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Nowak RP, Xiong Y, Kirmani N, Kalabathula J, Donovan KA, Eleuteri NA, Yuan JC, Fischer ES. Structure-Guided Design of a "Bump-and-Hole" Bromodomain-Based Degradation Tag. J Med Chem 2021; 64:11637-11650. [PMID: 34279939 DOI: 10.1021/acs.jmedchem.1c00958] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical biology tools to modulate protein levels in cells are critical to decipher complex biology. Targeted protein degradation offers the potential for rapid and dose-dependent protein depletion through the use of protein fusion tags toward which protein degraders have been established. Here, we present a newly developed protein degradation tag BRD4BD1L94V along with the corresponding cereblon (CRBN)-based heterobifunctional degrader based on a "bump-and-hole" approach. The resulting compound XY-06-007 shows a half-degradation concentration (DC50, 6 h) of 10 nM against BRD4BD1L94V with no degradation of off-targets, as assessed by whole proteome mass spectrometry, and demonstrates suitable pharmacokinetics for in vivo studies. We demonstrate that BRD4BD1L94V can be combined with the dTAG approach to achieve simultaneous degrader-mediated depletion of their respective protein fusions. This orthogonal system complements currently available protein degradation tags and enables investigation into the consequences resulting from rapid degradation of previously undruggable disease codependencies.
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Affiliation(s)
- Radosław P Nowak
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yuan Xiong
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Nadia Kirmani
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Joann Kalabathula
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Katherine A Donovan
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Nicholas A Eleuteri
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - J Christine Yuan
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Eric S Fischer
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
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Wang ES, Verano AL, Nowak RP, Yuan JC, Donovan KA, Eleuteri NA, Yue H, Ngo KH, Lizotte PH, Gokhale PC, Gray NS, Fischer ES. Acute pharmacological degradation of Helios destabilizes regulatory T cells. Nat Chem Biol 2021; 17:711-717. [PMID: 34035522 PMCID: PMC8162940 DOI: 10.1038/s41589-021-00802-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/19/2021] [Indexed: 02/02/2023]
Abstract
The zinc-finger transcription factor Helios is critical for maintaining the identity, anergic phenotype and suppressive activity of regulatory T (Treg) cells. While it is an attractive target to enhance the efficacy of currently approved immunotherapies, no existing approaches can directly modulate Helios activity or abundance. Here, we report the structure-guided development of small molecules that recruit the E3 ubiquitin ligase substrate receptor cereblon to Helios, thereby promoting its degradation. Pharmacological Helios degradation destabilized the anergic phenotype and reduced the suppressive activity of Treg cells, establishing a route towards Helios-targeting therapeutics. More generally, this study provides a framework for the development of small-molecule degraders for previously unligandable targets by reprogramming E3 ligase substrate specificity.
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Affiliation(s)
- Eric S. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston MA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Alyssa L. Verano
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston MA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Radosław P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston MA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - J. Christine Yuan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston MA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston MA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | | | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston MA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Kenneth H. Ngo
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Patrick H. Lizotte
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Prafulla C. Gokhale
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston MA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.,Correspondence to: Nathanael S. Gray (); Eric S. Fischer ()
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston MA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.,Correspondence to: Nathanael S. Gray (); Eric S. Fischer ()
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Gasic I, Groendyke BJ, Nowak RP, Yuan JC, Kalabathula J, Fischer ES, Gray NS, Mitchison TJ. Tubulin Resists Degradation by Cereblon-Recruiting PROTACs. Cells 2020; 9:E1083. [PMID: 32349222 PMCID: PMC7290497 DOI: 10.3390/cells9051083] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
Dysregulation of microtubules and tubulin homeostasis has been linked to developmental disorders, neurodegenerative diseases, and cancer. In general, both microtubule-stabilizing and destabilizing agents have been powerful tools for studies of microtubule cytoskeleton and as clinical agents in oncology. However, many cancers develop resistance to these agents, limiting their utility. We sought to address this by developing a different kind of agent: tubulin-targeted small molecule degraders. Degraders (also known as proteolysis-targeting chimeras (PROTACs)) are compounds that recruit endogenous E3 ligases to a target of interest, resulting in the target's degradation. We developed and examined several series of α- and β-tubulin degraders, based on microtubule-destabilizing agents. Our results indicate, that although previously reported covalent tubulin binders led to tubulin degradation, in our hands, cereblon-recruiting PROTACs were not efficient. In summary, while we consider tubulin degraders to be valuable tools for studying the biology of tubulin homeostasis, it remains to be seen whether the PROTAC strategy can be applied to this target of high clinical relevance.
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Affiliation(s)
- Ivana Gasic
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA;
| | - Brian J. Groendyke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; (R.P.N.); (J.C.Y.); (J.K.); (E.S.F.); (N.S.G.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Radosław P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; (R.P.N.); (J.C.Y.); (J.K.); (E.S.F.); (N.S.G.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - J. Christine Yuan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; (R.P.N.); (J.C.Y.); (J.K.); (E.S.F.); (N.S.G.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Joann Kalabathula
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; (R.P.N.); (J.C.Y.); (J.K.); (E.S.F.); (N.S.G.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; (R.P.N.); (J.C.Y.); (J.K.); (E.S.F.); (N.S.G.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; (R.P.N.); (J.C.Y.); (J.K.); (E.S.F.); (N.S.G.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy J. Mitchison
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA;
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Fu YX, Wang YH, Tong XS, Gong Z, Sun XM, Yuan JC, Zheng TT, Li C, Niu DQ, Dai HG, Liu XF, Mao YJ, Tang BD, Xue W, Huang YJ. EDACO, a derivative of myricetin, inhibits the differentiation of Gaoyou duck embryonic osteoclasts in vitro. Br Poult Sci 2019; 60:169-175. [PMID: 30722674 DOI: 10.1080/00071668.2018.1564239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
1. This study determined the effects of (E)-3-(2-(4-(3-(2,4-dimethoxyphenyl)acryloyl)phenoxy)ethoxy)-5,7-dimethoxy-2-(3,4,5-trimethoxyphenyl)-4H-chromen-4-one (EDACO) on the differentiation of Gaoyou duck embryonic osteoclasts cultured in vitro. 2. Bone marrow mononuclear cells (BM-MNC) were collected from 23-d-old Gaoyou duck embryos and induced by macrophage colony-stimulating factor and receptor activator of nuclear factor κB ligand in the presence of EDACO at different concentrations (i.e. 10, 20, 40, 80 and 160 µM). Tartrate-resistant acid phosphatase (TRAP) staining and resorption ability determination were conducted. 3. Results suggested that EDACO suppressed the shaping of positive multinucleated cells and the number of TRAP-positive cells in the 20, 40, 80 and 160 μM EDACO groups was significantly decreased (P < 0.05 or P < 0.01). Besides, the absorption activity of differentiated duck embryonic osteoclasts was significantly inhibited (P < 0.05) in both 80 and 160 μM EDACO groups. 4. Overall, EDACO can inhibit the differentiation of BM-MNC into mature osteoclasts in duck embryos.1.
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Affiliation(s)
- Y X Fu
- a Department of Bioscience , Bengbu Medical College , Bengbu , 233030 , PR China
| | - Y H Wang
- b State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering , Guizhou University , Huaxi District , Guiyang , 550025 , PR China
| | - X S Tong
- c College of Veterinary Medicine , Yangzhou University , Yangzhou , 225009 , PR China
| | - Z Gong
- a Department of Bioscience , Bengbu Medical College , Bengbu , 233030 , PR China
| | - X M Sun
- d Department of Clinical Medicine , Bengbu Medical College , Bengbu , 233030 , PR China
| | - J C Yuan
- a Department of Bioscience , Bengbu Medical College , Bengbu , 233030 , PR China
| | - T T Zheng
- a Department of Bioscience , Bengbu Medical College , Bengbu , 233030 , PR China
| | - C Li
- a Department of Bioscience , Bengbu Medical College , Bengbu , 233030 , PR China
| | - D Q Niu
- e Department of gynaecology and obstetrics , The Second Affiliated Hospital of Bengbu Medical College , Bengbu , 233030 , PR China
| | - H G Dai
- f Animal husbandry and veterinary bureau of Fengyang County , Chuzhou , 233100 , PR China
| | - X F Liu
- g Department of surgical oncology , The First Affiliated Hospital of Bengbu Medical College , Huaxi District , Bengbu , 233030 , PR China
| | - Y J Mao
- a Department of Bioscience , Bengbu Medical College , Bengbu , 233030 , PR China
| | - B D Tang
- a Department of Bioscience , Bengbu Medical College , Bengbu , 233030 , PR China
| | - W Xue
- b State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering , Guizhou University , Huaxi District , Guiyang , 550025 , PR China
| | - Y J Huang
- a Department of Bioscience , Bengbu Medical College , Bengbu , 233030 , PR China
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Yu Z, Liu J, Guo S, Xing C, Fan X, Ning M, Yuan JC, Lo EH, Wang X. Neuroglobin-overexpression alters hypoxic response gene expression in primary neuron culture following oxygen glucose deprivation. Neuroscience 2009; 162:396-403. [PMID: 19401220 DOI: 10.1016/j.neuroscience.2009.04.055] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 04/06/2009] [Accepted: 04/22/2009] [Indexed: 01/19/2023]
Abstract
Neuroglobin (Ngb) is a tissue globin specifically expressed in neurons. Our laboratory and others have shown that Ngb overexpression protects neurons against hypoxia/ischemia, but the underlying mechanisms remain poorly understood. Recent studies demonstrate that hypoxia/ischemia induces a multitude of spatially and temporally regulated responses in gene expression, and initial evidence suggested that Ngb might function in altering biological processes of gene expression. In this study, we asked how Ngb may help regulate genes responsive to hypoxia. Expression of hypoxic response genes following oxygen-glucose deprivation (OGD) was examined using mRNA arrays in neuroglobin-overexpressing transgenic (Ngb-Tg) and wild type (WT) mouse neurons. From a total of 113 genes on the microarray, mRNA expression of 65 genes was detected. Under rest condition, 14 genes were downregulated in Ngb-Tg neurons compared to WT. In WT neurons, after 4-h OGD followed by 4-h reoxygenation (O4/R4), 20 genes were significantly downregulated, and only Fos mRNA was significantly increased. However, out of the 20 downregulated genes in WT neurons, 12 of them were no longer significantly changed in Ngb-Tg neurons: Add1, Arnt2, Camk2g, Cstb, Dr1, Epas1, Gna11, Hif1a, Il6st, Khsrp, Mars and Rara. Among these 12 genes, 8 (Add1, Camk2g, Cstb, Dr1, Epas1, Gna11, Hif1a, Khsrp) were already reduced in Ngb-Tg neurons compared to WT under rest conditions. Additionally, three genes that initially showed no changes in WT neurons (Ctgf, Egfr and Pea15) were downregulated after OGD in the Ngb-Tg neurons. These findings suggest that Ngb overexpression modulates mRNA expression of multiple hypoxic response genes in the early phase after OGD/reoxygenation. Further studies on these gene networks and interactions may lead to better understanding of Ngb in signaling pathways that contribute to neuroprotection.
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Affiliation(s)
- Z Yu
- Neuroprotection Research Laboratory, Department of Neurology and Radiology, Massachusetts General Hospital, Program in Neuroscience, Harvard Medical School, 149 13th Street, Room 2411A, Charlestown, MA 02129, USA
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