title: Understanding Cytotoxicity and Cytostaticity in a High-Throughput Screening Collection.
abstract: While mechanisms of cytotoxicity and cytostaticity have been studied extensively from the biological side, relatively little is currently understood regarding areas of chemical space leading to cytotoxicity and cytostasis in large compound collections. Predicting and rationalizing potential adverse mechanism-of-actions (MoAs) of small molecules is however crucial for screening library design, given the link of even low level cytotoxicity and adverse events observed in man. In this study, we analyzed results from a cell-based cytotoxicity screening cascade, comprising 296 970 nontoxic, 5784 cytotoxic and cytostatic, and 2327 cytostatic-only compounds evaluated on the THP-1 cell-line. We employed an in silico MoA analysis protocol, utilizing 9.5 million active and 602 million inactive bioactivity points to generate target predictions, annotate predicted targets with pathways, and calculate enrichment metrics to highlight targets and pathways. Predictions identify known mechanisms for the top ranking targets and pathways for both phenotypes after review and indicate that while processes involved in cytotoxicity versus cytostaticity seem to overlap, differences between both phenotypes seem to exist to some extent. Cytotoxic predictions highlight many kinases, including the potentially novel cytotoxicity-related target STK32C, while cytostatic predictions outline targets linked with response to DNA damage, metabolism, and cytoskeletal machinery. Fragment analysis was also employed to generate a library of toxicophores to improve general understanding of the chemical features driving toxicity. We highlight substructures with potential kinase-dependent and kinase-independent mechanisms of toxicity. We also trained a cytotoxic classification model on proprietary and public compound readouts, and prospectively validated these on 988 novel compounds comprising difficult and trivial testing instances, to establish the applicability domain of models. The proprietary model performed with precision and recall scores of 77.9% and 83.8%, respectively. The MoA results and top ranking substructures with accompanying MoA predictions are available as a platform to assess screening collections.
authors: Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Cambridge, United Kingdom.
authors: Lewis H
authors: LH
authors: Mervin
authors: Discovery Sciences, AstraZeneca R&D , Waltham, United States.
authors: Qing
authors: Q
authors: Cao
authors: Discovery Sciences, AstraZeneca R&D , Cambridge Science Park, Cambridge, United Kingdom.
authors: Ian P
authors: IP
authors: Barrett
authors: Discovery Sciences, AstraZeneca R&D , Cambridge Science Park, Cambridge, United Kingdom.
authors: Mike A
authors: MA
authors: Firth
authors: Discovery Sciences, AstraZeneca R&D , Alderley Park, Macclesfield, United Kingdom.
authors: David
authors: D
authors: Murray
authors: Discovery Sciences, AstraZeneca R&D , Alderley Park, Macclesfield, United Kingdom.
authors: Lisa
authors: L
authors: McWilliams
authors: Discovery Sciences, AstraZeneca R&D , Alderley Park, Macclesfield, United Kingdom.
authors: Malcolm
authors: M
authors: Haddrick
authors: Discovery Sciences, AstraZeneca R&D , Alderley Park, Macclesfield, United Kingdom.
authors: Mark
authors: M
authors: Wigglesworth
authors: Discovery Sciences, AstraZeneca R&D , Mölndal, Sweden.
authors: Ola
authors: O
authors: Engkvist
authors: Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Cambridge, United Kingdom.
authors: Andreas
authors: A
authors: Bender
mesh_terms: D002453:Cell Cycle / Q000187:drug effects*; D002460:Cell Line; D002470:Cell Survival / Q000187:drug effects*; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans