A biochemistry-oriented drug design: synthesis, anticancer activity, enzymes inhibition, molecular docking studies of novel 1,2,4-triazole derivatives.

In this study, we researched the reactions of 5-(5-bromofuran-2-yl)-4-methyl-1,2,4-triazole-3-thiol and 5-thiophene-(3-ylmethyl)-4R-1,2,4-triazole-3-thiols with some halogen-containing compounds, a number of new compounds were synthesized (1.1-1.5 and 2.1-2.8). These compounds showed excellent to good inhibitory activities on acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes. For obtaining the effects of these compounds on AChE and BChE enzymes were determined spectrophotometrically according to Ellman. IC50 values of these enzymes were ranging between 1.63 and 17.68 nM for AChE and 8.71 and 84.02 nM for BChE. After, prostate cancer is the second leading cause of cancer-related mortality for men over the age of 65 in developed countries. Current treatment options remain limited in the treatment of advanced-stage prostate cancer leading to biochemical recurrence in almost 40% of the patients. Therefore, there is an urgent need for development of novel therapeutic tools for treatment of prostate cancer patients. In this study, we aimed at analyzing the potential of all compounds against prostate cancer cells. We found that, of the tested compounds, 2.1, 2.2 and 2.3 showed significant cytotoxic activities against PC3 prostate cancer cells, although their effect on the viability of normal prostate cells was limited. These findings suggest their selective targeting potential for prostate cancer cells and offer them as candidate therapeutic agents against prostate cancer. The inhibitory activities of some chemical compounds, such as (1.1-1.5 and 2.1-2.8) were assessed by performing the molecular docking study in the presence of AChE, BChE and prostate cancer protein. MM/GBSA methods are calculated binding free energy. Finally, ADME/T analysis was performed to examine the drug properties of the 13 studied molecules.Communicated by Ramaswamy H. Sarma.

Enhanced Method for the Synthesis and Comprehensive Characterization of 1-(4-Phenylquinolin-2-yl)propan-1-one.

We present an enhanced method for synthesizing a novel compound, 1-(4-phenylquinolin-2-yl)propan-1-one (3), through the solvent-free Friedländer quinoline synthesis using poly(phosphoric acid) as an assisting agent. The crystal structure of compound 3 is analyzed using FT-IR, and the chemical shifts of its 1H- and 13C NMR spectra are measured and calculated using B3LYP/6-311G(d,p), CAM-B3LYP/6-311G(d,p), and M06-2X/6-311G(d,p) basis sets in the gas phase. Additionally, the optimized geometry of quinoline 3 is compared with experimental X-ray diffraction values. Through density functional theory calculations, we explore various aspects of the compound's properties, including noncovalent interactions, Hirshfeld surface analysis, nonlinear optical properties, thermodynamic properties, molecular electrostatic potential, and frontier molecular orbitals. These investigations reveal chemically active sites within this quinoline derivative that contribute to its chemical reactivity.

Synthesis, nanostructuring and in silico studies of a new imine bond containing a macroheterocycle as a promising PBP-2a non-ß-lactam inhibitor.

This study is devoted to the synthesis of a 40-membered macroheterocycle with its further nanostructuring by magnetite nanoparticles. The mentioned macroheterocycle was synthesized by the [2+2] cyclocondensation of the oxygen-containing diamine with an aromatic dialdehyde in a non-catalytic medium and with no work-up procedure. The structure of the obtained macroheterocycle was studied by 1H and 13C nuclear magnetic resonance spectroscopy and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Furthermore, the nanosupramolecular complex of macroheterocycles with magnetite nanoparticles was obtained and investigated by Fourier-transform infrared and ultraviolet-visible spectroscopy methods. Shifts in the infrared spectra of the nanosupramolecular complex indicate the interaction through metal-aromatic ring non-covalent bonding. The shift is also observed for the C-O-C stretching band of ether bonds. The loading rate of macroheterocycles on magnetite nanoparticles was 18.6%. The morphology of the ensemble was studied by transmission electron microscopy, which confirmed the synthesis of nanospherical particles with a diameter range of 10-20 nm. Powder X-ray diffraction analysis showed patterns of cubic Fe3O4 nanoparticles with a crystallite size equal to 9.1 nm. The macroheterocycle and its nanosupramolecular complex were tested against Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus. The results have shown that the created complex has shown 64 times better activity against Staphylococcus aureus in comparison with the individual macroheterocycle and 32 times better activity in comparison with the pristine antibiotic Ampicillin as a control. In addition, computational analysis of the macroheterocycle was performed at the B3LYP/6-31G level in water. Molecular docking analyses for the macroheterocycle revealed Penicillin-binding protein PBP2a (5M18) from the transpeptidase family as a target protein in Staphylococcus aureus.

Design and in silico study of the novel coumarin derivatives against SARS-CoV-2 main enzymes.

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.

New anti-viral drugs for the treatment of COVID-19 instead of favipiravir.

The SARS-CoV-2 virus is a major problem in the world right now. Currently, all the attention of research centers and governments globally are focused on the investigation of vaccination studies and the discovery of small molecules that inhibit the SARS-CoV-2 virus in the treatment of patients. The goal of this study was to locate small molecules to be used against COVID19 instead of favipiravir. Favipiravir analogues were selected as drug candidates from the PubChem web tool. The RNA dependent RNA polymerase (RdRp) protein was selected as the target protein as favipiravir inhibits this protein in the human body. Initially, the inhibition activity of the studied compounds against RdRp of different virus types was investigated. Then, the inhibition properties of selected drug candidates and favipiravir were examined in detail against SARS-CoV-2 RdRp proteins. It was found that 2-oxo-1H-pyrazine-3-carboxamide performed better than favipiravir in the results of molecular docking, molecular mechanics Poisson-Boltzmann surface area (MM-PSBA) calculations, and ADME analyses.Communicated by Ramaswamy H. Sarma.

Pt-Ni@PC900 Hybrid Derived from Layered-Structure Cd-MOF for Fuel Cell ORR Activity.

Fuel cell technology is the supreme alternate option for the replacement of fossil fuel in the current era. Pt alloys can perform well as fuel cell electrodes for being used as catalytic materials to perform the very notorious oxygen reduction reaction. In this regard, first, a layered metal-organic framework with empirical formula [C8H10CdO7] n ·4H2O is synthesized and characterized using various experimental and theoretical techniques. Then, a nanostructured porous carbon material with a sheet morphology (PC900) having a high BET surface area of 877 m2 g-1 is fabricated by an inert-atmosphere thermal treatment of the framework upon heating up to 900 °C. Pt and Ni nanoparticles are embedded into PC900 to prepare a homogenized hybrid functional material, i.e., Pt-Ni@PC900. The Pt-Ni@PC900 hybrid is proved to be an excellent ORR catalyst in terms of half-wave potential and limiting current density with 7% Pt loading compared with the commercially available 20% Pt/C catalyst. Pt-Ni@PC900 also shows stability of current up to 12 h with only a very small variation in current. This work highlights the importance of Pt alloys in future large-scale commercial applications of fuel cells.

Structural, spectral characterization and molecular docking analyses of mer-ruthenium (II) complexes containing the bidentate chelating ligands.

In this study, we analyzed some monofunctional Ru (II) complexes containing chlorine, bromine and fluorine atoms around the central atom. The best calculation level among HF, B3LYP and M062X methods for [Ru (Cl-Ph-tpy)(NN)X]+ (X = F, Cl, Br) was determined in the light of Benchmark analysis and according to this analysis results, the best level is shown as B3LYP-LANL2DZ/6-31G(d). In addition to this, the spectroscopic data (IR, NMR and UV-Vis) were also obtained in agreement with experimental results. The tendency of anticancer activity and structural activity relationship (SAR) parameters are predicted with some quantum chemical methods. Surface and contour diagrams, as well as electron densities on mentioned complexes were interpreted through theoretically obtained results. Finally, the anticancer activity tendency of the relevant complexes on the human cervical carcinoma cell line (ID: 1 M17) is supported by molecular docking calculations.

Water mediated synthesis of 6-amino-5-cyano-2-oxo-N-(pyridin-2-yl)-4-(p-tolyl)-2H-[1,2'-bipyridine]-3-carboxamide and 6-amino-5-cyano-4-(4-fluorophenyl)-2-oxo-N-(pyridin-2-yl)-2H-[1,2'-bipyridine]-3-carboxamide - An experimental and computational studies with non-linear optical (NLO) and molecular docking analyses.

6-Amino-5-cyano-2-oxo-N-(pyridin-2-yl)-4-(p-tolyl)-2H-[1,2'-bipyridine]-3-carboxamide and 6-amino-5-cyano-4-(4-fluorophenyl)-2-oxo-N-(pyridin-2-yl)-2H-[1,2'-bipyridine]-3-carboxamide were synthesized through three-component reaction between N1,N3-di(pyridin-2-yl)-malonamide, aldehyde and malononitrile in water using triethylamine as a base at room temperature. Synthesized compounds were characterized by using different techniques (FT-IR, NMR and X-ray diffraction). Additionally, the mentioned compounds were investigated by computational chemistry methods. Obtained results were supported with calculated results. Additionally, NLO properties and molecular docking analyses of related compounds were examined in detail. The binding modes of the compounds 4a and 4b were explored with the colchicine binding site of tubulin, from molecular docking studies, remarkable interactions have been observed for 4a and 4b near to the colchicines binding site of tubulin that may contribute to the inhibition of tubulin polymerization and anticancer activity.

Synthesis of novel 1,10-phenanthroline derivatives and it used as probes for sensitive detection of Zn2+ and Cd2+ metal ions - Spectroscopic and theoretical approach.

A novel class of unexpected 1,10-phenanthrolinederivatives were synthesized from 2,3-dihydroacridin-4(1H)-ones with 3-aminonaphthalen-2-carboxylic acid in presence of phosphorus oxychloride at 130°C and simple perceptive emission intensity increasing assay was developed effectively to detect the very low concentrations of Zn2+ and Cd2+ ions. Emission intensity of compounds 3(a-c) directly related to the concentrations of Zn2+ and Cd2+ ions was due to metal chelating enhanced fluorescence (CHEF) effect and also its further validated by fluorescence lifetime measurement. Furthermore, the sensing mechanism for compounds 3(a-c) of Zn2+ and Cd2+ were sustained by theoretical calculations. Computational analysis results reveals that compounds 3(a-c) are more interested in Zn2+ ions than that of Cd2+ ions, while, compound 3c is more interested with Zn2+ and Cd2+ ions than those of the rest of the compounds. In addition, this proposed detection analysis has the direct application for monitoring Zn2+ and Cd2+ concentrations in tap and drinking water samples.

Investigations of structural, spectral and electronic properties of enrofloxacin and boron complexes via quantum chemical calculation and molecular docking.

Quantum chemical analyses were performed over enrofloxacin and boron complexes. The most stable isomer of enrofloxacin was examined at M062X/6-31+G(d) level in gas phase. Structural and spectral characterizations of enrofloxacin and its complexes were performed at same level of theory. MEP maps of studied compound were calculated via ESP charges analyses. Some quantum chemical descriptors (QCDs) were calculated to determine the non-linear optical (NLO) and biological reactivity of studied molecules. Furthermore, molecular docking calculations between boron complexes and a protein (ID: 2ITN and 2ITV) were done. ADME analyses were done in the determination of the best drug candidate. As a result, complex (3) was found as the best in the NLO applications and it was found that complex (1) and (3) have similar biological reactivity in lung cancer treatment.

Research of the substituent effect on non-linear optical properties of bis(difluoroboron)-1,2-bis((1H-pyrrol-2-yl)methylene)hydrazine (BOPHY) derivatives: Molecular simulation analyses.

Modelling studies of bis(difluoroboron)-1,2-bis((1H-pyrrol-2-yl)methylene)hydrazine (BOPHY) derivatives were completed at M06-2X/6-31+G(d) level in vacuo. Structural properties (geometric structure, bond lengths and angles), spectral electronic properties and non-linear optical properties (NLO) of related boron complexes were investigated. Geometric parameters of mentioned boron complexes and electronic structures of them were reported. IR spectrum of boron complexes is calculated in vacuo and potential energy distribution (PED) analyses of frequencies were done. UV-VIS spectrum were calculated in gas phase (ε = 1), toluene (ε = 2.3741), chloroform (ε = 4.7113), methanol (ε = 32.613), water (ε = 78.3553) and n-methylformamide-mixture (ε = 181.56) at M06-2X/6-31+G(d), wB97X-D/6-31+G(d) and CAM-B3LYP/6-31+G(d) levels. Wavelength of observed bands in UV-VIS spectrum was used in the interpretation of optical activity. Molecular orbital energy diagram (MOED), contour diagrams of certain molecular orbitals, density of state (DOS) spectrum and molecular electrostatic potential (MEP) maps are calculated to determination of electronic properties and NLO activity. Finally, some quantum chemical descriptors were calculated and analyzed in determination of NLO properties. It is found that compound 5 and 6 are found as the good materials for NLO applications.

Investigations over optical properties of boron complexes of benzothiazolines.

Quantum chemical analyses over benzothiazolines and their boron complexes are performed. In calculations, M06-2X method was selected with 6-31 + G(d,p) level. Structural and spectral (IR and NMR) characterization of studied compounds are done in detail. Quantum chemical descriptors (QCDs) are calculated to investigate the optical properties. Furthermore, molecular electrostatic potential (MEP) maps of the studied compounds are calculated by using electro-static potential (ESP) charges. According to QCDs and MEP maps, NLO properties of boron complexes are more than those of benzothiazolines and (Z)-2-((pyridin-2-ylmethylene)amino) benzenethiolatebutane-1,3-bis(olate)boron(III), complex (7), has the most NLO activity in studied compounds. Finally, solvent effect on NLO activity are investigated by calculating UV-vis spectrum in gas phase (ε = 1), toluene (ε = 2.3741), chloroform (ε = 4.7113), methanol (ε = 32.613), water (ε = 78.3553) and n-methylformamide-mixture (ε = 181.56). According to these spectra results, NLO activity mainly increases with increasing of polarizability of media.

Investigation of structural, electronic properties and docking calculations of some boron complexes with norfloxacin: A computational research.

Quantum chemical calculations are performed over BF2R (1), B(NO)2R (2), B(CN)2R (3) and B(CH3)2R (4) [R: 1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylate]. Mentioned boron complex with fluorine atoms which is BF2R are optimized at HF/6-31+G(d), B3LYP/6-31+G(d) and M062X/6-31+G(d) level and the best level is determined by comparison of experimental and calculated results. The best calculation level is determined as M06-2X/6-31+G(d) level. The other complexes are optimized at this level. Structural properties, IR and NMR spectrum are examined in detail. Additionally, biological activities of mentioned complexes are investigated by some quantum chemical descriptors (EHOMO, ELUMO, I, A, EGAP, η, σ, χ, CP, ω, N, ΔNmax and S) and molecular docking analyses. The interaction energies for complex (1), (2), (3) and (4) are calculated as -480.1, -443.6, -433.6 and -402.1 kJ mol-1, respectively. As a result, it is found that boron complex with fluorine atoms (BF2R) is the best candidate for anticancer drug.

Computational investigations of trans­platinum(II) oxime complexes used as anticancer drug.

Some platinum oxime complexes are optimized at HF/CEP-31G level which has been reported as the best level for these type complexes in the gas phase. IR spectrum is calculated and the new scale factor is derived. NMR spectrum is calculated at the same level of theory and examined in detail. Quantum chemical parameters which have been mainly used are investigated and their formulas are given in detail. Additionally, selected quantum chemical parameters of studied complexes are calculated. New theoretical IC50% formulas are derived and biological activity rankings of mentioned complexes are investigated.

Investigation of anticancer properties of caffeinated complexes via computational chemistry methods.

Computational investigations were performed for 1,3,7-trimethylpurine-2,6-dione, 3,7-dimethylpurine-2,6-dione, their Ru(II) and Os(III) complexes. B3LYP/6-311++G(d,p)(LANL2DZ) level was used in numerical calculations. Geometric parameters, IR spectrum, 1H-, 13C and 15N NMR spectrum were examined in detail. Additionally, contour diagram of frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) maps, MEP contour and some quantum chemical descriptors were used in the determination of reactivity rankings and active sites. The electron density on the surface was similar to each other in studied complexes. Quantum chemical descriptors were investigated and the anticancer activity of complexes were more than cisplatin and their ligands. Additionally, molecular docking calculations were performed in water between related complexes and a protein (ID: 3WZE). The most interact complex was found as Os complex. The interaction energy was calculated as 342.9kJ/mol.

Structural, spectral, NLO and MEP analysis of the [MgO2Ti2(OPr(i)ⁱⁱ)6], [MgO2Ti2(OPr(i)ⁱ)2(acac)4] and [MgO2Ti2(OPr(i)ⁱ)2(bzac)4] by DFT method.

Quantum chemical calculations are performed on [MgO2Ti2(OPr(i))6] and [MgO2Ti2(OPr(i))2(L)4] complexes. L is acetylacetonate (acac) and benzoylacetonate (bzac) anion. The crystal structures of these complexes have not been obtained as experimentally but optimized structures of these complexes are obtained as theoretically in this study. Universal force field (UFF) and DFT/B3LYP method are used to obtain optimized structures. Theoretical spectral analysis (IR, (1)H and (13)C NMR) is compared with their experimental values. A good agreement is found between experimental and theoretical spectral analysis. These results mean that the optimized structures of mentioned complexes are appropriate. Additionally, the active sites of mentioned complexes are determined by molecular electrostatic potential (MEP) diagrams and non-linear optical (NLO) properties are investigated.

Theoretical spectroscopic study of seven zinc(II) complex with macrocyclic Schiff-base ligand.

Seven zinc complexes, which are [ZnL(1)](2+), [ZnL(2)](2+), [ZnL(3)](2+), [ZnL(4)](2+), [ZnL(5)](2+), [ZnL(6)](2+) and [ZnL(7)](2+), are studied as theoretically. Structural parameters, vibration frequencies, electronic absorption spectra and (1)H and (13)C NMR spectra are obtained for Zn(II) complexes of macrocyclic penta and heptaaza Schiff-base ligand. Vibration spectra of Zn(II) complexes are studied by using Density Functional Theory (DFT) calculations at the B3LYP/LANL2DZ. The UV-VIS and NMR spectra of the zinc complexes are obtained by using Time Dependent-Density Functional Theory (TD-DFT) method and Giao method, respectively. The agreements are found between experimental data of [ZnL(5)](2+), [ZnL(6)](2+) and [ZnL(7)](2+) complex ions and their calculated results. The geometries of complexes are found as distorted pentagonal planar for [ZnL(1)](2+), [ZnL(2)](2+) and [ZnL(3)](2+) complex ions, distorted tetrahedral for [ZnL(4)](2+) complex ion and distorted pentagonal bipyramidal for [ZnL(5)](2+), [ZnL(6)](2+) and [ZnL(7)](2+) complex ions. Ranking of biological activity is determined by using quantum chemical parameters and this ranking is found as: [ZnL(7)](2+)>[ZnL(6)](2+)>[ZnL(5)](2+)>[ZnL(3)](2+)>[ZnL(2)](2+)>[ZnL(1)](2+).