An efficient new route to dihydropyranobenzimidazole inhibitors of HCV replication

A class of dihydropyranobenzimidazole inhibitors was recently discovered that acts against the hepatitis C virus (HCV) in a new way, binding to the IRES-IIa subdomain of the highly conserved 5' untranslated region of the viral RNA and thus preventing the ribosome from initiating translation. However, the reported synthesis of these compounds is lengthy and low-yielding, the intermediates are troublesome to purify, and the route is poorly structured for the creation of libraries. We report a streamlined route to this class of inhibitors in which yields are far higher and most intermediates are crystalline. In addition, a key variable side chain is introduced late in the synthesis, allowing analogs to be easily synthesized for optimization of antiviral activity.     

Orthogonal Ubiquitin Transfer through Engineered E1-E2 Cascades for Protein Ubiquitination

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Highlights? Orthogonal ubiquitin (UB) transfer pathway to synthesize specific UB-E2 conjugates ? Phage display to engineer UB-E1 and UB-E2 interactions ? Engineered xUB-xE1 and xE1-xE2 pairs with no cross-reactivities with native enzymes     

The challenge to quantify proteins with charge trains due to isoforms or conformers

Single proteins separated by 2-DE often show multiple spots spreading along the first dimension. In many cases, such charge trains are explained by isoform differences or by putative post-translational modifications including phosphorylation, glycosylation and others. We now report that individual spots of such charge trains on 2-D gels in fact often represent the same protein, but, apparently due to conformational changes, segregate to different isoelectric points. If MS analysis reveals protein identity, we therefore suggest integrating all individual spots within a charge train for quantification. Especially in quality control of pharmaceutical proteins, the integration of the spot groups of all active contents is preferable in order to obtain reproducible and reasonable quantitative results. However, most commercial software packages for gel analysis integrate the signals spot-wise. We provide an improved quantification tool for proteins with charge train groups. This calculation can be implemented using the MATLAB software and the self-developed "Correct Integration Software System" or the commercial software package Delta2D.     

Synthesis, characterization and examination of Gd[DO3A-hexylamine]-functionalized silica nanoparticles as contrast agent for MRI-applications

Spherical, nonporous and monodisperse silica nanoparticles (NPs) with a diameter of about 100 nm were synthesized and covalently functionalized with lanthanoid(III) (Ln=Gd or Y) chelate complexes, which serve as contrast agents (CAs) for magnetic resonance imaging (MRI). The materials were fully characterized after each synthetic step by different analytical methods, such as dynamic light scattering, scanning electron microscopy, DRIFT and NMR spectroscopy, thermogravimetry and elemental analysis, as well as zetapotential measurements. High surface concentrations of Gd(III) complexes (up to 50 μmol g(-1)) were determined by ICP-AES and T(1)-measurements, respectively. MRI experiments show the typical concentration-dependent increase of the longitudinal relaxation rate. T(1)-weighted images of samples with more than 25 μg NPs per 100 μL agar display a clear contrast enhancement in the agar layer. The transverse relaxivities r(2) of the materials are significantly higher than r(2) of the corresponding free Gd(III) complexes in water and medium, whereas the longitudinal relaxivities r(1) are slightly increased. Due to the high loading of Gd(III) complexes, the relaxivities per particle are remarkably high (up to 2.78×10(5) mM(-1) s(-1) for r(1)). Thus, new hybrid materials, based on nonporous silica NPs with high local relaxivity values were synthesized, which can serve as very effective CAs for MRI.     

Peptide-antibody complex as handle for single-molecule cut & paste

Molecule-by-molecule arrangement of proteins, for example, in enzymatic networks of predefined composition and proximity, is a major goal that may be accomplished by the single-molecule cut-and-paste technique (SMC&P). For this purpose, co-expressed anchors and handles as protein tags should be employed. As a first step in this direction, the authors develop an SMC&P design which exploits an antibody-peptide complex as a molecular handle.     

Sulfangolids, macrolide sulfate esters from Sorangium cellulosum

Sulfangolids are the first sulfate ester containing secondary metabolites from myxobacteria. The metabolites 1-4 and the structurally related kulkenon (5) were isolated from different strains of the species Sorangium cellulosum. In the course of isolation all metabolites proved to be rather sensitive due to their conjugated double bond systems and the strong acidic nature of the sulfate ester in sulfangolids. The relative configuration of sulfangolid C (3) was assigned by extensive 1D and 2D NMR analysis and molecular modelling. In addition, the biosynthesis of 3 was studied by feeding experiments.     

Lyapunov Spectra for All Ten Symmetry Classes of Quasi-one-dimensional Disordered Systems of Non-interacting Fermions

A random phase property is proposed for products of random matrices drawn from any one of the classical groups associated with the ten Cartan symmetry classes of non-interacting disordered Fermion systems. It allows to calculate the Lyapunov spectrum explicitly in a perturbative regime. These results apply to quasi-one-dimensional random Dirac operators which can be constructed as representatives for each of the ten symmetry classes. For those symmetry classes that correspond to two-dimensional topological insulators or superconductors, the random Dirac operators describing the one-dimensional boundaries have vanishing Lyapunov exponents and almost surely an absolutely continuous spectrum, reflecting the gapless and conducting nature of the boundary degrees of freedom.     

Application of explicitly correlated coupled-cluster methods to molecules containing post-3d main group elements

A benchmark of explicitly correlated CCSD(T)-F12 methods for the dimers Ga₂, As₂, Br₂ and diatomic molecules AsN, BrO, HBr, GaF, GaCl, GaBr, AsF, AsCl, BrF, and BrCl is presented. Equilibrium distances, harmonic vibrational frequencies, and dissociation energies are compared with extensive conventional CCSD(T) calculations using a variety of orbital basis sets and different ansätze for the explicitly correlated wavefunctions. Correlation of the 3d electrons has a strong effect, in particular on the equilibrium distances, and it is shown that this can be recovered very efficiently by the explicit correlation treatment. It is found that CCSD(T)-F12 calculations with new F12-specific cc-pVnZ-F12 basis sets give comparable accuracy to standard CCSD(T) calculations with very much larger aug-cc-pwCV(n+2)Z basis sets. The effects of higher order valence electron correlation (up to CCSDTQP) are also investigated in conventional calculations and are found to be significant in some cases.