Chemistry

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A $\pi$-electron rich supramolecular polymer as an efficient fluorescent sensor for electron deficient nitroaromatic explosives has been synthesized and the role of H-bonding in dramatic amplification of sensitivity/fluorescence quenching efficiency in the solid state has been established. {\textcopyright} The Royal Society of Chemistry 2011.

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Chemical Communications

Supramolecular polymer for explosives sensing: Role of H-bonding in enhancement of sensitivity in the solid state

A one-pot procedure for the efficient hydroazidation of alkenes involving hydroboration with catecholborane followed by reaction with benzenesulfonyl azide in the presence of a radical initiator is described. The regioselectivity is controlled by the hydroboration step and corresponds in most cases to an anti-Markovnikov regioselectivity. This procedure is applicable to a wide range of alkenes and gives excellent results with 1,2-disubstituted and trisubstituted alkenes. {\textcopyright} 2011 American Chemical Society.

Journal of the American Chemical Society

A radical procedure for the anti-markovnikov hydroazidation of alkenes

Photostability is one of the key issues in NIR dyes and we have previously reported a photostable CyNA library. Herein we report an ultra-photostable cyanine-based NIR fluorescence library, CyR, utilizing the stability component of CyNA. Efficient solid phase chemistry was also devised to provide a robust synthetic route to the new library. © The Royal Society of Chemistry 2011.

RSC Advances

Solid phase synthesis of ultra-photostable cyanine NIR dye library

A NIR death experience: A highly photostable NIR protein-labeling dye (CyNE790) that maintained excellent fluorescent properties after protein conjugation has been synthesized. Furthermore, the adequacy of the dye for NIR imaging was confirmed by showing that the recognition properties of a labeled anti-EGFR antibody remained unaffected. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemistry - An Asian Journal

A photostable near-infrared protein labeling dye for in vivo imaging

A highly efficient enantioselective SNAr reaction of chiral acyl bicyclic lactam with substituted-2,4-dinitrobenzenes was developed, affording products containing quarternary stereogenic centers. They are further utilized towards an enantioselective synthesis of spirooxoindoles. © 2011 The Royal Society of Chemistry.

Organic and Biomolecular Chemistry

Enantioselective synthesis of spirooxoindoles via chiral auxiliary (bicyclic lactam) controlled SNAr reactions

Structural biology of kinase and in particular of tyrosine kinase has given detailed insights into the intrinsic flexibility of the catalytic domain and has provided a rational basis for obtaining selective inhibitors. In this paper, we have studied the conformational flexibility of c-Abl tyrosine kinase complexed with Imatinib (STI), in the presence of TIP3P water in physiological conditions at neutral pH. The conformational studies suggest that the flexibility of activation loop is responsible to facilitate the nucleotide binding and release. Owing to the conformational adaptability, adenosine triphosphate (ATP) binds at a particular site in the loop region of the tyrosine kinase. The molecular mechanics Poisson- Boltzmann surface area methods are analysed, as is a free-energy pathways method, which shows the stable binding with free energy 26.04 kcal/mol for STI. The binding energy calculated by the Sietraj method is approximately the same as the experimental binding energy of STI with c-Abl kinase. It is suggested that the conserved glutamic acid and lysine residues are necessary for the stability and optimum activity of inhibitor. This study may be helpful in rational drug designing of new kinase inhibitors. © 2011 Taylor & Francis.

Molecular Simulation

Conformational flexibility and binding energy profile of c-Abl tyrosine kinase complexed with Imatinib: An insight from MD study

High throughput in silico methods have offered the tantalizing potential to drastically accelerate the drug discovery process. Yet despite significant efforts expended by academia, national labs and industry over the years, many of these methods have not lived up to their initial promise of reducing the time and costs associated with the drug discovery enterprise, a process that can typically take over a decade and cost hundreds of millions of dollars from conception to final approval and marketing of a drug. Nevertheless structure-based modeling has become a mainstay of computational biology and medicinal chemistry, helping to leverage our knowledge of the biological target and the chemistry of protein-ligand interactions. While ligand-based methods utilize the chemistry of molecules that are known to bind to the biological target, structure-based drug design methods rely on knowledge of the three-dimensional structure of the target, as obtained through crystallographic, spectroscopic or bioinformatics techniques. Here we review recent developments in the methodology and applications of structure-based and ligand-based methods and target-based chemogenomics in Virtual High Throughput Screening (VHTS), highlighting some case studies of recent applications, as well as current research in further development of these methods. The limitations of these approaches will also be discussed, to give the reader an indication of what might be expected in years to come. © 2011 Bentham Science Publishers.

Combinatorial Chemistry and High Throughput Screening

Current trends in virtual high throughput screening using ligand-based and structure-based methods

Computational Approaches in Cheminformatics and Bioinformatics

Molecular Descriptors for Biological Systems

The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5, 7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately. © 2011 International Union of Crystallography Printed in Singapore - all rights reserved.

Acta Crystallographica Section B: Structural Science

Structural analysis and multipole modelling of quercetin monohydrate - A quantitative and comparative study

An equimolar mixture of Ni(NO3)2.6H3O and pyridine-2-aldehyde with two equivalents of NaN3 in methanol in the presence of NaOMe resulted in the formation of light green precipitate which upon crystallization from dimethylformamide (DMF) yielded light green single crystals [{Ni2Na2(pic)4(N3) 2(H2O)2(MeOH)}.MeOH.3H2O]n (1) and [{Ni2Na2(pic)4(N3) 2(H2O)4}.2DMF.H2O]n (2) (pic = pyridine-2-carboxylate) at room temperature and high temperature (100°C), respectively. Variable temperature magnetic studies revealed the existence of overall ferromagnetic behaviour with J ̃ +10 cm-1 and D ̃ -2 to -7 cm-1 for 1 and 2, respectively. Negative D values as well as variation of D upon slight distortion of structure by varying reaction temperature were observed. The X-band Electron Paramagnetic Resonance (EPR) spectra of both 2 and 3 were recorded below 50 K. The structural distortion was also implicated from the EPR spectra. Density Functional Theory (DFT) calculations on both complexes were performed in two different ways to corroborate the magnetic results. Considering only NiII2 dimeric unit, results were J = +20.65 cm-1 and D = -3.16 cm -1 for 1 and J =+24.56 cm-1 and D =-4.67 cm-1 for 2. However, considering NiII2 NaI2 cubane as magnetic core the results were J =+16.35 cm-1 (1), +19.54 cm-1 (2); D =-3.05 cm-1 (1), -4.25 cm-1 (2). {\textcopyright} Indian Academy of Sciences.