Berberine analog of chloramphenicol exhibits a distinct mode of action and unveils ribosome plasticity

Chloramphenicol (CHL) is an antibiotic targeting the peptidyl transferase center in bacterial ribosomes. We synthesized a new analog, CAM-BER, by substituting the dichloroacetyl moiety of CHL with a positively charged aromatic berberine group. CAM-BER suppresses bacterial cell growth, inhibits protein synthesis in vitro, and binds tightly to the 70S ribosome. Crystal structure analysis reveals that the bulky berberine group folds into the P site of the peptidyl transferase center (PTC), where it competes with the formyl-methionine residue of the initiator tRNA. Our toe-printing data confirm that CAM-BER acts as a translation initiation inhibitor in stark contrast to CHL, a translation elongation inhibitor. Moreover, CAM-BER induces a distinct rearrangement of conformationally restrained nucleotide A2059, suggesting that the 23S rRNA plasticity is significantly higher than previously thought. CAM-BER shows potential in avoiding CHL resistance and presents opportunities for developing novel berberine derivatives of CHL through medicinal chemistry exploration. [Display omitted] •CAM-BER, berberine analog of chloramphenicol, binds to the 70S ribosome 40-fold stronger•Unlike parent chloramphenicol, CAM-BER inhibits translation initiation•Binding of CAM-BER causes an unseen rearrangement of 23S rRNA nucleotide A2059•CAM-BER is unlikely to induce the most common chloramphenicol resistance genes Here, Batool et al. synthesized a berberine derivative of a well-studied ribosome-targeting antibiotic chloramphenicol, CAM-BER, and showed that this new compound exhibits a distinctly different mode of binding and inhibition of the bacterial ribosome. Unlike other chloramphenicol analogs, CAM-BER is unlikely to induce resistance genes.