1
|
Zurlinden TJ, Saili KS, Rush N, Kothiya P, Judson RS, Houck KA, Hunter ES, Baker NC, Palmer JA, Thomas RS, Knudsen TB. Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity. Toxicol Sci 2021; 174:189-209. [PMID: 32073639 DOI: 10.1093/toxsci/kfaa014] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Stemina devTOX quickPredict platform is a human pluripotent stem cell-based assay that predicts the developmental toxicity potential based on changes in cellular metabolism following chemical exposure [Palmer, J. A., Smith, A. M., Egnash, L. A., Conard, K. R., West, P. R., Burrier, R. E., Donley, E. L. R., and Kirchner, F. R. (2013). Establishment and assessment of a new human embryonic stem cell-based biomarker assay for developmental toxicity screening. Birth Defects Res. B Dev. Reprod. Toxicol. 98, 343-363]. Using this assay, we screened 1065 ToxCast phase I and II chemicals in single-concentration or concentration-response for the targeted biomarker (ratio of ornithine to cystine secreted or consumed from the media). The dataset from the Stemina (STM) assay is annotated in the ToxCast portfolio as STM. Major findings from the analysis of ToxCast_STM dataset include (1) 19% of 1065 chemicals yielded a prediction of developmental toxicity, (2) assay performance reached 79%-82% accuracy with high specificity (> 84%) but modest sensitivity (< 67%) when compared with in vivo animal models of human prenatal developmental toxicity, (3) sensitivity improved as more stringent weights of evidence requirements were applied to the animal studies, and (4) statistical analysis of the most potent chemical hits on specific biochemical targets in ToxCast revealed positive and negative associations with the STM response, providing insights into the mechanistic underpinnings of the targeted endpoint and its biological domain. The results of this study will be useful to improving our ability to predict in vivo developmental toxicants based on in vitro data and in silico models.
Collapse
Affiliation(s)
| | | | | | | | | | | | - E Sidney Hunter
- National Health and Environmental Effects Research Laboratory (NHEERL), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, North Carolina
| | | | | | | | | |
Collapse
|
2
|
Cotterill JV, Palazzolo L, Ridgway C, Price N, Rorije E, Moretto A, Peijnenburg A, Eberini I. Predicting estrogen receptor binding of chemicals using a suite of in silico methods - Complementary approaches of (Q)SAR, molecular docking and molecular dynamics. Toxicol Appl Pharmacol 2019; 378:114630. [PMID: 31220507 DOI: 10.1016/j.taap.2019.114630] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/17/2019] [Accepted: 06/17/2019] [Indexed: 11/18/2022]
Abstract
With the aim of obtaining reliable estimates of Estrogen Receptor (ER) binding for diverse classes of compounds, a weight of evidence approach using estimates from a suite of in silico models was assessed. The predictivity of a simple Majority Consensus of (Q)SAR models was assessed using a test set of compounds with experimental Relative Binding Affinity (RBA) data. Molecular docking was also carried out and the binding energies of these compounds to the ERα receptor were determined. For a few selected compounds, including a known full agonist and antagonist, the intrinsic activity was determined using low-mode molecular dynamics methods. Individual (Q)SAR model predictivity varied, as expected, with some models showing high sensitivity, others higher specificity. However, the Majority Consensus (Q)SAR prediction showed a high accuracy and reasonably balanced sensitivity and specificity. Molecular docking provided quantitative information on strength of binding to the ERα receptor. For the 50 highest binding affinity compounds with positive RBA experimental values, just 5 of them were predicted to be non-binders by the Majority QSAR Consensus. Furthermore, agonist-specific assay experimental values for these 5 compounds were negative, which indicates that they may be ER antagonists. We also showed different scenarios of combining (Q)SAR results with Molecular docking classification of ER binding based on cut-off values of binding energies, providing a rational combined strategy to maximize terms of toxicological interest.
Collapse
Affiliation(s)
- J V Cotterill
- Fera Science Limited, Sand Hutton, York YO41 1LZ, UK
| | - L Palazzolo
- Università degli Studi di Milano, Dipartimento di Scienze Farmacologiche e Biomolecolari, Via Balzaretti 9, 20133 Milano, Italy
| | - C Ridgway
- Fera Science Limited, Sand Hutton, York YO41 1LZ, UK
| | - N Price
- Fera Science Limited, Sand Hutton, York YO41 1LZ, UK
| | - E Rorije
- Centre for Safety of Substances and Products, National Institute for Public Health and Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - A Moretto
- Università degli Studi di Milano, Dipartimento di Scienze Biomediche e Cliniche, Ospedale L. Sacco, Padiglione 17, Via G.B. Grassi 74, 20157 Milano, Italy
| | - A Peijnenburg
- Wageningen University & Research, Wageningen, The Netherlands
| | - I Eberini
- Università degli Studi di Milano, Dipartimento di Scienze Farmacologiche e Biomolecolari & DSRC, Via Balzaretti 9, 20133 Milano, Italy.
| |
Collapse
|
3
|
Theunissen PT, Beken S, Beyer BK, Breslin WJ, Cappon GD, Chen CL, Chmielewski G, De Schaepdrijver L, Enright B, Foreman JE, Harrouk W, Hew KW, Hoberman AM, Hui JY, Knudsen TB, Laffan SB, Makris SL, Martin M, McNerney ME, Siezen CL, Stanislaus DJ, Stewart J, Thompson KE, Tornesi B, Van der Laan JW, Weinbauer GF, Wood S, Piersma AH. Comparison of rat and rabbit embryo-fetal developmental toxicity data for 379 pharmaceuticals: on the nature and severity of developmental effects. Crit Rev Toxicol 2016; 46:900-910. [PMID: 27848393 PMCID: PMC8865449 DOI: 10.1080/10408444.2016.1224807] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regulatory non-clinical safety testing of human pharmaceuticals typically requires embryo–fetal developmental toxicity (EFDT) testing in two species (one rodent and one non-rodent). The question has been raised whether under some conditions EFDT testing could be limited to one species, or whether the testing in a second species could be decided on a case-by-case basis. As part of a consortium initiative, we built and queried a database of 379 compounds with EFDT studies (in both rat and rabbit animal models) conducted for marketed and non-marketed pharmaceuticals for their potential for adverse developmental and maternal outcomes, including EFDT incidence and the nature and severity of adverse findings. Manifestation of EFDT in either one or both species was demonstrated for 282 compounds (74%). EFDT was detected in only one species (rat or rabbit) in almost a third (31%, 118 compounds), with 58% (68 compounds) of rat studies and 42% (50 compounds) of rabbit studies identifying an EFDT signal. For 24 compounds (6%), fetal malformations were observed in one species (rat or rabbit) in the absence of any EFDT in the second species. In general, growth retardation, fetal variations, and malformations were more prominent in the rat, whereas embryo–fetal death was observed more often in the rabbit. Discordance across species may be attributed to factors such as maternal toxicity, study design differences, pharmacokinetic differences, and pharmacologic relevance of species. The current analysis suggests that in general both species are equally sensitive on the basis of an overall EFDT LOAEL comparison, but selective EFDT toxicity in one species is not uncommon. Also, there appear to be species differences in the prevalence of various EFDT manifestations (i.e. embryo–fetal death, growth retardation, and dysmorphogenesis) between rat and rabbit, suggesting that the use of both species has a higher probability of detecting developmental toxicants than either one alone.
Collapse
Affiliation(s)
- Peter T Theunissen
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands.,b Medicines Evaluation Board , Utrecht , The Netherlands.,c Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht (HU) , Utrecht , The Netherlands
| | - Sonja Beken
- d Federal Agency for Medicines and Health Products , Brussels , Belgium
| | | | - William J Breslin
- f Lilly Research Laboratories , Lilly Corporate Center , Indianapolis , IN , USA
| | - Gregg D Cappon
- g Pfizer Worldwide Research & Development , Groton , CT , USA
| | - Connie L Chen
- h ILSI-Health and Environmental Sciences Institute , Washington , DC , USA
| | | | | | | | | | - Wafa Harrouk
- m U.S. Food & Drug Administration , Silver Spring , MD , USA
| | - Kok-Wah Hew
- n Takeda Pharmaceutical Company , Deerfield , IL , USA
| | - Alan M Hoberman
- o Charles-River Laboratories, Preclinical Services , Horsham , PA , USA
| | | | - Thomas B Knudsen
- q U.S. Environmental Protection Agency, National Center for Computational Toxicology, Research Triangle Park , NC , USA
| | - Susan B Laffan
- r Safety Assessment, GlaxoSmithKline , King of Prussia , PA , USA
| | - Susan L Makris
- s U.S. Environmental Protection Agency, National Center for Environmental Assessment , Washington , DC , USA
| | - Matt Martin
- q U.S. Environmental Protection Agency, National Center for Computational Toxicology, Research Triangle Park , NC , USA
| | | | | | | | - Jane Stewart
- u Drug Safety & Metabolism, AstraZeneca , Macclesfield , UK
| | - Kary E Thompson
- t Drug Safety Evaluation, Bristol-Myers Squibb , New Brunswick , NJ , USA
| | | | - Jan Willem Van der Laan
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands.,b Medicines Evaluation Board , Utrecht , The Netherlands
| | | | - Sandra Wood
- w Merck Research Laboratories , Upper Gwynedd , Pennsylvania , USA
| | - Aldert H Piersma
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands.,x Institute for Risk Assessment Sciences, Faculty of Veterinary Sciences , Utrecht University , Utrecht , The Netherlands
| |
Collapse
|