title: Interactions of aminoglycoside antibiotics with rRNA.
abstract: Aminoglycoside antibiotics are protein synthesis inhibitors applied to treat infections caused mainly by aerobic Gram-negative bacteria. Due to their adverse side effects they are last resort antibiotics typically used to combat pathogens resistant to other drugs. Aminoglycosides target ribosomes. We describe the interactions of aminoglycoside antibiotics containing a 2-deoxystreptamine (2-DOS) ring with 16S rRNA. We review the computational studies, with a focus on molecular dynamics (MD) simulations performed on RNA models mimicking the 2-DOS aminoglycoside binding site in the small ribosomal subunit. We also briefly discuss thermodynamics of interactions of these aminoglycosides with their 16S RNA target.
authors.affiliation: Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland joanna@cent.uw.edu.pl.
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska
authors.affiliation: Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Marta
authors.initials: M
authors.lastname: Kulik
mesh_terms: D000617:Aminoglycosides / Q000737:chemistry* / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D006595:Hexosamines / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D006595:Hexosamines; D012336:RNA, Ribosomal, 16S; C007265:2-deoxystreptamine
keywords: MD simulations; aminoglycoside antibiotics; electrostatic interactions; molecular docking; rRNA; thermodynamics