Unique Biological Properties and Molecular Mechanism of 5,6-Bridged Quinolones

Abstract

We have characterized an early series of 5,6-bridged dioxinoquinolones which behaved strikingly different from typical quinolones. The 5,6-bridged dioxinoquinolones inhibited Escherichia coli DNA gyrase supercoiling activity but, unlike typical quinolones, failed to stimulate gyrase-dependent cleavable complex formation. Analogous unsubstituted compounds stimulated cleavable complex formation but were considerably less potent than the corresponding 5,6-bridged compounds. Consistent with a previous report (M. Antoine et al., Chim. Ther. 7:434-443, 1972) and contrary to established quinolone SAR trends, a compound with an N-1 methyl substitution (PGE-8367769) was more potent than its analog with an N-1 ethyl substitution (PGE-6596491). PGE-8367769 was shown to antagonize ciprofloxacin-mediated cleavable complex formation in a dose-dependent manner, suggesting an interaction with the gyrase-DNA complex that overlaps that of ciprofloxacin. Resistance to PGE-8367769 in E. coli was found to arise through missense mutations in gyrA, implicating DNA gyrase as the primary antibacterial target. Notably, only 1 of 15 distinct mutations selected on PGE-8367769 (D87G) has previously been implicated in quinolone resistance in E. coli. The remaining 14 mutations (E16V, G31V, R38L, G40A, Y50D, V70A, A84V, I89L, M135T, G173S, T180I, F217C, P218T, and F513C) have not been previously reported, and most were located outside of the traditional quinolone resistance-determining region. These novel GyrA mutations decreased sensitivity to 5,6-bridged dioxinoquinolones by four-to eightfold, whereas they did not confer resistance to other quinolones such as ciprofloxacin, clinafloxacin, or nalidixic acid. These results demonstrate that the 5,6-bridged quinolones act via a mechanism that is related to but qualitatively different from that of typical quinolones.The recent increase in multiple-drug-resistant bacterial infections has created a critical need to develop novel antibacterial drugs that elude existing mechanisms of resistance. Although the quinolone class is the second largest group of medically important antibacterial drugs, their future utility in the clinic is threatened by the increased rate of emergence of resistant bacteria. Quinolones target two related but functionally distinct and essential type II topoisomerases, DNA gyrase and topoisomerase IV (11,12,22,27). DNA gyrase introduces negative supercoils into DNA and is required to maintain the proper supercoiled state of the chromosome, whereas topoisomerase IV is required to decatenate interlinked replicated chromosomes. DNA gyrase is the primary target of most therapeutic quinolones in gram-negative bacteria, whereas topoisomerase IV is the primary target in gram-positive bacteria (10, 12). A defining feature of the quinolones is their ability to trap a covalent topoisomerase-DNA reaction intermediate termed the cleavable complex. These quinolone-topoisomerase-DNA ternary complexes block both DNA replication and RNA transcription and lead to the formation of lethal double...

Novel Bacterial Topoisomerase Inhibitors with Potent Broad-Spectrum Activity against Drug-Resistant Bacteria

“…Although no mutants were raised during the spontaneous frequency of resistance experiments against the compounds described here, whole-genome sequencing of the E. coli REDX06276 serial passage mutant revealed a single Arg38Leu substitution in the GyrA subunit. This mutation has been reported previously and conferred resistance to 5,6-bridged quinolones but not to other quinolones (36). Similarly, no cross-resistance to ciprofloxacin was found with the E. coli REDX06276 serial passage mutant (see Table S2 in the supplemental material).…”

NBTI 5463 Is a Novel Bacterial Type II Topoisomerase Inhibitor with Activity against Gram-Negative Bacteria and In Vivo Efficacy

“…Other bacterial topoisomerase inhibitors that appear to act on the DNA-bound form of the enzymes have been reported, yet they do not promote double-strand DNA cleavage complex formation. Among the gyramides (33), ES-1273 (34), and 5,6-bridged dioxinoquinolones (35), the last series also displayed slower killing kinetics in E. coli than fluoroquinolones. However, potencies against the topoisomerase IV enzyme were not reported.…”

Simocyclinone D8, an Inhibitor of DNA Gyrase with a Novel Mode of Action

“…There are, however, some similarities between simocyclinone D8 and an early series of 5,6-bridged quinolones, which were recently investigated (23). Like simocyclinone D8, these compounds inhibit gyrase supercoiling but do not stimulate gyrase-dependent cleavable complex formation.…”