Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening

Molecular descriptor (2D) and three dimensional (3D) shape based similarity methods are widely used in ligand based virtual drug design. In the present study pairwise structure comparisons among a set of 4858 DTP compounds tested in the NCI60 tumor cell line anticancer drug screen were computed using chemical hashed fingerprints and 3D molecule shapes to calculate 2D and 3D similarities, respectively. Additionally, pairwise biological activity similarities were calculated by correlating the 60 element vectors of pGI50 values corresponding to the cytotoxicity of the compounds across the NCI60 panel. Subsequently, we compared the power of 2D and 3D structural similarity metrics to predict the toxicity pattern of compounds. We found that while the positive predictive value and sensitivity of 3D and molecular descriptor based approaches to predict biological activity are similar, a subset of molecule pairs yielded contradictory results. By simultaneously requiring similarity of biological activities and 3D shapes, and dissimilarity of molecular descriptor based comparisons, we identify pairs of scaffold hopping candidates displaying characteristic core structural changes such as heteroatom/heterocycle change and ring closure. Attempts to discover scaffold hopping candidates of mitoxantrone recovered known Topoisomerase II (Top2) inhibitors, and also predicted new, previously unknown chemotypes possessing in vitro Top2 inhibitory activity

The Wiener polarity index of benzenoid systems and nanotubes

In this paper, we consider a molecular descriptor called the Wiener polarity index, which is defined as the number of unordered pairs of vertices at distance three in a graph. Molecular descriptors play a fundamental role in chemistry, materials engineering, and in drug design since they can be correlated with a large number of physico-chemical properties of molecules. As the main result, we develop a method for computing the Wiener polarity index for two basic and most commonly studied families of molecular graphs, benzenoid systems and carbon nanotubes. The obtained method is then used to find a closed formula for the Wiener polarity index of any benzenoid system. Moreover, we also compute this index for zig-zag and armchair nanotubes

A Novel Version of the Edge-Szeged Index

A novel version of the edge-Szeged index is proposed in parallel to the revised (vertex) Szeged index, and some properties, especially lower and upper bounds are established for this molecular descriptor. (doi: 10.5562/cca1889