Experimental and computational studies of the recognition of amino acids by galactosyl-imine and -amine derivatives: an attempt to understand the lectin-carbohydrate interactions

A galactosyl-naphthyl-imine-based derivative, 1-(beta-D-galactopyranosyl-1'-deoxy-1'-iminomethyl)-2-hydroxynaphthalene (GNI), and a galactosyl-naphthyl-amine-based derivative, 1-(galactopyranosyl-1'-deoxy-1'-aminomethyl)-2-hydroxynaphthalene (GNA), possessing an ONO binding core were studied for their recognition of naturally occurring amino acids using fluorescence and absorption spectroscopy, and the corresponding association constants were derived for the complexes formed. The complexes formed between GNI/GNA and amino acids were supported by electrospray ionization mass spectrometry (ESI/MS). The structures of the complexes were optimized by computational studies using density functional theory, and stabilization energies were computed for the complexes to substantiate the interactions present between GNI/GNA and amino acid. The interactions were found to be primarily hydrogen bonding in nature. These interactions are reminiscent of those present in the lectin-carbohydrate and glycosidase substrate. Thus, the carbohydrate moiety present in GNI shows high specificity toward the -COOH group of the amino acid, which may be relevant to such interactions present between the carbohydrates and the polypeptides.     

A domain adaptive stochastic collocation approach for analysis of MEMS under uncertainties

This work proposes a domain adaptive stochastic collocation approach for uncertainty quantification, suitable for effective handling of discontinuities or sharp variations in the random domain. The basic idea of the proposed methodology is to adaptively decompose the random domain into subdomains. Within each subdomain, a sparse grid interpolant is constructed using the classical Smolyak construction [S. Smolyak, Quadrature and interpolation formulas for tensor products of certain classes of functions, Soviet Math. Dokl. 4 (1963) 240–243], to approximate the stochastic solution locally. The adaptive strategy is governed by the hierarchical surpluses, which are computed as part of the interpolation procedure. These hierarchical surpluses then serve as an error indicator for each subdomain, and lead to subdivision whenever it becomes greater than a threshold value. The hierarchical surpluses also provide information about the more important dimensions, and accordingly the random elements can be split along those dimensions. The proposed adaptive approach is employed to quantify the effect of uncertainty in input parameters on the performance of micro-electromechanical systems (MEMS). Specifically, we study the effect of uncertain material properties and geometrical parameters on the pull-in behavior and actuation properties of a MEMS switch. Using the adaptive approach, we resolve the pull-in instability in MEMS switches. The results from the proposed approach are verified using Monte Carlo simulations and it is demonstrated that it computes the required statistics effectively.     

Fluoride removal using lanthanum incorporated chitosan beads

Highly selective material based on naturally occurring biomaterial namely chitosan has been designed for the defluoridation of water. Lanthanum incorporated chitosan beads (LCB) were prepared using precipitation method. The synthesis was optimized by varying different synthesis parameters namely lanthanum loading, complexation and precipitation time, strength of ammonia solution used for precipitation, drying time, etc. Lanthanum incorporated chitosan beads were characterized using SEM, FTIR, XRD and EDX. Surface area of LCB was observed to be 2.76 m² g⁻¹. The equilibrium adsorption data fitted well to Langmuir adsorption isotherm and showing maximum fluoride adsorption capacity of 4.7 mg g⁻¹ with negligible lanthanum release. Kinetic study reveals that adsorption of fluoride is fast and follows pseudo-first-order kinetics. The effect of pH was also studied and the best efficiency was observed at pH 5. Presence of sulphate, nitrate and chloride marginally affected the removal efficiency, however drastic reduction in fluoride uptake was observed in the presence of carbonate and bicarbonate. Negative value of change in free energy (ΔG°) and positive value of change in entropy (ΔS°) suggest the adsorption of fluoride by LCB is feasible and spontaneous process. Positive value of change in enthalpy (ΔH°) suggests the process of fluoride adsorption is endothermic in nature. Regeneration study reveals that 1 M ammonium chloride solution appears to be the promising regeneration media showing 81.22% regeneration. The adsorption capacity of LCB was similar in fluoride-contaminated ground water collected from Dhar district of Madhya Pradesh, India, as compared to simulated water.     

Gold-catalyzed intramolecular hydroamination of allenes: a case of chirality transfer

The hydroamination of allenes proceeded smoothly in the presence of gold catalysts to give the corresponding 2-vinyl pyrrolidines and piperidines in high yields. The reaction is very efficient and can be carried out with only 1-5 mol % catalyst at room temperature and under extremely mild conditions. As an example of chirality transfer, it is shown that aminoallene 1a (96% ee), synthesized from (S)-(−)-1-octyn-3-ol, was converted into the corresponding pyrrolidine 2a (94% ee) in 99% yield.     

Palladium-catalyzed intramolecular asymmetric hydroamination, hydroalkoxylation, and hydrocarbonation of alkynes

A conceptually novel approach for asymmetric intramolecular hydroamination, hydroalkoxylation and hydrocarbonation of alkynes using chiral palladium catalysts are described. The reactions of the aminoalkynes 5, alkynols 7, and alkynylmethines 9 in the presence of Pd2(dba)3 x CHCl3/PhCOOH/renorphos 4 in benzene (or benzene-hexane) at 100 degrees C gave the corresponding cyclization products (nitrogen heterocycles 6, oxygen heterocycles 8, and carbocycles 10) in good yields with good enantioselectivities. The origins of enantioselectivities in the hydroamination reaction are discussed based on DFT computations.     

A novel chemical biology and computational approach to expedite the discovery of new-generation polymyxins against life-threatening Acinetobacter baumannii

Multidrug-resistant Gram-negative bacteria represent a major medical challenge worldwide. New antibiotics are desperately required with ‘old’ polymyxins often being the only available therapeutic option. Here, we systematically investigated the structure–activity relationship (SAR) of polymyxins using a quantitative lipidomics-informed outer membrane (OM) model of Acinetobacter baumannii and a series of chemically synthesized polymyxin analogs. By integrating chemical biology and all-atom molecular dynamics simulations, we deciphered how each residue of the polymyxin molecule modulated its conformational folding and specific interactions with the bacterial OM. Importantly, a novel designed polymyxin analog FADDI-287 with predicted stronger OM penetration showed improved in vitro antibacterial activity. Collectively, our study provides a novel chemical biology and computational strategy to expedite the discovery of new-generation polymyxins against life-threatening Gram-negative ‘superbugs’.

Multidrug-resistant Gram-negative bacteria have been an urgent threat to global public health. Novel antibiotics are desperately needed to combat these ''superbugs''.     

Chirality Transfer and Memory of Chirality in Gold‐Catalyzed Reactions

Over the last few years, gold‐catalyzed reactions that involved chirality transfer and memory of chirality (MOC) have emerged as a powerful tool in enantioselective synthesis. This technique has allowed for the single‐step synthesis of enantioenriched compounds from readily available starting materials. This Focus Review discusses this emerging field with an emphasis on mechanistic aspects and their applications in synthetic organic chemistry.     

Consensus QSAR model for identifying novel H5N1 inhibitors

Due to the importance of neuraminidase in the pathogenesis of influenza virus infection, it has been regarded as the most important drug target for the treatment of influenza. Resistance to currently available drugs and new findings related to structure of the protein requires novel neuraminidase 1 (N1) inhibitors. In this study, a consensus QSAR model with defined applicability domain (AD) was developed using published N1 inhibitors. The consensus model was validated using an external validation set. The model achieved high sensitivity, specificity, and overall accuracy along with low false positive rate (FPR) and false discovery rate (FDR). The performance of model on the external validation set and training set were comparable, thus it was unlikely to be overfitted. The low FPR and low FDR will increase its accuracy in screening large chemical libraries. Screening of ZINC library resulted in 64,772 compounds as probable N1 inhibitors, while 173,674 compounds were defined to be outside the AD of the consensus model. The advantage of the current model is that it was developed using a large and diverse dataset and has a defined AD which prevents its use on compounds that it is not capable of predicting. The consensus model developed in this study is made available via the free software, PaDEL-DDPredictor.     

A one-pot catalysis: the strategic classification with some recent examples

In this "Emerging Area", the strategic classification of one-pot catalysis, i.e. cooperative, relay and sequential catalysis, is described. In order to illustrate this classification, we take the readers through a series of recent examples which utilize either metal-metal, metal-organo and organo-organo catalysts. The compilation clearly demonstrates the explosive growth and power of this field, which has become, in the last few years, an important technique particularly in the case of enantioselective catalysis.     

Photoluminescence of 2-(2′-hydroxy-5′-methylbenzoyl)-1,5-diphenylpyrrole in aqueous and β-cyclodextrin environments: manifestation of open and closed conformers

Steady-state fluorometric studies have been performed on 2-(2′-hydroxy-5′-methylbenzoyl)-1,5-diphenylpyrrole (HMBDPP) in aqueous and aqueous β-cyclodextrin (β-CD) environments at ambient temperature. The fluorophore mostly shows a single emission in aqueous solution. Addition of β-CD to the aqueous solution of the fluorophore results in the development of another emission band at higher energy. The difference in the fluorometric behaviour is assigned to a remarkable change in the polarity of the microenvironment within the supramolecular structural environment compared to that of the bulk aqueous phase. Semi-empirical calculation (AM1-SCI) rules out the possibility of intramolecular proton transfer reaction in any of the S₀, S₁ and T₁ states of the fluorophore. It is proposed that HMBDPP exists mostly in the intermolecularly hydrogen-bonded form (open conformer) in aqueous solution while within β-CD environment, it is the intramolecularly hydrogen-bonded form (closed conformer) that predominates.