New X-ray technique reveals metal ion role in antibiotic efficacy

Researchers from City St George’s, University of London 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.

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 co-led by Professor Mark Fisher from the Neuroscience and Cell Biology Research Institute at City St George’s, University of London, in collaboration with scientists at Imperial and Diamond Light Source.

Professor Mark Fisher, Professor of Molecular Biology from St George’s School of Health and Medical Sciences at City St George’s, University of London, who co-led the study, 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.”

X-ray scattering investigates the amount of energy produced by metal ions when an X-ray beam is applied. The change in energy released when X-ray beams of different energies are used reveals the identity of different metal ions and where they reside in biological structures.

At the Diamond Light Source synchrotron, X-rays from the I23 beamline 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.

This 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.”

Professor Mark Fisher, Professor of Molecular Biology from St George’s School of Health and Medical Sciences at City St George’s, University of London

This work follows a long-standing collaboration with structural biologist and co-lead Professor Mark Sanderson at Imperial, 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).