Aminoglycoside-hybrid ligands targeting the ribosomal decoding site.

The bacterial ribosome is the primary target for many classes of antibiotics including the aminoglycosides, tetracyclins, macrolides, and oxazolidinones, all of which interact predominantly with ribosomal RNA (rRNA), thereby interfering with cellular protein synthesis. 2] These antibiotics bind selectively to RNA sites that harbor unique sequence signatures that distinguish bacterial from eukaryotic targets. The aminoglycoside antibiotics of the related neomycin B and paromomycin classes, for example, induce translational miscoding by recognizing specifically the bacterial 16S rRNA at the decoding site, which differs by two bases from the eukaryotic sequence (Figure 1). In contrast, the aminoglycoside hygromycin B binds to a site that is conserved among bacteria and eukaryotes, inhibiting protein synthesis indiscriminately in organisms from both lineages. Consequently, hygromycin B, which blocks ribosomal translocation without causing significant miscoding, is toxic to eukaryotes and thus not used in anti-infective therapy. The binding sites of paromomycin and hygromycin B are located immediately adjacent to each other, within helix 44 of 16S rRNA, which plays a key role for mRNA decoding and has been implicated in movements during translocation. X-ray crystallographic studies on the whole ribosomal 30S subunit, individual domains of rRNA, and antibiotic complexes thereof have revealed three-dimensional structures of paromomycin and hygromycin B in complex with their RNA targets. 8,11] Comparison of the individual aminoglycoside complexes shows that the binding sites of paromomycin and hygromycin B are partially overlapping at the position of the U1406·U1495 base pair (Figure 1b, c). Mutations at these residues conferring resistance to either aminoglycoside, in agreement with the structural data, have been described. In this report, we outline an approach to develop novel lead structures based on aminoglycoside-hybrid ligands that were conceived to bridge between the paromomycin and hygromycin B binding sites in helix 44 of bacterial rRNA and thereby potentially interfere with ribosomal function. To obtain such bridging RNA binders, we designed compounds that combined the neamine core moiety of neomycin B, which is known to confer bacterial decoding-site-specific RNA binding, along with substituents at the 1and 6-positions of the 2-deoxystreptamine (2-DOS) ring, which were chosen to project into the hygromycin B binding site (Figure 1c). In the superimposition of the rRNA complexes of paromomycin and hygromycin B, the aminoglycosides overlap at the 2-DOS moieties, which adopt almost identical orientations, shifted by approximately 3 along the RNA helix. Ramakrishnan and co-workers have noted that this displacement corresponds exactly to the distance between neighboring residues in the RNA helix. This observation, along with the wide conservation of the 2-DOS moiety among natural aminoglycosides, emphasizes the role of the 2DOS ring system as a privileged scaffold for RNA recognition. Structural studies on aminoglycoside–RNA complexes have revealed that the 1and 3-amino groups of 2-DOS are predominantly involved in RNA base recognition. The hydroxy groups in the 4-, 5-, and 6-positions are often linked to additional sugar moieties. Many aminoglycosides of the potent neomycin and kanamycin classes of antibiotics carry a glucosamine-based substituent at the 4-position. The minimal aminoglycoside core structure of neamine, consisting of 2-DOS, linked at the 4-position to 2,6-diaminoglucose (Figure 1), interferes with protein synthesis at nanomolar concentration and shows moderate antibacterial potency (Table 1). Removal of the 5-hydroxy group leads to enhanced activity of the resulting 5-deoxyneamine against aminoglycoside-resistant bacteria (Table 1). Since the 2,5-dideoxystreptamine (2,5-dDOS) core of 5-deoxyneamine is readily available, we used it as a starting material for the synthesis of the novel RNA binders described herein (Figure 1d). [a] Dr. D. Vourloumis, G. C. Winters, Dr. K. B. Simonsen, M. Takahashi, Dr. B. K. Ayida Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121 (USA) Fax: (+1)858-527-1540 E-mail : [email protected] [b] S. Shandrick, Dr. Q. Zhao, Dr. Q. Han, Dr. T. Hermann Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121 (USA) Fax: (+1)858-527-1540 E-mail : [email protected] Supporting information for this article is available on the WWW under http://www.chembiochem.org or from the author.