Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model

Cross-beta amyloid is implicated in over 20 human diseases. Experiments suggest that specific sequence elements within amyloidogenic proteins play a major role in seeding amyloid formation. Identifying these seeding sequences is important for rationalizing the molecular mechanisms of amyloid formation and for elaborating therapeutic strategies that target amyloid. Theoretical techniques play an important role in facilitating the identification and structural characterization of putative seeding sequences; most amyloid species are not amenable to high resolution experimental structure techniques. In this study we have combined a coarse-grained physicochemical protein model with a highly efficient Monte Carlo sampling technique to identify amyloidogenic sequences in four proteins for which respective experimental peptide fragmentation data exist. Peptide sequences were defined as amyloidogenic if the ensemble structure predicted for three interacting peptides described a stable and regular three-stranded beta-sheet. For such peptides, free energies were calculated to provide a measure of amyloid propensity. The overall agreement between the experimental and predicted data is good, and we correctly identify several self-recognition motifs proposed to define the cross-beta amyloid fibril architectures of two of the proteins. Our results compare very favorably with those obtained using atomistic molecular dynamics methods, though our simulations are 30-40 times faster.     

A collaborative hit-to-lead investigation leveraging medicinal chemistry expertise with high throughput library design, synthesis and purification capabilities

High throughput screening (HTS) campaigns, where laboratory automation is used to expose biological targets to large numbers of materials from corporate compound collections, have become commonplace within the lead generation phase of pharmaceutical discovery. Advances in genomics and related fields have afforded a wealth of targets such that screening facilities at larger organizations routinely execute over 100 hit-finding campaigns per year. Often, 10(5) or 10(6) molecules will be tested within a campaign/cycle to locate a large number of actives requiring follow-up investigation. Due to resource constraints at every organization, traditional chemistry methods for validating hits and developing structure activity relationships (SAR) become untenable when challenged with hundreds of hits in multiple chemical families per target. To compound the issue, comparison and prioritization of hits versus multiple screens, or physical chemical property criteria, is made more complex by the informatics issues associated with handling large data sets. This article describes a collaborative research project designed to simultaneously leverage the medicinal chemistry and drug development expertise of the Novartis Institutes for Biomedical Research Inc. (NIBRI) and ArQule Inc.'s high throughput library design, synthesis and purification capabilities. The work processes developed by the team to efficiently design, prepare, purify, assess and prioritize multiple chemical classes that were identified during high throughput screening, cheminformatics and molecular modeling activities will be detailed.     

Gas‐phase functionalized carbon‐carbon coupling reactions catalyzed by Ni (II) complexes

Gas‐phase C―C coupling reactions mediated by Ni (II) complexes were studied using a linear quadrupole ion trap mass spectrometer. Ternary nickel cationic carboxylate complexes, [(phen)Ni (OOCR¹)]⁺ (where phen = 1,10‐phenanthroline), were formed by electrospray ionization. Upon collision‐induced dissociation (CID), they extrude CO₂ forming the organometallic cation [(phen)Ni(R¹)]⁺, which undergoes gas‐phase ion‐molecule reactions (IMR) with acetate esters CH₃COOR² to yield the acetate complex [(phen)Ni (OOCCH₃)]⁺ and a C―C coupling product R¹‐R². These Ni(II)/phenanthroline‐mediated coupling reactions can be performed with a variety of carbon substituents R¹ and R² (sp³, sp², or aromatic), some of them functionalized. Reaction rates do not seem to be strongly dependent on the nature of the substituents, as sp³‐sp³ or sp²‐sp² coupling reactions proceed rapidly. Experimental results are supported by density functional theory calculations, which provide insights into the energetics associated with the C―C bond coupling step.     

Interfacing Formate Dehydrogenase with Metal Oxides for the Reversible Electrocatalysis and Solar‐Driven Reduction of Carbon Dioxide

The integration of enzymes with synthetic materials allows efficient electrocatalysis and production of solar fuels. Here, we couple formate dehydrogenase ( FDH ) from Desulfovibrio vulgaris Hildenborough (DvH) to metal oxides for catalytic CO₂ reduction and report an in‐depth study of the resulting enzyme–material interface. Protein film voltammetry (PFV) demonstrates the stable binding of FDH on metal‐oxide electrodes and reveals the reversible and selective reduction of CO₂ to formate. Quartz crystal microbalance (QCM) and attenuated total reflection infrared (ATR‐IR) spectroscopy confirm a high binding affinity for FDH to the TiO₂ surface. Adsorption of FDH on dye‐sensitized TiO₂ allows for visible‐light‐driven CO₂ reduction to formate in the absence of a soluble redox mediator with a turnover frequency (TOF) of 11±1 s^?1. The strong coupling of the enzyme to the semiconductor gives rise to a new benchmark in the selective photoreduction of aqueous CO₂ to formate.     

Silver-mediated trifluoromethylation of arenes using TMSCF3

The silver-mediated C-H trifluoromethylation of aromatic substrates using TMSCF(3) is described. The development, optimization, and scope of these transformations are reported. AgCF(3) intermediates are proposed.     

(−)‐Englerin A is a Potent and Selective Activator of TRPC4 and TRPC5 Calcium Channels

Current therapies for common types of cancer such as renal cell cancer are often ineffective and unspecific, and novel pharmacological targets and approaches are in high demand. Here we show the unexpected possibility for the rapid and selective killing of renal cancer cells through activation of calcium‐permeable nonselective transient receptor potential canonical (TRPC) calcium channels by the sesquiterpene (?)‐englerin A. This compound was found to be a highly efficient, fast‐acting, potent, selective, and direct stimulator of TRPC4 and TRPC5 channels. TRPC4/5 activation through a high‐affinity extracellular (?)‐englerin A binding site may open up novel opportunities for drug discovery aimed at renal cancer.     

PAH formation under single collision conditions: reaction of phenyl radical and 1,3-butadiene to form 1,4-dihydronaphthalene

The crossed beam reactions of the phenyl radical (C(6)H(5), X(2)A(1)) with 1,3-butadiene (C(4)H(6), X(1)A(g)) and D6-1,3-butadiene (C(4)D(6), X(1)A(g)) as well as of the D5-phenyl radical (C(6)D(5), X(2)A(1)) with 2,3-D2-1,3-butadiene and 1,1,4,4-D4-1,3-butadiene were carried out under single collision conditions at collision energies of about 55 kJ mol(-1). Experimentally, the bicyclic 1,4-dihydronaphthalene molecule was identified as a major product of this reaction (58 ± 15%) with the 1-phenyl-1,3-butadiene contributing 34 ± 10%. The reaction is initiated by a barrierless addition of the phenyl radical to the terminal carbon atom of the 1,3-butadiene (C1/C4) to form a bound intermediate; the latter underwent hydrogen elimination from the terminal CH(2) group of the 1,3-butadiene molecule leading to 1-phenyl-trans-1,3-butadiene through a submerged barrier. The dominant product, 1,4-dihydronaphthalene, is formed via an isomerization of the adduct by ring closure and emission of the hydrogen atom from the phenyl moiety at the bridging carbon atom through a tight exit transition state located about 31 kJ mol(-1) above the separated products. The hydrogen atom was found to leave the decomposing complex almost parallel to the total angular momentum vector and perpendicularly to the rotation plane of the decomposing intermediate. The defacto barrierless formation of the 1,4-dihydronaphthalene molecule involving a single collision between a phenyl radical and 1,3-butadiene represents an important step in the formation of polycyclic aromatic hydrocarbons (PAHs) and their partially hydrogenated counterparts in combustion and interstellar chemistry.     

Comment: 2004's fastest organic and biomolecular chemistry!

In January 2004, the Royal Society of Chemistry launched Organic & Biomolecular Chemistry (OBC) - a journal promising to provide high quality research from all aspects of synthetic, physical and biomolecular organic chemistry. The journal was set to build upon the foundations laid down by its predecessor publications (J. Chem. Soc., Perkin Trans. 1 and J. Chem. Soc., Perkin Trans. 2) as well as complement the subject coverage already published in prestigious general chemistry journals such as Chemical Communications and Chemical Society Reviews. Nearly two years on, just how is the programme developing and what can the community expect to see from the Royal Society of Chemistry (RSC)?     

A series of novel lanthanide polyoxometalates: condensation of building blocks dependent on the nature of rare earth cations

A series of novel lanthanide polyoxomolybdates was synthesized by reaction of lanthanide cations with the Anderson type anion (TeMo(6)O(24))(6-). The polyoxometalates K(6n)(TeMo(6)O(24))(n)[(Ln(H(2)O)(7))(2)(TeMo(6)O(24))](n)[middle dot]16nH(2)O (Ln = Eu, Gd) and K(3n)[Ln(H(2)O)(5)(TeMo(6)O(24))](n)[middle dot]6nH(2)O (Ln = Tb, Dy, Ho, Er) were characterized by X-ray structure analysis, elemental analysis and IR spectroscopy. We found that the solid-state structures of Ln/(TeMo(6)O(24))(6-) compounds are strongly dependent on the lanthanide cations, and therefore represent a rare example for different arrangements of building units depending on the nature of the rare earth cations. While the Eu(3+) and Gd(3+) cations achieve ninefold coordination by seven water molecules and two terminal oxygen atoms of the (TeMo(6)O(24))(6-) anions, the Tb(3+), Dy(3+), Ho(3+) and Er(3+) cations are coordinated by five water molecules, two terminal oxygen atoms and one molybdenum-bridging oxygen atom belonging to the (TeMo(6)O(24))(6-) anion. The europium and gadolinium substituted compounds contain infinite one-dimensional [(Ln(H(2)O)(7))(2)(TeMo(6)O(24))](n) chains; the terbium, dysprosium, holmium and erbium compounds contain infinite one-dimensional [Ln(H(2)O)(5)(TeMo(6)O(24))](n)(3n-) chains.     

Non-linearity of calibration in the determination of anions by ion-chromatography with suppressed conductivity detection

Traces of simple inorganic anions may be determined by chromatographic separation with an alkaline eluent and conductimetric detection, which involves “suppressing” the background conductivity of the eluent by neutralization to form a sparingly dissociated species. Over a wide range of determinand concentration, e.g., two decades, non-linearity of the calibration may become evident, leading to errors of up to 100% at lower concentrations if linearity is assumed (a linear fit of the data usually gives a correlation coefficient>0.99, which may lead to false confidence). The curvature arises from displacement of eluent ions by the determinand and the consequent re-equilibration of the conjugate acid in the suppressed eluate. Even if the distribution of determinand in the peak is ideally Gaussian, the observed conductivity peak may be distorted and calibration will then be non-linear. The best linearity is obtained with the most strongly basic eluent, but other characteristics must also be considered, e.g., run time, peak separation. With a carbonate eluent, the curvature is demonstrated empirically for chloride, nitrate and sulphate calibrations. A second-order fit gives errors of < 10%. With a more strongly basic borate eluent, the deviation from linearity is negligible, but elution times are longer and may be inconvenient in some circumstances.