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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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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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