Basis for selective drug evasion of an aminoglycoside-resistance ribosomal RNA modification

Aminoglycosides disrupt the fidelity of bacterial protein synthesis, but their potent antibacterial activity is threatened by multiple resistance mechanisms, including methylation of their ribosomal RNA (rRNA) binding site. However, the impact of one such resistance-conferring methylation on N1 of helix 44 nucleotide A1408 (m1A1408) is highly variable with some aminoglycosides retaining significant potency. Here, we examine bacterial susceptibility to diverse aminoglycosides, determine high-resolution electron cryomicroscopy structures of m1A1408-modified 70S ribosome-aminoglycoside complexes, and perform molecular dynamics simulations to decipher the key determinants of such “resistance evasion.” Collectively, these analyses reveal how some aminoglycosides adapt their conformation to accommodate m1A1408, including the roles of specific ring substituents, balancing ligand strain and maintaining favorable interactions, as well as interactions made by additional functional groups that compensate for those disrupted by the modification. This work provides design principles that can guide future rational development of aminoglycosides refractory to resistance conferred by rRNA modifications.