Makale KoleksiyonuArticle Collecitonhttps://hdl.handle.net/11491/21532024-03-28T12:17:30Z2024-03-28T12:17:30ZEvaluation of Zerumbone as an EGFR Tyrosine Kinase Inhibitor by Molecular Docking MethodYonar, DilekBaba, BurcuKarayel, Arzuhttps://hdl.handle.net/11491/87892024-02-02T11:01:36Z2023-01-01T00:00:00ZEvaluation of Zerumbone as an EGFR Tyrosine Kinase Inhibitor by Molecular Docking Method
Yonar, Dilek; Baba, Burcu; Karayel, Arzu
Objective: EGFR-TK domain is of great importance in the initiation and progression of various cancer types, especially lung cancer. The existing EGFR-TK inhibitors have numerous side effects, which make them improper to be utilized as cancer therapeutics. In this study, we aimed to analyze the activity of zerumbone as an anticancer agent targeting EGFR by molecular docking approach and to evaluate its activity in comparison with curcumin. Material and Method: MEP and HOMO-LUMO analyses were achieved at B3LYP/6-31G(D,P) level to evaluate electrostatic interactions that affect binding of EGFR with zerumbone and curcumin. Their binding energies were determined by molecular docking and compared with erlotinib as reference ligand. Result and Discussion: Docking studies showed higher bindings (lower binding energy) for curcumin and zerumbone with binding energies -8.0 and -7.6 kcal/mol, respectively, compared to erlotinib (-7.3 kcal/mol). However, there is no significant difference between them. The ΔE energy gap of zerumbone was 5.09 eV which implies that this compound has more stability in comparison with curcumin (ΔE=3.68 eV) and erlotinib (ΔE=4.29eV). Also, zerumbone showed strong hydrogen bond interactions with EGFR, making it candidate as EGFR inhibitor, as did both in curcumin and erlotinib. It was concluded that zerumbone may have potential for inhibitory activity against EGFRTK.; Amaç: EGFR-TK bölgesi, başta akciğer kanseri olmak üzere çeşitli kanser türlerinin başlaması ve ilerlemesinde büyük önem taşımaktadır. Mevcut EGFR-TK inhibitörlerinin çeşitli yan etkilerinin varlığı, onların uygun kanser terapötikleri olarak kullanılmalarını sınırlandırmaktadır. Bu çalışmada, moleküler yerleştirme yaklaşımı ile EGFR'yi hedef alan bir antikanser ajan olarak zerumbonun aktivitesini analiz etmeyi ve aktivitesini kurkumin ile karşılaştırmalı olarak değerlendirmeyi amaçladık. Gereç ve Yöntem: EGFR'nin zerumbon ve kurkumin ile bağlanmasını etkileyen elektrostatik etkileşimleri değerlendirmek için B3LYP/6-31G(D,P) seviyesinde MEP ve HOMO-LUMO analizleri yapıldı. Bağlanma enerjileri moleküler yerleştirme ile belirlendi ve referans ligand olarak erlotinib ile karşılaştırıldı. Sonuç ve Tartışma: Yerleştirme çalışmaları, erlotinib (-7.3 kcal/mol) ile karşılaştırıldığında, sırasıyla -8.0 ve -7.6 kcal/mol bağlanma enerjileriyle kurkumin ve zerumbon için daha yüksek bağlanmalar (düşük bağlanma enerjisi) gösterdi. Ancak aralarında önemli bir fark gözlenmedi. Zerumbonun ΔE enerji aralığı 5.09 eV olarak bulundu. Bu sonuç, bu bileşiğin kurkumin (ΔE=3.68 eV) ve erlotinib ile karşılaştırıldığında (ΔE=4.29 eV) daha fazla kararlılığa sahip olduğu anlamına gelmektedir. Ayrıca, zerumbon EGFR ile güçlü hidrojen bağı etkileşimleri gösterdi ve bu da onun hem kurkumin hem de erlotinib'deki gibi EGFR inhibitörü olarak potansiyeli olduğunu göstermiştir. Zerumbonun EGFR-TK'ye karşı inhibitör aktiviteye sahip olabileceği sonucuna varıldı.
2023-01-01T00:00:00ZRevealing the effect of Co/Cu (d7/d9) cationic doping on an electronic acceptor ZnO nanocage surface for the adsorption of citric acid, vinyl alcohol, and sulfamethoxazole ligands: DFT-D3, QTAIM, IGM-NCI, and MD analysisGassoumi, B.Mahmoud, A.M. AhmedNasr, S.Karayel, ArzuÖzkınalı, Sevilhttps://hdl.handle.net/11491/87882024-02-02T10:39:51Z2023-01-01T00:00:00ZRevealing the effect of Co/Cu (d7/d9) cationic doping on an electronic acceptor ZnO nanocage surface for the adsorption of citric acid, vinyl alcohol, and sulfamethoxazole ligands: DFT-D3, QTAIM, IGM-NCI, and MD analysis
Gassoumi, B.; Mahmoud, A.M. Ahmed; Nasr, S.; Karayel, Arzu; Özkınalı, Sevil
The electron-spin duality and propagation of the active sites of free electrons are of interest for adsorbing the guests and fixing them with strong hydrogen bonds (HB). The coherence of the systems with the guests is one of the main parameters that favor the experimentation of new systems on primary column adsorption phenomena. The stability and the adaptable symmetries in all directions justify the use of a “nanocage” (ZnO) for studying adsorption phenomena. The formation of stable electronic charge transfer paths between sites occupied by very stable atomic orbitals ensures the success of the adsorption of the ligands. Electronic characterization (MES, FMO, DOS, and cationic doping) is used to describe the movement of the intra-Cu-Co/Zn19O20 electrons. The phenomena of charge transfer, stability, types of orbital occupations, adsorption sites, electron migration direction, conductivity, and reactivity of such systems are thoroughly explored. Based on these findings, the efficiency of a Cu–Co/Zn19O20 nanocage to adsorb three different ligands (medical ligands, prostate biomarkers, and antibiotics) is studied. From the reactivity parameter discussions, it is found that the copper or cobalt-doped nanocage-Citric Acid has a strongly electronegative index (4.40 eV and 4.91 eV) and hardness (1.99 eV and 1.82 eV) properties. The Fourier transform infrared analyses and orbital localizations (α and β) clearly demonstrate that the charge transfer occurs inter-surface, from nanocages to adsorbed ligands. Bader’s theory analysis for the adsorption ligands VA (Vinyl Alcohol), CA (Citric Acid), and SMX (Sulfamethoxazole) by the doped copper and cobalt nanocages demonstrates that these systems are much more adequate for adsorbing the ligand antibiotics than the other hosts. The highly adsorbent energy of sulfamethoxazole by Cu–Zn19O20 is equal to − 582.86 kJ. mol-1. The IGM-NCI/ELF analyses support these findings, revealing that the Cu/Co–Zn19O20 nanocages adsorb SMX via hydrogen bonding and van der Waals interactions, as they also did in DFT-D3 and FT-IR analyses. LOL analyses support this claim by visualizing single-pair spins in excess surrounding acceptor atoms (O) in the two systems. Molecular dynamics simulations show that SMX is quickly adsorbed by nanocages of Zn19O20 doped with copper (d9) or cobalt (d7).
2023-01-01T00:00:00ZVoltammetric Analysis of Thiram with Bimetallic Nanosensor and Investigation of Adsorption Mechanism by DFT-D3 MethodÇelik, MuratKanbeş Dindar, ÇiğdemKarayel, ArzuBozal Palabıyık, BurçinUslu, Bengihttps://hdl.handle.net/11491/87872024-02-02T10:22:38Z2023-01-01T00:00:00ZVoltammetric Analysis of Thiram with Bimetallic Nanosensor and Investigation of Adsorption Mechanism by DFT-D3 Method
Çelik, Murat; Kanbeş Dindar, Çiğdem; Karayel, Arzu; Bozal Palabıyık, Burçin; Uslu, Bengi
In this study, to detect thiram electrochemically, a simple nanosensor based on a glassy carbon electrode (GCE) modified with green-synthesized Ag and Au nanoparticles was designed. AuNPs@AgNPs/GCE nanosensor gave considerably greater signal for 5 ppm thiram in pH 3.0 phosphate buffer solution using adsorptive stripping differential pulse voltammetry compared to bare GCE. Under ideal conditions, the nanosensor produced a linear concentration calibration curve extending from 0.2 to 1.4 ppm for thiram, with limits of detection and quantification of 0.033 ppm and 0.100 ppm, respectively. The developed electrochemical bimetallic nanosensor demonstrated high sensitivity and stability, showing that it is a novel and promising platform for thiram determination. Furthermore, the nanosensor was used to assess thiram in human serum and recovery was obtained as 103.6%. DFT-D3 results showed that covalent modification of GCE with AuNPs/AgNPs occurs with the electron transfer between the electrode surface and thiram by bonding sulfur atoms of thiram to AgNPs and AuNPs. Both experimental and theoretical analyses showed that the modification with Ag and Au, GCE appeared to be a key property to improve the electronic activity at the surface and increase the charge transfer that facilitates the adsorption of the selected guest.
2023-01-01T00:00:00ZComputational Insight into Conformational Rearrangement and Intramolecular-H Bond Analysis of Some Calix[4]Arenes Including Acryloyl MoietyKarayel, Arzuhttps://hdl.handle.net/11491/80012021-11-01T18:18:18Z2019-01-01T00:00:00ZComputational Insight into Conformational Rearrangement and Intramolecular-H Bond Analysis of Some Calix[4]Arenes Including Acryloyl Moiety
Karayel, Arzu
The conformational analyses of Calix[4]arenes reveals four different stable structures (conformations); Cone, Partial Cone, 1,2-Alternate and 1,3-Alternate after employing a density functional theory (DFT) computational analysis. Intramolecular Hydrogen Bonds (IHBs) existing Calixarene core cause Cone conformation, supporting to be the best stable state in 1, 2 and 3 compounds. In addition, one needs Natural Bond Orbital (NBO) analyses of current compounds in order to understand nature of these IHBs. Specifically, it has been shown using NBO that the LP *?? interactions for O???O¯H IHBs and the delocalization LP ? ?* for O¯C=O are the major contributions to energy stabilization. Of all conformers of compound 4, Partial Cone has the lowest energy, which can be attributed to devoid of intramolecular hydrogen bond due to the absence of free phenolic groups.
2019-01-01T00:00:00Z