Researchers at City St George’s, University of London, in collaboration with scientists from Imperial and Diamond Light Source, have employed an innovative ultra-high precision X-ray scattering technique to identify and locate metal ions in bacteria that are vital for the optimal function of antibiotics. This discovery is considered a significant breakthrough that may lead to the development of new antibacterial drugs for various diseases.

Topoisomerase IV, an enzyme produced by many types of bacteria, is responsible for disentangling and separating newly-replicated DNA. This process is crucial for bacterial cell division and multiplication. Antibacterial drugs known as fluoroquinolones, such as delafloxacin, are used to target these bacteria by interacting with magnesium ions. These drugs bind to the enzyme-DNA complex, and once attached, they inhibit the enzyme’s function, thereby preventing bacterial cells from replicating.

Using X-ray beams at two defined energies, the team was able to determine the precise locations of the drug- and enzyme-bound magnesium ions. For the first time, the presence of potassium and chloride ions in the enzyme complex was also identified. The X-ray scattering technique utilized in this research allowed for an unprecedented level of precision, revealing the specific identities and positions of the metal ions involved.

Professor Mark Fisher, from the Neuroscience and Cell Biology Research Institute at City St George’s, University of London, co-led the research along with Professor Mark Sanderson from Imperial. Professor Fisher explained that many bacterial enzymes and antibiotic drugs are dependent on metal ions for their activities. By using X-ray scattering to unveil the identities and locations of these metal ions more precisely than ever before, new advancements in enzymology and drug development can now be pursued.

X-ray scattering is used to investigate the energy released by metal ions when exposed to an X-ray beam. By altering the energy of the beam, different metal ions can be identified based on changes in the energy emitted. This allowed the researchers to reveal not only the magnesium ions but also potassium and chloride ions within the biological structure of the enzyme complex.

The Diamond Light Source synchrotron, using X-rays from the I23 beamline, was utilized to study the delafloxacin-bound topoisomerase IV of Streptococcus pneumoniae. S. pneumoniae is known to be the primary cause of community-acquired pneumonia and other serious diseases, such as meningitis and sepsis. Pneumococcal pneumonia is particularly dangerous to young children and the elderly and is responsible for approximately one million deaths annually in children under five years of age worldwide.

This research builds upon an extensive collaboration between City St George’s, Imperial, and Diamond Light Source. Professor Mark Sanderson from Imperial emphasized that the success of this research was due to the merging of diverse expertise from different institutions. The combined efforts allowed the team to resolve key questions about the catalytic and structural roles of metal ions in bacterial DNA topoisomerases.

The precise identification and localization of metal ions within bacterial enzyme complexes represent a pivotal step toward understanding the mechanisms underlying antibiotic function. These findings are expected to be a springboard for the development of new antibacterial therapies targeting a variety of life-threatening bacterial infections.

Reference:

1. Wang, Beijia, Shabir Najmudin, Xiao-Su Pan, Vitaliy Mykhaylyk, Christian Orr, Armin Wagner, Lata Govada, Naomi E. Chayen, L. Mark Fisher, and Mark R. Sanderson. “Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in Type II DNA Topoisomerases.” Proceedings of the National Academy of Sciences 121, no. 41 (October 3, 2024). https://doi.org/10.1073/pnas.2413357121.

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