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Computational Design of a Potential Therapeutic Peptide Against Spike Protein of Sars-Cov-2 Publisher



Alibakhshi A1 ; Ahangarzadeh S2 ; Beikmohammadi L3, 10 ; Soltanmohammadi B4, 5 ; Bahrami AA6 ; Ranjbar MM7 ; Mohammadi E8, 9
Authors
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Authors Affiliations
  1. 1. Molecular Medicine Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
  2. 2. Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
  3. 3. Stem Cell and Regenerative Medicine Center of Excellence, Tehran University of Medical Sciences, Tehran, 14155-6559, Iran
  4. 4. Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
  5. 5. Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
  6. 6. Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
  7. 7. Razi Vaccine and Serum Research Institute, Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
  8. 8. Core Research Facilities, Isfahan University of Medical Sciences, Isfahan, Iran
  9. 9. Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
  10. 10. Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands

Source: Journal of Computational Biophysics and Chemistry Published:2021


Abstract

SARS-CoV-2 entrance to the host cells is started by the interaction between receptor binding domain (RBD) of the spike (S) protein on the virus with the angiotensin-converting enzyme 2 (ACE2) receptor which is very important in the onset of viral infection. Interference with this interaction can be a promising way to prevent Covid-19 infection. In this study, a novel potential therapeutic peptide was designed in silico based on the key interacting amino acids of ACE2 against SARS-CoV-2 S protein. In our computational analysis, a peptide consisting of residues 19-48 of ACE2 was chosen as the wild-type peptide. Based on this peptide, six mutant peptides (Mu-P1-6) were designed and then assessed in term of interaction with S protein. The result of protein-peptide docking by HADDOCK web server and then immunological analysis by SVMTriP epitope prediction tool leads to choose Mu-P3 as the best mutant. Molecular dynamics simulations of wild-type peptide-S protein complex and Mu-P3-S protein complex, showed Mu-P3 has better interaction with S protein than wild type peptide (interaction energies -897.14 vs. -784.13 (kJ/mol)) which can be a potential therapeutic peptide for Covid-19 pandemic. © 2021 Journal of Computational Biophysics and Chemistry. All Rights Reserved.
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