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
In order to assess the colonization efficacy of the oral probiotic Streptococcus salivarius K12, a rapid method for specific detection and enumeration of the strain was developed. Here, we describe a ...two-step TaqMan™ quantitative PCR assay using primer-probe combinations targeting genes of the locus encoding the lantibiotic bacteriocin salivaricin B.
Salivarisin B (Sal B) Lactobacillus salivarius M7 tarafından kodlanan bir proteindir. Bu protein pepsin, tiripsin, kimotiripsin gibi protein parçalayan enzimlerden etkilenmemelerine rağmen, diğer bir ...protein parçalayıcı enzim olan proteinaz K'ya karşı kısmen duyarlıdırlar. Sal B 3 ile 9 arası pH yelpazesinde aktiftir. Yapılan çalışmalarda, Sal B'nin Lactobacillus fermentum, Lactobacillus plantarum, ve Lactobacillus acidophilus gibi bir çok yakın akraba bakteriler ve Listeria monocytogenes. Streptococcus faecalis, Staphylococcus aureus, ve Staphylococcus epidermidis gibi akraba olmayan bakteriler üzerine etkili olduğu bulunmuştur. Sal B'nin etki şekli bakterisidal olup ölüm hücre parçalanmadan meydana gelmektedir. Lactobacillus salivarius M7'den Sal B kodlanması ve ifadesinden sorumlu genin yeri daha önce karakterize edilmiştir.
Salivaricin B (SalB) is a protein encoded by Lactobacillus saiivarius M7. This protein is insensitive to proteolytic enzymes, such as pepsin, trypsin, and chymotrypsin, but is partially sensitive to proteinase K. SalB is also stable and maintains its activity over a range of pHs, from 3 to 9. SalB was found to be effective against many closely related lactic acid bacteria such as, L fermentum, L plantarum, L acidophi/us and distantly related gram-positive bacteria, including Listeria monocytogenes, Streptococcus faecalis, Staphylococcus aureus and Staph. epidermidis. The mode of action of SalB was obviously bactericidal, and death occurs without bacterial lysis. The gene responsible for SalB production in L salivarius M7 had previously been characterized.
