66 results
Search Results
Now showing 1 - 10 of 66
Publication Restricted Molecular Structure, Vibrational Spectra, Molecular Docking, and ADMET Study of Cellulose Triacetate II(Pleiades Publishing Inc., 2020) Çelik, Sefa; Demirağ, A. Demet; Özel, Ayşen E.; AKYÜZ, SEVİMPeople have started to look for alternative sources because of the health problems created by petrochemical products used in all areas of human life and environmental problems that remain intact in nature for years. In this study, molecular structure analysis of cellulose triacetate II (CTA II) molecule, obtained from cellulose II and acetate, was carried out. There is an important relationship between the structure and activity of molecules, so it is very important to determine the geometric structure of a molecule. Therefore, using density functional theory (DFT) the most stable molecular geometries of the cellulose triacetate II monomer (C12H18O9) as well as dimer (C24H36O18), which included intermolecular H-bonding, were calculated. The analogous calculations were carried out for the (CTA-II)(2)nano-cluster (C24H34O17), which represents the local structure of CTA-II crystal, and created by binding the two most stable CTA II molecules by covalent bond. Scaled wavenumbers and potential energy distribution of the vibrational modes of CTA monomer and (CTA-II)(2)nano-cluster were computed. In order to evaluate the interaction of CTA II with theAspergillus nigercellulase enzyme,which is an important that is active in cellulose digestion and CTA II, molecular docking studies were carried out. H-binding interactions between CTA II (in monomeric, dimeric, and cluster forms) and the active site of theAspergillus nigercellulase enzyme were shown. Moreover, in silico ADMET prediction study was calculated for CTA-II monomer to predict its druglikeness properties.Publication Metadata only Structural and spectroscopic investigation on antioxidant dipeptide, L-Methionyl-L-Serine: A combined experimental and DFT study(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2017-06-05) Kecel Gündüz, Serda; Bıçak, Bilge; Çelik, Sefa; Özel, Ayşen E.; AKYÜZ, SEVİM; 110526; 277135; 110147; 10127; 110745The focus of this study is to determine the conformational, structural and vibrational properties of Methionyl-Serine dipeptide (L-Methionyl-L-Serine, Met-Ser), a biological active molecule. To investigate their energetically preferred conformations, molecular mechanics methods were utilized to determine the optimal conformations of the 3402 different dihedral angle values of the backbone and side chains. It was found that the extended (e) backbone shape in the LB conformational range was the most stable LMethionyl-L-Serine dipeptide conformation, with 3.12 kcal/mol of energy. Density Functional Theory (DFT) was used to determine the optimized geometry, the vibrational wavenumbers and modes of the title dipeptide values, with 6-31G (d,p) and 6-311++G (d,p) basis sets. The potential energy distribution data was used to carry out the assignment of the bands. In addition, the vibrational spectra of the most stable conformer and its dimer form were determined and the obtained results were compared with the experimental IR and Raman spectra in the solid phase. To determine the presence of intramolecular charge transfer, molecular dipole moment, polarizability and hyperpolarizability, the Natural Bond Orbital (NBO), HOMO LUMO calculations, the linear polarizability (alpha) and the first order hyperpolarizability (fio) value analyses of the investigated molecule were carried out using the DFT with the B3LYP/6-31++G(d,p) basis set. This study aims to determine a relatively stable conformation of antioxidant dipeptide and to investigate the molecular geometry, molecular vibrations and hydrogen bonding interactions between monomeric and dimeric forms of Methiony-Serine dipeptide. (C) 2017 Elsevier B.V. All rights reserved.Publication Restricted Molecular Modeling, DFT Quantum Chemical Analysis, and Molecular Docking on Edotecarin, an Indolocarbazole Anticancer Agent(Taylor & Francis Ltd., 2022) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.Edotecarin is an indolocarbazole class antitumor agent that has significant anticancer effects against various types of cancer, especially lung, breast, and stomach cancer.The conformation analysis of the edotecarin was performed using the PM3 method and six stable conformations were obtained.Afterwards the obtained lowest energy conformation was optimized at the DFT/B3LYP/6-31++G(d,p) level of theory. The vibrational wavenumbers, the highest occupied molecular orbital, the lowest unoccupied molecular orbital and molecular electrostatic potential of the most stable conformer of edotecarin were calculated at the DFT/B3LYP/6-31++G(d,p) level of theory.The molecular docking of the edotecarin molecule against DNA, Topoisomerase I, DNA-Topoisomerase I complex,alpha(5)beta(1) and alpha(IIb)beta(3) integrins were performed to reveal its binding modes and binding affinities.Publication Metadata only The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin(Taylor & Francis Inc, 530 Walnut Street, Ste 850, Philadelphia, Pa 19106 USA, 2017) Kecel Gündüz, Serda; Çelik, Sefa; Özel, Ayşen E.; AKYÜZ, SEVİM; 110526; 110147; 110745; 10127In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of beta-endorphin (glycy-L-glutamine, glycyl-glutamine, beta-endorphin(30-31)), which is an inhibitory neuropeptide synthesized from beta-endorphin(1-31) in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the phi, Psi, chi. dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with -.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO-LUMO energy gaps were computed using the DFT with the B3LYP/ 6-31++ G(d, p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-L-glutamine dipeptide.Publication Metadata only Structure and Vibrational Analysis of 5-Chlorouracil and its Dimers(2018) Akalın, Elif; Çelik, Sefa; AKYÜZ, SEVİM; 46357; 110147; 10127Publication Metadata only Binding Interactions of TYR-ILE-GYL-SER-ARG Ligand with Laminin Receptor Models(2017) Çelik, Sefa; Özel, Ayşen; AKYÜZ, SEVİM; 110147; 10127; 110745Publication Metadata only Investigation of Cellulose Molecular Structure and Docking Study With BgI Enzyme(2018) Demirağ, Demet; Çelik, Sefa; Özel, Ayşen; AKYÜZ, SEVİM; 110147; 110745; 10127Publication Restricted Molecular Structure, Molecular Docking and Absorption, Distribution, Metabolism, Excretion and Toxicity study of Cellulose II(Wiley-VCH Verlag GmbH, 2021) Çelik, Sefa; Demirağ, Aliye Demet; Özel, E. Ayşen; AKYÜZ, SEVİMCellulose is a renewable biopolymer which is the most abundant in nature, formed by binding of glucose units with beta-1,4 glycosidic bonds. Cellulose is divided into two groups as bacterial cellulose (BC) and vegetable cellulose. This study reports the interaction mechanism of Cellulose II, which is a BC, with the cellulase enzymes, determined by molecular docking method based on key-lock theory. The most stable molecular geometry of the Cellulose II molecule was determined by density functional theory using Gaussian 09 program. The scaled vibration frequencies of optimized geometry were calculated by using Molvib program. Molecular electrostatic potential and frontier molecular orbital analyses were performed. Molecular interactions between cellulose II and endoglucanase, exogluconase and beta-glucosidase II have been determined. Moreover, the drug likeness and ADMET properties of cellulose II were analyzed for the prediction of pharmacokinetic profiles.Publication Open Access Interactions Mechanism of Commonly Used Drugs for the Treatment of COVID-19(Bulletin of the Chemical Society of Ethiopia, 2020) Çelik, Sefa; Demirağ, A. Demet; Özel, Ayşen E.; AKYÜZ, SEVİMIn this study conformation analysis of seven drugs commonly used in the treatment of COVID-19 was performed. The most stable conformers of the drug molecules were used as initial data for docking analysis. Using the Cavityplus program, the probable most active binding sites of both apo and holo forms of COVID-19 main protease enzyme (M-P(ro)) and spike glycoprotein of SARSCoV-2 receptors were determined. The interaction mechanisms of the 7 FDA approved drugs (arbidol, colchicine, dexamethasone, favipiravir, galidesivir, hydroxychloroquine, remdesivir) were examined using the AutoDock Vina program. The six of the seven drugs were found to be more stable in binding to apo form of COVID-19 M-P(ro) and spike glycoprotein. Moreover, a set of molecular mechanics (MM) Poisson-Boltzmann (PB) surface area (SA) calculations on the investigated drugs-protein systems were performed and the estimated binding free energy of remdesivir and the apo form of MP' system was found to be the best. The interaction results of FDA drugs with the apo form of COVID-19 M-P(ro) and spike glycoprotein can play an important role for the treatment of COVID-19.Publication Restricted 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.