Exploring novel binding pockets in DNA gyrase and DNA topoisomerase IV to address antibiotic resistance
Lead Research Organisation:
University of Leeds
Department Name: Sch of Chemistry
Abstract
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Technical Summary
DNA gyrase is a type II topoisomerase that can supercoil DNA using the free energy of ATP hydrolysis. It is essential in bacteria but lacking from human cells. Its topoisomerase reaction involves the generation of transient double-stranded breaks in DNA. Interruption of the DNA breakage-reunion step of this reaction can lead to a lethal lesion in bacteria. These features have led to gyrase becoming a well-validated target for antibiotics. Most bacteria also contain a related enzyme, DNA topoisomerase IV, which can also be targeted by antibiotics. Fluoroquinolones (FQs), such as ciprofloxacin, target gyrase and topo IV, and have enjoyed widespread clinical success. However, resistance to FQs has become a serious problem and alternatives are urgently needed.
Working with GSK, Sanofi and other partners as part of an EU consortium (ENABLE), we have revealed novel unexploited drug-binding pockets, and compounds (thiophenes and IPYs) that inhibit gyrase and kill bacteria by binding to these pockets. Although the compounds themselves are unlikely to be taken forward to the clinic, this discovery presents us with the opportunity of exploiting these novel pockets to develop new compounds with potential as antibiotics. Using computational modelling methods, new compounds will be designed and synthesised (Leeds). These will be tested in in vitro assays with gyrase and topo IV from key bacterial species (JIC). This information will be fed back to the Leeds team to inform the design of new compounds. Complexes between gyrase/DNA and high-potency compounds will be subject to crystallography to ascertain the binding mode (JIC) and this information will be fed back to the design platform. Such compounds will be further analysed using microbiological assays and preliminary toxicity trials (JIC/Leeds). This programme aims to deliver a fundamental understanding of new drug-binding pockets and new compounds that could be taken forward in the future as potential antibiotics.
Working with GSK, Sanofi and other partners as part of an EU consortium (ENABLE), we have revealed novel unexploited drug-binding pockets, and compounds (thiophenes and IPYs) that inhibit gyrase and kill bacteria by binding to these pockets. Although the compounds themselves are unlikely to be taken forward to the clinic, this discovery presents us with the opportunity of exploiting these novel pockets to develop new compounds with potential as antibiotics. Using computational modelling methods, new compounds will be designed and synthesised (Leeds). These will be tested in in vitro assays with gyrase and topo IV from key bacterial species (JIC). This information will be fed back to the Leeds team to inform the design of new compounds. Complexes between gyrase/DNA and high-potency compounds will be subject to crystallography to ascertain the binding mode (JIC) and this information will be fed back to the design platform. Such compounds will be further analysed using microbiological assays and preliminary toxicity trials (JIC/Leeds). This programme aims to deliver a fundamental understanding of new drug-binding pockets and new compounds that could be taken forward in the future as potential antibiotics.
Publications
Grossman S
(2023)
Developments in Non-Intercalating Bacterial Topoisomerase Inhibitors: Allosteric and ATPase Inhibitors of DNA Gyrase and Topoisomerase IV.
in Pharmaceuticals (Basel, Switzerland)
M Orritt K
(2021)
Exploitation of a novel allosteric binding region in DNA gyrase and its implications for antibacterial drug discovery.
in Future medicinal chemistry
Orritt KM
(2022)
De novo design of type II topoisomerase inhibitors as potential antimicrobial agents targeting a novel binding region.
in RSC medicinal chemistry
| Description | Probing a novel allosteric binding site in Mycobacterium DNA gyrase to tackle TB and antimicrobial resistance |
| Amount | £89,037 (GBP) |
| Funding ID | ST/X508512/1 |
| Organisation | University of Leeds |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2026 |
| Description | Leeds-JIC collaboration |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We provide molecular design and synthetic chemistry expertise to this collaboration. Specifically, we design new molecular scaffolds using our de novo design software that are putative inhibitors of bacterial DNA gyrase and topoisomerase IV. We then synthesise these molecules in the laboratory and send to Professor Anthony Maxwell at the John Innes Centre where they are profiled for inhibition of bacterial DNA gyrases. Together, we aim to investigate a novel, allosteric binding site on bacterial DNA gyrase and provide evidence as to whether it is suitable for further antibiotic development to combat antimicrobial resistance (AMR). |
| Collaborator Contribution | Anthony Maxwell's laboratory provide biochemistry expertise of bacterial topoisomerases such as DNA gyrase and topoisomerase IV. The Maxwell lab profiles our compounds for (i) inhibition of E. coli DNA gyrase in a supercoiling assay (ii) inhibition of E. coli topoisomerase IV (iii) single or double stranded breaks in a cleavage assay (iv) inhibition of bacterial cells. Their lab also provides structural biology expertise, co-crystallising our active molecules in S. aureus DNA gyrase. Together, we aim to investigate a novel, allosteric binding site on bacterial DNA gyrase and provide evidence as to whether it is suitable for further antibiotic development to combat antimicrobial resistance (AMR). |
| Impact | Three publications from our current BBSRC grants (Anthony's BB/V006983/1): 1. Developments in Non-Intercalating Bacterial Topoisomerase Inhibitors: Allosteric and ATPase Inhibitors of DNA Gyrase and Topoisomerase IV', Grossman, S., Fishwick, C.W.G., McPhillie, M.J. Pharmaceuticals, 2023, 16(2), 261. Just Accepted doi:/10.3390/ph16020261. 2. De Novo Design of Type II Topoisomerase Inhibitors as Potential Antimicrobial Agents Targeting a Novel Binding Region', Orritt, K.M, Newell, J.F., Germe, T., Abbott, L.R., Jackson, H.L., Bury, B.K.L., Maxwell, A., McPhillie, M.J.*, Fishwick, C.W.G. RSC Medicinal Chemistry, 2022, doi:/10.1039/D2MD00049K. 3. Exploitation of a novel allosteric binding region in DNA gyrase and its implications for antibacterial drug discovery', Orritt, K.M., Maxwell, A., Fishwick, C.W.G., McPhillie, M.J.*, Future Medicinal Chemistry, 2021, 13(24), 2125-2127. doi: 10.4155/fmc-2021-0266 The collaboration is multi-disciplinary: medicinal chemistry, synthetic chemistry, biochemistry, structural biology. |
| Start Year | 2021 |
| Description | Be Curious 2023 (University of Leeds Public Engagement Event) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Martin McPhillie (grant co-I) developed and led a public engagement stall at the Be Curious event on computer-aided drug design and structural biology. The public are interested in how the next generation of medicines (including antibiotics) will be discovered, how computers can play a role, and we highlighted our work on new inhibitors for DNA gyrase. |
| Year(s) Of Engagement Activity | 2023 |