Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics

Qingsong Liu, Sivapriya Kirubakaran, Wooyoung Hur, Mario Niepel, Kenneth Westover, Carson C. Thoreen, Jinhua Wang, Jing Ni, Matthew P. Patricelli, Kurt Vogel, Steve Riddle, David L. Waller, Ryan Traynor, Takaomi Sanda, Zheng Zhao, Seong A. Kang, Jean Zhao, A. Thomas Look, Peter K. Sorger, David M. SabatiniNathanael S. Gray

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Abstract

Anintensive recent effort to develop ATP-competitivemTOR inhibitors has resulted in several potent and selective molecules such as Torin1, PP242, KU63794, and WYE354. These inhibitors are being widely used as pharmacological probes of mTOR-dependent biology. To determine the potency and specificity of these agents, we have undertaken a systematic kinome-wide effort to profile their selectivity and potency using chemical proteomics and assays for enzymatic activity, protein binding, and disruption of cellular signaling. Enzymatic and cellular assays revealed that all four compounds are potent inhibitors of mTORC1 and mTORC2, with Torin1 exhibiting ∼20-fold greater potency for inhibition of Thr-389 phosphorylation on S6 kinases (EC 50 = 2 nM) relative to other inhibitors. In vitro biochemical profiling at 10 μM revealed binding of PP242 to numerous kinases, although WYE354 and KU63794 bound only to p38 kinases and PI3K isoforms and Torin1 to ataxia telangiectasia mutated, ATM and Rad3-related protein, and DNA-PK. Analysis of these protein targets in cellular assays did not reveal any off-target activities for Torin1, WYE354, and KU63794 at concentrations below 1 μM but did show that PP242 efficiently inhibited the RET receptor (EC 50, 42 nM) and JAK1/2/3 kinases (EC 50, 780 nM). In addition, Torin1 displayed unusually slow kinetics for inhibition of the mTORC1/2 complex, a property likely to contribute to the pharmacology of this inhibitor. Our results demonstrated that, with the exception of PP242, available ATP-competitive compounds are highly selective mTOR inhibitors when applied to cells at concentrations below 1 μM and that the compounds may represent a starting point for medicinal chemistry efforts aimed at developing inhibitors of other PI3K kinase-related kinases.

Original languageEnglish (US)
Pages (from-to)9742-9752
Number of pages11
JournalJournal of Biological Chemistry
Volume287
Issue number13
DOIs
StatePublished - Mar 23 2012

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Sirolimus
Phosphotransferases
Adenosine Triphosphate
Kinetics
Assays
Enzyme Assays
Phosphatidylinositol 3-Kinases
Pharmacology
Ribosomal Protein S6 Kinases
Cell signaling
Ataxia Telangiectasia
Phosphorylation
Pharmaceutical Chemistry
Automatic teller machines
Protein Binding
Proteomics
Protein Isoforms
Proteins
Molecules
PP242

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

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Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics. / Liu, Qingsong; Kirubakaran, Sivapriya; Hur, Wooyoung; Niepel, Mario; Westover, Kenneth; Thoreen, Carson C.; Wang, Jinhua; Ni, Jing; Patricelli, Matthew P.; Vogel, Kurt; Riddle, Steve; Waller, David L.; Traynor, Ryan; Sanda, Takaomi; Zhao, Zheng; Kang, Seong A.; Zhao, Jean; Look, A. Thomas; Sorger, Peter K.; Sabatini, David M.; Gray, Nathanael S.

In: Journal of Biological Chemistry, Vol. 287, No. 13, 23.03.2012, p. 9742-9752.

Research output: Contribution to journalArticle

Liu, Q, Kirubakaran, S, Hur, W, Niepel, M, Westover, K, Thoreen, CC, Wang, J, Ni, J, Patricelli, MP, Vogel, K, Riddle, S, Waller, DL, Traynor, R, Sanda, T, Zhao, Z, Kang, SA, Zhao, J, Look, AT, Sorger, PK, Sabatini, DM & Gray, NS 2012, 'Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics', Journal of Biological Chemistry, vol. 287, no. 13, pp. 9742-9752. https://doi.org/10.1074/jbc.M111.304485
Liu, Qingsong ; Kirubakaran, Sivapriya ; Hur, Wooyoung ; Niepel, Mario ; Westover, Kenneth ; Thoreen, Carson C. ; Wang, Jinhua ; Ni, Jing ; Patricelli, Matthew P. ; Vogel, Kurt ; Riddle, Steve ; Waller, David L. ; Traynor, Ryan ; Sanda, Takaomi ; Zhao, Zheng ; Kang, Seong A. ; Zhao, Jean ; Look, A. Thomas ; Sorger, Peter K. ; Sabatini, David M. ; Gray, Nathanael S. / Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics. In: Journal of Biological Chemistry. 2012 ; Vol. 287, No. 13. pp. 9742-9752.
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AU - Niepel, Mario

AU - Westover, Kenneth

AU - Thoreen, Carson C.

AU - Wang, Jinhua

AU - Ni, Jing

AU - Patricelli, Matthew P.

AU - Vogel, Kurt

AU - Riddle, Steve

AU - Waller, David L.

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AU - Sanda, Takaomi

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AU - Zhao, Jean

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