Virtual Screening of Artemisia annua Phytochemicals as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human coronaviruses that emerged in China at Wuhan city, Hubei province during December 2019. Subsequently, SARS-CoV-2 has spread worldwide and caused millions of deaths around the globe. Several compounds and vaccines have been proposed to tackle this crisis. Novel recommended in silico approaches have been commonly used to screen for specific SARS-CoV-2 inhibitors of different types. Herein, the phytochemicals of Pakistani medicinal plants (especially Artemisia annua) were virtually screened to identify potential inhibitors of the SARS-CoV-2 main protease enzyme. The X-ray crystal structure of the main protease of SARS-CoV-2 with an N3 inhibitor was obtained from the protein data bank while A. annua phytochemicals were retrieved from different drug databases. The docking technique was carried out to assess the binding efficacy of the retrieved phytochemicals; the docking results revealed that several phytochemicals have potential to inhibit the SARS-CoV-2 main protease enzyme. Among the total docked compounds, the top-10 docked complexes were considered for further study and evaluated for their physiochemical and pharmacokinetic properties. The top-3 docked complexes with the best binding energies were as follows: the top-1 docked complex with a −7 kcal/mol binding energy score, the top-2 docked complex with a −6.9 kcal/mol binding energy score, and the top-3 docked complex with a −6.8 kcal/mol binding energy score. These complexes were subjected to a molecular dynamic simulation analysis for further validation to check the dynamic behavior of the selected top-complexes. During the whole simulation time, no major changes were observed in the docked complexes, which indicated complex stability. Additionally, the free binding energies for the selected docked complexes were also estimated via the MM-GB/PBSA approach, and the results revealed that the total delta energies of MMGBSA were −24.23 kcal/mol, −26.38 kcal/mol, and −25 kcal/mol for top-1, top-2, and top-3, respectively. MMPBSA calculated the delta total energy as −17.23 kcal/mol (top-1 complex), −24.75 kcal/mol (top-2 complex), and −24.86 kcal/mol (top-3 complex). This study explored in silico screened phytochemicals against the main protease of the SARS-CoV-2 virus; however, the findings require an experimentally based study to further validate the obtained results.     

Molecular Characterization of Bacterial Isolates from Soil Samples and Evaluation of their Antibacterial Potential against MDRS

Some soil microbes, with their diverse inhabitance, biologically active metabolites, and endospore formation, gave them characteristic predominance and recognition among other microbial communities. The present study collected ten soil samples from green land, agricultural and marshy soil sites of Khyber Pakhtunkhwa, Pakistan. After culturing on described media, the bacterial isolates were identified through phenotypic, biochemical and phylogenetic analysis. Our phylogenetic analysis revealed three bacterial isolates, A6S7, A1S6, and A1S10, showing 99% nucleotides sequence similarity with Brevibacillus formosus, Bacillus Subtilis and Paenibacillus dendritiformis. The crude extract was prepared from bacterial isolates to assess the anti-bacterial potential against various targeted multidrug-resistant strains (MDRS), including Acinetobacter baumannii (ATCC 19606), Methicillin-resistant Staphylococcus aureus (MRSA) (BAA-1683), Klebsiella pneumoniae (ATCC 13883), Pseudomonas aeruginosa (BAA-2108), Staphylococcus aureus (ATCC 292013), Escherichia coli (ATCC25922) and Salmonella typhi (ATCC 14028). Our analysis revealed that all bacterial extracts possess activity against Gram-negative and Gram-positive bacteria at a concentration of 5 mg/mL, efficiently restricting the growth of E. coli compared with positive control ciprofloxacin. The study concluded that the identified species have the potential to produce antimicrobial compounds which can be used to control different microbial infections, especially MDRS. Moreover, the analysis of the bacterial extracts through GC-MS indicated the presence of different antimicrobial compounds such as propanoic acid, oxalic acid, phenol and hexadecanoic acid.     

Synthesis of Starch-Grafted Polymethyl Methacrylate via Free Radical Polymerization Reaction and Its Application for the Uptake of Methylene Blue

In this research, a new biodegradable and eco-friendly adsorbent, starch-grafted polymethyl methacrylate (St-g-PMMA) was synthesized. The St-g-PMMA was synthesized by a free radical polymerization reaction in which methyl methacrylate (MMA) was grafted onto a starch polymer chain. The reaction was performed in water in the presence of a potassium persulfate (KPS) initiator. The structure and different properties of the St-g-PMMA was explored by FT-IR, 1H NMR, TGA, SEM and XRD. After characterization, the St-g-PMMA was used for the removal of MB dye. Different adsorption parameters, such as effect of adsorbent dose, effect of pH, effect of initial concentration of dye solution, effect of contact time and comparative adsorption study were investigated. The St-g-PMMA showed a maximum removal percentage (R%) of 97% towards MB. The other parameters, such as the isothermal and kinetic models, were fitted to the experimental data. The results showed that the Langmuir adsorption and pseudo second order kinetic models were best fitted to experimental data with a regression coefficient of R² = 0.93 and 0.99, respectively.     

Prospect of Anterior Gradient 2 homodimer inhibition via repurposing FDA-approved drugs using structure-based virtual screening

Anterior Gradient 2 (AGR2) has recently been reported as a tumor biomarker in various cancers, i.e., breast, prostate and lung cancer. Predominantly, AGR2 exists as a homodimer via a dimerization domain (E60-K64); after it is self-dimerized, it helps FGF2 and VEGF to homo-dimerize and promotes the angiogenesis and the invasion of vascular endothelial cells and fibroblasts. Up till now, no small molecule has been discovered to inhibit the AGR2–AGR2 homodimer. Therefore, the present study was performed to prepare a validated 3D structure of AGR2 by homology modeling and discover a small molecule by screening the FDA-approved drugs library on AGR2 homodimer as a target protein. Thirteen different homology models of AGR2 were generated based on different templates which were narrowed down to 5 quality models sorted by their overall Z-scores. The top homology model based on PDB ID?=?3PH9 was selected having the best Z-score and was further assessed by Verify-3D, ERRAT and RAMPAGE analysis. Structure-based virtual screening narrowed down the large library of FDA-approved drugs to ten potential AGR2–AGR2 homodimer inhibitors having FRED score lower than ? 7.8 kcal/mol in which the top 5 drugs’ binding stability was counter-validated by molecular dynamic simulation. To sum up, the present study prepared a validated 3D structure of AGR2 and, for the first time reported the discovery of 5 FDA-approved drugs to inhibit AGR2–AGR2 homodimer by using structure-based virtual screening. Moreover, the binding of the top 5 hits with AGR2 was also validated by molecular dynamic simulation.

Graphic abstract

A validated 3D structure of Anterior Gradient 2 (AGR2) was prepared by homology modeling, which was used in virtual screening of FDA-approved drugs library for the discovery of prospective inhibitors of AGR2–AGR2 homodimer.

     

Heat pipes: progress in thermal performance enhancement for microelectronics

Journal of Thermal Analysis and Calorimetry - The aim of this study is to oversee the impact of various techniques on thermal performance of heat pipes and to comprehensively cover the progress...     

Single nucleon distribution based on shell-model and matrix ensemble theory

An expression for the density of single nucleons in a heavy spherical nucleus is derived using the shell-model and matrix ensembles. It is shown that the theoretical expression gives an excellent fit to the density of nucleons for the nucleus¹⁹⁷Au obtained usinge-scattering data.     

Exact generator coordinate wave functions for some simple hamiltonians

We obtain the superconformal transformation laws of theN=4 supersymmetric Yang-Mills theory and explicitly demonstrate the closure of the algebra.     

Synthesis,characterization and biological analysis of transition metal complexes with macro cyclic ligands derived from adipic acid,ethylenediamine with diethyloxalate and diethylmalonate

Macro-cyclic ligands from adipic acid, ethylenediamine with diethyloxalate and diethylmalonate and their respective metal complexes of Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) with macro cyclic ligands (LO) and (LM) L [N,N′-bis(2-aminoethyl)hexanediamide] were synthesized successfully. These metal complexes were characterized by Fourier transform infrared, ultraviolet visible spectrometry, proton nuclear magnetic resonance spectroscopy, and mass Spectrometry, CHNS and thermogravimetric analysis. The elemental analysis confirms the structures for Mn(II), Co(II) and Ni(II) complexes similar to octahedral geometry, Cu(II) complexes as a square planar geometry and Zn(II) complexes in the tetrahedral geometry. The molar conductivities of all the metal complexes were taken in 10^?3 M DMSO, and values of all the metal complexes showed their electrolytic nature which indicates the presence of chloride ions. Thermal analysis supports as the metal complexes are thermally stable. The result of antimicrobial activity against various microorganisms confirms that the metal complexes are potent bactericides and fungicides than the ligand. Metal complexes of LO with Cu(II) and Zn(II) were found to be highly active against S. typhimurium than the complexes of LM.

Graphical abstract

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Estimation of Residual Nickel and Some Heavy Metals in Vanaspati Ghee

To convert vegetable edible oils into vanaspati ghee, nickel is used as a catalyst in the hydrogenation process. A simple and fast method for the trace level determination of nickel in ghee is reported. In this work different methods were applied for the extraction of residual nickel from ghee samples. Using toluene, benzene and carbon tetrachloride as organic solvents, an acid mixture was used for the extraction of nickel. Extracted nickel was quantified with atomic absorption and colorimetric methods. Among the organic solvents, toluene proved to be the best solvent mediating a 95% extraction of nickel from ghee samples. Nickel was extracted and determined in ten different brands of ghee and in all samples its amount was well above the permissible limit of WHO (0.2 μg/g). Other metals like lead, zinc, copper, and cadmium were also determined and their concentrations were found to be much below the WHO permissible limits.