Orally available designed miniproteins inhibit enterotoxigenic Bacteroides fragilis pathology by blocking toxin receptor binding
Year: 2026
Type: preprint
Abstract: Toxigenic bacterial infections in the gut are a significant contributor to the global burden of disease. Advanced tools for protein and live biotherapeutic engineering offer potentially transformative strategies for treating such diseases, while avoiding the collateral effects of traditional antibacterials. Here we used de novo protein design to identify inhibitors of the metzincin family protease Bacteroides fragilis toxin (BFT). These inhibitors, which bind distal to the active site, interfere with toxin-mediated E-cadherin cleavage and downstream proinflammatory signaling by blocking claudin-4 receptor binding. We tested the inhibitors as disulfide-stabilized variants administered directly to the cecum or in drinking water, as well as through in situ secretion by an engineered live biotherapeutic. Across these delivery modalities, the inhibitors successfully neutralized the toxin and effectively prevented BFT-associated gut pathology, including tumor formation. These results highlight the potential of de novo designed proteins as precise, non-antibiotic interventions to mitigate bacterial toxin-driven disease in the gut.
Authors: Pooja Srinivas, Victor Adebomi, Susan M. Markiewicz, Kang Wang, Denise Chac, Kristofer Lindenauer, Nishoni Huber, Zhihang Tao, Phat Luong, Stephen A. Rettie, Maisie W. Smith, Asim K. Bera, Alex Kang, Hannah Nguyen, Maika Schneider, Yaxi Wang, S. Brook Peterson, Min Dong, Ana A. Weil, Gaurav Bhardwaj, Joseph D. Mougous
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: green
Awards: G2004402655, Pixel Array Detector for Macromolecular Crystallography, Structure and Function of C. Difficile Toxins, Center for Biomolecular Structure (CBMS), UW Post-Baccalaureate Research Education Program (PREP), Molecular mechanism of tetanus neurotoxin pathogenesis, Genome-wide CRISPR-Cas9 screens in insect cells to characterize insecticidal toxins
OpenAlex ID: W7165754276