A Rationally Designed Antimicrobial Peptide from Structural and Functional Insight of Clostridium difficile Translation Initiation Factor 1

A significant increase of hospital-acquired bacterial infections during the COVID-19 pandemic has become an urgent medical problem. Clostridioides difficile is an urgent antibiotic-resistant bacterial pathogen and a leading causative agent of nosocomial infections. The increasing recurrence of C. difficile infection and antibiotic resistance in C. difficile has led to an unmet need for discovery of new compounds distinctly different from present antimicrobials, while antimicrobial peptides as promising alternatives to conventional antibiotics have attracted growing interest recently. Protein synthesis is an essential metabolic process in all bacteria and a validated antibiotic target. Initiation factor 1 from C. difficile (Cd-IF1) is the smallest of the three initiation factors that acts to establish the 30S initiation complex to initiate translation during protein biosynthesis. Here we report the solution NMR structure of Cd-IF1 which adopts a typical {beta}-barrel fold and consists of a five-stranded {beta}-sheet and one short -helix arranged in the sequential order {beta}1-{beta}2-{beta}3-1-{beta}4-{beta}5. The interaction of Cd-IF1 with the 30S ribosomal subunit was studied by NMR titration for the construction of a structural model of Cd-IF1 binding with the 30S subunit. The short -helix in IF1 was found to be critical for IF1 ribosomal binding. A peptide derived from this -helix was tested and displayed a high ability to inhibit the growth of C. difficile and other bacterial strains. These results provide a clue for rational design of new antimicrobials.