Browsing by Author "Sayiner H.S."

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An overview on lambda, epsilon, kappa, iota and zeta variants of covid-19 and its probability to merge with delta & delta plus, why it is a concern
(2022-10-15) Monajjemi M.; Sayiner H.S.; Kandemirli F.; Mollaamin F.
COVID-19 is caused by the virus SARS-CoV-2 that belongs to the Corona groups. The subgroups of the coronavirus families are α, β, γ, and δ coronavirus. On June 15, 2021, the string λ of SARS-CoV-2 was evaluated as a variant of interest via the World Health Organization. This string has a high prevalence in some parts of South American countries, but it occurred only occasionally in Brazil. This study confirms that mutations in the λ-spike protein can be destroyed the neutralizing antibodies and increase infectivity. Coronaviruses such as SARS-CoV-2 have an evolutionary superpower called “recombination” which permits the mixing of their genomes into novel combinations. Unlike regular mutation, which precedes slowly one change at a time, recombination can produce whole changes in a coronavirus genome. Although right now, is a concern, a mixing of λ with other variants such as is much more of a concern compared to alone variants. There is another item: the recombination can arise within the sample after it was taken from the infected person, not while it was inside their body.
Analysis of DNA protection, interaction and antimicrobial activity of isatin derivatives
(2019-02-01) Ganim M.A.; Baloglu M.C.; Aygun A.; Altunoglu Y.C.; Sayiner H.S.; Kandemirli F.; Sen F.
Isatin, thiosemicarbazone and their derivatives have been widely used in biological applications such as antimicrobial, antiviral and anticancer therapies. Herein, eight isatin and thiosemicarbazone derivative compounds were re-synthesized and evaluated for DNA binding analysis including DNA protection studies using plasmid DNA (pUC19) and DNA interaction experiments using calf thymus DNA (CT-DNA). All compounds were also utilized in vitro assay to assess the antimicrobial activity of compounds against different pathogenic bacterial strains. All isatin and thiosemicarbazone derivative compounds exhibited DNA protection activity which ranged from 23.5 to 59.5%. Among them, I3-(N-2-MP)-TSC had the greatest DNA protective activity. For DNA binding analysis, all compounds had the same constant concentration (40 μM), which interacts with CT-DNA. It was also observed that DNA interactions gave a high intrinsic binding constant (Kb = 1.72 × 104 M−1–9.73 × 105 M−1). Besides, several derivatives of isatin thiosemicarbazone exhibited significant and selective antibacterial activity with low concentration. These compounds primarily affected Gram-positive bacteria, but were not effective against P. vulgaris and E. coli. The Gram-positive methicillin-resistant S. aureus ATCC 43300 (MRSA) was the most influenced strain by these compounds. It was found that methyphenyl group at isatin was essential for its antibacterial activity for MRSA.
Carbazochrome carbon nanotube as drug delivery nanocarrier for anti-bleeding drug: quantum chemical study
(2022-01-01) Sayiner H.S.; Kandemirli F.; Dalgic S.S.; Monajjemi M.; Mollaamin F.
The interaction between drugs and single-walled carbon nanotubes is proving to be of fundamental interest for drug system of delivery and nano-bio-sensing. In this study, the interaction of pristine CNT with carbazochrome, an anti-hemorrhagic or hemostatic agent, was investigated with M06-2X functional and 6-31G* basis set. All probable positions of related adsorption for these kind drugs were thought-out to find out which one is energetically suitable. Based on the achieved data, the stronger interactions appeared the oxygen atom of C = O group and nitrogen atom of imine groups. The topology analysis of QTAIM (quantum theory of atoms in a molecule) method was accomplished to understand the properties of interactions between the CNT and carbazochrome. Frontier molecular orbital energies of all systems, global index including stiffness, softness, chemical Gibbs energies, and electrophilicity parameters, as well as some other important physical data such as dipole moment, polarizability, anisotropy polarisibility, and hyperpolaribility were calculated, evaluated, and then compared together. The essence of the formed bonding model progress along the reaction roots was further validated using electron localization function (ELF) calculations. The highest values of adsorption energies were determined in the range of 18.24 up to 22.12 kcal mol−1 for these kind systems. The acceptable recovery time of 849 s was obtained for the desorption of carbazochrome from the CNT surface under UV-light. The final results exhibit that carbazochrome can serve as a promising carrier and also as sensitive sensors in any kind of practical application.
Electronic-topological and neural network approaches to the structure-antimycobacterial activity relationships study on hydrazones derivatives
(2015-01-01) Kandemirli F.; Vurdu C.D.; Başaran M.A.; Sayiner H.S.; Shvets N.; Dimoglo A.; Kovalish V.; Polat T.
That the implementation of Electronic-Topological Method and a variant of Feed Forward Neural Network (FFNN) called as the Associative Neural Network are applied to the compounds of Hydrazones derivatives have been employed in order to construct model which can be used in the prediction of antituberculosis activity. The supervised learning has been performed using (ASNN) and categorized correctly 84.4% of them, namely, 38 out of 45. Ph1 pharmacophore and Ph2 pharmacophore consisting of 6 and 7 atoms, respectively were found. Anti-pharmacophore features socalled "break of activity" have also been revealed, which means that APh1 is found in 22 inactive molecules. Statistical analyses have been carried out by using the descriptors, such as EHOMO, ELUMO, ΔE, hardness, softness, chemical potential, electrophilicity index, exact polarizibility, total of electronic and zero point energies, dipole moment as independent variables in order to account for the dependent variable called inhibition efficiency. Observing several complexities, namely, linearity, nonlinearity and multi-co linearity at the same time leads data to be modeled using two different techniques called multiple regression and Artificial Neural Networks (ANNs) after computing correlations among descriptors in order to compute QSAR. Computations resulting in determining some compounds with relatively high values of inhibition are presented.
Evaluation of biological activity of 5-fluoro-isatin thiosemicarbazone derivatives
(2020-06-01) Ramadan M.A.G.; Baloglu M.C.; Altunoglu Y.C.; Kandemirli F.; Burhan H.; Aygün A.; Sayiner H.S.; Ozyigit F.; Şen F.
Isatin based materials can exhibit a wide range of biological activities including antimicrobial, antiviral, antifungal, anthelmintic, antitumor, anti-HIV, anti-inflammatory, antidepressant, antioxidant, anticonvulsant, antitubercular, analgesic, and central nervous system depressant activities. In this study, four compounds containing 5-Fluoro-isatin thiosemicarbazone with methoxyphenyl or methoxyphenyl in different positions and zinc complexes were evaluated based on their biological activities. Compound 2 was the strongest compound affecting gramnegative bacteria compared to the other compounds. Also, this compound indicated better antimicrobial activity than positive control antibiotics. Besides, compound 3 was the only compound that inhibited the growth of Salmonella spp. such as Salmonella enteritidis ATCC 13076 and Salmonella typhimurium NRRLE 4463. 5-Fluoro-Isatin thiosemicarbazone and its derivatives also showed DNA protection property from moderate to good protections. Among them, compound 4 displayed the highest DNA binding affinity. These compounds possessed a capacity for utilization as drugs or drug additives based on their effects on bacteria strains and DNA binding affinity.
Molecular structure vibrational & electronic properties of some isatin derivatives
(2021-01-01) Fkandermili F.K.; Aldibashi F.M.; Sayiner H.S.
In this study, Natural Bonding Orbitals (NBOs) were applied to isatin, 5‑fluoroisatin, 5‑chloroisatin, 5‑methylisatin and 5‑methoxyisatin using the Lee-Yang-Parr correlation functional B3LYP with 6‑311++G(2d,2p) basis set. Natural bonding analysis was performed to consider the transfer interactions of intra-molecular charge, pre-hybridization and electron density within the isatin, 5‑fluoroisatin, 5‑chloroisatin, 5‑methylisatin and 5‑methoxyisatin. In natural bonding orbital analysis, the wave functions of the electrons were explicated in sets of occupied Lewis type terms, (bonds or lone pairs) and sets of unoccupied non‑Lewis (anti‑bond and Rydberg) localized natural bonding orbitals. The electron density between these orbitals was correlated to stabilize the interaction of donor-acceptor orbitals. Second-order Perturbation Theory was employed to evaluate the stabilization energies of all possible interactions between donor and acceptor orbitals in natural bonding orbitals. The aim was to study the properties of these series and to produce a molecular geometry description, hyper-conjugative interactions, natural bond orbital (NBO) analysis and the HOMO‑LUMO energy gap-dependent properties that are important for the stability of structures. From the results, it can be noted that for all forms, the HOMO‑LUMO energy gap values decreased by substitution for the 5‑fluoroisatin, 5‑chloroisatin, 5‑methylisatin and 5‑methoxyisatin compounds and, with the exception of the deprotonated form in all the compounds, leading to less stable molecules. The anion form of the 5‑methoxyisatin compound and the cation form of the 5‑fluoroisatin, in which the HOMO‑LUMO energy gap values increased, became more stable. It also appeared that the 5‑CH3- and 5‑Cl groups caused an increase in the linear polarizability and anisotropic polarizability values in all forms; however, the 5‑OCH3 and 5‑F groups caused different effects in different forms. Furthermore, we concluded that the intramolecular hyper-conjugative interactions between bonded atoms changed by groups. These changes caused changes in the electron density values in the atoms, which in turn led to a change in the stabilization energy values of the isatin, 5‑fluoroisatin, 5‑chloroisatin, 5‑methylisatin and 5‑methoxyisatin.
Synthesis and characterization of new 1,3,4-thiadiazole derivatives: study of their antibacterial activity and CT-DNA binding
(2022-10-17) Sayiner H.S.; Yilmazer M.I.; Abdelsalam A.T.; Ganim M.A.; Baloglu C.; Altunoglu Y.C.; Gür M.; Saracoglu M.; Attia M.S.; Mahmoud S.A.; Mohamed E.H.; Boukherroub R.; Al-Shaalan N.H.; Alharthi S.; Kandemirli F.; Amin M.A.
1,3,4-Thiadiazole molecules (1-4) were synthesized by the reaction of phenylthiosemicarbazide and methoxy cinnamic acid molecules in the presence of phosphorus oxychloride, and characterized with UV, FT-IR, 13C-NMR, and 1H-NMR methods. DFT calculations (b3lyp/6-311++G(d,p)) were performed to investigate the structures' geometry and physiochemical properties. Their antibacterial activity was screened for various bacteria strains such as Enterobacter aerogenes, Escherichia coli ATCC 13048, Salmonella kentucky, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus and Gram positive such as Staphylococcus aureus ATCC 25923, Listeria monocytogenes ATCC 7644, Enterococcus faecium, Enterococcus durans, Staphylococcus aureus ATCC, Serratia marcescens, Staphylococcus hominis, Staphylococcus epidermidis, alfa Streptococcus haemolyticus, Enterococcus faecium and found to have an inhibitory effect on Klebsiella pneumoniae and Staphylococcus hominis, while molecules 1, 3 and 4 had an inhibitory effect on Staphylococcus epidermidis and alpha Streptococcus haemolyticus. The experimental results were supported by the docking study using the Kinase ThiM from Klebsiella pneumoniae. All the investigated compounds showed an inhibitory effect for the Staphylococcus epidermidis protein. In addition, the mechanism of the 1-4 molecule interaction with calf thymus-DNA (CT-DNA) was investigated by UV-vis spectroscopic methods.
The quantum chemical and QSAR studies on Acinetobacter baumannii oxphos inhibitors
(2018-05-01) Sayiner H.S.; Abdalrahm A.A.S.; Başaran M.A.; Kovalishyn V.; Kandemirli F.
Background: Acinetobacter is a Gram-negative, catalase-positive, oxidase-negative, non-motile, and no fermenting bacteria. Objective: In this study, some of the electronic and molecular properties, such as the highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital energy (ELUMO), the energy gap between EHOMO and ELUMO, Mulliken atomic charges, bond lengths, of molecules having impact on antibacterial activity against A. baumannii were studied. In addition, calculations of some QSAR descriptors such as global hardness, softness, electronegativity, chemical potential, global electrophilicity, nucleofugality, electrofugality were performed. Method: The descriptors having impact on antibacterial activity against A. baumannii have been investigated based on the usage of 29 compounds employing two statistical methods called Linear Regression and Artificial Neural Networks. Results: Artificial Neural Networks obtained accuracies in the range of 83-100% (for active/inactive classifications) and q2=0.63 for regression. Conclusion: Three ANN models were built using various types of descriptors with publicly available structurally diverse data set. QSAR methodologies used Artificial Neural Networks. The predictive ability of the models was tested with cross-validation procedure, giving a q2=0.62 for regression model and overall accuracy 70-95 % for classification models.
Voltammetric and theoretical study of the interaction of ceftriaxone with phenylalanine
(2018-01-01) Sayiner H.S.; Bakir T.; Kandemirli F.
The interaction between ceftriaxone and phenylalanine (PA) was investigated by cyclic voltammetry and quantum chemical study using DFT (density functional theory) method. The study was carried out in phosphate buffer solution (PBS) at pH 7.0 (which was also used as the supporting electrolyte) by directly dissolving it in twice distilled water. The voltammetric study of ceftriaxone showed well expressed redox peaks at 0.090 V on a GCE in phosphate buffer of pH 7.0 at 50 mVs-1. The cathodic peak currents were linear with different scan rates from 25 to 275 mVs-1 and the correlation coefficient was found to be 0.971 9 and 0.9592 for ceftriaxone and ceftriaxone-PA systems, respectively in the potential range of 0.8-(-0.2) V. The electron transfer rate constant (ks) was calculated for the reduction of ceftriaxone and ceftriaxone-PA interactions as 2.031 and 4.831 s-1, respectively. After the addition of PA to the ceftriaxone solution, the redox binding constant was obtained as K = 1.32×103 M-1 for ceftriaxone-PA interaction, and quantum chemical calculations were performed for ceftriaxone and ceftriaxone-PA complex by the B3LYP method.