Design and characterization of bivalent BET inhibitors

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Abstract

Cellular signaling is often propagated by multivalent interactions. Multivalency creates avidity, allowing stable biophysical recognition. Multivalency is an attractive strategy for achieving potent binding to protein targets, as the affinity of bivalent ligands is often greater than the sum of monovalent affinities. The bromodomain and extraterminal domain (BET) family of transcriptional coactivators features tandem bromodomains through which BET proteins bind acetylated histones and transcription factors. All reported antagonists of the BET protein BRD4 bind in a monovalent fashion. Here we describe, to our knowledge for the first time, a bivalent BET bromodomain inhibitor—MT1—which has unprecedented potency. Biophysical and biochemical studies suggest MT1 is an intramolecular bivalent BRD4 binder that is more than 100-fold more potent, in cellular assays, than the corresponding monovalent antagonist, JQ1. MT1 significantly (P < 0.05) delayed leukemia progression in mice, as compared to JQ1. These data qualify a powerful chemical probe for BET bromodomains and a rationale for further development of multidomain inhibitors of epigenetic reader proteins.

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Figure 1: Rational design of bivalent BET bromodomain inhibitors.
Figure 2: Heterodimeric bivalent inhibitors and activity optimization.
Figure 3: Biochemical and biophysical properties of bivalent inhibitors.
Figure 4: MT1: an intramolecular bivalent chemical probe of BET bromodomains.
Figure 5: Kinetic and antitumor advantage of dual-BET bromodomain inhibition.
Figure 6: Efficacy of dual-BET bromodomain inhibition in vivo.

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Acknowledgements

We thank J.A. Perry for critical reading of the manuscript and discussions. NMC797 cells were a gift from C. French (Brigham and Women's Hospital). Crystallographic work was based on research conducted at the Advanced Photon Source on the Northeastern Collaborative Access Team beamlines. We thank Mitsubishi Tanabe Pharma Corporation for nonresearch support of M.T. This research was supported by the William Lawrence and Blanche Hughes Foundation (J.E.B.), the Leukemia and Lymphoma Society (J.E.B.) and the US National Institutes of Health (CA066996-01A1, J.E.B.).

Author information

M.T. and J.M.R. designed and led the study under the supervision of J.E.B. M.T. designed bivalent molecules and performed organic chemistry and medicinal chemistry experiments. J.M.R. designed and performed biochemical, cellular, and in vivo experiments. J.P. performed BRD4(1) FP experiments. S.D.-P., H.-S.S. and S.L.D. performed crystallographic studies. H.S.S. performed SEC and ITC experiments. A.S. and T.G.S. performed in vivo studies. M.T., J.M.R. and J.E.B. wrote the manuscript with input from all authors.

Correspondence to James E Bradner.

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Competing interests

M.T. is a visiting scientist from Mitsubishi Tanabe Pharma Corporation and is supported by the company for nonresearch funds. J.E.B. is a founder of Tensha Therapeutics, a biotechnology company that develops drug-like derivatives of JQ1 as investigational cancer therapies. Dana-Farber Cancer Institute and M.T., J.M.R. and J.E.B. have filed patent applications (62/259,797, 62/261,703 and 62/338,968) that include MT1 and the analogs described in this manuscript. J.E.B. is an employee of the Novartis Institutes of BioMedical Research (effective 1 January 2016).

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Tanaka, M., Roberts, J., Seo, H. et al. Design and characterization of bivalent BET inhibitors. Nat Chem Biol 12, 1089–1096 (2016) doi:10.1038/nchembio.2209

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