The changes in the SARS-CoV-2 genome have resulted in the emergence of new variants. Some of the variants have been classified as variants of concern (VOC). These strains have higher transmission rate and improved fitness. One of the prevalent were the Omicron variant. Unlike previous VOCs, the Omicron possesses fifteen mutations on the spike
protein's receptor binding domain (RBD). The modifications of spike
protein's key
amino acid residues facilitate the virus' binding capability against ACE2, resulting in an increase in the infectiousness of Omicron variant. Consequently, investigating the prevention and treatment of the Omicron variant is crucial. In the present study, we aim to explore the binding capacity of twenty-two
bacteriocins derived from Lactic Acid Bacteria (LAB) against the Omicron variant by using
protein-peptidedocking and molecular dynamics (MD) simulations. The Omicron variant RBD was prepared by introducing fifteen mutations using PyMol. The
protein-
peptide complexes were obtained using HADDOCK v2.4 docking webserver. Top scoring complexes obtained from HADDOCK webserver were retrieved and submitted to the
PRODIGY server for the prediction of binding energies. RBD-
bacteriocin complexes were subjected to MD simulations. We discovered promising
peptide-based therapeutic candidates for the inhibition of Omicron variant for example
Salivaricin B,
Pediocin PA 1, Plantaricin W,
Lactococcin mmfii and
Enterocin A. The lead
bacteriocins, except
Enterocin A, are biosynthesized by food-grade lactic acid bacteria. Our study puts forth a preliminary information regarding potential utilization of food-grade LAB-derived
bacteriocins, particularly
Salivaricin B and
Pediocin PA 1, for
Covid-19 treatment and prophylaxis.Communicated by Ramaswamy H. Sarma.