Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome

• Published in: Nature communications 2023-08, Vol.14 (1), p.4666-12, Article 4666
• Main Authors: Seely, Savannah M., Parajuli, Narayan P., De Tarafder, Arindam, Ge, Xueliang, Sanyal, Suparna, Gagnon, Matthieu G.
• Format: Article
• Language: English
• Subjects: 101/28; 631/337/574/1789; 631/45/500; 631/535/1266; 631/57/2272/1590; 631/92/613; Amikacin; Amikacin - chemistry; Amikacin - metabolism; Amikacin - pharmacology; Aminoglycosides; Anti-Bacterial Agents - chemistry; Antibiotic resistance; Antibiotics; Bacteria; Binding sites; Biochemistry; Biokemi; Biologi med inriktning mot molekylärbiologi; Biologi med inriktning mot strukturbiologi; Biology with specialization in Molecular Biology; Biology with specialization in Structural Biology; Crystallography; Gram-negative bacteria; Humanities and Social Sciences; Kanamycin; Kanamycin - analysis; Kanamycin - metabolism; Kanamycin - pharmacology; Kinetics; Models, Molecular; multidisciplinary; Multidrug resistance; peptide release; ribosome; ribosome recycling; Ribosomes - metabolism; RNA, Transfer - metabolism; rRNA; Science; Science & Technology - Other Topics; Science (multidisciplinary); Transfer RNA; translation; Translocation; tRNA; tRNA translocation; X-ray crystallography
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-40416-5

Aminoglycosides are a class of antibiotics that bind to ribosomal RNA and exert pleiotropic effects on ribosome function. Amikacin, the semisynthetic derivative of kanamycin, is commonly used for treating severe infections with multidrug-resistant, aerobic Gram-negative bacteria. Amikacin carries the 4-amino-2-hydroxy butyrate (AHB) moiety at the N 1 amino group of the central 2-deoxystreptamine (2-DOS) ring, which may confer amikacin a unique ribosome inhibition profile. Here we use in vitro fast kinetics combined with X-ray crystallography and cryo-EM to dissect the mechanisms of ribosome inhibition by amikacin and the parent compound, kanamycin. Amikacin interferes with tRNA translocation, release factor-mediated peptidyl-tRNA hydrolysis, and ribosome recycling, traits attributed to the additional interactions amikacin makes with the decoding center. The binding site in the large ribosomal subunit proximal to the 3’-end of tRNA in the peptidyl (P) site lays the groundwork for rational design of amikacin derivatives with improved antibacterial properties. Here the authors use fast kinetics, X-ray crystallography, and cryo-EM to uncover the mechanism of ribosome inhibition by amikacin and kanamycin. They find that amikacin binds near the P-site tRNA, offering new strategies to fight antibiotic resistance.