Research Outputs
Identification of novel coumarin based compounds as potential inhibitors of the 3-Chymotrypsin-like main protease of Sars-Cov-2 Using Dft, molecular docking and molecular dynamics simulation studies
SARS-CoV-2 is the pandemic disease-causing agent COVID-19 with high infection rates. Despite the progress made in vaccine development, there is an urgent need for the identification of antiviral compounds that can tackle better the different phases of SARS-CoV-2. The main protease (Mpro or 3CLpro) of SARS-CoV-2 has a crucial role in viral replication and transcription. In this study, an in silico method was executed to elucidate the inhibitory potential of the synthesized 6-tert-octyl and 6-8-ditert-butyl coumarin compounds against the major protease of SARS-CoV-2 by comprehensive molecular docking and density functional theory (DFT), ADMET properties and molecular dynamics simulation approaches. Both compounds shown favorable interactions with the 3CLpro of the virus. From DFT calculations, HOMO-LUMO values and global descriptors indicated promising results for these compounds. Furthermore, molecular dynamics studies revealed that these ligand-receptor complexes remain stable during simulations and both compounds showed considerably high binding affinity to the main SARS-CoV-2 protease. The results of the study suggest that the coumarin compounds 6-tert-octyl and 6-8-ditert-butyl could be considered as promising scaffolds for the development of potential COVID-19 inhibitors after further studies.
Theoretical insight on structural activities and targets of Kaempferol Glycosides
Metabolite profile always hold important place for flavonoids as they are the major promoters of secondary metabolism in human body. For decades numerous flavonoids are explored for their structural activities which in turn helped them to meet various health promoting applications such as radical scavenging activity. Apart from conventional flavonoids their derivatives are also tend to exhibit similar kind of structural activity. Therefore, in the present work afzelin and juglanin – the glycosyl derivatives of kaemepferol an established flavonoid are subjected to structural activity relationship analysis using density functional theory. The structures of the two kaempferol glycosides are optimized and the optimized geometry is simulated to obtain frontier orbitals, electrostatic potential energy and molecular descriptors. The obtained results suggest that maximum amount of charge is accumulated over B-ring of two flavonoids, thus prefers to act as better electron donating region. Target predicted for two flavonoids over homosapien class reveal that the flavonoid highly prefers lyase and enzymatic targets for inhibition purpose.
Theoretical investigation of the molecular structure and molecular docking of etoricoxib
In this work, a computational chemical study of Etoricoxib was carried out at the X/6311G(d,p) (where X=B3LYP, M06 and B97XD) level of theory, at the gas, aqueous and ethanol phases. Through the chemical reactivity descriptors derived from the DFT, it was possible to find that Etoricoxib structure exhibits a major chemical activity in water and ethanol phases in comparison to the gas phase, which suggests this drug would be more active in biological solvents like in blood, tissues and places where the ciclooxigenasa 2 (COX)-2 is found. In addition, a molecular docking analysis was conducted to study the interaction of Etoricoxib with the COX-2 active site. The results suggest that Etoricoxib interacts with 19 amino acid residues inside the COX-2 active site.
Occurrence of chlorpyrifos in the atmosphere of the Araucanía Region in Chile using polyurethane foam-based passive air samplers
Little is known regarding the use and ambient levels of pesticides in Chilean agricultural regions. Chlorpyrifos (CPF) is one of the most used active ingredients in Chile and in the world. However, few investigations have been conducted to understand its environmental distribution and fate. In this study, PUF disk passive air samples were deployed during ~one year in two areas, Angol (5 sites) and Villarrica (2 sites), in the Araucanía Region. The concentration in air of CPF ranged from ten to thousands of pg m-3 (~20e14 600). The highest CPF concentrations were detected at the Angol sites (~14 600 pg m3) during period 2 (AugusteDecember 2008). These results were higher by a factor of ~10e15 than those detected in Villarica sites (~2000 pg m3) in period 1 (AprileJuly 2008). Seasonal CPF variations were observed, at both sites, within the sampling periods. Air back trajectory analyses showed that air masses from nearby agricultural zones contributed most of the CPF detected in Angol sites when the wind speed was low and at Villarrica when those sources were likely located north of the VMA site. These results provide initial data for CPF in the Chilean atmosphere and contribute new information to understanding distribution of CPF in Chilean environments.
Minor composition compounds of algerian herbal medicines as inhibitors of sars-cov-2 main protease: Molecular docking and admet properties prediction
The identification of drugs against the new coronavirus (SARS-CoV-2) is an important requirement. Natural products are substances that serve as sources of beneficial chemical molecules for the development of effective therapies. In this study, 187 natural compounds from Algerian herbal medicines were docked in the active site of SARS-CoV-2 main protease. The result indicates that Piperitol, Warfarin, cis-calamenen-10-ol and α-Cadinene are the structures with best affinity in the binding site of the studied enzyme and all of them respect the conditions mentioned in Lipinski’s rule and have acceptable ADMET proprieties; so, these compounds could have more potent antiviral treatment of COVID-19 than the studied compounds, and they have important pharmacokinetic properties and bioavailability.
A theoretical quantum study of the electronic properties of mentoxy dichloro phosphorous (C10H19OPCl2)
A theoretical quantum study of the organophosphorus compound with formula C10H19OPCl2 (MEPCL2) was carried out. The results of the calculations show excellent agreement between experimental and computed frequencies evaluated at the B3LYP/6-311++G(d,p) level of theory. A study of the electronic properties, such as excitation energies and wavelengths were performed employing the time-dependent DFT (TD-DFT) method. Global a chemical reactivity of MEPCL2 was analyzed through global reactivity descriptors, while its local reactivity was analyzed by mean maps of the electrostatic potential. Also, the orbital energies values suggest that a charge transfer is occurring within the molecule.
Preparation, identification and biological properties of new fluoride nanocompounds
Nanoparticles (NPs) of new fluoride (SrF2 and MgF2) nanocompounds were synthesized by the simple chemical method of precipitation in ethanol. Synthesis of the strontium fluoride (SrF2)-magnesium oxide (MgO) nanocomposite was achieved through the ultrasonic method. These prepared nanopowders were characterized through Fourier transform infrared (FT-IR) spectroscopy, ultraviolet–visible (UV–Vis) spectroscopy, Powder X-ray Diffraction (PXRD) and Scanning Electron Microscopy (SEM). FT-IR confirmed the purity of the synthesized fluoride NPs by evaluation of the vibrations, and UV–Visible showed the intense absorption peaks of NPs. PXRD analysis indicated the average of particle size, and SEM demonstrated a nearly spherical morphology of the NPs. The antibacterical properties of the nanopowders on Staphylococcus Aureus, Bacillus Subtilis and E. Aklay bacteria were studied, with the strongest effect by the magnesium fluoride (MgF2) NPs and the SrF2-MgO nanocomposite.
A DFT study on the efficacy of linking agents (Sulfur and Nitrogen) to connect Trans-azobenzene Sandwiched between two Gold Electrodes
Electronic structure calculations were performed to analyze the effectiveness of linking agents (sulfur and nitrogen) in connecting the trans-azobenzene sandwiched between two gold surfaces (Au-atoms). It was analyzed the dynamics of the load carrier and the electronic structure of the molecular backbone by applying an external electric field (EF), also a detailed structural, frontier orbital and natural bond orbital analysis (NBO) were performed. From the NBO analysis, it was possible to predict the path of charge flow in the molecular system. Electrostatic potential mapping allowed us to visualize the charge redistribution in the molecular system caused by the EF application. Our results indicate that when the nitrogen atom is used as a linking agent, the azo group of molecules may enhance their conductivity.
A computational study of the antioxidant power of eugenol compared to Vitamin C
The antioxidant power of eugenol and vitamin C was examined by analyzing the ability of these ligands to bind to the NADPH oxidase protein target and evaluating their bond interactions with critical residues. The results confirm that docked ligands are more stable in the specified active region of 2CDU during a MD simulation of 100 ns and 2CDU protein-ligand interactions with docked ligands showed significant hydrogen bond, hydrophobic, and water bridge formation. Eugenol exhibits hydrogen bond interactions with critical residues in the selective pocket in comparison to vitamin C. Also, eugenol had a similar binding orientation and very considerable stability in the selective pocket of 2CDU with a high binding energy with lipophilic energy. The electrostatic potential maps indicate that for eugenol, the –OH and –OCH3 sites, while that the –OH and –CO functional groups in vitamin C are responsible of the antioxidant activities of these compounds. HAT and SET mechanisms suggest that eugenol may become a better antioxidant than vitamin C.
New Phosphorus Compounds K[PCL3(X)] (X= SCN, CN): Preparation and DFT and spectroscopic studies
Two new phosphorus complexes, potassium trichlorothiocyanophosphate (III) (PTCTCP; K[PCl3(SCN)]) and potassium trichlorocyanophosphate (III) (PTCCP; K[PCl3(CN)]) were synthesized from the reaction of KSCN and KCN, respectively, with PCl3. The chemical formulas and compositions of these compounds were determined by elemental analysis and spectroscopic methods, such as phosphorus-31 nuclear magnetic resonance (NMR) spectroscopy (31P-NMR), Fourier transform infrared (FTIR) spectroscopy, ultraviolet-visible (UV-Vis) spectroscopy and mass spectrophotometry. All of the theoretical calculations and determinations of the properties of these compounds were performed as part of the Amsterdam Density Functional (ADF) program. Excitation energies were assessed using time-dependent perturbation density functional theory (TD-DFT). In addition, the molecular geometry was optimized and the frequencies and excitation energies were calculated using standard Slater-type orbital (STO) basis sets with triple-zeta quality double plus polarization functions (TZ2P) for all of the atoms. The assignment of the principal transitions and total densities of state (TDOS) for orbital analysis were performed using the GaussSum 2.2 program.