PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Article Citation - WoS: 24Citation - Scopus: 27In Silico Analysis of Bacteriocins From Lactic Acid Bacteria Against SARS-CoV(Springer, 2021-11-27) Erol, Ismail; Kotil, Seyfullah Enes; Fidan, Ozkan; Yetiman, Ahmet E.; Durdagi, Serdar; Ortakci, FatihThe COVID-19 pandemic caused by a novel coronavirus (SARS-CoV-2) is a serious health concern in the twenty-first century for scientists, health workers, and all humans. The absence of specific biotherapeutics requires new strategies to prevent the spread and prophylaxis of the novel virus and its variants. The SARS-CoV-2 virus shows pathogenesis by entering the host cells via spike protein and Angiotensin-Converting Enzyme 2 receptor protein. Thus, the present study aims to compute the binding energies between a wide range of bacteriocins with receptor-binding domain (RBD) on spike proteins of wild type (WT) and beta variant (lineage B.1.351). Molecular docking analyses were performed to evaluate binding energies. Upon achieving the best bio-peptides with the highest docking scores, further molecular dynamics (MD) simulations were performed to validate the structure and interaction stability. Protein-protein docking of the chosen 22 biopeptides with WT-RBD showed docking scores lower than -7.9 kcal/mol. Pediocin PA-1 and salivaricin P showed the lowest (best) docking scores of - 12 kcal/mol. Pediocin PA-1, salivaricin B, and salivaricin P showed a remarkable increase in the double mutant's predicted binding affinity with -13.8 kcal/mol, -13.0 kcal/mol, and -12.5 kcal/mol, respectively. Also, a better predicted binding affinity of pediocin PA-1 and salivaricin B against triple mutant was observed compared to the WT. Thus, pediocin PA-1 binds stronger to mutants of the RBD, particularly to double and triple mutants. Salivaricin B showed a better predicted binding affinity towards triple mutant compared to WT, showing that it might be another bacteriocin with potential activity against the SARS-CoV-2 beta variant. Overall, pediocin PA-1, salivaricin P, and salivaricin B are the most promising candidates for inhibiting SARS-CoV-2 (including lineage B.1.351) entrance into the human cells. These bacteriocins derived from lactic acid bacteria hold promising potential for paving an alternative way for treatment and prophylaxis of WT and beta variants.Article Citation - WoS: 35Citation - Scopus: 41AirBNB and COVID-19: Space-Time Vulnerability Effects in Six World-Cities(Elsevier Sci Ltd, 2022-12) Kourtit, Karima; Nijkamp, Peter; Osth, John; Turk, UmutThis study examines the COVID-19 vulnerability and subsequent market dynamics in the volatile hospitality market worldwide, by focusing in particular on individual Airbnb bookings-data for six world-cities in various continents over the period January 2020-August 2021. This research was done by: (i) looking into factual survival rates of Airbnb accommodations in the period concerned; (ii) examining place-based impacts of intracity location on the economic performance of Airbnb facilities; (iii) estimating the price responses to the pandemic by means of a hedonic price model. In our statistical analyses based on large volumes of time- and space-varying data, multilevel logistic regression models are used to trace `corona survivability footprints' and to estimate a hedonic price-elasticity-of-demand model. The results reveal hardships for the Airbnb market as a whole as well as a high volatility in prices in most cities. Our study highlights the vulnerability and `corona echoeffects' on Airbnb markets for specific accommodation segments in several large cities in the world. It adds to the tourism literature by testing the geographic distributional impacts of the corona pandemic on customers' choices regarding type and intra-urban location of Airbnb accommodations.