TR-Dizin İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/396
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Article Investigation of Antiviral Potential of Food Carotenoids and Apocarotenoids Against RNA-Dependent RNA Polymerase of Hepatitis C Virus(2022-09-30) Fidan, OzkanHepatitis C disease have been a global health threat and affects a significant portion of world population. Hepatitis C have also been a silent health threat for Turkiye, where there are around half million people infected with Hepatitis C Virus (HCV). Disease burden and mortality are expected to increase gradually in the next 20 years in Turkiye. Unavailability of enough data on the currently-available drugs in routine clinical practice, their side effects and interactions with other drugs, and their efficacies on the less common genotypes indicates the necessity of alternative treatment options. Natural products from herbal and medicinal plants can indeed provide an alternative as being drug-like dietary supplements. In particular, the carotenoids and apocarotenoids are underexplored in their antiviral potential, including anti-HCV activities. Therefore, we focused on the virtual screening of various carotenoids and apocarotenoids against the RNA-dependent RNA polymerase (RdRp) of HCV. Molecular docking experiments showed strong binding affinities of the ligands to both palm and thumb domains of RdRp of HCV. In fact, some of them such as neoxanthin, crocin, canthaxanthin and cryptoflavin bound quite strongly to both domains compared to native ligands and current antiviral drugs. MD simulation for neoxanthin-RdRp complex confirmed the stability of the ligand within the binding cavity of RdRp throughout 100 ns simulation. This clearly indicated the potential of carotenoids, specifically neoxanthin, as RdRp inhibitor in treating HCV. Thus, this study not only discovered anti-HCV drug candidates with the properties of easy-to-access and low cost, but also paved the way for the development of carotenoid or apocarotenoid based dietary supplement candidates for the prevention and treatment of HCV.Article In Silico Evaluation of the Potential of Natural Products From Chili Pepper as Antiviral Agents Against DNA-Directed RNA Polymerase of the Monkeypox Virus(2024-03-24) Fidan, Ozkan; Mujwar, SomduttThis study focused on the discovery of new drug candidates effective against the monkeypox virus. Virtual screening was performed to evaluate the potential of chili pepper natural products against homology-modeled DNA-directed RNA polymerase of the monkeypox virus using molecular docking. Our findings revealed that structurally similar triterpenes such as α-amyrin, β-amyrin, and β-sitosterol had strong binding affinities towards the DNA-directed RNA polymerase and can inhibit this pivotal viral enzyme. The stability of one of the drug candidate molecules, α-amyrin with the strongest binding affinity towards the binding cavity of the enzyme was also confirmed via molecular dynamics simulation. This study showed that α-amyrin is a promising DNA-directed RNA polymerase inhibitor to treat monkeypox disease. It also paves the way for the idea of the potential dietary supplement candidate for monkeypox patients.Article Computational Identification of MicroRNAs From Ssdna Viruses(2018-09-30) Demirci, Müşerref Duygu SaçarMicroRNAs (miRNAs) are post-transcriptional regulators of gene expression and the fact that they are associated with variousdisease phenotypes is one of the main reasons for their importance. The complexity of experimental detection of miRNAs dueto their characteristics led to the development of computational methods. In this work, a machine learning based approach wasapplied to identify and analyze potential miRNAs that might be originated from 60 single strand DNA (ssDNA) viruses’genomes. The results suggest that 53 of these viruses may possibly produce proper miRNA precursors. Moreover, thepossibility of these candidate miRNA precursors’ ability to generate mature miRNAs that could target human genes and viralgenomes has been tested. Overall, the outcomes of this research indicate that there might be another level of host-virusinteraction through miRNAs which requires further experimental confirmation.