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DOI10.1021/acs.jcim.6b00291
Informing the Human Plasma Protein Binding of Environmental Chemicals by Machine Learning in the Pharmaceutical Space: Applicability Domain and Limits of Predictability
Ingle, Brandall L.1; Veber, Brandon C.2,3; Nichols, John W.2; Tornero-Velez, Rogelio1
发表日期2016-11-01
ISSN1549-9596
卷号56期号:11页码:2243-2252
英文摘要

The free fraction of a xenobiotic in plasma (Fob) is an important determinant of chemical adsorption, tic distribution, metabolism, elimination, and toxicity, yet experimental plasma protein binding data are scarce for environmentally relevant chemicals. The presented work explores the merit of utilizing available pharmaceutical data to predict F-ub for environmentally relevant chemicals via machine learning techniques. Quantitative structure activity relationship (QSAR) models were constructed with k nearest neighbors (INN), support vector machines (SVM), and random forest (RF) machine learning algorithms from a training set of 1045 pharmaceuticals. The models were then evaluated with independent test sets of pharmaceuticals (200 compounds) and environmentally relevant ToxCast chemicals (406 total, in two groups of 238 and 168 compounds). The selection of a minimal feature set of 10-15 2D molecular descriptors allowed for both informative feature interpretation and practical applicability domain assessment via a bounded box of descriptor ranges and principal component analysis. The diverse pharmaceutical and environmental chemical sets exhibit similarities in terms of chemical space (99-82% overlap), as well as comparable bias and variance in constructed learning curves. All the models exhibit significant predictability with mean absolute errors (MAE) in the range of 0.10-0.18F(ub). The models performed best for highly bound chemicals (MAE 0.07-0.12), neutrals (MAE 0.11-0.14), and acids (MAE 0.14-0.17). A consensus model had the highest accuracy across both pharmaceuticals (MAE 0.151-0.155) and environmentally relevant chemicals (MAE 0.110-0.131). The inclusion of the majority of the ToxCast test sets within the AD of the consensus model, coupled with high prediction accuracy for these chemicals, indicates the model provides a QSAR for F-ub that is broadly applicable to both pharmaceuticals and environmentally relevant chemicals.


语种英语
WOS记录号WOS:000389116200012
来源期刊Journal of Chemical Information and Modeling
来源机构美国环保署
文献类型期刊论文
条目标识符http://gcip.llas.ac.cn/handle/2XKMVOVA/58113
作者单位1.US EPA, Off Res & Dev, Natl Exposure Res Lab, Res Triangle Pk, NC 27709 USA;
2.US EPA, Off Res & Dev, Natl Hlth Exposure Effects Res Lab, Duluth, MN 55804 USA;
3.Oak Ridge Inst Sci & Educ, Oak Ridge, TN 37830 USA
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Ingle, Brandall L.,Veber, Brandon C.,Nichols, John W.,et al. Informing the Human Plasma Protein Binding of Environmental Chemicals by Machine Learning in the Pharmaceutical Space: Applicability Domain and Limits of Predictability[J]. 美国环保署,2016,56(11):2243-2252.
APA Ingle, Brandall L.,Veber, Brandon C.,Nichols, John W.,&Tornero-Velez, Rogelio.(2016).Informing the Human Plasma Protein Binding of Environmental Chemicals by Machine Learning in the Pharmaceutical Space: Applicability Domain and Limits of Predictability.Journal of Chemical Information and Modeling,56(11),2243-2252.
MLA Ingle, Brandall L.,et al."Informing the Human Plasma Protein Binding of Environmental Chemicals by Machine Learning in the Pharmaceutical Space: Applicability Domain and Limits of Predictability".Journal of Chemical Information and Modeling 56.11(2016):2243-2252.
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