Orthogonal assay for validation of Tox21 PPARγ data and applicability to in silico prediction model

High-throughput screening data from the Tox21 database is used for prioritizing hazardous chemicals and building in silico-based toxicity prediction models. One of the Tox21 dataset, peroxisome proliferator-activated receptor-gamma (PPARγ), a nuclear receptor superfamily, identified various endpoints in HEK293 cells. PPARγ mediates various toxic effects when its receptors are activated or inhibited by ligands such as thiazolidinedione and GW9662. In this study, an orthogonal assay was constructed to verify the effectiveness of the Tox21 PPARγ data, and the effect of highly reliable data on in silico model construction was investigated. The orthogonal assay was a reporter gene assay based on the PPARγ ligand binding domain in CV-1 cells. Only 39% of agonists and 55% of antagonists had similar responses in CV-1 and HEK293 cells. Thus, the effectiveness of Tox21 data on PPARγ may vary depending on the cell line. However, in silico PLS-DA analysis with only high-reliability data (i.e., the same response in both cell lines), yielded more accurate prediction of the activity of potential chemical ligands, despite the small number of samples. Thus, obtaining reliable chemical screening data for PPARγ through orthogonal analysis, even for only limited chemicals, supports the construction of highly predictive in silico models with improved screening efficiency.

A Familiar Protein-Ligand Interaction Revisited with Multiple Methods

The interaction of hen egg white lysozyme with the trisaccharide tri-N-acetyl glucosamine has been well-characterized by biophysical methods and structural biology. In this chapter, we present a series of experiments designed to detect and quantify that interaction using several commonly available biophysical methods: thermal shift assay, fluorescence intensity, microscale thermophoresis, isothermal titration calorimetry, and surface plasmon resonance.These experiments have been used for teaching and troubleshooting in a core facility. By taking a set of representative data from several years of practical courses, we are able to demonstrate the robustness of the protocols, calculate confidence intervals for the dissociation constant from each method, and illustrate the degree of consistency between those methods when applied to a simple system in a single location by different experimenters.