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J Chem Inf Model. 2012 Nov 26;52(11):3064-73. doi: 10.1021/ci3001953. Epub 2012 Nov 6.

Multiple interaction regions in the orthosteric ligand binding domain of the α7 neuronal nicotinic acetylcholine receptor.

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1
Targacept, Inc., 200 East First Street, Suite 300, Winston-Salem, North Carolina 27101, USA. yunde.xiao@cubist.com

Abstract

Neuronal nicotinic receptors (nAChRs) belong to the Cys-loop family of ligand-gated ion channels and are formed from five subunits either as homologous or heterologous, oligomeric receptors, and are of interest as targets for treatment of a variety of central and peripheral nervous system disorders. Using a model of the homopentameric α7 nAChR extracellular region derived from the homologous acetylcholine binding protein (AChBP) from Aplysia California, binding modes of structurally diverse, high affinity α7 ligands were examined by docking to the orthosteric ligand binding domain. While all α7 ligands show similar interactions between the essential positively charged cationic center of the ligand and αTRP147 of the receptor (i.e., hydrogen bond to the tryptophan backbone carbonyl and cation-π interaction), docked poses of various ligands show the potential to interact with three additional regions within the binding domain, identified as regions 1, 2, and 3. Region 1 is located in the vicinity of Loop-E, involves ligand-protein interactions via a network of water-mediated hydrogen bonds, and is analogous to the region where pyridinyl groups are located in many of the AChBP-nicotinic ligand cocrystal structures. Ligands interacting with region 2 probe an area that spans from Loop-E to Loops-D and -F and may contribute to α7-selectivity over other nAChR subtypes. Several high affinity α7 ligands show strong interactions in this region. Region 3 is located near Loop-F of the protein and is analogous to an area involved in binding of an active metabolite derived from DMXBA, in an AChBP cocrystal structure. It appears that π-π interactions contribute to binding affinities of α7 nAChR ligands in this latter region, and further, this region may also contribute to α7-selectivity over other nAChR subtypes. Analysis of the resulting poses suggests that compounds with high α7 binding affinity do not require interactions across all regions simultaneously, but that interactions in multiple regions may enhance ligand binding and increase selectivity. Our results provide insight for further development of selective α7 nAChR ligands and may prove useful for the design of novel scaffolds for specific nicotinic therapeutic agents.

PMID:
23092444
DOI:
10.1021/ci3001953
[Indexed for MEDLINE]

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