Abstract
The 2019 coronavirus pandemic disease (COVID-19) is still declared a global pandemic by the World Health Organization (WHO). Therefore, an effort that is considered effective in finding therapeutic agents is needed to prevent the spread of COVID-19 infection. One of the steps that can be chosen is by utilizing antimicrobial peptides (AMPs) from animal venom by targeting the specific receptor of SARS-CoV-2, namely the main protease (Mpro). Through this research, a computational approach will be conducted to predict antiviral activity, including protein-peptide docking using PatchDock algorithm, to identify, evaluate, and explore the affinity and molecular interactions of four types of antimicrobial peptides (AMPs), such as Mucroporin, Mucroporin-M1, Mucroporin-S1, and Mucroporin-S2 derived from scorpion venom (Lychas mucronatus) against main protease (Mpro) SARS-CoV-2. These results were then confirmed using protein-peptide interaction dynamics simulations for 50 ns using Gromacs 2016 to observe the molecular stability to the binding site of SARS-CoV-2 Mpro. Based on protein-peptide docking simulations, it was proven that the Mucroporin S-1 peptides have a good affinity against the active site area of SARS-CoV-2 Mpro, with an ACE score of −779.56 kJ/mol. Interestingly, Mucroporin-S1 was able to maintain the stability of its interactions based on the results of RMSD, RMSF, and MM/PBSA binding free energy calculations. The results of the computational approach predict that the Mucroporin-S1 peptide is expected to be useful for further research in the development of new antiviral-based AMPs for the COVID-19 infectious disease.
Highlights
Coronaviruses (CoVs) are a large family of singlestranded RNA viruses that infect animals and humans and can cause several diseases in various system organs of the body, such as gastrointestinal, respiratory, hepatic, and neurology (Weiss, & Leibowitz, 2011)
All modeled antimicrobial peptides (AMPs) derived from scorpion venom (Lychas mucronatus) were simulated by the protein-peptide binding method to the main protease (Mpro) of SARS-CoV-2 that acts as a target macromolecule (Figure 1)
It can be predicted that each peptide molecule will occupy part of the SARS-CoV-2 Mpro based on its physicochemical properties
Summary
Coronaviruses (CoVs) are a large family of singlestranded RNA viruses that infect animals and humans and can cause several diseases in various system organs of the body, such as gastrointestinal, respiratory, hepatic, and neurology (Weiss, & Leibowitz, 2011). The SARS-CoV-2 Mpro macromolecules that have been prepared were identified, evaluated, and explored binding site areas that are most responsible for antimicrobial activity using BIOVIA Discovery Studio 2020 (BIOVIA, 2020). Analysis of the interaction stability of Mucroporin peptide molecules and SARS-CoV-2 Mpro macromolecules was carried out by calculating the residual values of RMSD and RMSF at the binding site during the simulation.
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