Abstract
Recently, an outbreak of a novel coronavirus disease (COVID-19) has reached pandemic proportions, and there is an urgent need to develop nutritional supplements to assist with prevention, treatment, and recovery. In this study, SARS-CoV-2 inhibitory peptides were screened from nut proteins in silico, and binding affinities of the peptides to the SARS-CoV-2 main protease (M pro ) and the spike protein receptor-binding domain (RBD) were evaluated. Peptide NDQF from peanuts and peptide ASGCGDC from almonds were found to have a strong binding affinity for both targets of the coronavirus. The binding sites of the NDQF and ASGCGDC peptides are highly consistent with the M pro inhibitor N3. In addition, NDQF and ASGCGDC exhibited an effective binding affinity for amino acid residues Tyr453 and Gln493 of the spike RBD. Molecular dynamics simulation further confirmed that the NDQF and ASGCGDC peptides could bind stably to the SARS-COV-2 M pro and spike RBD. In summary, nut protein may be helpful as nutritional supplements for COVID-19 patients, and the screened peptides could be considered a potential lead compound for designing entry inhibitors against SARS-CoV-2.
Keywords: Molecular docking; Molecular dynamics simulation; Nut proteins; SARS-COV-2 M(pro); SARS-CoV-2 spike RBD.
【저자키워드】 molecular docking, Molecular dynamics simulation, Nut proteins, SARS-COV-2 M(pro), SARS-CoV-2 spike RBD., 【초록키워드】 COVID-19, Treatment, coronavirus disease, SARS-CoV-2, coronavirus, pandemic, peptide, molecular docking, molecular dynamics, protease, in silico, novel coronavirus disease, SARS-CoV-2 main protease, binding affinity, Spike protein, SARS-CoV-2 Spike RBD, binding site, Molecular dynamics simulation, Novel coronavirus, Protein, outbreak, RBD, peptides, target, entry inhibitors, inhibitor, COVID-19 patients, Entry inhibitor, Amino acid, binding affinities, inhibitor N3, proportions, domain, M pro, amino acid residues, peanuts, inhibitory, amino acid residue, effective, develop, addition, evaluated, screened, exhibited, the spike protein, reached, assist, the SARS-CoV-2, 【제목키워드】 protease, SARS-CoV-2 spike protein, identification,