Using novel computational modelling approaches to address biased agonism at the Adenosine A1 receptor

Funder

Leverhulme Trust

Value

£274,306

Team

Christopher A Reynolds (Coventry University), Giuseppe Deganutti (Coventry University), Graham Ladds (University of Cambridge)

Collaborators

University of Cambridge

Dates

1 October 2017 to 31 December 2020

Project overview

G protein-coupled receptors (GPCRs) are fundamental to health, but the details of their activation mechanisms are complex. Consequently, we seek to apply cutting-edge advanced sampling molecular dynamics simulations, supported by laboratory experimentation, to address the complex biological issue of how G protein-coupled receptors (GPCRs) transition between multiple active states.

Our focus, the adenosine A1 receptor, is involved in cardiovascular function and is one of the receptors affected by caffeine (a drug found in coffee etc.). Experimental structures are now available for both the resting (inactive) and the main active state, but these do not give dynamic information. It is the array of different receptor shapes that we seek to model computationally using advanced molecular modelling, because it is these different conformations that contribute to biased signalling. Our focus is on the most applicable signalling pathways of the adenosine A1R receptor, namely those involving G proteins.

Our ultimate aim is to develop a Markov state model of the ligand binding process and how this leads to activation. With this in mind we have modified the supervised molecular dynamics (SuMD) method to describe ligand unbinding¹, and have further increased the amount of molecular dynamics (MD) sampling available through the development of the SuMD (path sampling) method². We have studied the binding and unbinding pathways of a number of adenosine A1 receptor agonists, including one ligand that shows G protein selectivity towards the G protein Gob, but not Goa or other G proteins.

Our collaborators have shown that this adenosine A1R agonist confers analgesia without cardiorespiratory depression because the negative cardiovascular effects are conveyed via Goa. In addition, adaptive sampling studies indicate that A1R allosteric modulators have divergent binding paths and may bind to multiple sites, but their intrinsic agonist activity is probably be due to some degree of orthosteric binding.⁴

Impact

Development of a modified supervised molecular dynamics (SuMD) method for studying ligand unbinding¹.

Further development of the SuMD method, namely the SuMD (path sampling) method to gain deeper insight into ligand (un)binding pathways through improved sampling².

Insight regarding the agonist (un)binding pathways to the adenosine A1 receptor orthosteric site².

Identification of an adenosine A1 agonist that activates Gob but not Goa - a rare example of G protein functional selectivity (In collaboration with B.G. Frenguelli, M.J. Wall, University of Warwick and M Lochner, University of Basel)³.

Identification of an adenosine A1R agonist that confers analgesia without cardiorespiratory depression (In collaboration with B.G. Frenguelli, M.J. Wall, University of Warwick and M Lochner, University of Basel)³.

Adaptive sampling studies on the mechanism of the adenosine A1R agonist that confers analgesia without cardiorespiratory depression; these studies highlight specific differences in the way Goa and Gob interact with the adenosine A1R receptor³.

Adaptive sampling studies give insight into the nature of allosteric ligand binding; such ligands may be useful clinic agents against the adenosine A1 receptor given the side effects that have impeded the development of agonists.⁴

Outputs

1. Deganutti, G.; Moro, S.; Reynolds, C. A. A Supervised Molecular Dynamics Approach to Unbiased Ligand-Protein Unbinding. J. Chem. Inf. Model. 2020, 60, 1804-1817.
2. Deganutti, G.; Barkan, K.; Preti, M.; Leuenberger, M.; Wall, M. J.; Frengielli, B. G.; Lochner, M.; Ladds, G.; Reynolds, C. A. Deciphering the Agonist Binding Mechanism to the Adenosine A1 Receptor. bioRxiv doi: https://doi.org/10.1101/2020.10.22.350827; submitted to ACS Pharmacol. and Trans. Sci., 2020.
3. Wall, J. M.; Hill, E.; Huckstepp, R.; Barkan, K.; Deganutti, G.; Leueberger, M.; Preti, B.; Winfield, I.; Wei, H.; Imlach, W.; Dean, E.; Hume, C.; Hayward, S.; Oliver, J.; Zhao, F. Y.; Spanswick, D.; Reynolds, C. A.; Lochner, M.; Ladds, G.; Frenguelli, B. G. A biased adenosine A1R agonist confers analgesia without cardiorespiratory depression. BioRxiv, https://www.biorxiv.org/content/10.1101/2020.04.04.023945v3.full, 2020.
4. Deganutti, G.; Barkan, K.; Ladds, G.; Reynolds, C. A. A multisite model of allosterism for the adenosine A1 receptor. BioRxiv, https://doi.org/10.1101/2020.10.14.338822, 2020.