tetano
Editor, Senior Moderator
Front Mol Biosci
. 2022 Jan 27;8:791642.
doi: 10.3389/fmolb.2021.791642. eCollection 2021.
Molecular Docking and Dynamics Studies to Explore Effective Inhibitory Peptides Against the Spike Receptor Binding Domain of SARS-CoV-2
Suvro Biswas[SUP] 1 [/SUP], Shafi Mahmud[SUP] 1 [/SUP], Mohasana Akter Mita[SUP] 1 [/SUP], Shamima Afrose[SUP] 1 [/SUP], Md Robiul Hasan[SUP] 1 [/SUP], Mst Sharmin Sultana Shimu[SUP] 1 [/SUP], Md Abu Saleh[SUP] 1 [/SUP], Gomaa Mostafa-Hedeab[SUP] 2 3 [/SUP], Mohammed Alqarni[SUP] 4 [/SUP], Ahmad J Obaidullah[SUP] 5 [/SUP], Gaber El-Saber Batiha[SUP] 6 [/SUP]
Affiliations
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic due to the high transmission and mortality rate of this virus. The world health and economic sectors have been severely affected by this deadly virus, exacerbated by the lack of sufficient efficient vaccines. The design of effective drug candidates and their rapid development is necessary to combat this virus. In this study, we selected 23 antimicrobial peptides from the literature and predicted their structure using PEP-FOLD 3.5. In addition, we docked them to the SARS-CoV-2 spike protein receptor-binding domain (RBD) to study their capability to inhibit the RBD, which plays a significant role in virus binding, fusion and entry into the host cell. We used several docking programs including HDOCK, HPEPDOCK, ClusPro, and HawkDock to calculate the binding energy of the protein-peptide complexes. We identified four peptides with high binding free energy and docking scores. The docking results were further verified by molecular dynamics (MD) simulations to characterize the protein-peptide complexes in terms of their root-mean-square fluctuation (RMSF), root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond formation. Allergenicity and toxicity predictions suggested that the peptides we identified were non-allergenic and non-toxic. This study suggests that these four antimicrobial peptides could inhibit the RBD of SARS-CoV-2. Future in vitro and in vivo studies are necessary to confirm this.
Keywords: RBD; SARS-CoV-2; molecular dynamics; peptide-protein docking; peptides.
. 2022 Jan 27;8:791642.
doi: 10.3389/fmolb.2021.791642. eCollection 2021.
Molecular Docking and Dynamics Studies to Explore Effective Inhibitory Peptides Against the Spike Receptor Binding Domain of SARS-CoV-2
Suvro Biswas[SUP] 1 [/SUP], Shafi Mahmud[SUP] 1 [/SUP], Mohasana Akter Mita[SUP] 1 [/SUP], Shamima Afrose[SUP] 1 [/SUP], Md Robiul Hasan[SUP] 1 [/SUP], Mst Sharmin Sultana Shimu[SUP] 1 [/SUP], Md Abu Saleh[SUP] 1 [/SUP], Gomaa Mostafa-Hedeab[SUP] 2 3 [/SUP], Mohammed Alqarni[SUP] 4 [/SUP], Ahmad J Obaidullah[SUP] 5 [/SUP], Gaber El-Saber Batiha[SUP] 6 [/SUP]
Affiliations
- PMID: 35187069
- PMCID: PMC8851422
- DOI: 10.3389/fmolb.2021.791642
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic due to the high transmission and mortality rate of this virus. The world health and economic sectors have been severely affected by this deadly virus, exacerbated by the lack of sufficient efficient vaccines. The design of effective drug candidates and their rapid development is necessary to combat this virus. In this study, we selected 23 antimicrobial peptides from the literature and predicted their structure using PEP-FOLD 3.5. In addition, we docked them to the SARS-CoV-2 spike protein receptor-binding domain (RBD) to study their capability to inhibit the RBD, which plays a significant role in virus binding, fusion and entry into the host cell. We used several docking programs including HDOCK, HPEPDOCK, ClusPro, and HawkDock to calculate the binding energy of the protein-peptide complexes. We identified four peptides with high binding free energy and docking scores. The docking results were further verified by molecular dynamics (MD) simulations to characterize the protein-peptide complexes in terms of their root-mean-square fluctuation (RMSF), root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond formation. Allergenicity and toxicity predictions suggested that the peptides we identified were non-allergenic and non-toxic. This study suggests that these four antimicrobial peptides could inhibit the RBD of SARS-CoV-2. Future in vitro and in vivo studies are necessary to confirm this.
Keywords: RBD; SARS-CoV-2; molecular dynamics; peptide-protein docking; peptides.