Kişi: AKYÜZ, SEVİM
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SEVİM
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- YayınKısıtlıMolecular 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.
- YayınKısıtlıAn Investigation on the Structure and Group Vibrations of Balenine Molecule by Matrix Isolation IR Spectroscopy, DFT and MP2 Based Calculations(Pergamon-Elsevier Science Ltd., 2022) Balcı, K.; Akkaya, Y.; Arman, C.; Gören, Y.; AKYÜZ, SEVİM; Hacker, AL; Van Vleet, HJ; Ritzhaupt, G.; Collier, W. B.Stable conformers of neutral balenine were scanned through molecular dynamics simulations and energy minimizations using Allinger's MM2 force field. For each of the found minimum-energy conformers, geometry optimization and thermochemistry calculations were performed by using B3LYP, MP2, G3MP2B3 methods, 6-31G(d), 6-311++G(d,p) and aug-cc-pvTZ basis sets. The calculation results have indicated that balenine has about twenty stable conformers whose relative energies are in the range of 0-9.5 kcal/mol. Three of these are thought to provide the major contribution to matrix isolation IR spectra of the molecule. Our solvent calculations using the polarized continuum model revealed the stable zwitterion structures which are predicted to dominate IR spectra of balenine in water and heavy water (D2O) solvents. Pulay's SQM-FF method was used in scaling of the harmonic force constants and vibrational spectral data calculated for the neutral and zwitterion structures. These refined calculation data together with those obtained from anharmonic frequency calculations enabled us to correctly interpret the matrix isolation IR spectrum of balenine and the tautomerism-based changes observed in its KBr IR and solution (D2O) IR spectra. The results revealed the crucial role of conformation and zwitterionic tautomerism on the structure and vibrational spectral data of the molecule.
- YayınKısıtlıMolecular Modeling, Dimer Calculations, Vibrational Spectra, and Molecular Docking Studies of 5-Chlorouracil(Springer, 2020) Akalın E.; Çelik S.; AKYÜZ, SEVİMThe structure and vibrational calculations of 5-chlorouracil (5-ClU) and its most stable dimer have been analyzed using the DFT method with B3LYP/6-31++G(d,p) and wb97xd/6-31++G(d,p), respectively. Vibrational calculations of the monomeric and dimeric forms were performed using both harmonic and anharmonic oscillator approximations with the same basis sets. A complete vibrational analysis of the molecule has been performed by combining experimental Raman, FT-IR spectral data and quantum chemical calculations. In addition, the DNA docking analysis of 5-ClU molecule was performed. A 5-ClU molecule binds to the active site of DNA by hydrogen bonding interactions. The results show that the docked ligand formed a stable complex with DNA with binding affi nity of –5.3 kcal/mol.
- YayınKısıtlıMolecular 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.
- YayınAçık ErişimCyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi(Süleyman Demirel Üniversitesi, 2021) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.Bu çalışmada HT-29, Hela ve MCF-7 hücre hatlarına karşı antikanser etkigösteren Cyclo(Tyr-Tyr) dipeptidinin olası en kararlı yedi konformasyonu tirozinaminoasitlerinin χ yan zincir dihedral açılarına bağlı olarak konformasyon analiziyapılarak belirlenmiştir. Konformasyon analizi sonrasında belirlenenkonformasyonlara ait geometrik yapılar, yan zincire ait dihedral açıdaki değişimlerve konformerlerin toplam ve bağıl enerjileri ile bu konformasyonların toplamenerjilerine katkı sağlayan van der Waals, elektrostatik, torsiyon enerji katkılarıayrı ayrı hesaplanmıştır. Konformasyon analizi ile belirlenen en kararlı konformer,Gaussian03 programı kullanılarak, DFT (Density Functional Teory), B3LYPfonksiyoneli ve 6-31++G(d,p) baz seti ile optimize edilmiş ve optimize yapınıntemel titreşim dalga sayıları aynı teori düzeyinde hesaplanmıştır. Ayrıca, IRşiddetleri, Raman aktiviteleri, potansiyel enerji dağılımları MOLVIB programıkullanılarak saptanmış, Simirra programı ile ölçeklendirilmiş Raman aktiviteleri,Raman şiddetlerine dönüştürülmüştür. Ek olarak bu dipeptidin dimerik formuoluşturulmuş ve DFT/B3LYP/6-31G(d,p) teori düzeyinde optimize edilerek halkayapıya ait w, φ, Ψ dihedral açıları monomer form ile karşılaştırmalı olarakverilmiştir. Dimerik yapının oluşumunda rol oynayan moleküller arası hidrojenbağları belirlenmiştir.
- YayınKısıtlıStructural Characterization and Drug Delivery System of Natural Growth-Modulating Peptide Against Glioblastoma Cancer(Springer, 2021) Budama-Kılınç, Yasemin; Keçel-Gündüz, Serda; Çakır-Koç, Rabia; Aslan, Bahar; Bıçak, Bilge; Kökçü, Yağmur; Özel, Ayşen E.; AKYÜZ, SEVİMThe aim of the current study was to design a drug delivery nano-system of natural growth-modulating peptide known as GHK that naturally occurs in human plasma, saliva, and urine and determine possible anticancer activity against glioblastoma cancer based on in-silico and in-vitro evaluations. In this current study, a drug delivery nano-system based on Poly(epsilon-caprolactone) (PCL) were prepared by a double emission-precipitation method with different preparation parameters for optimization. The characterization of the optimum nanoparticles was performed with Zeta-Sizer, Ultraviolet-Visible (UV-Vis), Fourier Transform Infrared spectroscopy (FT-IR) and Raman spectroscopy, and Transmission Electron Microscopy (TEM) methods. The optimum size of the GHK loaded PCL nanoparticle was prepared with a 232.5 +/- 0.72 nm average particle size, - 10.8 +/- 0.64 mV zeta potential, and a 0.029 polydispersity index, 82.3% of encapsulation efficiency and 73% of loaded efficiency. In vitro cytotoxicity test revealed that the GHK loaded PCL nanoparticles had anticancer effect on glioblastoma cells. In vitro release study showed the sustained release behavior of GHK from nanoparticles during the period of 10 days study. In addition, molecular dynamics and molecular docking calculations, in vitro release study, and cytotoxicity tests showed that GHK loaded PCL nanoparticles may be used effectively for glioblastoma cancer therapy.
- YayınKısıtlıUsing 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, Gözde; Yılmaz, SalihEndometriosis 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.
- YayınAçık ErişimInteractions 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.
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- YayınKısıtlıStructural 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.
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