Allosteric inhibition of PPM1D serine/threonine phosphatase via an altered conformational state.
| Title: | Allosteric inhibition of PPM1D serine/threonine phosphatase via an altered conformational state. |
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| Authors: | Miller PG; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.; Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Sathappa M; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Moroco JA; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Jiang W; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Qian Y; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Iqbal S; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Guo Q; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Giacomelli AO; Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.; Shaw S; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Vernier C; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Bajrami B; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Yang X; Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Raffier C; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Sperling AS; Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.; Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.; Gibson CJ; Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.; Kahn J; Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.; Jin C; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.; Ranaghan M; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Caliman A; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Brousseau M; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Fischer ES; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.; Lintner R; Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Piccioni F; Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Campbell AJ; Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Root DE; Broad Institute of MIT and Harvard University, Cambridge, MA, USA.; Garvie CW; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA. cgarvie@broadinstitute.org.; Ebert BL; Broad Institute of MIT and Harvard University, Cambridge, MA, USA. benjamin_ebert@dfci.harvard.edu.; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. benjamin_ebert@dfci.harvard.edu.; Howard Hughes Medical Institute, Bethesda, MD, USA. benjamin_ebert@dfci.harvard.edu. |
| Source: | Nature communications [Nat Commun] 2022 Jun 30; Vol. 13 (1), pp. 3778. Date of Electronic Publication: 2022 Jun 30. |
| Publication Type: | Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural |
| Language: | English |
| Journal Info: | Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: [London] : Nature Pub. Group |
| MeSH Terms: | Neoplasms*/drug therapy ; Neoplasms*/enzymology ; Neoplasms*/genetics ; Protein Phosphatase 2C*/antagonists & inhibitors ; Protein Phosphatase 2C*/chemistry ; Protein Phosphatase 2C*/genetics ; Protein Phosphatase 2C*/metabolism; Aminopyridines/pharmacology ; Dipeptides/pharmacology ; Serine/genetics ; Serine/metabolism ; Allosteric Site ; Humans ; Mutation ; Protein Conformation ; Structure-Activity Relationship |
| Abstract: | PPM1D encodes a serine/threonine phosphatase that regulates numerous pathways including the DNA damage response and p53. Activating mutations and amplification of PPM1D are found across numerous cancer types. GSK2830371 is a potent and selective allosteric inhibitor of PPM1D, but its mechanism of binding and inhibition of catalytic activity are unknown. Here we use computational, biochemical and functional genetic studies to elucidate the molecular basis of GSK2830371 activity. These data confirm that GSK2830371 binds an allosteric site of PPM1D with high affinity. By further incorporating data from hydrogen deuterium exchange mass spectrometry and sedimentation velocity analytical ultracentrifugation, we demonstrate that PPM1D exists in an equilibrium between two conformations that are defined by the movement of the flap domain, which is required for substrate recognition. A hinge region was identified that is critical for switching between the two conformations and was directly implicated in the high-affinity binding of GSK2830371 to PPM1D. We propose that the two conformations represent active and inactive forms of the protein reflected by the position of the flap, and that binding of GSK2830371 shifts the equilibrium to the inactive form. Finally, we found that C-terminal truncating mutations proximal to residue 400 result in destabilization of the protein via loss of a stabilizing N- and C-terminal interaction, consistent with the observation from human genetic data that nearly all PPM1D mutations in cancer are truncating and occur distal to residue 400. Taken together, our findings elucidate the mechanism by which binding of a small molecule to an allosteric site of PPM1D inhibits its activity and provides insights into the biology of PPM1D.; (© 2022. The Author(s).) |
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| Grant Information: | R35 CA253125 United States CA NCI NIH HHS; R01 HL082945 United States HL NHLBI NIH HHS; United States HHMI Howard Hughes Medical Institute; P01 CA066996 United States CA NCI NIH HHS; K12 CA087723 United States CA NCI NIH HHS; K08 CA263183 United States CA NCI NIH HHS |
| Substance Nomenclature: | 0 (Aminopyridines); 0 (Dipeptides); 0 (GSK2830371); 452VLY9402 (Serine); EC 3.1.3.16 (PPM1D protein, human); EC 3.1.3.16 (Protein Phosphatase 2C) |
| Entry Date(s): | Date Created: 20220630 Date Completed: 20220704 Latest Revision: 20250218 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC9246869 |
| DOI: | 10.1038/s41467-022-30463-9 |
| PMID: | 35773251 |
| Database: | MEDLINE |
Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural