Download MendeleyStructural basis of topoisomerase targeting by delafloxacin.
Najmudin, S., Pan, X.S., Wang, B., Govada, L., Chayen, N.E., Rubio, N., Shaffer, M.S.P., Rzepa, H.S., Fisher, L.M., Sanderson, M.R.(2025) Nat Commun 16: 5829-5829
- PubMed: 40595483
- DOI: https://doi.org/10.1038/s41467-025-60688-3
- Primary Citation of Related Structures:
8C41, 8QMB, 8QMC - PubMed Abstract:
Delafloxacin is a potent anionic fluoroquinolone approved for the treatment of respiratory infections that acts by trapping the DNA cleavage complexes of bacterial topoisomerase IV and gyrase. Its N-1-pyridinyl-, C-7-azetidinyl- and C-8-chlorine substituents confer enhanced antibiotic activity against bacteria resistant to other fluoroquinolones, but its mode of action is unclear. Here we present the X-ray crystal structures of a delafloxacin-DNA cleavage complex obtained by co-crystallization with Streptococcus pneumoniae topo IV using a graphene nucleant and solved at 2.0 and 2.4 Å resolution. The two Mg 2+ -chelated delafloxacin molecules intercalated at the DNA cleavage site are bound in an unusual conformation involving interacting out-of-plane N-1-aromatic- and C-8-chlorine- substituents. The unprecedented resolution allows comprehensive imaging of water-metal ion links integrating enzyme and DNA through drug-bound and active-site Mg 2+ ions plus the discovery of enzyme-bound K + ions. Our studies on delafloxacin action suggest that intrinsic target affinity contributes to its activity against quinolone-resistant bacteria.
- Molecular and Cellular Sciences Section, Neuroscience and Cell Biology Research Institute, City St George's, University of London, Cranmer Terrace, London, UK.
Organizational Affiliation:
