Designing antibiotics with inherent resistance to efflux as a transformative strategy to revive discovery against multidrug resistant pathogens

We report a novel Efflux Resistance Breaker (ERB) strategy that enables the design of antibiotics with inherent resistance to efflux, using fluoroquinolones as the model antibiotic class. These Efflux Resistance Breaker (ERB)-modified antibiotics maintain high intracellular concentrations resulting in bacterial death, even in the presence of multiple target mutations associated with resistance. The ERB-fluoroquinolones show notably better activity compared to parent fluoroquinolones in a variety of MDR bacteria with up to a 512-fold reduction in MIC (MIC90 0.03 to 2 µg/mL). The lead compounds, KSN-L22 and BL-7, showed MICs of 0.03 to 0.5 µg/mL against methicillin-resistant Staphylococcus aureus (MRSA), and demonstrated potent activity against Streptococcus pneumoniae, including MDR and PRSP isolates, as well as Enterococcus faecalis and Enterococcus faecium, including VanA, VanB and VanD phenotypes, with MICs of 0.125 to 1 µg/mL. They also showed MICs of 0.03 to 2 µg/mL against Acinetobacter baumannii, 0.03 to 2 µg/mL against Escherichia coli and 0.25 to 4 µg/mL against Klebsiella pneumoniae strains. The ERB-fluoroquinolones work by inhibiting both wild type and mutant (GyrA S84L) DNA gyrases (IC50 ~3.8 µg/mL). Both KSN-L22 and BL-7 showed vivo efficacy in a thigh infection model with 5-log reduction of bacterial load at both 20 and 50 mg/kg oral dose levels and excellent oral and IV pharmacokinetic/pharmacodynamic profiles. The compounds did not show any toxicity at 1200 mg/kg/day in mice. The off-target toxicity screen did not reveal any issues, including the hERG channel, and the compounds do not induce or inhibit cytochrome p450 enzymes. ERB technology offers a path to revitalise existing antibiotic classes and expand therapeutic options against resistant infections.