Identification of endogenous surrogate ligands for human P2Y receptors through an in silico search

G protein-coupled receptors (GPCRs) are distributed widely throughout the human body, and nearly 50% of current medicines act on a GPCR. GPCRs are considered to consist of seven transmembrane α-helices that form an α-helical bundle in which agonists and antagonists bind. A 3D structure of the target GPCR is indispensable for designing novel medicines acting on a GPCR. We have previously constructed the 3D structure of human P2Y₁ (hP2Y₁) receptor, a GPCR, by homology modeling with the 3D structure of bovine rhodopsin as a template. In the present study, we have employed an in silico screening for compounds that could bind to the hP2Y₁-receptor model using AutoDock 3.0. We selected 21 of the 30 top-ranked compounds, and by measuring intracellular Ca²⁺ concentration, we identified 12 compounds that activated or blocked the hP2Y₁ receptor stably expressed in recombinant CHO cells. 5-Phosphoribosyl-1-pyrophosphate (PRPP) was found to activate the hP2Y₁ receptor with a low ED₅₀ value of 15 nM. The Ca²⁺ assays showed it had no significant effect on P2Y₂, P2Y₆, or P2X₂ receptors, but acted as a weak agonist on the P2Y₁₂ receptor. This is the first study to rationally identify surrogate ligands for the P2Y-receptor family.