Viral 3CL(pro) as a Target for Antiviral Intervention Using Milk-Derived Bioactive Peptides

Viruses of the picornavirus-like supercluster mainly achieve cleavage of polyproteins into mature proteins through viral 3-chymotrypsin proteases (3C(pro)) or 3-chymotrypsin-like proteases (3CL(pro)). Due to the essential role in processing viral polyproteins, 3C(pro)/3CL(pro) is a drug target for treating viral infections. The 3CL(pro) is considered the main protease (M(pro)) of coronaviruses. In the current study, the SARS-CoV-2 M(pro) inhibitory activity of di- and tri-peptides (DTPs) resulted from the proteolysis of bovine milk proteins was evaluated. A set of 326 DTPs were obtained from virtual digestion of bovine milk major proteins. The resulted DTPs were screened using molecular docking. Twenty peptides (P1–P20) showed the best binding energies (ΔG(b) < − 7.0 kcal/mol). Among these 20 peptides, the top five ligands, namely P1 (RVY), P3 (QSW), P17 (DAY), P18 (QSA), and P20 (RNA), based on the highest binding affinity and the highest number of interactions with residues in the active site of M(pro) were selected for further characterization by ADME/Tox analyses. For further validation of our results, molecular dynamics simulation was carried out for P3 as one of the most favorable candidates for up to 100 ns. In comparison to N3, a peptidomimetic control inhibitor, high stability was observed as supported by the calculated binding energy of the M(pro)-P3 complex (− 59.48 ± 4.87 kcal/mol). Strong interactions between P3 and the M(pro) active site, including four major hydrogen bonds to HIS41, ASN142, GLU166, GLN189 residues, and many hydrophobic interactions from which the interaction with CYS145 as a catalytic residue is worth mentioning. Conclusively, milk-derived bioactive peptides, especially the top five selected peptides P1, P3, P17, P18, and P20, show promise as an antiviral lead compound. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10989-021-10284-y.