Antibiotics fight bacteria in different ways. Some kill bacteria by destroying their cell walls. Others bind to bacteria’s ribosomes, halting their ability to produce proteins. Over time, bacteria evolved defense mechanisms against these threats. One mechanism is a chemical modification of the ribosome that resembles a push pin on a chair, which interferes with the antibiotic’s ability to bind to its binding site.
Recently a team of scientists synthesized an antibiotic that can engage such modified ribosomes by pushing the “push pin” out of the way, as shown by an X-ray crystallography structural study conducted at the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory. Dubbed BT-33, the novel therapeutic is active against the deadliest and most antibiotic-resistant bacteria, known collectively as ESKAPE pathogens, as well as other gram-negative bacteria, in mice. Designed to attain its binding shape prior to binding, the antibiotic can serve as a powerful model for future antibiotics.
BT-33 belongs to a class of antibiotics called lincosamides, which bind to the ribosome and halt protein production. The primary lincosamide, clindamycin, was so widely used that bacteria developed numerous defenses against them, including acquiring new genes in healthcare settings that rendered lincosamides ineffective. Nevertheless, no new lincosamide has been approved since 1970.
The scientists behind BT-33 set out to fill that void. BT-33 is the third iteration of a molecule the team reported in Nature in 2021, called iboxamycin. It was followed by cresomycin, reported in Science, in 2024. Each iteration involved structural changes to different parts of the molecule that overall improved the molecule’s ability to bind to the ribosome. Each structural change was made possible by inventing new chemical combinations that had never existed before.
Iboxamycin, the first in the series, added a new chemical group at the top end of the clindamycin molecule. That addition alone was enough to enable iboxamycin to accomplish what clindamycin could not: It overcame the defense mechanism produced by the CFR gene.
The CFR gene, first identified in 2000, encodes a protein that installed a modification on the ribosome; much like putting a push pin on a chair, the modification makes it too uncomfortable for the antibiotic to bind. The addition of the chemical group in iboxamycin that is absent from clindamycin resulted in such a strong engagement of the drug with its “chair” that the push pin got moved out of the way.
Cresomycin, the second molecule in the series, was based on a revolutionary design hypothesis called preorganization: The scientists aimed to create a molecule that adopted its shape before binding to its target. To that end, the team added a unique ten-atom ring to the bottom, giving the molecule additional rigidity. Using NMR spectroscopy, they confirmed that the molecule in solution looked exactly the same as if it were already bound to the ribosome, confirming that their design hypothesis worked.
Cresomycin proved so powerful that it overcame the resistance of the six most resistant and dangerous bacteria, collectively given the acronym ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp).
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Image: Structure of BT-33 (yellow) bound to the catalytic center of the bacterial ribosome, showing the van der Waals contact of the fluorine atom (green) of BT-33 with the nucleotides of the ribosomal RNA (cyan).