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.
Highlights
The whole world is currently experiencing a pandemic which originated in the Chinese city of Wuhan in Hubei province in late December 2019
Venom extracted from hymenopteran insects, including the solitary bee Hylaeus signatus, is a prominent source of antimicrobial peptides (AMPs)
We found that several HYL peptides bind the receptor-binding domain (RBD) of SARS-CoV-2 in silico with favorable binding energy and stable conformations through 100 ns of molecular dynamics simulation
Summary
The whole world is currently experiencing a pandemic which originated in the Chinese city of Wuhan in Hubei province in late December 2019. This life-threatening agent was named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by WHO, which declared it as “the first pandemic of the 21st century” (De Wit et al, 2016; Dong et al, 2020; Gorbalenya et al, 2020; Li Q et al, 2020; Li X et al, 2020; Machhi et al, 2020; Zhu et al, 2020). As of November 16, 2021, there have been a total of 254,807,373 confirmed cases and 5,126,239 deaths
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
