Use of in Vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in Vivo Toxicity

Alexander Sedykh, Hao Zhu, Hao Tang, Liying Zhang, Ann Richard, Ivan Rusyn, Alexander Tropsha

Research output: Contribution to journalArticle

66 Citations (Scopus)

Abstract

Background: Quantitative high-throughput screening (qHTS) assays are increasingly being used to inform chemical hazard identification. Hundreds of chemicals have been tested in dozens of cell lines across extensive concentration ranges by the National Toxicology Program in collaboration with the National Institutes of Health Chemical Genomics Center. Objectives: Our goal was to test a hypothesis that dose-response data points of the qHTS assays can serve as biological descriptors of assayed chemicals and, when combined with conventional chemical descriptors, improve the accuracy of quantitative structure-activity relationship (QSAR) models applied to prediction of in vivo toxicity end points. Methods: We obtained cell viability qHTS concentration-response data for 1,408 substances assayed in 13 cell lines from PubChem; for a subset of these compounds, rodent acute toxicity half-maximal lethal dose (LD50) data were also available. We used the k nearest neighbor classification and random forest QSAR methods to model LD50 data using chemical descriptors either alone (conventional models) or combined with biological descriptors derived from the concentration-response qHTS data (hybrid models). Critical to our approach was the use of a novel noise-filtering algorithm to treat qHTS data. Results: Both the external classification accuracy and coverage (i.e., fraction of compounds in the external set that fall within the applicability domain) of the hybrid QSAR models were superior to conventional models. Conclusions: Concentration-response qHTS data may serve as informative biological descriptors of molecules that, when combined with conventional chemical descriptors, may considerably improve the accuracy and utility of computational approaches for predicting in vivo animal toxicity end points.

Original languageEnglish (US)
Pages (from-to)364-370
Number of pages7
JournalEnvironmental Health Perspectives
Volume119
Issue number3
DOIs
StatePublished - Mar 2011

Fingerprint

Quantitative Structure-Activity Relationship
High-Throughput Screening Assays
Lethal Dose 50
Cell Line
National Institutes of Health (U.S.)
Genomics
Toxicology
Noise
Rodentia
Cell Survival
In Vitro Techniques

Keywords

  • Acute toxicity
  • Animal testing
  • Computational toxicology
  • QSAR
  • Quantitative high-throughput screening

ASJC Scopus subject areas

  • Health, Toxicology and Mutagenesis
  • Public Health, Environmental and Occupational Health

Cite this

Use of in Vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in Vivo Toxicity. / Sedykh, Alexander; Zhu, Hao; Tang, Hao; Zhang, Liying; Richard, Ann; Rusyn, Ivan; Tropsha, Alexander.

In: Environmental Health Perspectives, Vol. 119, No. 3, 03.2011, p. 364-370.

Research output: Contribution to journalArticle

Sedykh, Alexander ; Zhu, Hao ; Tang, Hao ; Zhang, Liying ; Richard, Ann ; Rusyn, Ivan ; Tropsha, Alexander. / Use of in Vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in Vivo Toxicity. In: Environmental Health Perspectives. 2011 ; Vol. 119, No. 3. pp. 364-370.
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