Shape signatures: new descriptors for predicting cardiotoxicity in silico

Shape Signatures is a new computational tool that is being evaluated for applications in computational toxicology and drug discovery. The method employs a customized ray-tracing algorithm to explore the volume enclosed by the surface of a molecule and then uses the output to construct compact histograms (i.e., signatures) that encode for molecular shape and polarity. In the present study, we extend the application of the Shape Signatures methodology to the domain of computational models for cardiotoxicity. The Shape Signatures method is used to generate molecular descriptors that are then utilized with widely used classification techniques such as k nearest neighbors ( k-NN), support vector machines (SVM), and Kohonen self-organizing maps (SOM). The performances of these approaches were assessed by applying them to a data set of compounds with varying affinity toward the 5-HT(2B) receptor as well as a set of human ether-a-go-go-related gene (hERG) potassium channel inhibitors. Our classification models for 5-HT(2B) represented the first attempt at global computational models for this receptor and exhibited average accuracies in the range of 73-83%. This level of performance is comparable to using commercially available molecular descriptors. The overall accuracy of the hERG Shape Signatures-SVM models was 69-73%, in line with other computational models published to date. Our data indicate that Shape Signatures descriptors can be used with SVM and Kohonen SOM and perform better in classification problems related to the analysis of highly clustered and heterogeneous property spaces. Such models may have utility for predicting the potential for cardiotoxicity in drug discovery mediated by the 5-HT(2B) receptor and hERG.

Polyfunctional compounds containing the 4,6-dialkoxy-7-arylthioheptene moiety as synthetically useful intermediates. The course of lewis acid-induced transformations

Data on the selectivity of the Lewis acids induced transformations of the title compounds are presented, and the routes leading to formation of products containing either cyclohexane or 1,3-diene units are described.

Melting of a quasi-two-dimensional metallic system

We analyze the melting of a quasi-two-dimensional metallic system using the results of a series of Monte Carlo simulations of an array of Pb atoms. The system was chosen to model the melting behavior observed for the monolayer of Pb that segregates in the liquid-vapor interface of a dilute Pb in Ga alloy [B. Yang et al., Proc. Natl. Acad. Sci. USA 96, 13 009 (1999)]. Our calculations employed a realistic pair interaction potential between lead pseudoatoms, one that is known to describe accurately the properties of the three-dimensional metal near the melting point. Our results reveal that in the quasi-two-dimensional Pb system melting is a two-stage process which proceeds through formation of a stable intermediate hexatic phase, in agreement with the prediction of the Kosterlitz-Thouless-Halperin-Nelson-Young theory. Both the solid-to-hexatic and the hexatic-to-liquid transitions are found to be first order in our simulations.