Bacterial Carbonic Anhydrase Inhibitor CAI0019 Demonstrates Efficacy in Enterococcus faecium Septicemic Peritonitis Mouse Model While Sparing the Microbiome

Vancomycin-resistant enterococci are multidrug-resistant bacteria that as of 2021 continue to pervade the U.S. healthcare system as the second-most prevalent source of healthcare-acquired infections behind Escherichia coli. Given the limited treatment options for vancomycin-resistant enterococci and growing concerns about antibiotic-induced gut microbiome dysbiosis, there is an urgent need for narrow-spectrum antibiotics that can selectively target vancomycin-resistant enterococci while preserving the integrity of the gut microbiome. Previous studies have demonstrated the in vivo potential of orally dosed acetazolamide-based compounds to reduce vancomycin-resistant enterococci bioburden in the gastrointestinal tract and internal organs of mice. However, while it is hypothesized that these molecules inhibit bacterial carbonic anhydrases, the exact target of the acetazolamide scaffold in vancomycin-resistant enterococci has remained unconfirmed. Additionally, the impact of the scaffold on in vivo gut microbiome diversity remains uncharacterized. The work herein reports the chemoproteomic identification of α-carbonic anhydrase as the primary target of the acetazolamide scaffold in E. faecium and presents its uniqueness as a narrow-spectrum antibiotic target that can be exploited by CAI0019, a lead acetazolamide derivative with in vivo efficacy, while sparing gut microbiome diversity in mice. This work presents compelling data that not only confirm α-carbonic anhydrase as an antibiotic target in Enterococcus but also demonstrate that narrow-spectrum in vivo antienterococcal efficacy can be achieved through targeting α-carbonic anhydrase such that gut commensal microbiota remain unimpacted.