The published cryo-EM structure (PDB: 6DW0) of the GABA A receptor in complex with GABA was used as a starting template [34 (
link)]. The 6DW0 was prepared using a protein preparation wizard (Schrödinger, New York, NY, USA), where the bond orders were assigned and the structure was minimized. Each of the structures: chloroquine, erythromycin, metronidazole, minocycline, ofloxacin, (-)-epigallocatechin gallate, flumazenil, hydroxychloroquine, pentylenetetrazol, clarithromycin, and rifampicin, were built and optimized in a Spartan ‘20 Parallel Suite (Wavefunction, Irvine, CA, USA). Tautomers were generated for each ligand, and the dominant ionization states of acidic and basic functional groups were used, assuming pH 7.4 (Schrödinger, New York, NY, USA). QikProp was used to calculate the ADME properties of the 11 ligands tested (Schrödinger, New York, NY, USA). A receptor grid generator was used to place 10 Å × 10 Å × 10 Å boxes covering the whole receptor (Schrödinger, New York, NY, USA). All 11 ligands were run for each of the grid boxes generated in Glide SP, using flexible docking with enhanced conformational sampling by four-fold, and an expanded sampling for the selection of initial poses (Schrödinger, New York, NY, USA). The binding site for each ligand was chosen based on the most negative glide score. Erythromycin was not found to bind to any of the sites, and thus it was not carried forward. For each ligand–receptor complex, a minimization was run to reduce steric clashing between the ligand–receptor complex (Schrödinger, New York, NY, USA) using the VGSB solvation model. MMGBSA was run on each ligand–receptor complex to determine their relative affinities.
Kaplan A., Nash A.I., Freeman A.A., Lewicki L.G., Rye D.B., Trotti L.M., Brandt A.L, & Jenkins A. (2023). Commonly Used Therapeutics Associated with Changes in Arousal Inhibit GABAAR Activation. Biomolecules, 13(2), 365.