Crystal Structure and Pharmacological Characterization of a Novel N-Methyl-d-aspartate (NMDA) Receptor Antagonist at the GluN1 Glycine Binding Site

Kvist, Trine; Steffensen, Thomas Bielefeldt; Greenwood, Jeremy R.; Tabrizi, Fatemeh Mehrzad; Hansen, Kasper B.; Gajhede, Michael; Pickering, Darryl S.; Traynelis, Stephen F.; Kastrup, J.S.; Bräuner‐Osborne, Hans

doi:10.1074/jbc.m113.480210

Cited by 26 publications

(29 citation statements)

References 46 publications

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“…Most structural studies of NMDARs (or their fragments) investigate the glycan-free forms202324252627. The absence of glycans in the GluN1 LBD structures in the cited works was possibly a side effect of using E. coli as the expression system.…”

Section: Discussionmentioning

confidence: 99%

“…Binding (or unbinding) of agonists or coagonists is believed to result in a conformational change in the corresponding domain, namely clamshell-like closing (or opening) of the domain (Fig. 2)202324252627. If three events occur simultaneously: (1) glycine or D-serine binds to GluN1 LBD, (2) glutamate binds to GluN2 LBD, and (3) the magnesium ‘plug’ is released from the transmembrane domain (TMD) by an appropriately depolarized membrane voltage, then the ion channel pore opens and calcium cations enter the cell, triggering signal cascades responsible for synaptic plasticity1.…”

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confidence: 99%

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Computationally Discovered Potentiating Role of Glycans on NMDA Receptors

Sinitskiy

Stanley

Hackos³

et al. 2017

Sci Rep

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N-methyl-D-aspartate receptors (NMDARs) are glycoproteins in the brain central to learning and memory. The effects of glycosylation on the structure and dynamics of NMDARs are largely unknown. In this work, we use extensive molecular dynamics simulations of GluN1 and GluN2B ligand binding domains (LBDs) of NMDARs to investigate these effects. Our simulations predict that intra-domain interactions involving the glycan attached to residue GluN1-N440 stabilize closed-clamshell conformations of the GluN1 LBD. The glycan on GluN2B-N688 shows a similar, though weaker, effect. Based on these results, and assuming the transferability of the results of LBD simulations to the full receptor, we predict that glycans at GluN1-N440 might play a potentiator role in NMDARs. To validate this prediction, we perform electrophysiological analysis of full-length NMDARs with a glycosylation-preventing GluN1-N440Q mutation, and demonstrate an increase in the glycine EC50 value. Overall, our results suggest an intramolecular potentiating role of glycans on NMDA receptors.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Computationally Discovered Potentiating Role of Glycans on NMDA Receptors

Sinitskiy

Stanley

Hackos³

et al. 2017

Sci Rep

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“…TK40 (16)(17)(18)(19)(20) -and the glutamate site ligands-2-amino-5-phosphonopentanoic acid (D-AP5), (−)-PPDA, and NVP (18,21).…”

Section: Significancementioning

confidence: 99%

Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits

Lind

Mou

Tamborini

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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NMDA-type glutamate receptors are ligand-gated ion channels that contribute to excitatory neurotransmission in the central nervous system (CNS). Most NMDA receptors comprise two glycine-binding GluN1 and two glutamate-binding GluN2 subunits (GluN2A–D). We describe highly potent (S)-5-[(R)-2-amino-2-carboxyethyl]-4,5-dihydro-1H-pyrazole-3-carboxylic acid (ACEPC) competitive GluN2 antagonists, of which ST3 has a binding affinity of 52 nM at GluN1/2A and 782 nM at GluN1/2B receptors. This 15-fold preference of ST3 for GluN1/2A over GluN1/2B is improved compared with NVP-AAM077, a widely used GluN2A-selective antagonist, which we show has 11-fold preference for GluN1/2A over GluN1/2B. Crystal structures of the GluN1/2A agonist binding domain (ABD) heterodimer with bound ACEPC antagonists reveal a binding mode in which the ligands occupy a cavity that extends toward the subunit interface between GluN1 and GluN2A ABDs. Mutational analyses show that the GluN2A preference of ST3 is primarily mediated by four nonconserved residues that are not directly contacting the ligand, but positioned within 12 Å of the glutamate binding site. Two of these residues influence the cavity occupied by ST3 in a manner that results in favorable binding to GluN2A, but occludes binding to GluN2B. Thus, we reveal opportunities for the design of subunit-selective competitive NMDA receptor antagonists by identifying a cavity for ligand binding in which variations exist between GluN2A and GluN2B subunits. This structural insight suggests that subunit selectivity of glutamate-site antagonists can be mediated by mechanisms in addition to direct contributions of contact residues to binding affinity.

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“…For instance, the binding affinity of NMDA antagonist ifenprodil at GluN1/GluN2A is about 400-fold lower than at GluN1/GluN2B10. Of various subunits and their combinations, glycine can bind to GluN1 and GluN3 subunits1112 with pharmacological and structural differences in both binding sites1314. More importantly, it has been suggested that the glycine binding site of GluN1 is a potential pharmacological target for treating PD, schizophrenia, traumatic brain injury, and anxiety15161718.…”

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confidence: 99%

Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme

Leong

Syu

Ding

et al. 2017

Sci Rep

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The glycine-binding site of the N-methyl-D-aspartate receptor (NMDAR) subunit GluN1 is a potential pharmacological target for neurodegenerative disorders. A novel combinatorial ensemble docking scheme using ligand and protein conformation ensembles and customized support vector machine (SVM)-based models to select the docked pose and to predict the docking score was generated for predicting the NMDAR GluN1-ligand binding affinity. The predicted root mean square deviation (RMSD) values in pose by SVM-Pose models were found to be in good agreement with the observed values (n = 30, r2 = 0.928–0.988, = 0.894–0.954, RMSE = 0.002–0.412, s = 0.001–0.214), and the predicted pKi values by SVM-Score were found to be in good agreement with the observed values for the training samples (n = 24, r2 = 0.967, = 0.899, RMSE = 0.295, s = 0.170) and test samples (n = 13, q2 = 0.894, RMSE = 0.437, s = 0.202). When subjected to various statistical validations, the developed SVM-Pose and SVM-Score models consistently met the most stringent criteria. A mock test asserted the predictivity of this novel docking scheme. Collectively, this accurate novel combinatorial ensemble docking scheme can be used to predict the NMDAR GluN1-ligand binding affinity for facilitating drug discovery.

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Crystal Structure and Pharmacological Characterization of a Novel N-Methyl-d-aspartate (NMDA) Receptor Antagonist at the GluN1 Glycine Binding Site

Cited by 26 publications

References 46 publications

Computationally Discovered Potentiating Role of Glycans on NMDA Receptors

Computationally Discovered Potentiating Role of Glycans on NMDA Receptors

Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits

Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme

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