Sürdürülebilir Kalkınma Amaçları
Yayınlar
- MakaleAçık Erişim2026Scopus SJRQ2Synthesis and pharmacokinetic profiling of a novel pyrimidine imidazole based thiosemicarbazone derivative for BRAF inhibition in lung cancer therapy
Ekincioğlu, Yavuz; Kızıl, Hamit Emre; Güllü, Eda; Özkan, Elvan Hasanoğlu; Nartop, Dilek
This study presents the design, synthesis, and comprehensive evaluation of a novel thiosemicarbazone derivative containing a pyrimidine-imidazole (C11H11N8SCl) as a potential BRAF inhibitor for the treatment of non-small cell lung cancer. The compound was synthesized by a condensation reaction and characterized by elemental analysis, molar conductivity, SEM-EDS, FT-IR, 1H, and 13C-NMR spectral techniques. DFT calculations at the B3LYP/6-311 + + G(d, p) level revealed a HOMO-LUMO gap of 2.8 eV, indicating appropriate molecular stability and reactivity. Molecular docking studies with BRAF (PDB ID: 1UWH) demonstrated favorable binding affinity (-6.85 kcal/mol) with key interactions at ILE512, HIS509, HIS584, GLN529, GLU585, LYS590, VAL510, and LEU587 residues. In vitro cytotoxicity assays revealed that the compound possesses anticancer potential against H-460 cells, with a significant inhibitory effect observed at a concentration of 200 µg/mL. Combined with its favorable binding affinity toward BRAF kinase, these results suggest that the pyrimidine-imidazole thiosemicarbazone may serve as a potential lead scaffold for further development in targeted lung cancer therapy.ADME profiling confirmed the compound’s compliance with Lipinski’s rule of five parameters, supporting its potential as an orally active drug candidate. These findings suggest that our pyrimidine-imidazole thiosemicarbazone represents a promising scaffold for the development of targeted BRAF inhibitors for lung cancer therapy.
- MakaleAçık Erişim2026Scopus SJRQ3DFT-based structural and energetic characterisation of nitrogen-rich tetrazine/triazine derivatives with Kamlet-Jacobs performance predictions
Ekincioğlu, Yavuz; Kepceoğlu, Abdullah; Çakir, Zehra; Şentürk, Şükrü
Nitrogen-rich heterocycles are attractive candidates for next-generation energetic materials because they can deliver high heats of formation while producing relatively benign, N2-rich decomposition products. In this work, three nitrogen-rich frameworks 3,6-bis(tetrazol-5-yl)−1,2,4,5-tetrazine (H2BTTz), 2,4,6-tris(tetrazol-5-yl)−1,3,5-triazine (H3TTT), and 2,3,5,6-tetra(tetrazol-5-yl)pyrazine (H4TTP) were investigated using a combined conformational sampling and density functional theory (DFT) approach. Initial conformational searches were carried out with the MMFF method, and the lowest-energy structures were optimised at the DFT/B3LYP/6-311++G(d,p) level a widely used compromise between accuracy and computational cost for nitrogen-rich energetic molecules. Electronic structure analyses included frontier molecular orbitals, Mulliken and natural population charges, and molecular electrostatic potential maps. Energetic performance was evaluated through heats of formation, detonation velocity and pressure, and impact sensitivity estimates. Topological descriptors such as ELF, LOL, and NCI were analyzed using Multiwfn program. The calculated HOMO–LUMO gaps (3.54-4.90 eV) indicate electronically stable molecular frameworks. Gas-phase formation enthalpies were converted to condensed-phase values using a sublimation correction, and detonation properties were estimated via the Kamlet–Jacobs equations. The predicted performance follows the order H4TTP > H2BTTz > H3TTT. Although their detonation performance is lower than that of FOX-7 and CL-20, these nitrogen-rich systems remain promising candidates for reduced-sensitivity energetic materials and merit further experimental investigation.
AtıfScopus1WoS1OpenAlex1
İncele - MakaleAçık Erişim2025Theoretical Investigation of the Molecular Properties of the Fluoroaniline and Fluoroanisole Isomers
Kepceoğlu, Abdullah; Ekincioğlu, Yavuz
This research paper aims to analyse the molecular properties of fluoroaniline and fluoroanisole isomers through a range of theoretical methods. These methods include optimization of molecular structures, conformational analysis, and calculation of nonlinear optics (NLO) properties, frontier molecular orbital (HOMO-1, HOMO/SOMO, LUMO, LUMO+1) energies, chemical reactivity descriptors (ionization potentials - vertical and adiabatic, electron affinity, chemical hardness, softness, and electronegativity), molecular electrostatic potential (MEP), natural bonding orbital (NBO), and UV-Vis spectra. To achieve this, the density functional theory method with B3LYP functional and 6-311++G (d, p) basis set were used for the calculations. Additionally, the research examines the vertical and adiabatic ionization energy parameters of the molecules by constructing singly charged cation radicals. The outcome of this study provides valuable insights into the molecular properties of fluoroaniline and fluoroanisole isomers, which can be useful in the production of pharmaceuticals and agrochemicals.
AtıfOpenAlex1
İncele - MakaleAçık Erişim2025Scopus SJRQ2An Integrated In Vitro and In Silico Investigation of the Bioactive Properties of Wild Glycyrrhiza glabra var. glandulifera
Kızıl, Hamit Emre; Ulcay, Sibel; Ekincioğlu, Yavuz; Öğütçü, Hatice; Ağar, Güleray
This investigation examined methanol extracts obtained from the whole plant (encompassing all organs except roots), flowers, and fruits of wild Glycyrrhiza glabra var. glandulifera, a liquorice cultivar indigenous to the Cappadocia region of Türkiye, constituting the first comprehensive in vitro and in silico analysis of this species within the region. Anatomical identification revealed distinctive structural characteristics, including thick-walled epidermal cells in the stem, organized clusters of collenchyma cells, and well-defined sclerenchyma layers encompassing the vascular bundles. The petiole exhibited a characteristic heart-shaped morphology containing three vascular bundles, while foliar analysis demonstrated the presence of stomata on both adaxial and abaxial surfaces, accompanied by a bifacial mesophyll arrangement. The extracts demonstrated remarkable antimicrobial efficacy against both Gram-positive and Gram-negative bacteria, as well as various fungal species. Furthermore, significant cytotoxic activity was observed against non-small cell lung cancer (H460), with the whole plant extract exhibiting IC50 values of 117.8 µg/mL (24 h) and 105.6 µg/mL (48 h). Flower extracts demonstrated IC50 values of 116.8 µg/mL (24 h) and 112.7 µg/mL (48 h), while fruit extracts displayed superior potency with IC50 values of 104.4 µg/mL (24 h) and 63.09 µg/mL (48 h). Molecular docking analyses, conducted utilizing AutoDock Tools 1.5.6 and BIOVIA Discovery Studio Visualizer 4.5, revealed significant protein-ligand interactions, yielding optimal binding energy and inhibition constant values of -9.57 kcal/mol and 96.92 nM, respectively. The RMSD values were calculated based on structural variations between ligand-protein complexes during re-docking procedures. These findings underscore the substantial biological potential of Glycyrrhiza glabra var. glandulifera from Cappadocia, necessitating further comprehensive investigation.
AtıfScopus6WoS6OpenAlex5
İncele - MakaleAçık Erişim2025Scopus SJRQ1Anticancer (cytotoxic, anticlonogenic, antimetastatic, immunomodulatory actions) properties of 3,5-dibromosalicylaldehyde against glioblastoma cells and DFT analyses (FT-IR, Raman, NMR, UV) as well as a molecular docking study
Karakaş Sarıkaya, Ebru; Pehlivanoğlu, Suray; Türkmen, Merve Özcan; Ekincioğlu, Yavuz; Kostak, Feyza; Çelik, Sultan; Dereli, Ömer
Background Information: The primary objectives of this study were to characterize 3,5-dibromosalicylaldehyde (3,5-DBSA) and, investigate its antiproliferative, antimetastatic, cytotoxic, and immunoregulatory properties. NMR, Raman, UV, and FT-IR spectroscopies were used to characterize 3,5-DBSA. Potential conformations of 3,5-DBSA were evaluated using Spartan's MMFF method. Geometry optimization calculations using Gaussian software calculated conformation energy values. Results: Subsequently, Raman, FT-IR, UV (ethanol) and NMR (DMSO) parameters were calculated. The experimental spectrum was compared to theoretical spectroscopic data. The present investigation investigated 3,5-DBSA's anticancer properties; therefore, docking was done once the stable structure had been identified. Conclusion: Identifying stable structure is crucial to molecular docking studies. In order to identify the mechanism by which 3,5-DBSA binds to PI3K as a therapeutic target, molecular docking was utilized. This work is the first to show that 3,5-DBSA is cytotoxic, anticlonogenic, antimetastatic, and immunomodulatory in glioblastoma cell line U87MG compared to healthy fibroblast L929 cells. Cytotoxicity and anti-clonogenicity studies investigated 3,5-DBSA's antiproliferative activities, whereas wound healing assays assessed cell migration. The immunomodulatory effects of 3,5-DBSA in glioblastoma were assessed by measuring Netrin-1 and IL-6 protein levels. According to our findings, 3,5-DBSA may treat glioblastoma. Significance: This work analyzes 3,5-DBSA's conformational search, characterization, molecular docking, and structural and anticancer properties.
- MakaleAçık Erişim2024Determination of Cytotoxic and Apoptotic Properties of Lobaric Acid, a Secondary Metabolite of Lichen and Investigation of Its Theoretical Potential
Kizil, Hamit Emre; Agar, Guleray; Ekincioğlu, Yavuz
In this study, we aimed to elucidate some of the mechanisms of cell death induced by lobaric acid in A549 (human lung cancer) cells. For this purpose, the effects of cytotoxic concentrations on p53 and caspase-3 gene expressions were investigated. A549 cells were treated with varying concentrations of lobaric acid (12.5, 25, 50, and 100 µg/ml) for 48 hours and then their viability was evaluated and p53 and caspase-3 mRNA expressions were determined at statistically cytotoxic concentrations of 12.5, 50, and 100 µg/ml. According to beta-actin, it was determined that the increase in lobaric acid concentration revealed an upward trend in p53 and caspase-3 mRNA expressions. Furthermore, quantum chemical parameters such as frontier molecular orbitals, band gap energy and ionization potential, electronic affinity, chemical softness, chemical potential, electrophilicity index and chemical hardness were analyzed. Furthermore, molecular docking was performed to identify the binding sites and the binding behavior of lobaric acid to some target proteins (P53, Caspase-3 and Bcl-2).
AtıfOpenAlex3İncele - MakaleAçık Erişim2024Ab-initio Study of Structural, Spectroscopic and Electronic Properties of High Energy Explosive Molecules: DFT/TD-DFT Calculations
Kepceoğlu, Abdullah; Ekincioğlu, Yavuz
This research explores the ground state geometry and molecular properties of FOX-7 and nitroguanidine molecules, with a focus on their spectroscopic and electronic characteristics. Initially, the conformational space of each molecule was systematically scanned using molecular mechanic calculations and the most probable conformer structure was obtained for each molecule. Subsequently, geometry optimizations of molecules were conducted by using ab initio density functional theory (DFT) with Becke’s three-parameter hybrid-exchange functional, which combines the Lee–Yang–Parr correlation functional (B3LYP) method, and the standard 6-311++G(d,p) basis set. The theoretically determined geometrical parameters from optimized structure and experimental values available in the literature were compared, providing validation for the structural properties of both molecules. Furthermore, the stability and reactivity properties of both molecules are estimated in terms of HOMO-LUMO energies. Overall, this study contributes to a comprehensive understanding of the ground state geometry, molecular structure, and spectroscopic behavior of FOX-7 and nitroguanidine, paving the way for potential applications in various fields of science and technology.
AtıfOpenAlex1İncele - MakaleYayıncıda açık erişim2024Scopus SJRQ2Nonlinear optical properties of KnCl (n = 2-7) superalkali clusters
Şentürk, Şükrü; Fardad, Fraidoon; Ekincioğlu, Yavuz
The lowest energy structures along with the low lying isomer, stabilities, electronic properties, optical properties and nonlinear optical responses of KnCl (n = 2-7) clusters were studied within the density functional theory. The second order energy difference, dissociation energy and GH-L (HOMO-LUMO gap) point out that KnCl (n = 3, 5, 7) clusters are more stable. The calculated adiabatic ionization energies (AIE) for the KnCl (n = 2-6) clusters are in agreement with the measured ionization energies. The optical properties, namely optical electronegativity and refractive index, depends on the GH-L energy values. The K atom capped planar rhombus geometry of the K4Cl causes the noticeable vibrational frequency shift compared to the rest of IR spectra of the clusters. The first static hyperpolarizability (β o) values are in the range of 2.33 × 103-2.87 × 104 au and the second static hyperpolarizability varies between 5.74 × 106 au and 38.9 × 106 au for the cluster. The nonlinear optical response is due to the superalkali nature of KnCl (n = 2-7) clusters. From computed β vec values, the hyperpolarizability has projection on the dipole moment vector for the superalkalis except the K2Cl and K5Cl. The absorption spectra point out that KnCl (n = 6-7) clusters can be suitable as a NLO material since they have transparency in the deep UV region (λ< 300 nm).
AtıfScopus2WoS2OpenAlex3İncele - MakaleAçık Erişim2024Scopus SJRQ3Nonlinear optical response of LinClK (n = 1–6) superalkali clusters
Şentürk, Şükrü; Ekincioğlu, Yavuz; Doğan, Ümit
The geometrical structures, stabilities, electronic properties and nonlinear optical response of the halogen doped bimetallic LinClK (n = 1–6) clusters were studied within the density functional theory. Based on the dissociation energy, second order energy difference and GH-L (HOMO-LUMO gap), the LinClK (n = 2, 4, 6) clusters are more stable. According to their ionization energies, the clusters can be classified as a superalkali. From the NBO analysis, the clusters are excess electron systems. The obtained first static hyperpolarizability (o) values are in the range of 1.56 × 104 − 4.33 × 104 au while the second static hyperpolarizability vary within 2.47 × 106 au to 13.9 × 106 au for the LinClK (n = 1–6) superalkalis that are slightly higher than the nonlinear optical response of halogen doped monometallic clusters. More importantly, the Li5ClK is transparent in the deep UV region ( < 300 nm) among the superalkalis indicating that the Li5ClK superalkali can be a candidate structure as new member of NLO materials.
AtıfScopus1WoS1OpenAlex1İncele - MakaleAçık Erişim2024Analysis of the nonlinear optical properties, vibrational spectra, DFT method and photovoltaic performance of cyanidin-3-rutinoside chloride
Sarıkaya, Ebru Karakaş; Ekincioğlu, Yavuz; Bahçeli, Semiha; Dereli, Ömer
This study aims to identify a cyanidin-3-rutinoside chloride that exhibits both photovoltaic performance and nonlinear optical properties, which may be utilized in the field of optoelectronics. Prior to investigating these properties, the stable structure must be determined. For this purpose, its conformational analysis is performed by the Molecular Force Field method with the spartan program. The exact nature of the stable configuration has been ascertained by empirical evidence. The energy of the stable configuration is -1654184.76 kcal/mol, and its dipole moment is 9.94 Debye. Cyanidin-3-rutinoside chloride has been investigated using experimental FT-IR and Raman spectroscopies. Meanwhile, the DFT method at the B3LYP/6-311 + + G(d, p) level was employed in order to study the simulated FT-IR and Raman spectra, the HOMO-LUMO analysis, the molecular electrostatic potentials (MEP), and the non-linear optical (NLO) characteristics of the title molecule. The HOMO and LUMO energies are − 6.45 and − 3.64 electron volts (eV), respectively, with a gap value of 2.81 eV. Additionally, the title compound’s open-circuit voltage, the transition density matrix light-harvesting efficiency, driving force, and binding energy were calculated with by taking photovoltaic cell properties into account. Furthermore, investigations of hole reorganization energy, electron reorganization energy, and total reorganization energy were carried out at the B3LYP/6-31G(d, p) level for the cyanidin-3-rutinoside chloride of interest. In addition, density of state calculations and NBO were made at the B3LYP/6-31G(d, p) level. We calculated the following values for LHE,,,,, and : 0.06, 2.45 eV, 0.20 eV, 0.56 eV, 0.50 eV, 0.57 eV and 1.06 eV, respectively.
AtıfScopus9WoS10OpenAlex12İncele