From Fragment-screening to Fragment-growing - new strategies for drug discovery
Type-2 diabetes represents a major health problem in particular in industrialised countries and although many cases may be preventable by lifestyle changes, numbers are steadily rising. Human Glucose Kinase (GK) has been identified as one potential target for intervention but so far no drug targeting GK has been found. In this project we will employ and develop fragment-based methods to identify new lead compounds.
Background: Type-2 diabetes, also known as adult-onset diabetes is the most common form of this disease affecting between 150 and 400 million people worldwide. Although largely preventable by maintaining a normal weight and regular exercise, case numbers are expected to rise due to modern lifestyles and working practices. Hence, improved therapies for treatment and support of the necessary life-style changes are needed. Human Glucokinase, which catalyses the phosphorylation of glucose to glucose-6-phosphate has been identified as the key control point in the liver and pancreas for glucose homeostasis as glucose-6- phosphate is the entry point for both, glycolysis and glycogen synthesis. As both pathways reduce the glucose concentration, glucose kinase activators have recently been recognised as potential means to counterbalance the glycemic imbalance associated with type-2 diabetes.
Over the last decade fragment-based methods have made a major impact on drug discovery in academia and pharmaceutical research. Recent advances in high-throughput structure determination and the development of targeted fragment libraries were instrumental, however, one of the remaining bottlenecks is the translation from multiple fragment binding sites into a credible lead compound.
Objectives: The overall goal of the proposed project is to identify new chemical entities that act as allosteric activators of human GK and present lead candidates for future drug development using a new fragment-based drug discovery approach. These efforts will be supported with the expertise from CCDC to develop new algorithms to support fragment-linking and growing approach.
Expression of isoforms of glucokinases from human liver cells and beta cells in recombinant systems has already been established. After expression and purification, these enzymes will be characterised by biophysical and biochemical techniques. Crystals for fragment-based screening will be tested synchrotron sources.
In order to develop fragment hits into ligands, hits need to be chemically linked based on the conformation and the location on the target protein. In this work package we will develop a new strategy of fragment growing based on data base searches within the Cambridge Structural Database (CSD) which currently contains over 1 million 3-dimensional structures of organic and metal-organics compounds. This part of the project will be done in close collaboration with Dr. F. Stanzione from the CCDC. Any hits will inform the synthetic strategy to link fragments. Chemical synthesis of new compounds will be performed in the laboratories of our project partner, Prof. C. Cano in Newcastle.
Ligand validation – Any promising ligands will be verified in Durham by biochemical, biophysical and structural techniques in order to optimize design strategies.
Training & Skills
- Molecular biology, protein expression in recombinant systems
- Protein purification and quality control
- Crystallisation, X-ray crystallography
- Diffraction data collection
- Fragment-based screening
- Information retrieval from structural databases
- Molecular Modelling and Docking
- Python programming and/or
- Organic synthesis (depending on the candidate and the evolving collaboration)
- Biophysical techniques to investigate proteinligand and protein-protein interactions
Dr Ehmke Pohl
[Email Address Removed]
+44 (0) 191 33 43619
How to Apply
To apply for this project please visit the Durham University application portal to be found at: https://www.dur.ac.uk/study/pg/apply/
Please select the course code F1A201 for a PhD in Molecular Sciences for Medicine and indicate the reference MoSMed20-10 in the ‘Field of Study’ section of the application form.
Should you have any queries regarding the application process at Durham University please contact the Durham MoSMed CDT Manager, Emma Worden at: [Email Address Removed]