A new antibiotic from an uncultured bacterium binds to an immutable target

Shukla, R.; Peoples, A. J.; Ludwig, K. C.; Maity, S.; Derks, M. G. N.; Krueger, A. M.; de Benedetti, S.; Vermeulen, B. J. A.; Honorato, R. V.; Grein, F.; Lavore, F.; Bonvin, A. M. J. J.; Kubitscheck, U.; Breukink, E.; Achorn, C.; Nitti, A.; Schwalen, C. J.; Spoering, A. L.; Ling, L. L.; Hughes, D.; Lelli, M.; Roos, W. H.; Lewis, K.; Schneider, T.; Weingarth, M.

doi:10.1101/2023.05.15.540765

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bioRxiv · 10.1101/2023.05.15.540765

A new antibiotic from an uncultured bacterium binds to an immutable target

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Abstract

Antimicrobial resistance is a leading mortality factor worldwide. Here we report the discovery of clovibactin, a new antibiotic, isolated from uncultured soil bacteria. Clovibactin efficiently kills drug-resistant bacterial pathogens without detectable resistance. Using biochemical assays, solid-state NMR, and atomic force microscopy, we dissect its mode of action. Clovibactin blocks cell wall synthesis by targeting pyrophosphate of multiple essential peptidoglycan precursors (C55PP, Lipid II, LipidWTA). Clovibactin uses an unusual hydrophobic interface to tightly wrap around pyrophosphate, but bypasses the variable structural elements of precursors, accounting for the lack of resistance. Selective and efficient target binding is achieved by the irreversible sequestration of precursors into supramolecular fibrils that only form on bacterial membranes that contain lipid-anchored pyrophosphate groups. Uncultured bacteria offer a rich reservoir of antibiotics with new mechanisms of action that could replenish the antimicrobial discovery pipeline.

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Shukla, R., Peoples, A. J., Ludwig, K. C., Maity, S., Derks, M. G. N., Krueger, A. M., de Benedetti, S., Vermeulen, B. J. A., Honorato, R. V., Grein, F., Lavore, F., Bonvin, A. M. J. J., Kubitscheck, U., Breukink, E., Achorn, C., Nitti, A., Schwalen, C. J., Spoering, A. L., Ling, L. L., Hughes, D., Lelli, M., Roos, W. H., Lewis, K., Schneider, T., Weingarth, M.. 2023-05-15. A new antibiotic from an uncultured bacterium binds to an immutable target. https://doi.org/10.1101/2023.05.15.540765

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