Sulfur is the key ingredient for the π

Lincosamides are naturally occurring antibiotics that are effective against a variety of different types of bacterial infections. However, they possess a sulfur atom at a key location that makes them vulnerable to rapid metabolism in both animals and humans, reducing their usefulness in the clinic. Efforts to make a synthetic version without the sulfur atom have failed to generate a new antibiotic that is both long-lived and effective, and all the synthetic versions that do work still have the key sulfur.

One of these, a synthetic lincosamide called cresomycin (CRM), has potent antibiotic activity, even against multidrug-resistant strains, but still undergoes metabolic degradation at its sulfur atom. The excellent activity of CRM has renewed interest in the optimization of its structure and, in a recent publication, researchers from Harvard University and the University of Illinois at Chicago reported that they used CRM as a model to understand why sulfur plays such an important role in the action of this effective class of antibiotics. The work provides insights that may lead to new paradigms for antibiotic development.

The project was based on the premise that deciphering why the sulfur atom is essential to the antibiotic action of CRM would help lead to ideas for how to optimize its antibacterial activity and reduce its metabolic degradation. The team synthesized three new versions of CRM with replacement groups at the sulfur position, including an oxygen atom, to make O-CRM, a selenium atom, to make Se-CRM, and a methylene group to make C-CRM. Proton nuclear magnetic resonance spectra of the new versions suggested that they had identical conformational structures to CRM.

The next step was to test their activities in terms of antibiotic effects and metabolic stability. In tests against different bacterial strains, O-CRM and C-CRM had reduced activity but Se-CRM had almost identical activity to the parent CRM. In terms of metabolic stability, testing in an in vitro assay that recapitulates liver metabolism showed that O-CRM was very stable (two-fold more stable than CRM and four-fold more stable than Se-CRM) but that Se-CRM was not very stable and C-CRM was similar to CRM. This led to the conclusion that O-CRM is the most stable but has the lowest antibacterial activity and Se-CRM has good antibacterial activity but reduced stability.

Next, the researchers reasoned that other factors could affect the efficacy of the antibiotic, including how fast it gets into the bacteria, a factor called permeability, and how fast the bacterial system gets rid of it, a process called efflux. In permeability and efflux assays, all of the CRM analogs performed similarly, suggesting that the importance of the sulfur atom was not related to cellular accumulation. The team also assessed each CRM analog in displacement assays designed to test how well each antibiotic binds to its target, the bacterial 70S ribosome. Blocking the 70S ribosome, an essential part of the cellular machinery involved in bacterial protein production, is the basis of the antibiotic action of these drugs. The displacement assays confirmed that target engagement was indeed the key factor involved in the observed differences.

The next step was to solve the X-ray crystal structures of the CRM analogs in complex with the 70S ribosome target. In work done at the Northeastern Collaborative Access Team (NE-CAT) beamlines 24-ID-C and 24-ID-E at the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory, the group solved each of the four structures and determined that the overall structures were almost indistinguishable from each other. Each of the CRM analogs extends into the hydrophobic A-cleft site of the ribosome that normally receives the α-side chains of the tRNAs during bacterial protein synthesis. The CRM analogs all bind in the same way and make the same hydrogen bonds with their target.

In fact, all that appeared to be different were subtle changes in bond lengths that affect the van der Waals contacts between the antibiotic and the ribosome. Se-CRM and S-CRM have longer bond lengths and larger van der Waals radii that allow them to interact with the π-face of nucleobase G2505, while C-CRM and O-CRM simply don’t reach (Figure 1). The group further confirmed these findings with computational modeling experiments that supported their results from both the bench experiments and the structural data.

This work highlights the extraordinary sensitivity of these interactions to subtle changes of <1 Å in bond length and demonstrates why the arms race against bacteria is so challenging. A game of angströms rather than inches! In the next phase of this research, the group plans to work on blocking and shielding strategies that allow the essential sulfur atom to interact with the π-face of G2505, while providing it with some protection from metabolic enzymes in the liver. – Sandy Field

K.J.Y. Wu¹, E. Aleksandrova², P.J. Robinson¹, A.E. Benedetto¹, M. Yu¹, B.I.C. Tresco¹, D.N.Y. See¹, T. Jiang¹, A. Ramkissoon¹, C.F. Dunand¹, M.S. Svetlov¹, J. Lee¹, Y.S. Polikanov^1,2, A.G. Myers¹, “Why sulfur is important in lincosamide antibiotics,” Chem. 2025, 11, 7, 102480 (2025) https://doi.org/10.1016/j.chempr.2025.102480

Author affiliations: ¹Harvard University; ²University of Illinois Chicago.

We thank Dr. Michael Cameron for the collection of liver microsomal stability data. We thank the staff at NE-CAT beamlines 24-ID-C and 24-ID-E for help with X-ray diffraction data collection, especially Drs. Malcolm Capel, Frank Murphy, Surajit Banerjee, Igor Kourinov, David Neau, Jonathan Schuermann, Narayanasami Sukumar, Anthony Lynch, James Withrow, Kay Perry, Ali Kaya, and Cyndi Salbego. We thank Dr. Alexander Mankin and Dr. Mark Brönstrup for their invaluable insights over the course of our research. This work is based upon research conducted at the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P30-GM124165 to NE-CAT). The Eiger 16M detector on 24-ID-E beamline is funded by an NIH-ORIP HEI grant (S10-OD021527 to NE-CAT). This research used the resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. This work was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (R01-AI168228 to A.G.M. and R21-AI163466 to Y.S.P.), National Institute of General Medical Sciences of the National Institutes of Health (R01-GM132302 and R35-GM151957 to Y.S.P.), the Illinois State startup funds (to Y.S.P.), National Science Foundation (MCB-2345351 to M.S.S.), the Arnold O. Beckman Postdoctoral Fellowship in Chemical Sciences (to P.J.R.), the William F. Milton Fund (to J.L.), Wellcome Leap’s Supported Challenge Program in Quantum for Bio (to P.J.R., T.J., and J.L.). The funders had no role in study design, data collection and analysis, decision to publish, or manuscript preparation.

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