GABAA Receptor Ligands Often Interact with Binding Sites in the Transmembrane Domain and in the Extracellular Domain—Can the Promiscuity Code Be Cracked?

Abstract

Many allosteric binding sites that modulate gamma aminobutyric acid (GABA) effects have been described in heteropentameric GABA type A (GABAA) receptors, among them sites for benzodiazepines, pyrazoloquinolinones and etomidate. Diazepam not only binds at the high affinity extracellular “canonical” site, but also at sites in the transmembrane domain. Many ligands of the benzodiazepine binding site interact also with homologous sites in the extracellular domain, among them the pyrazoloquinolinones that exert modulation at extracellular α+/β− sites. Additional interaction of this chemotype with the sites for etomidate has also been described. We have recently described a new indole-based scaffold with pharmacophore features highly similar to pyrazoloquinolinones as a novel class of GABAA receptor modulators. Contrary to what the pharmacophore overlap suggests, the ligand presented here behaves very differently from the identically substituted pyrazoloquinolinone. Structural evidence demonstrates that small changes in pharmacophore features can induce radical changes in ligand binding properties. Analysis of published data reveals that many chemotypes display a strong tendency to interact promiscuously with binding sites in the transmembrane domain and others in the extracellular domain of the same receptor. Further structural investigations of this phenomenon should enable a more targeted path to less promiscuous ligands, potentially reducing side effect liabilities.

Structure-Guided Computational Methods Predict Multiple Distinct Binding Modes for Pyrazoloquinolinones in GABAA Receptors

“…Instead, net modulation was also influenced to some degree by all the sites at the upper TMD interfaces. These sites are otherwise known for conveying the action of ligands such as etomidate, barbiturates, or avermectin ( Lynagh and Lynch, 2012 ; Maldifassi et al, 2016 ; Iorio et al, 2020 ). In conclusion, the combined experimental evidence demonstrates that PQs depending on the details of the substitution patterns are ligands of at least five distinctive binding sites on a given GABA A R pentamer: The ECD α+/γ2− (benzodiazepine), the ECD α+/β−, the TMD β+/α− (etomidate), and the TMD α+ and γ+ containing interfaces ( Figure 5 ).…”

“…Historically, PQs have been developed as ligands of the high affinity benzodiazepine binding sites ( Iorio et al, 2020 ; Vega Alanis et al, 2020 ). In turn, a number of derivatives such as CGS 8216, CGS 9895, and others were used in pre-clinical research.…”

“…The involvement of the ECD α+/β− interface was demonstrated in three separate studies ( Ramerstorfer et al, 2011 ; Varagic et al, 2013b ; Maldifassi et al, 2016 ), of which one postulated additional binding sites that overlap with the “low affinity diazepam sites” ( Walters et al, 2000 ; Maldifassi et al, 2016 ). Thus, for a rational improvement of selectivity profiles more insight is needed concerning the use of multiple binding sites in a given receptor pentamer ( Iorio et al, 2020 ).…”

Allosteric GABAA Receptor Modulators—A Review on the Most Recent Heterocyclic Chemotypes and Their Synthetic Accessibility

“…Some benzodiazepines also bind at non-homologous sites located in the TMD [21,22]. These sites are thought to be the main site of action of intravenous anesthetics such as etomidate or propofol.…”

“…These sites are thought to be the main site of action of intravenous anesthetics such as etomidate or propofol. Promiscuous binding of chemotypes that bind at the high-affinity benzodiazepine binding site at both extracellular and TMD sites has been observed unexpectedly often [22]. In this review, ligands of the high-affinity benzodiazepine sites, the extracellular α+/β− interfaces, and the TMD sites with which barbiturates and etomidate interact are covered.…”