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Öğe Binding affinities of sanggenon derivatives as PTP1B inhibitors; using molecular dynamics and free energy calculations(Azerbaijan National Academy of Sciences, 2023) Kocakaya, Şafak ÖzhanRecently, protein tyrosine phosphatase 1B (PTP1B) inhibitors have become the frontier as possible target-ing for anti-cancer and antidiabetic drugs. The contemporary observe represents a pc assisted version to in-vestigate the importance of precise residues within the binding web site of PTP1B with numerous Sang-genon derivatives remoted from nature. Molecular dynamics (MD) simulations were performed to estimate the dynamics of the complexes, and absolute binding unfastened energies have been calculated with exclu-sive additives, and carried out through the usage of the Molecular Mechanics-Poisson-Boltzmann floor re-gion (MM-PB/SA) and Generalized Born surface vicinity (MM-GB/SA) strategies. The effects show that the expected free energies of the complexes are normally constant with the available experimental statis-tics. MM/GBSA free energy decomposition analysis shows that the residues Asp29, Arg24, Met258, and, Arg254 in the second active site in PTP1B are crucial for the excessive selectivity of the inhibitors.Öğe Docking studies of natural product derived carvacrol type aromatic monoterpenes against COVID-19 and comparison with used synthetic drugs: Potential of carvacryl acetate against SARS-CoV-2 (COVID-19)(Dicle Üniversitesi Fen Bilimleri Enstitüsü, 2023) Kocakaya, Şafak Özhan; Ertaş, Abdulselam; Yener, İsmail; Arıca, Enes; Dinçel, DemetThe COVID-19 pandemic that broken out in 2020 is becoming more worrying for the world. Although there is no 100 % success against COVID-19, certain synthetic drugs are currently used despite various side effects. Therefore, studies on the discovery of new treatment alternatives come to the fore. Studies so far show that natural products are still important resources for the discovery of new therapeutic agents. Plantderived essential oils are complex volatiles composed of various phytochemicals, mostly containing compounds such as sesquiterpenes, monoterpenes, and phenylpropanoids. In this study, especially thymol and carvacrol compounds specific to the Lamiaceae (Labiate) family and aromatic monoterpenes derived from these compounds were modeled against COVID-19. Results were compared with remdesivir, hydroxychloroquine, and favipiravir used as synthetic drugs. Dock and molecular dynamics simulations analyzed these molecules’ potential inhibitor efficiency of the SARS-CoV2 Mpro . Lipinski parameters and Docking results were demonstrated that ligands carvacrol (2), carvacryl acetate (11) and cuminaldehyde (12) are potential inhibitors towardsCOVID-19. According to the results, it is seen that medicinal aromatic herbs, which contain these volatile components with the fewer side effects than synthetic drugs, have the potential to be used as supplements in the pharmaceutical industry.Öğe Essential oil contents of Hypericum linarioides , H. helianthemoides, and H. lydium with their biological activities: Importance of Hypericum genus in the cosmeceutical and pharmaceutical industries(Springer, 2023) Akdeniz, Mehmet; Yener, İsmail; Ertaş, Abdülselam; Dincel, Demet; Fırat, Mehmet; Kocakaya, Şafak Özhan; Yigitkan, Serkan; Türkmenoğlu, Fatma Pınar; Aydın, Fırat; Kolak, UfukIn the literature, more than 3000 studies have been carried out on species in the Hypericum genus in the last ten years, especially for H. perforatum. The importance of Hypericum species in traditional medicine and modern medicine is increasing day by day. From this point of view, the chemical composition of H. linarioides, H. helianthemoides, and H. lydium essential oils was analyzed by GC-MS/FID. In addition, their antioxidant, cytotoxic and antimicrobial activities along with their enzyme inhibitory potentials (cholinesterase, urease, tyrosinase, elastase and, collagenase) were defined. Also, in vitro and in silico studies of the major components of the species have been carried out on the studied enzymes. H. linarioides and H. helianthemoides were found to be rich in monoterpene hydrocarbons (63.96% and 43.86%, respectively), and H. lydium in sesquiterpene hydrocarbons (48.41%). The major components were indicated as α-pinene for H. linarioides (50.39%) and for H. helianthemoides (36.84%), and β-selinene for H. lydium (10.12%). H. lydium essential oil exhibited very high cytotoxic activity on breast cancer (MCF-7) (selectivity indices SI: 12) and colon cancer (HT-29) (SI: 2) cell lines. In particular, the selectivity indice value in MCF-7 cell lines of H. lydium could have natural therapeutic potential for breast cancer. H. lydium possessed neuropharmacological potential due to its high anticholinesterase activity. Since H. linarioides indicated high anti-aging potential (tyrosinase, elastase, and collagenase enzyme inhibitory activities), it could be used in the cosmetic industry.Öğe The molecular modeling of novel inhibitors of protein tyrosine phosphatase 1B based on catechol by MD and MM-GB (PB)/SA calculations(Korean Chemical Society, 2014) Kocakaya, Şafak ÖzhanBinding modes of a series of catechol derivatives such as protein tyrosine phosphatase 1B (PTP1B) inhibitors were identified by molecular modeling techniques. Docking, molecular dynamics simulations and free energy calculations were employed to determine the modes of these new inhibitors. Binding free energies were calculated by involving different energy components using the Molecular Mechanics-Poisson-Boltzmann Surface Area and Generalized Born Surface Area methods. Relatively larger binding energies were obtained for the catechol derivatives compared to one of the PTP1B inhibitors already in use. The Molecular Mechanics/ Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicated that the hydroxyl functional groups and biphenyl ring system had favorable interactions with Met258, Tyr46, Gln262 and Phe182 residues of PTP1B. The results of hydrogen bound analysis indicated that catechol derivatives, in addition to hydrogen bonding interactions, Val49, Ile219, Gln266, Asp181 and amino acid residues of PTP1B are responsible for governing the inhibitor potency of the compounds. The information generated from the present study should be useful for the design of more potent PTP1B inhibitors as anti-diabetic agents.Öğe Proflavin içeren, (+)-Duocarmycin antibiyotiği analoglarının sentezlenmesi ve DNA üzerine etkilerinin araştırılması(2013) Kızıl, Murat; Tanrıkurt, Emen; Aytekin, Çetin; Kocakaya, Şafak Özhan; Çeken, Bircan Toprancı; Pirinççioğlu, Mihdiye[Abstract Not Available]
