Identification of the antiepileptic racetam binding site in the synaptic vesicle protein 2A by molecular dynamics and docking simulations.

Josã© Correa-Basurto,Gema L Ramã­Rez-Salinas,Ã“Scar A Pã©Rez-Gonzã¡Lez,Josã© Trujillo-Ferrara,Bryan V Phillips-Farfã¡N,Marlet Martã­Nez-Archundia,Julieta G Mendoza-Torreblanca,Antonio Romo-Mancillas,Roberto I Cuevas-Hernã¡Ndez

doi:10.3389/fncel.2015.00125

Abstract

Synaptic vesicle protein 2A (SV2A) is an integral membrane protein necessary for the proper function of the central nervous system and is associated to the physiopathology of epilepsy. SV2A is the molecular target of the anti-epileptic drug levetiracetam and its racetam analogs. The racetam binding site in SV2A and the non-covalent interactions between racetams and SV2A are currently unknown; therefore, an in silico study was performed to explore these issues. Since SV2A has not been structurally characterized with X-ray crystallography or nuclear magnetic resonance, a three-dimensional (3D) model was built. The model was refined by performing a molecular dynamics simulation (MDS) and the interactions of SV2A with the racetams were determined by docking studies. A reliable 3D model of SV2A was obtained; it reached structural equilibrium during the last 15 ns of the MDS (50 ns) with remaining structural motions in the N-terminus and long cytoplasmic loop. The docking studies revealed that hydrophobic interactions and hydrogen bonds participate importantly in ligand recognition within the binding site. Residues T456, S665, W666, D670 and L689 were important for racetam binding within the trans-membrane hydrophilic core of SV2A. Identifying the racetam binding site within SV2A should facilitate the synthesis of suitable radio-ligands to study treatment response and possibly epilepsy progression.

Highlights

Epilepsy is the most common chronic brain disorder that affects people of all ages
Because positron emission tomography (PET) requires the use of a radio-ligand to label the protein target, as a first approximation to synthesize a radio-ligand with a high affinity and specificity, we investigated the specific binding site(s) for racetams in Synaptic vesicle protein 2A (SV2A) and the residues involved in their interaction
The root mean square deviation (RMSD) results showed that SV2A reached equilibrium in the last 15 ns of the molecular dynamics simulation (MDS) and this was in agreement with the radius of gyration (Rg) values

Summary

Introduction

Epilepsy is the most common chronic brain disorder that affects people of all ages. More than 50 million people worldwide have epilepsy (WHO, 2014). Epileptic seizures and/or epileptogenesis may functionally alter brain regions involved in cognitive processing, contributing to the progressive nature of epilepsy; neurodegenerative cellular mechanisms may participate. To cure epilepsy, both epileptogenesis and the associated neuro-degeneration have to be stopped and, if possible, reversed. Both epileptogenesis and the associated neuro-degeneration have to be stopped and, if possible, reversed This will require early detection through biomarkers that can reliably predict disease progression (Ono and Galanopoulou, 2012)

Methods

Results

Conclusion