Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens

Oana Ursu, Sara J.C. Gosline, Neil Beeharry, Lauren Fink, Vikram Bhattacharjee, Shao-Shan Huang, Yan Zhou, Tim Yen, Ernest Fraenkel

Research output: Contribution to journalArticle

Abstract

Small molecule screens are widely used to prioritize pharmaceutical development. However, determining the pathways targeted by these molecules is challenging, since the compounds are often promiscuous. We present a network strategy that takes into account the polypharmacology of small molecules in order to generate hypotheses for their broader mode of action. We report a screen for kinase inhibitors that increase the efficacy of gemcitabine, the first-line chemotherapy for pancreatic cancer. Eight kinase inhibitors emerge that are known to affect 201 kinases, of which only three kinases have been previously identified as modifiers of gemcitabine toxicity. In this work, we use the SAMNet algorithm to identify pathways linking these kinases and genetic modifiers of gemcitabine toxicity with transcriptional and epigenetic changes induced by gemcitabine that we measure using DNaseI-seq and RNA-seq. SAMNet uses a constrained optimization algorithm to connect genes from these complementary datasets through a small set of protein-protein and protein-DNA interactions. The resulting network recapitulates known pathways including DNA repair, cell proliferation and the epithelial-to-mesenchymal transition. We use the network to predict genes with important roles in the gemcitabine response, including six that have already been shown to modify gemcitabine efficacy in pancreatic cancer and ten novel candidates. Our work reveals the important role of polypharmacology in the activity of these chemosensitiz-ing agents.

Original languageEnglish (US)
Article numbere0185650
JournalPLoS One
Volume12
Issue number10
DOIs
StatePublished - Oct 1 2017

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gemcitabine
Polypharmacology
phosphotransferases (kinases)
Phosphotransferases
pancreatic neoplasms
modifiers (genes)
Pancreatic Neoplasms
Molecules
Toxicity
toxicity
Genes
proteins
DNA repair
Proteins
Epithelial-Mesenchymal Transition
Chemotherapy
epigenetics
DNA
Constrained optimization
Cell proliferation

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Ursu, O., Gosline, S. J. C., Beeharry, N., Fink, L., Bhattacharjee, V., Huang, S-S., ... Fraenkel, E. (2017). Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens. PLoS One, 12(10), [e0185650]. https://doi.org/10.1371/journal.pone.0185650

Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens. / Ursu, Oana; Gosline, Sara J.C.; Beeharry, Neil; Fink, Lauren; Bhattacharjee, Vikram; Huang, Shao-Shan; Zhou, Yan; Yen, Tim; Fraenkel, Ernest.

In: PLoS One, Vol. 12, No. 10, e0185650, 01.10.2017.

Research output: Contribution to journalArticle

Ursu, O, Gosline, SJC, Beeharry, N, Fink, L, Bhattacharjee, V, Huang, S-S, Zhou, Y, Yen, T & Fraenkel, E 2017, 'Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens', PLoS One, vol. 12, no. 10, e0185650. https://doi.org/10.1371/journal.pone.0185650
Ursu O, Gosline SJC, Beeharry N, Fink L, Bhattacharjee V, Huang S-S et al. Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens. PLoS One. 2017 Oct 1;12(10). e0185650. https://doi.org/10.1371/journal.pone.0185650
Ursu, Oana ; Gosline, Sara J.C. ; Beeharry, Neil ; Fink, Lauren ; Bhattacharjee, Vikram ; Huang, Shao-Shan ; Zhou, Yan ; Yen, Tim ; Fraenkel, Ernest. / Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens. In: PLoS One. 2017 ; Vol. 12, No. 10.
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