Browsing by Author "deniz karatas"

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    Phytochemicals of Hibiscus sabdariffa with Therapeutic Potential against SARS-CoV-2: A Molecular Docking Study
    (2023) EMEL AKBABA; deniz karatas
    In this study, the possible interactions of 17 phytochemicals that were reported as the most abundant biomolecules of Hibiscus sabdariffa, including many organic acids as well as catechin and quercetin derivatives, with 3CLpro and PLpro proteases of SARS-CoV-2 have been investigated via molecular docking. Caffeoylshikimic acid/3CLpro showed the lowest binding energy (-7.72 kcal/mol) with seven H-bonds. The second-lowest binding energy was computed in the chlorogenic acid/3CLpro complex (-7.18 kcal/mol), which was found to form 6 H-bonds. Also, low binding energies of cianidanol (-7.10 kcal/mol), cryptochlorogenic acid (-6.67 kcal/mol), and kaempferol (-6.82 kcal/mol) were calculated to 3CLpro with several H-bond interactions. Nelfinavir (-10.16 kcal/mol) and remdesivir (-6.40 kcal/mol), which have been used against COVID-19, were obtained to have low binding energies to 3CLpro with 3 H-bond formations each. On the other hand, the nicotiflorin/PLpro complex, which had the lowest binding energy (-7.40 kcal/mol), was found to have only 1 H-bond interaction. The second-lowest binding energy was reported in chlorogenic acid/PLpro (-7.20 kcal/mol), which was found to possess four H-bonds. On the other hand, epigallocatechin gallate/PLpro, which was shown to have a -5.95 kcal/mol binding energy, was found to form 8 H-bond interactions. Furthermore, the quercetin pentosylhexoside/PLpro complex was monitored to have low binding energy (-6.54 kcal/mol) with 9 H-bonds, which stands as the highest number of H-bonds in all complexes. Therefore, several molecules of Hibiscus sabdariffa were found to have strong binding affinity to the main proteases of SARS-CoV-2. This study suggests many compounds, including caffeoylshikimic acid and nicotiflorin, to inhibit 3CLpro and PLpro activities. As a result, numerous chemicals derived from Hibiscus sabdariffa have the potential to be employed therapeutically against SARS-CoV-2 infection.
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    Prebiotic Chemistry and Sepiolite: A Density Functional Theory Approach
    (2024) deniz karatas
    Sepiolite, a natural clay mineral, offers a large surface area due to its fibrous structure, allowing it to exhibit adsorption properties. In this study, the molecular interactions of sepiolite, a biocompatible clay mineral known as a biomaterial, and purine and pyrimidine molecules forming the bases of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) molecules were modeled by Density Functional Theory. In addition to geometry optimization, calculations of interaction energy, bond critical points, and electrostatic potential revealed that essential molecules for our source of life interact with basal surface of the clay. For example, the best interaction energies between bases/sepiolite were found to be -127.47 kJ/mol for guanine and -121.35 kJ/mol for cytosine, respectively. Looking at the modeling results, one of the most important factors affecting the interaction energies is hydrogen bonding. To reveal this, bond critical point analysis was performed, and it was computed that a large amount of intermolecular interaction energies came from hydrogen bonds. For example, it was calculated that approximately 70% of the total energy in the guanine/TOT (two tetrahedra and one octahedron) model comes from hydrogen bonds. Furthermore, this value for the cytosine/TOT model was found to be around 72%. The most effective indices in these two models are 145 and 135, with the H- bond energies recorded as -22.41 and -31.41 kJ/mol, respectively. Considering all analyses, it can be concluded that basal surfaces of sepiolite serve as suitable hosts for nitrogenous bases, which are the basic components of life. The aim of this study is to show that sepiolite offers an important surface feature to protect and stabilize DNA and RNA nucleic acid bases, which are necessary for the existence of living organisms, and to reveal the existence of a robust adsorption interaction between sepiolite and bases, thanks to the surface and chemical properties of sepiolite.