What is the potential of G protein-coupled receptor [corrected] allosteric sites in drug design?

In silico mapping of allosteric ligand binding sites in type-1 cannabinoid receptor

The recent resolution of the crystal structure of type-1 cannabinoid receptor (CB₁ ) and the discovery of novel modulators for this target open the way to the possibility of elucidating the structural requirements for CB₁ binding, and thereby facilitate a rational drug design. Compounds that target the orthosteric site of CB₁ in some cases have shown side effects. Allosteric modulators could potentially avoid these side effects by influencing binding and/or efficacy of orthosteric ligands. Here, we summarize and compare previous data on different putative allosteric binding sites observed in CB₁ homology models with an in silico docking study of the recently published crystal structure of the same receptor on endogenous and natural hydrophobic ligands that act as positive allosteric modulators and negative allosteric modulators of CB₁ . In particular, a lipid-exposed pocket targeted by most of the tested molecules is reported and discussed.

Demystifying P2Y1 Receptor Ligand Recognition through Docking and Molecular Dynamics Analyses

We performed a molecular modeling analysis of 100 nucleotide-like bisphosphates and 46 non-nucleotide arylurea derivatives previously reported as P2Y₁R binders using the recently solved hP2Y₁R structures. We initially docked the compounds at the X-ray structures and identified the binding modes of representative compounds highlighting key patterns in the structure-activity relationship (SAR). We subsequently subjected receptor complexes with selected key agonists (2MeSADP and MRS2268) and antagonists (MRS2500 and BPTU) to membrane molecular dynamics (MD) simulations (at least 200 ns run in triplicate, simulation time 0.6-1.6 μs per ligand system) while considering alternative protonation states of nucleotides. Comparing the temporal evolution of the ligand-protein interaction patterns with available site-directed mutagenesis (SDM) data and P2Y₁R apo state simulation provided further SAR insights and suggested reasonable explanations for loss/gain of binding affinity as well as the most relevant charged species for nucleotide ligands. The MD analysis also predicted local conformational changes required for the receptor inactive state to accommodate nucleotide agonists.