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The tightest non-aminoglycoside ligand for the bacterial ribosomal RNA A-site

A research group at Tohoku University has made a significant discovery with positive implications for the development of bacteria fighting drugs. The aminoacyl-tRNA site (A-site) of the 16S RNA decoding region in the bacterial ribosome looks promising for a new era of antibiotic drug development.

Traditional aminoglycoside antibiotics are problematic given their high toxicity and the potential for resistance development. The research at Tohoku University focused on bacterial A-site binding small ligands whose structures are distinct from the aminoglycoside family, which offer potential for the development of novel drugs that treat bacterial infections with a reduction in the problems associated with traditional antibiotics.

The research group led by Dr. S. Nishizawa and Dr. Y. Sato (Department of Chemistry, Graduate School of Science) has reported a novel small ligand, ATMND-C2-NH2 that has the tightest binding affinity for the bacterial A-site among the non-aminoglycoside ligands.

ATMND-C2-NH2 shows a significant fluorescent quenching response upon selective binding to the internal loop of the bacterial (Escherichia coli) A-site-containing model RNA.
ATMND-C2-NH2 has also proven useful as an indicator for assessing ligand/A-site interactions.

The results obtained by the research group offer a rational basis for the generation of novel A-site binding ligands with a view toward novel antibiotics with less toxicity and minimum resistance development.


Chemical structure of ATMND-C2-NH2 and sequence of the bacterial (Escherichia coli) A-site-containing RNA model used in this study. It also shows the possible structure of the complex between ATMND-C2-NH2 (green color) and internal loop of A-site.
Copyright: Seiichi Nishizawa

Publication Details:
Title: Fluorescent trimethylated naphthyridine derivative with an aminoalkyl side chain as the tightest non-aminoglycoside ligand for the bacterial A-site RNA
Authors: Yusuke Sato, Masafumi Rokugawa, Sho Ito, Sayaka Yajima, Hiroki Sugawara, Norio Teramae and Seiichi Nishizawa
Journal: Chemistry-An European Journal
DOI: 10.1002/chem.201802320
Embargo date: 18th Sep 2018

Yusuke Sato
Department of Chemistry, Graduate School of Science, Tohoku University
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