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.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
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.
References
Antibiotic Resistance Threats in the United States (US Department of Health and Human Services, CDC, 2019).
Fenton, S., Stephenson, D. & Weder, C. Pseudomembranous colitis associated with antibiotic therapy—an emerging entity. Can. Med. Assoc. J. 111, 1110–1111 (1974). 1114.
Bartlett, J. G., Chang, T. W., Gurwith, M., Gorbach, S. L. & Onderdonk, A. B. Antibiotic-associated pseudomembranous colitis due to toxin-producing clostridia. N. Engl. J. Med. 298, 531–534 (1978).
Theriot, C. M. et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat. Commun. 5, 3114 (2014).
Abt, M. C., McKenney, P. T. & Pamer, E. G. Clostridium difficile colitis: pathogenesis and host defence. Nat. Rev. Microbiol. 14, 609–620 (2016).
Oksi, J., Anttila, V.-J. & Mattila, E. Treatment of Clostridioides (Clostridium) difficile infection. Ann. Med. 52, 12–20 (2020).
Williams, D. H., Williamson, M. P., Butcher, D. W. & Hammond, S. J. Detailed binding sites of the antibiotics vancomycin and ristocetin A: determination of intermolecular distances in antibiotic/substrate complexes by use of the time-dependent NOE. J. Am. Chem. Soc. 105, 1332–1339 (1983).
Nitanai, Y. et al. Crystal structures of the complexes between vancomycin and cell-wall precursor analogs. J. Mol. Biol. 385, 1422–1432 (2009).
Johnson, S. et al. Vancomycin, metronidazole, or tolevamer for Clostridium difficile infection: results from two multinational, randomized, controlled trials. Clin. Infect. Dis. 59, 345–354 (2014).
Louie, T. J. et al. Fidaxomicin versus vancomycin for Clostridium difficile infection. N. Engl. J. Med. 364, 422–431 (2011).
Xu, F. et al. A genetics-free method for high-throughput discovery of cryptic microbial metabolites. Nat. Chem. Biol. 15, 161–168 (2019).
Rekharsky, M. et al. Thermodynamics of interactions of vancomycin and synthetic surrogates of bacterial cell wall. J. Am. Chem. Soc. 128, 7736–7737 (2006).
Gerhard, U., Mackay, J. P., Maplestone, R. A. & Williams, D. H. The role of the sugar and chlorine substituents in the dimerization of vancomycin antibiotics. J. Am. Chem. Soc. 115, 232–237 (1993).
Mackay, J. P., Gerhard, U., Beauregard, D. A., Maplestone, R. A. & Williams, D. H. Dissection of the contributions toward dimerization of glycopeptide antibiotics. J. Am. Chem. Soc. 116, 4573–4580 (1994).
Barna, J. C. & Williams, D. H. The structure and mode of action of glycopeptide antibiotics of the vancomycin group. Annu. Rev. Microbiol. 38, 339–357 (1984).
Nicolaou, K. C., Boddy, C. N., Bräse, S. & Winssinger, N. Chemistry, biology, and medicine of the glycopeptide antibiotics. Angew. Chem. Int. Ed. Engl. 38, 2096–2152 (1999).
Kahne, D., Leimkuhler, C., Lu, W. & Walsh, C. Glycopeptide and lipoglycopeptide antibiotics. Chem. Rev. 105, 425–448 (2005).
Perkins, H. R. Specificity of combination between mucopeptide precursors and vancomycin or ristocetin. Biochem. J. 111, 195–205 (1969).
Nieto, M. & Perkins, H. R. Modifications of the acyl-d-alanyl-d-alanine terminus affecting complex-formation with vancomycin. Biochem. J. 123, 789–803 (1971).
Kannan, R. et al. Function of the amino sugar and N-terminal amino acid of the antibiotic vancomycin in its complexation with cell wall peptides. J. Am. Chem. Soc. 110, 2946–2953 (1988).
Booth, P. M. & Williams, D. H. Preparation and conformational analysis of vancomycin hexapeptide and aglucovancomycin hexapeptide. J. Chem. Soc. Perkin Trans. 1 12, 2335–2339 (1989).
Schäfer, M., Schneider, T. R. & Sheldrick, G. M. Crystal structure of vancomycin. Structure 4, 1509–1515 (1996).
Arthur, M. et al. Evidence for in vivo incorporation of d-lactate into peptidoglycan precursors of vancomycin-resistant enterococci. Antimicrob. Agents Chemother. 36, 867–869 (1992).
Lee, J.-G., Sagui, C. & Roland, C. First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini. J. Am. Chem. Soc. 126, 8384–8385 (2004).
Lee, J.-G., Sagui, C. & Roland, C. Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues. J. Phys. Chem. B. 109, 20588–20596 (2005).
Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648–5652 (1993).
Lee, C., Yang, W. & Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B. 37, 785–789 (1988).
Tomasi, J., Mennucci, B. & Cammi, R. Quantum mechanical continuum solvation models. Chem. Rev. 105, 2999–3094 (2005).
Avogadro: an open-source molecular builder and visualization tool v.1.20 (Avogadro Chemistry, 2022).
Hanwell, M. D. et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J. Cheminform. 4, 17 (2012).
Rappe, A. K., Casewit, C. J., Colwell, K. S., Goddard, W. A. & Skiff, W. M. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 114, 10024–10035 (1992).
Berenbaum, M. C. A method for testing for synergy with any number of agents. J. Infect. Dis. 137, 122–130 (1978).
Yang, J. & Yang, H. Antibacterial activity of Bifidobacterium breve against Clostridioides difficile. Front. Cell Infect. Microbiol. 9, 288 (2019).
Deng, H. et al. Bacteroides fragilis prevents Clostridium difficile infection in a mouse model by restoring gut barrier and microbiome regulation. Front. Microbiol. 9, 2976 (2018).
Casas, V. D. L., Miller, S., Herbert, D. L. & Jiang, Z.-D. In vitro effects of probiotics on Clostridium difficile toxin production and sporulation. Int. Arch. Public Health Community Med. 4, 40 (2020).
Campbell, J. et al. An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus. Antimicrob. Agents Chemother. 56, 1810–1820 (2012).
Wenzel, M. et al. A flat embedding method for transmission electron microscopy reveals an unknown mechanism of tetracycline. Commun. Biol. 4, 306 (2021).
Mcguire, J. M., Wolfe, R. N. & Ziegler, D. W. Vancomycin, a new antibiotic. II. In vitro antibacterial studies. Antibiot. Annu. 3, 612–618 (1955).
Goldstein, B. P. Resistance to rifampicin: a review. J. Antibiot. 67, 625–630 (2014).
Kim, S. J., Cegelski, L., Preobrazhenskaya, M. & Schaefer, J. Structures of Staphylococcus aureus cell-wall complexes with vancomycin, eremomycin, and chloroeremomycin derivatives by 13C{19F} and 15N{19F} rotational-echo double resonance. Biochemistry 45, 5235–5250 (2006).
Culp, E. J. et al. Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling. Nature 578, 582–587 (2020).
Ganeshapillai, J., Vinogradov, E., Rousseau, J., Weese, J. S. & Monteiro, M. A. Clostridium difficile cell-surface polysaccharides composed of pentaglycosyl and hexaglycosyl phosphate repeating units. Carbohydr. Res. 343, 703–710 (2008).
Campbell, J. et al. Synthetic lethal compound combinations reveal a fundamental connection between wall teichoic acid and peptidoglycan biosyntheses in Staphylococcus aureus. ACS Chem. Biol. 6, 106–116 (2011).
Swoboda, J. G. et al. Discovery of a small molecule that blocks wall teichoic acid biosynthesis in Staphylococcus aureus. ACS Chem. Biol. 4, 875–883 (2009).
Willing, S. E. et al. Clostridium difficile surface proteins are anchored to the cell wall using CWB2 motifs that recognise the anionic polymer PSII. Mol. Microbiol. 96, 596–608 (2015).
Mitachi, K. et al. Novel FR-900493 analogues that inhibit the outgrowth of Clostridium difficile spores. ACS Omega 3, 1726–1739 (2018).
Lebedev, A. A. et al. JLigand: a graphical tool for the CCP4 template-restraint library. Acta Crystallogr. D. Biol. Crystallogr. 68, 431–440 (2012).
Honorato, R. V. et al. Structural biology in the clouds: the WeNMR-EOSC ecosystem. Front. Mol. Biosci. 8, 729513 (2021).
van Zundert, G. C. P. et al. The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J. Mol. Biol. 428, 720–725 (2016).
Dominguez, C., Boelens, R. & Bonvin, A. M. J. J. HADDOCK: a protein–protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125, 1731–1737 (2003).
Abraham, M. J., van der Spoel, D., Lindahl, E., Hess, B. & the GROMACS Development Team. GROMACS User Manual version 2019.3 (GROMACS, 2019).
Lindorff-Larsen, K. et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78, 1950–1958 (2010).
Abraham, M. J. et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).
Atilano, M. L. et al. Teichoic acids are temporal and spatial regulators of peptidoglycan cross-linking in Staphylococcus aureus. Proc. Natl Acad. Sci. USA 107, 18991–18996 (2010).
Usenik, A. et al. The CWB2 cell wall-anchoring module is revealed by the crystal structures of the Clostridium difficile cell wall proteins Cwp8 and Cwp6. Structure 25, 514–521 (2017).
Yu, F. et al. Glycopeptide antibiotic teicoplanin inhibits cell entry of SARS-CoV-2 by suppressing the proteolytic activity of cathepsin L. Front. Microbiol. 13, 884034 (2022).
Kwon, Y.-J., Kim, H.-J. & Kim, W.-G. Complestatin exerts antibacterial activity by the inhibition of fatty acid synthesis. Biol. Pharm. Bull. 38, 715–721 (2015).
Kaneko, I., Fearon, D. T. & Austen, K. F. Inhibition of the alternative pathway of human complement in vitro by a natural microbial product, complestatin. J. Immunol. 124, 1194–1198 (1980).
Olsen, M. A., Yan, Y., Reske, K. A., Zilberberg, M. D. & Dubberke, E. R. Recurrent Clostridium difficile infection is associated with increased mortality. Clin. Microbiol. Infect. 21, 164–170 (2015).
Enoch, D. A. et al. Risk of complications and mortality following recurrent and non-recurrent Clostridioides difficile infection: a retrospective observational database study in England. J. Hosp. Infect. 106, 793–803 (2020).
Kabsch, W. XDS. Acta Crystallogr. D. Biol. Crystallogr. 66, 125–132 (2010).
Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D. Biol. Crystallogr. 69, 1204–1214 (2013).
Sheldrick, G. M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D. Biol. Crystallogr. 66, 479–485 (2010).
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr. 66, 486–501 (2010).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–221 (2010).
Vanommeslaeghe, K., Raman, E. P. & MacKerell, A. D. Jr. Automation of the CHARMM general force field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J. Chem. Inf. Model. 52, 3155–3168 (2012).
Frisch, M. J. et al. Gaussian 09 Rev. E.01 (Gaussian Inc., 2009).
Grimme, S., Antony, J., Ehrlich, S. & Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 132, 154104 (2010).
CLSI. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically (Clinical and Laboratory Standards Institute, 2018).
CLSI. Methods for Antimicrobial Susceptibility Testing of Anaerobic Bacteria (Clinical and Laboratory Standards Institute, 2018).
Krogstad, D. J. & Moellering, R. C. Jr in Antibiotics in Laboratory Medicine (ed. Lorian, V.) 537–595 (Williams & Wilkins Co., 1986).
Schaub, R. E. & Dillard, J. P. Digestion of peptidoglycan and analysis of soluble fragments. Bio-Protoc. 7, e2438 (2017).
Schüttelkopf, A. W. & van Aalten, D. M. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D. Biol. Crystallogr. 60, 1355–1363 (2004).
Bayly, C. I., Cieplak, P., Cornell, W. & Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97, 10269–10280 (1993).
Frisch, M. J. et al. Gaussian 16 Rev. C.01 (Gaussian Inc., 2016).
Sousa da Silva, A. W. & Vranken, W. F. ACPYPE—antechamber Python parser interface. BMC Res. Notes 5, 367 (2012).
Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435–447 (2008).
Hess, B. P-LINCS: a parallel linear constraint solver for molecular simulation. J. Chem. Theory Comput. 4, 116–122 (2008).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
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.
Author information
Authors and Affiliations
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
Ethics declarations
Competing interests
M.R.S. is a co-founder of Cryptyx Bioscience. Some of the authors have filed a provisional patent application related to this project.
Peer review
Peer review information
Nature Chemical Biology thanks the anonymous reviewers for their contribution to the peer review of this work.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Supplementary Information
Supplementary Tables 1–13 and Figs. 1–16.
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.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41589-024-01651-z