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Molecular Modelling of P2X receptor agonism and antagonism

Primary Supervisor: Dr Ralf Schmid, Department of Molecular and Cell Biology

PhD project title: Molecular Modelling of P2X receptor agonism and antagonism

University of Registration: University of Leicester

Project outline:

    P2X receptors (P2XRs) form a family of ligand-gated ion channels activated upon binding of extracellular ATP (for review see [1]). In humans, there are seven P2XR paralogs (P2XR1-P2XR7) that have intracellular N- and C-termini, two transmembrane domains and an extracellular ligand binding domain. P2XR assemble as trimeric ion channels which after channel opening allow the influx of small cations. P2XR paralogs have distinct roles and show tissue specific expression raising their therapeutic potential. For instance P2X3R, P2X4R and P2X7R are drug targets for pain treatment and inflammatory diseases. With the recent publication of X-ray structures of P2XRs in different states the time has come for molecular modelling and molecular dynamics simulations to gain a deeper understanding of how these ion channels function at the molecular level. The proposed project will investigate two major aspects of P2XR function, the molecular underpinnings of agonism, and the mechanism of allosteric antagonism.

    Agonism. The key question for receptor function is how the agonist ATP and its derivatives trigger the opening of the channel, and how the receptor transits back from the open, ATP-bound to the closed state via a desensitized state. In preliminary work we have characterised structural requirements for agonist action [2]. Based on this we want to further investigate and characterise the transition between different states of the receptor using Markov State modelling of unbiased molecular dynamics simulations, and steered molecular dynamics simulations.

    Allosteric antagonism. We recently characterised an allosteric binding site in the P2X7R by site directed mutagenesis and molecular modelling [3]. This site was confirmed by X-ray structures of the panda P2X7R with allosteric antagonists bound, which allowed us to confirm the accuracy of our modelling approach. The project aims to characterise the energetics of P2X7R allosteric binding by taking advantage of recent progress in free energy perturbation calculations and the characterisation of the chemical inhibitor space with descriptors based on molecular dynamics. Establishing accurate free energy calculations and quantitative pharmacore descriptors for allosteric P2X7R inhibitors are extremely useful for lead optimization, for classification of known antagonists and filtering candidates from virtual screening.

    References:

    1. Schmid & Evans (2019), Annual Review of Physiology 81, 43-62.
    2. Fryatt et al. (2016), Scientific reports 6, 32918.
    3. Allsopp et al. Scientific Reports (2017), 7, 725. 

    BBSRC Strategic Research Priority: Understanding the Rules of Life: Structural Biology

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      Techniques that will be undertaken during the project:

      • Homology modelling
      • Molecular dynamics simulations of membrane proteins
      • Markov State models
      • Free energy calculations
      • Ligand docking with receptor and ligand flexibility

      Contact: Dr Ralf Schmid, University of Leicester