Annual Review 2024-2025

D I A M O N D L I G H T S O U R C E L I M I T E D 19 Tearing down bacterial membranes with new antibiotics According to the UN Environment Programme, bacteria resistant to existing antibiotics cause approximately one million deaths each year. Some bacteria, including strains of the gut pathogen Escherichia coli or the lung pathogen Klebsiella pneumoniae, are resistant to multiple antibiotics, limiting treatment options. These bacteria possess two bacterial membranes, the outer of which is studded with fatty carbohydrates called lipopolysaccharides (LPS) that play an essential role in reinforcing the membrane’s integrity. Researchers at Uppsala University in Sweden are designing compound series that obstruct LPS synthesis. They merged a compound previously developed by AstraZeneca with a new compound and found a potent blocker that inhibits an essential enzyme called LpxH by binding to part of the active site. Since this enzyme is conserved in many species, drugs that target it could potentially have broad- spectrum use, much like the cephalosporin drugs used to treat many Gram-negative microbes. Their newly fashioned molecule, which they called JEDI-1444, worked in bacteria with functioning efflux pumps, suggesting it is potent enough to kill bacteria even if they expel some of the compound from the cell. By further refining the compound’s structure, they ended up with two new molecules called EBL-3647 and EBL-3599 bearing corrections that improved the stability and solubility of the compounds and reduced their interactions with serum proteins. Finally, they administered both compounds to mice and found that neither induced side effects, suggesting these compound series might be safe. Testing them out on mice infected with K. pneumoniae showed that a single dose of either compound could partially lower bacterial numbers. Infections with E. coli were more promising: the same treatment cleared the infection to undetectable levels. In the next steps, researchers will continue assessing the compounds’ safety and efficacy with further animal tests and subsequent human trials. DOI: 10.1073/pnas.2317274121 Targeted destruction of disease-related proteins While most conventional drugs work by inhibiting proteins, not all proteins are easy to block in this fashion. Drug developers are investigating new classes of drugs that mark proteins for degradation in the cell. A large, barrel-shaped structure called the proteasome drives this breakdown process, and a protein called Cereblon behaves as an usher, delivering proteins to the proteasome for destruction. Some drugs act as “molecular glue”, sticking to Cereblon and altering its structure so that it binds to target proteins. Other drugs called proteolysis targeting chimeras (PROTACs) bind to target proteins and Cereblon, bridging the two together. Thus, an in-depth understanding of Cereblon’s morphology is crucial for drug investigations. However, scientists have struggled to determine high-resolution structures of this protein in the past due to complications with its synthesis and stability. Researchers from the University of Dundee developed a highly stable, easily purified M A C R OMO L E C U L A R C RY S TA L L O G R A P H Y G R O U P X-ray crystallography experiments at Diamond’s I04-1 beamline revealed that the new compound, JEDI-1444, binds to the LPS- synthesising enzyme in the same place as substrates, suggesting it may interfere with the active site. Image credit: Douglas Huseby; adapted from the PNAS publication in accordance with CC-BY 4.0 license.