Structural and Mechanistic Insights into Atypical Bacterial Topoisomerase Inhibitors

Novel bacterial topoisomerase inhibitors (NBTIs) targeting DNA gyrase and topoisomerase IV constitute a new antibacterial class for deadly pathogens such as MRSA. While most NBTIs induce gyrase-mediated single-strand DNA breaks, a subset of amide NBTIs induces both single-strand and double-strand DNA breaks. Here, we report the X-ray crystal structures of two such amide NBTIs, <b>148</b> and <b>185</b>, and demonstrate an unusual binding mode characterized by engagement of both GyrA D83 and R122. The synthesis of two isosteric triazole NBTIs is also described, one of which (<b>342</b>) affords only single-strand DNA breaks, while the other (<b>276</b>) also induces both single- and double-strand DNA breaks. A combination of docking and molecular dynamics simulations is employed to further investigate the potential structural underpinnings of differences in DNA cleavage.