Design, Synthesis and Biological Evaluation of Inhibitors for DNA Gyrase and Topoisomerase IV as Novel Antibacterials

Antimicrobial resistance (AMR) poses an existential threat to humanity. By 2050, it is predicted that bacterial superbugs will be responsible for 10 million global deaths annually – more than cancer. Between now and 2050, the cost in terms of lost global production is estimated to cost the world economy $100 trillion if action is not taken. As disease-causing bacteria evolve rapidly, they can evade our existing arsenal of antibiotics through the development of various resistance mechanisms, rendering current therapeutics ineffective. It is imperative that we increase our development and production of new antibiotics to replace those that have already become obsolete. An exciting approach in gaining a foothold for treating infections caused by resistant bacteria is to focus on a recently discovered binding region on DNA gyrase, a well-validated target protein belonging to the topoisomerase family of enzymes. These proteins control how bacteria modulate their DNA ahead of cell division, and disruption of this process results in a bactericidal effect. Using a combination of advanced in silico molecular design methods such as virtual inhibitor docking and de novo design, alongside modern synthetic chemistry techniques, five novel inhibitor families were designed and synthesised as potential antibiotic drug leads. Four of these designs, the biphenyl-, tricyclic-, quinazoline- and pyrazolone-based series, offered significant promise following in vitro evaluations against Escherichia coli DNA gyrase, exhibiting IC50 values in the medium-to-low micromolar range. The most potent of these inhibitors possesses a level of inhibition that is 10-20-fold less than that of the fluoroquinolone-based inhibitors; a class of potent antibiotic drugs used in the clinic that simultaneously target not only DNA gyrase, but another type II topoisomerase: topoisomerase IV. This dual-targeting mechanism means that emergence of resistance to these compounds is therefore slower than more traditional drugs, but ultimately still inevitable. Despite being at a very early stage of discovery, a crucial advantage of our compounds is that they bind to an allosteric site within the protein that is remote of where the fluoroquinolones bind. As such, they are consequently not cross-resistant with them. A second of these inhibitors possesses a moderate equipotency against both gyrase and topoisomerase IV, a characteristic yet to be achieved in novel allosteric inhibitors for this site. Bacteria are yet to evolve any form of resistance in this region, holding great promise for the development of additional weapons to use in humanity’s fight against AMR.