Chapter 10 Molecular recognition in P2 receptors: Ligand development aided by molecular modeling and mutagenesis

Abstract

Publisher Summary As molecular modeling of cloned G protein-coupled receptor (GPCR) sequences using a rhodopsin template has been refined, it has become possible to generate hypotheses for location of the binding sites that are consistent with mutagenesis results and ligand specificities. To obtain an energetically refined 3-D structure of the ligand–receptor complex, the chapter introduces a new computational approach, a “cross docking” procedure, which simulates the reorganization of the native receptor induced by the ligand. The molecular basis for recognition by human P2Y 1 receptors of the selective, competitive antagonist MRS 2179 is probed using site-directed mutagenesis and molecular modeling. The model was derived from primary sequence comparison, secondary structure predictions, and 3-D homology building, using rhodopsin as a template, and was consistent with data obtained from mutagenesis studies. A putative nucleotide binding site was localized, following a cross docking procedure to obtain energetically refined 3-D structures of the ligand–receptor complexes, and used to predict which residues are likely to be in proximity to agonists and antagonists. Molecular modeling using PowerFit has suggested a possible model of superimposition of two classes of antagonists, nucleotides related to MRS 2179, and non-nucleotides related to pyridoxal phosphate.