New X-ray technique reveals role of metal ions in antibiotic effectiveness

Researchers from City St George’s, University of London have used a new ultra-high-precision X-ray scattering technique to reveal 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 untangles and separates newly replicated DNA into complex structures within the bacteria to allow cells to divide and multiply.

Antibacterial medicines called fluoroquinolones – eg delafloxacin – which can kill a wide range of bacteria that “seek” magnesium ions and bind to this complex structure. Once bound, the drug exerts its lethal effects by blocking the action of topoisomerase and ultimately prevents bacterial cell proliferation.

Using X-ray beams at two defined energies, the team determined the exact location of magnesium ions bound to drugs and enzymes, and globally, identified the presence of potassium and chloride ions in the enzyme complex.

The researchers say this discovery could jump-start the development of new antibacterial drugs for a range of diseases.

The research, published in PNASco-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 bacteria-killing drugs depend on metal ions for their activities. Our discovery by X-ray scattering revealed identities and locations of metal ions with greater precision than before and should be the springboard for new advances in enzymology and drug development.”

X-ray scattering investigates the amount of energy produced by metal ions when a beam of X-rays 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 are located in biological structures.

At the Diamond Light Source synchrotron, X-rays from beamline I23 provided new insights into the delafloxacin-bound topoisomerase IV of Streptococcus pneumoniaea bacterium that is the leading cause of community-acquired pneumonia and causes other life-threatening illnesses, including meningitis and sepsis. Pneumococcal pneumonia is common in the young and the elderly and is responsible for approximately one million deaths worldwide in children under the age of five each year.

This greater understanding of fluoroquinolones, their topoisomerase targets and the role of magnesium, potassium and chloride ions will hopefully aid drug design to address the growing problem of drug-resistant disease.”

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-leader 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 very different expertise to resolve fundamental questions about the catalytic and structural role of ions in DNA topoisomerases.”

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