Periodic Reporting for period 1 - PyroSuL (Pyrophosphate Surrogates with Low polarity as part of glycosyltransferase ligands)
Période du rapport: 2021-01-01 au 2022-12-31
Glycosilation is an enzymatic process where biomolecules are tagged with carbohydrates. This is a fundamental process for the maturation of every protein our bodies synthetise, or for the signalling tags our cells bear on their surface, which enable them to communicate with the environment. But there is much yet to be discovered and understood about these processes.
What we know is the glycosylation machinery is affected in several diseases. For instance, tumoral cells protect themselves from being attacked by the immune system by modifying their signalling tags on their surface, or to enhance the metastasis development. So it is important to have tools to control this glycosylation machinery to promote or inhibit it according to therapeutical needs when the scope is treating a disease.
For this aim, during the last decades the scientific community has done huge efforts to create new compounds able to control this glycosylation machinery, and one of the possibilities is the development of molecules able to interact with glycosyltransferases, which are the enzymes responsible of glycosylation. However, this is a very challenging task, due to the nature of the natural substrates of these enzymes and the difficulty to design and synthetise molecules with good pharmacological properties to be used as potential therapeutics.
In this context, the objective of this MSCA-IF is designing small molecular fragments that can be used in the preparation of new glycosyltransferase inhibitors with better pharmacological properties that would make them suitable candidates for therapeutic drugs.
What we know is the glycosylation machinery is affected in several diseases. For instance, tumoral cells protect themselves from being attacked by the immune system by modifying their signalling tags on their surface, or to enhance the metastasis development. So it is important to have tools to control this glycosylation machinery to promote or inhibit it according to therapeutical needs when the scope is treating a disease.
For this aim, during the last decades the scientific community has done huge efforts to create new compounds able to control this glycosylation machinery, and one of the possibilities is the development of molecules able to interact with glycosyltransferases, which are the enzymes responsible of glycosylation. However, this is a very challenging task, due to the nature of the natural substrates of these enzymes and the difficulty to design and synthetise molecules with good pharmacological properties to be used as potential therapeutics.
In this context, the objective of this MSCA-IF is designing small molecular fragments that can be used in the preparation of new glycosyltransferase inhibitors with better pharmacological properties that would make them suitable candidates for therapeutic drugs.
Unfortunately, the COVID-19 pandemic had an important effect on the performance of this project. The health authorities in the UK, as well as the University executive, kept all the personnel working from home for the first 6 months of the fellowship. This had an impact not only in my initial steps, but also in the parts of the project done in collaboration with other research groups.
For the most of the 9 first months the work was fundamentally computer based. A comprehensive study of all the human glycosyltransferases (GTs) was carried out, to analyse the common features and how they recognise their substrates. This resulted in the categorisation of all the human GTs in 3 categories, making patent how well conserved the recognition site for the substrates are, specially for the pyrophosphate unit, scope of this project.
Afterwards a comprehensive docking study was performed to identify small molecular fragments that might bind to the pyrophosphate recognition site. Due to the pandemic restrictions, this computational work was extended to develop a reliable methodology to better assess the binding potential of these fragments, based on a double molecular dynamics simulations – docking process (2MD-Dock)
With the most promising candidates, several potential ligands were designed, containing a uridine/guanidine unit to enhance the recognition to the protein, and a 2MD-Dock process was followed to better evaluate the potential biological activity.
When we were able to be back at normal work, the synthetic part of the project was carried out. In order to prepare and evaluate the higher number of ligands in the minimum time, simple synthetic methodologies were developed to obtain reaction crudes pure enough for biological evaluation with NMR, even if the yields are yet to be improved.
The biological evaluation step was also affected by the pandemic situation and fewer human glycosyltrasnsferases were available. Nonetheless, some of the new ligands were successfully evaluated and showed a promising affinity towards the GTs employed, being in some cases in the same order of magnitude as UDP/GDP (a natural substrate) according to competition experiments. Now, purification and further analysis are to be done.
During the fellowship I applied for a permanent position at the University of East Anglia as lecturer in NMR which I successfully secured, being the incorporation to the post the reason for a early termination of the fellowship.
The work done in this project has been presented in different seminars within the University and presented to conferences as the European NMR conference (Euromar) celebrated in the Netherlands and the NMR discussion group meeting in Manchester, both in the summer of 2022.
It is expected that I will publish in peer-review journals at least 3 articles, which due to the lack of time haven’t been prepared yet.
For the most of the 9 first months the work was fundamentally computer based. A comprehensive study of all the human glycosyltransferases (GTs) was carried out, to analyse the common features and how they recognise their substrates. This resulted in the categorisation of all the human GTs in 3 categories, making patent how well conserved the recognition site for the substrates are, specially for the pyrophosphate unit, scope of this project.
Afterwards a comprehensive docking study was performed to identify small molecular fragments that might bind to the pyrophosphate recognition site. Due to the pandemic restrictions, this computational work was extended to develop a reliable methodology to better assess the binding potential of these fragments, based on a double molecular dynamics simulations – docking process (2MD-Dock)
With the most promising candidates, several potential ligands were designed, containing a uridine/guanidine unit to enhance the recognition to the protein, and a 2MD-Dock process was followed to better evaluate the potential biological activity.
When we were able to be back at normal work, the synthetic part of the project was carried out. In order to prepare and evaluate the higher number of ligands in the minimum time, simple synthetic methodologies were developed to obtain reaction crudes pure enough for biological evaluation with NMR, even if the yields are yet to be improved.
The biological evaluation step was also affected by the pandemic situation and fewer human glycosyltrasnsferases were available. Nonetheless, some of the new ligands were successfully evaluated and showed a promising affinity towards the GTs employed, being in some cases in the same order of magnitude as UDP/GDP (a natural substrate) according to competition experiments. Now, purification and further analysis are to be done.
During the fellowship I applied for a permanent position at the University of East Anglia as lecturer in NMR which I successfully secured, being the incorporation to the post the reason for a early termination of the fellowship.
The work done in this project has been presented in different seminars within the University and presented to conferences as the European NMR conference (Euromar) celebrated in the Netherlands and the NMR discussion group meeting in Manchester, both in the summer of 2022.
It is expected that I will publish in peer-review journals at least 3 articles, which due to the lack of time haven’t been prepared yet.
The preliminary results from this project will have an important impact withing the glycobiology community as it opens a new door for the development of glycosyltransferases inhibitor with better pharmacological properties and enhanced therapeutic potential.