Mapping the fluorophilicity of a hydrophobic pocket: synthesis and biological evaluation of tricyclic thrombin inhibitors directing fluorinated alkyl groups into the p pocket

In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effects on binding into the hydrophobic proximal (P) pocket, lined by Tyr 60A and Trp 60D, His 57, and Leu 99. The synthesis of the tricyclic scaffolds was based on the 1,3-dipolar cycloaddition of azomethine ylides, derived from L-proline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide. Introduction of alkyl, alkenyl, and partially fluorinated alkyl residues was achieved upon substitution of a sulfonyl group by mixed Mg/Zn organometallics followed by oxidation/deoxyfluorination, as well as oxidation/reduction/deoxyfluorination sequences. In contrast, the incorporation of perfluoroalkyl groups required a stereoselective nucleophilic addition reaction at the "upper" carbonyl group of the tricycles, thereby yielding scaffolds with an additional OH, F, or OMe group, respectively. All newly prepared inhibitors showed potent biological activity, with inhibitory constants (K(i) values) in the range of 0.008-0.163 microM. The X-ray crystal structure of a protein-ligand complex revealed the exact positioning of a difluoromethyl substituent in the tight P pocket. Fluorophilic characteristics are attributed to this hydrophobic pocket, although the potency of the inhibitors was found to be modulated by steric rather than electronic factors.     

Knowledge-based systems in civil engineering: Three case studies

Although substantial advances have been achieved in last twenty years, in practice we are still far from taking full advantage of the potential of knowledge-based systems (KBS). Very few KBS have survived their evaluation period and only one third of those that were initially reported as successful are still in use. The primary purpose of the paper is to report on three KBS applications that have been developed for research purposes in the field of civil engineering. The main challenge underlying all three projects has been to develop computer support systems that would induce changes and improvements to the way that engineers solve their everyday problems. A great deal of effort has been put into eliciting knowledge and reasoning strategies from engineering experts with the aim of building up a computer model of their expertise in order to assist engineers in their decision-making processes. The paper closes by highlighting the principal achievements and the main issues concerning the future development of KBS for solving real life problems.     

Activity‐Based Protein Profiling of Rhomboid Proteases in Liposomes

Although activity‐based protein profiling (ABPP) has been used to study a variety of enzyme classes, its application to intramembrane proteases is still in its infancy. Intramembrane proteolysis is an important biochemical mechanism for activating proteins residing within the membrane in a dormant state. Rhomboid proteases (intramembrane serine proteases) are embedded in the lipid bilayers of membranes and occur in all phylogenetic domains. The study of purified rhomboid proteases has mainly been performed in detergent micelle environments. Here we report on the reconstitution of rhomboids in liposomes. Using ABPP, we have been able to detect active rhomboids in large and giant unilamellar vesicles. We have found that the inhibitor profiles of rhomboids in micelles and liposomes are similar, thus validating previous inhibitor screenings. Moreover, fluorescence microscopy experiments on the liposomes constitute the first steps towards activity‐based imaging of rhomboid proteases in membrane environments.     

Electrochemical determination of elemental sulfur in Brazilian naphtha: method and validation

Sulfur compounds in petroleum have caused several problems such as corrosion of equipment, lack of high quality final products, and emission of toxic gases into the environment. Elemental sulfur can increase these problems, since small amounts of it turn mercaptans into potential corrosion agents. This paper describes the applicability of a voltammetric method to quantify elemental sulfur in Brazilian naphtha samples. Elemental sulfur was quantified in synthetic and real samples using square wave voltammetry and a hanging mercury drop electrode. The method was found to have low limits of detection (0.003 mg L⁻¹) and quantification (0.009 mg L⁻¹) and a good recovery range (94.0–108.6%). This voltammetric method has potential for use in elemental sulfur determination in naphtha samples containing mercaptans and aliphatic and aromatic disulfides.     

Hydrazine oxidation catalyzed by ruthenium hexacyanoferrate-modified glassy carbon electrode

A ruthenium (III) hexacyanoferrate (Ru(HCF)) film coated on a glassy carbon electrode was explored as an electrocatalyst for hydrazine oxidation. Surface cyclic voltammograms of Ru(HCF) film showed four reversible one-electron redox waves. Two, which corresponded to the redox processes of Ru(III)/Ru(IV) and Fe(II)/Fe(III), were identified to be responsible for the catalytic activity of hydrazine oxidation. Kinetic studies using potential scan rate dependency, Tafel plots, and rotating disk electrode technique found that this catalyzed hydrazine oxidation was a complete four-electron/four-proton process producing N₂, with the rate determining step possibly a one-electron process with a transfer coefficient (α) of ~0.31–0.36. In addition, based on kinetic analysis and findings in the literature, we propose a possible reaction mechanism for catalyzed hydrazine oxidation in order to facilitate further understanding.     

Phospholipid Distribution and Phospholipid Fatty Acids of the Tropical Tunicates <Emphasis Type="Italic">Eudistoma</Emphasis> sp. and <Emphasis Type="Italic">Leptoclinides uniorbis</Emphasis>

Two tunicates, Eudistoma sp. and Leptoclinides uniorbis, collected from the tropical waters off Djibouti were investigated for lipids and phospholipid (PL) fatty acids. PL accounted for 38.2% of the total lipids in Eudistoma sp. and for 30.2% in L. uniorbis. PL classes were quantified by normal-phase high-performance liquid chromatography using an evaporative light-scattering detector and revealed essential differences. Eudistoma sp. contained mainly phosphatidylcholine (PC, 70.3% of total PL) and lysophosphatidylcholine (LPC, 11.9%) and was devoid of phosphatidylserine (PS), whereas the major PL of L. uniorbis was PS (59.1%) followed by PC (22.5%) and LPC (8.8%). Gas chromatography–mass spectrometry analyses of fatty acid (FA) derivatives revealed 38 FA in Eudistoma sp., and 35 FA in L. uniorbis, ranged from C₁₂ to C₂₄ chain lengths. Polyunsaturated FA accounted for 25.9% in Eudistoma sp. and for 32.3% in L. uniorbis. Interestingly, L. uniorbis contained a high percentage (16.7%) of the 20:5n-3 acid (8.9% in Eudistoma sp.) and the 18:4n-3 acid (4.1%). Significant levels of the 20:4n-6 acid were observed in both organisms (7.8 and 6.0% respectively). Eudistoma sp. contained the rare 20:3n-7 acid (2.3%) only recorded to date in hydrothermal vent animals. The cyclopropane dihydrosterculic acid was identified in both tunicates (0.7 and 0.5% respectively). These latter FA, together with some unusual branched saturated and monounsaturated FA, revealed the occurrence of associated bacteria in the tunicates. Another noticeable feature was a series of eight C₁₆ to C₁₈ aldehyde dimethylacetals revealing the presence of plasmalogens at 5.0% in Eudistoma sp. and 14.2% in L. uniorbis. The results of this study were compared with those previously published for other tunicates regarding mainly PL content and FA composition.