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Öğe Advancing Pyrrole Synthesis through DDQ Catalysis: A Comprehensive Research Incorporating DFT, ADMT, and Molecular Docking Analysis(Wiley-V C H Verlag Gmbh, 2024) Serdaroglu, Goncaguel; Uludag, Nesimi; Uestuen, ElvanThe construction of pyrroles is an important heterocyclic group comprising many compounds with interesting properties that have led to numerous applications in various fields. We delineate a new synthetic method for the rapid construction of tree-substituted pyrroles from readily available ketoximes as starting materials and also a new mechanism and method has been proposed. It is presented that substituted pyrroles were efficiently synthesized in high yields (up to 81 % yield) through the cyclization reaction of starting ketoximes mediated by 2,3-dichlor-5,6-dicyanobenzoquinone (DDQ). Utilizing this protocol various pyrrole derivatives were synthesized from diethyl acetylene dicarboxylate (DEAD). We then developed the dehydrogenation reaction mechanism of this formation, also studied in detail, also all synthesized compounds were analyzed in detail by spectroscopic techniques (FT-IR, 1H NMR, 13CNMR) which were compared with the computational data estimated at B3LYP/6-311G** level. The thermochemical and electronic properties of the pyrroles were evaluated after optimizing and then confirming the equilibrium structures. ADMT scores were also considered to estimate/elucidate the possible bioavailability tendencies as well as the toxicity. In addition, the interactions of the optimized molecules were evaluated by molecular docking methods against BSA Bovine Serum Albumin and LIF Leukemia Inhibitory Factor. The results obtained from this study will ideally provide a fundamental source in contemporary drug design in terms of both the key electronic properties underlying the possible reactivity features and toxicity. The pyrrole compounds were synthesized and characterized by spectroscopic tools (FT-IR, NMR). The DFT computations were performed to predict possible reactivity directions and sites. The ADMT (Absorption distribution, metabolism, and toxicity) features were calculated to evaluate the possible pharmacokinetics and bioavailability as well as the harmful effect in both medicinal and environmental respects. The molecular Docking studies were applied to compounds.imageÖğe Computational Study of Coumarin Compounds as Potential Inhibitors of Casein Kinase 2: DFT, 2D-QSAR, ADMET and Molecular Docking Investigations(Taylor & Francis Ltd, 2024) Chennai, Hind Yassmine; Belaidi, Salah; Ouassaf, Mebarka; Sinha, Leena; Prasad, Onkar; Serdaroglu, Goncaguel; Chtita, SamirCasein kinase 2 (CK2) is an ubiquitous, essential, and highly pleiotropic protein kinase whose abnormally high constitutive activity is suspected to underlie its pathogenic potential in neoplasia and other diseases. Recently, there has been a notable increase in interest in the use of casein kinase 2 (CK2) inhibitors to improve the treatment of a specific form of cancer while minimizing the risk of undesirable side effects. Recently, using different virtual screening approaches, we have identified several novel CK2 inhibitors. In particular, we have discovered that the coumarin moiety can be considered an attractive CK2 inhibitor scaffold. In the present work, quantitative structure-activity relationship (QSAR) analysis has been employed to envisage the inhibitory effects of 32 coumarin derivatives on the CK2 protein. The most efficient model is found by using multiple linear regression (MLR). Its capability is considered by the external and internal validation values found (R2 = 0.884, Q2cv = 0.822, R2pred = 0.821, and R2p = 0.811), which aligned well with Tropsha and Golbraikh's approach. The highest docking score founded for the newly designed coumarins is -7.50 kcal mol-1, which indicates that candidates can bind to the CK2 receptor with greater affinity. Based on the results of the ADMET properties and drug similarity analyses, a DFT investigation was conducted to confirm the stability of the newly explored compounds. It appears that the most stable complexes are those of compound with the highest binding affinity with a lower risk of toxicit & eacute;.Öğe In silico ADMET and DFT analysis of methoxy substituted curcumin derivatives(Elsevier, 2024) Afrdi, Muhammad Bilal; Sardar, Haseeba; Serdaroglu, Goncaguel; Shah, Syed Wadood Ali; Alsharif, Khalaf F.; Khan, HaroonThe current study aimed to predict drug ability of methoxy group substituted curcumin derivatives (MC1 to MC4) using ADMETLab 3.0 and DFT approaches. Almost all derivatives exhibited satisfactory physicochemical properties and medicinal chemistry. Pharmacokinetic profile revealed that all derivatives showed higher Caco-2 cell predicted permeability and exhibited a P-glycoprotein (Pgp) inhibitor capability, while non-of them is a Pgpsubstrate. MC1 and MC2 exhibited favorable human intestinal absorption (HIA) values. MC1 was in favor of better oral bioavailability. Values for plasma protein binding and volume of distribution were optimum for MC1 and MC2. All compounds were unable to cross blood brain barrier. Fraction unbound in the plasma was moderate for all compounds. All derivatives exhibited moderate clearance rate, while having ultra short half-lives. Toxicity profile was moderate for almost all compounds. Similarly, the DFT computations of the compounds of the curcumin derivatives were conducted at B3LYP/6-311G** level to predict and then assess the key electronic characteristics underlying the bioactivity. Accordingly, the MC4 molecule (Delta Egap = 3.883 eV) would prefer to interact with the external molecular system more than the other molecules due to having the biggest energy gap. The Delta Nmax (2.328 eV) and Delta epsilon back-donat. (-0.422 eV) scores implied that MC1 would have more charge transfer capability and the lowest stability via back donation among the compounds. In short, the derivative (MC1 to MC4) exhibited strong extrinsic therapeutic properties and therefore stand eligible for further in vitro and in vivo studies.Öğe Spectroscopic, crystal structure and DFT-assisted studies of some nickel(II) chelates of a heterocyclic-based NNO donor aroylhydrazone: in vitro DNA binding and docking studies(Springer, 2024) Nair, Yamuna; Joy, Francis; Vinod, T. P.; Vineetha, M. C.; Kurup, M. R. Prathapachandra; Kaya, Savas; Serdaroglu, GoncaguelFive new nickel(II) complexes have been synthesised with an NNO donor tridentate aroylhydrazone (HFPB) employing the chloride, nitrate, acetate and perchlorate salts, and all the complexes are physiochemically characterized. Elemental analyses suggested stoichiometries as Ni(FPB)(NO3)]& BULL;2H(2)O (1), [Ni(HFPB)(FPB)]Cl (2), [Ni(FPB)(OAc)(DMF)] (3), [Ni(FPB)(ClO4)]& BULL;DMF (4), [Ni(FPB)(2)] (5). Aroylhydrazone is found coordinating in deprotonated iminolate form in four of the complexes (1, 3, 4, 5) however in one case (complex 2), two aroylhydrazone moieties are binding to the metal centre in the neutral and anionic forms. The structure of the bisligated complex 5, found using single crystal X ray diffraction studies confirmed that the metal has a distorted octahedral N4O2 coordination environment, with each of the two deprotonated ligands coordinating through the pyridine nitrogen, imino-hydrazone nitrogen and the enolate oxygen of the hydrazone moiety. To compare and study, the electronic interactions and stabilities of the metal complexes, various quantum chemical parameters were calculated. Moreover, Hirshfeld surface analysis was carried out for complex 5 to determine the intermolecular interactions. The biophysical attributes of the ligand and complex 5 have been investigated with CT-DNA and experimental outcomes show that the Ni(II) complex exhibited higher binding propensity towards DNA as compared to ligand. Furthermore, to specifically understand the type of interactions of the metal complexes with DNA, molecular docking studies were effectuated. In addition, the electronic and related reactivity behaviors of the ligand and five Ni(II) complexes were studied using B3LYP/6-31 + + G**/LANL2DZ level. As expected, the obtained results from Natural Bond Orbital (NBO) computations displayed that the resonance interactions (n -> pi* and pi -> pi*) play a determinant role in evaluating the chemical attributes of the reported compounds.Öğe The synthesis and spectroscopic characterization of (+)-demethoxyaspidospermine: Density functional theory calculations of the structural, electronic, and non-linear optic and spectroscopic properties(Sage Publications Ltd, 2019) Serdaroglu, Goncaguel; Uludag, Nesimi(+)-Demethoxyaspidospermine was synthesized via the acylation of aspidospermidine with acetic anhydride, and the structure was determined by elemental analysis and Fourier-transform infrared and nuclear magnetic resonance spectroscopic tools and was supported by the simulated spectroscopic studies. Next, the stable geometries obtained by the conformational analysis performed at the B3LYP/6-31G(d, p) level were used for further investigations carried out in B3LYP and M06-2X functionals, and Hartree-Fock (HF) method, employed by the 6-311++G(d, p) basis set. Also, the natural bond orbital analysis revealed that the most contribution to the lowering of the stabilization energy came from n -> pi* and pi -> pi* interactions. Moreover, the non-linear optic analysis has shown that the title compound can be a useful agent in the optoelectronic devices because of the optical properties. Also, the chemical reactivity tendency for nucleophilic or electrophilic attack reactions on the compound was evaluated by frontier molecular orbital analysis, and the reactive sites of the compound was shown by highest molecular orbital and lowest unoccupied orbital amplitudes and molecular electrostatic potential diagrams.
