Factor Xa: Simulation studies with an eye to inhibitor design

Factor Xa is a serine protease which activates thrombin and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is at the crossroads of the extrinsic and intrinsic pathways of coagulation and, hence, has become an important target for the design of anti-thrombotics (inhibitors). It is not known to be involved in other processes than hemostasis and its binding site is different to that of other serine proteases, thus facilitating selective inhibition. The design of high-affinity selective inhibitors of factor Xa requires knowledge of the structural and dynamical characteristics of its active site. The three-dimensional structure of factor Xa was resolved by X-ray crystallography and refined at 2.2 Å resolution by Padmanabhan and collaborators. In this article we present results from molecular dynamics simulations of the catalytic domain of factor Xa in aqueous solution. The simulations were performed to characterise the mobility and flexibility of the residues delimiting the unoccupied binding site of the enzyme, and to determine hydrogen bonding propensities (with protein and with solvent atoms) of those residues in the active site that could interact with a substrate or a potential inhibitor. The simulation data is aimed at facilitating the design of high-affinity selective inhibitors of factor Xa.     

Determination by LC of Polyphenols in Italian Red Wine

A reversed-phase liquid chromatographic method, optimised for the separation of trans-, and cis-resveratrol, catechin, epicatechin, quercetin and rutin, is reported. Separation was achieved using a C18 column and a gradient elution with acetonitrile and 5% formic acid aqueous solution. The analyses required an equilibration period of 10 min and a run time of 25 min for completion. Identification was based on retention characteristics and by relative UV spectra, obtained by photodiode array detector and were compared with commercial standards. Analyses were performed without any sample pre-treatment. Detection was carried out by UV–Vis detector at three different wavelengths. The detection limit ranged from 0.16 μgm L⁻¹ (cis-resveratrol) to 1.5 μgm L⁻¹ (+)-catechin. Investigation was extended to quantitative determination of phenol compounds in Italian red wine and to investigate the stability of the six antioxidants.     

GC–MS analysis of phenolic compounds in fuels after conversion to trifluoroacetate esters

The GC–MS characteristics of trifluoroacetate esters of phenolic compounds are discussed. Linear temperature programmed retention indices and total ion current MS response factors of over 120 phenolic esters are reported. The main GC advantages from analysis of trifluoroacetate esters as compared to plain phenols are enhanced volatility and improved resolution. For example, the elution temperature of a given phenol is typically 50 °C greater than that of the corresponding trifluoroacetate ester. Also, while retention of compounds with two trifluoroacetate groups is only moderately greater than mono esters, underivatized dihydroxy compounds are very difficult to elute from any GC column. Complete resolution of isomeric C₀-, C₁- and C₂-alkylphenol esters is readily achieved on conventional fused silica GC columns; resolution of the corresponding underivatized compounds requires specialized GC columns with low temperature limits. In general, mass spectra of trifluoroacetate esters are more characteristic of a given structure than those of the corresponding phenols and may be more rigorously interpreted towards structural elucidation. A table in the report summarizes some of the more important spectral features used in compound identification. Example applications in analysis of coal-, shale- and petroleum-derived materials are presented. Selected ion monitoring is used to determine individual phenolic components in whole distillates; reconstructed ion chromatograms are used to illustrate distributions of selected species as a function of fuel storage and thermal stress.     

Stoichiometric and catalytic methods of asymmetric synthesis of nonproteinogenic α-and β-amino acids via transition metal coordination compounds

The complexes of glycine, -alanine, and -alanine with (S)-[N-(N-benzylprolyl)amino] benzophenone formed by Ni(II) and Cu(II) ions and Schiff bases enter into different nucleophilic and electrophilic reactions with the formation of diastereoisomeric complexes which decompose into proteinogenic and nonproteinogenic L-amino acids with a high chemical yield and elevated optical purity (70–90%). Optically pure amino acids can be obtained from diastereoisomerically pure complexes after the complexes are separated by recrystallization of the mixture of diastereoisomeric complexes formed. A new type of interphase catalysts of C-alkylation of achiral Schiff bases was proposed. The catalysts are positively charged Ni(II) and Cu(II) complexes of Schiff bases of chiral diamines. In some cases, these complexes have a higher activity and capacity to execute asymmetric alkylation than traditional chiral interphase catalysts based on cinchonidine.Based on materials in the section report by Yu. N. Belokon' to the 7th European Symposium on Organic Chemistry, ESOC-7.A. N. Nesmeyanov Institute of Organoelemental Compounds, Russian Academy of Sciences, 117813 Moscow. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 5, pp. 1106–1127, May, 1992.     

Convexlike and concavelike conditions in alternative,minimax, and minimization theorems

Convexlike and concavelike conditions are of interest for extensions of the Von Neumann minimax theorem. Since the beginning of the 80's, these conditions also play a certain role in deriving generalized alternative theorems of the Gordan, Motzkin, and Farkas type and Lagrange multiplier results for constrained minimization problems.In this paper, we study various known convexlike conditions for vector-valued functions on a set and investigate convexlike and concavelike conditions for real-valued functions on a product setC×D, where we are mainly interested in the relationships between these conditions. At the end of the paper, we point out several conclusions from our results for the above-mentioned mathematical fields.The author is indebted to Dr. R. Reemtsen and Dr. V. Jeyakumar for their helpful comments during the preparations of this paper.     

X-ray and IR spectroscopic studies of specific intermolecular interactions inN′-substituted isonicotinohydrazides

_N-Thenylidene- andN-(o-nitrobenzylidene)hydrazides of isonicotinic acid have been studied by X-ray structural analysis and IR spectroscopy. In the crystalline state, these molecules are linked through intermolecular N—H ... Np_y hydrogen bonds. Carbonyl groups are not involved in intermolecular hydrogen bonds. However, it was found that the C=O group participates in an attractive interaction with the sulfur atom of the thiophene group. The energy of this interaction is comparable with the energies of intermolecular C=O ... H—N hydrogen bonds in amides.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 896–900, April, 1996.     

Thermal Decomposition of Bi(III), Cd(II), Pb(II) and Cu(II) Thiocyanates

Thermal decomposition of Bi(SCN)₃, Cd(SCN)₂, Pb(SCN)₂ and Cu(SCN)₂ has been studied. The thermal analysis curves and the diffraction patterns of the solid intermediate and final products of the pyrolysis are presented. The gaseous products of the decomposition (SO₂ and CO₂) were detected and quantitatively determined. Thermal, X-ray and chemical analyses have been used to establish the nature of the reactions occurring at each stage in the decomposition.This revised version was published online in November 2005 with corrections to the Cover Date.     

Determination of acidic sites and binding toxic metal ions on cumin surface using nonideal competitive adsorption model

A fundamental study of the application of cumin biomass in the recovery of Cu and Zn metal ion uptake from food and drinks is carried out at different pH's and at fixed ionic strength. The chemical characteristics of protein in cumin seeds were investigated. Results showed that cumin contains 18.25% crude protein, which includes 18 amino acids. The main reactive groups on protein cumin are amino and carboxylic groups of dicarboxylic amino acids, leading to a pH-dependent charge. Therefore, the cumin surface is considered as a heterogeneous system. To describe protonation behavior in a heterogeneous cumin biomass (cumin/0.1 M NaNO(3)) system, acid-base titrations have been performed with conductometric and potentiometric titration. Measurement of the reactivity of cumin surface in the adsorption of Cu and Zn metal ions and determination of metal binding at different pH's were also carried out. To solve broad and ill-defined titration curves, a simplified version of nonideal competitive analysis (NICA) by Plette et al.) was applied. The results show that the sorption of the bivalent metal ions onto the whole surface of cumin could be attributed to a monodentate binding to one site mainly carboxylic-type site.     

Supercritical Propanol-Water Synthesis and Comprehensive Size Characterisation of Highly Crystalline anatase TiO2 Nanoparticles

Highly crystalline anatase TiO₂ nanoparticles have been synthesised in less than 1 min in a supercritical propanol-water mixture using a continuous flow reactor. The synthesis parameter space (T, P, concentration) has been explored and the average particle size can be accurately controlled within 10-18 nm with narrow size distributions (2-3 nm). At subcritical conditions amorphous products are obtained, whereas a broad range of T and P in the supercritical regime gives 11-14 nm particles. At high temperature and pressure, the particles size increase to 18 nm. The nanoparticles have been extensively characterised with powder X-ray diffraction (PXRD), transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) with excellent agreement on size and size distribution parameters. The SAXS analysis suggests disk-shaped particles with diameters that are approximately double the height. For comparison, a series of conventional autoclave sol-gel syntheses have been carried out. These also produce phase-pure anatase nanoparticles, but with much broader size distributions and at much longer synthesis times (hours). The study demonstrates that synthesis in supercritical fluids is a very promising method for manipulating the size and size distribution of nanoparticles, thus removing one of the key limitations in many applications of nanomaterials.