An approach to computer-aided inhibitor design: Application to cathepsin L

Summary We have developed an approach to search for molecules that can be used as lead compounds in designing an inhibitor for a given proteolytic enzyme when the 3D structure of a homologous protein is known. This approach is based on taking the cast of the binding pocket of the protease and comparing its dimensions with that of the dimensions of small molecules. Herein the 3D structure of papain is used to model cathepsin L using the comparative modeling technique. The cast of the binding pocket is computed using the crystal structure of papain because the structures of papain and the model of cathepsin L are found to be similar at the binding site. The dimensions of the cast of the binding site of papain are used to screen for molecules from the Cambridge Structural Database (CSD) of small molecules. Twenty molecules out of the 80 000 small molecules in the CSD are found to have dimensions that are accommodated by the papain binding pocket. Visual comparison of the shapes of the cast and the 20 screened molecules resulted in identifying brevotoxin b, a toxin isolated from the red tide dinoflagellate Ptycho brevis (previously classified as Gymonodium breve), as the structure that best fits the binding pocket of papain. We tested the proteolytic activity of papain and cathepsin L in the presence of brevotoxin b and found inhibition of papain and cathepsin L with K_is of 25 M and 0.6 M, respectively. We also compare our method with a more elaborate method in the literature, by presenting our results on the computer search for inhibitors of the HIV-1 protease.     

On the existence of ‘glycine barium nitrate potassium nitrate’ crystal

It is proved that a so called novel nonlinear optical glycine barium nitrate potassium nitrate single crystal grown by slow evaporation solution growth technique by Ravishankar et al. (Optik, 2013) is actually the well-known γ-glycine crystal.     

Simulation of local ion transport in lamellar block copolymer electrolytes based on electron micrographs

A method is presented to relate local morphology and ionic conductivity in a solid, lamellar block copolymer electrolyte for lithium batteries, by simulating conductivity through transmission electron micrographs. The electrolyte consists of polystyrene‐block‐poly(ethylene oxide) mixed with lithium bis(trifluoromethanesulfonyl) imide salt (SEO/LiTFSI), where the polystyrene phase is structural phase and the poly(ethylene oxide)/LiTFSI phase is ionically conductive. The electric potential distribution is simulated in binarized micrographs by solving the Laplace equation with constant potential boundary conditions. A morphology factor, f, is reported for each image by calculating the effective conductivity relative to a homogenous conductor. Images from two samples are examined, one annealed with large lamellar grains and one unannealed with small grains. The average value of f is 0.45 ± 0.04 for the annealed sample, and 0.37 ± 0.03 for the unannealed sample, both close to the value predicted by effective medium theory, 1/2. Simulated conductivities are compared to published experimental conductivities. The value of f_Unannealed/f_Annealed is 0.82 for simulations and 6.2 for experiments. Simulation results correspond well to predictions by effective medium theory but do not explain the experimental measurements. Observation of nanoscale morphology over length scales greater than the size of the micrographs (～1 μm) may be required to explain the experimental results. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 266–274     

meta-Nitration of Arenes Bearing ortho/para Directing Group(s) Using C−H Borylation

Herein, we report the meta-nitration of arenes bearing ortho/para directing group(s) using the iridium-catalyzed C−H borylation reaction followed by a newly developed copper(II)-catalyzed transformation of the crude aryl pinacol boronate esters into the corresponding nitroarenes in a one-pot fashion. This protocol allows the synthesis of meta-nitrated arenes that are tedious to prepare or require multistep synthesis using the existing methods. The reaction tolerates a wide array of ortho/para-directing groups, such as −F, −Cl, −Br, −CH₃, −Et, −iPr −OCH₃, and −OCF₃. It also provides regioselective access to the nitro derivatives of π-electron-deficient heterocycles, such as pyridine and quinoline derivatives. The application of this method is demonstrated in the late-stage modification of complex molecules and also in the gram-scale preparation of an intermediate en route to the FDA-approved drug Nilotinib. Finally, we have shown that the nitro product obtained by this strategy can also be directly converted to the aniline or hindered amine through Baran's amination protocol.     

Can a ‘magnesium sulfate admixtured l-threonine’ crystal be grown by slow evaporation solution growth method?

Slow evaporation of an aqueous solution containing l-threonine and magnesium sulphate heptahydrate, results in the fractional crystallization of the less soluble l-threonine crystal and not any novel optoelectronic ‘magnesium sulfate admixtured l-threonine’ crystal as reported by Puhal Raj et al. in Optik, 124 (2013) 6887–6891.     

Sulfonated rGO from waste dry cell graphite rod and its hybrid with PANI as electrode for supercapacitor

Journal of Solid State Electrochemistry - Development of high-performance energy storage devices is a vital research area to meet the present-day energy demand. In the work carried toward the...