Intrinsically disordered proteins as novel drug targets for antimicrobial therapy

The evolution of drug resistance, particularly in the context of antibiotics, is a fundamental and ever-escalating challenge for global healthcare. Drug resistant pathogens have important implications for patient prognosis in a clinical setting, and are associated with an increased cost of treatment and higher mortality rates[1] . A lack of antibiotics in development with novel mechanisms of action has compounded the emergence of multi-drug resistant infections, and many analogue-based antimicrobial agents become the subject of resistance shortly after their approval to market[2]. This has eroded the current supply of effective therapies for serious infections at a global scale, prompting research into the identification of unique targets for the sustainable development of antibiotics that do not rapidly evolve resistance[3] . Intrinsically disordered proteins (IDPs) contain a low population of hydrophobic amino acids. These biological macromolecules lack a unique three-dimensional structure in their native state in aqueous solution. Although they are the focus of much current research in the fields of bioengineering and medicine – such as neurodegenerative diseases[4] and cancer[5] – IDPs are not typically considered within the framework of antimicrobial resistance (AMR). In this project, bacterial disordered proteins are proposed as a novel linkage to AMR, and the hypothesis that bacterial IDPs are innovative drug targets for antimicrobial therapy is explored.

Leveraging a detailed bioinformatics analysis, putative IDPs in ESKAPEE pathogens that show potential as either (1) resistance factors, (2) antimicrobial drug targets, or (3) targets for antibiotic re-sensitisation are identified. The ESKAPEE pathogens encompass seven highly virulent and resistant bacteria: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli. To further substantiate the relationship between intrinsic disorder and AMR, and to highlight the clinical translatability of this research, small molecule and biologic therapies were designed to inhibit the expression of selected IDPs in vivo. Through the execution of loss-of-function assays, it was demonstrated that inhibiting the expression of specific disordered proteins improves antibiotic efficacy against a laboratory strain of E. coli K12 BW25113. The results from these data-driven investigations (spanning multi-omics, systems biology, and small-scale cell culture experiments) illuminate a previously unexplored relationship between bacterial IDPs and AMR.