venom gland Transcriptome analysis of Iranian yellow scorpion,“Odontobuthus doriae” derived some putative antimicrobial peptide with anti-SARS-CoV-۲ effect

SARS-CoV-۲ is from enveloped virus family responsible for the COVID-۱۹ pandemic. No e cient drugs currently available for treatment of infection caused specifically by this virus. Therefore, searching for effective therapeutic treatments for severe illness caused SARS-CoV-۲ 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-۲ e↵ects of these peptides have been reported until now. In this study antiviral e↵ects of two predicted antimicrobial peptides (ODAMP۴, ODAMP۵) from Iranian yellow scorpion “Odontobuthus doriae” were assessed by Computational methods. Two predicted peptides with potential of antiviral activities were selected from the cDNA library that have been constructed by our research team from Iranian scorpion “Odontobuthus doriae”. ۳D model of peptides was designed with I-TASSER. The models were refined by a ۲۰۰ ns Molecular Dynamics (MD) simulation by using Gromacs ۲۰۲۱.۲ software. Refined models were Docked with RBD domain of SARS-CoV-۲ spike protein by using HADDOCK software. Docking of human ACE۲ peptide with RBD domain also assessed at the same time. The docked complexes (RBD-peptide and RBD-ACE۲) were refined again by a ۱۰۰ ns MD simulation and then analyzed. The results from molecular docking based on HADDOCK Score and Z-score showed that ODAMP۵ peptide has a high a nity for RBD domain compared to another peptides. the results of molecular dynamics simulation which were done after docking for ۱۰۰ns showed ODAMP۵ has a high stability and a nity to the RBD domain of covid-۱۹ spike protein to ODAMP۴ and human ACE۲. In fact, this peptide can be a good candidate for used as a factor to inhibit the RBD domain of SARS-COV۲ virus in in clinical studies with pharmacological purposes.

کلیدواژه ها:

COVID-۱۹ ، Antimicrobial peptide ، Iranian yellow scorpion ، Molecular Dynamics simulation ، Molecular Docking