P-positions in modular extensions to Nim

In this paper, we consider a modular extension to the game of Nim, which we call m-Modular Nim, and explore its optimal strategy. In m-Modular Nim, a player can either make a standard Nim move or remove a multiple of m tokens in total. We develop a winning strategy for all m with 2 heaps and for odd m with any number of heaps.     

Production,Purification and Characterisation of a Potential Fibrinolytic Protease from Endophytic <Emphasis Type="Italic">Xylaria curta</Emphasis> by Solid Substrate Fermentation

The present investigation highlights the optimal conditions for production of a non-toxic, bi-functional fibrinolytic enzyme xylarinase produced by endophytic fungus Xylaria curta by solid substrate fermentation using rice chaff medium. The purified enzyme is a monomeric protein with a molecular mass of ～33 kDa. The enzyme exhibits cleavage of Aα and Bβ chains of fibrin(ogen) and has no effect on γ chain. The optimal fibrinolytic activity of the enzyme was observed at 35 °C and pH 8. The fibrinolytic activity was enhanced in the presence of Ca²⁺, whereas it was completely inhibited in the presence of Fe²⁺ and Zn²⁺ ions and inhibitors like EDTA and EGTA suggesting it to be a metalloprotease. The K _m and V _max of the enzyme for azocasein were 326 μM and 0.13 μM min^?1. The N-terminal sequence of the enzyme (SNGPLPGGVVWAG) was same when compared to xylarinase isolated from culture broth of X. curta. Thus, xylarinase could be exploited as a potent clot busting enzyme which could be produced on large scale using solid substrate fermentation.     

An expeditious route to sterically encumbered nonproteinogenic α-amino acid precursors using allylboronic acids

A diastereoselective allylation of N-tert-butane sulfinyl α-iminoesters using allylboronic acids is developed to obtain optically active non-proteinogenic α-amino acid precursors in good yields and diastereoselectivities. Gram-scale synthesis, broad tolerance of functional groups, excellent stereodivergence, post-synthetic modifications, and easy removal of the chiral auxiliary are some of the key highlights. The protocol is applicable to various amino acids and short peptides, resulting in the incorporation of these precursors at the N-terminal position.

A diastereoselective allylation of N-tert-butane sulfinyl α-iminoesters using allylboronic acids is developed to obtain optically active non-proteinogenic α-amino acid precursors in good yield and diastereoselectivities.     

Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein

P-glycoprotein (Pgp) is a major efflux pump in humans, overexpressed in a variety of cancers and associated with the development of multi-drug resistance. Allosteric modulation by various ligands (e.g., transport substrates, inhibitors, and ATP) has been biochemically shown to directly influence structural dynamics, and thereby, the function of Pgp. However, the molecular details of such effects, particularly with respect to the role and involvement of the surrounding lipids, are not well established. Here, we employ all-atom molecular dynamics (MD) simulations to study the conformational landscape of Pgp in the presence of a high-affinity, third-generation inhibitor, tariquidar, in comparison to the nucleotide-free (APO) and the ATP-bound states, in order to characterize the mechanical effects of the inhibitor that might be of relevance to its blocking mechanism of Pgp. Simulations in a multi-component lipid bilayer show a dynamic equilibrium between open(er) and more closed inward-facing (IF) conformations in the APO state, with binding of ATP shifting the equilibrium towards conformations more prone to ATP hydrolysis and subsequent events in the transport cycle. In the presence of the inhibitor bound to the drug-binding pocket within the transmembrane domain (TMD), Pgp samples more open IF conformations, and the nucleotide binding domains (NBDs) become highly dynamic. Interestingly, and reproduced in multiple independent simulations, the inhibitor is observed to facilitate recruitment of lipid molecules into the Pgp lumen through the two proposed drug-entry portals, where the lipid head groups from the cytoplasmic leaflet penetrate into and, in some cases, translocate inside the TMD, while the lipid tails remain extended into the bulk lipid environment. These “wedge” lipids likely enhance the inhibitor-induced conformational restriction of the TMD leading to the differential modulation of coupling pathways observed with the NBDs downstream. We suggest a novel inhibitory mechanism for tariquidar, and potentially for related third-generation Pgp inhibitors, where lipids are seen to enhance the inhibitory role in the catalytic cycle of membrane transporters.

Lipid invasion of P-glycoprotein, enhanced by binding of an inhibitor.     

Effect of 100 keV N+ ion irradiation on the organic single crystal of hippuric acid for nonlinear optical applications

The potential organic nonlinear optical material of hippuric acid (HA) single crystal has been grown by the slow evaporation solution growth technique using N, N-dimethylformamide as the solvent. Single crystals of pure HA were irradiated at room temperature with 100 keV Nitrogen (N⁺) ions at fluence 1×10¹⁶ and 5×10¹⁶ ions/cm². The pure and irradiated HA single crystals were characterized by different characterization technique. The photoluminescence and UV–visible absorption were performed at room temperature. The crystalline perfection of the pure and irradiated single crystals has been examined by high-resolution X-ray diffraction. Vickers microhardness technique was used to study the effect on the mechanical strength of the crystal at different ion fluences. The structural changes were analyzed by powder X-ray diffraction analysis. The functional groups of the synthesized compound have been identified by Fourier transform infrared spectroscopy. The dielectric constant and dielectric loss as a function of frequency were analyzed at room temperature.     

Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins

Proteins can sample a broad landscape as they undergo conformational transition between different functional states. At the same time, as key players in almost all cellular processes, proteins are important drug targets. Considering the different conformational states of a protein is therefore central for a successful drug-design strategy. Here we introduce a novel docking protocol, termed extended-ensemble docking, pertaining to proteins that undergo large-scale (global) conformational changes during their function. In its application to multidrug ABC-transporter P-glycoprotein (Pgp), extensive non-equilibrium molecular dynamics simulations employing system-specific collective variables are first used to describe the transition cycle of the transporter. An extended set of conformations (extended ensemble) representing the full transition cycle between the inward- and the outward-facing states is then used to seed high-throughput docking calculations of known substrates, non-substrates, and modulators of the transporter. Large differences are predicted in the binding affinities to different conformations, with compounds showing stronger binding affinities to intermediate conformations compared to the starting crystal structure. Hierarchical clustering of the binding modes shows all ligands preferably bind to the large central cavity of the protein, formed at the apex of the transmembrane domain (TMD), whereas only small binding populations are observed in the previously described R and H sites present within the individual TMD leaflets. Based on the results, the central cavity is further divided into two major subsites, first preferably binding smaller substrates and high-affinity inhibitors, whereas the second one shows preference for larger substrates and low-affinity modulators. These central subsites along with the low-affinity interaction sites present within the individual TMD leaflets may respectively correspond to the proposed high- and low-affinity binding sites in Pgp. We propose further an optimization strategy for developing more potent inhibitors of Pgp, based on increasing its specificity to the extended ensemble of the protein, instead of using a single protein structure, as well as its selectivity for the high-affinity binding site. In contrast to earlier in silico studies using single static structures of Pgp, our results show better agreement with experimental studies, pointing to the importance of incorporating the global conformational flexibility of proteins in future drug-discovery endeavors.

Functional states of P-glycoprotein formed during its full transition cycle (red to blue), captured by molecular dynamics simulations, form a structural framework for extended-ensemble docking of small-molecule ligands of diverse activities.     

catena‐Poly[[[triaqua­cobalt(II)]‐μ‐2,6‐dioxo‐1,2,3,6‐tetra­hydro­pyrimidine‐4‐carboxyl­ato(2–)] 1.72‐hydrate]

The Co^II ion in the title complex {[Co(C₅H₂N₂O₄)(H₂O)₃]·1.72H₂O}_n, has a distorted octa­hedral coordination geometry comprised of three water ligands, one deprotonated pyrimidine N atom and an adjacent carboxyl­ate O atom of one orotate ligand. The sixth coordination site is occupied by an exocyclic O atom from a neighbouring orotate moiety, and through this inter­action a helicoidal chain is formed. The mol­ecules are linked by intra­molecular O_water—H⋯O and inter­molecular N—H⋯O and O_water—H⋯O hydrogen bonds, forming a three‐dimensional network.     

Influence of density-dependent symmetry energy on elliptical flow

The effect of density-dependent symmetry energy on elliptical flow is studied using the isospin-dependent quantum molecular dynamics model (IQMD). We have used the reduced isospin-dependent cross-section with hard (H) equation of state to study the sensitivity of the elliptical flow to symmetry energy in the energy range 50-1000MeV/nucleon. The elliptical flow becomes zero at a particular energy termed as transition energy. A systematic effort has been made to pin down the transition energy for the density-dependent symmetry energy.     

Design,synthesis and exploration of in silico α-amylase and α-glucosidase binding studies of pyrrolidine-appended quinoline-constrained compounds

Research on Chemical Intermediates - A series of new pyrrolidine-appended phenoxy-substituted quinoline derivatives were synthesized using 2-chloro-3-formyl quinoline. Initially, the second...