1
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Shevalev R, Bischof L, Sapegin A, Bunev A, Olga G, Kantin G, Kalinin S, Hartmann MD. Discovery and characterization of potent spiro-isoxazole-based cereblon ligands with a novel binding mode. Eur J Med Chem 2024; 270:116328. [PMID: 38552426 DOI: 10.1016/j.ejmech.2024.116328] [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: 12/27/2023] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 04/21/2024]
Abstract
The vast majority of current cereblon (CRBN) ligands is based on the thalidomide scaffold, relying on glutarimide as the core binding moiety. With this architecture, most of these ligands inherit the overall binding mode, interactions with neo-substrates, and thereby potentially also the cytotoxic and teratogenic properties of the parent thalidomide. In this work, by incorporating a spiro-linker to the glutarimide moiety, we have generated a new chemotype that exhibits an unprecedented binding mode for glutarimide-based CRBN ligands. In total, 16 spirocyclic glutarimide derivatives incorporating an isoxazole moiety were synthesized and tested for different criteria. In particular, all ligands showed a favorable lipophilicity, and several were able to outperform the binding affinity of thalidomide as a reference. In addition, all compounds showed favorable cytotoxicity profiles in myeloma cell lines and human peripheral blood mononuclear cells. The novel binding mode, which we determined in co-crystal structures, provides explanations for these improved properties: The incorporation of the spiro-isoxazole changes both the conformation of the glutarimide moiety within the canonical tri-trp pocket and the orientation of the protruding moiety. In this new orientation it forms additional hydrophobic interactions and is not available for direct interactions with the canonical neo-substrates. We therefore propose this chemotype as an attractive building block for the design of PROTACs.
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Affiliation(s)
- Robert Shevalev
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia
| | - Luca Bischof
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Alexander Sapegin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexander Bunev
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russia
| | - Grigor'eva Olga
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russia
| | - Grigory Kantin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia
| | - Stanislav Kalinin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia.
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany.
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2
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Steinebach C, Bricelj A, Murgai A, Sosič I, Bischof L, Ng YLD, Heim C, Maiwald S, Proj M, Voget R, Feller F, Košmrlj J, Sapozhnikova V, Schmidt A, Zuleeg MR, Lemnitzer P, Mertins P, Hansen FK, Gütschow M, Krönke J, Hartmann MD. Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs. J Med Chem 2023; 66:14513-14543. [PMID: 37902300 PMCID: PMC10641816 DOI: 10.1021/acs.jmedchem.3c00851] [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: 05/12/2023] [Revised: 09/11/2023] [Accepted: 10/05/2023] [Indexed: 10/31/2023]
Abstract
Immunomodulatory imide drugs (IMiDs) such as thalidomide, pomalidomide, and lenalidomide are the most common cereblon (CRBN) recruiters in proteolysis-targeting chimera (PROTAC) design. However, these CRBN ligands induce the degradation of IMiD neosubstrates and are inherently unstable, degrading hydrolytically under moderate conditions. In this work, we simultaneously optimized physiochemical properties, stability, on-target affinity, and off-target neosubstrate modulation features to develop novel nonphthalimide CRBN binders. These efforts led to the discovery of conformationally locked benzamide-type derivatives that replicate the interactions of the natural CRBN degron, exhibit enhanced chemical stability, and display a favorable selectivity profile in terms of neosubstrate recruitment. The utility of the most potent ligands was demonstrated by their transformation into potent degraders of BRD4 and HDAC6 that outperform previously described reference PROTACs. Together with their significantly decreased neomorphic ligase activity on IKZF1/3 and SALL4, these ligands provide opportunities for the design of highly selective and potent chemically inert proximity-inducing compounds.
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Affiliation(s)
| | - Aleša Bricelj
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Arunima Murgai
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Izidor Sosič
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Luca Bischof
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Yuen Lam Dora Ng
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Christopher Heim
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Samuel Maiwald
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Matic Proj
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Rabea Voget
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Felix Feller
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Janez Košmrlj
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, SI 1000 Ljubljana, Slovenia
| | - Valeriia Sapozhnikova
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
- Max
Delbrück
Center for Molecular Medicine, D-13125 Berlin, Germany
- German
Cancer Consortium (DKTK), Partner Site Berlin, DKFZ, D-69120 Heidelberg, Germany
| | - Annika Schmidt
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Maximilian Rudolf Zuleeg
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Patricia Lemnitzer
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Philipp Mertins
- Max
Delbrück
Center for Molecular Medicine, D-13125 Berlin, Germany
- Berlin
Institute of Health, D-10178 Berlin, Germany
| | - Finn K. Hansen
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Jan Krönke
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
- German
Cancer Consortium (DKTK), Partner Site Berlin, DKFZ, D-69120 Heidelberg, Germany
| | - Marcus D. Hartmann
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
- Interfaculty
Institute of Biochemistry, University of
Tübingen, D-72076 Tübingen, Germany
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3
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Kuchta R, Heim C, Herrmann A, Maiwald S, Ng YLD, Sosič I, Keuler T, Krönke J, Gütschow M, Hartmann MD, Steinebach C. Accessing three-branched high-affinity cereblon ligands for molecular glue and protein degrader design. RSC Chem Biol 2023; 4:229-234. [PMID: 36908700 PMCID: PMC9994103 DOI: 10.1039/d2cb00223j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
The Petasis borono-Mannich reaction was employed for an alternative entry towards three-branched cereblon ligands. Such compounds are capabable of making multiple interactions with the protein surface and possess a suitable linker exit vector. The high-affinity ligands were used to assemble prototypic new molecular glues and proteolysis targeting chimeras (PROTACs) targeting BRD4 for degradation. Our results highlight the importance of multicomponent reactions (MCRs) in drug discovery and add new insights into the rapidly growing field of protein degraders.
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Affiliation(s)
- Robert Kuchta
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 Bonn D-53121 Germany
| | - Christopher Heim
- Max Planck Institute for Biology Tübingen Tübingen D-72076 Germany .,Interfaculty Institute of Biochemistry, University of Tübingen Tübingen 72076 Germany
| | | | - Samuel Maiwald
- Max Planck Institute for Biology Tübingen Tübingen D-72076 Germany
| | - Yuen Lam Dora Ng
- Charité, Department of Internal Medicine with Focus on Hematology, Oncology and Tumor Immunology Berlin D-12203 Germany
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana Ljubljana SI-1000 Slovenia
| | - Tim Keuler
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 Bonn D-53121 Germany
| | - Jan Krönke
- Charité, Department of Internal Medicine with Focus on Hematology, Oncology and Tumor Immunology Berlin D-12203 Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 Bonn D-53121 Germany
| | - Marcus D Hartmann
- Max Planck Institute for Biology Tübingen Tübingen D-72076 Germany .,Interfaculty Institute of Biochemistry, University of Tübingen Tübingen 72076 Germany
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 Bonn D-53121 Germany
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4
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Heim C, Spring AK, Kirchgäßner S, Schwarzer D, Hartmann MD. Cereblon neo-substrate binding mimics the recognition of the cyclic imide degron. Biochem Biophys Res Commun 2023; 646:30-35. [PMID: 36701892 DOI: 10.1016/j.bbrc.2023.01.051] [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: 12/31/2022] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
In targeted protein degradation, immunomodulatory drugs (IMiDs) or cereblon (CRBN) E3 ligase modulatory drugs (CELMoDs) recruit neo-substrate proteins to the E3 ubiquitin ligase receptor CRBN for ubiquitination and subsequent proteasomal degradation. While the structural basis of this mechanism is generally understood, we have only recently described the recognition mode of the natural CRBN degron. In this communication, we reveal that the IMiD- or CELMoD-mediated binding of neo-substrates closely mimics the recognition of natural degrons. In crystal structures, we identify a conserved binding mode for natural degron peptides with an elaborate hydrogen bonding network involving the backbone of each of the six C-terminal degron residues, without the involvement of side chains. In a structural comparison, we show that neo-substrates recruited by IMiDs or CELMoDs emulate every single hydrogen bond of this network and thereby explain the origins of the largely sequence-independent recognition of neo-substrates. Our results imply that the V388I substitution in CRBN does not impair natural degron recognition and complete the structural basis for the rational design of CRBN effectors.
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Affiliation(s)
- Christopher Heim
- Max Planck Institute for Biology, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany; NanoTemper Technologies GmbH, Munich, Germany
| | | | - Sören Kirchgäßner
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Marcus D Hartmann
- Max Planck Institute for Biology, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
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5
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Krasavin M, Adamchik M, Bubyrev A, Heim C, Maiwald S, Zhukovsky D, Zhmurov P, Bunev A, Hartmann MD. Synthesis of novel glutarimide ligands for the E3 ligase substrate receptor Cereblon (CRBN): Investigation of their binding mode and antiproliferative effects against myeloma cell lines. Eur J Med Chem 2023; 246:114990. [PMID: 36476642 DOI: 10.1016/j.ejmech.2022.114990] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
To expand the chemical toolkit for targeted protein degradation, we report the generation of a new series of non-thalidomide Cereblon (CRBN) ligands. Readily available 2-methylidene glutarimide was converted to a series of 2-((hetero)aryl(methyl))thio glutarimides via the thio-Michael addition reaction. The compounds thus synthesized were evaluated for their affinity to the thalidomide-binding domain of human CRBN and their binding modes studied via X-ray crystallography. This helped identify several promising glutarimide derivatives which bind stronger to CRBN compared to thalidomide and contain a functional group which permits further chemical conjugation. Oxidation of the sulfur atom in a select group of 2-((hetero)aryl(methyl))thio glutarimides produced the respective sulfones which were found to possess a markedly stronger antiproliferative profile against multiple myeloma cell lines and a sophisticated structural binding mode with additional hydrogen bonding interactions. The newly identified Cereblon ligands form the basis for the synthesis of novel PROTAC protein degraders.
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Affiliation(s)
- Mikhail Krasavin
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation; Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russian Federation.
| | - Maria Adamchik
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Andrey Bubyrev
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Christopher Heim
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Samuel Maiwald
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Daniil Zhukovsky
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Petr Zhmurov
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Alexander Bunev
- Medicinal Chemistry Center, Togliatti State University, Togliatti, 445020, Russian Federation
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
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6
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Fuchs O. Targeting cereblon in hematologic malignancies. Blood Rev 2023; 57:100994. [PMID: 35933246 DOI: 10.1016/j.blre.2022.100994] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/28/2023]
Abstract
The protein cereblon (CRBN) is a substrate receptor of the cullin 4-really interesting new gene (RING) E3 ubiquitin ligase complex CRL4CRBN. Targeting CRBN mediates selective protein ubiquitination and subsequent degradation via the proteasome. This review describes novel thalidomide analogs, immunomodulatory drugs, also known as CRBN E3 ubiquitin ligase modulators or molecular glues (avadomide, iberdomide, CC-885, CC-90009, BTX-1188, CC-92480, CC-99282, CFT7455, and CC-91633), and CRBN-based proteolysis targeting chimeras (PROTACs) with increased efficacy and potent activity for application in hematologic malignancies. Both types of CRBN-binding drugs, molecular glues, and PROTACs stimulate the interaction between CRBN and its neosubstrates, recruiting target disease-promoting proteins and the E3 ubiquitin ligase CRL4CRBN. Proteins that are traditionally difficult to target (transcription factors and oncoproteins) can be polyubiquitinated and degraded in this way. The competition of CRBN neosubstrates with endogenous CRBN-interacting proteins and the pharmacology and rational combination therapies of and mechanisms of resistance to CRL4CRBN modulators or CRBN-based PROTACs are described.
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Affiliation(s)
- Ota Fuchs
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12800 Praha 2, Czech Republic.
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7
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Watson ER, Novick S, Matyskiela ME, Chamberlain PP, de la Peña AH, Zhu J, Tran E, Griffin PR, Wertz IE, Lander GC. Molecular glue CELMoD compounds are regulators of cereblon conformation. Science 2022; 378:549-553. [PMID: 36378961 PMCID: PMC9714526 DOI: 10.1126/science.add7574] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Cereblon (CRBN) is a ubiquitin ligase (E3) substrate receptor protein co-opted by CRBN E3 ligase modulatory drug (CELMoD) agents that target therapeutically relevant proteins for degradation. Prior crystallographic studies defined the drug-binding site within CRBN's thalidomide-binding domain (TBD), but the allostery of drug-induced neosubstrate binding remains unclear. We performed cryo-electron microscopy analyses of the DNA damage-binding protein 1 (DDB1)-CRBN apo complex and compared these structures with DDB1-CRBN in the presence of CELMoD compounds alone and complexed with neosubstrates. Association of CELMoD compounds to the TBD is necessary and sufficient for triggering CRBN allosteric rearrangement from an open conformation to the canonical closed conformation. The neosubstrate Ikaros only stably associates with the closed CRBN conformation, illustrating the importance of allostery for CELMoD compound efficacy and informing structure-guided design strategies to improve therapeutic efficacy.
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Affiliation(s)
- Edmond R. Watson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Scott Novick
- Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
- UF Scripps Biomedical Research, University of Florida, Jupiter, FL 33458, USA
| | | | | | | | - Jinyi Zhu
- Bristol-Myers Squibb, San Diego, CA 92121, USA
| | - Eileen Tran
- Bristol-Myers Squibb, San Diego, CA 92121, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
- UF Scripps Biomedical Research, University of Florida, Jupiter, FL 33458, USA
| | | | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
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8
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Heim C, Spring AK, Kirchgäßner S, Schwarzer D, Hartmann MD. Identification and structural basis of C-terminal cyclic imides as natural degrons for cereblon. Biochem Biophys Res Commun 2022; 637:66-72. [DOI: 10.1016/j.bbrc.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
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9
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Yamamoto J, Ito T, Yamaguchi Y, Handa H. Discovery of CRBN as a target of thalidomide: a breakthrough for progress in the development of protein degraders. Chem Soc Rev 2022; 51:6234-6250. [PMID: 35796627 DOI: 10.1039/d2cs00116k] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Progress in strategies aimed at breaking down therapeutic target proteins has led to a paradigm shift in drug discovery. Thalidomide and its derivatives are the only protein degraders currently used in clinical practice. Our understanding of the molecular mechanism of action of thalidomide and its derivatives has advanced dramatically since the identification of cereblon (CRBN) as their direct target. The binding of thalidomide derivatives to CRBN, a substrate recognition receptor for Cullin 4 RING E3 ubiquitin ligase (CRL4), induces the recruitment of non-native substrates to CRL4CRBN and their subsequent degradation. This discovery was a breakthrough in the current rapid development of protein-degrading agents because clarification of the mechanism of action of thalidomide derivatives has demonstrated the clinical value of these compounds. This review provides an overview of the mechanism of action of thalidomide and its derivatives and describes perspectives for protein degraders.
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Affiliation(s)
- Junichi Yamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takumi Ito
- Institute of Medical Science, Tokyo Medical University, Shinjuku, Tokyo 160-8402, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroshi Handa
- Center for Future Medical Research, Tokyo Medical University, Shinjuku, Tokyo 160-8402, Japan.
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