Computational Modelling
The structure of the α5 subunits contained in the A-type γ-aminobutyric acid receptor (GABAAR) subtype formed by two α5, two β3 and one γ2 subunit was modelled based on the Cryo-EM structure 6A96 downloaded from the protein data bank (http://www.rcsb.org./pdb). Then, the complete GABAAR was modelled. Potential pockets that were large enough to bind the ligands were identified using the icmPocketfinder tool present in the ICM-Pro software (www.molsoft.com). The pocket selected was present at the interface of the subunits α5 and γ2 and was analogous to that which binds benzodiazepine in the GABAAR, the human β3 homopentamer. (PDB id: 4COF). The volume of the pocket was 435.6Å3.
The ligands were sketched using the LigEdit module and docked in the receptor using the docking module. The template-based docking protocol was used. The spatial orientation of benzodiazepine was selected as reference template to dock the compounds. Grid maps were generated around the template, which defined a binding site encompassed in a grid of 20 x 20 x 20Å3. Docking was run with an effort of 5, storing all alternative conformations. A maximum of 25 docked conformations were generated. The final conformation was chosen based on strongest interaction energy. Visualisation of the docked poses was done by using ICM-Pro Molsoft molecular modelling package.