Fluorescent Trimethylated Naphthyridine Derivative with an Aminoalkyl Side Chain as the Tightest Non‐aminoglycoside Ligand for the Bacterial A‐site RNA

• Published in: Chemistry : a European journal Vol. 24; no. 52; pp. 13862 - 13870
• Main Authors: Sato, Yusuke, Rokugawa, Masafumi, Ito, Sho, Yajima, Sayaka, Sugawara, Hiroki, Teramae, Norio, Nishizawa, Seiichi
• Format: Journal Article
• Language: English
• Published: Germany Wiley Subscription Services, Inc 18.09.2018
• Subjects: Aminoglycoside antibiotics; Aminoglycosides; Aminoglycosides - chemistry; Anti-Bacterial Agents - chemistry; Antibiotics; Bacteria; bacterial A-site; Binding; Binding Sites; Chains; Chemistry; Decoding; Drug Resistance, Bacterial; E coli; Escherichia coli - chemistry; Fluorescence; fluorescence indicator displacement assay; Fluorescent Dyes - chemistry; Fluorescent indicators; Ligands; Models, Molecular; Molecular interactions; Molecular modelling; Molecular Structure; naphthyridine; Naphthyridines - chemistry; non-aminoglycoside ligand; Nucleic Acid Conformation; Ribonucleic acid; RNA; RNA, Bacterial - chemistry; rRNA; Structure-Activity Relationship; Thermodynamics; tRNA; non-aminoglycoside ligand; fluorescence indicator displacement assay; naphthyridine; fluorescence; bacterial A-site
• ISSN: 0947-6539; 1521-3765
• DOI: 10.1002/chem.201802320

The bacterial ribosomal decoding region of the aminoacyl‐tRNA site (A‐site) is one of the most validated target RNAs for antibiotic agents. Although natural aminoglycosides are well‐characterized A‐site binding ligands, high off‐target effects and the growing emergence of bacterial resistance against aminoglycosides limit their clinical use. To circumvent these concerns with the aminoglycoside family, non‐aminoglycoside A‐site binding ligands have great potential as novel antibiotics against bacterial infections. This work describes a new class of small heterocyclic ligands based on the 2‐amino‐5,6,7‐trimethyl‐1,8‐naphthyridine (ATMND) structure for the bacterial (Escherichia coli) A‐site. ATMND possessing an aminoethyl side chain is found to strongly and selectively bind to the internal loop of the A‐site (Kd=0.44 μm; pH 7.0, I=0.06 m, 5 °C). Significantly, this ligand shows the tightest binding reported to date among non‐aminoglycoside ligands. The binding study based on the thermodynamics and molecular modelling reveals key molecular interactions of ATMND‐C2‐NH2 for high affinity to the A‐site. This ligand is also demonstrated to be applicable to the fluorescence indicator displacement assay for assessing ligand/A‐site interactions. Tight binding to bacterial A‐site: 2‐Amino‐5,6,7‐trimethyl‐1,8‐naphthyridine (ATMND) possessing an aminoethyl side chain was developed as the strong and selective binder to the internal loop of the bacterial A‐site. This ligand shows the tightest binding reported to date among non‐aminoglycoside ligands. Also, this ligand was demonstrated to be applicable to the fluorescence indicator displacement assay for assessing ligand/A‐site interactions.