Structure-Based Design and Synthesis of Apramycin–Paromomycin Analogues: Importance of the Configuration at the 6′-Position and Differences between the 6′-Amino and Hydroxy Series

• Published in: Journal of the American Chemical Society Vol. 139; no. 41; pp. 14611 - 14619
• Main Authors: Mandhapati, Appi Reddy, Yang, Guanyu, Kato, Takayuki, Shcherbakov, Dimitri, Hobbie, Sven N, Vasella, Andrea, Böttger, Erik C, Crich, David
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 18.10.2017; Amer Chemical Soc
• Subjects: Anti-Bacterial Agents - chemical synthesis; Anti-Bacterial Agents - chemistry; antibacterial properties; Chemistry; Chemistry, Multidisciplinary; diastereomers; Gram-positive bacteria; moieties; Nebramycin - analogs & derivatives; Nebramycin - chemical synthesis; Nebramycin - chemistry; neomycin; Neomycin - analogs & derivatives; Paromomycin - analogs & derivatives; Paromomycin - chemical synthesis; pathogens; Physical Sciences; ribosomes; Ribosomes - metabolism; Science & Technology; therapeutics; translation (genetics); RIBOSOMAL-RNA METHYLATION; ANTIBACTERIAL ACTIVITY; DRUG DISCOVERY; A-SITE; CRYSTAL-STRUCTURES; BACTERIAL-RESISTANCE; ACUTE TOXICITY; MITOCHONDRIAL 1555A-GREATER-THAN-G MUTATION; AMINOGLYCOSIDE ANTIBIOTICS; CARBOXYLIC-ACIDS
• ISSN: 0002-7863; 1520-5126; 1520-5126
• DOI: 10.1021/jacs.7b07754

The preparation of a series of four analogues of the aminoglycoside antibiotics neomycin and paromomycin is described in which ring I, involved in critical binding interactions with the ribosomal target, is replaced by an apramycin-like dioxabicyclo[4.4.0]­octane system. The effect of this modification is to lock the hydroxymethyl side chain of the neomycin or paromomycin ring I, as part of the dioxabicyclooctane ring, into either the gauche–gauche or the gauche–trans conformation (respectively, axial or equatorial to the bicyclic system). The antiribosomal activity of these compounds is investigated with cell-free translation assays using both bacterial ribosomes and recombinant hybrid ribosomes carrying eukaryotic decoding A site cassettes. Compounds substituted with an equatorial hydroxyl or amino group in the newly formed ring are considerably more active than their axial diastereomers, lending strong support to crystallographically derived models of aminoglycoside–ribosome interactions. One such bicyclic compound carrying an equatorial hydroxyl group has activity equal to that of the parent yet displays better ribosomal selectivity, predictive of an enhanced therapeutic index. A paromomycin analog lacking the hydroxymethyl ring I side chain is considerably less active than the parent. Antibacterial activity against model Gram negative and Gram positive bacteria is reported for selected compounds, as is activity against ESKAPE pathogens and recombinant bacteria carrying specific resistance determinants. Analogues with a bicyclic ring I carrying equatorial amino or hydroxyl groups mimicking the bound side chains of neomycin and paromomycin, respectively, show excellent activity and, by virtue of their novel structure, retain this activity in strains that are insensitive to the parent compounds.