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

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Abstract

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 GABAA receptor (GABAAR), including some benzodiazepines. The ligands satisfy the Lipinski rules and contain a pharmacophore core that has been previously reported to be a GABAAR 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 GABAAR 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 GABAAR–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 GABAAR–D1, and GABAAR–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.

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Acknowledgments

We thank CONACYT (Grant: 132353), CYTED: 214RT0482 and SIP (project 20140252)-COFAA-PIFI/IPN for financial support. Thanks to Cinthya Czajkowski Ph.D. (University of Wisconsin-Madison) for providing us with the GABAAR coordinate. In memory of Dr. J. Samuel Cruz-Sánchez.

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Authors and Affiliations

  1. Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina IPN, 11340, Mexico City, Mexico

    Margarita Virginia Saavedra-Vélez, José Correa-Basurto, Martiniano Bello, Roberto Cuevas-Hernández & José Trujillo-Ferrara

  2. Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico

    Margarita Virginia Saavedra-Vélez

  3. Centro de Investigaciones Cerebrales, Universidad Veracruzana, Xalapa, Veracruz, Mexico

    Eloy Gasca-Pérez

  4. Unidad de Servicios de Apoyo en Resolución Analítica, Universidad Veracruzana, A. P. 575, Xalapa, Veracruz, Mexico

    Myrna H. Matus, Eloy Gasca-Pérez, Rosa Virginia García-Rodríguez & Fernando Rafael Ramos-Morales

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  1. Margarita Virginia Saavedra-Vélez
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  2. José Correa-Basurto
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Correspondence to José Correa-Basurto or Fernando Rafael Ramos-Morales.

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Saavedra-Vélez, M.V., Correa-Basurto, J., Matus, M.H. et al. Seeking potential anticonvulsant agents that target GABAA receptors using experimental and theoretical procedures. J Comput Aided Mol Des 28, 1217–1232 (2014). https://doi.org/10.1007/s10822-014-9798-z

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