Poster abstracts

Poster number 117 submitted by Hyosuk Seo

Peptides targeting modified helix 69 of 23S rRNA in bacterial ribosomes

Hyosuk Seo (Department of Chemistry, Wayne State University, Detroit, MI 48202), Christine S. Chow (Department of Chemistry, Wayne State University, Detroit, MI 48202)

Abstract:
Due to the rise of antibiotic resistance, there is a need for discovery of new targets and development of novel drugs.¹ In this study, we are targeting helix 69 (H69) of 23S ribosomal RNA (rRNA) in E. coli ribosomes with peptides as potential new antibacterial compounds.² This RNA contains highly conserved nucleotides, in addition to three pseudouridine modifications. Helix 69 is located in the 50S subunit of the ribosome, specifically at the interface with the 30S subunit, and plays important roles in translation.³ Peptides were chosen as possible drug candidates to target modified H69 because they have reasonable stability and can be easily modified.⁴ Phage display was performed in order to screen for linear heptapeptides that target H69 under various conditions, such as high and low pH, differing magnesium concentrations, or in the presence of competitor RNAs.⁵ After four rounds of selection, the bound phage were analyzed and several consensus sequences were identified. These peptides were synthesized by using solid-phase synthesis techniques, purified by HPLC, and characterized by MALDI mass spectrometry. Binding assays with H69 revealed peptides with moderate affinity. Future studies will involve optimization of these peptides for enhanced binding and selectivity for modified H69.

References:
1. G. Taubes. The bacteria fight back. Science 2008, 321 (5887), 356.
2. J. Frank, R. K. Agrawal. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 2000, 406 (6793), 318.
3. A. Bakin, J. Ofengand. Four newly located pseudouridylate residues in Escherichia coli 23S Ribosomal RNA are all at the peptidyltransferase center: analysis by the application of new sequencing technique. Biochemistry 1993, 32 (37), 9754.
4. R. B. Merrifield. Solid phase peptide synthesis. I. The synthesis of a tetrapeptide, J. Am. Chem. Soc. 1963, 85, 2149.
5. G. P. Smith. Surface presentation of protein epitopes using bacteriophage expression systems. Curr. Opin. Biotechnol. 1991, 2 (5), 668.

Keywords: Helix 69, Peptides, Phage display