Due to the rise of antibiotic resistance, there is a need for discovery of new targets and development of novel drugs. 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. 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. Peptides were chosen as possible drug candidates to target modified H69 because they have reasonable stability and can be easily modified. 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. After four rounds of selection, the sequences of 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 studies such as fluorescent indicator displacement assay, anisotropy and ESI-MS with H69 revealed peptides with moderate affinity. Current studies involve optimization of these peptides for enhanced binding and selectivity for modified H69.

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

248th National Meeting (2014)

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