Discovery of an efficacious KDM5B PROTAC degrader GT-653 up-regulating IFN response genes in prostate cancer

Eur J Med Chem. 2024 Jun 5:272:116494. doi: 10.1016/j.ejmech.2024.116494. Epub 2024 May 10.

Abstract

Epigenetic alterations promote cancer development by regulating the expression of various oncogenes and anti-oncogenes. Histone methylation modification represents a pivotal area in epigenetic research and numerous publications have demonstrated that aberrant histone methylation is highly correlated with tumorigenesis and development. As a key histone demethylase, lysine-specific demethylase 5B (KDM5B) demethylates lysine 4 of histone 3 (H3K4) and serves as a transcriptional repressor of certain tumor suppressor genes. Meanwhile, KDM5B inhibits STING-induced intrinsic immune response of tumor cells or recruits SETDB1 through non-enzymatic function to silence reverse transcription elements to promote immune escape. The conventional small molecule inhibitors can only inhibit the enzymatic function of KDM5B with no effect on the non-enzymatic function. In the article, we present the development of the first series of KDM5B degraders based on CPI-455 to inhibit the non-enzymatic function. Among them, GT-653 showed optimal KDM5B degradation efficiency in a ubiquitin proteasome-dependent manner. GT-653 efficiently reduced KDM5B protein levels without affecting KDM5B transcription. Interestingly, GT-653 increased H3K4me3 levels and activated the type-I interferon signaling pathway in 22RV1 cells without significant phenotypic response on cell proliferation.

Keywords: Epigenetic alterations; KDM5B; PROTAC; STING; Type-I interferon.

MeSH terms

  • Antineoplastic Agents* / chemical synthesis
  • Antineoplastic Agents* / chemistry
  • Antineoplastic Agents* / pharmacology
  • Cell Line, Tumor
  • Cell Proliferation / drug effects
  • Dose-Response Relationship, Drug
  • Drug Discovery
  • Drug Screening Assays, Antitumor
  • Humans
  • Interferons / metabolism
  • Jumonji Domain-Containing Histone Demethylases* / antagonists & inhibitors
  • Jumonji Domain-Containing Histone Demethylases* / metabolism
  • Male
  • Molecular Structure
  • Nuclear Proteins
  • Prostatic Neoplasms* / drug therapy
  • Prostatic Neoplasms* / metabolism
  • Prostatic Neoplasms* / pathology
  • Proteolysis / drug effects
  • Repressor Proteins
  • Structure-Activity Relationship
  • Up-Regulation / drug effects

Substances

  • KDM5B protein, human
  • Jumonji Domain-Containing Histone Demethylases
  • Antineoplastic Agents
  • Interferons
  • Nuclear Proteins
  • Repressor Proteins