Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling

J Med Chem. 2022 Feb 10;65(3):1898-1914. doi: 10.1021/acs.jmedchem.1c01265. Epub 2022 Feb 1.

Abstract

RAS is a major anticancer drug target which requires membrane localization to activate downstream signal transduction. The direct inhibition of RAS has proven to be challenging. Here, we present a novel strategy for targeting RAS by stabilizing its interaction with the prenyl-binding protein PDE6D and disrupting its localization. Using rationally designed RAS point mutations, we were able to stabilize the RAS:PDE6D complex by increasing the affinity of RAS for PDE6D, which resulted in the redirection of RAS to the cytoplasm and the primary cilium and inhibition of oncogenic RAS/ERK signaling. We developed an SPR fragment screening and identified fragments that bind at the KRAS:PDE6D interface, as shown through cocrystal structures. Finally, we show that the stoichiometric ratios of KRAS:PDE6D vary in different cell lines, suggesting that the impact of this strategy might be cell-type-dependent. This study forms the foundation from which a potential anticancer small-molecule RAS:PDE6D complex stabilizer could be developed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Cell Membrane / metabolism
  • Cyclic Nucleotide Phosphodiesterases, Type 6 / metabolism*
  • Humans
  • Peptides / pharmacology*
  • Protein Binding / drug effects*
  • Proto-Oncogene Proteins p21(ras) / analysis*
  • Proto-Oncogene Proteins p21(ras) / antagonists & inhibitors*
  • Proto-Oncogene Proteins p21(ras) / metabolism
  • Signal Transduction / drug effects*

Substances

  • KRAS protein, human
  • Peptides
  • PDE6D protein, human
  • Cyclic Nucleotide Phosphodiesterases, Type 6
  • HRAS protein, human
  • Proto-Oncogene Proteins p21(ras)