Development of PDE6D and CK1α Degraders through Chemical Derivatization of FPFT-2216

J Med Chem. 2022 Jan 13;65(1):747-756. doi: 10.1021/acs.jmedchem.1c01832. Epub 2021 Dec 29.

Abstract

Immunomodulatory drugs are a class of drugs approved for the treatment of multiple myeloma. These compounds exert their clinical effects by inducing interactions between the CRL4CRBN E3 ubiquitin ligase and a C2H2 zinc finger degron motif, resulting in degradation of degron-containing targets. However, although many cellular proteins feature the degron motif, only a subset of those are degradable via this strategy. Here, we demonstrated that FPFT-2216, a previously reported "molecular glue" compound, degrades PDE6D, in addition to IKZF1, IKZF3, and CK1α. We used FPFT-2216 as a starting point for a focused medicinal chemistry campaign and developed TMX-4100 and TMX-4116, which exhibit greater selectivity for degrading PDE6D and CK1α, respectively. We also showed that the region in PDE6D that interacts with the FPFT-2216 derivatives is not the previously pursued prenyl-binding pocket. Moreover, we found that PDE6D depletion by FPFT-2216 does not impede the growth of KRASG12C-dependent MIA PaCa-2 cells, highlighting the challenges of drugging PDE6D-KRAS. Taken together, the approach we described here represents a general scheme to rapidly develop selective degraders by reprogramming E3 ubiquitin ligase substrate specificity.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites
  • Casein Kinase Ialpha* / antagonists & inhibitors
  • Cell Line, Tumor
  • Cell Proliferation
  • Cyclic Nucleotide Phosphodiesterases, Type 6* / antagonists & inhibitors
  • Humans
  • Immunotherapy
  • Kinetics
  • Phosphodiesterase Inhibitors* / chemical synthesis
  • Phosphodiesterase Inhibitors* / pharmacology

Substances

  • Casein Kinase Ialpha
  • CSNK1A1 protein, human
  • Cyclic Nucleotide Phosphodiesterases, Type 6
  • PDE6D protein, human
  • Phosphodiesterase Inhibitors
  • 3-(4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl)piperidine-2,6-dione