Anionic Oligothiophenes Compete for Binding of X‐34 but not PIB to Recombinant Aβ Amyloid Fibrils and Alzheimer's Disease Brain‐Derived Aβ

Deposits comprised of amyloid‐β (Aβ) are one of the pathological hallmarks of Alzheimer's disease (AD) and small hydrophobic ligands targeting these aggregated species are used clinically for the diagnosis of AD. Herein, we observed that anionic oligothiophenes efficiently displaced X‐34, a Congo Red analogue, but not Pittsburgh compound B (PIB) from recombinant Aβ amyloid fibrils and Alzheimer's disease brain‐derived Aβ. Overall, we foresee that the oligothiophene scaffold offers the possibility to develop novel high‐affinity ligands for Aβ pathology only found in human AD brain, targeting a different site than PIB.     

Microwave-enhanced alpha-arylation of a protected glycine in water: evaluation of 3-phenylglycine derivatives as inhibitors of the tuberculosis enzyme, glutamine synthetase

A microwave-enhanced, palladium-catalyzed protocol for the alpha-arylation of a protected glycine in neat water is described. This reaction proceeds rapidly, under non-inert conditions, to afford a range of phenylglycine derivatives in moderate to good yields. Based on this alpha-arylation, a number of aryl L-methionine-SR-sulfoximine (MSO) analogues were prepared and evaluated for their Mycobacterium tuberculosis glutamine synthetase (TB-GS) inhibitory activity.     

DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations

Molecular orbital calculations of the complex between DNA-ERE (estrogen response element) and ER (estrogen receptor)-DBD (DNA-binding domain) were performed using the fragment molecular orbital (FMO) method, which enables large-scale MO (molecular orbital) calculations by reducing the computational cost and by significantly increasing efficiency for parallel computation. Such a large system, which contains 3354 atoms, is impractical via conventional MO methods due to the immense computational cost. Details of the interaction between DNA-ERE and ER-DBD were revealed in this study as follows by using the FMO calculations to analyze the interfragment interaction energies (IFIEs) and the electrostatic potentials (ESPs). An area with a high positive ESP is identified on the DNA-binding side of ER-DBD and is the main driving force behind access to the DNA. The position of the ER-DBD monomer can be fixed on a phosphate group of DNA-ERE by the strong electrostatic interactions, whereas the rotation cannot be fixed. In contrast, both the position and rotation of the ER-DBD dimer can be fixed and can therefore form the stable (ER-DBD)2...DNA-ERE complex. Dimerization of the ER-DBD monomers, each of which have a charge of +5 , is mainly due to large attractive interaction energies of the second Zn fragments. The base pairs in the consensus sequence of DNA-ERE interact only with the recognition helix located in the major groove due to the large shielding effect of the phosphate groups of DNA. The recognition helix has weaker interactions with the base pairs than the electrostatic interactions with the phosphate groups. Thus, the DNA-binding machinery of the ER-DBD dimer, which can secure the recognition helix in the major groove of DNA, is crucial for interactions between the recognition helix and base pairs.     

Charge recombination versus charge separation in donor-bridge-acceptor systems

Optimizing the ratio of the rates for charge separation (CS) over charge recombination (CR) is crucial to create long-lived charge-separated states. Mastering the factors that govern the electron transfer (ET) rates is essential when trying to achieve molecular-scale electronics, artificial photosynthesis, and also for the further development of solar cells. Much work has been put into the question of how the donor-acceptor distances and donor-bridge energy gaps affect the electronic coupling, V(DA), and thus the rates of ET. We present here a unique comparison on how these factors differently influence the rates for CS and CR in a porphyrin-based donor-bridge-acceptor model system. Our system contains three series, each of which focuses on a separate charge-transfer rate-determining factor, the donor-acceptor distance, the donor-bridge energy gap, and last, the influence of the electron acceptor on the rate for charge transfer. In these three series both CS and CR are governed by superexchange interactions which make a CR/CS comparative study ideal. We show here that the exponential distance dependence increases slightly for CR compared to that for CS as a result of the increased tunneling barrier height for this reaction, in accordance with the McConnell superexchange model. We also show that the dependence on the tunneling barrier height is different for CS and CR. This difference is highly dependent on the electron acceptor and thus cannot solely be explained by the differences in the frontier orbitals of the electron donor in these porphyrin systems.     

Catalysis of the cleavage of uridine 3'-2,2,2-trichloroethylphosphate by a designed helix-loop-helix motif peptide

A 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle has been designed to catalyze the hydrolysis of phosphodiesters. The active site on the surface of the folded catalyst is composed of two histidine and four arginine residues, with the capacity to provide general acid, general base, and/or nucleophilic catalysis as well as transition state stabilization. Uridine 3'-2,2,2 trichloroethylphosphate (2) is a mimic of RNA with a leaving group pKa of 12.3. Its hydrolysis is energetically less favorable than that of commonly used model substrates with p-nitrophenyl leaving groups and therefore a more realistic model for the design of catalysts capable of cleaving RNA. The second-order rate constant for the hydrolysis of 2 at pH 7.0 by the polypeptide catalyst was 418 x 10(-6) M-1 s-1, and that of the imidazole catalyzed reaction was 1.66 x 10(-6) M-1 s-1. The pH dependence suggested that catalysis is due to the unprotonated form of a residue with a pKa of around 5.3, and the observed kinetic solvent isotope effect of 1.9 showed that there is significant hydrogen bonding in the transition state, consistent with general acid-base catalysis. The rate constant ratio k2(Pep)/k2(Im) of 252 is probably due to a combination of nucleophilic and general acid-base catalysis, as well as transition state stabilization. Substrate binding was weak since no sign of saturation kinetics was observed for substrate concentrations in the range from 5 to 40 mM. The results provide a platform for the further development of catalysts for RNA cleavage with a potential role in the development of drugs.     

Nearest-neighbor oxygen distances in liquid water and ice observed by x-ray Raman based extended x-ray absorption fine structure

We report the nearest-neighbor oxygen-oxygen radial distribution function (NN O-O RDF) of room temperature liquid water and polycrystalline ice Ih (-16.8 degrees C) obtained by x-ray Raman based extended x-ray absorption fine structure (EXAFS) spectroscopy. The spectra of the two systems were taken under identical experimental conditions using the same procedures to obtain the NN O-O RDFs. This protocol ensured a measurement of the relative distance distribution with very small systematic errors. The NN O-O RDF of water is found to be more asymmetric (tail extending to longer distances) with longer average distance (2.81 A for water and 2.76 A for ice) but a slightly shorter peak position (2.70 A for water and 2.71 A for ice). The refinement also showed a small but significant contribution from the linear O-H-O multiple scattering signal. The high sensitivity to short range distances of the EXAFS probe will set further restrictions to the range of possible models of liquid water.     

The REX-ISOLDE project

The Radioactive Beam Experiment REX-ISOLDE [1–3] is a pilot experiment at ISOLDE (CERN) testing the new concept of post acceleration of radioactive ion beams by using charge breeding of the ions in a high charge state ion source and the efficient acceleration of the highly charged ions in a short LINAC using modern ion accelerator structures. In order to prepare the ions for the experiments singly charged radioactive ions from the on-line mass separator ISOLDE will be cooled and bunched in a Penning trap, charge bred in an electron beam ion source (EBIS) and finally accelerated in the LINAC. The LINAC consists of a radiofrequency quadrupole (RFQ) accelerator, which accelerates the ions up to 0.3 MeV/u, an interdigital H-type (IH) structure with a final energy between 1.1 and 1.2 MeV/u and three seven gap resonators, which allow the variation of the final energy. With an energy of the radioactive beams between 0.8 MeV/u and 2.2 MeV/u a wide range of experiments in the field of nuclear spectroscopy, astrophysics and solid state physics will be addressed by REX-ISOLDE. This revised version was published online in July 2006 with corrections to the Cover Date.     

Crystal Structure of BaNb6.3(1)Ti3.6(1)O16 containing Nb6O12, fused Ti3O13 Clusters and Ti3O10 Units

A new phase, BaNb_6.3(1)Ti_3.6(1)O₁₆, has been synthesised. Electron diffraction studies indicate an hexagonal substructure with unit cell parameters a ≈ 8.9 Å and c ≈ 9.5 Å. In some of the ED patterns superstructure reflections are present, indicating a supercell with a = √3 · a_sub and c = c_sub. However, X‐ray single‐crystal diffraction studies of a crystallite yielding reflections corresponding to the supercell revealed it to be monoclinic, with the unit cell parameters a = 26.811(2) Å, b = 15.4798(2) Å, c = 9.414(2) Å, β = γ = 90° and α = 90.0(3)°. The average crystal structure was refined, using the subcell with a = 8.937(2) Å, b = 15.479(2) Å, c = 9.414(2) Å, β = γ = 90° and α = 90.0(3)°, space group Cm11, and Z = 4, to R_I = 3.24% and R_wI = 3.44%. The structure can be described as an hexagonal close packing layers of Nb₆ octahedra, Ba, and O atoms (A1, A2) and layers of O atoms (B1, B2), appearing in the packing sequence: A1B1A2B2. The Nb₆ octahedra are found in isolated Nb₆O₁₂O₆ clusters, and the Ti atoms in Ti₃O₁₃ and Ti₃O₁₀ units in octahedral and tetrahedral voids formed by O atoms, respectively. The Ti positions were found to be only partly occupied. Microanalysis indicates that some Nb atoms are located in the Ti₃ triangles. A model is presented that interprets these not fully occupied Ti₃ triangles as a result of a superimposing of three different structures. Two of these consist of two fused Ti₃O₁₃ units, forming an Ti₆O₁₉ unit, and a Ti₃O₁₀ unit, while the third consists of alternating Ti₃O₁₃ units.     

Synthesis of Tetracyclic Analogues of Calcitriol (1α,25‐Dihydroxyvitamin D3) with Side‐Chain‐Locked Spatial Orientations at C(20)

We present our first results on the synthesis of a new class of conformationally restricted vitamin D analogues bearing an extra five‐membered ring formed by linking C(18) and C(21). Two analogues of calcitriol ( 1 ) with unsaturations at the extra ring and the lateral chain were prepared. The triene system was introduced by the convergent Wittig Horner approach developed by Lythgoe [8] and F. Hoffmann‐La Roche [9]. The key steps in the preparation of the requisite fragments were: i) the long‐distance functionalization of ketal 11 at C(18), ii) the ring closure on 15 through an intramolecular aldol condensation to give the α,β‐unsaturated ketone 10 , and iii) the Pd‐catalyzed installation of the side chains.