QSAR modeling using automatically updating correction libraries: application to a human plasma protein binding model

It is assumed that compounds occupying the same region of model space will be subject to similar errors in prediction, and hence, where these errors are known, they can be applied to predictions. Thus, any available measured data can be used to refine predictions of query compounds. This study describes the application of a correction library to a human plasma protein binding model. Compounds that have been measured since the model was built are entered into the library to improve predictions of current compounds. Time-series simulations were conducted to measure the time dependence of the correction library. This study demonstrates significant improvements in predictions where a library is applied, compared with both a static model and an updating model that includes recently measured data.     

Metalloporphyrin Dendrimers with Folding Arms

Rigid and flexible linkers are combined in the new dendrimer shown schematically in the picture, which contains nine metalloporphyrin units (Porph). The construction is such that the four “arms” of the dendrimer can fold in a cooperative and predetermined manner in response to added 1,4-diazabicyclo[2.2.2]octane (DABCO).     

Synthesis and characterisation of low density porous polymers by reversible addition-fragmentation chain transfer (RAFT)

PolyHIPE foams with densities of 0.05–0.1 g cm^?3 have been prepared by the polymerisation of the continuous phase of high internal phase emulsions (HIPEs). The internal aqueous phase in HIPE occupies more than 74 % of the total volume, which leads to highly porous and open-cell morphologies. In this paper a method of preparing polyHIPE foams by using reversible addition-fragmentation chain transfer (RAFT) polymerisation has been investigated. Polystyrene-co-polymethyl methacrylate (PS-co-PMMA) has been studied and by using a variety of characterisation methods, it was possible to compare the polyHIPEs prepared by the conventional free radical polymerisation (FRP) to those by RAFT polymerisation. Scanning electron microscopy images have confirmed the presence of a cellular polyHIPE structure. PS-co-PMMA polyHIPEs made by RAFT have significantly narrower molecular weight distribution with values for the polydispersity index (PDI) for PS-co-PMMA between 1.46 and 2.08 compared to 4.68 observed by FRP. The effects of different concentrations of the RAFT agent on structure, glass transition temperature (T _g) and PDI of PS-co-PMMA polyHIPE foams are presented.     

Structural characterization of ß-amyloid oligomer-aggregates by ion mobility mass spectrometry and electron spin resonance spectroscopy

Formation and accumulation of fibrillar plaques and aggregates of ß-amyloid peptide (Aß) in brain have been recognized as characteristics of Alzheimer’s disease (AD). Oligomeric aggregates of Aß are considered critical intermediates leading to progressive neurodegeneration; however, molecular details of the oligomerization and aggregation pathway and the structures of Aß-oligomers are hitherto unclear. Using an in vitro fibril formation procedure of Aß(1–40), ß-amyloid aggregates were prepared and insoluble aggregates separated from soluble products by centrifugation. In this study, ion mobility mass spectrometry (IM-MS) was applied in combination with electron paramagnetic resonance spectroscopy (EPR) to the identification of the components of Aß-oligomers, and to their structural and topographical characterization. The formation of Aß-oligomers and aggregates was monitored by gel electrophoresis, and Aß-oligomer bands were identified by in-gel tryptic digestion and matrix-assisted laser desorption ionization–mass spectrometry (MALDI-MS) to consist predominantly of Aß(1–40) peptide. First, ion mobility-MS studies of soluble Aß-aggregates prepared by incubation for 5 days were performed on a quadrupole time-of-flight mass spectrometer and revealed (1) the presence of at least two different conformational states, and (2), the formation of Met-35 oxidized products. For estimation of the size of Aß-aggregates using EPR spectroscopy, a modified Aß(1–40) peptide containing an additional N-terminal cysteine residue was prepared, and a 3-(2-iodoacetamido)-2,2,5,5-tetramethyl-1-pyrrolidinyloxy radical spin label derivative (IPSL) was coupled by S-alkylation. The EPR spectra of the spin-labeled Cys-Aß(1–40) oligomers were matched with spectra simulations using a multi-component simulation strategy, resulting in complete agreement with the gel electrophoresis results.     

Giant excitonic Zeeman splittings in colloidal Co2+ -doped ZnSe quantum dots

Colloidal Co(2+):ZnSe diluted magnetic semiconductor quantum dots (DMS-QDs) were prepared by the hot injection method and studied spectroscopically. Ligand-field electronic absorption and magnetic circular dichroism (MCD) spectra confirm homogeneous substitutional speciation of Co(2+) in the ZnSe QDs. Absorption spectra collected at various times throughout the syntheses reveal that dopants are absent from the central cores of the QDs but are incorporated at a constant concentration during nanocrystal growth. The undoped cores are associated with dopant exclusion from the ZnSe critical nuclei. Analysis of low-temperature electronic absorption and MCD spectra revealed excitonic Zeeman splitting energies (DeltaE(Zeeman)) of these Co(2+):ZnSe QDs that were substantially smaller than anticipated from bulk Co(2+):ZnSe data. This reduction in DeltaE(Zeeman) is explained quantitatively by the absence of dopants from the QD cores, where dopant-exciton overlap would be greatest. Since dopant exclusion from nucleation appears to be a general phenomenon for DMS-QDs grown by direct chemical methods, we propose that DeltaE(Zeeman) will always be smaller in colloidal DMS-QDs grown by such methods than in the corresponding bulk materials.     

Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins

Agouti (ASIP) and Agouti-related protein (AgRP) are endogenous antagonists of melanocortin receptors that play critical roles in the regulation of pigmentation and energy balance, respectively, and which arose from a common ancestral gene early in vertebrate evolution. The N-terminal domain of ASIP facilitates antagonism by binding to an accessory receptor, but here we show that the N-terminal domain of AgRP has the opposite effect and acts as a prodomain that negatively regulates antagonist function. Computational analysis reveals similar patterns of evolutionary constraint in the ASIP and AgRP C-terminal domains, but fundamental differences between the N-terminal domains. These studies shed light on the relationships between regulation of pigmentation and body weight, and they illustrate how evolutionary structure function analysis can reveal both unique and common mechanisms of action for paralogous gene products.     

Thiamine models and perspectives on the mechanism of action of thiamine-dependent enzymes

Thiamine dependent enzymes catalyze ligase and lyase reactions near a carbonyl moiety. Chemical models for these reactions serve as useful tools to substantiate a detailed mechanism of action. This tutorial review covers all such studies performed thus far, emphasizing the role of each part around the active site and the conformation of the cofactor during catalysis.