Initial computational assessment of the binding mode of Diazepam Binding Inhibitor to GABAARs

ZAMARREÑO, F.; AMUNDARAIN, M.J.; COSTABEL, M.; OBIOL D.J.

San Luis

Congreso; XLVIII Reunión Anual de la Sociedad Argentina de Biofísica; 2019

SAB - Sociedad Argentina de Biofísica

GABAA receptors are the main mediators of the fast inhibitory response in the central nervous system of mammals. These members of the Cys-loop family are activated by g-Aminobutyric acid, and are modulated by a myriad of pharmacologically relevant compounds such as benzodiazepines, neurosteroids and alcohol. Moreover, it has been shown that a 10 kDa protein, named DBI (Diazepam Binding Inhibitor) and small peptides derived from its tryptic digestion interact with GABAARs through the benzodiazepines binding site, acting as allosteric modulators. DBI and its peptides are expressed in the brain, both in astrocytes and neurons. However, details about the interaction and the allosteric effects remain unspecified. The aim of this research is to study the interaction between the small peptides and DBI protein, and the α1β2γ2 GABAAR through in silico methods, namely docking and classic molecular dynamics simulations. The structure for the receptor was obtained from homology modeling (based on the β3 homopentamer PDB ID: 4COF) and DBI was obtained from PDB ID: 2FJ9. Docking simulations were performed with HADDOCK webserver, and GROMACS4.6.5 was employed for the molecular dynamics simulations. The complexes were evaluated through the webservers HyPPI and PRODIGY, in addition to careful inspection of the interactions and standard structure analysis. First, four peptides were studied: N41-K53, T42-K53, E43-K-53 and R44-K53. R44-K53 (OP peptide) showed the best scores, and a binding mode comprising a stable C-end inside the cavity, which is in agreement with the experimental data available. In addition, the interaction of the whole protein was assessed and a plausible binding mode was found with good scores. The complex was stable during the MD simulation and DBI interacted with loops involved in mechanisms of opening/closing of the channel. This work presents the first computational assessments of the interaction between GABAA receptors and DBI protein and peptides.