DOCKING ANALYSIS OF THE INTERACTION OF PROPOXAZEPAM WITH BIOTARGETS THAT REGULATE ITS MECHANISM OF ACTION AND PHARMACOLOGICAL ACTIVITY
Authors:   Odesa I.I. Mechnykov National University, Ukraine, Akisheva Alina , Valivodz Iryna ,   A.V. Bogatsky Physical-Chemical Institute of the National Academy of Sciences of Ukraine, Ukraine
Published: December 2023

One of 1.4-benzodiazepine 3-alcoxy derivatives – propoxazepam, possessing high analgetic action, also effectively suppresses experimental seizures of different etiology. Unexpected combination of pharmacological spectrum components suggests its different binding sites of GABAA receptor subunits.The aim of the work was docking analysis of the interaction of Propoxazepam with biotargets that mediate its mechanism of action and pharmacological activity (using experimental data of the propoxazepam conformation and calculated data for the three-dimensional structure of the ligand-binding site and subsequent docking to characterize its binding to this receptor)/Materials and methods. X-ray diffraction studies of the compound were performed using Xcalibur 3 single crystal X-ray diffractometer. Calculation of the molecular docking parameters was performed using the iGEMDOCK v2.1 program for the GABA receptor (GABA (A) R-beta3 homopentamer, 4COF), the molecular structures of propoxazepam conformers were prepared using ChemAxon (MarvinSketch 17.11.0); study the binding energy of the TRPV1 receptor with the researched compounds, PDB: 8GFA – Cryo-EM structure of human TRPV1 in complex with the analgesic drug SB-366791 was used. The protein was modelled by using Protein Preparation of Schrodinger Suite; the protein structure was prepared by adding hydrogen atoms, optimizing hydrogen bonds. The ligands were prepared by LigPrep module of Schrödinger suite before proceeding for docking. The ligands were minimized using OPLS4 force field in Schrödinger suite. The docking and QSAR prediction were carried out with propoxazepam, SB-366791, RTX, capsazepin, capsaicin, diazepam, oxazepam, 3-hydroxopropoxazepam. To study the effect of the studied ligands on the NMDA receptor, it was used PDB:7EU7 – structure of the human GluN1-GluN2A NMDA receptor in complex with S-ketamine, glycine and glutamate.Results. Based on the X-ray diffraction analysis, the coordinates of the atoms, bond lengths and valence angles in the propoxazepam molecule were calculated, it was found that it forms crystallographic twins as racemate. The molecular docking method showed that propoxazepam has several binding sites with the energy of complex formation from -78.64 to -85.29 kcal/mol exist on the isolated site of the GABA-receptor. The docking score of propoxazepam (-7.30 kcal/mol) indicates a stronger interaction with the TRPV1 receptor compared to oxazepam (-6.82 kcal/mol), 3-hydroxopropoxazepam (-6.49 kcal/mol), and capsazepin (-6.39 kcal/mol). Propoxazepam creates hydrogen bond with TYR 511 of the TRPV1 receptor as referent ligand SB-366791.Conclusions. The highest contribution to the formation of the bond of the complex is carried out by residues of polar amino acids (serine, asparagine, methionine and arginine in polar binding sub-center). However, also for individual conformers, aromatic amino acids, predominantly phenylalanine (Phe-31, Ala-135 – hydrophobic binding sub-center) make a significant contribution. According to QSAR modelling, all studied compounds (3-hydroxopropoxazepam, diazepam, oxazepam, propoxazepam) have low pIC50 values, which could indicate a relatively low potency or affinity for TRPV1. The computational prediction, propoxazepam has one of the highest docking scores for (-6.77 kcal/mol), kynurenic acid (-6.60 kcal/mol), ketamine (5,34 kcal/mol) and N-methyl-D-aspartate (-4.32 kcal/mol). As a result of docking with the above ligands, it can be noted that most often a hydrogen bond was formed between Asn 616 with the carbonyl group (H acceptor) or the secondary amine group and Phe 613 with the secondary amine group. The best pharmacophore (AHHR1) has been selected based on ketamine structure, which consist of H-bond acceptor site (A1), H-hydrophobic sites (H3, H2) and an aromatic ring (R5).