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TitleDe novo design of mini-protein binders broadly neutralizing Clostridioides difficile toxin B variants.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 8521, Year 2024
Publish dateOct 2, 2024
AuthorsXinchen Lv / Yuanyuan Zhang / Ke Sun / Qi Yang / Jianhua Luo / Liang Tao / Peilong Lu /
PubMed AbstractClostridioides difficile toxin B (TcdB) is the key virulence factor accounting for C. difficile infection-associated symptoms. Effectively neutralizing different TcdB variants with a universal ...Clostridioides difficile toxin B (TcdB) is the key virulence factor accounting for C. difficile infection-associated symptoms. Effectively neutralizing different TcdB variants with a universal solution poses a significant challenge. Here we present the de novo design and characterization of pan-specific mini-protein binders against major TcdB subtypes. Our design successfully binds to the first receptor binding interface (RBI-1) of the varied TcdB subtypes, exhibiting affinities ranging from 20 pM to 10 nM. The cryo-electron microscopy (cryo-EM) structures of the mini protein binder in complex with TcdB1 and TcdB4 are consistent with the computational design models. The engineered and evolved variants of the mini-protein binder and chondroitin sulfate proteoglycan 4 (CSPG4), another natural receptor that binds to the second RBI (RBI-2) of TcdB, better neutralize major TcdB variants both in cells and in vivo, as demonstrated by the colon-loop assay using female mice. Our findings provide valuable starting points for the development of therapeutics targeting C. difficile infections (CDI).
External linksNat Commun / PubMed:39358329 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.2 Å
Structure data

39072

8y9b

EMDB-39072, PDB-8y9b:
TcdB1 in complex with mini-binder
Method: EM (single particle) / Resolution: 3.2 Å

39073

8y9c

EMDB-39073, PDB-8y9c:
De novo design mini-binder in complex with TcdB4
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • clostridioides difficile (bacteria)
  • synthetic construct (others)
KeywordsTOXIN/DE NOVO PROTEIN / Mini-binder against C.difficle infection / TOXIN-DE NOVO PROTEIN complex / De novo design mini-binder against C.difficle toxin B / DE NOVO PROTEIN

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