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- ArticleYalnız künye2025Novel europium(III), terbium(III), and gadolinium(III) Schiff base complexes: Synthesis, structural, photoluminescence, antimicrobial, antioxidant, and molecular docking studies
Sogukomerogullari, Hatice Gamze; Başaran, Eyüp; Kepekçi, Remziye Aysun; Türkmenoğlu, Burçin; Sarıoğlu, Ahmet Oral; Köse, Muhammet
Three lanthanide (III) complexes, L-Eu, L-Tb, and L-Gd, were synthesized using a Schiff base ligand (H2L) composed of (2,2′-(thiophene-2,5-diylbis(methaneylyl-idene))bis(azaneylyl-idene))diphenol. Complexes with the generic formula LnL(Cl)(H2O)·xH2O, where L is the ligand, was studied using elemental analysis, spectrum analysis (IR, mass- UV–Vis), and molar conductivity. Next, the photoluminescence characteristics of the lanthanide complexes were investigated. An assessment was conducted to ascertain the antioxidant activity of the synthetic compounds compared with that of the stable free radical DPPH. The antibacterial activity of the Schiff base metal complexes was assessed against a strain of yeast as well as against a number of Gram-positive and Gram-negative bacteria. Computational studies were also performed to elucidate the mechanisms of the antimicrobial and antioxidant effects. In molecular docking, 1LL9, 6J2O, 3JPU, 2MBR, and 1HD2 crystal structures were determined as targets and the docking score values of H2L, L-Tb, L-Gd, and L-Eu compounds for these targets were calculated.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2025Synthesis of newly designed hydrazones, in vitro and in silico studies, and structure-activity relationship
Sıcak, Yusuf; Başaran, Eyüp; Türkmenoğlu, Burçin; Öztürk, Mehmet
Herein, new N'-(substituted benzylidene)-3,5-dihydroxybenzohydrazide (1–13) series were synthesized, and their antioxidant, anticholinesterase, anti-tyrosinase, anti-urease, and antidiabetic activities were investigated together with in silico studies. The synthesized derivates were characterized using molecular spectroscopy, and the structure-activity relationships (SAR) were discussed for all tested biological assays. According to activity results, compound 3 exhibited excellent antioxidant activity in all tests, while compound 1 demonstrated the best acetylcholinesterase (AChE) inhibitory and butyrylcholinesterase (BChE) inhibitory activities. On the other hand, compound 11 showed excellent tyrosinase inhibitory (IC50:3.02±0.10 mM) and urease inhibitory (IC50:9.21±0.27 µM) activity. Moreover, among the synthesized compounds, compound 6 was detected as the best antidiabetic compound by inhibiting α-amylase (IC50:30.68±0.94 µM) and α-glycosidase (IC50:41.35±0.03 µM) enzymes, which were related with the antidiabetic activity. Molecular docking analysis confirmed AChE, BChE, tyrosinase, urease, α-amylase, and α-glucosidase inhibitory activities. In line with the findings obtained from in vitro bioactivity results and molecular docking analysis, hydrazone compounds are a suitable class of organic compounds for developing acetylcholinesterase, butyrylcholinesterase, urease, α-amylase, and α-glucosidase inhibitors.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2025Thiophene-based hydrazones and their metal complexes: Synthesis, structure affirmation, antioxidant and cytotoxic activity, photoluminescence, molecular docking, and ADMET studies
Sarıoğlu, Ahmet Oral; Bulut, Zafer; Türkmenoğlu, Burçin; Yumrutaş, Pınar; Mısır, Büşra Albayrak; Karaküçük-İyidoğan, Ayşegül; Oruç-Emre, Emine Elçin
This work involves the synthesis of N'-(2‑hydroxy-3‑methoxy-5-nitrobenzylidene)thiophene-2-carbohydrazide (HL1) and N'-(2‑hydroxy-5‑methoxy-3-nitrobenzylidene)thiophene-2-carbohydrazide (HL2) and their complexes with Cu(II), Ni(II), and Fe(II), as well as the investigation of their photoluminescence properties, cytotoxic, and antioxidant activities. Elemental analysis, molar conductivity, FT-IR, UV–Vis, TGA, LC-MS/MS, and 1H and 13C NMR (only for ligands) were used to determine the chemical structures of all compounds. Two complementary tests (CUPRAC and DPPH assays) were used to evaluate the antioxidant activities of the compounds. The results suggested that compound [Fe(L2)2] (L2-Fe) was found to have good radical scavenging power compared to α-tocopherol in the CUPRAC assay. The newly synthesized thiophene-based hydrazones and their metal complexes were screened for in vitro cytotoxic activity assessments against A549 and BEAS-2B cell lines and were found to show high cellular toxicity at lower doses on the A549 cell line. In particular, the Cu(II) complexes ([Cu(L1)2] (L1–Cu) and [Cu(L2)2] (L2–Cu)) exhibited the inhibitory effect against A549 cells with IC50 values of 5.1 and 6.93 μM, respectively. In order to the anticancer and antioxidant effects of the active compounds, the possible interaction mechanisms between novel compounds and target proteins were performed computationally by the molecular docking study. In conclusion, the study provided preliminary information about some biological properties of ligands and their Cu(II) complexes. It revealed that thiophene-based hydrazones may play a crucial role in drug applications. Also compounds that could be drug candidates were compared with both experimental and computational data.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2025N2O2 Schiff-Base nickel(II) and iron(III) template complexes of 2-hydroxy-5-ethoxyacetophenone S-methylthiosemicarbazone: Synthesis, characterization, DFT calculations, molecular docking, and antioxidant activity
Poladian, Qumars; İlhan-Ceylan, Berat; Bölükbaşı-Yalçınkaya, Olcay; Türkmenoğlu, Burçin; Kurt, Yasemin
Two new complexes, [Ni (L)] (1) and [Fe (L)Cl] (2), were synthesized through template condensation of 2-hydroxy-5-ethoxyacetophenone S-methylthiosemicarbazone (H2L1) with 2-hydroxy-4-methoxybenzaldehyde in the presence of nickel(II) and iron(III) ions. The complexes were characterized using elemental analysis, magnetic measurements, FT-IR, UV–Vis, ESI-MS and 1H NMR spectra. In order to gain further insights into their structural features, Density Functional Theory (DFT) calculations were employed to optimize the geometries and predict vibrational frequencies of the complexes, providing valuable insights into their structural stability and bonding interactions. The frontier molecular orbital (HOMO and LUMO) analyses were conducted for the optimized geometries to evaluate the electronic properties and chemical reactivity. The computational results confirmed the proposed square-planar geometry for (1) and square-pyramidal geometry for (2). TD-DFT analyses predicted the theoretical UV–Vis spectra and compared with experimental spectra. Molecular docking analyses were performed with EGFR (PDB ID: 4HJO) and B-DNA (PDB ID: 1BNA). Binding parameters and ADME analyses were also conducted. The antioxidant capacity of the compounds were examined using the CUPRAC (cupric reducing antioxidant capacity) method, and their radical scavenging activity was determined by the DPPH (1,1-Diphenyl-2-picrylhydrazyl) assay. [Ni(L)] exhibited higher antioxidant activity compared to [Fe(L)Cl] and the ligand (H2L1) in the CUPRAC assay.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye20253D-QSAR modeling with selection of local reactive descriptors (LRD) and molecular docking studies on diarylpyrazole-benzenesulfonamide derivatives
Güzel, Yahya; Karakaya, Sevcan; Wang, Lichang; Türkmenoğlu, Burçin; Kızılcan, Dilek Şeyma
The understanding of the interaction mechanism between ligands and receptors depends on the performance of the descriptors. In this study, the electrophilic and nucleophilic interactions of diarylpyrazole-benzenesulfonamide derivatives active on human carbonic anhydrase in 3D space were analyzed using different types of Local Reactivity Descriptors (LRDs). Three different classes of descriptors used in the Molecular Conformer Electron Topology (MCET) method: (1) Atomic charge, (2) Frontier Molecular Orbital (FMO) and (3) Fukui and Klopman indices. To assess the effect of changing LRD types on the ligand side, the variations in dimensions and values of the parameters on the receptor side were calculated for 3D quantitative structure-activity relationship (3D-QSAR) models. Each model was evaluated using the Leave One Out-Cross Validation (LOO-CV) method on the training set from the split molecule series and then validated on the external test set. As a result of comparing the different LRD types, a model with satisfactory values of Q2 = 0.933 and R2 = 0.964 was selected, which consisted of the electrostatic charge and LUMO coefficient under the Klopman Index (K_I) class. The activity changes at the interaction points between the ligand and receptor (L-R) were plotted to show the Auxiliary Group (AG) and Anti Pharmacophore Shielding (APS) groups. In addition to ligand-based drug design, the binding interactions between the ligand and the identified targets were investigated through molecular docking, one of the most widely used methods in structure-based drug design.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2025ADME predictions and molecular docking insights for novel Gypsogenin–chalcone hybrids and chalcones as antitumor and antimicrobial agents
Emirdağ, Safiye; Ulusoy, Nafia Gökçe; Kahriman, Nuran; Serdaroğlu, Vildan; Türkmenoğlu, Burçin; Yaylı, Nurettin
The cytotoxicity and antimicrobial efficacy of novel semisynthesized Gypso-Anhd chalcone hybrids (C1–C27) and methoxy‑substituted hydroxychalcones (A1–A27) were evaluated in the following six cancer cell lines: A549, HeLa, HEK293, SHSY5Y, MDA-MB-231, and PANC-1. These derivatives exhibited significant antimicrobial activity, against G+ bacteria (Bacillus subtilis, Enterococcus faecalis, and Staphylococcus aureus), G- bacteria (Escherichia coli and Pseudomonas aeruginosa) and Candida albicans. Among hydroxychalcone derivatives, A19, A25, and A26, demonstrated superior antiproliferative activity compared doxorubicin, with IC50 values of 1.43 ± 0.02 μM (A19, A549), 1.04 ± 0.02 μM (A25, HeLa), 0.90 ± 0.14 μM (A25, HEK293), 0.25 ± 0.03 μM (A25, SHSY5Y), 1.18 ± 0.03 μM (A26, MDA-MB-231), and 0.99 ± 0.03 μM (A26, PANC-1). Likewise, hybrid derivatives C12, C14, and C26 exhibited higher antiproliferative activity than doxorubicin, with IC50 values of 1.33 ± 1.14 μM (C26, A549), 9.51 ± 0.03 μM (C12, HeLa), 4.09 ± 0.65 μM (C26, HEK293), 1.79 ± 0.09 μM (C12, SHSY5Y), 7.97 ± 0.84 μM (C26, MDA-MB-231), and 3.71 ± 0.49 μM (C14, PANC-1). Molecular docking studies confirmed target-specific interactions for all synthesized derivatives. ADME analyses indicated favorable pharmacokinetic profiles, while hydroxy and methoxy substitutions modulated bioactivity, highlighting their potential as anticancer drug candidates.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2025Copper(II), cobalt(II), nickel(II), and iron(II) mixed complexes formed by Schiff base and 1,10-phenanthroline as secondary chelates: Preparation, characterization, antimicrobial, antioxidant, and molecular docking studies
Sogukomerogullari, Hatice Gamze; Sarıoğlu, Ahmet Oral; Kepekçi, Remziye Aysun; Türkmenoğlu, Burçin; Morcali, Mehmet Hakan
This study details the synthesis and characterization of new metal complexes formed by combining 2-((2-mercaptophenylimino)methyl)-4-methoxy-6-nitrophenol (L1) and 1,10-phenantroline (L2) ligands. The ligand (L1) and its mixed-ligand complexes with Co (II), Cu (II), Fe (II), and Ni (II) salts was analyzed using elemental analysis, FT-IR, UV–Vis, mass spectrometry, 1H and 13C NMR, magnetic susceptibility, and molar conductivity studies. The development of non-electrolytic compounds in a 1:1:1 M (L1:M:L2) ratio was verified by elemental analysis and conductance measurements. The complexes displayed an octahedral configuration. Biological uses of newly synthesized complexes were suggested by their antibacterial and antioxidant properties. Especially, the Fe (II) complex exhibited higher antimicrobial activity than free ligand on all the tested microbial strains according to the results of agar disc difffusion assay (inhibition zones ranging from 09.50 ± 0.70 and 19.50 ± 0.70 mm) and broth microdilution test (MIC values ranging between 97.66 and 781.25 μM) The highest antioxidant activity, among ligand and its metal complexes, were recorded for Ni (II) complex with IC50 value 59.17 ± 01.94 μM. The compounds with antimicrobial and antioxidant effects were further investigated via in silico approaches. The binding parameter values were calculated for the effectiveness of [FeL1L2H2O].3H2O complexes on the antimicrobial target and [NiL1L2H2O].2H2O complexes on the antioxidant target in molecular docking.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2025Antitumor effects of dicyanoaurate(I)-based complexes: In vivo and in silico insights using the HT29 xenograft model
Aydin, Ali; Kısa, Dursun; Türkmenoğlu, Burçin; Karadağ, Ahmet
Colorectal adenocarcinoma, the second deadliest malignancy, is characterized by chromosomal instability and mismatch repair deficiencies, leading to apoptosis resistance. Previously, we developed Au(I) complexes [Ni(hydeten)Au2(CN)4] (C1), [Ni(bishydeten)Au2(CN)4] (C2), and [Cd(edbea)2][Au(CN)2]2.H2O (C3) that induce apoptosis in cancer cells without toxicity to normal cells in vitro. In this study, we evaluate the in vivo antitumor efficacy of these Au(I) complexes, assessing tumor volume, survival rate, and protein markers related to cell cycle, apoptosis, and oxidative stress through immunohistochemistry, gene expression, and ELISA assays. Molecular docking studies of the complexes with proteins revealed the best binding interactions. In molecular docking analysis, compounds C1, C2, and C3 interacted with more than one target. The best interaction results were obtained with PI3K alpha target among these targets. ETotal energy values presenting the docking score value on PI3K alpha (PDB ID:5ITD) were calculated as -1653.5 kJ/mol for C1, -1863.4 kJ/mol for C2, and -2420.4 kJ/mol for C3. In the HT29 xenograft tumor model, treatment with Au(I) complexes (0.5 mg/kg) resulted in a significant reduction in tumor volume and increased survival. Histopathological analysis confirmed minimal side effects on tissues, while assessment of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) levels indicated that the mechanism of action was not based on oxidative stress-induced cell death. Overall, Au(I) complexes demonstrated selective low toxicity and antitumor effects via apoptosis, suggesting their potential as therapeutic agents for colorectal adenocarcinoma.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2024Investigation of Newly Synthesized Fluorinated Isatin-Hydrazones by In Vitro Antiproliferative Activity, Molecular Docking, ADME Analysis, and e-Pharmacophore Modeling
Başaran, Eyüp; Köprü, Semiha; Akkoç, Senem; Türkmenoğlu, Burçin
In this study, we investigated the in vitro antiproliferative activities and performed computational studies of newly synthesized fluorinated isatin-hydrazones. The chemical structures of the synthesized compounds were confirmed by FT-IR, 1D NMR (1H- and 13C NMR and APT), 2D NMR (HETCOR and HMBC), and elemental analysis. All compounds (1-15) were tested in human lung (A549) and liver (HepG2) cancer cell lines for 72 h. The compounds were screened against a healthy embryonic kidney cell line (HEK-293T) under the same conditions to determine their toxic effects. According to the results obtained, one of the compounds, in particular, compound 8 was effective at inhibiting the growth of cancerous cells, and its effects on both cancer cell lines were similar to IC50 values of 42.43 and 48.43 μM for A549 and HepG2, respectively. Compound 8, which was determined to be the best anticancer agent in vitro, was chosen to interact with the target via molecular docking. This selected ligand (compound 8) interacted with the targets 4HJO, 4ASD, 3POZ, and 7TZ7, and docked into the active sites. The docking score, Glide energy, and Glide emodel values were calculated and determined to be lower than those of the reference compound cisplatin. The pharmacokinetic properties, stability, and drug-likeness parameters of all designed compounds were estimated using SwissADME. Finally, the binding affinities of compound 8 for all four targets were calculated using the MM-GBSA method.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2024Synthesis, Characterization, Investigation of Anticancer Activity and Molecular Docking Studies of N2O2 Type Schiff Base Ligand and Metal Complexes
Türkmenoğlu, Mustafa; Yıldırım, Sümeyra Tuna; Altay, Ahmet; Türkmenoğlu, Burçin
Schiff base ligands and their metal complexes play a great important role in pharmaceutical sciences because of their wide and significant activities. They are versatile pharmacophores for the design and discovery of many drugs. In this study, a Schiff base ligand and its complexes were synthesized. Some spectroscopic techniques such as FT-IR, 1H-NMR, 13C-NMR, XRD, SEM, and UV-Vis were used for structural characterization. Antiproliferative activities of the synthesized ligand and complexes were investigated on the human breast (MCF-7) and colon (HT-29) cancer cell lines by XTT [2,3-Bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium] method. The obtained data showed that the ligand and complexes exhibited dose-dependent and cell-selective in vitro antiproliferative activity on the tested cell line. In addition, it was determined that complexes showed statistically higher cytotoxic activity compared to the ligand. The binding parameter values and the important amino acids in the binding site were determined between the possible lead compounds synthesized by molecular docking from in silico approaches and the target. A molecular docking study of the cobalt complex was performed against Bcl-2 (PDB ID:4IEH) and DNA recognition (PDB ID:423D) targets. In conclusion, these data show that the synthesized Schiff base ligand and metal complexes have the potential to be evaluated as a chemotherapeutic agent.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2024Histopathological, Antioxidant, and Enzyme Activity of Boronic Incorporated Catechin Compound: Screening of Bioactivity with Molecular Docking Studies
Paşa, Salih; Atlan, Metin; Temel, Hamdi; Türkmenoğlu, Burçin; Ertaş, Abdulselam; Okan, Aslı; Yilmaz, Seher; Ateş, Şükrü
Abstract: Objective: Boron structures play a crucial role in biological treatments due to their unique chemical properties. They are used in pharmaceuticals for their potential as enzyme inhibitors and as anti-inflammatory agents. Boron-containing compounds are also explored in drug delivery systems, leveraging their ability to cross cell membranes effectively. Additionally, boron-based materials are studied for their applications in biomaterials, such as wound healing and tissue engineering, highlighting their diverse applications in biological treatments. Methods: The study aims to elucidate the biological properties of catechin, a natural phenolic compound, by modifying it with phenylboronic acid. The Catechin-based boronic compound (CBC) was synthesized. The antioxidant and enzyme activity were studied. Histopathological experiments to vital organs and molecular docking studies were also conducted. Results and Discussion: The (CBC) showed meaningful antioxidant and enzyme activity when compared to standards. The effect of the (CBC) on tissues was demonstrated by in vivo experiments. Histopathological evaluation of vital organs in male Sprague Dawley rats was demonstrated by Hematoxylin–Eosin staining. The study has supported the antioxidant property of (CBC), also has a natural origin based on its structure. Besides, the antiurease and antityrosinase activities of catechin were tested for the first time. Furthermore, in silico approaches also supported the acceptable biological activity results that were experimentally examined. The interactions of AChE, BChE, urease, and tyrosinase enzymes with the (CBC) were investigated theoretically via molecular docking, and the binding parameter values were also shared. The (CBC) demonstrated radical scavenging activity. The in vivo experiments on rats were carried out and the (CBC) showed no negative effects on the vital organs. It was seen that the experimental results were in good agreement with the theoretical calculations. Conclusions: The analysis of the crystal structures of AChE, BChE, urease, and tyrosinase enzymes in relation to the compound (CBC) yielded striking results, highlighting the compound’s promising potential as a therapeutic agent.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2024Determination of the interactions of a schiff base with different targets via molecular docking and cytotoxic activity studies
Türkmenoğlu, Burçin; Bayar, İrem; Kökbudak, Zülbiye; Akkoc, Senem
The pyrimidine nucleus is a vital pharmacophore that exhibits excellent pharmacological activity. A Schiff base containing a pyrimidine nucleus was obtained in two steps. This compound was assessed on the human prostate (PC3) and liver (HepG2) cancer cell lines using the MTT method. The prepared compound 3 was determined to have a high cytotoxic effect towards prostate cancer with an IC50 value of 9.32 μM. Since experimental prostate and liver cancer studies were examined, the molecular docking study's target structures were determined accordingly. In molecular docking studies, compound 3 interacted in silico with the crystal structure of the human HER2 kinase domain (PDB Id: 3PP0), the crystal structure of VEGFR-2 (PDB Id: 4ASD), and the crystal structure of EGFR tyrosine kinase (PDB Id: 4HJO), respectively. As a result of these interactions, binding energy values were calculated, and binding modes were determined. Additional in vitro and in vivo experiments targeting other cancer cell lines will provide deeper insight into the anticancer spectrum of this compound and new studies on this compound will be planned in the following years. Furthermore, optimizing and studying such pyrimidine-based Schiff base compounds for improved selectivity and potency against prostate cancer is also considered to be valuable as it may increase the potential to capture potential drug candidates.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2024Synthesis of new sulfonamide derivatives: Investigation of their interactions with carbonic anhydrase and cholinesterase enzymes by in vitro and in silico evaluations
Kurban, Muhammet Gürkan; Çakmak, Reşit; Başaran, Eyüp; Türkmenoğlu, Burçin; Şentürk, Murat
In this study, a series of novel sulfonamide derivatives (6–10) bearing an aryl sulfonate moiety was designed, and synthesized for the first time, and their inhibitory activities against human carbonic anhydrase isoenzymes (hCA II and I), acetylcholinesterase (AChE), and butyrylcholinesterase (BChE) were investigated by in vitro and silico studies. The chemical structures of the derivatives were elucidated by elemental analysis and spectral techniques. All tested hybrids showed remarkably low nanomolar inhibition with Kı values of in the range of 8.98 ± 0.10 to 14.56 ± 0.41 nM against hCA I, 7.73 ± 0.10 to 13.85 ± 0.32 nM against hCA II, 12.90 ± 0.29 to 16.38 ± 0.41 nM against AChE, and 6.21 ± 0.09 to 14.52 ± 0.38 nM against BChE. Overall, the majority of these molecules inhibited these metabolic enzymes significantly more than acetazolamide (AZA) and neostigmine. Moreover, the biological effects of the compounds produced were assessed through computational studies of target enzymes. In this regard, in silico ADMET properties were evaluated to determine the physicochemical properties of target compounds. The calculated results support the biological activity results.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2024Clustering of atoms relative to vector space in the Z-matrix coordinate system and ‘graphical fingerprint’ analysis of 3D pharmacophore structure
Kızılcan, Dilek Şeyma; Güzel, Yahya; Türkmenoğlu, Burçin
The behavior of a molecule within its environment is governed by chemical fields present in 3D space. However, beyond local descriptors in 3D, the conformations a molecule assumes, and the resulting clusters also play a role in influencing structure–activity models. This study focuses on the clustering of atoms according to the vector space of four atoms aligned in the Z-Matrix Reference system for molecular similarity. Using 3D-QSAR analysis, it was aimed to determine the pharmacophore groups as interaction points in the binding region of the β2-adrenoceptor target of fenoterol stereoisomers. Different types of local reactive descriptors of ligands have been used to elucidate points of interaction with the target. Activity values for ligand-receptor interaction energy were determined using the Levenberg–Marquardt algorithm. Using the Molecular Comparative Electron Topology method, the 3D pharmacophore model (3D-PhaM) was obtained after aligning and superimposing the molecules and was further validated by the molecular docking method. Best guesses were calculated with a non-output validation (LOO-CV) method. Finally, the data were calculated using the ‘graphic fingerprint’ technique. Based on the eLKlopman (Electrostatic LUMO Klopman) descriptor, the Q2 value of this derivative set was calculated as 0.981 and the R2ext value is calculated as 0.998.
RDL Kalıcı Kaydıİncele - CorrectionAçık Erişim2024Erratum to: Histopathological, Antioxidant, and Enzyme Activity of Boronic Incorporated Catechin Compound: Screening of Bioactivity with Molecular Docking Studies (Russian Journal of Bioorganic Chemistry, (2024), 50, 4, (1446-1465), 10.1134/S1068162024040216)
Paşa, Salih; Atlan, Metin; Temel, Hamdi; Türkmenoğlu, Burçin; Ertaş, Abdulselam; Okan, Aslı; Yilmaz, Seher; Ateş, Şükrü
In the article some errors were made and data was not included. 1. There is a missing data as figure in “Histochemical Results” section 2. In the AUTHOR CONTRIBUTION section the authors made a mistake. The contributions for two authors should be as: “The author AO—histopathological evaluation; the author SY—in vivo experiments; the author ŞA— in vivo experiments.” 3. The following revised sentence can be added to “In vivo experiment procedure” section: “This study, which was carried out on experimental animals, was approved by the Erciyes University Animal Experiments Department Local Ethics Committee.” 4. In the ETHICS APPROVAL AND CONSENT TO PARTICIPATES section the authors indicated the protocol number incorrectly. Correct protocol number: 24/162.The original article can be found online at https://doi.org/10.1134/S1068162024040216.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2023New pyrimidine-N-β-D-glucosides: synthesis, biological evaluation, and molecular docking investigations
Kahri̇Man, Nuran; Peker, Kıvanç; Serdaroğlu, Vildan; Aydin, Ali; Türkmenoğlu, Burçin; Usta, Asu; Yayli, Nurettin
In this study, syntheses of new pyrimidine-coupled N-β-glucosides and tetra-O-acetyl derivatives were carried out. All glycoconjugates were investigated in comparison with known chemotherapeutic agents in terms of their antimicrobial and anticancer functions and DNA/protein binding affinities. Spectral data showed that all glycoside derivatives were obtained by diastereoselectivity as β-anomers. Both tested groups exhibited strong antiproliferative activity (2.29–66.84 µg/mL), but some of them had sufficiently ideal % cytotoxicity values (10.01%–16.78%). And also all synthetic compounds exhibited remarkable antibacterial activity against human pathogenic bacteria. Binding of these compounds to CT-DNA resulted in significant changes in spectral properties, consistent with groove binding. Molecular docking studies of some compounds revealed that the docking score, complex energy, and MM-GBSA ΔGBind energy values were consistent with the experimental results, which showed that the new compounds were potent chemotherapeutic agents. Overall bioactivity results suggest that these compounds may be candidates as new chemotherapeutic agents and deserve further pharmacological evaluation.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2023In silico and biological activity evaluation of quercetin-boron hybrid compounds, anti-quorum sensing effect as alternative potential against microbial resistance
Temel, Hamdi; Atlan, Metin; Türkmenoğlu, Burçin; Ertaş, Abdulselam; Erdönmez, Demet; Çalışkan, Ufuk Koca
Boronic acid compounds and the natural flavonoid compound quercetin were handled to synthesize two novel ligands encoded as B1(2,2′-(1,4-phenylenebis (benzo [1,3,2] dioxaborole-2,5-diyl)) bis (3,5,7-trihydroxy-4H- chromen-4-one) and B2(3.3.6. 3,5,7-trihydroxy-2-(2-(6-methoxypyridin-3-yl)benzo[d][1,3,2]dioxaborol-5-yl)− 4 H-chromene-4). Antioxidant activities of ligands were investigated by DPPH, ABTS and CUPRAC methods. Cholinesterase inhibition effects of ligands were determined by acetylcholinesterase and butyrylcholinesterase enzyme inhibition methods, cytotoxic effects of ligands were applied to healthy breast and colon cancer cell lines by MTT method, and urease and tyrosinase enzyme activities were determined. Antimicrobial properties of the compounds were analyzed by detecting their anti-QS potentials on Chromobacterium violaceum biosensor strain. Both compounds were found to have significant antioxidant effects compared to controls. It was determined that the compound B1 at 1–10 µg/mL was more active than the reference compounds (α-TOC and BHT). Moreover, the enzyme activity studies on ligands demonstrated that acetylchoinesterase and butyrylcholinesterase enzyme inhibitions were higher than the reference compounds. As expected, boron derivatives exhibited respectable activity against the biofilms of Escherichia coli (E. coli) and P. aeruginosa (P. aeruginosa). These results demonstrate the potential applicability of boron derivatives in the treatment of biofilm-associated infections and provide a practical strategy for the design of new boron-based antimicrobial materials. In silico molecular docking studies were performed on ligands to identify newly synthesized compounds. The binding parameter values and binding sites of the compounds were also determined. In conclusion, our studies showed that newly synthesized hybrid compounds could be solutions for antimicrobial resistance and enzyme-related disorders.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2023Focusing on New Piperazinyl-methyl-3(2H)pyridazinone Based Derivatives: Design, Synthesis, Anticancer Activity and Computational Studies
Merde, İrem Bozbey; Önel, Gülce Taşkor; Akkoç, Senem; Karaköy, Zeynep; Türkmenoğlu, Burçin
Heterocyclics containing pyridazinone and piperazine structures are potential anticancer agents in the treatment of cancer disease caused by increasing the number of abnormal cells disrupting body biochemistry. There is a need for the design of more biocompatible drugs for the treatment of cancer with minimal side effects. For this purpose, a series of piperazinyl-methyl-3(2H)pyridazinone based compounds were synthesized and their anticancer activities were studied in vitro and in silico. The chemical structures of all the new compounds 3 (a–k) were identified by spectral analysis. The new compounds were screened in human lung and colon cancer cell lines to learn about their cytotoxic effects. The importance of the structure activity relationship was seen in this study and the compounds containing methoxy groups on the phenyl ring (3 a, 3 b, 3 e–3 g) were found to have higher cytotoxic effects than those without. It was determined that one of these compounds (3 a) demonstrated significant cytotoxic effect against both cell lines for 72 h as in vitro. The geometry of the synthesized 3 a ligand was optimized using the hybrid B3LYP functional density functional theory (DFT). Molecular docking study of 3 a compound was performed against EGFR (PDB ID : 1M17) and VEGFR-2 (PDB ID: 2RL5) molecular targets.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2023Diastereoselective Synthesis, Characterization, Investigation of Anticancer, Antibacterial Activities, In Silico Approaches and DNA/BSA Binding Affinities of Novel Pyrimidine-Sugar Derivatives
Kahriman, Nuran; Serdaroğlu, Vildan; Aydın, Ali; Türkmenoğlu, Burçin; Usta, Asu
Eighteen novel carbohydrate conjugates (1-9) and their tetra-O-acetyl derivatives (10-18) were synthesized in total and evaluated for their biological properties, including antimicrobial and anticancer functions, and DNA/protein binding affinities. The compounds were prepared by firstly glycosylation and secondly acetylation methods. The structures of all compounds were elucidated by spectral analysis and the results showed that the glycoconjugates were obtained by diastereoselectivity as pure β- anomer. To observe cell proliferation, cytotoxicity and microdilution, different cancer cell lines (Hep3B, A549, HeLa, C6, HT29, MCF7) were treated with pyrimidine N-β-D-glycosides (1-9) and their tetra-O-acetyl derivatives (10-18). These new carbohydrate conjugates and the controls showed the same non-toxic property to the cells, while 10-18 displayed lower cytotoxic potency than 1-9. And to support the experimental results of some compounds (8, 9, 17, and 18) whose pharmacological properties were determined, molecular docking studies were performed, which belonged to the in silico methods. The values of the binding parameters of these compounds with different receptors were determined by molecular docking. Studies on pathogenic bacteria revealed that both groups of new compounds exhibited significant antimicrobial activity with low concentrations (31.25-125 µg/mL). Significant data have been obtained indicating that they can bind to DNA via groove binding, with binding constants ranging from 1.1 × 103 to 4.0 × 104. In summary, preliminary information indicates that acetylated derivatives (10-18) have effective pharmacological properties.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2023Effect of fermented concentrated potato protein on milk yield and fertility parameters in dairy cows in the prepartum and postpartum periods
Aktuğ, Eray; Baytok, Erol; Türkmenoğlu, Burçin
This study aims to determine the effects of fermented concentrated potato protein (FCPP) which showed very high levels of indole acetic acid (IAA) on milk yield, fertility, and level of insulin-like growth factor 1 (IGF-1) parameters in pregnant dairy cows and pregnant heifers. In total, sixty Holstein cattle were enrolled in the study. The animals were divided into three groups, as control group (n=20), 25 g FCPP group (n=20), and 50 g FCPP group (n=20). Besides, these main groups were also divided into two sub-groups, as primiparous (n=10) and multiparous cows (n=10). Oral administration of FCPP started two weeks (14±4 days) before expected parturition and continued until postpartum day 100. The affinity of IAA found in FCPP pellets to 5HT1 and JAK2 receptors, which is thought to be related to IGF-1 release, was determined by the molecular docking method that receptor affinities were found as-5.8637 kcal/mol and-4.3857 kcal/mol, respectively. Blood IGF-1 profile was followed at 7 different time points throughout the study. It was detected that the IGF-1 concentrations have significant difference in terms of both time and groups (P<0.05). Furthermore, there was a significant difference in interaction of time and parity (P<0.05). The results showed that average and total 100-day milk yield was not affected by FCCP supplementation (P>0.05). FCPP supplementation generally has improved the mathematical data of fertility parameters, but no statistical significance was detected except for calving-conception interval. It was found that calving-conception interval reduce by 16.8% in primiparous cows supplemented with 25 g FCPP. The pregnancy rates in control, 25 g and 50 g FCPP were found as 72.2 %, 78.9 % and 88.9 %, respectively (P>0.05). This study has concluded that fermented concentrated potato protein (which has indole acetic acid-indole compounds) may improve the productivity of dairy cows supplemented in transition period and it has suggested that further research must be done for its usage and beneficial effects in dairy cows.
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