Person: YILMAZ, GÖZDE
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Öğr.Gör.
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YILMAZ
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GÖZDE
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Publication Shedding Light Into the Biological Activity of Aminopterin, Via Molecular Structural, Docking, and Molecular Dynamics Analyses(Taylor & Francis Inc., 2023) Çelik, Sefa; YILMAZ, GÖZDE; AKYÜZ, SEVİM; Özel, Ayşen E.In this study, the structural and anticancer properties of aminopterin, as well as its antiviral characteristics, were elucidated. The preferred conformations of the title molecule were investigated with semiempirical AM1 method, and the obtained the lowest energy conformer was then optimized by using density functional (DFT/B3LYP) method with 6-311++G(d,p) as basis set. The vibrational frequencies of the optimized structure were calculated by the same level of theory and were compared with the experimental values. The vibrational assignments were performed based on the computed potential energy distribution (PED) of the vibrational modes. The molecular electrostatic potential (MEP) and frontier molecular orbitals (HOMO, LUMO) analyses were carried out for the optimized structure and the chemical reactivity has been scrutinized. To enlighten the biological activity of aminopterin as anticancer and anti-COVID-19 agents, aminopterin was docked into DNA, & alpha;(IIB)& beta;(3) and & alpha;(5)& beta;(1)integrins, human dihydrofolate reductase, main protease (M-pro) of SARS-CoV-2 and SARS-CoV-2/ACE2 complex receptor. The binding mechanisms of aminopterin with the receptors were clarified. The molecular docking results revealed the strong interaction of the aminopterin with DNA (-8.2 kcal/mol), & alpha;(IIB)& beta;(3) and & alpha;(5)& beta;(1) integrins (-9.0 and -10.8 kcal/mol, respectively), human dihydrofolate reductase (-9.7 kcal/mol), M-pro of SARS-CoV-2 (-6.7 kcal/mol), and SARS-CoV-2/ACE2 complex receptor (-8.1 kcal/mol). Moreover, after molecular docking calculations, top-scoring ligand-receptor complexes of the aminopterin with SARS-CoV-2 enzymes (6M03 and 6M0J) were subjected to 50 ns all-atom MD simulations to investigate the ligand-receptor interactions in more detail, and to determine the binding free energies accurately. The predicted results indicate that the aminopterin may significantly inhibit SARS-CoV-2 infection. Thus, in this study, as both anticancer and anti-COVID-19 agents, the versatility of the biological activity of aminopterin was shown.Publication Structural and Spectral Analysis of Anticancer Active Cyclo(Ala-His) Dipeptide(Taylor & Francis Inc., 2020) Çelik, Sefa; YILMAZ, GÖZDE; Özel, Ayşen E.; AKYÜZ, SEVİMThe theoretically possible most stable conformation of the cyclic dipeptide, which has a significant anticancer activity, was examined by conformational analysis method and then by DFT calculations. With DFT calculations, cyclo(Ala-His) dipeptide was found to be more stable in boat form than in planar conformation. Moreover, conformations of the dimeric forms of the title molecule were investigated. The dimeric forms of the cyclo(Ala-His) dipeptide were created by combining two identical cyclo(Ala-His) monomers, in lowest energy configuration and as a result three energetically possible dimeric structures were obtained. The solid phase FTIR and Raman spectra of cyclo(Ala-His) have been recorded. The spectra were interpreted with the aid of quantum chemical calculations based on density functional theory, using B3LYP and wb97xd methods with 6-311++G(d,p) basis set, in order to elucidate structural and spectral properties of the investigated molecule. Experimental vibrational spectra are found to be in accord with the simulated vibrational spectra. The assignment of the vibrational modes was performed depending on the calculated potential energy distribution (PED).In slicomolecular docking of cyclo(Ala-His) was also carried out with DNA. The drug likeness and ADMET properties were analyzed for the prediction of pharmacokinetic profiles. The results revealed that the compound has the potential to be the leading molecule in the drug discovery process.Publication Using Raman Spectroscopy to Investigate the Molecular Level Characteristics of Endometriosis(Pleiades Publishing Inc., 2020) AKYÜZ, SEVİM; Çelik, Sefa; Usta, Abdullah Taner; Özel, Ayşen E.; Yılmaz, Salih; YILMAZ, GÖZDEEndometriosis is a benign gynecologic disorder. It is particularly common among young women and may make pregnancy difficult. In this study molecular level characterization of endometriosis tissues were performed using Raman spectroscopy in combination with multivariate statistical analysis. Three hundred sixty six Raman spectra recorded from different points of seventy two tissue samples, taken from the cyst walls of twelve patients were examined. Principle component analysis (PCA) followed by linear discriminant analysis (LDA) were performed on the Raman data, and the samples were then classified into three groups: severe, moderate, and weak endometriosis. In the severe endometriosis group, the relative band intensities of DNA were increased. Moreover, increase in pyrrole moieties and kynurenine were seen. The results show that endometriosis severity correlates to increase in DNA concentration, and degradation of tryptophan due to increased indoleamine-pyrrole 2,3-dioxygenase (IDO) activity, and an increase in kynurenine concentration and pyrrole intermediate. It is concluded that Raman spectroscopy is capable of providing a quick diagnosis, ahead of the pathology result being reported.