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Carbazole derivatives: Synthesis, spectroscopic characterization, antioxidant activity, molecular docking study, and the quantum chemical calculations
(Elsevier, 2021) Serdaroğlu, Goncagül; Uludağ, Nesimi; Erçağ, Erol; Sugumar, Paramasivam; Rajkumar, Parthasarathi
A various carbazole derivativeswere synthesized for the synthesis 2,3-Dihydro-1H-carbazol-4(9H)-one O-acetyl oxime (3), ethyl 2-(2,3,4,9-tetrahydrospiro[carbazole-1,2'-[1,3]dithiolane]-2-yl)acetate (5), 2- hydroxyethyl {2,3,4,9-tetrahydrospiro[1H-carbazole-1,2'[1,3]dithiolane-4-one]-2-yl}-acetamide (7). These products (3, 5, and 7) were characterized by the spectroscopic techniques (IR, H-1 NMR, C-13 NMR and elemental analysis). Then, the observed FT-IR and NMR peaks of the studied compounds were compared with the calculated values. The FMO analyses disclosed that the (5) would prefer intermolecular interactions more than intramolecular interactions because of its higher energy gap. NBO analyses displayed that the n ->Pi* and Pi ->Pi* interactionswere responsible for the lowering of the stabilization energy. Themolecular docking studies showed that (5) exhibited highest binding affinitywith the human glutathione reductase at binding site (-7.21 kcal/mol). Also, the antioxidant activities were investigated using the CUPRAC method, and TEAC coefficient implied that compound (3) have an antioxidant property. In addition, docking calculations of the compound (3), (5), and(7) were performed on bacterial tyrosinase enzyme and human glutathione reductase protein. (C) 2021 Elsevier B.V. All rights reserved.
Cr(VI) adsorption on binary and ternary composites of raw cocoa shell with magnetic nanoparticle and Prussian blue
(Elsevier B.V., 2022) Erçağ, Erol; Kanmaz, N.; Buğdaycı, M.; Hızal, J.
Binary and ternary composites of raw cocoa shell (CS) were investigated as novel adsorbents for chromate (Cr(VI)) ions adsorption. CS incorporated with magnetite nanoparticle (MNP) and MNP-Prussian blue (MNP-PB) composites of CS were fabricated for the first time in this study. The characterization of the adsorbents was performed by using Fourier-transform infrared (FTIR), BET/N2 surface area analysis, particle size and zeta potential measurements, X-ray powder diffraction (XRD) and scanning electron microscopy (SEM) analysis. The measured zeta potential values are high enough to point out stable aqueous suspensions. The efficiency of Cr(VI) adsorption were examined by evaluating the effects of contact time and initial chromate concentration. The kinetic behaviors of all adsorbents fitted Pseudo Second Order Model. The adsorption capacities were calculated as 23.36, 10.73 and 11.76 mg CrO42?/g adsorbent on CS, MNP-CS and MNP-PB-CS, respectively. Additionally, the pH dependency of the adsorption was investigated by considering surface acidity properties of CS and species distribution of Cr(VI) ions at different pHs. As a result, it was observed that the HCrO4? species was responsible for adsorption at pHs between 2 and 8. © 2021
Cyanomethylation of 2,3,4,9-tetrahydro-1H-carbazol-1-one based on using two different reagents: Antioxidant activity and DFT studies
(Elsevier, 2022) Serdaroğlu, Goncagül; Uludağ, Nesimi; Erçağ, Erol
C-2 and C-6 monoalkyl nitrile substituted reactant (1), which constitute the tricyclic framework of carbazole derivatives along with the substructure of the Strychnos alkaloids family, have been synthesized by using different bases to produce substitution reactions. In addition, the antioxidant capacity of the synthesized compound by the CUPRAC (cupric reducing antioxidant capacity) method was evaluated and the obtained TEAC (Trolox equivalent antioxidant capacity) coefficient implied that product (2) has antioxidant feature. The B3LYP/6-311G(d,p) level calculations were performed in the gas phase, and the optimized geometries obtained from these calculations were used for the solvation media calculations. The SMD variation of the IEFPCM (polarized continuum model) was used to conduct the quantum chemical calculations in the solvent environment such as CHCl3, CH3OH, and H2O (water, epsilon=78.4). Also, the NMR chemical shifts of the products were calculated using GIAO (Gauge-Independent Atomic Orbital) approach and compared with the corresponding experimental data. The TD-DFT calculations disclosed that the observed peaks for both products were attributed to the n -> pi* and pi -> pi* excitations. Moreover, NBO analysis revealed that the n -> pi* and pi -> pi* interactions have a great importance for lowering the stabilization energy for all compounds. Also, the FMO (Frontier Moleular Orbital) analyses implied that the product P2 would prefer the intermolecular interactions would rather than the intramolecular interactions. (C) 2021 Published by Elsevier B.V.
Design and in silico study of the novel coumarin derivatives against SARS-CoV-2 main enzymes
(Taylor and Francis Ltd., 2020) Özdemir, Mücahit; Köksoy, Baybars; Ceyhan, Deniz; Sayın, Koray; Erçağ, Erol; Bulut, Mustafa; Yalçın, Bahattin
The novel coronavirus (SARS-CoV-2) causes severe acute respiratory syndrome and can be fatal. In particular, antiviral drugs that are currently available to treat infection in the respiratory tract have been experienced, but there is a need for new antiviral drugs that are targeted and inhibit coronavirus. The antiviral properties of organic compounds found in nature, especially coumarins, are known and widely studied. Coumarins, which are also metabolites in many medicinal drugs, should be investigated as inhibitors against coronavirus due to their pharmacophore properties (low toxicity and high pharmacokinetic properties). The easy addition of substituents to the chemical structures of coumarins makes these structures unique for the drug design. This study focuses on factors that increase the molecular binding and antiviral properties of coumarins. Molecular docking studies have been carried out to five different proteins (Spike S1-subunit, NSP5, NSP12, NSP15, and NSP16) of the SARS-CoV-2 and two proteins (ACE2 and VKORC1) of human. The best binding scores for 17 coumarins were determined for NSP12 (NonStructural Protein-12). The highest score (–10.01 kcal/mol) in the coumarin group is 2-morpholinoethan-1-amine substituted coumarin. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analyses of selected ligand-protein complexes were performed. The binding energies in each 5 ns were calculated and it was found that the interaction between ligand and target protein were stable. Communicated by Ramaswamy H. Sarma. © 2020 Informa UK Limited, trading as Taylor & Francis Group.
Development of a gold nanoparticles-based colorimetric sensor for the indirect determination of ammonium dinitramide and tetryl
(Elsevier B.V., 2021) Mamatioğlu, F.; Üzer, A.; Erçağ, Erol; Apak, R.
Ammonium dinitramide (ADN) is a strong, environmentally friendly oxidizer used in composite solid rocket propellants. As there is no reliable colorimetric sensor for ADN assay applicable to in-field screening, we developed a sensitive and practical sensing method to determine it in the presence of other explosives and possible interferents, based on the detection of nitrite formed from ADN degradation under UV light in a slightly alkaline (i.e. of lower alkalinity than needed to hydrolyze nitramines) solution by a nanoparticle-based colorimetric sensor. The ADN-derived nitrite formed a colored product via a Griess reaction using gold nanoparticles modified with 4–aminothiophenol (4-ATP-AuNPs) along with a coupling reagent N-(1-naphthyl)ethylene diamine (NED) for forming an azo dye. The method used for ADN detection could also be applied to tetryl samples at a different wavelength. The limit of detection (LOD) was 0.012 mg L?1 for ADN and 0.615 mg L?1 for tetryl. Interference effects of energetic materials like trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and pentaerythritol tetranitrate (PETN) to ADN determination could be overcome. In addition, common soil ions did not adversely affect the nanosensor performance. The developed method was statistically validated against reference voltammetric, UV, and HPLC methods using t- and F- tests. © 2021 Elsevier B.V.
Efficient removal of indigo dye by using sulfonated poly (ether ether ketone) (sPEEK), montmorillonite (MMT) and sPEEK-MMT composites as novel adsorbent
(Elsevier, 2022) Hizal, Julide; Yılmazoğlu, Mesut; Kanmaz, Nergiz; Erçağ, Erol
In this study, indigo blue (IB) was adsorbed on individual sulfonated poly (ether ether ketone) (sPEEK), montmorillonite (MMT) and sPEEK-MMT composites for the first time. Characterizations were performed by using XRD, FTIR, SEM, HR-TEM and BET/N-2 surface area analyses, particle size and zeta potential measurements. Approximately 91% of initial amount of IB in aqueous solution was adsorbed by all adsorbents at the end of equilibrium time. The highest maximum adsorption capacity reported in literature was achieved by using sPEEK-MMT (1:10) with Qmax as 833.30 mg IB/g adsorbent. Therefore, it can be presented as an innovative adsorbent to limit IB emissions.
Electrochemical determination of boron using the signal suppression of mannitol on a gold nanoparticle coated p-Aminothiophenol polymer electrode
(Elsevier Inc., 2021) Sağlam, Şener; Üzer, Ayşem; Erçağ, Erol; Apak, Reşat
In this study, a glassy carbon electrode (GCE) modified with gold nanoparticles (AuNPs) and coated with electropolymerized p-aminothiophenol (p-ATP) was used as a modified electrode (GC/AuNPs/PATP electrode) for the indirect electrochemical determination of boron (B) using boric acid-mannitol complexation. The developed electrode showed good electroactivity for B determination. Firstly the current intensity of mannitol was measured, then B (as H3BO3) was added to the medium and the unreacted mannitol was measured. The decrement in current intensity was recorded against B concentration to build linear calibration curves within the range of 5–50 mg L?1 of B using square wave voltammetry (SWV), and the oxidation peak potential of mannitol was observed at 0.97 V. The limit of detection (LOD) and limit of quantification (LOQ) were 1.43 mg L?1 and 4.77 mg L?1, respectively. Boron (5 mg L?1) was determined with quantitative recovery in the presence of 100-fold concentration (except 5-fold for Fe3+) levels of the potentially interferent ions (Cl?, SO42?, HCO3?, CO32?, NO32?, PO43?, NH4+, Cu2+, Mg2+, Ca2+, Na+, K+, Fe3+) in water using the proposed SWV method. Fe3+ and Cu2+ interferences could be overcome with cation exchange resin removal. Additionally, boron was determined in synthetic and real seawater samples. The proposed SWV method was statistically validated against the spectrophotometric carmine method using seawater, antibacterial hand sanitizer gel and boron/potassium nitrate (BPN) pyrotechnic formulation. © 2021 Elsevier B.V.
Magnetite nanoparticles-based hydroxyl radical scavenging activity assay of antioxidants using N, N-dimethyl-p-phenylenediamine probe
(TUBITAK, 2020) Can, Z.; Keskin, B.; Arda, A.; Erçağ, Erol; Apak, M.R.
Excessive amounts of reactive oxygen species (ROS), unless counterbalanced by antioxidants, can cause cellular damage under oxidative stress conditions; therefore, antioxidative defenses against ROS must be measured. With the development of nanotechnology, nanoparticles have found numerous applications in science, health, and industries. Magnetite nanoparticles (Fe3O4:MNPs) have attracted attention because of their peroxidase-like activity. In this study, hydroxyl radicals (·OH) generated by MNPs-catalyzed degradation of H2O2 converted the N,N-dimethyl-p-phenylenediamine (DMPD) probe into its colored DMPD·+ radical cation, which gave an absorbance maximum at ? = 553 nm. In the presence of antioxidants, ·OH was partly scavenged by antioxidants and produced less DMPD·+, causing a decrease in the 553 nm-absorbance. Antioxidant concentrations were calculated with the aid of absorbance differences between the reference and sample solutions. The linear working ranges and trolox equivalent antioxidant capacity coefficients of different classes of antioxidants were determined by applying the developed method. In addition, binary and ternary mixtures of antioxidants were tested to observe the additivity of absorbances of mixture constituents. The method was applied to real samples such as orange juice and green tea. Student t-test, F tests, and the Spearman's rank correlation coefficient were used for statistical comparisons. © 2020 TUBITAK. All rights reserved.
Magnetite nanoparticles-based hydroxyl radical scavenging activity assay of antioxidants using N, N-dimethyl-p-phenylenediamine probe
(Scientific Technical Research Council Turkey-Tubitak, 2020) Can, Ziya; Keskin, Büşra; Arda, Ayşem; Erçağ, Erol; Apak, Mustafa Reşat
Excessive amounts of reactive oxygen species (ROS), unless counterbalanced by antioxidants, can cause cellular damage under oxidative stress conditions; therefore, antioxidative defenses against ROS must be measured. With the development of nanotechnology, nanoparticles have found numerous applications in science, health, and industries. Magnetite nanoparticles (Fe3O4:MN Ps) have attracted attention because of their peroxidase-like activity. In this study, hydroxyl radicals (center dot OH) generated by MNPs-catalyzed degradation of H2O2 converted the N,N-dimethyl-p-phenylenediamine (DMPD) probe into its colored DMPD center dot+. radical cation, which gave an absorbance maximum at lambda = 553 nm. In the presence of antioxidants, center dot OH was partly scavenged by antioxidants and produced less DMPD center dot+, causing a decrease in the 553 nm-absorbance. Antioxidant concentrations were calculated with the aid of absorbance differences between the reference and sample solutions. The linear working ranges and trolox equivalent antioxidant capacity coefficients of different classes of antioxidants were determined by applying the developed method. In addition, binary and ternary mixtures of antioxidants were tested to observe the additivity of absorbances of mixture constituents. The method was applied to real samples such as orange juice and green tea. Student t-test, F tests, and the Spearman's rank correlation coefficient were used for statistical comparisons.
Structural characterization and biological evaluation of uracil-appended benzylic amines as acetylcholinesterase and carbonic anhydrase I and II inhibitors
(Elsevier B.V., 2023) Bulut, Z.; Abul, N.; Poslu, A.H.; Gülçin, İ.; Ece, A.; Erçağ, Erol; Koz, Ö.; Erçağ, Erol
A series of novel uracil-appended benzylic amines were synthesized through reductive amination with moderate to good yields (30–84% yields). In situ prepared 5-(arylidene)-6-aminouracils with the condensation reaction between 5,6-diamino-1,3-dimethyluracil and substituted salicylaldehydes were reduced by excess sodium borohydride. All of the compounds were characterized using FT-IR, 1H NMR, 13C NMR spectroscopy and elemental analysis. The inhibition abilities of novel uracil-appended benzylic amines (1–9) were evaluated against acetylcholinesterase (AChE) and human carbonic anhydrase I and II (hCA I and II) isoenzymes that are linked to some global disorders such as Alzheimer's disease (AD), epilepsy, diabetes and glaucoma. The compounds exhibited inhibition profiles with Ki values ranging from 2.28±0.41 nM to 5.25±0.75 nM for AChE, 36.10±5.22–110.31±54.81 nM for hCA I and 16.33±4.91–72.03±28.86 for hCA II. Tacrine was used as a reference inhibitor for AChE and exhibited a Ki value of 2.59±0.92 nM against the AChE enzyme. On the other hand, Acetazolamide was used as a standard inhibitor towards hCA I and hCA II isoforms with Ki values of 31.38±8.56 nM and 18.72±1.67 nM, respectively. The results of enzyme inhibition associated with some global metabolic diseases indicate that novel uracil-appended benzylic amines may have the potential to develop new drugs to treat some common diseases such as Alzheimer's disease (AD), epilepsy and glaucoma. Molecular docking simulations were conducted to explain the binding interactions of compounds with AChE, hCA I and hCA II. Pharmacokinetic profiles were predicted to be within the acceptable ranges. © 2023 Elsevier B.V.
Synthesis and molecular docking study of novel COVID-19 inhibitors
(Scientific Technical Research Council Turkey-Tubitak, 2021) Gerçek, Zuhal; Ceyhan, Deniz; Erçağ, Erol
In 2020, the world tried to combat the corona virus (COVID-19) pandemic. A proven treatment method specific to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is still not found. In this study, seven new antiviral compounds were designed for COVID-19 treatment. The ability of these compounds to inhibit COVID-19's RNA processing was calculated by the molecular docking study. It has been observed that the compounds can have high binding affinities especially against NSP12 (between -9.06 and -8.00 kcal/mol). The molecular dynamics simulation of NSP12-ZG 7 complex proved the stability of interaction. The synthesis of two most active molecules was performed by one-pot reaction and characterized by FT-IR, H-1-NMR, C-13-NMR, and mass spectroscopy. The compounds presented with their synthesis are inhibitory core structures against SARS-CoV-2 infection.
Synthesis and molecular docking study of novel COVID-19 inhibitors
(TUBITAK, 2021) GERÇEK, Z.; Ceyhan, Deniz; Erçağ, Erol
In 2020, the world tried to combat the corona virus (COVID-19) pandemic. A proven treatment method specific to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is still not found. In this study, seven new antiviral compounds were designed for COVID-19 treatment. The ability of these compounds to inhibit COVID-19's RNA processing was calculated by the molecular docking study. It has been observed that the compounds can have high binding affinities especially against NSP12 (between -9.06 and -8.00 kcal/mol). The molecular dynamics simulation of NSP12-ZG 7 complex proved the stability of interaction. The synthesis of two most active molecules was performed by one-pot reaction and characterized by FT-IR, 1H-NMR, 13C-NMR, and mass spectroscopy. The compounds presented with their synthesis are inhibitory core structures against SARS-CoV-2 infection. © 2021 TUBITAK. All rights reserved.
Synthesis of thiophene derivatives: Substituent effect, antioxidant activity, cyclic voltammetry, molecular docking, DFT, and TD-DFT calculations
(Elsevier, 2022) Uludağ, Nesimi; Serdaroğlu, Goncagül; Sugumar, Paramasivam; Rajkumar, Parthasarathi; Çolak, Naki; Erçağ, Erol
The efficient pathway 6-methyl-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carboxylate derivatives have been synthesized. Due to the promising biochemical reactivity, the bioactive agent synthesis in the frame of the thiophene moiety is one of the main objectives of the contemporary scientific disciplines. The structures of all the presently synthesized compounds were confirmed using spectroscopic methods (UV-vis, FT-IR, H-1 NMR, C-13 NMR). The cyclic voltammetry (CV) of three compounds (1-3) was performed using a bare ITO electrode and a Nafion modified ITO (Indium Tin Oxide) electrode. The antioxidant properties of these compounds were explored by the CUPRAC method and TEAC (Trolox equivalent total antioxidant capacity) coefficients revealed that the antioxidant capacity of the compounds was ranking as follows: compound 2 (C-2) > compound 3 (C-3) > compound 1 (C-1). The docking studies displayed that compound 1 was the most active compound against Escherichia coli thymidylate synthase (TS). The TD-DFT calculations displayed that two observed peaks on the UV-vis spectra of the thiophenes were related to the n & nbsp;-> pi* and pi & nbsp;-> pi* transitions. Also, NBO (Natural Bond Orbital) analysis indicated that the resonance interactions (n & nbsp;-> pi* and pi & nbsp;-> pi*) in the ground state of all compounds had an essential role in the decreasing of the stabilization energy. The antioxidant activity and molecular docking results were supported by the electrodonating power and hardness indexes in addition to the NBO results. (C)& nbsp;2022 Elsevier B.V. All rights reserved.
Ultrasound phantom with solids mimicking cancerous tissue for needle breast biopsy
(Scientific And Technological Research Council Turkey, 2022) Yayla, Işık İpek Avcı; Bilal, Melis; Salmaslıoğlu, Artur; Erçağ, Erol; Sezer, Esma; Ustamehmetoğlu, Belkıs
This study aimed at synthesizing hydrogels to simulate opaque breast tissue (BT) and coloured cancerous tissues (CT) at different densities of the designed phantom to improve the biopsy-related skills along with ultrasonography. Both tissues are tear-resistant and therefore, the phantom can be trained multiple times in order to lower the price and improve the eye-hand coordination of users. For this purpose, self-healing (SH) polyacrylamide (PAAm) hydrogels (SH hydrogel) obtained by free-radical polymerization of AAm, in the presence of chemical cross-linker, BAAm, physical cross-linker stearyl methacrylate, C18, and ammonium persulfate APS as initiator were used in the design of phantoms. Psyllium was added to the BT to differentiate density and obtain human skin color and it could be distinguished from the CT which was also colored with methyl violet. BT and CTs were characterized with FTIR spectroscopy, mechanical, swelling, and refractive index measurements. Designing phantoms from BT and CT were characterized by ultrasonography, mechanical tests, observation of needle track after biopsy, and stabilization tests to follow the self-healing behaviours of tissues with time. As a result of this study, self-healing, low-cost, and suitable for multi-usage ultrasonographic phantom for needle breast biopsy was designed and cancerous tissue was successfully detected.

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