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.