Using Chemical Structure Information to Develop Predictive Models for In Vitro Toxicokinetic Parameters to Inform High-throughput Risk-assessment

The toxicokinetic (TK) parameters fraction of the chemical unbound to plasma proteins and metabolic clearance are critical for relating exposure and internal dose when building in vitro-based risk assessment models. However, experimental toxicokinetic studies have only been carried out on limited chemicals of environmental interest (~1000 chemicals with TK data relative to tens of thousands of chemicals of interest). This work evaluated the utility of chemical structure information to predict TK parameters in silico; development of cluster-based read-across and quantitative structure-activity relationship models of fraction unbound or fub (regression) and intrinsic clearance or Cl_int (classification and regression) using a dataset of 1487 chemicals; utilization of predicted TK parameters to estimate uncertainty in steady-state plasma concentration (C_ss); and subsequent in vitro-in vivo extrapolation analyses to derive bioactivity-exposure ratio (BER) plot to compare human oral equivalent doses and exposure predictions using androgen and estrogen receptor activity data for 233 chemicals as an example dataset. The results demonstrate that fub is structurally more predictable than Cl_int. The model with the highest observed performance for fub had an external test set RMSE/σ=0.62 and R²=0.61, for Cl_int classification had an external test set accuracy = 65.9%, and for intrinsic clearance regression had an external test set RMSE/σ=0.90 and R²=0.20. This relatively low performance is in part due to the large uncertainty in the underlying Cl_int data. We show that C_ss is relatively insensitive to uncertainty in Cl_int. The models were benchmarked against the ADMET Predictor software. Finally, the BER analysis allowed identification of 14 out of 136 chemicals for further risk assessment demonstrating the utility of these models in aiding risk-based chemical prioritization.

Changes in global gene and protein expression during early mouse liver carcinogenesis induced by non-genotoxic model carcinogens oxazepam and Wyeth-14,643

We hypothesized that the mouse liver tumor response to non-genotoxic carcinogens would involve some common early gene and protein expression changes that could ultimately be used to predict chemical hepatocarcinogenesis. In order to identify a panel of genes to test, we analyzed global differences in gene and protein expression in livers from B6C3F1 mice following dietary treatment with two rodent carcinogens, the benzodiazepine anti-anxiety drug oxazepam (2500 p.p.m.) and the hypolipidemic agent Wyeth (Wy)-14,643 (500 p.p.m.) compared with livers from untreated mice. Male mice were exposed for 2 weeks and 1, 3 or 6 months to oxazepam or Wy-14,643 in an age-matched study design. By histopathological evaluation, no liver preneoplastic foci or tumors were detected at 6 months in treated or control groups. By cDNA microarray analysis [NIEHS Mouse Chip (8700 genes); n = 3 individual livers/group, four hybridizations/sample], expression of 36 genes or 220 genes were changed relative to control livers following 6 months of oxazepam or Wy-14,643 treatment, respectively. To obtain a more comprehensive picture of gene/protein expression changes, we also conducted a proteomics study by 2D-gel electrophoresis followed by matrix assisted laser desorption/ionization-mass spectrometry on cytoplasmic, nuclear, and microsomal subcellular fractions of the same liver samples utilized for the cDNA microarray analysis. Real-time PCR, western blot analysis and immunohistochemistry were utilized for validation and to expand the results to other time points. Cyp2b20, growth arrest- and damage-inducible gene beta (Gadd45beta), tumor necrosis factor alpha-induced protein 2 and insulin-like growth factor binding protein 1 (Igfbp5) genes and proteins were upregulated by oxazepam, and Cyp2b20, Cyclin D1, proliferating cell nuclear antigen, Igfbp5, Gadd45beta and cell death-inducing DNA fragmentation factor alpha subunit-like effector A exhibited higher expression after Wy-14,643 treatment. Most of these genes/proteins were also deregulated at 2 weeks. There appeared to be more distinct than common changes in the expression of carcinogenesis-related genes/proteins between the two compounds, suggesting that the major carcinogenic pathways are different for these compounds and may be distinct for different chemical classes.