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Structure paper

TitleStructural insights into binding of therapeutic channel blockers in NMDA receptors.
Journal, issue, pagesNat Struct Mol Biol, Vol. 29, Issue 6, Page 507-518, Year 2022
Publish dateMay 30, 2022
AuthorsTsung-Han Chou / Max Epstein / Kevin Michalski / Eve Fine / Philip C Biggin / Hiro Furukawa /
PubMed AbstractExcitatory signaling mediated by N-methyl-D-aspartate receptor (NMDAR) is critical for brain development and function, as well as for neurological diseases and disorders. Channel blockers of NMDARs ...Excitatory signaling mediated by N-methyl-D-aspartate receptor (NMDAR) is critical for brain development and function, as well as for neurological diseases and disorders. Channel blockers of NMDARs are of medical interest owing to their potential for treating depression, Alzheimer's disease, and epilepsy. However, precise mechanisms underlying binding and channel blockade have remained limited owing to challenges in obtaining high-resolution structures at the binding site within the transmembrane domains. Here, we monitor the binding of three clinically important channel blockers: phencyclidine, ketamine, and memantine in GluN1-2B NMDARs at local resolutions of 2.5-3.5 Å around the binding site using single-particle electron cryo-microscopy, molecular dynamics simulations, and electrophysiology. The channel blockers form different extents of interactions with the pore-lining residues, which control mostly off-speeds but not on-speeds. Our comparative analyses of the three unique NMDAR channel blockers provide a blueprint for developing therapeutic compounds with minimal side effects.
External linksNat Struct Mol Biol / PubMed:35637422 / PubMed Central
MethodsEM (single particle)
Resolution2.97 - 4.3 Å
Structure data

24946

7saa

EMDB-24946, PDB-7saa:
Glycine and glutamate bound GluN1a-GluN2B NMDA receptors in non-active 1 conformation at 2.97 Angstrom resolution
Method: EM (single particle) / Resolution: 2.97 Å

24947

7sab

EMDB-24947, PDB-7sab:
Phencyclidine-bound GluN1a-GluN2B NMDA receptors
Method: EM (single particle) / Resolution: 4.3 Å

24948

7sac

EMDB-24948, PDB-7sac:
S-(+)-ketamine bound GluN1a-GluN2B NMDA receptors at 3.69 Angstrom resolution
Method: EM (single particle) / Resolution: 3.69 Å

24949

7sad

EMDB-24949, PDB-7sad:
Memantine-bound GluN1a-GluN2B NMDA receptors
Method: EM (single particle) / Resolution: 3.96 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-GLY:
GLYCINE / Glycine

ChemComp-GLU:
GLUTAMIC ACID / Glutamic acid

ChemComp-1PC:
1-(PHENYL-1-CYCLOHEXYL)PIPERIDINE / Phencyclidine

ChemComp-JC9:
(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one / antidepressant*YM / Esketamine

ChemComp-377:
Memantine / medication*YM / Memantine

Source
  • rattus norvegicus (Norway rat)
KeywordsTRANSPORT PROTEIN / Ligand-gated ion channel / ionotropic glutamate receptor / synaptic protein / voltage-gate ion channel / voltage-gated ion channel

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