Dermaseptin-Based Antiviral Peptides to Prevent COVID-19 through In Silico Molecular Docking Studies against SARS-CoV-2 Spike Protein

Abstract

A pandemic coronavirus disease of 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now been declared a global pandemic by the World Health Organization. The search for new drugs, especially by utilizing antiviral peptides is a very potential area. Through this study, protein-peptide docking and protein-protein docking simulations were conducted using in silico methods to identify, evaluate, and explore the molecular affinity and interaction of dermaseptin peptide molecules produced by frogs of the genus Phyllomedusa against the SARS-CoV-2 spike protein macromolecule, and its effect on attachment to the surface of the ACE-2 (Angiotensin Converting Enzyme-2) receptor. Protein-peptide docking simulation results show that dermaseptin-S9 peptide molecule has the best affinity to the active site of SARS-CoV-2 spike protein macromolecule binding site, with a binding free energy value of −792.93 kJ/mol. Then the results of protein-protein docking simulations proved that dermaseptin-S9 peptide molecule was able to prevent the attachment of SARS-CoV-2 spike protein to the surface of the ACE-2 receptor, with a total energy value of 517.85 kJ/mol. Therefore, it is hoped that dermaseptin-S9 peptide molecule can be further studied in the development of novel antiviral peptide candidates for the control of COVID-19 infectious disease.

SARS-CoV-2 spike protein-, main protease- and papain-like-protease-targeting peptides from seed proteins following gastrointestinal digestion: An in silico study

“…In response to the COVID-19 pandemic, there is a need to develop countermeasures urgently. This has fueled current interest among researchers to adopt molecular docking and other in silico approaches to evaluate the potential of existing antiviral drugs and bioactive natural products in targeting SARS-CoV-2 ( Fakih, 2020 ). Molecular docking has been widely exploited as structure-based drug discovery tool owing to its quick, low-cost and precise prediction of the biological activity and interactions of ligands with target molecules.…”

Identification of the molecular mechanism of christinin compounds from Arabian bidara leaves (Ziziphus spina-christi L.) on microorganisms that cause female genital problems through computational approaches

“…The crystal structure of target protein macromolecules that has been downloaded from the Protein Data Bank web is then prepared first using MGLTools 1.5.6 software with AutoDock 4.2. The macromolecule preparation stage for this target protein is carried out by removing water molecules and natural ligands, adding polar hydrogen atoms, and calculating Gasteiger's partial charge (Fakih, 2020).…”

Antiviral peptides from aquatic organisms: Functionality and potential inhibitory effect on SARS-CoV-2

“…Other studies have predicted the efficacy of antiviral peptides against SARS-CoV-2 through computational approaches. For instance, Dermaseptin-s9 peptide showed the best affinity to the active site of SARS-CoV-2 macromolecule in protein-peptide docking simulation ( Fakih, 2020 ). Similarly, Ling et al (2020) designed antiviral peptides through in silico modelling seeking compounds capable of preventing SARS-CoV-2 membrane fusion, which could be used in the prevention and treatment of COVID-19 pandemic.…”