Design and synthesis of new aminoglycoside antibiotics containing neamine as an optimal core structure: Correlation of antibiotic activity with in vitro inhibition of translation

The structure and activity of the pseudodisaccharide core found in aminogly coside antibiotics was probed with a series of synthetic analogues in which the position of amino groups was varied around the glucopyranose ring. The naturally occurring structure neamine was the best in the series according to assays for in vitro RNA binding and antibiotic activity. With this resu lt in hand, neamine was used as a common core structure for the synthesis o f new antibiotics, which were evaluated for binding to models of the Escher ichia coli 16S A-site ribosomal RNA, in vitro protein synthesis inhibition, and antibiotic activity. Analysis of RNA binding revealed some correlation between the relative affinity and specificity of RNA binding and antibacte rial efficacy. However, the correlation was not linear. This result led us to develop the in vitro translation assay in an effort to better understand aminoglycoside-RNA interactions. A linear correlation between in vitro tra nslation inhibition and antibiotic activity was observed. In addition, IC(5 0)s in the protein synthesis assay were typically lower than the K(d)s Obta ined for RNA binding, suggesting that binding of these compounds to intact ribosomes is tighter in these cases than binding to the model RNA oligonucl eotides. This reflects possible differences in RNA conformation between int act ribosomes and the free RNA of the model system, or possible high-affini ty ribosomal binding sites in addition to the A-site RNA.