(34a) Rational Design of Peptide Nucleic Acid Antibiotics 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 rapidly design, synthesize, and test antibiotic peptide nucleic acids (PNAs), which can block translation of bacterial RNA via sequence-specific binding. In this study we sought to target PNAs to essential genes 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 sequences of 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 filter for sequences with good solubility and low self-complementarity. The PNAs used in this study were selected from that filtered set based on their targeting of varied essential gene pathways including metabolism, cell signaling, and stress response. 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 and inhibit growth as a monotherapy. Our full process from the design of the PNAs to in-house synthesis to testing can be achieved in 5 days or less, which represents an extremely rapid development in comparison to traditional antibiotics screening. These results demonstrate our ability to quickly and rationally design species-specific therapies for treatment of MDR infections via non-traditional pathways. Furthermore, this technology’s success has far-reaching implications for controlling protein translation in bacterial, viral, and mammalian systems in biopharmaceuticals, metabolic engineering, and other areas.