Cross-talk between allosteric and orthosteric binding sites of γ-amino butyric acid type A receptors (GABA_A-Rs): A computational study revealing the structural basis of selectivity

The γ-amino butyric acid type A receptors (GABAA-Rs) are GABA-gated chloride ion channels that mediate fast inhibitory neurotransmissions. Due to their essential role in normal brain function, neuromodulatory therapies are targeted at them for restoring GABA-mediated inhibition. The receptor modulation by benzodiazepine (BZD) shows therapeutically useful actions. The mechanisms, by which BZD-site performs selective transduction while modulating GABAA-Rs, and its correlation with the occurrence of sedation is not fully known. In pursuance, we performed a computational study starting from modeling of α2-subtype GABAA-R, docking of α1/2-selective ligands followed by molecular dynamics simulations of the obtained complexes. The results show that during early stages of activation, a) allosteric binding initiate structural changes through BZD-site for GABA-elicited activation; b) selective BZD-binders positively modulate orthosteric GABA-bound site with fin-like C- and F-loop movements, which supports twisting of inner and outer β-barrel; c) modulation by α1/2-selective ligands was only evident at site 1, mimicking mandatory doubly bound state; d) strength of allosteric communication was prominent for α2-modulators, however, the basic nature of allosteric-orthosteric site cross-talk remains same for both α1/2-modulators; and e) ratio of hydrophobic:hydrophilic ligand contact surface decides α2-selectivity, less value of ratio favors it. These insights would enable us to design better α2-selective modulator/s. Altogether our computational study reveals early stages of allosteric modulation, highlighting subtype selective activation and pathways recommending GABA binding sites during selective modulation. Communicated by Ramaswamy H. Sarma