Volume 10, Issue 4 (3-2024)
jhbmi 2024, 10(4): 386-399 |
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Mortezaali S, Zarrabi M. The Study of the Binding Ability of Antimicrobial Peptides to Spike Protein of the Coronavirus by Docking and Molecular Dynamics Simulation. jhbmi 2024; 10 (4) :386-399
URL: http://jhbmi.ir/article-1-836-en.html
URL: http://jhbmi.ir/article-1-836-en.html
Ph.D. in Biophysics, Assistant Professor, Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
Abstract: (169 Views)
Introduction: Since the start of 2020, SARS-CoV-2 has infected a significant number of individuals, prompting extensive research. Antimicrobial peptides can be considered as a promising treatment for emerging viral pathogens due to their safety, efficacy, and specificity.
Method: In this study, first, 104 natural antiviral peptides were chosen from APD databases. Then, the third structure of proteins was modeled by PEP-FOLD 3 server. The structures were refined and optimized for docking operation. Subsequently, peptide-protein docking was performed using AutoDock Vina. The most favorable peptide-protein complex, chosen based on binding energy, was employed for molecular simulation using GROMACS. The simulation was carried out for 100 ns at 310° K and pH=7. Gromos54a7 force field was used in this study and the SPC water model was used as solvent.
Results: The obtained results from molecular dynamics examine the stability of complex structure and energy calculations. RMSD, RMSF, radius of gyration, and SASA analyses indicate the stability of the peptide-protein complex during the simulation. Additionally, LJ, CL, HBond, and ΔG analyses were conducted to calculate the energy interactions between the peptide and the Spike protein.
Conclusion: The results indicate that antimicrobial peptides can effectively bind to the SARS-CoV-2 spike protein, acting as inhibitors with a favorable binding energy. Consequently, these peptides can be employed for therapeutic and experimental studies of COVID-19.
Method: In this study, first, 104 natural antiviral peptides were chosen from APD databases. Then, the third structure of proteins was modeled by PEP-FOLD 3 server. The structures were refined and optimized for docking operation. Subsequently, peptide-protein docking was performed using AutoDock Vina. The most favorable peptide-protein complex, chosen based on binding energy, was employed for molecular simulation using GROMACS. The simulation was carried out for 100 ns at 310° K and pH=7. Gromos54a7 force field was used in this study and the SPC water model was used as solvent.
Results: The obtained results from molecular dynamics examine the stability of complex structure and energy calculations. RMSD, RMSF, radius of gyration, and SASA analyses indicate the stability of the peptide-protein complex during the simulation. Additionally, LJ, CL, HBond, and ΔG analyses were conducted to calculate the energy interactions between the peptide and the Spike protein.
Conclusion: The results indicate that antimicrobial peptides can effectively bind to the SARS-CoV-2 spike protein, acting as inhibitors with a favorable binding energy. Consequently, these peptides can be employed for therapeutic and experimental studies of COVID-19.
Type of Study: Original Article |
Subject:
Bioinformatics
Received: 2023/12/25 | Accepted: 2024/03/5
Received: 2023/12/25 | Accepted: 2024/03/5
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