Targeting MarA to Inhibit Efflux

ended

Antibiotic resistance is a growing global crisis and current predictions suggest that by 2050 drug resistant bacteria will cause up to 10 million deaths a year globally. Bacteria employ many mechanisms to become resistant to antibiotics. One important mechanism is antibiotic efflux where membrane bound efflux pumps actively pump molecules, including antibiotics, out of bacterial cells. The RND-family AcrAB efflux pump confers multi-drug resistance in many Gram-negative bacteria including Escherichia coli and is commonly over-produced in antibiotic resistant clinical isolates. Regulation of RND efflux pump expression is complex but in E. coli the master regulator is the AraC/XylS family global transcription factor MarA. In spite of its relevant role up to now no inhibitor targeting this protein has been published. In this project we aim to develop efflux inhibitors that prevent transcription of acrAB by inhibiting MarA and to test their efficacy by measuring AcrAB expression and activity. In order to design the inhibitors we will analyse MarA structure and its direct DNA interactions based on available crystal structures. We will design oligonucleotides acting as a transcriptional factor decoy that modulate transcription by sequestering MarA from their endogenous DNA binding sites (RO1). We will also design peptides acting as inhibitors by blocking DNA-MarA interactions (RO1). Nextly we will measure the affinity of the inhibitor-MarA complexes by in vitro biochemical assays (RO2) and in vivo experiments (RO3). In RO4, we will crystallize the most promising inhibitor-MarA complexes in order to improve their efficacy after structure analysis. Successful development of these inhibitors will open an avenue in the fight against antibiotic resistance conferred by increased efflux pump activity. Training in efflux pumps to complement her existing skills in protein structure analysis will position the ER as a future research leader in the antibiotic resistance field.