Discovery of a Tri-substituted Furan Antibacterial That Is More Active against Quinolone-resistant DNA Gyrase Than Wild-type

Background: Bacterial DNA gyrase is the clinically-validated antibacterial target of quinolone antibiotics. However, clinical resistance to quinolones has become common in many bacterial pathogens. Here, we report the discovery of a novel class of DNA gyrase inhibitor that is more potent against quinolone-resistant isolates.

Methods: Gyrase supercoiling and DNA cleavage assays were employed to identify gyrase inhibitors. Macromolecular synthesis (MMS) and spontaneous resistant mutant isolation were used to confirm antibacterial mode of action.

Results: We identified a tri-substituted furan from the output of an E. coli IVR (in vitro replication) HTS of the GSK compound collection. It showed supercoiling inhibition (IC₅₀ of ~10 uM) and induced both single- and double-stranded DNA cleavage with E. coli gyrase. Antibacterial profiling of the tri-substituted furan gave MIC of 2 – 8 ug/ml against common Gram-positive pathogens as well as efflux mutants of several Gram-negative pathogens. Strikingly, it had significantly more potent MIC against quinolone-resistant MRSA than quinolone-sensitive isolates (MIC₉₀ of 0.06 vs 4 ug/ml, respectively). Using S. aureus isogenic mutants we showed a 16-fold hypersensitivity to the tri-substituted furan in an isolate carrying the GyrA S84L mutation compared to its parent. This was confirmed at the enzyme level as the tri-substituted furan was 10 times more potent against E. coli gyrase carrying the corresponding GyrA mutation than the wild type (wt) gyrase. MMS analysis showed that the tri-substituted furan specifically inhibited DNA synthesis in S. aureus wt and GyrA S84L mutant strains. Spontaneous mutants resistant to the tri-substituted furan were isolated from a S. aureus quinolone-resistant isolate and mutations were mapped to GyrA confirming the antibacterial mode of action is via inhibition of DNA gyrase.

Conclusion: We clearly demonstrated that the tri-substituted furan is a more potent inhibitor of gyrase containing a common quinolone-resistant mutation than wt gyrase resulting in more potent MICs against clinical quinolone-resistant isolates. This novel class of DNA gyrase inhibitor warrants further study to determine the potential to combat clinical resistance to quinolones when combined with a quinolone antibiotic.