Mapping the Binding of GluN2B-Selective N-Methyl-D-aspartate Receptor Negative Allosteric Modulators

Burger, P. B., Yuan, H. J., Karakas, E., Geballe, M., Furukawa, H., Liotta, D. C., Snyder, J. P., Traynelis, S. F. (2012) Mapping the Binding of GluN2B-Selective N-Methyl-D-aspartate Receptor Negative Allosteric Modulators. Molecular Pharmacology, 82 (2). pp. 344-359. ISSN 0026-895X

URL: http://www.ncbi.nlm.nih.gov/pubmed/22596351
DOI: 10.1124/mol.112.078568

Abstract

We have used recent structural advances in our understanding of the N-methyl-D-aspartate (NMDA) receptor amino terminal domain to explore the binding mode of multiple diaryl GluN2B-selective negative allosteric modulators at the interface between the GluN1 and GluN2B amino-terminal domains. We found that interaction of the A ring within the binding pocket seems largely invariant for a variety of structurally distinct ligands. In addition, a range of structurally diverse linkers between the two aryl rings can be accommodated by the binding site, providing a potential opportunity to tune interactions with the ligand binding pocket via changes in hydrogen bond donors, acceptors, as well as stereochemistry. The most diversity in atomic interactions between protein and ligand occur in the B ring, with functional groups that contain electron donors and acceptors providing additional atomic contacts within the pocket. A cluster of residues distant to the binding site also control ligand potency, the degree of inhibition, and show ligand-induced increases in motion during molecular dynamics simulations. Mutations at some of these residues seem to distinguish between structurally distinct ligands and raise the possibility that GluN2B-selective ligands can be divided into multiple classes. These results should help facilitate the development of well tolerated GluN2B subunit-selective antagonists.

Item Type: Paper
Uncontrolled Keywords: amino-terminal domain anti-ischemic agents nmda receptor nr2b subunit antagonist properties pi interactions ifenprodil protein subtype mechanisms
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > NMDA receptor
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein receptor
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types
CSHL Authors:
Communities: CSHL labs > Furukawa lab
CSHL Post Doctoral Fellows
Depositing User: Matt Covey
Date Deposited: 31 Jan 2013 20:54
Last Modified: 02 May 2013 19:10
PMCID: PMC3400845
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26911

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