Docking of 1,4-Benzodiazepines in the α₁/γ₂GABA_AReceptor Modulator Site

Abstract

Positive allosteric modulation of the GABA A receptor (GABA A R) via the benzodiazepine recognition site is the mechanism whereby diverse chemical classes of therapeutic agents act to reduce anxiety, induce and maintain sleep, reduce seizures, and induce conscious sedation. The binding of such therapeutic agents to this allosteric modulatory site increases the affinity of GABA for the agonist recognition site. A major unanswered question, however, relates to how positive allosteric modulators dock in the 1,4-benzodiazepine (BZD) recognition site. In the present study, the X-ray structure of an acetylcholine binding protein from the snail Lymnea stagnalis and the results from site-directed affinity-labeling studies were used as the basis for modeling of the BZD binding pocket at the ␣ 1 /␥ 2 subunit interface. A tethered BZD was introduced into the binding pocket, and molecular simulations were carried out to yield a set of candidate orientations of the BZD ligand in the binding pocket. Candidate orientations were refined based on known structureactivity and stereospecificity characteristics of BZDs and the impact of the ␣ 1 H101R mutation. Results favor a model in which the BZD molecule is oriented such that the C5-phenyl substituent extends approximately parallel to the plane of the membrane rather than parallel to the ion channel. Application of this computational modeling strategy, which integrates sitedirected affinity labeling with structure-activity knowledge to create a molecular model of the docking of active ligands in the binding pocket, may provide a basis for the design of more selective GABA A R modulators with enhanced therapeutic potential.

Orthosteric and benzodiazepine cavities of the α1β2γ2 GABAA receptor: insights from experimentally validated in silico methods

“…Both precision and recall indices are high. Moreover, this configuration agrees well with those proposed by previous works (Berezhnoy et al, 2009; and with experimental information (Clayton et al, 2007, Table 5 -SI). We compared this docking pose with those reported by Richter et al (2012), finding our model resembles their second ranked mode, since it places the pending phenyl ring inside the lipophilic cavity in the back of the binding site, in contrast to their best binding pose which orients the ring outwards.…”

“…Furthermore, there are other non-benzodiazepine ligands of this site, which include the imidazopyridine Zolpidem and the cyclopyrrolone Eszopiclone (S-zopiclone) ( Figure 3). Acetylcholine-binding proteins and non-eukaryotic receptors such as ELIC (Erwinia ligand-gated ion channel), GLIC (Gloeobacter ligand-gated ion channel) and invertebrate Glutamate receptors have been extensively used in the past as templates to model mammalian Cys-Loop receptors (Berezhnoy, Gibbs, & Farb, 2009;Bertaccini, Yoluk, Lindahl, & Trudell, 2013;Carpenter, Lau, & Lightstone, 2012;Carpenter & Lightstone, 2016;Cromer, Morton, & Parker, 2002;Ernst, Brauchart, Boresch, & Sieghart, 2003;Hénin, Salari, Murlidaran, & Brannigan, 2014;Puthenkalam et al, 2016;Sander et al, 2011;Thompson, Lester, & Lummis, 2010;Xie, Sha, Wang, & Cheng, 2013). However, in 2014 the first 3D structure of a GABA A receptor was published by Miller and Aricescu .…”

A Unified Model of the GABAA Receptor Comprising Agonist and Benzodiazepine Binding Sites

“…Homology models, on the other hand, have had little practical impact on the design process despite a number of models reported in the literature [15]–[25]. The models were mainly built using the homologous acetylcholine binding proteins (AChBPs) as templates.…”

GABA A Receptor Family: Overview on Structural Characterization

“…γ 2 Met130, ubicada en la parte posterior y superior del sitio, no está en contacto directo con diazepam, pero sí lo está con residuos que interactúan directamente con el ligando como α 1 Tyr210 y Los valores de precisión y sensibilidad son altos para el mejor modelo. Además, esta configuración concuerda con aquellas propuestas en estudios in silico previos [260,261]. La pose encontrada para diazepam se corresponde con una de las propuestas por Richter et.al.…”