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Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A

Nature Chemical Biology volume 13, pages 785–792 (2017)Cite this article

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Abstract

S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzyme turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.

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Figure 1: PF-9366 inhibition of Mat2A.
Figure 2: Structure of the Mat2A–PF-9366 complex that overlaps the Mat2B binding site.
Figure 3: Mat2A ligand induced structural dynamics probed by hydrogen–deuterium exchange mass spectrometry (HDX–MS).
Figure 4: Kinetic consequences of PF-9366 and Mat2B binding.
Figure 5: PF-9366 and Mat2B modulation of Mat2A in H520 lung cancer cells.
Figure 6: Mat2A is upregulated in response to inhibition.

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References

  1. Timp, W. & Feinberg, A.P. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat. Rev. Cancer 13, 497–510 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Lu, S.C. & Mato, J.M. S-adenosylmethionine in liver health, injury, and cancer. Physiol. Rev. 92, 1515–1542 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Halim, A.B., LeGros, L., Geller, A. & Kotb, M. Expression and functional interaction of the catalytic and regulatory subunits of human methionine adenosyltransferase in mammalian cells. J. Biol. Chem. 274, 29720–29725 (1999).

    CAS  PubMed  Google Scholar 

  4. Kotb, M. & Kredich, N.M. Regulation of human lymphocyte S-adenosylmethionine synthetase by product inhibition. Biochim. Biophys. Acta 1039, 253–260 (1990).

    CAS  PubMed  Google Scholar 

  5. LeGros, H.L. Jr., Geller, A.M. & Kotb, M. Differential regulation of methionine adenosyltransferase in superantigen and mitogen stimulated human T lymphocytes. J. Biol. Chem. 272, 16040–16047 (1997).

    CAS  PubMed  Google Scholar 

  6. Nordgren, K.K. et al. Methionine adenosyltransferase 2A/2B and methylation: gene sequence variation and functional genomics. Drug Metab. Dispos. 39, 2135–2147 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Cai, J., Mao, Z., Hwang, J.J. & Lu, S.C. Differential expression of methionine adenosyltransferase genes influences the rate of growth of human hepatocellular carcinoma cells. Cancer Res. 58, 1444–1450 (1998).

    CAS  PubMed  Google Scholar 

  8. Jani, T.S. et al. Inhibition of methionine adenosyltransferase II induces FasL expression, Fas-DISC formation and caspase-8-dependent apoptotic death in T leukemic cells. Cell Res. 19, 358–369 (2009).

    CAS  PubMed  Google Scholar 

  9. Cai, J., Sun, W.M., Hwang, J.J., Stain, S.C. & Lu, S.C. Changes in S-adenosylmethionine synthetase in human liver cancer: molecular characterization and significance. Hepatology 24, 1090–1097 (1996).

    CAS  PubMed  Google Scholar 

  10. Frau, M., Feo, F. & Pascale, R.M. Pleiotropic effects of methionine adenosyltransferases deregulation as determinants of liver cancer progression and prognosis. J. Hepatol. 59, 830–841 (2013).

    CAS  PubMed  Google Scholar 

  11. Martínez-Chantar, M.L. et al. Methionine adenosyltransferase II β subunit gene expression provides a proliferative advantage in human hepatoma. Gastroenterology 124, 940–948 (2003).

    PubMed  Google Scholar 

  12. Chen, H. et al. Role of methionine adenosyltransferase 2A and S-adenosylmethionine in mitogen-induced growth of human colon cancer cells. Gastroenterology 133, 207–218 (2007).

    CAS  PubMed  Google Scholar 

  13. Liu, Q. et al. Silencing MAT2A gene by RNA interference inhibited cell growth and induced apoptosis in human hepatoma cells. Hepatol. Res. 37, 376–388 (2007).

    CAS  PubMed  Google Scholar 

  14. Lombardini, J.B., Coulter, A.W. & Talalay, P. Analogues of methionine as substrates and inhibitors of the methionine adenosyltransferase reaction. Deductions concerning the conformation of methionine. Mol. Pharmacol. 6, 481–499 (1970).

    CAS  PubMed  Google Scholar 

  15. Lombardini, J.B. & Sufrin, J.R. Chemotherapeutic potential of methionine analogue inhibitors of tumor-derived methionine adenosyltransferases. Biochem. Pharmacol. 32, 489–495 (1983).

    CAS  PubMed  Google Scholar 

  16. Sviripa, V.M. et al. 2′,6′-Dihalostyrylanilines, pyridines, and pyrimidines for the inhibition of the catalytic subunit of methionine S-adenosyltransferase-2. J. Med. Chem. 57, 6083–6091 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Attia, R.R. et al. Selective targeting of leukemic cell growth in vivo and in vitro using a gene silencing approach to diminish S-adenosylmethionine synthesis. J. Biol. Chem. 283, 30788–30795 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Hester, J.B. Jr., Rudzik, A.D. & VonVoigtlander, P.F. 1-(Aminoalkyl)-6-aryl-4-H-s-triazolo[4,3-a][1,4]benzodiazepines with antianxiety and antidepressant activity. J. Med. Chem. 23, 392–402 (1980).

    CAS  PubMed  Google Scholar 

  19. Shafqat, N. et al. Insight into S-adenosylmethionine biosynthesis from the crystal structures of the human methionine adenosyltransferase catalytic and regulatory subunits. Biochem. J. 452, 27–36 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Murray, B. et al. Structure and function study of the complex that synthesizes S-adenosylmethionine. IUCrJ 1, 240–249 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Marjon, K. et al. MTAP deletions in cancer create vulnerability to targeting of the MAT2A/PRMT5/RIOK1 axis. Cell Rep. 15, 574–587 (2016).

    CAS  PubMed  Google Scholar 

  22. Murray, B. et al. Crystallography captures catalytic steps in human methionine adenosyltransferase enzymes. Proc. Natl. Acad. Sci. USA 113, 2104–2109 (2016).

    CAS  PubMed  Google Scholar 

  23. Finkelstein, J.D. Methionine metabolism in mammals. J. Nutr. Biochem. 1, 228–237 (1990).

    CAS  PubMed  Google Scholar 

  24. del Pino, M.M.S., Corrales, F.J. & Mato, J.M. Hysteretic behavior of methionine adenosyltransferase III. Methionine switches between two conformations of the enzyme with different specific activity. J. Biol. Chem. 275, 23476–23482 (2000).

    CAS  PubMed  Google Scholar 

  25. Orenstein, J.M. & Marsh, W.H. Incorporation in vivo of methionine and ethionine into and the methylation and ethylation of rat liver nuclear proteins. Biochem. J. 109, 697–699 (1968).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Liu, Q. et al. Hypoxia induces genomic DNA demethylation through the activation of HIF-1α and transcriptional upregulation of MAT2A in hepatoma cells. Mol. Cancer Ther. 10, 1113–1123 (2011).

    CAS  PubMed  Google Scholar 

  27. Panayiotidis, M.I. et al. Activation of a novel isoform of methionine adenosyl transferase 2A and increased S-adenosylmethionine turnover in lung epithelial cells exposed to hyperoxia. Free Radic. Biol. Med. 40, 348–358 (2006).

    CAS  PubMed  Google Scholar 

  28. Ramani, K. et al. Leptin's mitogenic effect in human liver cancer cells requires induction of both methionine adenosyltransferase 2A and 2β. Hepatology 47, 521–531 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Wang, X. et al. Expression of methionine adenosyltransferase 2A in renal cell carcinomas and potential mechanism for kidney carcinogenesis. BMC Cancer 14, 196 (2014).

    PubMed  PubMed Central  Google Scholar 

  30. Yang, H., Li, T.W., Peng, J., Mato, J.M. & Lu, S.C. Insulin-like growth factor 1 activates methionine adenosyltransferase 2A transcription by multiple pathways in human colon cancer cells. Biochem. J. 436, 507–516 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Zhang, T. et al. Overexpression of methionine adenosyltransferase II alpha (MAT2A) in gastric cancer and induction of cell cycle arrest and apoptosis in SGC-7901 cells by shRNA-mediated silencing of MAT2A gene. Acta Histochem. 115, 48–55 (2013).

    CAS  PubMed  Google Scholar 

  32. Mavrakis, K.J. et al. Disordered methionine metabolism in MTAP/CDKN2A-deleted cancers leads to dependence on PRMT5. Science 351, 1208–1213 (2016).

    CAS  PubMed  Google Scholar 

  33. Kornev, A.P. & Taylor, S.S. Dynamics-driven allostery in protein kinases. Trends Biochem. Sci. 40, 628–647 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Süel, G.M., Lockless, S.W., Wall, M.A. & Ranganathan, R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10, 59–69 (2003).

    PubMed  Google Scholar 

  35. Tomasi, M.L., Li, T.W., Li, M., Mato, J.M. & Lu, S.C. Inhibition of human methionine adenosyltransferase 1A transcription by coding region methylation. J. Cell. Physiol. 227, 1583–1591 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Yang, H. et al. Role of promoter methylation in increased methionine adenosyltransferase 2A expression in human liver cancer. Am. J. Physiol. Gastrointest. Liver Physiol. 280, G184–G190 (2001).

    CAS  PubMed  Google Scholar 

  37. Maegley, K.A., Krivacic, C., Bingham, P., Liu, W. & Brooun, A. Comparison of a high-throughput mass spectrometry method and radioactive filter binding to assay the protein methyltransferase PRMT5. Assay Drug Dev. Technol. 13, 235–240 (2015).

    CAS  PubMed  Google Scholar 

  38. Wiseman, T., Williston, S., Brandts, J.F. & Lin, L.N. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 179, 131–137 (1989).

    CAS  PubMed  Google Scholar 

  39. Vonrhein, C. et al. Data processing and analysis with the autoPROC toolbox. Acta Crystallogr. D Biol. Crystallogr. 67, 293–302 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Burke, J.E., Perisic, O., Masson, G.R., Vadas, O. & Williams, R.L. Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110α (PIK3CA). Proc. Natl. Acad. Sci. USA 109, 15259–15264 (2012).

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank members of the Pfizer La Jolla Analytical Chemistry group (W. Ferrell, C. Aurigemma, and P. Tran) for project support, and thank E. Johnson, M. Calabrese and A. Zorba for helpful comments and discussion.

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Author notes

  1. Casey L Quinlan and Stephen E Kaiser: These authors contributed equally to this work.

Authors and Affiliations

  1. Oncology Research and Development, Pfizer Inc., San Diego, California, USA

    Casey L Quinlan, Dawn Nowlin, Rita Grantner, Shannon Karlicek-Bryant, Stephen G Dann, Xiaoli Wang, Peter A Wells & Stephan K Grant

  2. Oncology Medicinal Chemistry, Pfizer Inc., San Diego, California, USA

    Stephen E Kaiser, Ben Bolaños, Jun Li Feng, Kevin Freeman-Cook & Al E Stewart

  3. Drug Safety and Pharmacology, Pfizer Inc., San Diego, California, USA

    Stephen Jenkinson

  4. ORIC Pharmaceuticals, South San Francisco, California, USA

    Valeria R Fantin

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Contributions

C.L.Q. conceptualized, executed, and analyzed the kinetic and cellular studies. S.E.K. conceived the crystallographic study, collected and analyzed crystallographic data, solved crystal structures and made figures; B.B. designed, executed and analyzed the HDX–MS experiments; D.N. designed and oversaw the screening campaign and follow-up compound triage; R.G. performed cell assays and quantitative western blotting analysis; S.K.-B. performed ITC experiments and analysis; J.L.F. expressed and purified the recombinant enzymes; S.J. designed and performed that selectivity screening; K.F.-C. purified and analyzed PF-9366; S.G.D. performed shRNA studies; X.W. performed qtPCR on PF-9366 treated cells; P.A.W. oversaw and analyzed kinetic experiments; V.R.F. conceptualized and oversaw the drug discovery effort; A.E.S. designed and reviewed structural and protein science experiments and data; S.K.G. oversaw and directed the biochemical and screening work; C.L.Q. and S.E.K. wrote the paper with contributions from all authors.

Corresponding authors

Correspondence to Casey L Quinlan or Stephen E Kaiser.

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All authors were employed by Pfizer, Inc. at the time this work was conducted.

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Quinlan, C., Kaiser, S., Bolaños, B. et al. Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A. Nat Chem Biol 13, 785–792 (2017). https://doi.org/10.1038/nchembio.2384

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