Computational studies on δ-branch G protein-coupled P2Y and related orphan receptors

Abstract

G protein-coupled receptors (GPCRs) represent an attractive target for drug development as the modulation of their activity can induce a desired physiological response to treat pathological conditions. Given the knowledge about the receptor’s three-dimensional architecture as well as the binding site of ligands, computational methods can be applied to design novel compounds and investigate the behavior of the complex. In this work, binding modes of ligands at GPCRs of the purinergic P2Y receptor family, namely P2Y₂ and P2Y₄, as well as the related orphan receptor GPR18 were studied in order to identify key interactions and structural features important for receptor functionality. <br /> Since no X-ray crystal structures of the investigated receptors were solved to this point, homology models based on related proteins were generated for this purpose. Subsequently, molecular docking and mutagenesis studies were performed. Here, involvement of positively charged residues in the binding of the phosphate groups of the endogenous P2Y nucleotide agonists ATP and UTP, as well as accommodation of their nucleobase by lipophilic and aromatic residues were observed in the putative orthosteric binding site. Structure-activity relationships of anthraquinone-derived antagonists were elucidated and binding mode differences between both investigated P2Y subtypes were discussed. Further, those findings were used to supplement a structure-based virtual high-throughput screening campaign of 3.2 million molecules at human P2Y₂R. Using complexes with AR-C118925, the most potent selective P2Y2R inhibitor described so far, three novel molecular antagonist scaffolds displaying micromolar potency were discovered. <br /> Taking the collected insights on relevant ionic locks into account, binding modes of agonist &Delta;9-tetrahydrocannabinol (THC) and imidazothiazinone antagonists at GPR18 were assessed in molecular dynamics simulations to detect sidechain interaction partners involved in the stabilization of different receptor conformations. <br /> The presented knowledge and characterization of key interactions contributes to the understanding of those targets and will facilitate future drug development.