Towards intelligent drug design system: Application of artificial dipeptide receptor library in QSAR-oriented studies

The pharmacophore properties of a new series of potential purinoreceptor (P2X) inhibitors determined using a coupled neural network and the partial least squares method with iterative variable elimination (IVE-PLS) are presented in a ligand-based comparative study of the molecular surface by comparative molecular surface analysis (CoMSA). Moreover, we focused on the interpretation of noticeable variations in the potential selectiveness of interactions of individual inhibitor-receptors due to their physicochemical properties; therefore, the library of artificial dipeptide receptors (ADP) was designed and examined. The resulting library response to individual inhibitors was arranged in the array, preprocessed and transformed by the principal component analysis (PCA) and PLS procedures. A dominant absolute contribution to PC1 of the Glu attached to heptanoic gating acid and Phe bonded to the linker m-phenylenediamine/triazine scaffold was revealed by the PCA. The IVE-PLS procedure indicated the receptor systems with predominant Pro bonded to the linker and Glu, Gln, Cys and Val directly attached to the gating acid. The proposed comprehensive ligand-based and simplified structure-based methodology allows the in-depth study of the performance of peptide receptors against the tested set of compounds.NC

Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N4-hydroxy-dCMP

Endogenous thymidylate synthases, isolated from tissues or cultured cells of the same specific origin, have been reported to show differing slow-binding inhibition patterns. These were reflected by biphasic or linear dependence of the inactivation rate on time and accompanied by differing inhibition parameters. Considering its importance for chemotherapeutic drug resistance, the possible effect of thymidylate synthase inhibition by post-translational modification was tested, e.g. phosphorylation, by comparing sensitivities to inhibition by two slow-binding inhibitors, 5-fluoro-dUMP and N4-hydroxy-dCMP, of two fractions of purified recombinant mouse enzyme preparations, phosphorylated and non-phosphorylated, separated by metal oxide/hydroxide affinity chromatography on Al(OH)3 beads. The modification, found to concern histidine residues and influence kinetic properties by lowering Vmax, altered both the pattern of dependence of the inactivation rate on time from linear to biphasic, as well as slow-binding inhibition parameters, with each inhibitor studied. Being present on only one subunit of at least a great majority of phosphorylated enzyme molecules, it probably introduced dimer asymmetry, causing the altered time dependence of the inactivation rate pattern (biphasic with the phosphorylated enzyme) and resulting in asymmetric binding of each inhibitor studied. The latter is reflected by the ternary complexes, stable under denaturing conditions, formed by only the non-phosphorylated subunit of the phosphorylated enzyme with each of the two inhibitors and N5,10-methylenetetrahydrofolate. Inhibition of the phosphorylated enzyme by N4-hydroxy-dCMP was found to be strongly dependent on [Mg2+], cations demonstrated previously to also influence the activity of endogenous mouse TS isolated from tumour cells

An analysis of non-isothermal primary crystallization kinetics of Fe95Si5 amorphous alloy

The paper describes the primary crystallization of metallic Fe95Si5 glass which was studied by differential scanning calorimetry (DSC) with non-isothermal methods. The activation energy of crystal transformation was calculated with the equations proposed by Kissinger, Mahadevan and a modified version of the equation developed by Augis and Bennett. Activation energy was determined at Ea = 242.0 - 254.2 kJ / mol, subject to the applied method. The Avrami exponent of crystallization in the amorphous phase n was determined in the range of n = 2.40 - 2.52, depending on the method of calculating the transformation of activation energy

Metallic alloy with shape memory – selected properties and engineering aspects

In the case of shape memory alloys (SMA), a form to which a material is expected to return during heating can be repeatedly programmed, whereas other related properties can be individually adjusted. It was found that most producers of commercial assortment based on SMA as well as traders are seldom willing to lift the veil of secrecy on this topic. In the context of own experimental studies, the authors made a reference to the technical aspects of some post-treatments of a Ni-Ti alloy with a view to further practical application, e.g. the design and construction of machinery and structures with the involvement of SMA. For these purposes, high-temperature shape setting trials were carried out using various parameters of heat treatment with no secrecy surrounding the procedures applied. Some of the tested parameters proved effective, whereas some were less useful. Following the activation of the reverse transformation by heating, a somewhat different behaviour was observed, and simultaneously one of the crucial material temperatures was determined. The paper as a whole is reported from a specifically engineering/technical point of view, which is continuously emphasized in the content of the presented article

Effects of Friction Plate Hardness and Surface Orientation on the Frictional Properties of Cereal Grain

The objective of this study was to evaluate the effects of the friction plate hardness and surface orientation of a friction plate on the angle and coefficient of static friction of cereal kernels. The angle of static friction of kernels representing four major cereal species was measured on six friction plates with different hardness. The friction plates were placed in position where their surface orientation was perpendicular or parallel relative to their inclination tilt. The experimental material comprised the so-called flat seed units, where each unit consisted of three spaced kernels. The angle of static friction of every flat seed unit was measured with a dedicated device in three replications, and average values of that angle were calculated. The kernels’ angle of static friction varied considerably from 13° to 33° within the analyzed range of changes in the surface characteristics of friction plates. The average angle of static friction was influenced mainly by the surface orientation of the friction plate that came into contact with cereal kernels. The angle of static friction was 17.5% to 56.5% higher when the friction plate had perpendicular rather than parallel surface orientation. The frictional properties of kernels were less influenced by plate hardness, and clear relationships were not observed in this respect. The kernels’ coefficient of static friction remained fairly constant within the analyzed range of plate hardness values, and it was estimated at 0.4 on plates with a perpendicular surface orientation and at 0.3 on plates with a parallel surface orientation

Properties of Phosphorylated Thymidylate Synthase

Thymidylate synthase (TS) may undergo phosphorylation endogenously in mammalian cells, and as a recombinant protein expressed in bacterial cells, as indicated by the reaction of purified enzyme protein with Pro-Q® Diamond Phosphoprotein Gel Stain (PGS). With recombinant human, mouse, rat, Trichinella spiralis and Caenorhabditis elegans TSs, expressed in E. coli, the phosphorylated, compared to non-phosphorylated recombinant enzyme forms, showed a decrease in Vmax(app), bound their cognate mRNA (only rat enzyme studied), and repressed translation of their own and several heterologous mRNAs (human, rat and mouse enzymes studied). However, attempts to determine the modification site(s), whether endogenously expressed in mammalian cells, or recombinant proteins, did not lead to unequivocal results. Comparative ESI-MS/analysis of IEF fractions of TS preparations from parental and FdUrd-resistant mouse leukemia L1210 cells, differing in sensitivity to inactivation by FdUMP, demonstrated phosphorylation of Ser(10) and Ser(16) in the resistant enzyme only, although PGS staining pointed to modification of both L1210 TS proteins. The TS proteins phosphorylated in bacterial cells were shown by (31)P NMR to be modified only on histidine residues, like potassium phosphoramidate (KPA)-phosphorylated TS proteins. NanoLC-MS/MS, enabling the use of CID and ETD peptide fragmentation methods, identified several phosphohistidine residues, but certain phosphoserine and phosphothreonine residues were also implicated. Molecular dynamics studies, based on the mouse TS crystal structure, allowed one to assess potential of several phosphorylated histidine residues to affect catalytic activity, the effect being phosphorylation site ̵ dependent