Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Synthesis of self‐healing polyurethane urea‐based supramolecular materials

Supramolecular polyurethane ureas are expected to have superior mechanical properties primarily due to the reversible, noncovalent interactions such as hydrogen bonding interactions. We synthesized polyurethane prepolymers from small molecular weight of poly(tetramethylene ether)glycol and isophorone diisocyanates, which were end capped with propylamine to synthesize polyurethane ureas with high contents of urea and urethane groups for hydrogen‐bonding formations to facilitate self‐healing. The effects of polyurethane urea molecular weight (3000 ≤ M_n ≤ 9000), crosslinking, and cutting direction were studied in terms of thermal, mechanical, and morphological properties with an emphasis on the self‐healing efficiency. It was found that the thermal self‐healability was more pronounced as the molecular weight of polyurethane urea decreased, showing a maximum of more than 96% with 3000 M_n when the sample was cut along the stretch direction. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 468–474     

Studies on metabolites and metabolic pathways of bulleyaconitine A in rat liver microsomes using LC‐MSn combined with specific inhibitors

Bulleyaconitine A (BLA) from Aconitum bulleyanum plants is usually used as anti‐inflammatory drug in some Asian countries. It has a variety of bioactivities, and at the same time some toxicities. Since the bioactivities and toxicities of BLA are closely related to its metabolism, the metabolites and the metabolic pathways of BLA in rat liver microsomes were investigated by HPLC–MSⁿ. In this research, the 12 metabolites of BLA were identified according to the results of HPLC‐MSⁿ data and the relevant literature. The results showed that there are multiple metabolites of BLA in rat liver microsomes, including demethylation, deacetylation, dehydrogenation deacetylation and hydroxylation. The major metabolic pathways of BLA in rat liver microsomes were clarified by HPLC‐MS combined with specific inhibitors of CYP450 isoforms. As a result, CYP3A and 2C were found to be the principal CYP isoforms contributing to the metabolism of BLA. Moreover, CYP2D6 and 2E1 are also more important CYP isoforms for the metabolism of BLA. While CYP1A2 only affected the formation rate of M11, its effect on the metabolism of BLA is very small. Copyright © 2014 John Wiley & Sons, Ltd.     

Finding any given 2‐factor in sparse pseudorandom graphs efficiently

Given an $n$‐vertex pseudorandom graph $G$ and an $n$‐vertex graph $H$ with maximum degree at most two, we wish to find a copy of $H$ in $G$, that is, an embedding $\phi :V\left(H\right)\to V\left(G\right)$ so that $\phi \left(u\right)\phi \left(v\right)\in E\left(G\right)$ for all $uv\in E\left(H\right)$. Particular instances of this problem include finding a triangle‐factor and finding a Hamilton cycle in $G$. Here, we provide a deterministic polynomial time algorithm that finds a given $H$ in any suitably pseudorandom graph $G$. The pseudorandom graphs we consider are $\left(p,\lambda \right)$‐bijumbled graphs of minimum degree which is a constant proportion of the average degree, that is, $\mathrm{\Omega }\left(pn\right)$. A $\left(p,\lambda \right)$‐bijumbled graph is characterised through the discrepancy property: $|e\left(A,B\right)?p|A||B||<\lambda \sqrt{|A||B|}$ for any two sets of vertices $A$ and $B$. Our condition $\lambda =O(p^{2}n/\log n)$ on bijumbledness is within a log factor from being tight and provides a positive answer to a recent question of Nenadov. We combine novel variants of the absorption‐reservoir method, a powerful tool from extremal graph theory and random graphs. Our approach builds on our previous work, incorporating the work of Nenadov, together with additional ideas and simplifications.     

Microwave‐assisted polycondensation of 4‐octylaniline with dibromoarylene

The Pd‐catalyzed polycondensation of 4‐octylaniline with various dibromoarylenes was carried out under microwave heating. Microwave heating led to a decrease in the reaction time and an increase in the molecular weight of the polymers as compared to conventional heating. Microwave heating also allowed the catalyst loading to be reduced to 1 mol %, yielding polymerization results that were comparable to those under conventional heating and 5 mol % catalyst. Investigations regarding field‐effect transistors and organic photovoltaic cells using the obtained poly(arylamine) with azobenzene units revealed that increasing the molecular weight of the polymer led to improved device performance, including hole mobility and power conversion efficiency. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 536–542     

Synthesis of diisocyanides with phenolic groups and their polymerization to helically chiral poly(quinoxaline‐2,3‐diyl)s

The development of synthetic routes which lead to five new diisocyanide monomers with one or two phenolic groups is described. Their polymerization behavior is studied with Pd‐ and Ni‐based initiators, as well as under microwave irradiation. The polymerizability is mainly dominated by steric effects as is concluded from experiments using different protecting groups. Chiroptical properties of these new polymers are studied by CD‐spectroscopy. After deprotection, helically chiral poly(quinoxalin‐2,3‐diyl)s are obtained which display a Brønsted function attached to a stereolabile biaryl axis whose configuration should be influenced by the chiral polymer backbone. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 1320–1329     

Highly dispersed palladium nanoclusters incorporated in amino‐functionalized silica spheres for the selective hydrogenation of succinic acid to γ‐butyrolactone

Highly dispersed palladium nanoclusters incorporated on amino‐functionalized silica sphere surfaces (Pd/SiO₂‐NH₂) were fabricated by a simple one‐pot synthesis utilizing 3‐(2‐aminoethylamino)propyltrimethoxysilane (AAPTS) as coordinating agent. Uniform palladium nanoclusters with an average size of 1.1 nm can be obtained during the co‐condensation of tetraethyl orthosilicate and AAPTS owing to the strong interaction between palladium species and amino groups in AAPTS. The palladium particle size can be controlled by addition of AAPTS and plays a significant role in the catalytic performance. The Pd/SiO₂‐NH₂ catalyst exhibits high catalytic activity for succinic acid hydrogenation with 100% conversion and 94% selectivity towards γ‐butyrolactone using 1,4‐dioxane as solvent at 240°C and 60 bar for 4 h. Moreover, the Pd/SiO₂‐NH₂ catalyst is robust and readily reusable without loss of its catalytic activity. Copyright © 2015 John Wiley & Sons, Ltd.