• A Corrigendum to this article was published on 19 July 2016

This article has been updated

Abstract

Serine is both a proteinogenic amino acid and the source of one-carbon units essential for de novo purine and deoxythymidine synthesis. In the canonical pathway of glucose-derived serine synthesis, Homo sapiens phosphoglycerate dehydrogenase (PHGDH) catalyzes the first, rate-limiting step. Genetic loss of PHGDH is toxic toward PHGDH-overexpressing breast cancer cell lines even in the presence of exogenous serine. Here, we used a quantitative high-throughput screen to identify small-molecule PHGDH inhibitors. These compounds reduce the production of glucose-derived serine in cells and suppress the growth of PHGDH-dependent cancer cells in culture and in orthotopic xenograft tumors. Surprisingly, PHGDH inhibition reduced the incorporation into nucleotides of one-carbon units from glucose-derived and exogenous serine. We conclude that glycolytic serine synthesis coordinates the use of one-carbon units from endogenous and exogenous serine in nucleotide synthesis, and we suggest that one-carbon unit wasting thus may contribute to the efficacy of PHGDH inhibitors in vitro and in vivo.

  • Compound

    N-(4-methylpyridin-2-yl)-4-(3-(trifluoromethyl)phenyl)piperazine-1-carbothioamide

  • Compound

    N-(4,6-dimethylpyridin-2-yl)-4-[5-(trifluoromethyl)pyridin-2-yl]piperazine-1-carbothioamide

  • Compound

    N-(4,6-dimethylpyridin-2-yl)-4-[[4-(trifluoromethyl)phenyl]methyl]piperazine-1-carbothioamide

  • Compound

    N-(4,6-dimethylpyridin-2-yl)-4-pyridin-4-ylpiperazine-1-carbothioamide

  • Compound

    N-(4,6-dimethylpyridin-2-yl)-1H-imidazole-1-carbothioamide

  • Compound

    1-(5-(trifluoromethyl)pyridin-2-yl)piperazine

  • Compound

    tert-butyl 4-(4-(trifluoromethyl)benzyl)piperazine-1-carboxylate

  • Compound

    4-(4-(trifluoromethyl)benzyl)piperazin-1-ium trifluoroacetate

  • Compound

    1-(pyridin-4-yl)piperazine

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Change history

  • 28 June 2016

    In the version of this article initially published, the author omitted some funding sources: NIH (R03 DA034602-01A1, R01 CA129105, R01 CA103866, and R37 AI047389 to D.M.S.) and the US Department of Defense (W81XWH-14-PRCRP-IA to D.M.S.). The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We thank T. Wang and E. Edenberg for critical reading of the manuscript, S. Murphy for assistance with mouse experiments, and J. Pacold of the Lawrence Berkeley National Laboratory for assistance in interpreting Tm data. This research is supported by the Sally Gordon Fellowship of the Damon Runyon Cancer Research Foundation (DRG-112-12), a Department of Defense Breast Cancer Research Program Postdoctoral Fellowship (BC120208), and an ASTRO Resident Seed Grant (RA-2011-1) (all to M.E.P.)., by Susan G. Komen for the Cure (grant to R.L.P.), by an EMBO Long-Term Fellowship (to M.A.-R.), by the NIH (R03 DA034602-01A1, R01 CA129105, R01 CA103866, and R37 AI047389 to D.M.S.), by the US Department of Defense (W81XWH-14-PRCRP-IA to D.M.S.) and by the Stewart Trust (to D.M.S.). D.M.S. is an investigator of the Howard Hughes Medical Institute.

Author information

Affiliations

  1. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.

    • Michael E Pacold
    • , Sze Ham Chan
    • , Lotteke J Y M Swier
    • , Walter W Chen
    • , Steve Cho
    • , Elizaveta Freinkman
    • , Monther Abu-Remaileh
    • , Chieh Min Liu
    • , Minerva Zhou
    • , Min Jung Koh
    • , Haeyoon Chung
    •  & David M Sabatini
  2. Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Michael E Pacold
    • , Sze Ham Chan
    • , Lotteke J Y M Swier
    • , Walter W Chen
    • , Steve Cho
    • , Monther Abu-Remaileh
    • , Chieh Min Liu
    • , Minerva Zhou
    • , Min Jung Koh
    • , Haeyoon Chung
    •  & David M Sabatini
  3. Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.

    • Michael E Pacold
    • , Sze Ham Chan
    • , Caroline A Lewis
    • , Lotteke J Y M Swier
    • , Walter W Chen
    • , Lucas B Sullivan
    • , Brian P Fiske
    • , Steve Cho
    • , Monther Abu-Remaileh
    • , Chieh Min Liu
    • , Minerva Zhou
    • , Min Jung Koh
    • , Haeyoon Chung
    • , Shawn M Davidson
    • , Alba Luengo
    • , Matthew G Vander Heiden
    •  & David M Sabatini
  4. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Michael E Pacold
    • , Sze Ham Chan
    • , Lotteke J Y M Swier
    • , Walter W Chen
    • , Steve Cho
    • , Monther Abu-Remaileh
    • , Chieh Min Liu
    • , Minerva Zhou
    • , Min Jung Koh
    • , Haeyoon Chung
    •  & David M Sabatini
  5. Dana-Farber Cancer Institute, Longwood Center, Boston, Massachusetts, USA.

    • Michael E Pacold
    •  & Nathanael S Gray
  6. Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Michael E Pacold
    •  & Sze Ham Chan
  7. National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA.

    • Kyle R Brimacombe
    • , Jason M Rohde
    • , Amy Q Wang
    • , Xin Xu
    • , Adam Yasgar
    • , Li Liu
    • , Ganesha Rai
    • , Min Shen
    •  & Matthew B Boxer
  8. New York University Langone Medical Center, New York, New York, USA.

    • Richard Possemato
  9. Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, New York, USA.

    • Kıvanç Birsoy
  10. Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel–Canada, The Hebrew University–Hadassah Medical School, Jerusalem, Israel.

    • Yoav D Shaul
  11. University of Texas Southwestern Medical Center, Dallas, Texas, USA..

    • Kenneth D Westover

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Contributions

M.E.P. and D.M.S. conceived of the study and designed most of the experiments with advice from N.S.G. M.E.P. performed most of the experiments (in vitro assays, cell viability and proliferation, western blots, xenografts, knockdowns, and metabolomics) with assistance from L.J.Y.M.S., S.H.C., R.P., S.W.C., M.Z., E.F., K.B., M.A.-R., Y.D.S., C.M.L., H.C., M.J.K., W.W.C., and K.D.W. and in discussion with C.A.L., B.P.F., L.B.S. and M.G.V.H., K.R.B. and M.B.B. helped design and carried out the quantitative high-throughput screen. J.M.R., L.L., G.R., and M.B.B. designed and carried out structure–activity relationship (SAR) analysis and synthesis of all compounds. A.Y. assisted with additional in vitro assays, and A.Q.W. and X.X. designed and carried out pharmacokinetic analyses. M.S. was responsible for chemoinformatics during the screen and for SAR. S.M.D., A.L., and M.G.V.H. designed and carried out in vivo isotope tracing experiments. M.E.P. and D.M.S. wrote and all authors edited the manuscript.

Competing interests

D.M.S. is a founder and holds equity in Raze Therapeutics, which has interest in targeting one-carbon metabolism in cancer. M.E.P. is a consultant to and holds equity in Raze Therapeutics.

Corresponding author

Correspondence to David M Sabatini.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Results, Supplementary Table 1 and Supplementary Figures 1–9.

  2. 2.

    Supplementary Note

    Synthetic Procedures

Excel files

  1. 1.

    Supplementary Data Set 1

    Selectivity profile of NCT-502, NCT-503 and inactive compound. The activity of NCT-502, NCT-503 and the inactive compound was tested against a panel of 168 GPCR candidates.

About this article

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DOI

https://doi.org/10.1038/nchembio.2070

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