A new approach towards peptidosulfonamides: synthesis of potential inhibitors of bacterial peptidoglycan biosynthesis enzymes MurD and MurE

Peptidosulfonamides are an emerging group of peptidomimetics with a variety of applications in medicinal chemistry. We present a novel approach to the synthesis of peptidosulfonamides, and apply it to a series of new potential inhibitors of the bacterial peptidoglycan biosynthesis enzymes MurD and MurE. The synthesis was conducted via N-phthalimido β-aminoethanesulfonyl chlorides, which are new building blocks for the synthesis of peptidosulfonamides. In the most crucial step, sulfonic acids or their sodium salts were converted into the corresponding sulfonyl chlorides using an excess of either SOCl₂ or SOCl₂/DMF, and then coupled to the C-protected amino acid. None of the compounds significantly inhibited MurD, however, some inhibited MurE; one had an IC₅₀ below 200 μM, which constitutes a promising starting point for further development. Molecular modelling simulations were performed on two analogues to investigate the absence of inhibitory activity of the sulfonamide compounds on MurD.     

Enzyme binding selectivity prediction: alpha-thrombin vs trypsin inhibition

In the present work we explore the possibility of an in-depth computational analysis of available experimental X-ray structures in the specific case of a series of alpha-thrombin and trypsin complexes with their respective inhibitors for the development of a novel scoring function based on molecular electrostatic potential computed at the contact surface in the enzyme-inhibitor molecular complex. We subsequently employ the chemometrical approach to determine which are the interactions in the large volume of data that determine the resulting experimental binding constant between ligand and receptor. The results of the model evaluated with molecules in the independent validation set show that a reasonable average error of 1.30 log units of the difference between experimental and calculated binding constants was achieved in the system thrombin-trypsin, which is comparable with those of methods from the literature. Furthermore, by a careful preparation of the Kohonen top layer in the artificial neural network approach that is normally perceived as a "black box device", we have been able to follow the implications of the structure of the inhibitor-enzyme complex for the inhibitor's binding constant. The method appears to be suitable for evaluation of selectivity in structurally similar enzymatic systems, which is currently an important problem in drug design.     

Effects of fish farm loading on sea grass Posidonia oceanica at Vrgada Island (Central Adriatic): a nitrogen stable isotope study

Analyses of nitrogen stable isotopes in the marine sea grass Posidonia oceanica were used to investigate the influence of fish farming on the coastal ecosystem of Vrgada Island in the Murter Sea, Central Adriatic. The results show a statistically significant ¹⁵N enrichment (up to 4.7‰ at p?<?0.005) in P. oceanica leaf and shoot tissues from fish cage sites with respect to the unaffected offshore reference site of Lumbarda Reef Flat (Kornati Islands). Heavy nitrogen enrichment was also detected in other benthic organisms analysed during this study and is attributed to the absorption and assimilation of ¹⁵N-enriched fish farm derived nitrogen waste.     

Effects of fish farm loading on sea grass Posidonia oceanica at Vrgada Island (Central Adriatic): a nitrogen stable isotope study

Analyses of nitrogen stable isotopes in the marine sea grass Posidonia oceanica were used to investigate the influence of fish farming on the coastal ecosystem of Vrgada Island in the Murter Sea, Central Adriatic. The results show a statistically significant 15N enrichment (up to 4.7 per thousand at p < 0.005) in P. oceanica leaf and shoot tissues from fish cage sites with respect to the unaffected offshore reference site of Lumbarda Reef Flat (Kornati Islands). Heavy nitrogen enrichment was also detected in other benthic organisms analysed during this study and is attributed to the absorption and assimilation of 15N-enriched fish farm derived nitrogen waste.     

Regioselective Synthesis of 5- and 3-Hydroxy-N-Aryl-1H-Pyrazole-4-Carboxylates and Their Evaluation as Inhibitors of Plasmodium falciparum Dihydroorotate Dehydrogenase

In silico evaluation of various regioisomeric 5- and 3-hydroxy-substituted alkyl 1-aryl-1H-pyrazole-4-carboxylates and their acyclic precursors yielded promising results with respect to their binding in the active site of dihydroorotate dehydrogenase of Plasmodium falciparum (PfDHODH). Consequently, four ethyl 1-aryl-5-hydroxy-1H-pyrazole-4-carboxylates and their 3-hydroxy regioisomers were prepared by two-step syntheses via enaminone-type reagents or key intermediates. The synthesis of 5-hydroxy-1H-pyrazoles was carried out using the literature protocol comprising acid-catalyzed transamination of diethyl [(dimethylamino)methylene]malonate with arylhydrazines followed by base-catalyzed cyclization of the intermediate hydrazones. For the synthesis of isomeric methyl 1-aryl-3-hydroxy-1H-pyrazole-4-carboxylates, a novel two-step synthesis was developed. It comprises acylation of hydrazines with methyl malonyl chloride followed by cyclization of the hydrazines with tert-butoxy-bis(dimethylamino)methane. Testing the pyrazole derivatives for the inhibition of PfDHODH showed that 1-(naphthalene-2-yl)-5-hydroxy-1H-pyrazole-4-carboxylate and 1-(naphthalene-2-yl)-, 1-(2,4,6-trichlorophenyl)-, and 1-[4-(trifluoromethyl)phenyl]-3-hydroxy-1H-pyrazole-4-carboxylates (~30% inhibition) were slightly more potent than a known inhibitor, diethyl α-{[(1H-indazol-5-yl)amino]methylidene}malonate (19% inhibition).     

A method for semi-continuous measurement of dissolved elemental mercury in industrial and natural waters

Mercury in aqueous systems can be present in different chemical forms. Of these, dissolved elemental Hg(0) (DEM) is of great importance because it can readily be partitioned between air and water. Analytical methods used for determining DEM are conventionally based on removal of Hg(0) by purging, pre-concentration on gold and detection by either cold vapour atomic absorption (CV-AAS) or atomic fluorescence spectrophotometry (CV-AFS). At present, there is no agreed protocol for the measurement of DEM in aqueous samples. A new method is described here, which is based on continuous stripping of DEM by mercury-free nitrogen in a flow injection mode and detection by CV-AAS. The partitioning of DEM between aqueous and gas phases is largely dependent on the composition of the former. Moreover, calibration using the standard addition method is not possible due to the reactivity of DEM introduced from calibration solutions. Calibration is therefore done by reference measurements using a manual method for DEM involving quantitative removal and CV-AFS detection. DEM is then determined in the water sample by applying the partitioning factor. The optimised method is precise, sensitive and linear over a wide concentration range. It has provided comparable results with the manual method when applied on board a research vessel in the Mediterranean Sea (0.02–0.05 ng L^?1) and during a pilot laboratory-scale experiment on industrial aqueous media from wet flue gas desulphurisation (WFGD) equipment (2–300 ng L^?1).     

Standardisation of a European measurement method for the determination of mercury in deposition: results of the field trial campaign and determination of a measurement uncertainty and working range

A standard method for the measurement of mercury in deposition is currently being finalised by Working Group 25 of the European Committee for Standardisation’s Technical Committee 264 ‘Air Quality’, in response to the requirements of the European Union’s Fourth Air Quality Daughter Directive. This paper reports the results of a field measurement programme which was undertaken to assess the uncertainty of the proposed standard method, define its working range and determine its compliance with the required data quality objectives of the Fourth Air Quality Daughter Directive.     

Extended Global Convergence Framework for Unconstrained Optimization

An extension of the global convergence framework for unconstrained derivative-free optimization methods is presented. The extension makes it possible for the framework to include optimization methods with varying cardinality of the ordered direction set. Grid-based search methods are shown to be a special case of the more general extended global convergence framework. Furthermore,the required properties of the sequence of ordered direction sets listed in the definition of grid-based methods are relaxed and simplified by removing the requirement of structural equivalence.     

Energy Minimizing Mountain Ascent

In this article, an optimal mountain ascent is studied as a particular problem of a human walking over a rugged terrain. First, an approximation of the terrain is constructed using particular smooth splines??macro-elements. Then a functional measuring the energy consumption along boundary curves of a macro-element is defined. Finally, the corresponding discrete problem of finding the optimal path on a mesh of curves is applied. Numerical results on real-life data indicate that computed paths are a good approximation of hiking paths in nature.     

Optimization of gradient profiles in ion-exchange chromatography using computer simulation programs

Optimization procedure of gradient separations in ion-exchange chromatography using simplex optimization method in combination with the computer simulation program for ion-exchange chromatography is presented. The optimization of parameters describing gradient profile for the separation in ion chromatography is based on the optimization criterion obtained from calculated chromatograms. The optimization criterion depends on the parameters used for calculations and thus exhibits the quality of gradient conditions for the separation of the analytes. Simplex method is used to calculate new gradient profiles in order to reach optimum separations for the selected set of analytes. The Simplex algorithm works stepwise, for each new combination of parameters that describe the gradient profile a new calculation is performed and from the calculated chromatogram the optimization criterion is determined. The proposed method is efficient and may reduce the time and cost of analyses of complex samples with ion-exchange chromatography.