9MF4

De novo designed minibinder complexed with Clostridioides difficile Toxin B

Summary for 9MF4

• Entry DOI: 10.2210/pdb9mf4/pdb
• EMDB information: 48223
• Descriptor: Toxin B, De novo designed cspg67 minibinder (2 entities in total)
• Functional Keywords: tcdb, minibinder, de novo, inhibitor, toxin
• Biological source: Clostridioides difficile; More
• Total number of polymer chains: 2
• Total formula weight: 277408.07

Authors

Miletic, S.,Li, Z.,Ragotte, R.J.,Melnyk, R. (deposition date: 2024-12-09, release date: 2025-09-17, Last modification date: 2025-10-08)

Primary citation

Ragotte, R.J.,Liang, H.,Tam, J.,Miletic, S.,Berman, J.M.,Palou, R.,Weidle, C.,Li, Z.,Glogl, M.,Beilhartz, G.L.,Carr, K.D.,Borst, A.J.,Coventry, B.,Wang, X.,Rubinstein, J.L.,Tyers, M.,Schramek, D.,Melnyk, R.A.,Baker, D.
De novo design of potent inhibitors of clostridial family toxins.
Proc.Natl.Acad.Sci.USA, 122:e2509329122-e2509329122, 2025

PubMed Abstract: remains a leading cause of hospital-acquired infections, with its primary virulence factor, toxin B (TcdB), responsible for severe colitis and recurrent disease. The closely related toxin, TcsL, from , causes a rarer but often fatal toxic shock syndrome, particularly in gynecological and obstetric contexts. We report the de novo design of small protein minibinders that directly neutralize TcdB and TcsL by preventing their entry into host cells. Using deep learning and Rosetta-based approaches, we generated high-affinity minibinders that protect cells from intoxication with picomolar potency and, in the case of TcsL, prolonged survival following lethal toxin challenge in mice. The designed proteins against TcdB demonstrate exceptional stability in proteolytic and acidic environments, making them well-suited for oral delivery-a valuable feature for treating infections localized to the gastrointestinal tract. For TcsL, potent inhibitors were identified from 48 initial designs and 48 optimized designs, highlighting the potential of computational design for rapidly developing countermeasures against life-threatening bacterial toxins.

PubMed: 40982695
DOI: 10.1073/pnas.2509329122

Experimental method

ELECTRON MICROSCOPY (3.02 Å)