Computer Simulation of Interaction of Natto-derived Peptides with DPP-IV and SARS-CoV-2 Mpro
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Abstract:
People with diabetes have a significantly higher mortality rate of coronavirus disease 2019 (COVID-19) than the general population, and the symptoms can be alleviated by inhibiting the activity of the key enzyme of type 2 diabetes, dipeptidyl peptidase-4 (DPP-IV), which is the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 Mpro). The UniProt, NCBI, and PDB databases were used to search the natto protein. Based on the BIOPBP-UWM database, a computer simulation of the hydrolysis of natto proteins by gastrointestinal proteases (pepsin, trypsin, and chymotrypsin) was conducted. Finally, molecular docking technology was used to study the ability of natto-protein-derived polypeptides to bind to DPP-IV and SARS-CoV-2 Mpro, and the amino acid residues involved in the interaction and the type of molecular forces were analyzed. The sugar transporters were found to strongly bind with the two enzymes. In particular, peptides with the sequences ISQPR, TIPVR, and STVTR had high binding scores (≤-130) for both enzymes and, therefore, were identified as inhibitory peptides of both DPP-IV and SARS-CoV-2 Mpro. Thus, natto protein has the potential to alleviate the symptoms of type 2 diabetes and be used as a nutritional supplement for people infected with COVID-19.
