Macrolide-ketolide inhibition of MLS-resistant ribosomes is improved by alternative drug interaction with domain II of 23S rRNA

The macrolide antibiotic erythromycin and its 6-O-methyl derivative (clarit hromycin) bind to bacterial ribosomes primarily through interactions with n ucleotides in domains II and V of 23S rRNA. The domain II interaction occur s 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 approximate to 100-f old 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 mu tation disrupts the drug-domain V contact and leads to a further > 25 000-f old decrease in the binding of RU 56006. Drug binding to resistant ribosome s can be improved over 3000-fold by forming an alternative and more effecti ve 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 dat a indicate that simultaneous drug interactions with domains II and V streng then 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.