Metabolic Modifier Screen Reveals Secondary Targets of Protein Kinase Inhibitors within Nucleotide Metabolism

Cell Chem Biol. 2020 Feb 20;27(2):197-205.e6. doi: 10.1016/j.chembiol.2019.10.012. Epub 2019 Nov 13.

Abstract

Biosynthesis of the pyrimidine nucleotide uridine monophosphate (UMP) is essential for cell proliferation and is achieved by the activity of convergent de novo and salvage metabolic pathways. Here we report the development and application of a cell-based metabolic modifier screening platform that leverages the redundancy in pyrimidine metabolism for the discovery of selective UMP biosynthesis modulators. In evaluating a library of protein kinase inhibitors, we identified multiple compounds that possess nucleotide metabolism modifying activity. The JNK inhibitor JNK-IN-8 was found to potently inhibit nucleoside transport and engage ENT1. The PDK1 inhibitor OSU-03012 (also known as AR-12) and the RAF inhibitor TAK-632 were shown to inhibit the therapeutically relevant de novo pathway enzyme DHODH and their affinities were unambiguously confirmed through in vitro assays and co-crystallization with human DHODH.

Keywords: cancer metabolism; phenotypic screening; pyrimidine metabolism; target identification.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Cell Line, Tumor
  • Cell Survival / drug effects
  • Crystallography, X-Ray
  • Drug Design
  • Equilibrative Nucleoside Transporter 1 / antagonists & inhibitors*
  • Equilibrative Nucleoside Transporter 1 / metabolism
  • Humans
  • Molecular Dynamics Simulation
  • Oxidoreductases Acting on CH-CH Group Donors / antagonists & inhibitors*
  • Oxidoreductases Acting on CH-CH Group Donors / genetics
  • Oxidoreductases Acting on CH-CH Group Donors / metabolism
  • Protein Kinase Inhibitors / chemistry*
  • Protein Kinase Inhibitors / metabolism
  • Protein Kinase Inhibitors / pharmacology
  • Pyrimidine Nucleosides / metabolism*
  • Small Molecule Libraries / chemistry

Substances

  • Equilibrative Nucleoside Transporter 1
  • Protein Kinase Inhibitors
  • Pyrimidine Nucleosides
  • Small Molecule Libraries
  • Oxidoreductases Acting on CH-CH Group Donors
  • dihydroorotate dehydrogenase