Probing a novel allosteric binding site in Mycobacterium DNA gyrase to tackle TB and antimicrobial resistance

Background
Antimicrobial resistance (AMR) undermines the effectiveness of antibiotics. Fluoroquinolones are frontline antibiotics that treat bacterial infections via the inhibition of DNA gyrase. A recently characterised allosteric site on Staphylococcus aureus DNA gyrase offers the potential for the design of allosteric inhibitors of gyrase. Since the allosteric site is distinct from the fluoroquinolone-binding site, allosteric inhibitors can overcome fluoroquinolone resistance observed in the clinic (point mutations in gyrase). The project aims to investigate this allosteric site in Mycobacterium tuberculosis (Mtb) which has been unexplored to date, but has high amino acid conservation compared to the sequence of S. aureus gyrase.
Objectives
1. Use computational techniques and homology modelling to build a structural model of the Mtb allosteric site.
2. Use computational medicinal chemistry to design potent inhibitors of Mtb.
3. Ascertain the mode of action of the allosteric inhibitors: do they bind to the nicked or cleaved DNA complex?
4. Establish synergy of allosteric inhibitors with fluoroquinolones.
Novelty
1.4 million people died of TB in 2019 and bovine TB is a major infectious disease in cattle. Multi-drug resistance (XDR)-TB are strains resistance to nearly all frontline antibiotics. Therefore, new investigations into viable therapeutic targets is required such as this allosteric site.
Timeliness
This work capitalises on our recent discovery of Escherichia coli gyrase allosteric inhibitors with cellular activity against Mtb (MIC90 8 uM). The supervisory team have an established track record in investigating small molecule inhibition of bacterial DNA gyrase. All the methodologies for these studies have been established.
Experimental Approach
The student will be trained in computational medicinal chemistry (to understand protein structure, ligand-protein interactions, computer-aided drug design) and synthetic chemistry. Synthesised molecules will be characterized using a combination of biochemistry and crystallography to ascertain their mode of Mtb gyrase inhibition.