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Title: Discovery of a chemical probe for PRDM9

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.

Authors:
 [1];  [1];  [2];  [1];  [3]; ORCiD logo [3];  [3];  [1];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1];  [1];  [1];  [3]; ORCiD logo [3]; ORCiD logo [1]; ORCiD logo [4] more »; ORCiD logo [5];  [6];  [7]; ORCiD logo [8]; ORCiD logo [2]; ORCiD logo [6];  [6]; ORCiD logo [6];  [6]; ORCiD logo [4] « less
  1. Univ. of Toronto, ON (Canada). Structural Genomics Consortium
  2. Univ. of Toronto, ON (Canada). Structural Genomics Consortium and Princess Margaret Cancer Centre
  3. Agency for Science, Technology and Research (A*STAR), (Singapore). Inst. of Molecular and Cell Biology (IMCB)
  4. Univ. of Toronto, ON (Canada). Structural Genomics Consortium and Dept. of Pharmacology and Toxicology
  5. Agency for Science, Technology and Research (A*STAR), (Singapore). Inst. of Molecular and Cell Biology (IMCB); National Univ. of Singapore (NUS) (Singapore). Dept. of Biochemistry
  6. Merck & Co, Inc., Kenilworth, NJ (United States)
  7. Agency for Science, Technology and Research (A*STAR), (Singapore). Inst. of Molecular and Cell Biology (IMCB); Icahn School of Medicine at Mount Sinai, New York, NY (United States)
  8. Univ. of Toronto, ON (Canada). Structural Genomics Consortium; Nature Research Center, Vilnius (Luthuania)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC); AbbVie; Bayer Pharma AG; Boehringer Ingelheim; Canada Foundation for Innovation (CFI); Eshelman Institute for Innovation; Genome Canada through Ontario Genomics Institute; Innovative Medicines Initiative (EU/EFPIA); Janssen; Merck KGaA; MSD; Novartis Pharma AG; Ontario Ministry of Research, Innovation and Science (MRIS); Pfizer; São Paulo Research Foundation (FAPESP); Takeda; Wellcome; Natural Sciences and Engineering Research Council of Canada (NSERC)
OSTI Identifier:
1624225
Grant/Contract Number:  
AC02-06CH11357; 115766; NMRC/OFIRG/0032/2017; NRF-CRP17-2017-06
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 60 APPLIED LIFE SCIENCES; science & technology - other topics; chemical tools; drug discovery; histone post-translational modifications; transferases

Citation Formats

Allali-Hassani, Abdellah, Szewczyk, Magdalena M., Ivanochko, Danton, Organ, Shawna L., Bok, Jabez, Ho, Jessica Sook Yuin, Gay, Florence P. H., Li, Fengling, Blazer, Levi, Eram, Mohammad S., Halabelian, Levon, Dilworth, David, Luciani, Genna M., Lima-Fernandes, Evelyne, Wu, Qin, Loppnau, Peter, Palmer, Nathan, Talib, S. Zakiah A., Brown, Peter J., Schapira, Matthieu, Kaldis, Philipp, O’Hagan, Ronan C., Guccione, Ernesto, Barsyte-Lovejoy, Dalia, Arrowsmith, Cheryl H., Sanders, John M., Kattar, Solomon D., Bennett, D. Jonathan, Nicholson, Benjamin, and Vedadi, Masoud. Discovery of a chemical probe for PRDM9. United States: N. p., 2019. Web. https://doi.org/10.1038/s41467-019-13652-x.
Allali-Hassani, Abdellah, Szewczyk, Magdalena M., Ivanochko, Danton, Organ, Shawna L., Bok, Jabez, Ho, Jessica Sook Yuin, Gay, Florence P. H., Li, Fengling, Blazer, Levi, Eram, Mohammad S., Halabelian, Levon, Dilworth, David, Luciani, Genna M., Lima-Fernandes, Evelyne, Wu, Qin, Loppnau, Peter, Palmer, Nathan, Talib, S. Zakiah A., Brown, Peter J., Schapira, Matthieu, Kaldis, Philipp, O’Hagan, Ronan C., Guccione, Ernesto, Barsyte-Lovejoy, Dalia, Arrowsmith, Cheryl H., Sanders, John M., Kattar, Solomon D., Bennett, D. Jonathan, Nicholson, Benjamin, & Vedadi, Masoud. Discovery of a chemical probe for PRDM9. United States. https://doi.org/10.1038/s41467-019-13652-x
Allali-Hassani, Abdellah, Szewczyk, Magdalena M., Ivanochko, Danton, Organ, Shawna L., Bok, Jabez, Ho, Jessica Sook Yuin, Gay, Florence P. H., Li, Fengling, Blazer, Levi, Eram, Mohammad S., Halabelian, Levon, Dilworth, David, Luciani, Genna M., Lima-Fernandes, Evelyne, Wu, Qin, Loppnau, Peter, Palmer, Nathan, Talib, S. Zakiah A., Brown, Peter J., Schapira, Matthieu, Kaldis, Philipp, O’Hagan, Ronan C., Guccione, Ernesto, Barsyte-Lovejoy, Dalia, Arrowsmith, Cheryl H., Sanders, John M., Kattar, Solomon D., Bennett, D. Jonathan, Nicholson, Benjamin, and Vedadi, Masoud. Tue . "Discovery of a chemical probe for PRDM9". United States. https://doi.org/10.1038/s41467-019-13652-x. https://www.osti.gov/servlets/purl/1624225.
@article{osti_1624225,
title = {Discovery of a chemical probe for PRDM9},
author = {Allali-Hassani, Abdellah and Szewczyk, Magdalena M. and Ivanochko, Danton and Organ, Shawna L. and Bok, Jabez and Ho, Jessica Sook Yuin and Gay, Florence P. H. and Li, Fengling and Blazer, Levi and Eram, Mohammad S. and Halabelian, Levon and Dilworth, David and Luciani, Genna M. and Lima-Fernandes, Evelyne and Wu, Qin and Loppnau, Peter and Palmer, Nathan and Talib, S. Zakiah A. and Brown, Peter J. and Schapira, Matthieu and Kaldis, Philipp and O’Hagan, Ronan C. and Guccione, Ernesto and Barsyte-Lovejoy, Dalia and Arrowsmith, Cheryl H. and Sanders, John M. and Kattar, Solomon D. and Bennett, D. Jonathan and Nicholson, Benjamin and Vedadi, Masoud},
abstractNote = {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.},
doi = {10.1038/s41467-019-13652-x},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {12}
}

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