Computational prediction of ligand binding in peptide G-protein coupled receptors

Sammanfattning: G-protein coupled receptors (GPCRs) are a superfamily of membrane receptors involved in a wide variety of biological processes, and their malfunction is associated with many diseases. Consequently, GPCRs are targeted by one-third of the drugs on the market, and constitute the focus of active public and private research in the search of more effective drugs. The GPCR families that are activated by endogenous peptides are particularly challenging for the drug design process, which in this case contemplates peptides, peptidomimetics and small molecules, as selective activators (agonists) or blockers (antagonists) of the particular receptor subtype of interest. This process benefits of a detailed understanding of how known ligands bind to the receptors. Homology modelling, molecular dynamics (MD) and free energy perturbation (FEP) are computational methods used to predict binding modes and binding affinities. In this thesis, these techniques are applied (and even further developed) in combination with novel experimental data provided by our collaborators, in order to elucidate the molecular determinants of endogenous peptide ligands, analogues and mimetics to two families of peptide-binding receptors: the neuropeptide Y (NPY) and the Angiotensin II receptors.The NPY signaling system is responsible for the regulation of food intake and its malfunction is connected to obesity, a risk factor for diseases such as diabetes and cancer. In this thesis, we focused on the elucidation of the binding mode of endogenous peptide ligands and studied the structural effect of receptor mutants, with the aim of helping in future drug design on the Y2 receptor subtype, as well as understanding the effect of receptor polymorphisms on the Y4 subtype. We further used this system to refine and test our computational protocol for the prediction of binding free energies, by characterizing the binding mode of a peptidomimetic antagonist to the Y1 receptor.The AT2 receptor is another interesting drug target, as its activation by the Angiotensin II peptide elicits responses that counterbalance the hypertensive effects caused by activation of the AT1 receptor by the same ligand. Moreover, AT2 is upregulated in events of tissue damage. We characterized the chemical evolution of peptide and peptidomimetic agonists at this receptor, with the aim to identify a set of pharmacophoric points and key interactions with AT2. The outcome of this study allowed the establishment of a clear explanation of structure-activity relationships, and will be the starting point for further ligand-design efforts at this receptor.