A new high-precision X-ray scattering technique shows location & identity of metal ions in bacteria that are crucial for antibiotics to work optimally

“The success of such a project is dependent on attaining high quality crystals of the protein DNA drug complex” Professor Naomi Chayen Head of the Crystallization Group in Computational and Systems Medicine, Imperial College London

Researchers from Imperial College London, City St George’s, University of London and Diamond have used a new ultra-high precision x-ray scattering technique to unveil the location and identity of metal ions in bacteria that are crucial for antibiotics to work optimally.

Many types of bacteria produce an enzyme molecule called topoisomerase IV, which disentangles and separates newly-replicated DNA in complex structures within bacteria to enable the cells to divide and multiply.

Antibacterial drugs called fluoroquinolones - e.g. delafloxacin – that can kill a wide-range of bacteria ‘seek-out’ magnesium ions and bind to this complex structure. Once bound, the drug exerts its lethal effects by blocking the topoisomerase from working, and ultimately prevents bacterial cells from multiplying.

By using X-ray beams at two defined energies, the team determined the exact location of drug- and enzyme-bound magnesium ions, and in a world-first, they identified the presence of potassium and chloride ions in the enzyme complex.

 "By producing high quality crystals, we managed to observe strong anomalous scattering signals essential for ion identification for a new fluoroquinolone-stabilised topoisomerase complex at Diamond beamline i23." Beijia Wang, Research Postgraduate and first author

The researchers say that this breakthrough could initiate the development of new antibacterial drugs for an array of diseases.

The research, published in PNAS, was performed by Professor Naomi Chayen’s Team (Department of Metabolism, Digestion and Reproduction) in collaboration with City St George’s, University of London and Diamond Light Source. It was co-led by Imperial’s Professor Mark Sanderson and Professor Mark Fisher from St George’s.

Springboard for new advancements

Professor Mark Fisher said: “Many enzymes and important drugs that kill bacteria are dependent on metal ions for their activities. Our breakthrough using X-ray scattering has unveiled metal ion identities and locations more precisely than before and should be the springboard for new advancements in enzymology and drug development.”

This collaborative work provided new insights on the delafloxacin-bound topoisomerase IV of Streptococcus pneumoniae, a bacterium which is the main cause of community-acquired pneumonia and causes other life-threatening diseases including meningitis and sepsis. Pneumococcal pneumonia is prevalent in the young and old and is responsible for around one million deaths worldwide in children under five every year.

The greater understanding of fluoroquinolones, their topoisomerase targets and the role of magnesium, potassium and chloride ions will hopefully aid the design of drugs to counter the growing problem of drug-resistant diseases.

Long-standing collaboration

This work follows a long-standing collaboration between Professor Mark Sanderson, a structural biologist at Imeprial's Department of Metabolism, Digestion and Reproduction and Professor Mark Fisher, who together, have solved the structure of many topoisomerase-drug complexes that are vital for advancing antibacterial drug development.

Professor Mark Sanderson, co-lead of the study at Imperial, said: "This research would not have been possible without bringing together groups at City St George's, Imperial and the Diamond synchrotron with greatly differing expertise to resolve key questions on the catalytic and structural role of ions in DNA topoisomerases."

This research was supported by the Medical Research Council (MRC).

Content for this news item was taken from a City St George’s, University of London press release.

Wang, B., et al. (2024). Experimental localization of metal-binding sites reveals the role of metal ions in type II DNA topoisomerases. Proceedings of the National Academy of Sciences. doi.org/10.1073/pnas.2413357121.