A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase

We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of l- and d-alanine using pyridoxal 5-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for d-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects.This article describes the development of a receptor-based pharmacophore model for AlaR, taking into account receptor flexibility (i.e. a `dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1sft) with a d-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing.The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets.     

Polymers from a levopimaric acid–acrylonitrile Diels–Alder adduct: Synthesis and characterization

The Diels–Alder adduct of levopimaric acid with acrylonitrile was efficiently prepared from resin acids. Excellent addition reaction yields (ca. 95%) were obtained. The adduct was converted into polyamides by polycondensation with diamines. When the same adduct was subjected to a dehydrodecarboxylation reaction, a novel ketone dinitrile derivative was obtained. This trifunctional product was also converted into polyamides by polycondensation with diamines. When the ketone dinitrile was hydrolyzed in the presence of alkalies and the reaction product was chlorinated, a ketone diacid chloride was obtained. A polyester was synthesized by the polycondensation of the diacid chloride with a diol. The structures of the Diels–Alder adduct, ketone dinitrile derivative, ketone diacid chloride, and polymers were established by means of elemental analysis, IR and NMR spectroscopy, and molecular weight determinations. Both the polyamides and the polyester were low‐molecular‐weight polymers soluble in polar solvents. The thermal behavior of the monomers and polymers was evaluated by thermogravimetric analysis. The thermal studies showed that the polymers were fairly thermostable substances, except the polyester, which appeared to be a substance with good thermal stability. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6308–6322, 2005     

CDM predictions of creep damage initiation and growth in ferritic steel weldments in a medium-bore branched pipe under constant pressure at 590° C using a four-material weld model

The paper reports the use of three-dimensional creep continuum damage mechanics techniques to study the creep failure of a medium-bore low-alloy ferritic-steel cylinder–cylinder branched pressure vessel welded connection, tested at a constant pressure of 4 MPa, at a uniform temperature of 590°C. The development of computational techniques is reported to analyse this problem with a four-material model of the welded connection which includes: parent, type IV, heat-affected zone (HAZ) and weld materials. The results of analyses are presented for two sets of creep damage constitutive equations. For both equation sets, lifetimes are conservatively, yet accurately predicted; however, the results of metallographic examinations of a tested vessel are not accurately predicted. To overcome this deficiency further analyses of the vessel are recommended which include: a coarse-grained HAZ (CGHAZ), adjacent to the weld material; and, more-refined finite element modelling.     

Possible High Power Laser Construction Using a New Discharge Type-Heated Cathode Discharge in the Copper Vapours Continuously Evaporated from the Anode

The possibility to build a high power copper laser using a new type of discharge – heated cathode discharge in the copper vapours continuously evaporated from a melted spot on the anode surface is analysed. From the experimental data on this new discharge type, the equivalent pressure of the copper atoms in the discharge space has been obtained. This pressure can be as high as 1 torr. The density of the power in the discharge volume is evaluated to be more than 1 kW/cm³.     

Utilization of α-olefins obtained by pyrolysis of waste high density polyethylene to synthesize α-olefin-succinic-anhydride based cold flow improvers

A new route of utilization of α-olefin rich hydrocarbon fractions obtained by waste polymer pyrolysis was investigated. α-olefin-succinic-anhydride intermediate-based pour point depressant additives for diesel fuel were synthesized, in which reactions needed α-olefins were obtained by pyrolysis of waste high-density polyethylene (HDPE). Fraction of α-olefins was produced by the de-polymerization of plastic waste in a tube reactor at 500℃ in the absence of catalysts and air. C_17~22 range of mixtures of olefins and paraffins were separated for synthesis and then, these hydrocarbons were reacted with maleic-anhydride (MA) for formation of α-olefin-succinic-anhydride intermediates. The olefin-rich hydrocarbon fraction contained approximately 60% of olefins, including 90%~95% α-olefins. Other intermediates were produced in the same way by using commercial C₂₀ α-olefin instead of C_17~22 olefin mixture. The two different experimental intermediates with number average molecular weights of 1850g/mol and 1760g/mol were reacted with different alcohols: 1-butanol, 1-hexanol, 1-octanol, i-butanol, and c-hexanol to produce their ester derivatives. The synthesized ten experimental pour point depressants were added in different concentrations to conventional diesel fuel, which had no other additive content before. The structure and efficiency of experimental additives were followed by different standardized and non-standardized methods. Results showed that the experimental additives on the basis of the product of waste pyrolysis were able to decrease not only the pour but also the cloud point and cold filter plugging point (CFPP) of diesel fuel, whose effects could be observed even if the concentration of additives was low. Furthermore, all additives had anti-wear and anti-friction effects in diesel fuel.     

Novel cellulose esters derived from the levopimaric acid-maleic anhydride adduct: synthesis,characterization, and properties

Synthesis of maleated pimaric acid (MPA) cellulose esters is first reported in this work. Cellulose esterification was performed by reacting microcrystalline cellulose with monoacid chloride of MPA (MPA-Cl) in presence of pyridine as catalyst and reaction medium. The syntheses were started in a heterogeneous solid–liquid reaction medium, but as the reaction advanced, the reaction mass turned into a homogeneous solution. The effects of MPA-Cl/anhydroglucose unit molar ratio, reaction temperature, and reaction duration on the yield and degree of substitution (DS) of cellulose esters (CEs) were investigated. CEs with DS ranging from 2.6 to 2.8 were achieved at molar ratios of 5.5–6.0 after 12–16 h at 118 °C. The purified products were characterized by elemental analysis, IR and ¹³C-NMR spectroscopy, and thermogravimetric analysis. CEs are soluble or partially soluble in usual organic solvents, depending on DS. Transparent films were prepared using CE-cyclohexanone solutions.     

An alternating direction scheme on a nonuniform mesh for reaction-diffusion parabolic problems

In this paper we develop a numerical method for two-dimensionaltime-dependent reaction-diffusion problems. This method, whichcan immediately be generalized to higher dimensions, is shownto be uniformly convergent with respect to the diffusion problems.This method, which can immediately be generalized to higherdimensions, is shown to be uniformly convergent with respectto the diffusion parameter.     

Exchange bias and spin valve systems with Fe–Mn antiferromagnetic pinning layers, obtained by the thermo-ionic vacuum arc method

Exchange bias and spin valve systems with Fe–Mn antiferromagnetic layers of different Fe concentrations were obtained by the thermo-ionic vacuum arc method. The adherence of the multilayer system to the Si substrate depends on the Fe–Mn composition. The overall roughness depends on the growing order of the antiferromagnetic/ferromagnetic layers. Very low blocking temperatures for exchange bias were observed for the considered compositions of the Fe–Mn layer. The coercive forces of both the pinned and the free layers of spin valve structures can be considerably modified along a large set of samples simultaneously prepared.     

Spin configurations and interfacial diffusion in exchange bias and spin valve systems with Ir–Mn antiferromagnetic pinning layers

Exchange bias and spin valve structures with Fe as ferromagnetic layers selectively enriched in ⁵⁷Fe and Ir–Mn of different compositions as antiferromagnetic pinning layers have been prepared by r.f. sputtering. Conversion Electron Mössbauer Spectroscopy and Magneto Optic Kerr Effect have shown that the local structure and interactions in the whole ferromagnetic layers, with direct influence on their magnetic reversal processes, depend on growing order of the layers and composition of the AF layer. Interfacial atomic diffusion is the main reason of perturbing the local structure of the ferromagnet. Mössbauer Spectroscopy is a powerfool tool which allows a detailed analysis of local configurations, in order to optimize the magnetic and giant magnetoresistive parameters of such multilayers of important technological applications.