Lab rotation project description
In this mini-project of our triangle, you will predict how novel allosteric modulators interact with the intracellular CXCR2 allosteric binding site. CXCR2 is a membrane-bound protein residing at the cell surface which belongs to family A of the G protein-coupled receptors (GPCRs). Allosteric ligands are those that bind to topographically distinct regions of the receptor, relative to the endogenous (orthosteric) ligand binding site. Until now, the development of allosteric ligands for family A GPCRs has focused on extracellular allosteric binding sites that tend to overlap with the orthosteric ligand entry channel at the top of the GPCR. Recently, x-ray crystal structures have been published for a small number of GPCRs (2-adrenoceptor, CCR2 and CCR9 chemokine receptors), which reveal an intracellular binding pocket, targetable by small molecules.
Whilst currently, there is no x-ray crystal structure for the CXCR2, mutagenesis studies have identified a series of residues on the intracellular face of this receptor which affect the binding of three structurally distinct ligands, believed to share a common intracellular binding site.
The aim of this training project will be to use state-of-the-art computational modelling methods to predict the detailed molecular structure of CXCR2 in complex with these ligands. This data will then guide the rational design and synthesis of improved ligands, including fluorescent probes (chemistry rotation). This training project will provide you with experience in:
• computational methods for predicting protein structure (homology modelling)
• computational methods for predicting ligand binding sites (docking, and potentially molecular dynamics)
• use of molecular graphics and modelling methods for ligand design.
This arm of the triangle will be supervised by Professor Charlie Laughton (BSMC, School of Pharmacy). Initially you will build models for the CXCR2 receptor using data from structurally-related proteins whose X-ray structure is known (the technique of homology modelling). The ways in which known and potential new allosteric modulators (from the chemistry arm of the training triangle) might bind to the intracellular allosteric site in these protein models will then be predicted (docking studies and, potentially, molecular dynamics simulations).