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Potent and specific antibiotic combination therapy against Clostridioides difficile

Abstract

Keratinicyclins and keratinimicins are recently discovered glycopeptide antibiotics. Keratinimicins show broad-spectrum activity against Gram-positive bacteria, while keratinicyclins form a new chemotype by virtue of an unusual oxazolidinone moiety and exhibit specific antibiosis against Clostridioides difficile. Here we report the mechanism of action of keratinicyclin B (KCB). We find that steric constraints preclude KCB from binding peptidoglycan termini. Instead, KCB inhibits C. difficile growth by binding wall teichoic acids (WTAs) and interfering with cell wall remodeling. A computational model, guided by biochemical studies, provides an image of the interaction of KCB with C. difficile WTAs and shows that the same H-bonding framework used by glycopeptide antibiotics to bind peptidoglycan termini is used by KCB for interacting with WTAs. Analysis of KCB in combination with vancomycin (VAN) shows highly synergistic and specific antimicrobial activity, and that nanomolar combinations of the two drugs are sufficient for complete growth inhibition of C. difficile, while leaving common commensal strains unaffected.

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Fig. 1: Structures of GPAs studied herein and binding assays with the peptidoglycan tripeptide.
Fig. 2: X-ray crystal structures and alignments of KMA and KCB.
Fig. 3: Synergy and TEM analysis of VAN and KCB.
Fig. 4: Interaction of KCB with PS-II, a C. difficile-specific WTA.
Fig. 5: Model for the mode of action of KCB against C. difficile.

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Data availability

Atomic coordinates and structure factors for KMA and KCB have been deposited in the PDB under accession numbers 7LKC and 7LTB, respectively. Other relevant data supporting the findings of this study are available within the Article, source data and supplementary materials. Datasets are also available from the corresponding authors upon reasonable request. Source data are provided with this paper.

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Acknowledgements

We are grateful to V. Vandavasi at Princeton University’s Biophysics Core Facility for assistance with ITC experiments, J. Musaev and A. Kaledin at Emory University’s Cherry L. Emerson Center for Scientific Computation for assistance with DFT calculations and MD simulations, as well as the Edward C. Taylor 3rd Year Fellowship in Chemistry (to V.T.C.) and the National Institutes of Health (grant nos. 1R35GM147557 to K.M.D. and 1R01GM129496 to M.R.S.) for support of this work.

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Authors

Contributions

V.T.C., K.L.M., K.M.D. and M.R.S. conceived of the study. V.T.C. performed all biochemical experiments with assistance from Y.L. on the TEM studies. K.L.M. conducted all computational experiments with assistance from T.C.B. on the MD simulations. F.X. provided KCB for crystallographic studies. K.M.D. and P.D.J. solved the crystal structure of KCB. V.T.C., K.L.M., K.M.D. and M.R.S. wrote the manuscript with contributions from all authors.

Corresponding authors

Correspondence to Katherine M. Davis or Mohammad R. Seyedsayamdost.

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M.R.S. is a co-founder of Cryptyx Bioscience. Some of the authors have filed a provisional patent application related to this project.

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Supplementary information

Supplementary Information

Supplementary Tables 1–13 and Figs. 1–16.

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Supplementary Video

Animation of the alignment of KMA and KCB. Monomer A is displayed for each GPA.

Supplementary Data

Statistical source data for Supplementary Figs. 1, 4–6, 8, 11 and 14–16.

Source data

Source Data Fig. 1

Statistical source data.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 4

Statistical source data.

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Chioti, V.T., McWhorter, K.L., Blue, T.C. et al. Potent and specific antibiotic combination therapy against Clostridioides difficile. Nat Chem Biol 20, 924–933 (2024). https://doi.org/10.1038/s41589-024-01651-z

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