Modeling of αk/γ2 (k = 1, 2, 3 and 5) interface of GABAA receptor and docking studies with zolpidem:: Implications for selectivity

The three-dimensional models of the alpha k/gamma 2 (k = 1, 2, 3 and 5) interface of GABA(A) receptors, which included the agonist-binding site, were constructed and validated by molecular modeling technology. To investigate the mechanism of a subunit selectivity of zolpidem, docking calculations were used to illustrate the potential binding modes of zolpidem with different a subtypes. The results revealed that there were three reasons resulting in the distinct binding affinity of zolpidem to different alpha subtype. Firstly, the number of hydrogen bonds of agonist-receptor complex would determine the magnitude of binding affinity. Secondly, the His residue in loop A of a subunit was indicated as a key role of benzodiazepine binding. Thirdly, the side chain of Glu in loop C reduced the affinity of zolpidem to those receptors containing alpha 2, alpha 3 or alpha 5 subunits. (c) 2007 Elsevier Inc. All rights reserved.