engaging host cell receptors and entering target cells.
What You Need to Know
C difficile toxin B (TcdB), the primary virulence factor driving diarrhoea and colitis, was structurally resolved bound to inhibitory bile acids at 2.9 Å and 3.3 Å using cryo-electron microscopy.
Bile acids bind the toxin’s C-terminal CROP domain, allosterically masking both receptor-binding sites and preventing host cell recognition.
A gut-restricted synthetic bile acid (sBA-2) remained localized in the intestine after oral dosing and protected mice from toxin-induced C difficile disease pathology in preclinical models.
Building on these structural insights, the research team synthesized gut-restricted bile acid derivatives designed to evade intestinal bile acid reuptake transporters, thereby prolonging local activity within the gut lumen. One candidate compound, sBA-2, demonstrated intestinal retention following oral administration and significantly protected mice from toxin-induced C difficile disease pathology in preclinical models.
Notably, this therapeutic strategy targets toxin activity rather than bacterial viability, distinguishing it from antibiotic-based treatments that can disrupt the gut microbiota and contribute to recurrent infection. By neutralizing TcdB directly within the intestinal lumen, sBA-2 mitigated disease severity while preserving microbiome integrity.
The authors conclude that defining the structural basis of bile acid–mediated TcdB inhibition provides a foundation for developing orally deliverable, precision therapeutics for C difficile infection, with the potential to reduce recurrence and improve outcomes without microbiome disruption.
References
1.Miletic, S., Icho, S., Li, Z. et al. Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin. Nat Microbiol 10, 3215–3228 (2025). https://doi.org/10.1038/s41564-025-02179-1
