Models of steroid binding based on the minimum deviation of structurally assigned 13C NMR spectra analysis (MiDSASA)

This paper develops a quantitative k-nearest neighbors modeling technique. The technique is used to demonstrate that a compound's biological binding activity to a receptor can be calculated from the minimum of the square root of the sum of squared deviations (SSSD) of a structurally assigned chemical shift on a template between the unknown compound to be predicted and a set of known compounds with known activities. When building models of biological activity, nonlinear relationships are built into the input training data. If a model is developed by selecting only compounds with minimum structurally assigned chemical shift deviations from the unknown compound, some of the nonlinear relationships can be removed. The smaller the total chemical shift deviation between a compound with known activity and another compound with unknown activity, the more likely it will have similar biological, chemical, and physical properties. This means that a model can be produced without rigorous statistics or neural networks. This technique is similar to structure-activity relationship (SAR) modeling, but instead of relying on substructure fragments to produce a model, this new model is based on minimum chemical shift differences on those substructure fragments. We refer to this method as minimum deviation of structurally assigned spectra analysis (MiDSASA) modeling. Modeling by the minimum deviation concept can be applied to other chemoinformatic data analyses such as metabolite concentrations in metabolic pathways for metabolomics research. A MiDSASA template model for 30 steroids binding the corticosterone binding globulin based on the activity factors of the two nearest compounds had a correlation of 0.88. A MiDSASA template model for 50 steroids binding the aromatse enzyme based on the average activity of the four nearest compounds had a correlation of 0.71.     

Investigative proteomics: identification of an unknown plant virus from infected plants using mass spectrometry

We describe the identification of a previously uncharacterized plant virus that is capable of infecting Nicotiana spp. and Arabidopsis thaliana. Protein extracts were first prepared from leaf tissue of uninfected tobacco plants, and the proteins were visualized with two-dimensional electrophoresis (2-DE). Matching gels were then run using protein extracts of a tobacco plant infected with tobacco mosaic virus (TMV). After visual comparison, the proteins spots that were differentially expressed in infected plant tissues were cut from the gels and analyzed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Tandem mass spectrometry data of individual peptides was searched with SEQUEST. Using this approach we demonstrated a successful proof-of-concept experiment by identifying TMV proteins present in the total protein extract. The same procedure was then applied to tobacco plants infected with a laboratory viral isolate of unknown identity. Several of the differentially expressed protein spots were identified as proteins of potato virus X (PVX), thus successfully identifying the causative agent of the uncharacterized viral infection. We believe this demonstrates that HPLC-MS/MS can be used to successfully characterize unknown viruses in infected plants.     

Hexaphosphapentaprismane: a new gateway to organophosphorus cage compound chemistry

Several independent synthetic routes are described leading to the formation of a novel unsaturated tetracyclic phosphorus carbon cage compound tBu4C4P6 (1), which undergoes a light-induced valence isomerization to produce the first hexaphosphapentaprismane cage tBu4C4P6 (2). A second unsaturated isomer tBu4C4P6 (9) of 1 and the bis-[W(CO)5] complex 13 of 1 are stable towards similar isomerization reactions. Another starting material for the synthesis of the hexaphosphapentaprismane cage tBu4C4P6 (2) is the trimeric mercury complex [(tBu4C4P6)Hg]3 (11), which undergoes elimination of mercury to afford the title compound 2. Single-crystal X-ray structural determinations have been carried out on compounds 1, 2, 9, 11, and 13.     

The simplest coronoids: Hollow hexagons

Hollow hexagons form a subclass of primitive coronoid systems. The macrocyclic aromatic hydrocarbon kekulene corresponds to a hollow hexagon. The hollow hexagons for given numbers of hexagonal units (h) were enumerated by computer aid, but also an analytical solution for the numbers of hollow hexagons was achieved. For the Kekulé structure counts (k) of a hollow hexagon a general formula is reported. Also the maximum and minimumK numbers are considered.This article is Part VI of the series Enumeration and Classification of Coronoid Hydrocarbons. For Part V, see ref. [36].     

Role of thiol-disulfide exchange in insulin binding to its receptor.

The effects of reduction by DTT, oxidation by DTNB and treatment with NEM on the thiol contents and insulin binding to its receptor in mice liver membranes were studied. Reduction with DTT leads to a parallel increase in the thiol content and the specific binding of insulin to the membrane. Scatchard analysis of the results shows little change in the number of binding sites but a twofold increase of the binding constant. Washing the membrane with bound insulin by a DTT containing buffer results in a more marked increase in the release of bound insulin than washing with buffer alone, suggesting that part of the insulin is bound to its receptor by covalent disulfide linkages through a thiol-disulfide exchange reaction and reduction with DTT leads to a marked increase in this "disulfide-linked" insulin. Treatment with DTNB or NEM of the DTT-reduced membrane seems to reverse the effect of DTT reduction, although the reaction of the untreated membrane with DTNB or NEM had little or no effect on the specific binding of insulin. It is suggested that initially, part of the thiols responsible for the exchange reaction may not be available for reaction with DTNB and reduction with DTT generates further thiols leading to increased specific binding in general and increased insulin binding to the receptor through covalent disulfide linkages in particular.     

Clays as selective catalysts in organic synthesis

Suitably modified smectite clays can be very selective catalysts for a wide range of organic reactions. While it has long been known that such materials can act as Bronsted and Lewis acids, it has been shown recently that they are also effective Diels-Alder catalysts. A selection of illustrative reactions is given which emphasises their wide range of use, their selectivity, and the ease of work-up after reaction. In each case, mechanistic information is presented, e.g., on the site of reaction (whether interlayer or surface), rate determining steps, etc. The regiochemical consequences of the restricted reaction space are stressed.Based on material presented at the Fourth International Symposium on Inclusion Phenomena and the Third International Symposium on Cyclodextrins, Lancaster, U.K., 20–25 July 1986.     

Collision-induced dissociations of substituted benzyl anions: Deprotonated 2-Phenyl-1,3-dithiane

Deprotonated 2-phenyl-1,3-dithiane undergoes competitive losses of H˙, C₃H₆ C₂H₄S, C₃H₄S, C₇H₆S, C₁₀H₁₀ and C₁₀H₁₀S upon collisional activation. The elimination of H occurs from the phenyl ring. The loss of C₃H₆ occurs by simple cleavage of the dithiane ring. All other processes involve specific proton transfer followed by either cleavage or internal nucleophilic displacement.     

MEASUREMENT OF CELL LYSIS BY LIGHT SCATTERING

Abstract— A method is presented which is capable of continuously monitoring the degree of hemolysis in erythrocyte suspensions too dilute to be monitored by conventional light transmission techniques. Scattered light is used to non-destructively assess hemolysis in sparse monolayers which are particularly well suited to many photohemolytic studies. The small angle scattering (<10°), measured here, shows a transient decline as cells settle in a culture dish and then is constant if no lysis occurs. Lysis is indicated by a decrease in scattered light to < 20% of initial intensity when lysis is complete. The light used to monitor lysis is restricted to wavelengths longer than 700 nm which is outside the absorption band of many. photosensitizers of current interest, and is a wavelength range at which light scattering is relatively independent of changes in cell volume. In photohemolytic studies with phloxine B lysis values from light scattering are shown to correlate well with lysis values from hemoglobin release. An apparatus is described which is capable of periodically measuring lysis in eight suspensions without intervention by the experimenter.