Impact of Target Warhead and Linkage Vector on Inducing Protein Degradation: Comparison of Bromodomain and Extra-Terminal (BET) Degraders Derived from Triazolodiazepine (JQ1) and Tetrahydroquinoline (I-BET726) BET Inhibitor Scaffolds

J Med Chem. 2018 Jan 25;61(2):504-513. doi: 10.1021/acs.jmedchem.6b01912. Epub 2017 Jun 22.

Abstract

The design of proteolysis-targeting chimeras (PROTACs) is a powerful small-molecule approach for inducing protein degradation. PROTACs conjugate a target warhead to an E3 ubiquitin ligase ligand via a linker. Here we examined the impact of derivatizing two different BET bromodomain inhibitors, triazolodiazepine JQ1 and the more potent tetrahydroquinoline I-BET726, via distinct exit vectors, using different polyethylene glycol linkers to VHL ligand VH032. Triazolodiazepine PROTACs exhibited positive cooperativities of ternary complex formation and were more potent degraders than tetrahydroquinoline compounds, which showed negative cooperativities instead. Marked dependency on linker length was observed for BET-degrading and cMyc-driven antiproliferative activities in acute myeloid leukemia cell lines. This work exemplifies as a cautionary tale how a more potent inhibitor does not necessarily generate more potent PROTACs and underscores the key roles played by the conjugation. The provided insights and framework for structure-activity relationships of bivalent degraders are anticipated to have wide future applicability.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aminoquinolines / chemistry*
  • Azepines / chemistry*
  • Benzoates / chemistry*
  • Calorimetry
  • Cell Cycle Proteins
  • Chemistry Techniques, Synthetic
  • Drug Evaluation, Preclinical / methods
  • HL-60 Cells
  • HeLa Cells
  • Humans
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / metabolism
  • Proteolysis / drug effects*
  • Proto-Oncogene Proteins c-myc / metabolism
  • RNA-Binding Proteins / metabolism
  • Structure-Activity Relationship*
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism
  • Triazoles / chemistry*
  • Von Hippel-Lindau Tumor Suppressor Protein / chemistry
  • Von Hippel-Lindau Tumor Suppressor Protein / metabolism

Substances

  • 4-(1-acetyl-4-((4-chlorophenyl)amino)-2-methyl-1,2,3,4-tetrahydroquinolin-6-yl)benzoic acid
  • Aminoquinolines
  • Azepines
  • BRD3 protein, human
  • BRD4 protein, human
  • Benzoates
  • Cell Cycle Proteins
  • Nuclear Proteins
  • Proto-Oncogene Proteins c-myc
  • RNA-Binding Proteins
  • Transcription Factors
  • Triazoles
  • WEB 2086
  • Von Hippel-Lindau Tumor Suppressor Protein
  • VHL protein, human