The macrolide-ketolide antibiotic binding site is formed by structures in domains II and V of 23S ribosomal RNA

The macrolide antibiotic erythromycin interacts with bacterial 23S ribosoma l RNA (rRNA) making contacts that are limited to hairpin 35 in domain II of the rRNA and to the peptidyl transferase loop in domain V. These two regio ns are probably folded dose together in the 23S rRNA tertiary structure and form a binding pocket for macrolides and other drug types. Erythromycin ha s been derivatized by replacing the L-cladinose moiety at position 3 by a k eto group (forming the ketolide antibiotics) and by an alkyl-aryl extension at positions 11/12 of the lactone ring. All the drugs footprint identicall y within the peptidyl transferase loop, giving protection against chemical modification at A2058, A2059 and G2505, and enhancing the accessibility of A2062. However, the ketolide derivatives bind to ribosomes with widely vary ing affinities compared with erythromycin. This variation correlates with d ifferences in the hairpin 35 footprints. Erythromycin enhances the modifica tion at position A752. Removal of cladinose lowers drug binding 70-fold, wi th concomitant loss of the A752 footprint. However, the 11/12 extension str engthens binding 10-fold, and position A752 becomes protected. These findin gs indicate how drug derivatization can improve the inhibition of bacteria that have macrolide resistance conferred by changes in the peptidyl transfe rase loop.