Mimetic sugar nucleotides to probe a strategic bacterial dehydrogenase enzyme
Lead Research Organisation:
Keele University
Department Name: Faculty of Natural Sciences
Abstract
This work will use exploratory scientific research to help further understand the way that the infectious bacterium and opportunistic pathogen, P. aeruginosa, regulates its own biosynthetic processes. Infections caused by P. aeruginosa are particularly harmful for sufferers of cystic fibrosis and one critical process that this bacterium utilises here is the production of a protective biofilm, which contributes to the ineffectiveness of standard antibiotic treatments used against it. Bacterial biofilm formation processes are governed by enzymes, which control the formation of key biological building blocks for assembly into the more complex, ultimate biofilm system. It is here that organic chemists can use their expertise to build new molecules to mimic the building blocks used by bacteria, effectively creating a molecular tool to investigate and understand a given enzyme mechanism in more detail. The molecular tools needed to do this are called sugar nucleotides and their construction is an intricate, exciting and diverse activity. Using such tools, important new information about enzyme structure and function can be collected, which could contribute towards instigating new approaches to disrupt specific enzyme activity and potentially arrest normal bacterial biofilm development. It is the purpose of this research to initiate an essential, molecular-level understanding of how a critical enzyme-controlled process operates within this pathogen.
Planned Impact
The necessity to successfully treat bacterial infections that can have a debilitating effect on the quality of human life is essential. We as a society rely profoundly upon the advancement of medicine to discover new and effective solutions to address such infections and ensure posterity. Such advances can be aided, in the first instance, by innovative contributions from scientific research within the field of biological chemistry that investigate the basis behind the molecular machinery responsible for bacterial biosynthesis. Ultimately this could instigate a pathway towards new therapeutic targets with the potential to deliver new antibacterial agents. However, before this can happen, synthetic chemists must use their expertise to build molecular tools, capable of probing and trying to understand the mechanisms by which individual pieces of these bacterial biosynthetic machineries operate. This research aims to do just that, through investigating the mechanism of an unexplored, yet pivotal, step in the biosynthesis of the opportunistic pathogen, P. aeruginosa. Beneficiaries of such research within the immediate scientific communities will include: synthetic chemists, enzymologists, bacteriologists, biochemists and structural biologists. Upon delivery of a clearer understanding regarding this process, a broader group of beneficiaries can be envisaged, which could ultimately include the medical and pharmaceutical sectors. The scientific approach described herein will be of significant benefit to the UK chemical biology and biological chemistry footprint, strengthening its presence and international competitiveness within worldwide glycomics research. It will additionally benefit scientific education through increased knowledge and opportunity for the next generation of scientists to evolve their research, based on new understanding.
Publications
Keenan T
(2023)
Reverse thiophosphorylase activity of a glycoside phosphorylase in the synthesis of an unnatural Manß1,4GlcNAc library.
in Chemical science
Dolan JP
(2023)
Virtual screening, identification and in vitro validation of small molecule GDP-mannose dehydrogenase inhibitors.
in RSC chemical biology
Ahmadipour S
(2022)
Synthesis of C6-modified mannose 1-phosphates and evaluation of derived sugar nucleotides against GDP-mannose dehydrogenase.
in Beilstein journal of organic chemistry
Ahmadipour S
(2022)
Sweet targets: sugar nucleotide biosynthesis inhibitors.
in Future medicinal chemistry
Beswick L
(2020)
Inhibition of the GDP-d-Mannose Dehydrogenase from Pseudomonas aeruginosa Using Targeted Sugar Nucleotide Probes.
in ACS chemical biology
Ní Cheallaigh A
(2020)
Chemical synthesis of a sulfated d-glucosamine library and evaluation of cell proliferation capabilities.
in Carbohydrate research
Beswick L
(2020)
Exploring anomeric glycosylation of phosphoric acid: Optimisation and scope for non-native substrates.
in Carbohydrate research
Beswick L
(2019)
Chemical and enzymatic synthesis of the alginate sugar nucleotide building block: GDP-d-mannuronic acid.
in Carbohydrate research
Description | A first series of chemical biology tools for the enzyme under study were created and evaluated. Chemical and enzymatic routes to a diverse series of sugar nucleotide targets were established. In addition, we have now discovered and reported the first ever example of a sugar nucleotide inhibitor for the enzyme under study A PDRA was trained in chemical and enzymatic synthesis alongside developing skills in enzyme assay capability |
Exploitation Route | Antimicrobial strategies against Pseudomonas aeruginosa |
Sectors | Pharmaceuticals and Medical Biotechnology |
Description | Chemoenzymatic approaches to explore polysaccharide structure-property relationships |
Amount | £100,000 (GBP) |
Funding ID | 2508788 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2021 |
End | 01/2025 |
Description | PolyMod: Designer Polysaccharide Modification |
Amount | £100,000 (GBP) |
Funding ID | 2307983 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2019 |
End | 09/2023 |
Description | Small molecules to target large molecules: In silico identification of Pseudomonas aeruginosa GDP-mannose dehydrogenase inhibitors |
Amount | £10,000 (GBP) |
Organisation | Royal Society of Chemistry |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 06/2021 |
End | 07/2022 |
Title | GMD Assay |
Description | GMD assay established to monitor enzyme function and quantify inhibition by tracking NADH readout |
Type Of Material | Technology assay or reagent |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Further funding, further screening of potential inhibitors with new collborators |
URL | https://pubs.acs.org/doi/10.1021/acs.orglett.9b00967 |
Description | Collaboration between Keele University and the John Innes Centre |
Organisation | John Innes Centre |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Chemical synthesis of a series of modified glycosyl 1-phosphates |
Collaborator Contribution | Hosting and training of a PDRA to complete chemoenzymatic synthesis using the glycosyl 1-phosphates and the subsequent assaying of these compounds against the bacterial enzyme target |
Impact | Synthetic chemistry Biological chemistry Enzymology |
Start Year | 2018 |
Description | Collaboration with University of Toronto/Hospital for Sick Kids |
Organisation | University of Toronto |
Country | Canada |
Sector | Academic/University |
PI Contribution | Synthesis and characterisation of sugar nucleotides and small molecules for structural biology studies |
Collaborator Contribution | Structural biology work to obtain crystallographic evidence of protein+ligand (inhibitors) identified through the EPSRC grant |
Impact | None yet |
Start Year | 2021 |
Description | In silico docking work to identify small molecule inhibitors |
Organisation | Hacettepe University |
Country | Turkey |
Sector | Academic/University |
PI Contribution | Structural characterisation and testing of small molecules identified from in silico docking work. this includes a new collaboration "in house" at Keele with Dr Johannes Reynission who has also also contributed in silico studies. |
Collaborator Contribution | In silico identification of GDP-mannose dehydrogenase inhibitors against Pseudomonas aeruginosa from an in-house compound collection |
Impact | None yet |
Start Year | 2021 |