Synthesis of 9H-pyrrolo[2,1-b][1,3,6]benzothiadiazocin-10(11H)-one 4,4-dioxide,a potential anti-HIV-1 agent

Starting from 2-(2-aminophenylthio)-1-ethoxycarbonylmethyl-1H-pyrrole a four-step synthesis of 9H-pyrrolo[2,1-b][1,3,6]benzothiadiazocin-10(11H)-one 4,4-dioxide, a new heterocycle related to anti-HIV-1 tricyclic non-nucleoside agents, is described.     

Molecular geometry and electronic structure of chlorosubstituted trans- and cis-stilbene derivatives

Geometrical structures of several chlorostilbenes were determined from ultraviolet absorption spectra in solution by calculations based on the simple LCAO molecular orbital method. Dipole moments were evaluated for all derivatives without a center of symmetry in the calculated geometry. The results are in good agreement with experimental data.

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Zusammenfassung Die geometrischen Strukturen einiger Chlorostilbene werden aus den UV-Absorptionsspektren in Lösung mittels einfacher MO-LCAO Berechnungen erhalten. Für alle Verbindungen, deren berechnete Struktur kein Symmetriezentrum aufweist, werden die Dipolmomente bestimmt. Die Resultate stehen in gutem Einklang mit den experimentellen Daten.

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Résumé Les structures géométriques de plusieurs chlorostilbènes ont été déterminées à partir des spectres d'absorption ultraviolette en solution par des calculs fondés sur la méthode simple des orbitales moléculaires. Pour tous les dérivés sans centre de symétrie les moments dipolaires ont été évalués à l'aide de la géométrie calculée. Les résultats sont en bon accord avec l'expérience.

     

Primary thermal degradation processes occurring in poly(phenylenesulfide) investigated by direct pyrolysis–mass spectrometry

The thermal degradation Processes which occur in poly(phenylenesulfide) (PPS) have been studied by direct pyrolysis-mass spectrometry (DPMS). The structure of the compounds evolved in the overall temperature range of PPS decomposition (400–700°C) suggests the occurrence of several thermal decomposition steps. At the onset of the thermal degradation (430–450°C) this polymer decomposes with the formation of cyclic oligomers, generated by a simple cylization mechanism either initiated at the—SH end groups or by the exchange between the inner sulfur atoms along the polymer chain. At higher temperature (> 500°C) another decomposition reaction takes over with the formation of aromatic linear thiols. The formation of thiodibenzofuran units by a subsequent dehydrogenation reaction occurs in the temperature range of 550–650°C; in fact, pyrolysis products with a quasi-ladder structure have also been detected. Ultimately, above 600°C, extrusion of sulfur from the pyrolysis residue occurs with the maximum evolution at the end of decomposition (about 700°C). It appears, therefore, that the residue obtained at high temperature tends to have a crosslinked graphite-like structure from which the bonded sulfur is extruded. © 1994 John Wiley & Sons, Inc.     

Blue silver: a very sensitive colloidal Coomassie G-250 staining for proteome analysis

A modified Neuhoff's colloidal Coomassie Blue G-250 stain is reported, dubbed "blue silver" on account of its considerably higher sensitivity, approaching the one of conventional silver staining. The main modifications, as compared to Neuhoff's protocol, were: a 20% increment in dye concentration (from 0.1% up to 0.12%) and a much higher level of phosphoric acid in the recipe (from 2% up to 10%). The "blue silver" exhibits a much faster dye uptake (80% during the first hour of coloration, vs. none with a commercial preparation from Sigma). Even at equilibrium (24 h staining), the "blue silver" exhibits a much higher sensitivity than all other recipes, approaching (but lower than) the one of the classical silver stain. Measurements of stain sensitivity after sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of bovine serum albumin (BSA) gave a detection limit (signal-to-noise ratio > 3) of 1 ng in a single zone. The somewhat lower sensitivity of "blue silver" as compared to classical silvering protocols in the presence of aldehydes is amply compensated for by its full compatibility with mass spectrometry of eluted polypeptide chains, after a two-dimensional map analysis, thus confirming that no dye is covalently bound (or permanently modifies) to any residue in the proteinaceous material. It is believed that the higher level of phosphoric acid in the recipe, thus its lower final pH, helps in protonating the last dissociated residues of Asp and Glu in the polypeptide coils, thus greatly favoring ionic anchoring of dye molecules to the protein moiety. Such a binding, though, must be followed by considerable hydrophobic association with the aromatic and hydrophobic residues along the polypeptide backbone.     

PHOTOOXIDATION OF HORSE AND SPERM-WHALE MYOGLOBIN SENSITIZED BY THE HEME GROUP

Abstract —The irradiation of horse and sperm-whale Fe 3 * or Fe 2* myoglobins with visible light showed that axial ligands that render the heme diamagnetic (e.g. O₂, CO or CN^-) endow the hemoproteins with a marked photosensitivity. In contrast, high-spin myoglobins are unaffected by visible light. These findings appear to be of general validity for all hemo-proteins and are in agreement with the involvment of the triplet state of the heme as the reactive intermediate. In all cases, the overall photoprocess occurs within a very narrow spatial range, leading to specific modification of these photooxidizable side chains adjacent to the chromophore. Therefore, this technique can be used to probe the environment of the prosthetic group in hemoproteins. In particular, our data suggest that, in horse myoglobin, histidines-93 and -64 represent the heme-linked and the distal imidazole groups, respectively; moreover, the thioether function of methionine-131 must be nearer the heme in horse than in sperm-whale myoglobin. The selectivity of the photoreaction can be further enhanced by a suitable choice of the sixth ligand, and/or by controlling the pH of the irradiated solution. For example, for both proteins, irradiation of the cyanide derivative results in specific photooxidation of the proximal histidine, whereas irradiation of horse CO-ferromyoglobin at pH values below 6 causes specific photooxidation of methionine-131. Consequently, this photooxidative procedure can also be utilized to monitor conformational changes upon binding of the heme with different ligands, as well as to achieve the selective modification of amino acid residues, which are usually buried inside the protein molecule.     

Considerations in compound database preparation--"hidden" impact on virtual screening results

Structure-based virtual screening (SBVS) utilizing docking algorithms has become an essential tool in the drug discovery process, and significant progress has been made in successfully applying the technique to a wide range of receptor targets. In silico validation of virtual screening protocols before application to a receptor target using a corporate or commercially available compound collection is key to establishing a successful process. Ultimately, retrieval of a set of active compounds from a database of inactives is required, and the metric of enrichment (E) is habitually used to discern the quality of separation of the two. Numerous reports have addressed the performance of docking algorithms with regard to the quality of binding mode prediction and the issue of postprocessing "hit lists" of docked ligands. However, the impact of ligand database preprocessing has yet to be examined in the context of virtual screening and prioritization of compounds for biological evaluation. We provide an insight into the implications of cheminformatic preprocessing of a validation database of compounds where multiple protonated, tautomeric, stereochemical, and conformational states have been enumerated. Several commonly used methods for the generation of ligand conformations and conformational ensembles are examined, paired with an exhaustive rigid-body algorithm for the docking of different "multimeric" compound representations to the ligand binding site of the human estrogen receptor alpha. Chemgauss, a shapegaussian scoring function with intrinsic chemical knowledge, was combined with PLP as a consensus-scoring scheme to rank output from the docking protocol and enrichment rates calculated for each screen. The overheads of CPU consumption and the effect on relative database size (disk requirement) for each of the protocols employed are considered. Assessment of these parameters indicates that SBVS enrichments are highly dependent on the initial cheminformatic treatment(s) used in database construction. The interplay of SMILES representations, stereochemical information, protonation state enumeration, and ligand conformation ensembles are critical in achieving optimum enrichment rates in such screening.     

Facile synthesis of 5-(α-alkyl-substituted) furans

2-Halo, 2-hydroxy- or 2-alkoxyalkyl substituted furans are easily synthesized under acidic conditions by intramolecular cyclization of α,β-unsaturated 1,4-diketones by a simple and cheap procedure. Some aspects of the mechanism are discussed.     

Protein adsorption equilibrium and kinetics in multimodal cation exchange resins

Protein adsorption equilibria and kinetics are obtained experimentally for two multimodal cation exchange resins—Nuvia cPrime, which is based on a polymeric matrix, and Capto MMC, which is based on an agarose matrix. In both resins, the ligand contains a phenyl group, a carboxyl group, and a peptide bond but with a different arrangement. Transmission electron microscopy and inverse size exclusion chromatography indicate a bimodal distribution of pores in Nuvia cPrime, including small pores with 10 nm radius and pores larger than 400 nm, and a monodispersed distribution of pores in Capto MMC, averaging 32 nm in radius. Potentiometric titration curves show similar buffering ranges and pK _a values for the ligands in both resins and a slightly higher ligand density for Nuvia cPrime. Equilibrium binding capacities for lysozyme and a monoclonal antibody (mAb) are also similar for both resins at comparable pH and salt concentrations, although Capto MMC shows a weaker dependence on salt concentration as a result of its more hydrophobic character. The main difference is the adsorption kinetics of the mAb, which is the larger of the two proteins studied. For both resins, as shown by means of confocal laser scanning miscopy, the adsorption kinetics is controlled by pore diffusion. Capto MMC with its smaller pores has a slower rate of mass transfer than Nuvia cPrime. As a result, for the mAb, much higher column dynamic binding capacities are obtained for Nuvia cPrime than for Capto MMC.     

A numerical eigenvalue study of preconditioned non‐equilibrium transport equations

The finite element integration of non‐equilibrium contaminant transport in porous media yields sparse, unsymmetric, real or complex equations, which may be solved by iterative projection methods, such as Bi‐CGSTAB and TFQMR, on condition that they are effectively preconditioned. To ensure a fast convergence, the eigenspectrum of the preconditioned equations has to be very compact around unity. Compactness is generally measured by the spectral condition number. In difficult advection‐dominated problems, however, the condition number may be large and nevertheless, convergence may be good. A numerical study of the preconditioned eigenspectrum of a representative test case is performed using the incomplete triangular factorization. The results show that preconditioning eliminates most of the original complex eigenvalues, and that compactness is not necessarily jeopardized by a large condition number. Quite surprisingly, it is shown that the preconditioned complex problem may have a more compact real eigenspectrum than the equivalent real problem. Copyright © 1999 John Wiley & Sons, Ltd.