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

AMUNDARAIN, MARÍA JULIA; DIEGO OBIOL; FERNANDO ZAMARREÑO; MARCELO D. COSTABEL

San Luis

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

Sociedad Argentina de Biofísica

GABAA receptors are the main mediators of the fast inhibitory response in the centralnervous system of mammals. These members of the Cys-loop family are activated by gAminobutyric acid, and are modulated by a myriad of pharmacologically relevantcompounds such as benzodiazepines, neurosteroids and alcohol. Moreover, it has beenshown that a 10 kDa protein, named DBI (Diazepam Binding Inhibitor) and small peptidesderived from its tryptic digestion interact with GABAARs through the benzodiazepinesbinding site, acting as allosteric modulators. DBI and its peptides are expressed in thebrain, both in astrocytes and neurons. However, details about the interaction and theallosteric effects remain unspecified.The aim of this research is to study the interaction between the small peptides and DBIprotein, and the α1β2γ2 GABAAR through in silico methods, namely docking and classicmolecular dynamics simulations. The structure for the receptor was obtained fromhomology modeling (based on the β3 homopentamer PDB ID: 4COF) and DBI wasobtained from PDB ID: 2FJ9. Docking simulations were performed with HADDOCKwebserver, and GROMACS4.6.5 was employed for the molecular dynamics simulations.The complexes were evaluated through the webservers HyPPI and PRODIGY, in additionto 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 (OPpeptide) showed the best scores, and a binding mode comprising a stable C-end insidethe cavity, which is in agreement with the experimental data available. In addition, theinteraction of the whole protein was assessed and a plausible binding mode was foundwith good scores. The complex was stable during the MD simulation and DBI interactedwith loops involved in mechanisms of opening/closing of the channel.This work presents the first computational assessments of the interaction betweenGABAA receptors and DBI protein and peptides.