امیر عباس برزگری سرخه

Background and Aim: Using computational methods, it is possible to examine the interaction of chemical compounds with proteins before conducting experimental experiments, and after ensuring that the compounds are more likely to bind to the target, they can be tested in the laboratory or in living systems. Molecular modeling is a powerful tool for the study of structure-activity relationships (SAR) in the research-based pharmaceutical industry. According to the results of our previous research, the analgesic effect of intra-paragigantocellularis lateralis 17β-estradiol on the formalin-induced inflammatory pain might be mediated via NMDA receptors in Male Rats. This study investigated the antinociceptive role of 17β-estradiol and its interaction with the NMDA receptor by molecular docking. Methods: NMDA receptor pdb file was downloaded from Protein Data Bank (PDB) with the code 6WI1. Also, 20 SDF files for 17β-estradiol were downloaded from the ZINC database. The active site was delimited based on reported residues at PDB and complemented with searching of close residues until 6 Å far crystallized protein supported by Molegro Virtual Docker Tools. All molecular docking assays were carried out using flexible residues. Ligand and protein were docked employing Molegro Virtual Docker. The strongest docked pose, residual interactions maps were obtained with Molegro Molecular Viewer for compounds that exhibited the highest affinity energy. Results: The results of molecular docking were first analyzed in terms of affinity energy. 20 compounds of 17β-estradiol were tested via molecular docking. From docked compounds, the eleventh top pose of 17β-estradiol with the code ZINC000028107026 was found strongest docked pose, which demonstrated to achieve an important strong affinity with NMDA (–62.7826 kcal/mol). Four hydrogen bondings (Asn 689A, IIe 688A, Glu 793D, and Leu 797D) and five steric interactions (Asn 689A, IIe 688A, Glu 793D, Glu 790D, and Leu 797D) between amino groups