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Tuning G protein-coupled receptor pharmacology with a novel drug design approach
Secondary Supervisor(s): Dr Hoor Ayub
University of Registration: Coventry University
BBSRC Research Themes:
Project Outline
The pituitary adenylate cyclase-activating polypeptide type 1 receptor (PAC1R) and the parathyroid hormone-1 receptor (PTH1R) are two related class B G protein-coupled receptors (GPCRs) that are therapeutic targets in depression, posttraumatic stress disorder, chronic pain, migraine, and osteoporosis. Our earlier work on water-mediated interactions in another class B agonist1 and the recent discovery of PCO371, an unselective agonist with a novel intracellular mode of binding2, offers us the timely opportunity to explore the role of water-mediated interactions in improving the binding and selectivity of PCO371 analogues.
GPCRs are the most abundant proteins on the surface of human cells and are targets for more than one-third of all approved drugs. However, just a handful of non-peptide agonists for PAC1R or PTH1R are known and are used only as tool compounds to study receptor pharmacology.
PCO371 is a recently characterised agonist able to activate several class B GPCRs with a novel mechanism of action that diverges from the canonical one2. Remarkably, it binds to the intracellular side of PAC1R and PTH1R (Figure 1), stabilising the receptors in the active state. PCO371 does not discern between PAC1R and PTH1R because their structure is conserved and there are no receptor-specific amino acids for increasing selectivity. The knowledge gap we will address is the poor selectivity of PCO371, which limits its relevance as a template for the design of new PAC1R and PTH1R agonists.
We hypothesise that selectivity is achievable by employing an integrated approach that considers flexibility and structural water molecules within the PCO371 binding site. Flexibility and transitory interactions regulate GPCR functioning; water molecules are key players in GPCR activation.
Figure 1. a) PCO371 intracellular binding site within PTH1R; b) structure of PCO371. (Adapted from ref. 2).
Objectives
The overarching project objective is to design novel agonists with a PCO371-like mechanism but improved selectivity between PAC1R and PTH1R. Three parallel strands of work will aim at:
- Computationally map and experimentally validate PAC1R and PTH1R cryptic (transient) sub-pockets. Binding selectivity will be achieved by targeting receptor-specific sub-pockets;
- Computationally map and experimentally validate differences between PAC1R and PTH1R in specific water molecules within the PCO371 binding site. Binding selectivity can be achieved by displacing weakly-bound receptor-specific water molecules, enhancing binding stability for PAC1R or PTH1R
- Computationally understand and experimentally validate the binding path of PCO371 to design structural modifications with more rapid binding. Binding selectivity towards PAC1R or PTH1R can be achieved by tuning the receptor occupancy kinetics (i.e. binding kon and koff).
Methods
The PhD student will learn in silico and experimental techniques, acquiring a complete set of transferable scientific skills. Molecular modelling and computational drug design methods will comprehend the virtual screening of molecular databases and advanced molecular dynamics simulations. Experimental techniques will cover receptor-agonist binding and signalling activity analysis in live mammalian cell line systems. We have genetically engineered mammalian cells that overexpress wild-type PTH1R and PAC1R and will employ site-directed mutagenesis to generate receptor mutants to complement and validate PCO371 computational work.
Impact
Non-peptidic agonists for PAC1R and PTH1R can pave the way to novel drugs administered orally rather than by injection as is currently necessary for peptides, with enormous pharmaceutical gains in drug delivery and patient compliance in osteoporosis, hypoparathyroidism, migraine and psycho and neuro-pathologies. Importantly, our novel approach is transferable to other class B GPCRs.
References
1. Deganutti, G. et al. Nature 577, 432–436 (2020).
2. Kobayashi, K. et al. Nature 618, 1085–1093 (2023).
