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A PHGDH inhibitor reveals coordination of serine synthesis and one-carbon unit fate

A Corrigendum to this article was published on 19 July 2016

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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.

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Figure 1: Identification and characterization of small-molecule PHGDH inhibitors.
Figure 2: Target engagement and efficacy of PHGDH inhibitors.
Figure 3: In vitro and in vivo efficacy of PHGDH inhibitors.
Figure 4: PHGDH inhibition in a PHGDH-dependent cell line unexpectedly reduces the incorporation of exogenous serine into dTMP and AMP.
Figure 5: SHMT1 mediates the loss of nucleotide labeling induced by PHGDH inhibition.

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  • 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

Authors and Affiliations

Authors

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.

Corresponding author

Correspondence to David M Sabatini.

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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.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Table 1 and Supplementary Figures 1–9. (PDF 12061 kb)

Supplementary Note

Synthetic Procedures (PDF 173 kb)

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. (XLSX 429 kb)

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Pacold, M., Brimacombe, K., Chan, S. et al. A PHGDH inhibitor reveals coordination of serine synthesis and one-carbon unit fate. Nat Chem Biol 12, 452–458 (2016). https://doi.org/10.1038/nchembio.2070

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