Narrow-Spectrum Oxadiazole Antibacterials that Target Cell−Wall Septation in Clostridioides difficile and Spare the Gut Microbiota

Abstract Recurrence of infection is a challenge in treatment of Clostridioides difficile infection (CDI), observed in 25% of patients. The first-line antibiotics disturb the gut microbiota, exacerbating the already disrupted commensal gut homeostasis and allow for C. difficile colonization. Narrow-spectrum antibiotics are critical for selective targeting of C. difficile while preserving beneficial gut flora, thereby mitigating recurrence. Our study investigates a novel class of highly selective, nitroimidazole-based oxadiazole antibacterials. We detail the chemical basis for their exceptional selectivity against C. difficile over commensal bacteria and elucidate their mechanism of action. Oxadiazole 2 inhibits penicillin-binding proteins 1 and 3 involved in septal peptidoglycan biosynthesis during vegetative cell division. We further demonstrate by whole-genome sequencing that treatment of mice with oxadiazole 2 does not disrupt the gut microflora and confers an impediment to colonization by C. difficile. This work is foundational for development of a new generation of narrow-spectrum therapeutics to combat CDI.