Antimicrobial peptoids: Investigating the mechanisms of a novel class of therapeutics against the ESKAPE pathogens

The global burden of multidrug resistant bacteria requires the rapid development of alternatives for conventional antibiotics. One group of bacterial pathogens known as the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have been shown to rapidly acquire antibiotic resistance. Antimicrobial peptides (AMPs) are a promising solution in the fight against antibiotic resistant bacteria. These small molecules naturally occur in the innate immune system of nearly all organisms and are potent against many pathogens, including the ESKAPE pathogens. Although extensive research has been done on the therapeutic potential of AMPs, their clinical success has been limited due to their instability and cytotoxicity. Maxwell Biosciences has developed AMP analogues known as peptoids. Peptoids are N-substituted glycine oligomer peptidomimetics, meaning active side chains are linked to a nitrogen backbone instead of a carbon backbone. This change in structure makes them resistant to proteolysis as they can no longer form hydrogen bonds within their main chain. These have been shown to be highly effective at inactivating ESKAPE pathogens, but their exact mechanism is not fully understood. A number of peptoids are currently in development with various modifications to their biochemical structures. Preliminary data has shown that susceptibility to different peptoids varies between bacterial pathogens and even within different strains of the same pathogen. As genetic markers have been linked to antibiotic susceptibility in the ESKAPE pathogens, this project will test the hypothesis that the variable susceptibility to different peptoids is genetically determined. Here, Staphylococcus aureus will be used a model ESKAPE pathogen. Genes that are associated with increased susceptibility to each peptoid will be identified using a Transposon Directed Insertion-site Sequencing (TraDIS) genomic screen. Peptoids can be grouped by their structure and functional group, therefore the generated datasets for each peptoid will be compared to identify genes associated with sensitivity to analogous peptoids. This data will be used to propose genetic markers that can be used to predict how effective peptoids will be against a S. aureus infection. To confirm the identified genetic links between peptoid structure and bacterial sensitivity, knockout mutants with be constructed in an S.aureus strain. To test the peptoids' predicted phenotype, the minimal inhibitory and bactericidal concentration will be determined. Identifying markers of sensitivity to different peptoid structures could help predict which of the peptoids would be most effective against a given pathogen activity and even inform the development of future peptoid structures. This would suggest that peptoid treatment could be tailored to individual clinical infections and lead to an optimal outcome using a precision medicine approach.