A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists

• DOI: 10.1124/mol.115.103036
• Publication Date: 2016-02-25T03:48:33Z
• Authors: David Stroebel; Derek L. Buhl; John D. Knafels; Pranab K. Chanda; Michael Green; Simone Sciabola; Laetitia Mony; Pierre Paoletti; Jayvardhan Pandit
• Keywords: Models, Molecular; 0301 basic medicine; Molecular Conformation; Expert Systems; Ligands; [SCCO]Cognitive science; 03 medical and health sciences; Allosteric Regulation; Piperidines; Membrane Transport Modulators; Animals; Humans; Protein Interaction Domains and Motifs; Adrenergic alpha-Antagonists; Oxadiazoles; Binding Sites; [SCCO.NEUR]Cognitive science/Neuroscience; Imidazoles; Computational Biology; Articles; Drugs, Investigational; Molecular Docking Simulation; Protein Subunits; Amino Acid Substitution; Mutation

N-methyl-d-aspartate receptors (NMDARs) are glutamate-gated ion channels that play key roles in brain physiology and pathology. Because numerous pathologic conditions involve NMDAR overactivation, subunit-selective antagonists hold strong therapeutic potential, although clinical successes remain limited. Among the most promising NMDAR-targeting drugs are allosteric inhibitors of GluN2B-containing receptors. Since the discovery of ifenprodil, a range of GluN2B-selective compounds with strikingly different structural motifs have been identified. This molecular diversity raises the possibility of distinct binding sites, although supporting data are lacking. Using X-ray crystallography, we show that EVT-101, a GluN2B antagonist structurally unrelated to the classic phenylethanolamine pharmacophore, binds at the same GluN1/GluN2B dimer interface as ifenprodil but adopts a remarkably different binding mode involving a distinct subcavity and receptor interactions. Mutagenesis experiments demonstrate that this novel binding site is physiologically relevant. Moreover, in silico docking unveils that GluN2B-selective antagonists broadly divide into two distinct classes according to binding pose. These data widen the allosteric and pharmacological landscape of NMDARs and offer a renewed structural framework for designing next-generation GluN2B antagonists with therapeutic value for brain disorders.