WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
Browse
2 results
Search Results
Article Citation - WoS: 6Citation - Scopus: 7Exploring the Binding Capacity of Lactic Acid Bacteria Derived Bacteriocins Against RBD of SARS-CoV Omicron Variant by Molecular Simulations(Taylor & Francis inc, 2023-01-02) Erol, Ismail; Kotil, Seyfullah Enes; Ortakci, Fatih; Durdagi, SerdarThe 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. SarmaArticle Citation - WoS: 26Citation - Scopus: 33Characterization of Genomic, Physiological, and Probiotic Features Lactiplantibacillus Plantarum DY46 Strain Isolated From Traditional Lactic Acid Fermented Shalgam Beverage(Elsevier, 2022-04) Yetiman, Ahmet E.; Keskin, Abdullah; Darendeli, Busra Nur; Kotil, Seyfullah Enes; Ortakci, Fatih; Dogan, MahmutLactiplantibacillus plantarum is a significant probiotic where it could be found in ubiquitous niches. In this study, a new Lb. plantarum strain DY46 was isolated from a traditional lactic-acid-fermented beverage called shalgam. The whole genome of the DY46 was sequenced and obtained sequences were assembled into a 3.32 Mb draft genome using PATRIC (3.6.8.). The DY46 genome consists of a single circular chromosome of 3,332,827 bp that is predicted to carry 3219 genes, including 61 tRNA genes, 2 rRNA operons. The genome has a GC content of 44.3% includes 98 predicted pseudogenes, 25 complete or partial transposases and 3 intact prophages. The genes encoding enzymes related in the intact EMP (Embden-Meyerhof-Parnas) and PK (phosphoketolase) pathways were predicted using BlastKOALA which is an indicator of having facultative heterofermentative pathways. DY46 genome also predicted to carry genes of Pln E, Pln F and Pln K showing the antimicrobial potential of this bacterium which can be linked to in vitro antagonism tests that DY46 can inhibit S.enterica sv. Typhimurium ATCC14028, K. pneumonie ATCC13883, and P. vulgaris ATCC8427. Moreover, it is determined that all resistome found in its genome were intrinsically originated and the strain was found to be tolerant to acid and bile concentrations by mimicking human gastrointestinal conditions. In conclusion, L. plantarum DY46 is a promising bacterium that appears to have certain probiotic properties, confirmed by "in vitro" and "in silico" analyses, and is a potential dietary supplement candidate that may provide functional benefits to the host.