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

From Fragment to Lead: A Structure-Guided Approach Towards a Selective FGFR2 Inhibitor

Fibroblast growth factor receptors (FGFRs) are implicated in a range of cancers with several pan-kinase and selective-FGFR inhibitors currently being evaluated in clinical trials for FGFR-implicated malignancies. Pan-FGFR inhibitors often cause toxic side-effects via off-target inhibition and very few examples of subtype-selective inhibitors exist. Herein, we describe a structure-guided approach towards the development of a selective FGFR2 inhibitor. De novo design was carried out on an existing fragment series that exhibited moderate sub-micromolar activity against FGFRs 1–3. Subsequent synthesis, biological evaluation, and iterative rounds of SBDD led to an inhibitor with nM potency that exhibited moderate selectivity for FGFR2 over FGFR1/3. Subtle changes to the lead inhibitor resulted in a complete loss of selectivity for FGFR2. Subsequent X-ray crystallographic studies revealed significant morphological differences in the P-loop flanking the ATP-binding pocket which appeared to be determined by which inhibitor was bound. It was posited that this dynamic phenomenon was fundamental to the selectivity of these compounds and complementary to current theories surrounding sub-type FGFR2 selectivity. In addition, several derivatives exhibited low µM potency against FGFR1/2-activated cell lines and underlined the potential of these compounds for development into medicines for the treatment of FGFR-driven cancers

De Novo Design of Type II Topoisomerase Inhibitors as Potential Antimicrobial Agents Targeting a Novel Binding Region

By 2050 it is predicted that antimicrobial resistance will be responsible for 10 million global deaths annually, costing the world economy $100 trillion. Clearly, strategies to address this problem are required as bacterial evolution is rendering our current antibiotics ineffective. The discovery of an allosteric binding site on the established antibacterial target DNA gyrase offers a new medicinal chemistry strategy, as this site is distinct from the fluoroquinolone-DNA site binding site. Using in silico molecular design methods, we have designed and synthesised a novel series of biphenyl-based inhibitors inspired by the published thiophene allosteric inhibitor. This series was evaluated in vitro against E. coli DNA gyrase, exhibiting IC50 values in the low micromolar range. The structure-activity relationship reported herein suggests insights to further exploit this allosteric site, offering a pathway to overcome fluoroquinolone resistance