title: A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists.
abstract: 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.
authors.affiliation: Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.).
authors.forename: David
authors.initials: D
authors.lastname: Stroebel
authors.affiliation: Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.) Derek.Buhl@pfizer.com Pierre.Paoletti@ens.fr Jayvardhan.Pandit@pfizer.com.
authors.forename: Derek L
authors.initials: DL
authors.lastname: Buhl
authors.affiliation: Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.).
authors.forename: John D
authors.initials: JD
authors.lastname: Knafels
authors.affiliation: Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.).
authors.forename: Pranab K
authors.initials: PK
authors.lastname: Chanda
authors.affiliation: Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.).
authors.forename: Michael
authors.initials: M
authors.lastname: Green
authors.affiliation: Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.).
authors.forename: Simone
authors.initials: S
authors.lastname: Sciabola
authors.affiliation: Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.).
authors.forename: Laetitia
authors.initials: L
authors.lastname: Mony
authors.affiliation: Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.) Derek.Buhl@pfizer.com Pierre.Paoletti@ens.fr Jayvardhan.Pandit@pfizer.com.
authors.forename: Pierre
authors.initials: P
authors.lastname: Paoletti
authors.affiliation: Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.) Derek.Buhl@pfizer.com Pierre.Paoletti@ens.fr Jayvardhan.Pandit@pfizer.com.
authors.forename: Jayvardhan
authors.initials: J
authors.lastname: Pandit
mesh_terms: D000317:Adrenergic alpha-Antagonists / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D000494:Allosteric Regulation / Q000187:drug effects; D019943:Amino Acid Substitution; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology; D015507:Drugs, Investigational / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D005103:Expert Systems; D006801:Humans; D007093:Imidazoles / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D008024:Ligands; D049990:Membrane Transport Modulators / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D009154:Mutation; D010069:Oxadiazoles / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D010880:Piperidines / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D054730:Protein Interaction Domains and Motifs; D021122:Protein Subunits / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011724:Pyridazines / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D011743:Pyrimidines / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D016194:Receptors, N-Methyl-D-Aspartate / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000378:metabolism; D029867:Xenopus Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D000317:Adrenergic alpha-Antagonists; D015507:Drugs, Investigational; C000609739:EVT-101; D007093:Imidazoles; D008024:Ligands; D049990:Membrane Transport Modulators; C579629:N-(3-(3-(4-methylbenzyl)-1,2,4-oxadiazol-5-yl)cyclopentyl)-1H-pyrazolo(3,4-d)pyrimidin-4-amine; C121001:NR2B NMDA receptor; D010069:Oxadiazoles; D010880:Piperidines; D021122:Protein Subunits; D011724:Pyridazines; D011743:Pyrimidines; D016194:Receptors, N-Methyl-D-Aspartate; D011993:Recombinant Fusion Proteins; D029867:Xenopus Proteins; C010739:ifenprodil