Seeking potential anticonvulsant agents that target GABAA receptors using experimental and theoretical procedures

• Published in: Journal of computer-aided molecular design 2014-12, Vol.28 (12), p.1217-1232
• Main Authors: Saavedra-Vélez, Margarita Virginia, Correa-Basurto, José, Matus, Myrna H., Gasca-Pérez, Eloy, Bello, Martiniano, Cuevas-Hernández, Roberto, García-Rodríguez, Rosa Virginia, Trujillo-Ferrara, José, Ramos-Morales, Fernando Rafael
• Format: Article
• Language: English
• Subjects: Animal Anatomy; Anticonvulsants - chemistry; Anticonvulsants - therapeutic use; Binding Sites; Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; GABA-A Receptor Antagonists - chemistry; GABA-A Receptor Antagonists - therapeutic use; Histology; Humans; Ligands; Molecular Dynamics Simulation; Morphology; Physical Chemistry; Protein Conformation; Receptors, GABA-A - chemistry; Receptors, GABA-A - metabolism; Seizures - drug therapy; Seizures - pathology
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-014-9798-z

The aim of this study was to identify compounds that possess anticonvulsant activity by using a pentylenetetrazol (PTZ)-induced seizure model. Theoretical studies of a set of ligands, explored the binding affinities of the ligands for the GABA A receptor (GABA A R), including some benzodiazepines. The ligands satisfy the Lipinski rules and contain a pharmacophore core that has been previously reported to be a GABA A R activator. To select the ligands with the best physicochemical properties, all of the compounds were analyzed by quantum mechanics and the energies of the highest occupied molecular orbital and lowest unoccupied molecular orbital were determined. Docking calculations between the ligands and the GABA A R were used to identify the complexes with the highest Gibbs binding energies. The identified compound D1 (dibenzo( b,f )(1,4)diazocine-6,11(5H,12H)-dione) was synthesized, experimentally tested, and the GABA A R–D1 complex was submitted to 12-ns-long molecular dynamics (MD) simulations to corroborate the binding conformation obtained by docking techniques. MD simulations were also used to analyze the decomposition of the Gibbs binding energy of the residues involved in the stabilization of the complex. To validate our theoretical results, molecular docking and MD simulations were also performed for three reference compounds that are currently in commercial use: clonazepam (CLZ), zolpidem and eszopiclone. The theoretical results show that the GABA A R–D1, and GABA A R–CLZ complexes bind to the benzodiazepine binding site, share a similar map of binding residues, and have similar Gibbs binding energies and entropic components. Experimental studies using a PTZ-induced seizure model showed that D1 possesses similar activity to CLZ, which corroborates the predicted binding free energy identified by theoretical calculations.