In Silico Study of Pacific oyster Antiviral Polypeptides as Potential Inhibitory Compounds for SARS-CoV-2 Main Protease

Abstract

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel pathogen that has triggered a pneumonia outbreak, and despite the measures, the pandemic still continues to occur. Objectives: The molecular docking analysis was used to test whether the human immunodeficiency virus 1 (HIV-1) protease inhibitory peptides. These marine polypeptides were isolated from the hydrolysate of Pacific oyster. Methods: Molecular docking process was performed using Molegro Virtual Docker software. The protein data bank file of the crystal structure of COVID-19 main protease in complex with an inhibitor N3 (ID 6LU7) was obtained from the PubChem data source. After preparing protein and removing water and internal ligand, the major cavity was selected for the next step, the docking procedure. Afterward, the MolDock score, Rerank score, Total interaction energy (between energy), and HBond item were calculated. The Remdesivir was used as a positive control in the docking project. Results: The results of the docking step were evaluated based on several bioinformatics docking scores, including MolDock score, Rerank score, Total interaction energy (between energy), and HBond. The hydrogen bond of remdesivir was -6.03673, and Leu-Leu-Glu-Tyr-Ser-Ileu polypeptide was -6.44185. The Rerank score of remdesivir was -98.9254 and for Leu-Leu-Glu-Tyr-Ser-Ileu polypeptide was -107.821. Of the two screened Pacific oyster polypeptides, the score of Leu-Leu-Glu-Tyr-Ser-Ileu ligand was higher than remdesivir. Conclusions: This study demonstrated that Pacific oyster compounds may have the potency to be evolved as an anti-COVID-19 main protease drug to fight against the novel coronavirus; however, preclinical and clinical trials are needed for further experimental and/or clinical scientific validation.