1
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Winter GE. Extrapolating Lessons from Targeted Protein Degradation to Other Proximity-Inducing Drugs. ACS Chem Biol 2024; 19:2089-2102. [PMID: 39264973 DOI: 10.1021/acschembio.4c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
Targeted protein degradation (TPD) is an emerging pharmacologic strategy. It relies on small-molecule "degraders" that induce proximity of a component of an E3 ubiquitin ligase complex and a target protein to induce target ubiquitination and subsequent proteasomal degradation. Essentially, degraders thus expand the function of E3 ligases, allowing them to degrade proteins they would not recognize in the absence of the small molecule. Over the past decade, insights gained from identifying, designing, and characterizing various degraders have significantly enhanced our understanding of TPD mechanisms, precipitating in rational degrader discovery strategies. In this Account, I aim to explore how these insights can be extrapolated to anticipate both opportunities and challenges of utilizing the overarching concept of proximity-inducing pharmacology to manipulate other cellular circuits for the dissection of biological mechanisms and for therapeutic purposes.
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Affiliation(s)
- Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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2
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Wilms G, Schofield K, Maddern S, Foley C, Shaw Y, Smith B, Basantes LE, Schwandt K, Babendreyer A, Chavez T, McKee N, Gokhale V, Kallabis S, Meissner F, Rokey SN, Dunckley T, Montfort WR, Becker W, Hulme C. Discovery and Functional Characterization of a Potent, Selective, and Metabolically Stable PROTAC of the Protein Kinases DYRK1A and DYRK1B. J Med Chem 2024; 67:17259-17289. [PMID: 39344427 DOI: 10.1021/acs.jmedchem.4c01130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Small-molecule-induced protein degradation has emerged as a promising pharmacological modality for inactivating disease-relevant protein kinases. DYRK1A and DYRK1B are closely related protein kinases that are involved in pathological processes such as neurodegeneration, cancer development, and adaptive immune homeostasis. Herein, we report the development of the first DYRK1 proteolysis targeting chimeras (PROTACs) that combine a new ATP-competitive DYRK1 inhibitor with ligands for the E3 ubiquitin ligase component cereblon (CRBN) to induce ubiquitination and subsequent proteasomal degradation of DYRK1A and DYRK1B. The lead compound (DYR684) promoted fast, efficient, potent, and selective degradation of DYRK1A in cell-based assays. Interestingly, an enzymatically inactive splicing variant of DYRK1B (p65) resisted degradation. Compared to competitive kinase inhibition, targeted degradation of DYRK1 by DYR684 provided improved suppression of downstream signaling. Collectively, our results identify DYRKs as viable targets for PROTAC-mediated degradation and qualify DYR684 as a useful chemical probe for DYRK1A and DYRK1B.
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Affiliation(s)
- Gerrit Wilms
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Kevin Schofield
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy The University of Arizona, Tucson, Arizona 85721, United States
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Shayna Maddern
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher Foley
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yeng Shaw
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy The University of Arizona, Tucson, Arizona 85721, United States
| | - Breland Smith
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - L Emilia Basantes
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Katharina Schwandt
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Aaron Babendreyer
- Institute of Molecular Pharmacology, RWTH Aachen University, Aachen 52074, Germany
| | - Timothy Chavez
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Nicholas McKee
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy The University of Arizona, Tucson, Arizona 85721, United States
| | - Vijay Gokhale
- BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
| | - Sebastian Kallabis
- Core Facility Translational Proteomics, Institute of Innate Immunity, University Hospital Bonn, Bonn 53127, Germany
| | - Felix Meissner
- Department of Systems Immunology and Proteomics, Institute of Innate Immunity, University Hospital Bonn, Bonn 53127, Germany
| | - Samantha N Rokey
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Travis Dunckley
- ASU-Banner Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - William R Montfort
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Walter Becker
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Christopher Hulme
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy The University of Arizona, Tucson, Arizona 85721, United States
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
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3
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Mi D, Huang A, Song J, Chen Y. A long march for targeted protein degradation in the new era: expanding E3 ligases. Future Med Chem 2024:1-3. [PMID: 39373160 DOI: 10.1080/17568919.2024.2409618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 09/17/2024] [Indexed: 10/08/2024] Open
Affiliation(s)
- Dazhao Mi
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Anxin Huang
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jingfeng Song
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Yihua Chen
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan, 650500, China
- Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming, Yunnan, 650500, China
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4
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Baek K, Metivier RJ, Roy Burman SS, Bushman JW, Yoon H, Lumpkin RJ, Abeja DM, Lakshminarayan M, Yue H, Ojeda S, Verano AL, Gray NS, Donovan KA, Fischer ES. Unveiling the hidden interactome of CRBN molecular glues with chemoproteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612438. [PMID: 39314457 PMCID: PMC11419069 DOI: 10.1101/2024.09.11.612438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Targeted protein degradation and induced proximity refer to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of glues remains challenging, unbiased discovery methods are needed to unveil hidden chemical targets. Here we establish a high throughput affinity purification mass spectrometry workflow in cell lysates for the unbiased identification of molecular glue targets. By mapping the targets of 20 CRBN-binding molecular glues, we identify 298 protein targets and demonstrate the utility of enrichment methods for identifying novel targets overlooked using established methods. We use a computational workflow to estimate target confidence and perform a biochemical screen to identify a lead compound for the new non-ZF target PPIL4. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying new drug-induced protein interactions in cell lysates.
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Affiliation(s)
- Kheewoong Baek
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rebecca J. Metivier
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shourya S. Roy Burman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonathan W. Bushman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan J. Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dinah M. Abeja
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Megha Lakshminarayan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Samuel Ojeda
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alyssa L. Verano
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford Medical School, Stanford University, Stanford, CA, 94305, USA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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5
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Arkinson C, Dong KC, Gee CL, Martin A. Mechanisms and regulation of substrate degradation by the 26S proteasome. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00778-0. [PMID: 39362999 DOI: 10.1038/s41580-024-00778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2024] [Indexed: 10/05/2024]
Abstract
The 26S proteasome is involved in degrading and regulating the majority of proteins in eukaryotic cells, which requires a sophisticated balance of specificity and promiscuity. In this Review, we discuss the principles that underly substrate recognition and ATP-dependent degradation by the proteasome. We focus on recent insights into the mechanisms of conventional ubiquitin-dependent and ubiquitin-independent protein turnover, and discuss the plethora of modulators for proteasome function, including substrate-delivering cofactors, ubiquitin ligases and deubiquitinases that enable the targeting of a highly diverse substrate pool. Furthermore, we summarize recent progress in our understanding of substrate processing upstream of the 26S proteasome by the p97 protein unfoldase. The advances in our knowledge of proteasome structure, function and regulation also inform new strategies for specific inhibition or harnessing the degradation capabilities of the proteasome for the treatment of human diseases, for instance, by using proteolysis targeting chimera molecules or molecular glues.
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Affiliation(s)
- Connor Arkinson
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Ken C Dong
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Christine L Gee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Andreas Martin
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.
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6
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Chen Y, Xia Z, Suwal U, Rappu P, Heino J, De Wever O, De Geest BG. Dual-ligand PROTACS mediate superior target protein degradation in vitro and therapeutic efficacy in vivo. Chem Sci 2024:d4sc03555k. [PMID: 39391379 PMCID: PMC11462456 DOI: 10.1039/d4sc03555k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 09/27/2024] [Indexed: 10/12/2024] Open
Abstract
Proteolysis targeting chimeras (PROTACs) are revolutionizing the drug development landscape due to their unique ability to selectively degrade disease-associated proteins. Conventional PROTACs are bivalent entities that induce ubiquitination and subsequent proteolysis of a chosen protein of interest (POI) by forming a ternary complex with an E3 ligase. We hypothesized that dual-ligand PROTACs, featuring two copies each of a POI ligand and an E3 ligase ligand, would facilitate the formation of high-avidity, long-lived ternary complexes inside cells, thereby increasing POI degradation potency. To this end, we developed a convergent synthesis route, using l-aspartic acid as a building block for homodimer synthesis, followed by copper-catalyzed azide-alkyne cycloaddition (CuAAC) to conjugate both dimers through a flexible linker. Dual-ligand PROTACs achieved up to a tenfold increase in degradation efficiency and a hundredfold increase in cytotoxicity in vitro across various cancer cell lines compared to their single-ligand counterparts. Furthermore, dual-ligand PROTACs sustain prolonged protein degradation, up to 60 hours after pulsing and washout. In vivo, in a mouse tumor model, the superior therapeutic activity of dual ligand PROTACs was observed.
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Affiliation(s)
- Yong Chen
- Department of Pharmaceutics, Ghent University 9000 Ghent Belgium
- Cancer Research Institute Ghent 9000 Ghent Belgium
| | - Zihan Xia
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University 9000 Ghent Belgium
- Cancer Research Institute Ghent 9000 Ghent Belgium
| | - Ujjwal Suwal
- Department of Life Technologies, InFLAMES Flagship, University of Turku 20520 Turku Finland
| | - Pekka Rappu
- Department of Life Technologies, InFLAMES Flagship, University of Turku 20520 Turku Finland
| | - Jyrki Heino
- Department of Life Technologies, InFLAMES Flagship, University of Turku 20520 Turku Finland
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University 9000 Ghent Belgium
- Cancer Research Institute Ghent 9000 Ghent Belgium
| | - Bruno G De Geest
- Department of Pharmaceutics, Ghent University 9000 Ghent Belgium
- Cancer Research Institute Ghent 9000 Ghent Belgium
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7
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Goebel GL, Giannino N, Lampe P, Qiu X, Schloßhauer JL, Imig J, Sievers S, Wu P. Profiling Cellular Morphological Changes Induced by Dual-Targeting PROTACs of Aurora Kinase and RNA-Binding Protein YTHDF2. Chembiochem 2024; 25:e202400183. [PMID: 38837838 DOI: 10.1002/cbic.202400183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/07/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are new chemical modalities that degrade proteins of interest, including established kinase targets and emerging RNA-binding proteins (RBPs). Whereas diverse sets of biochemical, biophysical and cellular assays are available for the evaluation and optimizations of PROTACs in understanding the involved ubiquitin-proteasome-mediated degradation mechanism and the structure-degradation relationship, a phenotypic method profiling the cellular morphological changes is rarely used. In this study, first, we reported the only examples of PROTACs degrading the mRNA-binding protein YTHDF2 via screening of multikinase PROTACs. Second, we reported the profiling of cellular morphological changes of the dual kinase- and RBP-targeting PROTACs using the unbiased cell painting assay (CPA). The CPA analysis revealed the high biosimilarity with the established aurora kinase cluster and annotated aurora kinase inhibitors, which reflected the association between YTHDF2 and the aurora kinase signaling network. Broadly, the results demonstrated that the cell painting assay can be a straightforward and powerful approach to evaluate PROTACs. Complementary to the existing biochemical, biophysical and cellular assays, CPA provided a new perspective in characterizing PROTACs at the cellular morphology.
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Affiliation(s)
- Georg L Goebel
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Nicole Giannino
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Philipp Lampe
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Compound Management and Screening Center, Otto-Hahn Str. 15, Dortmund, 44227, Germany
| | - Xiaqiu Qiu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Jeffrey L Schloßhauer
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Jochen Imig
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Compound Management and Screening Center, Otto-Hahn Str. 15, Dortmund, 44227, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
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8
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Huber AD, Lin W, Poudel S, Miller DJ, Chen T. PROTAC-mediated activation, rather than degradation, of a nuclear receptor reveals complex ligand-receptor interaction network. Structure 2024:S0969-2126(24)00385-X. [PMID: 39389062 DOI: 10.1016/j.str.2024.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/30/2024] [Accepted: 09/13/2024] [Indexed: 10/12/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules containing a ligand for a protein of interest linked to an E3 ubiquitin ligase ligand that induce protein degradation through E3 recruitment to the target protein. Small changes in PROTAC linkers can have drastic consequences, including loss of degradation activity, but the structural mechanisms governing such changes are unclear. To study this phenomenon, we screened PROTACs of diverse targeting modalities and identified dTAG-13 as an activator of the xenobiotic-sensing pregnane X receptor (PXR), which promiscuously binds various ligands. Characterization of dTAG-13 analogs and precursors revealed interplay between the PXR-binding moiety, linker, and E3 ligand that altered PXR activity without inducing degradation. A crystal structure of PXR ligand binding domain bound to a precursor ligand showed ligand-induced binding pocket distortions and a linker-punctured tunnel to the protein exterior at a region incompatible with E3 complex formation, highlighting the effects of linker environment on PROTAC activity.
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Affiliation(s)
- Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 1000, Memphis, TN 38105-3678, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 1000, Memphis, TN 38105-3678, USA
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 1000, Memphis, TN 38105-3678, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 1000, Memphis, TN 38105-3678, USA.
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9
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Zhuang Z, Byun WS, Kozicka Z, Dwyer BG, Donovan KA, Jiang Z, Jones HM, Abeja DM, Nix MN, Zhong J, Słabicki M, Fischer ES, Ebert BL, Gray NS. Discovery of electrophilic degraders that exploit S NAr chemistry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.25.615094. [PMID: 39386645 PMCID: PMC11463635 DOI: 10.1101/2024.09.25.615094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Targeted covalent inhibition (TCI) and targeted protein degradation (TPD) have proven effective in pharmacologically addressing formerly 'undruggable' targets. Integration of both methodologies has resulted in the development of electrophilic degraders where recruitment of a suitable E3 ubiquitin ligase is achieved through formation of a covalent bond with a cysteine nucleophile. Expanding the scope of electrophilic degraders requires the development of electrophiles with tempered reactivity that enable selective ligase recruitment and reduce cross-reactivity with other cellular nucleophiles. In this study, we report the use of chemical moieties that enable nucleophilic aromatic substitution (SNAr) reactions in the rational design of electrophilic protein degraders. Appending an SNAr covalent warhead to several preexisting small molecule inhibitors transformed them into degraders, obviating the need for a defined E3 ligase recruiter. The SNAr covalent warhead is versatile; it can recruit various E3 ligases, including DDB1 and CUL4 associated factor 11 (DCAF11), DDB1 and CUL4 associated factor 16 (DCAF16), and possibly others. The incorporation of an SNAr covalent warhead into the BRD4 inhibitor led to the discovery of degraders with low picomolar degradation potency. Furthermore, we demonstrate the broad applicability of this approach through rational functional switching from kinase inhibitors into potent degraders.
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Affiliation(s)
- Zhe Zhuang
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- These authors contributed equally: Zhe Zhuang, Woong Sub Byun
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- These authors contributed equally: Zhe Zhuang, Woong Sub Byun
| | - Zuzanna Kozicka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brendan G. Dwyer
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zixuan Jiang
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Hannah M. Jones
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Dinah M. Abeja
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Meredith N. Nix
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jianing Zhong
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
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10
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Fan AT, Gadbois GE, Huang HT, Jiang J, Sigua LH, Smith ER, Wu S, Dunne-Dombrink K, Goyal P, Tao AJ, Sellers W, Fischer ES, Donovan KA, Ferguson FM. A Kinetic Scout Approach Accelerates Targeted Protein Degrader Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.612508. [PMID: 39345570 PMCID: PMC11429919 DOI: 10.1101/2024.09.17.612508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Bifunctional molecules such as targeted protein degraders induce proximity to promote gain-of-function pharmacology. These powerful approaches have gained broad traction across academia and the pharmaceutical industry, leading to an intensive focus on strategies that can accelerate their identification and optimization. We and others have previously used chemical proteomics to map degradable target space, and these datasets have been used to develop and train multiparameter models to extend degradability predictions across the proteome. In this study, we now turn our attention to develop generalizable chemistry strategies to accelerate the development of new bifunctional degraders. We implement lysine-targeted reversible-covalent chemistry to rationally tune the binding kinetics at the protein-of-interest across a set of 25 targets. We define an unbiased workflow consisting of global proteomics analysis, IP/MS of ternary complexes and the E-STUB assay, to mechanistically characterize the effects of ligand residence time on targeted protein degradation and formulate hypotheses about the rate-limiting step of degradation for each target. Our key finding is that target residence time is a major determinant of degrader activity, and this can be rapidly and rationally tuned through the synthesis of a minimal number of analogues to accelerate early degrader discovery and optimization efforts.
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Affiliation(s)
- Angela T. Fan
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Gillian E. Gadbois
- Department of Chemistry and Biochemistry, University of California, San Diego
| | | | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Logan H. Sigua
- Medical Scientist Training Program, University of California, San Diego
| | - Emily R. Smith
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Sitong Wu
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Kara Dunne-Dombrink
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Andrew J. Tao
- Department of Chemistry and Biochemistry, University of California, San Diego
| | | | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston
| | - Fleur M. Ferguson
- Department of Chemistry and Biochemistry, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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11
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Whittaker MK, Bendzunas GN, Shirani M, LeClair TJ, Shebl B, Dill TC, Coffino P, Simon SM, Kennedy EJ. Targeted Degradation of Protein Kinase A via a Stapled Peptide PROTAC. ACS Chem Biol 2024; 19:1888-1895. [PMID: 39137166 PMCID: PMC11420944 DOI: 10.1021/acschembio.4c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) are bifunctional molecules that bind and recruit an E3 ubiquitin ligase to a targeted protein of interest, often through the utilization of a small molecule inhibitor. To expand the possible range of kinase targets that can be degraded by PROTACs, we sought to develop a PROTAC utilizing a hydrocarbon-stapled peptide as the targeting agent to bind the surface of a target protein of interest. In this study, we describe the development of a proteolysis-targeting chimera, dubbed Stapled Inhibitor Peptide - PROTAC or StIP-TAC, linking a hydrocarbon-stapled peptide with an E3 ligase ligand for targeted degradation of Protein Kinase A (PKA). This StIP-TAC molecule stimulated E3-mediated protein degradation of PKA, and this effect could be reversed by the addition of the proteasomal inhibitor MG-132. Further, StIP-TAC treatment led to a significant reduction in PKA substrate phosphorylation. Since many protein targets of interest lack structural features that make them amenable to small molecule targeting, development of StIP-TACs may broaden the potential range of protein targets using a PROTAC-mediated proteasomal degradation approach.
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Affiliation(s)
- Matthew K Whittaker
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - George N Bendzunas
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Mahsa Shirani
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York 10065, United States
| | - Timothy J LeClair
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Bassem Shebl
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York 10065, United States
| | - Taylor C Dill
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Philip Coffino
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York 10065, United States
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York 10065, United States
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
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12
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Taylor JD, Barrett N, Martinez Cuesta S, Cassidy K, Pachl F, Dodgson J, Patel R, Eriksson TM, Riley A, Burrell M, Bauer C, Rees DG, Cimbro R, Zhang AX, Minter RR, Hunt J, Legg S. Targeted protein degradation using chimeric human E2 ubiquitin-conjugating enzymes. Commun Biol 2024; 7:1179. [PMID: 39300128 DOI: 10.1038/s42003-024-06803-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 08/29/2024] [Indexed: 09/22/2024] Open
Abstract
Proteins can be targeted for degradation by engineering biomolecules that direct them to the eukaryotic ubiquitination machinery. For instance, the fusion of an E3 ubiquitin ligase to a suitable target binding domain creates a 'biological Proteolysis-Targeting Chimera' (bioPROTAC). Here we employ an analogous approach where the target protein is recruited directly to a human E2 ubiquitin-conjugating enzyme via an attached target binding domain. Through rational design and screening we develop E2 bioPROTACs that induce the degradation of the human intracellular proteins SHP2 and KRAS. Using global proteomics, we characterise the target-specific and wider effects of E2 vs. VHL-based fusions. Taking SHP2 as a model target, we also employ a route to bioPROTAC discovery based on protein display libraries, yielding a degrader with comparatively weak affinity capable of suppressing SHP2-mediated signalling.
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Affiliation(s)
- Jonathan D Taylor
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK.
| | - Nathalie Barrett
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Sergio Martinez Cuesta
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Katelyn Cassidy
- Protein Sciences, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Waltham, MA, 02451, USA
| | - Fiona Pachl
- Protein Sciences, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Waltham, MA, 02451, USA
| | - James Dodgson
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Radhika Patel
- Centre for Genomics Research, Dynamic Omics, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Tuula M Eriksson
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Aidan Riley
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Matthew Burrell
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Christin Bauer
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - D Gareth Rees
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Raffaello Cimbro
- Centre for Genomics Research, Dynamic Omics, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Andrew X Zhang
- Protein Sciences, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Waltham, MA, 02451, USA
| | - Ralph R Minter
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - James Hunt
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK.
| | - Sandrine Legg
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
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13
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Gregory JA, Hickey CM, Chavez J, Cacace AM. New therapies on the horizon: Targeted protein degradation in neuroscience. Cell Chem Biol 2024; 31:1688-1698. [PMID: 39303702 DOI: 10.1016/j.chembiol.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/22/2024]
Abstract
This minireview explores the burgeoning field of targeted protein degradation (TPD) and its promising applications in neuroscience and clinical development. TPD offers innovative strategies for modulating protein levels, presenting a paradigm shift in small-molecule drug discovery and therapeutic interventions. Importantly, small-molecule protein degraders specifically target and remove pathogenic proteins from central nervous system cells without the drug delivery challenges of genomic and antibody-based modalities. Here, we review recent advancements in TPD technologies, highlight proteolysis targeting chimera (PROTAC) protein degrader molecules with proximity-induced degradation event-driven and iterative pharmacology, provide applications in neuroscience research, and discuss the high potential for translation of TPD into clinical settings.
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Affiliation(s)
| | | | - Juan Chavez
- Arvinas, Inc., 5 Science Park, New Haven, CT 06511, USA
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14
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Lampe GD, Liang AR, Zhang DJ, Fernández IS, Sternberg SH. Structure-guided engineering of type I-F CASTs for targeted gene insertion in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613948. [PMID: 39345383 PMCID: PMC11429998 DOI: 10.1101/2024.09.19.613948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Conventional genome editing tools rely on DNA double-strand breaks (DSBs) and host recombination proteins to achieve large insertions, resulting in a heterogeneous mixture of undesirable editing outcomes. We recently leveraged a type I-F CRISPR-associated transposase (CAST) from the Pseudoalteromonas Tn7016 transposon (PseCAST) for DSB-free, RNA-guided DNA integration in human cells, taking advantage of its programmability and large payload capacity. PseCAST is the only characterized CAST system that has achieved human genomic DNA insertions, but multiple lines of evidence suggest that DNA binding may be a critical bottleneck that limits high-efficiency activity. Here we report structural determinants of target DNA recognition by the PseCAST QCascade complex using single-particle cryogenic electron microscopy (cryoEM), which revealed novel subtype-specific interactions and RNA-DNA heteroduplex features. By combining our structural data with target DNA library screens and rationally engineered protein mutations, we uncovered CAST variants that exhibit increased integration efficiency and modified PAM stringency. Structure predictions of key interfaces in the transpososome holoenzyme also revealed opportunities for the design of hybrid CASTs, which we leveraged to build chimeric systems that combine high-activity DNA binding and DNA integration modules. Collectively, our work provides unique structural insights into type I-F CAST systems while showcasing multiple diverse strategies to investigate and engineer new RNA-guided transposase architectures for human genome editing applications.
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Affiliation(s)
- George D. Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Ashley R. Liang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Present Address: Tornado Bio, San Francisco, CA, USA
| | - Dennis J. Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Present Address: Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Israel S. Fernández
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
| | - Samuel H. Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY, USA
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15
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Pliatsika D, Blatter C, Riedl R. Targeted protein degradation: current molecular targets, localization, and strategies. Drug Discov Today 2024; 29:104178. [PMID: 39276920 DOI: 10.1016/j.drudis.2024.104178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/23/2024] [Accepted: 09/10/2024] [Indexed: 09/17/2024]
Abstract
Targeted protein degradation (TPD) has revolutionized drug discovery by selectively eliminating specific proteins within and outside the cellular context. Over the past two decades, TPD has expanded its focus beyond well-established targets, exploring diverse proteins beyond cancer-related ones. This evolution extends the potential of TPD to various diseases. Notably, TPD can target proteins at demanding locations, such as the extracellular matrix (ECM) and cellular membranes, presenting both opportunities and challenges for future research. In this review, we comprehensively examine the exciting opportunities in the burgeoning field of TPD, highlighting different targets, their cellular environment, and innovative strategies for modern drug discovery.
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Affiliation(s)
- Dimanthi Pliatsika
- Institute of Chemistry and Biotechnology, Competence Center for Drug Discovery, Zurich University of Applied Sciences, CH-8820 Wädenswil, Switzerland
| | - Cindy Blatter
- Institute of Chemistry and Biotechnology, Competence Center for Drug Discovery, Zurich University of Applied Sciences, CH-8820 Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Competence Center for Drug Discovery, Zurich University of Applied Sciences, CH-8820 Wädenswil, Switzerland.
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16
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Tsai JM, Nowak RP, Ebert BL, Fischer ES. Targeted protein degradation: from mechanisms to clinic. Nat Rev Mol Cell Biol 2024; 25:740-757. [PMID: 38684868 DOI: 10.1038/s41580-024-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/02/2024]
Abstract
Targeted protein degradation refers to the use of small molecules to induce the selective degradation of proteins. In its most common form, this degradation is achieved through ligand-mediated neo-interactions between ubiquitin E3 ligases - the principal waste disposal machines of a cell - and the protein targets of interest, resulting in ubiquitylation and subsequent proteasomal degradation. Notable advances have been made in biological and mechanistic understanding of serendipitously discovered degraders. This improved understanding and novel chemistry has not only provided clinical proof of concept for targeted protein degradation but has also led to rapid growth of the field, with dozens of investigational drugs in active clinical trials. Two distinct classes of protein degradation therapeutics are being widely explored: bifunctional PROTACs and molecular glue degraders, both of which have their unique advantages and challenges. Here, we review the current landscape of targeted protein degradation approaches and how they have parallels in biological processes. We also outline the ongoing clinical exploration of novel degraders and provide some perspectives on the directions the field might take.
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Affiliation(s)
- Jonathan M Tsai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Institute of Structural Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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17
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Kadier K, Niu T, Ding B, Chen B, Qi X, Chen D, Cheng X, Fang Y, Zhou J, Zhao W, Liu Z, Yuan Y, Zhou Z, Dong X, Yang B, He Q, Cao J, Jiang L, Zhu CL. PROTAC-Mediated HDAC7 Protein Degradation Unveils Its Deacetylase-Independent Proinflammatory Function in Macrophages. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309459. [PMID: 39049738 PMCID: PMC11423193 DOI: 10.1002/advs.202309459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/25/2024] [Indexed: 07/27/2024]
Abstract
Class IIa histone deacetylases (Class IIa HDACs) play critical roles in regulating essential cellular metabolism and inflammatory pathways. However, dissecting the specific roles of each class IIa HDAC isoform is hindered by the pan-inhibitory effect of current inhibitors and a lack of tools to probe their functions beyond epigenetic regulation. In this study, a novel PROTAC-based compound B4 is developed, which selectively targets and degrades HDAC7, resulting in the effective attenuation of a specific set of proinflammatory cytokines in both lipopolysaccharide (LPS)-stimulated macrophages and a mouse model. By employing B4 as a molecular probe, evidence is found for a previously explored role of HDAC7 that surpasses its deacetylase function, suggesting broader implications in inflammatory processes. Mechanistic investigations reveal the critical involvement of HDAC7 in the Toll-like receptor 4 (TLR4) signaling pathway by directly interacting with the TNF receptor-associated factor 6 and TGFβ-activated kinase 1 (TRAF6-TAK1) complex, thereby initiating the activation of the downstream mitogen-activated protein kinase/nuclear factor-κB (MAPK/NF-κB) signaling cascade and subsequent gene transcription. This study expands the insight into HDAC7's role within intricate inflammatory networks and highlights its therapeutic potential as a novel target for anti-inflammatory treatments.
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Affiliation(s)
- Kailibinuer Kadier
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Tian Niu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Baoli Ding
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Boya Chen
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xuxin Qi
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Danni Chen
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xirui Cheng
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yizheng Fang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Jiahao Zhou
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Wenyi Zhao
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
| | - Zeqi Liu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yi Yuan
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Zhan Zhou
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
| | - Xiaowu Dong
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, 310058, P. R. China
- School of Medicine, Hangzhou City University, Hangzhou, 310015, P. R. China
| | - Qiaojun He
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, 310058, P. R. China
- Center for Drug Safety Evaluation and Research of Zhejiang University, Hangzhou, 310058, P. R. China
| | - Ji Cao
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, 310058, P. R. China
| | - Li Jiang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
| | - Cheng-Liang Zhu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
- Center for Drug Safety Evaluation and Research of Zhejiang University, Hangzhou, 310058, P. R. China
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18
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Huang HT, Lumpkin RJ, Tsai RW, Su S, Zhao X, Xiong Y, Chen J, Mageed N, Donovan KA, Fischer ES, Sellers WR. Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates. Nat Chem Biol 2024; 20:1227-1236. [PMID: 38514884 DOI: 10.1038/s41589-024-01590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Protein ubiquitylation controls diverse processes within eukaryotic cells, including protein degradation, and is often dysregulated in disease. Moreover, small-molecule degraders that redirect ubiquitylation activities toward disease targets are an emerging and promising therapeutic class. Over 600 E3 ubiquitin ligases are expressed in humans, but their substrates remain largely elusive, necessitating the development of new methods for their discovery. Here we report the development of E3-substrate tagging by ubiquitin biotinylation (E-STUB), a ubiquitin-specific proximity labeling method that biotinylates ubiquitylated substrates in proximity to an E3 ligase of interest. E-STUB accurately identifies the direct ubiquitylated targets of protein degraders, including collateral targets and ubiquitylation events that do not lead to substrate degradation. It also detects known substrates of E3 ligase CRBN and VHL with high specificity. With the ability to elucidate proximal ubiquitylation events, E-STUB may facilitate the development of proximity-inducing therapeutics and act as a generalizable method for E3-substrate mapping.
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Affiliation(s)
- Hai-Tsang Huang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ryan W Tsai
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Shuyao Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xu Zhao
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yuan Xiong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - James Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nada Mageed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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19
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Yang J, Wu Y, Zhu Q, Qu X, Ou H, Liu H, Wei Y, Ge D, Lu C, Jiang B, Song X. Discovery of a first-in-class protein degrader for the c-ros oncogene 1 (ROS1). Bioorg Chem 2024; 150:107590. [PMID: 38955003 DOI: 10.1016/j.bioorg.2024.107590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/16/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
The c-ros oncogene 1 (ROS1), an oncogenic driver, is known to induce non-small cell lung cancer (NSCLC) when overactivated, particularly through the formation of fusion proteins. Traditional targeted therapies focus on inhibiting ROS1 activity with ROS 1 inhibitors to manage cancer progression. However, a new strategy involving the design of protein degraders offers a more potent approach by completely degrading ROS1 fusion oncoproteins, thereby effectively blocking their kinase activity and enhancing anti-tumour potential. Utilizing PROteolysis-TArgeting Chimera (PROTAC) technology and informed by molecular docking and rational design, we report the first ROS1-specific PROTAC, SIAIS039. This degrader effectively targets multiple ROS1 fusion oncoproteins (CD74-ROS1, SDC4-ROS1 and SLC34A2-ROS1) in engineered Ba/F3 cells and HCC78 cells, demonstrating anti-tumour effects against ROS1 fusion-driven cancer cells. It suppresses cell proliferation, induces cell cycle arrest, and apoptosis, and inhibits clonogenicity. The anti-tumour efficacy of SIAIS039 surpasses two approved drugs, crizotinib and entrectinib, and matches that of the top inhibitors, including lorlatinib and taletrectinib. Mechanistic studies confirm that the degradation induced by 039 requires the participation of ROS1 ligands and E3 ubiquitin ligases, and involves the proteasome and ubiquitination. In addition, 039 exhibited excellent oral bioavailability in a mouse xenograft model, highlighting its potential for clinical application. In conclusion, our study presents a promising and novel therapeutic strategy for ROS1 fusion-positive NSCLC by targeting ROS1 fusion oncoproteins for degradation, laying the foundation for the development of further PROTAC and offering hope for patients with ROS1 fusion-positive NSCLC.
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Affiliation(s)
- Jiawen Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Yifan Wu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qiaoliang Zhu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xiaojuan Qu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Hongyue Ou
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haixia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yongqi Wei
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chunlai Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Xiaoling Song
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
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20
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Li Z, Liu HY, He Z, Chakravarty A, Golden RP, Jiang Z, You I, Yue H, Donovan KA, Du G, Che J, Tse J, Che I, Lu W, Fischer ES, Zhang T, Gray NS, Yang PL. Discovery of Potent Degraders of the Dengue Virus Envelope Protein. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405829. [PMID: 39145423 DOI: 10.1002/advs.202405829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/26/2024] [Indexed: 08/16/2024]
Abstract
Targeted protein degradation has been widely adopted as a new approach to eliminate both established and previously recalcitrant therapeutic targets. Here, it is reported that the development of small molecule degraders of the envelope (E) protein of dengue virus. Two classes of bivalent E-degraders are developed by linking two previously reported E-binding small molecules, GNF-2, and CVM-2-12-2, to a glutarimide-based recruiter of the CRL4CRBN ligase to effect proteosome-mediated degradation of the E protein. ZXH-2-107 (based on GNF-2) is an E-degrader with ABL inhibitory activity while ZXH-8-004 (based on CVM-2-12-2) is a selective and potent E-degrader. These two compounds provide proof of concept that difficult-to-drug targets such as a viral envelope protein can be effectively eliminated using a bivalent degrader and provide starting points for the future development of a new class of direct-acting antiviral drugs.
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Affiliation(s)
- Zhengnian Li
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Han-Yuan Liu
- Department of Microbiology and Immunology, Stanford University School of Medicine, 279 Campus Drive, Palo Alto, CA, 94305, USA
| | - Zhixiang He
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, 02115, USA
| | - Antara Chakravarty
- Department of Microbiology and Immunology, Stanford University School of Medicine, 279 Campus Drive, Palo Alto, CA, 94305, USA
| | - Ryan P Golden
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Zixuan Jiang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | | | - Katherine A Donovan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, 02115, USA
| | - Guangyan Du
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, 02115, USA
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, USA
| | - Jason Tse
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Isaac Che
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Wenchao Lu
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, 02115, USA
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, 290 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Priscilla L Yang
- Department of Microbiology and Immunology, Stanford University School of Medicine, 279 Campus Drive, Palo Alto, CA, 94305, USA
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21
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Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Rutter JC, Lumpkin RJ, Sandoval B, Jin CY, Schmoker AM, Ficarro SB, Cheong H, Metivier RJ, Wang MY, Xu S, Byun WS, Groendyke BJ, You I, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Sperling HT, Marto JA, Qi J, Nowak RP, Donovan KA, Słabicki M, Gray NS, Fischer ES, Ebert BL. Template-assisted covalent modification underlies activity of covalent molecular glues. Nat Chem Biol 2024:10.1038/s41589-024-01668-4. [PMID: 39075252 DOI: 10.1038/s41589-024-01668-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/05/2024] [Indexed: 07/31/2024]
Abstract
Molecular glues are proximity-inducing small molecules that have emerged as an attractive therapeutic approach. However, developing molecular glues remains challenging, requiring innovative mechanistic strategies to stabilize neoprotein interfaces and expedite discovery. Here we unveil a trans-labeling covalent molecular glue mechanism, termed 'template-assisted covalent modification'. We identified a new series of BRD4 molecular glue degraders that recruit CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). Through comprehensive biochemical, structural and mutagenesis analyses, we elucidated how pre-existing structural complementarity between DCAF16 and BRD4BD2 serves as a template to optimally orient the degrader for covalent modification of DCAF16Cys58. This process stabilizes the formation of BRD4-degrader-DCAF16 ternary complex and facilitates BRD4 degradation. Supporting generalizability, we found that a subset of degraders also induces GAK-BRD4BD2 interaction through trans-labeling of GAK. Together, our work establishes 'template-assisted covalent modification' as a mechanism for covalent molecular glues, which opens a new path to proximity-driven pharmacology.
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Affiliation(s)
- Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle W Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Justine C Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cyrus Y Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anna M Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hakyung Cheong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rebecca J Metivier
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michelle Y Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Brian J Groendyke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Logan H Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan M Tsai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Felix C Majewski
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Haniya T Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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22
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Jarusiewicz JA, Yoshimura S, Actis M, Li Y, Fu X, Yang L, Narina S, Pruett-Miller SM, Zhou S, Wang X, High AA, Nishiguchi G, Yang JJ, Rankovic Z. Development of an Orally Bioavailable LCK PROTAC Degrader as a Potential Therapeutic Approach to T-Cell Acute Lymphoblastic Leukemia. J Med Chem 2024; 67:11868-11884. [PMID: 38973320 DOI: 10.1021/acs.jmedchem.4c00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Despite significant advances over recent years, the treatment of T cell acute lymphoblastic leukemia (T-ALL) remains challenging. We have recently shown that a subset of T-ALL cases exhibited constitutive activation of the lymphocyte-specific protein tyrosine kinase (LCK) and were consequently responsive to treatments with LCK inhibitors and degraders such as dasatinib and dasatinib-based PROTACs. Here we report the design, synthesis and in vitro/vivo evaluation of SJ45566, a potent and orally bioavailable LCK PROTAC.
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Affiliation(s)
- Jamie A Jarusiewicz
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Satoshi Yoshimura
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Marisa Actis
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yong Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xiang Fu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Shilpa Narina
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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23
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Xiao Y, Yuan Y, Liu Y, Lin Z, Zheng G, Zhou D, Lv D. Targeted Protein Degradation: Current and Emerging Approaches for E3 Ligase Deconvolution. J Med Chem 2024; 67:11580-11596. [PMID: 38981094 DOI: 10.1021/acs.jmedchem.4c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Targeted protein degradation (TPD), including the use of proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) to degrade proteins, is an emerging strategy to develop novel therapies for cancer and beyond. PROTACs or MGDs function by inducing the proximity between an E3 ligase and a protein of interest (POI), leading to ubiquitination and consequent proteasomal degradation of the POI. Notably, one major issue in TPD is the lack of ligandable E3 ligases, as current studies predominantly use CUL4CRBN and CUL2VHL. The TPD community is seeking to expand the landscape of ligandable E3 ligases, but most discoveries rely on phenotypic screens or serendipity, necessitating systematic target deconvolution. Here, we examine and discuss both current and emerging E3 ligase deconvolution approaches for degraders discovered from phenotypic screens or monovalent glue chemistry campaigns, highlighting future prospects for identifying more ligandable E3 ligases.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
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24
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Lynch TL, Marin VL, McClure RA, Phipps C, Ronau JA, Rouhimoghadam M, Adams AM, Kandi S, Wolke ML, Shergalis AG, Potts GK, Nacham O, Richardson P, Kakavas SJ, Chhor G, Jenkins GJ, Woller KR, Warder SE, Vasudevan A, Reitsma JM. Quantitative Measurement of Rate of Targeted Protein Degradation. ACS Chem Biol 2024; 19:1604-1615. [PMID: 38980123 DOI: 10.1021/acschembio.4c00262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Targeted protein degradation (TPD) is a therapeutic approach that leverages the cell's natural machinery to degrade targets instead of inhibiting them. This is accomplished by using mono- or bifunctional small molecules designed to induce the proximity of target proteins and E3 ubiquitin ligases, leading to ubiquitination and subsequent proteasome-dependent degradation of the target. One of the most significant attributes of the TPD approach is its proposed catalytic mechanism of action, which permits substoichiometric exposure to achieve the desired pharmacological effects. However, apart from one in vitro study, studies supporting the catalytic mechanism of degraders are largely inferred based on potency. A more comprehensive understanding of the degrader catalytic mechanism of action can help aspects of compound development. To address this knowledge gap, we developed a workflow for the quantitative measurement of the catalytic rate of degraders in cells. Comparing a selective and promiscuous BTK degrader, we demonstrate that both compounds function as efficient catalysts of BTK degradation, with the promiscuous degrader exhibiting faster rates due to its ability to induce more favorable ternary complexes. By leveraging computational modeling, we show that the catalytic rate is highly dynamic as the target is depleted from cells. Further investigation of the promiscuous kinase degrader revealed that the catalytic rate is a better predictor of optimal degrader activity toward a specific target compared to degradation magnitude alone. In summary, we present a versatile method for mapping the catalytic activity of any degrader for TPD in cells.
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Affiliation(s)
- Thomas L Lynch
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Violeta L Marin
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Ryan A McClure
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Colin Phipps
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Judith A Ronau
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Milad Rouhimoghadam
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Ashley M Adams
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Soumya Kandi
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Malerie L Wolke
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Andrea G Shergalis
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Gregory K Potts
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Omprakash Nacham
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Paul Richardson
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Stephan J Kakavas
- Target Enabling Technologies, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Gekleng Chhor
- Target Enabling Technologies, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Gary J Jenkins
- Quantitative, Translational & ADME Sciences, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Kevin R Woller
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Scott E Warder
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Anil Vasudevan
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
| | - Justin M Reitsma
- Technology & Therapeutic Platforms, AbbVie Incorporated, 1 North Waukegan Rd., North Chicago, Illinois 60064, United States
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25
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HAMILTON GERHARD, EGGERSTORFER MARIETHERESE, STICKLER SANDRA. Development of PROTACS degrading KRAS and SOS1. Oncol Res 2024; 32:1257-1264. [PMID: 39055890 PMCID: PMC11267056 DOI: 10.32604/or.2024.051653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/24/2024] [Indexed: 07/28/2024] Open
Abstract
The Kirsten rat sarcoma virus-son of sevenless 1 (KRAS-SOS1) axis drives tumor growth preferentially in pancreatic, colon, and lung cancer. Now, KRAS G12C mutated tumors can be successfully treated with inhibitors that covalently block the cysteine of the switch II binding pocket of KRAS. However, the range of other KRAS mutations is not amenable to treatment and the G12C-directed agents Sotorasib and Adragrasib show a response rate of only approximately 40%, lasting for a mean period of 8 months. One approach to increase the efficacy of inhibitors is their inclusion into proteolysis-targeting chimeras (PROTACs), which degrade the proteins of interest and exhibit much higher antitumor activity through multiple cycles of activity. Accordingly, PROTACs have been developed based on KRAS- or SOS1-directed inhibitors coupled to either von Hippel-Lindau (VHL) or Cereblon (CRBN) ligands that invoke the proteasomal degradation. Several of these PROTACs show increased activity in vitro and in vivo compared to their cognate inhibitors but their toxicity in normal tissues is not clear. The CRBN PROTACs containing thalidomide derivatives cannot be tested in experimental animals. Resistance to such PROTACS arises through downregulation or inactivation of CRBN or factors of the functional VHL E3 ubiquitin ligase. Although highly active KRAS and SOS1 PROTACs have been formulated their clinical application remains difficult.
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Affiliation(s)
- GERHARD HAMILTON
- Institute of Pharmacology, Medical University of Vienna, Vienna, 1090, Austria
| | | | - SANDRA STICKLER
- Institute of Pharmacology, Medical University of Vienna, Vienna, 1090, Austria
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26
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Sobierajski T, Małolepsza J, Pichlak M, Gendaszewska-Darmach E, Błażewska KM. The impact of E3 ligase choice on PROTAC effectiveness in protein kinase degradation. Drug Discov Today 2024; 29:104032. [PMID: 38789027 DOI: 10.1016/j.drudis.2024.104032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
Proteolysis targeting chimera (PROTACs) provide a novel therapeutic approach that is revolutionizing drug discovery. The success of PROTACs largely depends on the combination of their three fragments: E3 ligase ligand, linker and protein of interest (POI)-targeting ligand. We summarize the pivotal significance of the precise combination of the E3 ligase ligand with the POI-recruiting warhead, which is crucial for the successful execution of cellular processes and achieving the desired outcomes. Therefore, the key to our selection was the use of at least two ligands recruiting two different ligases. This approach enables a direct comparison of the impacts of the specific ligases on target degradation.
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Affiliation(s)
- Tomasz Sobierajski
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Joanna Małolepsza
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Marta Pichlak
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland
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27
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Koldenhof P, Bemelmans MP, Ghosh B, Damm-Ganamet KL, van Vlijmen HWT, Pande V. Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases. Proteins 2024; 92:819-829. [PMID: 38337153 DOI: 10.1002/prot.26675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/12/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
Proteolysis Targeting Chimeras (PROTACs) are an emerging therapeutic modality and chemical biology tools for Targeted Protein Degradation (TPD). PROTACs contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. There are over 600 E3 ligases known so far, but only a handful have been exploited for TPD applications. A key reason for this is the scarcity of ligands binding various E3 ligases and the paucity of structural data available, which complicates ligand design across the family. In this study, we aim to progress PROTAC discovery by proposing a shortlist of E3 ligases that can be prioritized for covalent targeting by performing systematic structural ligandability analysis on a chemoproteomic dataset of potentially reactive cysteines across hundreds of E3 ligases. One of the goals of this study is to apply AlphaFold (AF) models for ligandability evaluations, as for a vast majority of these ligases an experimental structure is not available in the protein data bank (PDB). Using a combination of pocket features, AF model quality and additional aspects, we propose a shortlist of E3 ligases and corresponding cysteines that can be prioritized to potentially discover covalent ligands and expand the PROTAC toolbox.
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Affiliation(s)
- Patrick Koldenhof
- Computer-Aided Drug Design, Janssen Pharmaceuticals, Beerse, Belgium
| | | | - Brahma Ghosh
- Discovery Chemistry, Janssen Pharmaceuticals, Spring House, Pennsylvania, USA
| | | | | | - Vineet Pande
- Computer-Aided Drug Design, Janssen Pharmaceuticals, Beerse, Belgium
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28
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Verma SK, Witkin KL, Sharman A, Smith MA. Targeting fusion oncoproteins in childhood cancers: challenges and future opportunities for developing therapeutics. J Natl Cancer Inst 2024; 116:1012-1018. [PMID: 38574391 PMCID: PMC11223828 DOI: 10.1093/jnci/djae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/19/2024] [Accepted: 03/24/2024] [Indexed: 04/06/2024] Open
Abstract
Fusion oncoproteins are associated with childhood cancers and have proven challenging to target, aside from those that include kinases. As part of its efforts for targeting childhood cancers, the National Cancer Institute recently conducted a series on Novel Chemical Approaches for Targeting Fusion Oncoproteins. Key learnings on leading platforms and technologies that can be used to advance the development of molecular therapeutics that target fusion oncoproteins in childhood cancers are described. Recent breakthroughs in medicinal chemistry and chemical biology provide new ground and creative strategies to exploit for the development of targeted agents for improving outcomes against these recalcitrant cancers.
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Affiliation(s)
- Sharad K Verma
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keren L Witkin
- Division of Cancer Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anu Sharman
- Division of Cancer Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Malcolm A Smith
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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29
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Ichikawa S, Payne NC, Xu W, Chang CF, Vallavoju N, Frome S, Flaxman HA, Mazitschek R, Woo CM. The cyclimids: Degron-inspired cereblon binders for targeted protein degradation. Cell Chem Biol 2024; 31:1162-1175.e10. [PMID: 38320555 DOI: 10.1016/j.chembiol.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/02/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024]
Abstract
Cereblon (CRBN) is an E3 ligase substrate adapter widely exploited for targeted protein degradation (TPD) strategies. However, achieving efficient and selective target degradation is a preeminent challenge with ligands that engage CRBN. Here, we report that the cyclimids, ligands derived from the C-terminal cyclic imide degrons of CRBN, exhibit distinct modes of interaction with CRBN and offer a facile approach for developing potent and selective bifunctional degraders. Quantitative TR-FRET-based characterization of 60 cyclimid degraders in binary and ternary complexes across different substrates revealed that ternary complex binding affinities correlated strongly with cellular degradation efficiency. Our studies establish the unique properties of the cyclimids as versatile warheads in TPD and a systematic biochemical approach for quantifying ternary complex formation to predict their cellular degradation activity, which together will accelerate the development of ligands that engage CRBN.
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Affiliation(s)
- Saki Ichikawa
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - N Connor Payne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wenqing Xu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chia-Fu Chang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nandini Vallavoju
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Spencer Frome
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hope A Flaxman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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30
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Li Z, Liu HY, He Z, Chakravarty A, Golden RP, Jiang Z, You I, Yue H, Donovan KA, Du G, Che J, Tse J, Che I, Lu W, Fischer ES, Zhang T, Gray NS, Yang PL. Discovery of Potent Degraders of the Dengue Virus Envelope Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596987. [PMID: 38854003 PMCID: PMC11160776 DOI: 10.1101/2024.06.01.596987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Targeted protein degradation has been widely adopted as a new approach to eliminate both established and previously recalcitrant therapeutic targets. Here we report the development of small molecule degraders of the envelope (E) protein of dengue virus. We developed two classes of bivalent E-degraders, linking two previously reported E-binding small molecules, GNF-2 and CVM-2-12-2, to a glutarimide-based recruiter of the CRL4CRBN ligase to effect proteosome-mediated degradation of the E protein. ZXH-2-107 (based on GNF-2) is an E degrader with ABL inhibition while ZXH-8-004 (based on CVM-2-12-2) is a selective and potent E-degrader. These two compounds provide proof-of-concept that difficult-to-drug targets such as a viral envelope protein can be effectively eliminated using a bivalent degrader and provide starting points for the future development of a new class antiviral drugs.
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Affiliation(s)
- Zhengnian Li
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Han-Yuan Liu
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
| | - Zhixiang He
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Antara Chakravarty
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
| | - Ryan P. Golden
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Zixuan Jiang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Hong Yue
- 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
| | - Guangyan Du
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Jason Tse
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Isaac Che
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Wenchao Lu
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - 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
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Priscilla L. Yang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
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31
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Reinecke M, Brear P, Vornholz L, Berger BT, Seefried F, Wilhelm S, Samaras P, Gyenis L, Litchfield DW, Médard G, Müller S, Ruland J, Hyvönen M, Wilhelm M, Kuster B. Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors. Nat Chem Biol 2024; 20:577-585. [PMID: 37904048 PMCID: PMC11062922 DOI: 10.1038/s41589-023-01459-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/22/2023] [Indexed: 11/01/2023]
Abstract
Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover such probes, we profiled 1,183 compounds from drug discovery projects in lysates of cancer cell lines using Kinobeads. The resulting 500,000 compound-target interactions are available in ProteomicsDB and we exemplify how this molecular resource may be used. For instance, the data revealed several hundred reasonably selective compounds for 72 kinases. Cellular assays validated GSK986310C as a candidate SYK (spleen tyrosine kinase) probe and X-ray crystallography uncovered the structural basis for the observed selectivity of the CK2 inhibitor GW869516X. Compounds targeting PKN3 were discovered and phosphoproteomics identified substrates that indicate target engagement in cells. We anticipate that this molecular resource will aid research in drug discovery and chemical biology.
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Affiliation(s)
- Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Larsen Vornholz
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Benedict-Tilmann Berger
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Florian Seefried
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David William Litchfield
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Jürgen Ruland
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
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32
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Zhu D, Liang H, Du Z, Liu Q, Li G, Zhang W, Wu D, Zhou X, Song Y, Yang C. Altered Metabolism and Inflammation Driven by Post-translational Modifications in Intervertebral Disc Degeneration. RESEARCH (WASHINGTON, D.C.) 2024; 7:0350. [PMID: 38585329 PMCID: PMC10997488 DOI: 10.34133/research.0350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024]
Abstract
Intervertebral disc degeneration (IVDD) is a prevalent cause of low back pain and a leading contributor to disability. IVDD progression involves pathological shifts marked by low-grade inflammation, extracellular matrix remodeling, and metabolic disruptions characterized by heightened glycolytic pathways, mitochondrial dysfunction, and cellular senescence. Extensive posttranslational modifications of proteins within nucleus pulposus cells and chondrocytes play crucial roles in reshaping the intervertebral disc phenotype and orchestrating metabolism and inflammation in diverse contexts. This review focuses on the pivotal roles of phosphorylation, ubiquitination, acetylation, glycosylation, methylation, and lactylation in IVDD pathogenesis. It integrates the latest insights into various posttranslational modification-mediated metabolic and inflammatory signaling networks, laying the groundwork for targeted proteomics and metabolomics for IVDD treatment. The discussion also highlights unexplored territories, emphasizing the need for future research, particularly in understanding the role of lactylation in intervertebral disc health, an area currently shrouded in mystery.
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Affiliation(s)
- Dingchao Zhu
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Huaizhen Liang
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Zhi Du
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Qian Liu
- College of Life Sciences,
Wuhan University, Wuhan 430072, Hubei Province, China
| | - Gaocai Li
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Weifeng Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Di Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Xingyu Zhou
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Yu Song
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical College,
Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
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33
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Hernández-Morán BA, Taylor G, Lorente-Macías Á, Wood AJ. Degron tagging for rapid protein degradation in mice. Dis Model Mech 2024; 17:dmm050613. [PMID: 38666498 PMCID: PMC11073515 DOI: 10.1242/dmm.050613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
Degron tagging allows proteins of interest to be rapidly degraded, in a reversible and tuneable manner, in response to a chemical stimulus. This provides numerous opportunities for understanding disease mechanisms, modelling therapeutic interventions and constructing synthetic gene networks. In recent years, many laboratories have applied degron tagging successfully in cultured mammalian cells, spurred by rapid advances in the fields of genome editing and targeted protein degradation. In this At a Glance article, we focus on recent efforts to apply degron tagging in mouse models, discussing the distinct set of challenges and opportunities posed by the in vivo environment.
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Affiliation(s)
- Brianda A. Hernández-Morán
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Gillian Taylor
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Álvaro Lorente-Macías
- Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XR, UK
| | - Andrew J. Wood
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
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34
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Poirson J, Cho H, Dhillon A, Haider S, Imrit AZ, Lam MHY, Alerasool N, Lacoste J, Mizan L, Wong C, Gingras AC, Schramek D, Taipale M. Proteome-scale discovery of protein degradation and stabilization effectors. Nature 2024; 628:878-886. [PMID: 38509365 DOI: 10.1038/s41586-024-07224-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
Targeted protein degradation and stabilization are promising therapeutic modalities because of their potency, versatility and their potential to expand the druggable target space1,2. However, only a few of the hundreds of E3 ligases and deubiquitinases in the human proteome have been harnessed for this purpose, which substantially limits the potential of the approach. Moreover, there may be other protein classes that could be exploited for protein stabilization or degradation3-5, but there are currently no methods that can identify such effector proteins in a scalable and unbiased manner. Here we established a synthetic proteome-scale platform to functionally identify human proteins that can promote the degradation or stabilization of a target protein in a proximity-dependent manner. Our results reveal that the human proteome contains a large cache of effectors of protein stability. The approach further enabled us to comprehensively compare the activities of human E3 ligases and deubiquitinases, identify and characterize non-canonical protein degraders and stabilizers and establish that effectors have vastly different activities against diverse targets. Notably, the top degraders were more potent against multiple therapeutically relevant targets than the currently used E3 ligases cereblon and VHL. Our study provides a functional catalogue of stability effectors for targeted protein degradation and stabilization and highlights the potential of induced proximity screens for the discovery of new proximity-dependent protein modulators.
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Affiliation(s)
- Juline Poirson
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Hanna Cho
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Akashdeep Dhillon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shahan Haider
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ahmad Zoheyr Imrit
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mandy Hiu Yi Lam
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Nader Alerasool
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Lacoste
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lamisa Mizan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Daniel Schramek
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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35
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Bouvier C, Lawrence R, Cavallo F, Xolalpa W, Jordan A, Hjerpe R, Rodriguez MS. Breaking Bad Proteins-Discovery Approaches and the Road to Clinic for Degraders. Cells 2024; 13:578. [PMID: 38607017 PMCID: PMC11011670 DOI: 10.3390/cells13070578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) describe compounds that bind to and induce degradation of a target by simultaneously binding to a ubiquitin ligase. More generally referred to as bifunctional degraders, PROTACs have led the way in the field of targeted protein degradation (TPD), with several compounds currently undergoing clinical testing. Alongside bifunctional degraders, single-moiety compounds, or molecular glue degraders (MGDs), are increasingly being considered as a viable approach for development of therapeutics, driven by advances in rational discovery approaches. This review focuses on drug discovery with respect to bifunctional and molecular glue degraders within the ubiquitin proteasome system, including analysis of mechanistic concepts and discovery approaches, with an overview of current clinical and pre-clinical degrader status in oncology, neurodegenerative and inflammatory disease.
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Affiliation(s)
- Corentin Bouvier
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
| | - Rachel Lawrence
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Francesca Cavallo
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Wendy Xolalpa
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62209, Morelos, Mexico;
| | - Allan Jordan
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Roland Hjerpe
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Manuel S. Rodriguez
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
- Pharmadev, UMR 152, Université de Toulouse, IRD, UT3, 31400 Toulouse, France
- B Molecular, Centre Pierre Potier, Canceropôle, 31106 Toulouse, France
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36
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Robbins DW, Noviski MA, Tan YS, Konst ZA, Kelly A, Auger P, Brathaban N, Cass R, Chan ML, Cherala G, Clifton MC, Gajewski S, Ingallinera TG, Karr D, Kato D, Ma J, McKinnell J, McIntosh J, Mihalic J, Murphy B, Panga JR, Peng G, Powers J, Perez L, Rountree R, Tenn-McClellan A, Sands AT, Weiss DR, Wu J, Ye J, Guiducci C, Hansen G, Cohen F. Discovery and Preclinical Pharmacology of NX-2127, an Orally Bioavailable Degrader of Bruton's Tyrosine Kinase with Immunomodulatory Activity for the Treatment of Patients with B Cell Malignancies. J Med Chem 2024; 67:2321-2336. [PMID: 38300987 DOI: 10.1021/acs.jmedchem.3c01007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Bruton's tyrosine kinase (BTK), a member of the TEC family of kinases, is an essential effector of B-cell receptor (BCR) signaling. Chronic activation of BTK-mediated BCR signaling is a hallmark of many hematological malignancies, which makes it an attractive therapeutic target. Pharmacological inhibition of BTK enzymatic function is now a well-proven strategy for the treatment of patients with these malignancies. We report the discovery and characterization of NX-2127, a BTK degrader with concomitant immunomodulatory activity. By design, NX-2127 mediates the degradation of transcription factors IKZF1 and IKZF3 through molecular glue interactions with the cereblon E3 ubiquitin ligase complex. NX-2127 degrades common BTK resistance mutants, including BTKC481S. NX-2127 is orally bioavailable, exhibits in vivo degradation across species, and demonstrates efficacy in preclinical oncology models. NX-2127 has advanced into first-in-human clinical trials and achieves deep and sustained degradation of BTK following daily oral dosing at 100 mg.
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Affiliation(s)
- Daniel W Robbins
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Mark A Noviski
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Ying Siow Tan
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Zef A Konst
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Aileen Kelly
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Paul Auger
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Nivetha Brathaban
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Robert Cass
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Ming Liang Chan
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Ganesh Cherala
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Matthew C Clifton
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Stefan Gajewski
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Timothy G Ingallinera
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Dane Karr
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Daisuke Kato
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Jun Ma
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Jenny McKinnell
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Joel McIntosh
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Jeff Mihalic
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Brent Murphy
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Jaipal Reddy Panga
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Ge Peng
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Janine Powers
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Luz Perez
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Ryan Rountree
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Austin Tenn-McClellan
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Arthur T Sands
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Dahlia R Weiss
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Jeffrey Wu
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Jordan Ye
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Cristiana Guiducci
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Gwenn Hansen
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
| | - Frederick Cohen
- Nurix Therapeutics, Inc., 1700 Owens St., San Francisco, California 94158, United States
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Nalawansha DA, Mangano K, den Besten W, Potts PR. TAC-tics for Leveraging Proximity Biology in Drug Discovery. Chembiochem 2024; 25:e202300712. [PMID: 38015747 DOI: 10.1002/cbic.202300712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
Chemically induced proximity (CIP) refers to co-opting naturally occurring biological pathways using synthetic molecules to recruit neosubstrates that are not normally encountered or to enhance the affinity of naturally occurring interactions. Leveraging proximity biology through CIPs has become a rapidly evolving field and has garnered considerable interest in basic research and drug discovery. PROteolysis TArgeting Chimera (PROTAC) is a well-established CIP modality that induces the proximity between a target protein and an E3 ubiquitin ligase, causing target protein degradation via the ubiquitin-proteasome system. Inspired by PROTACs, several other induced proximity modalities have emerged to modulate both proteins and RNA over recent years. In this review, we summarize the critical advances and opportunities in the field, focusing on protein degraders, RNA degraders and non-degrader modalities such as post-translational modification (PTM) and protein-protein interaction (PPI) modulators. We envision that these emerging proximity-based drug modalities will be valuable resources for both biological research and therapeutic discovery in the future.
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Affiliation(s)
| | - Kyle Mangano
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Willem den Besten
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
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Torres-Ayuso P, Katerji M, Mehlich D, Lookingbill SA, Sabbasani VR, Liou H, Casillas AL, Chauhan SS, Serwa R, Rubin MR, Marusiak AA, Swenson RE, Warfel NA, Brognard J. PIM1 targeted degradation prevents the emergence of chemoresistance in prostate cancer. Cell Chem Biol 2024; 31:326-337.e11. [PMID: 38016478 PMCID: PMC10922308 DOI: 10.1016/j.chembiol.2023.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 08/08/2023] [Accepted: 10/29/2023] [Indexed: 11/30/2023]
Abstract
PIM kinases have important pro-tumorigenic roles and mediate several oncogenic traits, including cell proliferation, survival, and chemotherapeutic resistance. As a result, multiple PIM inhibitors have been pursued as investigational new drugs in cancer; however, response to PIM inhibitors in solid tumors has fallen short of expectations. We found that inhibition of PIM kinase activity stabilizes protein levels of all three PIM isoforms (PIM1/2/3), and this can promote resistance to PIM inhibitors and chemotherapy. To overcome this effect, we designed PIM proteolysis targeting chimeras (PROTACs) to target PIM for degradation. PIM PROTACs effectively downmodulated PIM levels through the ubiquitin-proteasome pathway. Importantly, degradation of PIM kinases was more potent than inhibition of catalytic activity at inducing apoptosis in prostate cancer cell line models. In conclusion, we provide evidence of the advantages of degrading PIM kinases versus inhibiting their catalytic activity to target the oncogenic functions of PIM kinases.
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Affiliation(s)
- Pedro Torres-Ayuso
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, NIH, Frederick, MD 21702, USA; Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Meghri Katerji
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Dawid Mehlich
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, NIH, Frederick, MD 21702, USA; Laboratory of Molecular OncoSignalling, IMol Polish Academy of Sciences, 00-783 Warsaw, Poland; Doctoral School of the Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Sophia A Lookingbill
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Venkata R Sabbasani
- Chemistry and Synthesis Center, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Hope Liou
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | | | - Shailender S Chauhan
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Remigiusz Serwa
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, 00-783 Warsaw, Poland
| | - Maxine R Rubin
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Anna A Marusiak
- Laboratory of Molecular OncoSignalling, IMol Polish Academy of Sciences, 00-783 Warsaw, Poland
| | - Rolf E Swenson
- Chemistry and Synthesis Center, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Noel A Warfel
- University of Arizona Cancer Center, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA.
| | - John Brognard
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, NIH, Frederick, MD 21702, USA.
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Lane IC, Kembuan G, Carreiro J, Kann MC, Lin W, Bouffard AA, Kreuzer J, Morris R, Schneider EM, Kim JY, Zou C, Salas-Benito D, Gasser JA, Leick MB, Słabicki M, Haas W, Maus MV, Jan M. Genetic retargeting of E3 ligases to enhance CAR T cell therapy. Cell Chem Biol 2024; 31:338-348.e5. [PMID: 37989314 PMCID: PMC10922718 DOI: 10.1016/j.chembiol.2023.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 08/09/2023] [Accepted: 10/27/2023] [Indexed: 11/23/2023]
Abstract
Chimeric antigen receptor (CAR) T cell therapies are medical breakthroughs in cancer treatment. However, treatment failure is often caused by CAR T cell dysfunction. Additional approaches are needed to overcome inhibitory signals that limit anti-tumor potency. Here, we developed bifunctional fusion "degrader" proteins that bridge one or more target proteins and an E3 ligase complex to enforce target ubiquitination and degradation. Conditional degradation strategies were developed using inducible degrader transgene expression or small molecule-dependent E3 recruitment. We further engineered degraders to block SMAD-dependent TGFβ signaling using a domain from the SARA protein to target both SMAD2 and SMAD3. SMAD degrader CAR T cells were less susceptible to suppression by TGFβ and demonstrated enhanced anti-tumor potency in vivo. These results demonstrate a clinically suitable synthetic biology platform to reprogram E3 ligase target specificity for conditional, multi-specific endogenous protein degradation, with promising applications including enhancing the potency of CAR T cell therapy.
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Affiliation(s)
- Isabel C Lane
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Gabriele Kembuan
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Jeannie Carreiro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael C Kann
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - William Lin
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Amanda A Bouffard
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Johannes Kreuzer
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert Morris
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Joanna Y Kim
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Charles Zou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Diego Salas-Benito
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica A Gasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark B Leick
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Mikołaj Słabicki
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wilhelm Haas
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marcela V Maus
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Max Jan
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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40
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Nguyen TM, Sreekanth V, Deb A, Kokkonda P, Tiwari PK, Donovan KA, Shoba V, Chaudhary SK, Mercer JAM, Lai S, Sadagopan A, Jan M, Fischer ES, Liu DR, Ebert BL, Choudhary A. Proteolysis-targeting chimeras with reduced off-targets. Nat Chem 2024; 16:218-228. [PMID: 38110475 PMCID: PMC10913580 DOI: 10.1038/s41557-023-01379-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 10/13/2023] [Indexed: 12/20/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) are molecules that induce proximity between target proteins and E3 ligases triggering target protein degradation. Pomalidomide, a widely used E3 ligase recruiter in PROTACs, can independently degrade other proteins, including zinc-finger (ZF) proteins, with vital roles in health and disease. This off-target degradation hampers the therapeutic applicability of pomalidomide-based PROTACs, requiring development of PROTAC design rules that minimize off-target degradation. Here we developed a high-throughput platform that interrogates off-target degradation and found that reported pomalidomide-based PROTACs induce degradation of several ZF proteins. We generated a library of pomalidomide analogues to understand how functionalizing different positions of the phthalimide ring, hydrogen bonding, and steric and hydrophobic effects impact ZF protein degradation. Modifications of appropriate size on the C5 position reduced off-target ZF degradation, which we validated through target engagement and proteomics studies. By applying these design principles, we developed anaplastic lymphoma kinase oncoprotein-targeting PROTACs with enhanced potency and minimal off-target degradation.
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Affiliation(s)
- Tuan M Nguyen
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Vedagopuram Sreekanth
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Arghya Deb
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Praveen K Tiwari
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Veronika Shoba
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Santosh K Chaudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jaron A M Mercer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Sophia Lai
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ananthan Sadagopan
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Max Jan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA.
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41
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Wang Y, Zheng J, Long Y, Wu W, Zhu Y. Direct degradation and stabilization of proteins: New horizons in treatment of nonalcoholic steatohepatitis. Biochem Pharmacol 2024; 220:115989. [PMID: 38122854 DOI: 10.1016/j.bcp.2023.115989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is featured with excessive hepatic lipid accumulation and its global prevalence is soaring. Nonalcoholic steatohepatitis (NASH), the severe systemic inflammatory subtype of NAFLD, is tightly associated with metabolic comorbidities, and the hepatocytes manifest severe inflammation and ballooning. Currently the therapeutic options for treating NASH are limited. Potent small molecules specifically intervene with the signaling pathways that promote pathogenesis of NASH. Nevertheless they have obvious adverse effects and show long-term ineffectiveness in clinical trials. It poses the fundamental question to efficiently and safely inhibit the pathogenic processes. Targeted protein degradation (TPD) belongs to the direct degradation strategies and is a burgeoning strategy. It utilizes the small molecules to bind to the target proteins and recruit the endogenous proteasome, lysosome and autophagosome-mediated degradation machineries. They effectively and specifically degrade the target proteins. It has exhibited promising therapeutic effects in treatment of cancer, neurodegenerative diseases and other diseases in a catalytic manner at low doses. We critically discuss the principles of multiple direct degradation strategies, especially PROTAC and ATTEC. We extensively analyze their emerging application in degradation of excessive pathogenic proteins and lipid droplets, which promote the progression of NASH. Moreover, we discuss the opposite strategy that utilizes the small molecules to recruit deubiquinases to stabilize the NASH/MASH-suppressing proteins. Their advantages, limitations, as well as the solutions to address the limitations have been analyzed. In summary, the innovative direct degradation strategies provide new insights into design of next-generation therapeutics to combat NASH with optimal safety paradigm and efficiency.
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Affiliation(s)
- Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, PR China.
| | - Jianan Zheng
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China
| | - Yun Long
- Department of Endocrinology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, PR China
| | - Wenyi Wu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China
| | - Yutong Zhu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China
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42
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Peng X, Hu Z, Zeng L, Zhang M, Xu C, Lu B, Tao C, Chen W, Hou W, Cheng K, Bi H, Pan W, Chen J. Overview of epigenetic degraders based on PROTAC, molecular glue, and hydrophobic tagging technologies. Acta Pharm Sin B 2024; 14:533-578. [PMID: 38322348 PMCID: PMC10840439 DOI: 10.1016/j.apsb.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 02/08/2024] Open
Abstract
Epigenetic pathways play a critical role in the initiation, progression, and metastasis of cancer. Over the past few decades, significant progress has been made in the development of targeted epigenetic modulators (e.g., inhibitors). However, epigenetic inhibitors have faced multiple challenges, including limited clinical efficacy, toxicities, lack of subtype selectivity, and drug resistance. As a result, the design of new epigenetic modulators (e.g., degraders) such as PROTACs, molecular glue, and hydrophobic tagging (HyT) degraders has garnered significant attention from both academia and pharmaceutical industry, and numerous epigenetic degraders have been discovered in the past decade. In this review, we aim to provide an in-depth illustration of new degrading strategies (2017-2023) targeting epigenetic proteins for cancer therapy, focusing on the rational design, pharmacodynamics, pharmacokinetics, clinical status, and crystal structure information of these degraders. Importantly, we also provide deep insights into the potential challenges and corresponding remedies of this approach to drug design and development. Overall, we hope this review will offer a better mechanistic understanding and serve as a useful guide for the development of emerging epigenetic-targeting degraders.
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Affiliation(s)
- Xiaopeng Peng
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Zhihao Hu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Limei Zeng
- College of Basic Medicine, Gannan Medical University, Ganzhou 314000, China
| | - Meizhu Zhang
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Congcong Xu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Benyan Lu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Chengpeng Tao
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Weiming Chen
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Wen Hou
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huichang Bi
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wanyi Pan
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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43
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Chowdhury SR, Chuong P, Mgbemena VE, Statsyuk A. Development of a PROTAC Targeting Chk1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573733. [PMID: 38260247 PMCID: PMC10802242 DOI: 10.1101/2023.12.30.573733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
A series of Chk1 degraders were designed and synthesized. The degraders were developed through the conjugation of a promiscuous kinase binder and thalidomide. One of the degraders PROTAC-2 was able to decrease Chk1 levels in a concentration-dependent manner in A375 cells. The developed probes can be useful for the development of selective and more potent Chk1 degraders.
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Affiliation(s)
- Sandipan Roy Chowdhury
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Health 2, 4349 Martin Luther King Boulevard, Houston, Texas, 77204
| | - Patrick Chuong
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Health 2, 4349 Martin Luther King Boulevard, Houston, Texas, 77204
| | - Victoria E Mgbemena
- Department of Biology, MD and S Brailsford College of Arts and Sciences, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Alexander Statsyuk
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Health 2, 4349 Martin Luther King Boulevard, Houston, Texas, 77204
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44
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Ru J, Wang Y, Li Z, Wang J, Ren C, Zhang J. Technologies of targeting histone deacetylase in drug discovery: Current progress and emerging prospects. Eur J Med Chem 2023; 261:115800. [PMID: 37708798 DOI: 10.1016/j.ejmech.2023.115800] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Histone deacetylases (HDACs) catalyze the hydrolysis of acetyl-l-lysine side chains in histones and non-histones, which are key to epigenetic regulation in humans. Targeting HDACs has emerged as a promising strategy for treating various types of cancer, including myeloma and hematologic malignancies. At present, numerous small molecule inhibitors targeting HDACs are actively being investigated in clinical trials. Despite their potential efficacy in cancer treatment, HDAC inhibitors suffer from multi-directional selectivity and preclinical resistance issues. Hence, developing novel inhibitors based on cutting-edge medicinal chemistry techniques is essential to overcome these limitations and improve clinical outcomes. This manuscript presents an extensive overview of the properties and biological functions of HDACs in cancer, provides an overview of the current state of development and limitations of clinical HDAC inhibitors, and analyzes a range of innovative medicinal chemistry techniques that are applied. These techniques include selective inhibitors, dual-target inhibitors, proteolysis targeting chimeras, and protein-protein interaction inhibitors.
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Affiliation(s)
- Jinxiao Ru
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuxi Wang
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China
| | - Zijia Li
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, USA
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Jifa Zhang
- Department of Neurology, Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China.
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45
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Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A biotin targeting chimera (BioTAC) system to map small molecule interactomes in situ. Nat Commun 2023; 14:8016. [PMID: 38049406 PMCID: PMC10695998 DOI: 10.1038/s41467-023-43507-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/12/2023] [Indexed: 12/06/2023] Open
Abstract
Understanding how small molecules bind to specific protein complexes in living cells is critical to understanding their mechanism-of-action. Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules would provide advantages over target-focused approaches, including the ability to detect previously unknown ligand targets and complexes. However, there are few current methods for unbiased profiling of small molecule interactomes. To address this, we envisioned a technology that would combine the sensitivity and live-cell compatibility of proximity labelling coupled to mass spectrometry, with the specificity and unbiased nature of chemoproteomics. In this manuscript, we describe the BioTAC system, a small-molecule guided proximity labelling platform that can rapidly identify both direct and complexed small molecule binding proteins. We benchmark the system against µMap, photoaffinity labelling, affinity purification coupled to mass spectrometry and proximity labelling coupled to mass spectrometry datasets. We also apply the BioTAC system to provide interactome maps of Trametinib and analogues. The BioTAC system overcomes a limitation of current approaches and supports identification of both inhibitor bound and molecular glue bound complexes.
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Affiliation(s)
- Andrew J Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gillian E Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bridget T Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth J Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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46
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Castelo-Soccio L, Kim H, Gadina M, Schwartzberg PL, Laurence A, O'Shea JJ. Protein kinases: drug targets for immunological disorders. Nat Rev Immunol 2023; 23:787-806. [PMID: 37188939 PMCID: PMC10184645 DOI: 10.1038/s41577-023-00877-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2023] [Indexed: 05/17/2023]
Abstract
Protein kinases play a major role in cellular activation processes, including signal transduction by diverse immunoreceptors. Given their roles in cell growth and death and in the production of inflammatory mediators, targeting kinases has proven to be an effective treatment strategy, initially as anticancer therapies, but shortly thereafter in immune-mediated diseases. Herein, we provide an overview of the status of small molecule inhibitors specifically generated to target protein kinases relevant to immune cell function, with an emphasis on those approved for the treatment of immune-mediated diseases. The development of inhibitors of Janus kinases that target cytokine receptor signalling has been a particularly active area, with Janus kinase inhibitors being approved for the treatment of multiple autoimmune and allergic diseases as well as COVID-19. In addition, TEC family kinase inhibitors (including Bruton's tyrosine kinase inhibitors) targeting antigen receptor signalling have been approved for haematological malignancies and graft versus host disease. This experience provides multiple important lessons regarding the importance (or not) of selectivity and the limits to which genetic information informs efficacy and safety. Many new agents are being generated, along with new approaches for targeting kinases.
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Affiliation(s)
- Leslie Castelo-Soccio
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hanna Kim
- Juvenile Myositis Pathogenesis and Therapeutics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Massimo Gadina
- Translational Immunology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Pamela L Schwartzberg
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Arian Laurence
- Department of Immunology, Royal Free London Hospitals NHS Foundation Trust, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
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47
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Xiao Y, Hale S, Awasthee N, Meng C, Zhang X, Liu Y, Ding H, Huo Z, Lv D, Zhang W, He M, Zheng G, Liao D. HDAC3 and HDAC8 PROTAC dual degrader reveals roles of histone acetylation in gene regulation. Cell Chem Biol 2023; 30:1421-1435.e12. [PMID: 37572669 PMCID: PMC10802846 DOI: 10.1016/j.chembiol.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 05/19/2023] [Accepted: 07/22/2023] [Indexed: 08/14/2023]
Abstract
HDAC3 and HDAC8 have critical biological functions and represent highly sought-after therapeutic targets. Because histone deacetylases (HDACs) have a very conserved catalytic domain, developing isozyme-selective inhibitors remains challenging. HDAC3/8 also have deacetylase-independent activity, which cannot be blocked by conventional enzymatic inhibitors. Proteolysis-targeting chimeras (PROTACs) can selectively degrade a target enzyme, abolishing both enzymatic and scaffolding function. Here, we report a novel HDAC3/8 dual degrader YX968 that induces highly potent, rapid, and selective degradation of both HDAC3/8 without triggering pan-HDAC inhibitory effects. Unbiased quantitative proteomic experiments confirmed its high selectivity. HDAC3/8 degradation by YX968 does not induce histone hyperacetylation and broad transcriptomic perturbation. Thus, histone hyperacetylation may be a major factor for altering transcription. YX968 promotes apoptosis and kills cancer cells with a high potency in vitro. YX968 thus represents a new probe for dissecting the complex biological functions of HDAC3/8.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Seth Hale
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nikee Awasthee
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Chengcheng Meng
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Haocheng Ding
- Department of Biostatistics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Mei He
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
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48
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Kim Y, Seo P, Jeon E, You I, Hwang K, Kim N, Tse J, Bae J, Choi HS, Hinshaw SM, Gray NS, Sim T. Targeted kinase degradation via the KLHDC2 ubiquitin E3 ligase. Cell Chem Biol 2023; 30:1414-1420.e5. [PMID: 37567174 PMCID: PMC10839117 DOI: 10.1016/j.chembiol.2023.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/17/2023] [Accepted: 07/18/2023] [Indexed: 08/13/2023]
Abstract
Chemically induced protein degradation is a powerful strategy for perturbing cellular biochemistry. The predominant mechanism of action for protein degrader drugs involves an induced proximity between the cellular ubiquitin-conjugation machinery and a target. Unlike traditional small molecule enzyme inhibition, targeted protein degradation can clear an undesired protein from cells. We demonstrate here the use of peptide ligands for Kelch-like homology domain-containing protein 2 (KLHDC2), a substrate adapter protein and member of the cullin-2 (CUL2) ubiquitin ligase complex, for targeted protein degradation. Peptide-based bivalent compounds that can induce proximity between KLHDC2 and target proteins cause degradation of the targeted factors. The cellular activity of these compounds depends on KLHDC2 binding. This work demonstrates the utility of KLHDC2 for targeted protein degradation and exemplifies a strategy for the rational design of peptide-based ligands useful for this purpose.
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Affiliation(s)
- Younghoon Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Pooreum Seo
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Eunhye Jeon
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Inchul You
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Kyubin Hwang
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Namkyoung Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jason Tse
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Juhyeon Bae
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Ha-Soon Choi
- Magicbullettherapeutics Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Stephen M Hinshaw
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA 94305, USA.
| | - Nathanael S Gray
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA 94305, USA.
| | - Taebo Sim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea; Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
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49
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Julio AR, Shikwana F, Truong C, Burton NR, Dominguez E, Turmon AC, Cao J, Backus K. Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564067. [PMID: 38014036 PMCID: PMC10680658 DOI: 10.1101/2023.10.30.564067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Protein homeostasis is tightly regulated, with damaged or misfolded proteins quickly eliminated by the proteasome and autophagosome pathways. By co-opting these processes, targeted protein degradation technologies enable pharmacological manipulation of protein abundance. Recently, cysteine-reactive molecules have been added to the degrader toolbox, which offer the benefit of unlocking the therapeutic potential of 'undruggable' protein targets. The proteome-wide impact of these molecules remains to be fully understood and given the general reactivity of many classes of cysteine-reactive electrophiles, on- and off-target effects are likely. Using chemical proteomics, we identified a cysteine-reactive small molecule degrader of the SARS-CoV-2 nonstructural protein 14 (nsp14), which effects degradation through direct modification of cysteines in both nsp14 and in host chaperones together with activation of global cell stress response pathways. We find that cysteine-reactive electrophiles increase global protein ubiquitylation, trigger proteasome activation, and result in widespread aggregation and depletion of host proteins, including components of the nuclear pore complex. Formation of stress granules was also found to be a remarkably ubiquitous cellular response to nearly all cysteine-reactive compounds and degraders. Collectively, our study sheds light on complexities of covalent target protein degradation and highlights untapped opportunities in manipulating and characterizing proteostasis processes via deciphering the cysteine-centric regulation of stress response pathways.
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Affiliation(s)
- Ashley R Julio
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Flowreen Shikwana
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Cindy Truong
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
| | - Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Emil Dominguez
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
| | - Alexandra C Turmon
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Jian Cao
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Keriann Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095 (USA)
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095 (USA)
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095 (USA)
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50
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Cruite J, Nowak R, Donovan KA, Ficarro SB, Huang H, Liu H, Liu Y, Marto JA, Metivier RJ, Fischer ES, Jones LH. Covalent Stapling of the Cereblon Sensor Loop Histidine Using Sulfur-Heterocycle Exchange. ACS Med Chem Lett 2023; 14:1576-1581. [PMID: 37974938 PMCID: PMC10641907 DOI: 10.1021/acsmedchemlett.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023] Open
Abstract
Site-specific modification of amino acid residues in protein binding pockets using sulfonyl exchange chemistry expands the druggable proteome by enabling the development of covalent modulators that target residues beyond cysteine. Sulfonyl fluoride and triazole electrophiles were incorporated previously into the cereblon (CRBN) molecular glue degrader EM12, to covalently engage His353 within the CRBN sensor loop, but these probes had poor human plasma stability. Attenuation of intrinsic reactivity through the development of sulfonyl pyrazoles, imidazoles, and nucleobases enhanced plasma stability, and several compounds retained efficient labeling of His353. For example, sulfonyl imidazole EM12-SO2Im covalently blocked the CRBN binding site and possessed excellent metabolic stability in human plasma, liver microsomes, and hepatocytes. These results highlight the potential suitability of sulfonyl imidazole and related sulfur(VI)-diazole exchange (SuDEx) warheads for covalent drug development and further exemplify the therapeutic promise of site-specific histidine targeting.
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Affiliation(s)
- Justin
T. Cruite
- Center
for Protein Degradation, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Radosław
P. Nowak
- Center
for Protein Degradation, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Katherine A. Donovan
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Scott B. Ficarro
- Department
of Cancer Biology, Department of Oncologic Pathology, Blais Proteomics
Center, and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Huang Huang
- Center
for Protein Degradation, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Hu Liu
- Center
for Protein Degradation, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yingpeng Liu
- Center
for Protein Degradation, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jarrod A. Marto
- Department
of Cancer Biology, Department of Oncologic Pathology, Blais Proteomics
Center, and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Rebecca J. Metivier
- Center
for Protein Degradation, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
| | - Eric S. Fischer
- Center
for Protein Degradation, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Lyn H. Jones
- Center
for Protein Degradation, 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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