2D binary QSAR modeling of LPA3 receptor antagonism

Comparative modeling of lipid receptors

Comparative modeling is a powerful technique to generate models of proteins from families already represented by members with experimentally characterized three-dimensional structures. The method is particularly important for modeling membrane-bound receptors in the G Protein-Coupled Receptor (GPCR) family, such as many of the lipid receptors (such as the cannabinoid, prostanoid, lysophosphatidic acid, sphingosine 1-phosphate, and eicosanoid receptor family members), as these represent particularly challenging targets for experimental structural characterization methods. Although challenging modeling targets, these receptors have been linked to therapeutic indications that vary from nociception to cancer, and thus are of interest as therapeutic targets. Accurate models of lipid receptors are therefore valuable tools in the drug discovery and optimization phases of therapeutic development. This chapter describes the construction and evaluation of comparative structural models of lipid receptors beginning with the selection of template structures.

An application of two MIFs-based tools (Volsurf+ and Pentacle) to binary QSAR: the case of a palinurin-related data set of non-ATP competitive glycogen synthase kinase 3β (GSK-3β) inhibitors

VolSurf+ and GRIND descriptors extract the information present in MIFs calculated by GRID: the first are simpler to interpret and generally applied to ADME-Tox topics, whereas the latter are more sophisticated and thus more suited for pharmacodynamics events. Here we present a study which compares binary QSAR models obtained with VolSurf+ descriptors and GRIND for a data set of non-ATP competitive GSK-3β inhibitors chemically related to palinurin for which the biological activity is expressed in binary format. Results suggest not only that the simpler Volsurf+ descriptors are good enough to predict and chemically interpret the investigated phenomenon but also a bioactive conformation of palinurin which may guide future design of ATP non-competitive GSK-3 inhibitors.