Computational investigation of drug bank compounds against 3C-like protease (3CLpro) of SARS-CoV-2 using deep learning and molecular dynamics simulation

Blocking the main replicating enzyme, 3 Chymotrypsin-like protease (3CL^pro) is the most promising drug development strategy against the SARS-CoV-2 virus, responsible for the current COVID-19 pandemic. In the present work, 9101 drugs obtained from the drug bank database were screened against SARS-CoV-2 3CL^pro prosing deep learning, molecular docking, and molecular dynamics simulation techniques. In the initial stage, 500 drug-screened by deep learning regression model and subjected to molecular docking that resulted in 10 screened compounds with strong binding affinity. Further, five compounds were checked for their binding potential by analyzing molecular dynamics simulation for 100 ns at 300 K. In the final stage, two compounds {4-[(2s,4e)-2-(1,3-Benzothiazol-2-Yl)-2-(1h-1,2,3-Benzotriazol-1-Yl)-5-Phenylpent-4-Enyl]Phenyl}(Difluoro)Methylphosphonic Acid and 1-(3-(2,4-dimethylthiazol-5-yl)-4-oxo-2,4-dihydroindeno[1,2-c]pyrazol-5-yl)-3-(4-methylpiperazin-1-yl)urea were screened as potential hits by analyzing several parameters like RMSD, Rg, RMSF, MMPBSA, and SASA. Thus, our study suggests two potential drugs that can be tested in the experimental conditions to evaluate the efficacy against SARS-CoV-2. Further, such drugs could be modified to develop more potent drugs against COVID-19.

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An overview of degradation in solid oxide fuel cells-potential clean power sources

Journal of Solid State Electrochemistry - Solid oxide fuel cells (SOFCs) have emerged as the potential power generating devices, being profoundly effective, biofuel-based, and causing negligible...     

Application of a UPLC‐MS/MS method for the analysis of alosetron in human plasma to support a bioequivalence study in healthy males and females

A simple, rapid and sensitive ultra‐performance liquid chromatography–tandem mass spectrometry (UPLC‐MS/MS) method has been developed and validated for the determination of alosetron (ALO) in human plasma. The assay method involved solid‐phase extraction of ALO and ALO 13C‐d3 as internal standard (IS) on a LichroSep DVB‐HL (30 mg, 1 cm³) cartridge. The chromatography was performed on an Acquity UPLC BEH C₁₈ (50 × 2.1 mm, 1.7 µm) column using acetonitrile and 2.0 mm ammonium formate, pH 3.0 adjusted with 0.1% formic acid (80:20, v/v) as the mobile phase in an isocratic mode. For quantitative analysis, the multiple reaction monitoring transitions studied were m/z 295.1/201.0 for ALO and m/z 299.1/205.1 for IS in the positive ionization mode. The method was validated over a concentration range of 0.01–10.0 ng/mL for ALO. Post‐column infusion experiment showed no positive or negative peaks in the elution range of the analyte and IS after injection of extracted blank plasma. The extent of ion‐suppression/enhancement, expressed as IS‐normalized matrix factor, varied from 0.96 to 1.04. The assay recovery was within 97–103% for ALO and IS. The method was successfully applied to support a bioequivalence study of 1.0 mg alosetron tablets in 28 healthy Indian male and female subjects. Copyright © 2015 John Wiley & Sons, Ltd.     

Chemical Perturbation of Oncogenic Protein Folding: from the Prediction of Locally Unstable Structures to the Design of Disruptors of Hsp90–Client Interactions

Protein folding quality control in cells requires the activity of a class of proteins known as molecular chaperones. Heat shock protein-90 (Hsp90), a multidomain ATP driven molecular machine, is a prime representative of this family of proteins. Interactions between Hsp90, its co-chaperones, and client proteins have been shown to be important in facilitating the correct folding and activation of clients. Hsp90 levels and functions are elevated in tumor cells. Here, we computationally predict the regions on the native structures of clients c-Abl, c-Src, Cdk4, B-Raf and Glucocorticoid Receptor, that have the highest probability of undergoing local unfolding, despite being ordered in their native structures. Such regions represent potential ideal interaction points with the Hsp90-system. We synthesize mimics spanning these regions and confirm their interaction with partners of the Hsp90 complex (Hsp90, Cdc37 and Aha1) by Nuclear Magnetic Resonance (NMR). Designed mimics selectively disrupt the association of their respective clients with the Hsp90 machinery, leaving unrelated clients unperturbed and causing apoptosis in cancer cells. Overall, selective targeting of Hsp90 protein–protein interactions is achieved without causing indiscriminate degradation of all clients, setting the stage for the development of therapeutics based on specific chaperone:client perturbation.     

Rapid extraction and quantitative detection of the herbicide diuron in surface water by a hapten-functionalized carbon nanotubes based electrochemical analyzer

A solid phase extraction micro-cartridge containing a non-polar polystyrene absorbent matrix was coupled with an electrochemical immunoassay analyzer (EIA) and used for the ultra-sensitive detection of the phenyl urea herbicide diuron in real samples. The EIA was fabricated by using carboxylated carbon nanotubes (CNTs) functionalized with a hapten molecule (an amine functionalized diuron derivative). Screen printed electrodes (SPE) were modified with these haptenized CNTs and specific in-house generated anti diuron antibodies were used for bio-interface development. The immunodetection was realized in a competitive electrochemical immunoassay format using alkaline phosphatase labeled secondary anti-IgG antibody. The addition of 1-naphthyl phosphate substrate resulted in the production of an electrochemically active product, 1-naphthol, which was monitored by using differential pulse voltammetry (DPV). The assay exhibited excellent sensitivity and specificity having a dynamic response range of 0.01 pg mL(-1) to 10 μg mL(-1) for diuron with a limit of detection of around 0.1 pg mL(-1) (n = 3) in standard water samples. The micro-cartridge coupled hapten-CNTs modified SPE provided an effective and efficient electrochemical immunoassay for the real-time monitoring of pesticides samples with a very high degree of sensitivity.     

Antituberculosis agent diaportheone B: synthesis, absolute configuration assignment, and anti-TB activity of its analogues

First synthesis of diaportheone B, an antituberculosis agent isolated from endophytic fungus Diaporthe sp. P133 is reported using two complementary routes, a one step and a three-step sequence. The absolute configuration of diaportheone B was determined by using X-ray crystal structure analysis of its dibromo derivative. In addition, we have prepared several close analogues of diaportheone B and determined their anti-TB potential using Alamar-blue assay (H(37)Rv).     

Some Anisotropic Homogeneous Cosmological Models in Self-creation Cosmology

The paper presents an exact solution of cylindrically symmetric cosmological models which are of Petrov type-I or Petov type-D in Barber’s second self-creation theory of gravitation. Some physical and geometrical properties of these models are also discussed.     

Protein assisted fluorescence enhancement of a dansyl containing fluorescent reagent: detection of Hg+ ion in aqueous medium

Intramolecular charge transfer (ICT) based fluorescent reagents containing a dansyl fluorophore have been synthesized and characterized. The reagent 1 and its complex, 1+Hg(2+) in sodium acetate buffer (pH 6.7) revealed considerable fluorescence enhancement (switched-on) in the presence of bovine serum albumin (BSA) with 10 ppb detection sensitivity. (1)H NMR spectral analysis suggests complexation between 1 and Hg(2+) ion involving the N,N-dimethylamino and carboxylic functions.     

Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers

The reliability of molecular simulations largely depends on the quality of the empirical force field parameters. Force fields used in lipid simulations continue to be improved to enhance the agreement with experiments for a number of different properties. In this work, we have carried out molecular dynamics simulations of neat DMPC bilayers using united‐atom Berger force field and three versions of all‐atom CHARMM force fields. Three different systems consisting of 48, 72, and 96 lipids were studied. Both particle mesh Ewald (PME) and spherical cut‐off schemes were used to evaluate the long‐range electrostatic interactions. In total, 21 simulations were carried out and analyzed to find out the dependence of lipid properties on force fields, system size, and schemes to calculate long‐range interactions. The acyl chain order parameters calculated from Berger and the recent versions of CHARMM simulations have shown generally good agreement with the experimental results. However, both sets of force fields deviate significantly from the experimentally observed P‐C dipolar coupling values for the carbon atoms that link the choline and glycerol groups with the phosphate groups. Significant differences are also observed in several headgroup parameters between CHARMM and Berger simulations. Our results demonstrate that when changes were introduced to improve CHARMM force field using PME scheme, all the headgroup parameters have not been reoptimized. The headgroup properties are likely to play a significant role in lipid–lipid, protein–lipid, and ligand–lipid interactions and hence headgroup parameters in phospholipids require refinement for both Berger and CHARMM force fields. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2010