Molecular Insights into DNA Cleavage by Novel Bacterial Topoisomerase Inhibitors

Infections with multidrug-resistant bacterial strains place an ever-growing burden on public health. As such, it is imperative that the development of new antibiotics keeps pace with this constantly evolving threat. Novel bacterial topoisomerase inhibitors (NBTIs) represent a promising class of antibacterial that have demonstrated clinical success in targeting the essential bacterial topoisomerase enzymes, DNA gyrase and topoisomerase IV. Conventional models suggest that NBTI treatment induces a buildup of gyrase-mediated single-strand DNA breaks (SSBs) in bacteria, ultimately resulting in cell death. However, the precise mechanism through which NBTIs cause DNA damage remains poorly understood, impeding the rational development of compounds with higher specificity and effectiveness. To address this knowledge gap, we looked to a small subclass of NBTIs that induce both single- and double-strand DNA breaks (DSBs). Using newly resolved DNA gyrase crystal structures bound to DSB-inducing NBTIs as targets, we computationally docked five DSB-inducing and nine SSB-inducing NBTIs to assess their binding interactions. We then conducted extensive molecular dynamics simulations to investigate the binding site interactions that may contribute to different DNA cleavage mechanisms . These insights represent an initial step toward a deeper mechanistic understanding of NBTI function.