(188j) Peptide Nucleic Acid Antibiotics Design and Screening Against Multidrug Resistant Bacteria

Multidrug-resistant (MDR) infections are an urgent global health concern which is exacerbated by a lack of new antibiotics in the pharmaceutical pipeline. Rational design of antibiotics can improve upon current antibiotic screening techniques and quickly create therapies that are specifically targeted to MDR bacteria. Here we develop new classes of antibiotics by targeting non-traditional pathways and genes using peptide nucleic acids (PNAs) which block translation of bacterial RNA via sequence-specific binding. In this study we sought to target PNAs to essential genes in pathways including metabolism, cell signaling, and stress response in MDR clinical isolates of carbapenem-resistant Escherichia coli, extended-spectrum beta-lactamase Klebsiella pneumoniae, New Delhi Metallo-beta-lactamase-1 carrying Klebsiella pneumoniae, and MDR Salmonella enterica. We created a library of 303 PNA sequences—originating from the E. coli essential genes of the Keio collection—and used genome alignment tools to predict which of these PNAs would both avoid incidental non-target inhibition within the E. coli genome and target an analogous gene within the other MDR strains. Additionally, we used a custom sequence analysis tool to select sequences with good solubility and low self-complementarity. The five PNAs used in this study were then selected from that filtered set based on their targeting of the desired essential gene pathways. Though these MDR clinical isolates were found to be resistant to most classes of antibiotics, with genome sequencing revealing as high as sixteen resistance genes, the PNAs we designed were able to potentiate the activity of traditional antibiotics. These findings demonstrate our ability to rationally design and screen PNAs for the treatment of MDR infections by targeting non-traditional antibiotic pathways. Furthermore, our results have far-reaching implications for the control of bacterial protein translation in medical settings as well as in metabolic engineering and other fields.