1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Antiviral effect assessment of some venom gland peptides from Iranian yellow scorpion, “Odontobuthus doriae” against SARS-CoV-2 with the aim of drug development
Paper ID : 1297-ICB10
Authors:
maryam Naderi Soorki *
گروه زیست شناسی، دانشکده علوم،دانشگاه شهید چمران اهواز، اهواز، ایران
Abstract:
SARS-CoV-2 is from enveloped virus family responsible for the COVID-19 pandemic. No efficient drugs currently available for treatment of infection caused specifically by this virus. Therefore, searching for effective therapeutic treatments for severe illness caused SARS-CoV-2 is crucial. Scorpion venoms are significant sources of peptides with pharmaceutical potential including antivirals. Although, some studies determined the antiviral effects of some scorpion peptides on the other members of Coronaviridae family, but no anti-SARS-CoV-2 effects of these peptides have been reported until now. In this study antiviral effects of three predicted antimicrobial peptides (ODAMP1, ODAMP2 and ODAMP3) from Iranian yellow scorpion “Odontobuthus doriae” were assessed by Computational methods.
Methods: 3D model of selected potent antimicrobial peptides was designed with I-TASSER. The best models based on Z-score and Ramachandran plot were. Themodels were refined by a 200 ns Molecular Dynamics (MD) simulation by using Gromacs 2021.2 software. Refined models were Docked with RBD domain of SARS-CoV-2 spike protein by using HADDOCK software. Docking of human ACE2 peptide with RBD domain also assessed at the same time. The docked complexes (RBD-peptide and RBD-ACE2) were refined again by a 100 ns MD simulation and then analyzed.
Result & discussion: the results of 3D-model designing and models refinement showed one cluster for ODAMP1 and 2 cluster for each one of the ODAMP2 and ODAMP3. The results from molecular docking based on HADDOCK Score and Z-score showed that ODAMP1 peptide has a high affinity for RBD domain compared to other peptides but the results of molecular dynamics simulation showed ODAMP2 has a high stability and affinity to the RBD domain of covid-19 spike protein among the three peptides. In fact, this peptide can be a good candidate for used as a factor to inhibit the RBD domain of Sars-COV2 virus in in clinical studies with pharmacological purposes.
Keywords:
COVID-19, Antimicrobial peptide, Iranian yellow scorpion, Molecular Dynamics simulation, Molecular Docking
Status : Paper Accepted (Poster Presentation)