Machine learning on drug-specific data to predict small molecule teratogenicity

Pregnant women are an especially vulnerable population, given the sensitivity of a developing fetus to chemical exposures. However, prescribing behavior for the gravid patient is guided on limited human data and conflicting cases of adverse outcomes due to the exclusion of pregnant populations from...

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Bibliographic Details
Published inbioRxiv
Main Authors Challa, Anup P, Beam, Andrew L, Shen, Min, Peryea, Tyler, Lavieri, Robert R, Lippmann, Ethan S, Aronoff, David M
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 30.11.2019
Subjects
Artificial intelligence
Biological activity
Clinical trials
Fetuses
Learning algorithms
Machine learning
Pregnancy
Structure-activity relationships
Teratogenicity
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Summary:Pregnant women are an especially vulnerable population, given the sensitivity of a developing fetus to chemical exposures. However, prescribing behavior for the gravid patient is guided on limited human data and conflicting cases of adverse outcomes due to the exclusion of pregnant populations from randomized, controlled trials. These factors increase risk for adverse drug outcomes and reduce quality of care for pregnant populations. Herein, we propose the application of artificial intelligence to systematically predict the teratogenicity of a prescriptible small molecule from information inherent to the drug. Using unsupervised and supervised machine learning, our model probes all small molecules with known structure and teratogenicity data published in research-amenable formats to identify patterns among structural, meta-structural, and in vitro bioactivity data for each drug and its teratogenicity score. With this workflow, we discovered three chemical functionalities that predispose a drug towards increased teratogenicity and two moieties with potentially protective effects. Our models predict three clinically-relevant classes of teratogenicity with AUC = 0.8 and nearly double the predictive accuracy of a blind control for the same task, suggesting successful modeling. We also present extensive barriers to translational research that restrict data-driven studies in pregnancy and therapeutically 'orphan' pregnant populations. Collectively, this work represents a first-in-kind platform for the application of computing to study and predict teratogenicity. Footnotes * https://github.com/apchalla/teratogenicity-qsar.
DOI:10.1101/860627