Related Experiment Video
Updated: Jan 1, 2026
Direct Measurement of KDM1A Target Engagement Using Chemoprobe-based Immunoassays
Published on: June 13, 2019
Discovery of a chemical probe for PRDM9
Abdellah Allali-Hassani1, Magdalena M Szewczyk1, Danton Ivanochko1,2
1Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
Abstract:
PRDM9 is a PR domain containing protein which trimethylates histone 3 on lysine 4 and 36. Its normal expression is restricted to germ cells and attenuation of its activity results in altered meiotic gene transcription, impairment of double-stranded breaks and pairing between homologous chromosomes. There is growing evidence for a role of aberrant expression of PRDM9 in oncogenesis and genome instability. Here we report the discovery of MRK-740, a potent (IC50: 80 ± 16 nM), selective and cell-active PRDM9 inhibitor (Chemical Probe). MRK-740 binds in the substrate-binding pocket, with unusually extensive interactions with the cofactor S-adenosylmethionine (SAM), conferring SAM-dependent substrate-competitive inhibition. In cells, MRK-740 specifically and directly inhibits H3K4 methylation at endogenous PRDM9 target loci, whereas the closely related inactive control compound, MRK-740-NC, does not. The discovery of MRK-740 as a chemical probe for the PRDM subfamily of methyltransferases highlights the potential for exploiting SAM in targeting SAM-dependent methyltransferases.
Insights
Researchers developed MRK-740, a potent chemical probe that inhibits PRDM9 methyltransferase activity. This discovery offers a new tool for studying PRDM9
Area of Science:
- Biochemistry
- Molecular Biology
- Epigenetics
Background:
- PRDM9 is a key methyltransferase regulating histone modifications and meiosis.
- Aberrant PRDM9 expression is linked to oncogenesis and genome instability.
- Targeting PRDM9 offers potential therapeutic strategies.
Purpose of the Study:
- To discover and characterize a potent and selective chemical probe for PRDM9.
- To investigate the mechanism of PRDM9 inhibition.
- To validate the probe's activity in cellular contexts.
Main Methods:
- High-throughput screening and biochemical assays to identify PRDM9 inhibitors.
- Structural studies to elucidate the binding mode of the inhibitor.
- Cell-based assays to assess target engagement and specificity.
Main Results:
- Discovery of MRK-740, a potent (IC50: 80 ± 16 nM) and selective PRDM9 inhibitor.
- MRK-740 binds to the substrate-binding pocket and interacts with S-adenosylmethionine (SAM).
- MRK-740 demonstrates cell-specific inhibition of H3K4 methylation at PRDM9 target loci.
Conclusions:
- MRK-740 serves as a valuable chemical probe for studying PRDM9 function.
- The findings highlight the potential of targeting SAM-dependent methyltransferases.
- This work opens avenues for developing novel cancer therapies.
