Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site

Paromomycin is an aminoglycosidic antibiotic that targets the RNA of the bacterial small ribosomal subunit. It binds in the A-site, which is one of the three tRNA binding sites, and affects translational fidelity by stabilizing two adenines (A1492 and A1493) in the flipped-out state. Experiments have shown that various mutations in the A-site result in bacterial resistance to aminoglycosides. In this study, we performed multiple molecular dynamics simulations of the mutated A-site RNA fragment in explicit solvent to analyze changes in the physicochemical features of the A-site that were introduced by substitutions of specific bases. The simulations were conducted for free RNA and in complex with paromomycin. We found that the specific mutations affect the shape and dynamics of the binding cleft as well as significantly alter its electrostatic properties. The most pronounced changes were observed in the U1406C∶U1495A mutant, where important hydrogen bonds between the RNA and paromomycin were disrupted. The present study aims to clarify the underlying physicochemical mechanisms of bacterial resistance to aminoglycosides due to target mutations. Author Summary: In hospitals throughout the world, aminoglycosidic antibiotics are used to combat even the most severe bacterial infections. However, the continuous emergence of resistant bacteria has created an urgent need to improve these antibiotics. Aminoglycosides bind to bacterial ribosomal RNA. Experiments have shown that specific point mutations in the RNA confer high resistance against aminoglycosides in bacteria. We performed molecular dynamics simulations of the aminoglycosidic binding site model after introducing various mutations. Here, we show that even single nucleotide substitutions can significantly change the physicochemical features of the binding site. In addition, we hypothesize why certain mutations result in bacterial resistance to aminoglycosides.