Structure-activity relationships among the kanamycin aminoglycosides: role of ring I hydroxyl and amino groups

Abstract

The kanamycins form an important subgroup of the 4,6-disubstituted 2-deoxystreptamine aminoglycoside antibiotics, comprising kanamycin A, kanamycin B, tobramycin, and dibekacin. These compounds interfere with protein synthesis by targeting the ribosomal decoding A site, and they differ in the numbers and locations of amino and hydroxy groups of the glucopyranosyl moiety (ring I). We synthesized kanamycin analogues characterized by subtle variations of the 2' and 6' substituents of ring I. The functional activities of the kanamycins and the synthesized analogues were investigated (i) in cell-free translation assays on wild-type and mutant bacterial ribosomes to study drug-target interaction, (ii) in MIC assays to assess antibacterial activity, and (iii) in rabbit reticulocyte translation assays to determine activity on eukaryotic ribosomes. Position 2' forms an intramolecular H bond with O5 of ring II, helping the relative orientations of the two rings with respect to each other. This bond becomes critical for drug activity when a 6'-OH substituent is present.

Fig 1

Kanamycin A binding to the bacterial A site. (A) Kanamycin A complexed to the bacterial A site. The neamine core (rings I and II) is shown in yellow, and ring III is shown in gray; 16S rRNA residues are indicated. Note the stacking interaction of the compound's ring I with rRNA residue G1491 and the two hydrogen bonds between ring I and rRNA residue A1408 (N6′-N1 A1408 and O5′-N6 A1408; indicated by the orange dashed lines). The blue dotted lines indicate the hydrogen bonds between C1409 and G1491. (B) Description of contacts between kanamycin A and specific rRNA nucleotides. W, water. The views are based on the crystal structure described previously (13).

Fig 2

Activities of kanamycins on rabbit reticulocyte ribosomes. (Top) Inhibition of luciferase mRNA translation and IC₅₀s (μM) (inset). Conc., concentration. (Bottom) Drug-induced misreading.