Computer-aided design of a factor Xa inhibitor by using MCSS functionality maps and a CAVEAT linker search

We have investigated a new approach to efficiently find a novel inhibitor against a serine protease (i.e. an activated coagulation factor X, FXa) by using de novo design programs and the X-ray crystal structure of the target enzyme. FXa is a coagulant enzyme that generates thrombin (a serine protease) and participates in both intrinsic and extrinsic coagulation pathways. We adopted multiple copy simultaneous search (MCSS) and CAVEAT linker search techniques, which disclosed a novel FXa inhibitor (T01312) consisting of two binding moieties (the benzamidinyl and adamantyl groups) and a linker unit (the carboxybenzylamine group). The inhibitory activity of T01312 against FXa was determined to be a small K(i)-value of 48nM, which is two orders of magnitude smaller than that against thrombin. An X-ray crystal analysis of T01312 complexed with trypsin (an analogue of FXa) and docking studies of T01312 with trypsin and FXa showed that: (i) the benzamidinyl group is a predominant binding moiety in the anionic pocket (S1 site) with an asparatic acid residue; (ii) a hydrophobic pocket (S4 site) is the binding site of the adamantyl group; (iii) the carboxylate group of the linker contributes to the selectivity for FXa against thrombin. Thus, the combination of the knowledge of the X-ray crystal structure of the target molecule with MCSS and CAVEAT linker search techniques proved to be an effective hit-finding method that does not require the screening of huge compound libraries.     

Carbon materials modified by plasma treatment as electrodes for supercapacitors

The carbon material was modified by RF plasma with various reactive gases: O₂, Ar and CO₂. Physicochemical properties of the final carbon products were characterized using different techniques such as gas adsorption method and XPS. Plasma modified materials enriched in oxygen functionalities were investigated as electrodes for supercapacitors in acidic medium. The electrochemical measurements have been carried out using cyclic voltammetry, galvanostatic charge/discharge and impedance spectroscopy. The electrochemical measurements have confirmed that capacity characteristics are closely connected with a type of plasma exposition. Modification processes have an influence on the kind and amount of surface functional groups in the carbon matrix. The moderate increase of capacity of carbon materials modified by plasma has been observed using symmetric two-electrode systems. Whereas investigations made in three-electrode system proved that the suitable selection of plasma modification parameters allows to obtain promising negative and positive electrode materials for supercapacitor application.     

Chemical composition of Pinus sibirica nut oils

The chemical composition of oil obtained from Pinus sibirica was investigated. The nonpolar lipids were the predominant lipid fraction while the triacylglycerols were the major component of this fraction. α‐ and γ‐tocopherols were the dominant tocopherols in pine oils. Eleven fatty acids (FA) were identified in pine nut oil. The unsaturated FA comprised over 90% of the total FA. Of these, polyunsaturated FA accounted for 66% of the total FA. 18:2 and 18:3 acids were the dominant unsaturated FA, while palmitic and stearic acids were the major saturated FA. Three unusual FA, namely 10,13‐octadecadienoic, gorlic and 11,13‐eicosadienoic acid, were tentatively identified in pine nut oil.     

The effect of baking of various kinds of raw meat from different animal species and meat with functional additives on nitrosamine contamination level

The studies aimed to determine the occurrence and formation of nitrosamine contamination levels with dimethylnitrosamine (DMNA) and diethylnitrosamine (DENA) in meat of various kinds, species and genders of farm animals slaughtered at meat processing plants all over Poland. The meat after cooling, cutting and jointing was classified, then comminuted and divided into several experimental variants. Moreover, the effect of the most frequent functional additives used in food industry, such as sodium chloride and sodium ascorbate, and baking process upon the level of the meat pollution was researched. Nitrosamine (DMNA and DENA) concentrations were assessed by Varian 3400 gas chromatograph coupled with Finnigan MAT ITD 800 spectrometer. The quantitative and qualitative states of respective nitrosamines were determined by comparing the chromatogram values.     

Characterization and Quantification of Selenoprotein P: Challenges to Mass Spectrometry

Selenoprotein P (SELENOP) is an emerging marker of the nutritional status of selenium and of various diseases, however, its chemical characteristics still need to be investigated and methods for its accurate quantitation improved. SELENOP is unique among selenoproteins, as it contains multiple genetically encoded SeCys residues, whereas all the other characterized selenoproteins contain just one. SELENOP occurs in the form of multiple isoforms, truncated species and post-translationally modified variants which are relatively poorly characterized. The accurate quantification of SELENOP is contingent on the availability of specific primary standards and reference methods. Before recombinant SELENOP becomes available to be used as a primary standard, careful investigation of the characteristics of the SELENOP measured by electrospray MS and strict control of the recoveries at the various steps of the analytical procedures are strongly recommended. This review critically discusses the state-of-the-art of analytical approaches to the characterization and quantification of SELENOP. While immunoassays remain the standard for the determination of human and animal health status, because of their speed and simplicity, mass spectrometry techniques offer many attractive and complementary features that are highlighted and critically evaluated.     

Synthesis and Interfacial Activity of Novel Heterogemini Sulfobetaines in Aqueous Solution

Three new heterogemini sulfobetaines and their chloride salts were synthesised. The interfacial activities of the obtained chlorides in aqueous solution were studied by equilibrium and dynamic surface tension measurements. The critical micelle concentration, surface excess concentration, minimum area per surfactant molecule and standard Gibbs energy of adsorption as well as micelle lifetime and diffusion coefficient were determined. The adsorption properties and micelle lifetime of these compounds significantly depend on the length of alkyl chain. The critical micelle concentration decreases with increasing chain length of the compounds considered. The values of the diffusion coefficient of N‐alkyl‐N‐methyl‐N‐(3‐sulfopropyl)‐6‐(N‐alkyl‐N‐methylamino)hexylammonium chloride tend to decrease as the concentration is increased.     

Phytochemical Content and Antioxidant Properties of Seeds of Unconventional Oil Plants

The lipophilic and hydrophilic antioxidants were evaluated in eight plants: safflower (Carthamus tinctorius), viper’s bugloss (Echium vulgare), quince (Cydonia vulgaris), evening primrose (Oenothera biennis), rose mosqueta (Rosa affinis rubiginosa), black seed (Nigella sativa), sea buckthorn (Hippophae rhamnoides) and borage (Borago officinales). The highest amounts of tocopherols were contained in seeds of borage and sea buckthorn (66.9 mg/100 g and 45.9 mg/100 g, respectively). The sea buckthorn seed lipids had the highest amount of total sterols (10.4 mg/g of lipids). The predominant form was campesterol. Sitosterol was the major sterol in the lipids of other tested seeds. The content of phenolic compounds ranged from 736.5 mg/100 g dry matter (d.m.) (evening primrose) to 74.8 mg/100 g d.m. (safflower). The highest antioxidant activity, expressed in % scavenged DPPH· free radicals, was observed for evening primrose (91.2%), while the lowest for safflower (36.2%). The correlation coefficient between the level of phenolic compounds and antioxidant activity was 0.53.     

Presence of two forms of methylated (–)‐epigallocatechin‐3‐gallate in green tea

Crude catechins extract from Chinese green tea were fractionated using Sephadex LH‐20 column chromatography. The fraction containing (–)‐epigallocatechin‐3‐gallate (EGCG) was then subjected to a semipreparative high‐performance liquid chromatography (HPLC). Using a mobile phase of water : dimethyl formamide : methanol : acetic acid (157 : 49 : 2 : 1 v/v/v/v( the mixture of two methylated catechins was separated and isolated. According to mass spectrometry (MS) and nuclear magnetic resonance (¹H‐NMR) date, these compounds were identified as (–)‐epigallocatechin‐3‐(3‐O‐methylgallate) and (–)‐epigallocatechin‐3‐(4‐O‐methylgallate).     

Catalyst-free synthesis, morphology evaluation and photocatalytic properties of pristine and calcinated titanate nanorods

Titanate nanorods with high photocatalytic activity was successfully synthesized through a simple catalyst-free hydrothermal method. The photocatalytic degradation of a model organic dye (Reactive Red 198) was accelerated by the calcination of the nanorods prior the reaction. The calcination of nanorods did not modify their morphology, however the crystallinity of the samples was significantly improved. Therefore, the quality of the samples is a key parameter determining their activity in the investigated photocatalytic process. The as-produced and annealed catalysts were characterized by high-resolution transmission electron microscopy (HR-TEM), X-ray diffraction (XRD), Diffuse Reflectance (DR) UV-Vis and resonance Raman spectroscopy.