Antimicrobial peptides of the apidaecin family inhibit the bacterial ribosome by multimodal mechanisms involving three different sites on the large ribosomal subunit

Proline-rich antimicrobial peptides (PrAMPs) inhibit bacterial ribosomes by binding to the polypeptide exit tunnel (PET) near the peptidyl transferase center. Api137, an optimized derivative of honeybee apidaecin, traps the release factor (RF) at the ribosome, thereby arresting the ribosomes at stop codons. This study shows that Api137 occupies a second binding site near the exit of the PET and represses protein translation independently of RF1-trapping. Api88, the C-terminally amidated (-CONH2) analog of Api137 (-COOH), binds in a slightly shifted manner to the same regions without RF trapping, presumably by interfering with the translation process. Api88 also binds to a pocket deep within domain III of the 23S rRNA. In conclusion, Api88 and Api137 inhibit ribosomes through different multimodal mechanisms. These mechanisms have likely reduced the emergence of bacterial resistance and contributed to the evolutionary success of this structurally diverse group of PrAMPs, providing a promising pool for drug development efforts.