title: Macrolide-ketolide inhibition of MLS-resistant ribosomes is improved by alternative drug interaction with domain II of 23S rRNA.
abstract: The macrolide antibiotic erythromycin and its 6-O-methyl derivative (clarithromycin) bind to bacterial ribosomes primarily through interactions with nucleotides in domains II and V of 23S rRNA. The domain II interaction occurs between nucleotide A752 and the macrolide 3-cladinose moiety. Removal of the cladinose, and substitution of a 3-keto group (forming the ketolide RU 56006), results in loss of the A752 interaction and an approximately 100-fold drop in drug binding affinity. Within domain V, the key determinant of drug binding is nucleotide A2058 and substitution of G at this position is the major cause of drug resistance in some clinical pathogens. The 2058G mutation disrupts the drug-domain V contact and leads to a further > 25 000-fold decrease in the binding of RU 56006. Drug binding to resistant ribosomes can be improved over 3000-fold by forming an alternative and more effective contact to A752 via alkyl-aryl groups linked to a carbamate at the drug 11/12 position (in the ketolide antibiotics HMR 3647 and HMR 3004). The data indicate that simultaneous drug interactions with domains II and V strengthen binding and that the domain II contact is of particular importance to achieve binding to the ribosomes of resistant pathogens in which the domain V interaction is perturbed.
authors.affiliation: Department of Molecular Biology, Odense University, DK-5230 Odense M, Denmark. srd@molbiol.ou.dk
authors.forename: S
authors.initials: S
authors.lastname: Douthwaite
authors.forename: L H
authors.initials: LH
authors.lastname: Hansen
authors.forename: P
authors.initials: P
authors.lastname: Mauvais
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001483:Base Sequence; D001665:Binding Sites; D017291:Clarithromycin / Q000494:pharmacology; D004347:Drug Interactions; D004352:Drug Resistance, Microbial; D004917:Erythromycin / Q000031:analogs & derivatives*; D004926:Escherichia coli / Q000187:drug effects; D048628:Ketolides; D018942:Macrolides; D008826:Microbial Sensitivity Tests; D008969:Molecular Sequence Data; D009154:Mutation; D011500:Protein Synthesis Inhibitors / Q000494:pharmacology*; D012338:RNA, Ribosomal, 23S / Q000187:drug effects* / Q000235:genetics; D012270:Ribosomes / Q000187:drug effects* / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D048628:Ketolides; D018942:Macrolides; D011500:Protein Synthesis Inhibitors; D012338:RNA, Ribosomal, 23S; C118442:RU 56006; C105420:RU 64004; D004917:Erythromycin; D017291:Clarithromycin; C106791:telithromycin