Assessment of Homology Templates and an Anesthetic Binding Site within the γ-Aminobutyric Acid Receptor

Abstract

Background Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). While its molecular structure remains unknown, significant progress has been made towards understanding its interactions with anesthetics via molecular modeling. Methods The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50’s. Results Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between alpha and beta subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. Conclusion Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed correlation of ligand docking scores with experimentally measured GABAaR potentiation.

γ-Aminobutyric Acid Type A Receptor Modulation by Etomidate Analogs

“…33–36 In the CoMFA approach, there are no a priori assumptions regarding the nature of the protein binding site. Instead, the molecular (i.e.…”

“…However, progress in that direction is being made through the construction of homology models that seek to approximate the receptor’s structure by utilizing structurally similar proteins. 33,34 With further refinement and validation of these models or the production of a high-resolution heteromeric GABA A receptor crystal structure, it may be possible to unambiguously identify amino acids at the etomidate binding site that are the important determinants of receptor (and therefore hypnotic) potency and account for our pharmacophore model.…”

Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics

“…Recent NMR structures of isolated nicotinic receptor transmembrane domains (Bondarenko et al, 2012) further clarified the topological map and informed its use as a modeling template. Moreover, the determination of homologous X-ray structures from bacteria Dutzler, 2008, 2009;Bocquet et al, 2009) and C. elegans (Hibbs and Gouaux, 2011) to #3.3 Å resolution have confirmed the conservation of receptor conformation across species and provided increasingly well-defined templates for homology modeling (Bertaccini et al, 2013).…”

“…However, the utility of these methods in identifying new drugs remains to be demonstrated, particularly given that the receptors of greatest therapeutic interest (GABA A and glycine receptors) exhibit ion selectivity and modulation properties distinct from structurally-characterized receptors (GLIC and ELIC). The recently determined structure of GluCl (Hibbs and Gouaux, 2011) may prove a more useful template given its selectivity for anions and excellent alignment with other eukaryotic receptors (Bertaccini et al, 2013); however, the structural relevance of the bulky ivermectin molecule cocrystallized at the transmembrane subunit interface in this structure remains to be determined. Notably, docking of etomidate to GABA A receptor homology models based on both GLIC and GluCl corroborated functional evidence for binding (Chiara et al, 2012), supporting these structures as templates for future drug screening.…”

“…The glutamategated chloride channel (GluCl) from Caenorhabditis elegans rose to particular significance as the first eukaryotic member of this receptor family whose structure has been determined at atomic resolution (Hibbs and Gouaux, 2011). This receptor may prove a particularly valuable template for homology modeling, given its high degree of sequence conservation with human GABA A and glycine receptors (Bertaccini et al, 2013). In addition to glutamate, this channel is activated by ivermectin (Cully et al, 1994), which also allosterically modulates human homologs, such as GABA A (Sigel and Baur, 1987), glycine (Shan et al, 2001), and nicotinic acetylcholine receptors (Krause et al, 1998).…”