1
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Jiang W, Shaw S, Rush J, Dumont N, Kim J, Singh R, Skepner A, Khodier C, Raffier C, Yan N, Schluter C, Yu X, Szuchnicki M, Sathappa M, Kahn J, Sperling AS, McKinney DC, Gould AE, Garvie CW, Miller PG. Identification of Small Molecule Inhibitors of PPM1D Using a Novel Drug Discovery Platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595001. [PMID: 38826457 PMCID: PMC11142126 DOI: 10.1101/2024.05.20.595001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Protein phosphatase, Mg2+/Mn2+ dependent 1D (PPM1D), is a serine/threonine phosphatase that is recurrently activated in cancer, regulates the DNA damage response (DDR), and suppresses the activation of p53. Consistent with its oncogenic properties, genetic loss or pharmacologic inhibition of PPM1D impairs tumor growth and sensitizes cancer cells to cytotoxic therapies in a wide range of preclinical models. Given the therapeutic potential of targeting PPM1D specifically and the DDR and p53 pathway more generally, we sought to deepen our biological understanding of PPM1D as a drug target and determine how PPM1D inhibition differs from other therapeutic approaches to activate the DDR. We performed a high throughput screen to identify new allosteric inhibitors of PPM1D, then generated and optimized a suite of enzymatic, cell-based, and in vivo pharmacokinetic and pharmacodynamic assays to drive medicinal chemistry efforts and to further interrogate the biology of PPM1D. Importantly, this drug discovery platform can be readily adapted to broadly study the DDR and p53. We identified compounds distinct from previously reported allosteric inhibitors and showed in vivo on-target activity. Our data suggest that the biological effects of inhibiting PPM1D are distinct from inhibitors of the MDM2-p53 interaction and standard cytotoxic chemotherapies. These differences also highlight the potential therapeutic contexts in which targeting PPM1D would be most valuable. Therefore, our studies have identified a series of new PPM1D inhibitors, generated a suite of in vitro and in vivo assays that can be broadly used to interrogate the DDR, and provided important new insights into PPM1D as a drug target.
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Affiliation(s)
- Wei Jiang
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Subrata Shaw
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Jason Rush
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Nancy Dumont
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - John Kim
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Ritu Singh
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Adam Skepner
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Carol Khodier
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Cerise Raffier
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Ni Yan
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Cameron Schluter
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Xiao Yu
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Mateusz Szuchnicki
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Murugappan Sathappa
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Josephine Kahn
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Adam S. Sperling
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David C. McKinney
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Alexandra E. Gould
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Colin W. Garvie
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Peter G. Miller
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
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2
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Qin R, Fan X, Ding R, Qiu Y, Chen X, Liu Y, Lin M, Wang H. Research advancements on the involvement of E3 ubiquitin ligase UBR5 in gastrointestinal cancers. Heliyon 2024; 10:e30284. [PMID: 38707379 PMCID: PMC11066684 DOI: 10.1016/j.heliyon.2024.e30284] [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: 09/24/2023] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024] Open
Abstract
E3 ubiquitin ligases comprise a family of ubiquitination-catalyzing enzymes that have been extensively researched and are considered crucial components of the ubiquitin-proteasome system involved in various diseases. The ubiquitin-protein ligase E3 component n-recognition 5 (UBR5) is an E3 ubiquitin-protein ligase that has garnered considerable interest of late. Recent studies demonstrate that UBR5 undergoes high-frequency mutations, chromosomal amplification, and/or abnormalities during expression of various malignant tumors. These alterations correlate with the biological behaviors and prognoses of malignancies, such as tumor invasion, metastasis, and resistance to chemotherapeutic agents. This study aimed to comprehensively elucidate the biological functions of UBR5, and its role and relevance in the context of gastrointestinal cancers. Furthermore, this article expounds a scientific basis to explore the molecular mechanisms underlying gastrointestinal cancers and developing targeted therapeutic strategies for their remediation.
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Affiliation(s)
- Rong Qin
- Department of Gastroenterology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, 650051, China
| | - Xirui Fan
- Department of Gastroenterology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, 650051, China
| | - Rui Ding
- Department of Gastroenterology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, 650051, China
| | - Yadan Qiu
- Department of Gastroenterology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, 650051, China
| | - Xujia Chen
- Department of Gastroenterology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, 650051, China
| | - Yanting Liu
- Department of Gastroenterology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, 650051, China
| | - Minjuan Lin
- Department of Gastroenterology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, 650051, China
| | - Hui Wang
- Department of Gastroenterology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, 650051, China
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3
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Duan CY, Li Y, Zhi HY, Tian Y, Huang ZY, Chen SP, Zhang Y, Liu Q, Zhou L, Jiang XG, Ullah K, Guo Q, Liu ZH, Xu Y, Han JH, Hou J, O'Connor DP, Xu G. E3 ubiquitin ligase UBR5 modulates circadian rhythm by facilitating the ubiquitination and degradation of the key clock transcription factor BMAL1. Acta Pharmacol Sin 2024:10.1038/s41401-024-01290-z. [PMID: 38740904 DOI: 10.1038/s41401-024-01290-z] [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: 01/01/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
The circadian clock is the inner rhythm of life activities and is controlled by a self-sustained and endogenous molecular clock, which maintains a ~ 24 h internal oscillation. As the core element of the circadian clock, BMAL1 is susceptible to degradation through the ubiquitin-proteasome system (UPS). Nevertheless, scant information is available regarding the UPS enzymes that intricately modulate both the stability and transcriptional activity of BMAL1, affecting the cellular circadian rhythm. In this work, we identify and validate UBR5 as a new E3 ubiquitin ligase that interacts with BMAL1 by using affinity purification, mass spectrometry, and biochemical experiments. UBR5 overexpression induced BMAL1 ubiquitination, leading to diminished stability and reduced protein level of BMAL1, thereby attenuating its transcriptional activity. Consistent with this, UBR5 knockdown increases the BMAL1 protein. Domain mapping discloses that the C-terminus of BMAL1 interacts with the N-terminal domains of UBR5. Similarly, cell-line-based experiments discover that HYD, the UBR5 homolog in Drosophila, could interact with and downregulate CYCLE, the BMAL1 homolog in Drosophila. PER2-luciferase bioluminescence real-time reporting assay in a mammalian cell line and behavioral experiments in Drosophila reveal that UBR5 or hyd knockdown significantly reduces the period of the circadian clock. Therefore, our work discovers a new ubiquitin ligase UBR5 that regulates BMAL1 stability and circadian rhythm and elucidates the underlying molecular mechanism. This work provides an additional layer of complexity to the regulatory network of the circadian clock at the post-translational modification level, offering potential insights into the modulation of the dysregulated circadian rhythm.
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Affiliation(s)
- Chun-Yan Duan
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, 123 St Stephen's Green, Dublin 2, D02 YN77, Dublin, Ireland
| | - Yue Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Hao-Yu Zhi
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Yao Tian
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, 2 Sipailou Road, Nanjing, 210096, China
| | - Zheng-Yun Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, 215123, China
| | - Su-Ping Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Yang Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Qing Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Liang Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Xiao-Gang Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Kifayat Ullah
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Qing Guo
- Department of Human Anatomy and Cytoneurobiology, Medical School of Soochow University, Suzhou, 215123, China
| | - Zhao-Hui Liu
- Department of Human Anatomy and Cytoneurobiology, Medical School of Soochow University, Suzhou, 215123, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, 215123, China
| | - Jun-Hai Han
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, 2 Sipailou Road, Nanjing, 210096, China
| | - Jiajie Hou
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Darran P O'Connor
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, 123 St Stephen's Green, Dublin 2, D02 YN77, Dublin, Ireland
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China.
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, China.
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4
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Tsai JM, Nowak RP, Ebert BL, Fischer ES. Targeted protein degradation: from mechanisms to clinic. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00729-9. [PMID: 38684868 DOI: 10.1038/s41580-024-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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5
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Zhang S, Valenzuela LF, Zatulovskiy E, Mangiante L, Curtis C, Skotheim JM. The G1/S transition is promoted by Rb degradation via the E3 ligase UBR5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.03.560768. [PMID: 37873473 PMCID: PMC10592979 DOI: 10.1101/2023.10.03.560768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Mammalian cells make the decision to divide at the G1/S transition in response to diverse signals impinging on the retinoblastoma protein Rb, a cell cycle inhibitor and tumor suppressor. Rb is inhibited by two parallel pathways. In the canonical pathway, Cyclin D-Cdk4/6 kinase complexes phosphorylate and inactivate Rb. In the second, recently discovered pathway, Rb's concentration decreases during G1 to promote cells progressing through the G1/S transition. However, the mechanisms underlying this second pathway are unknown. Here, we found that Rb's concentration drop in G1 and recovery in S/G2 is controlled by phosphorylation-dependent protein degradation. In early G1 phase, un- and hypo-phosphorylated Rb is targeted by the E3 ligase UBR5. UBR5 knockout cells have higher Rb concentrations in early G1, exhibit a lower G1/S transition rate, and are more sensitive to Cdk4/6 inhibition. This last observation suggests that UBR5 inhibition can strengthen the efficacy of Cdk4/6 inhibitor-based cancer therapies.
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Affiliation(s)
- Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA 94305
| | | | | | | | | | - Jan M. Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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6
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Horn-Ghetko D, Hopf LVM, Tripathi-Giesgen I, Du J, Kostrhon S, Vu DT, Beier V, Steigenberger B, Prabu JR, Stier L, Bruss EM, Mann M, Xiong Y, Schulman BA. Noncanonical assembly, neddylation and chimeric cullin-RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex. Nat Struct Mol Biol 2024:10.1038/s41594-024-01257-y. [PMID: 38605244 DOI: 10.1038/s41594-024-01257-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/26/2024] [Indexed: 04/13/2024]
Abstract
Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, 'cullin-RING' and 'RBR', are individually found in several hundred human E3 ligases, and collaborate with E2 enzymes to catalyze ubiquitylation. However, the vertebrate-specific CUL9 complex with RBX1 (also called ROC1), of interest due to its tumor suppressive interaction with TP53, uniquely encompasses both cullin-RING and RBR domains. Here, cryo-EM, biochemistry and cellular assays elucidate a 1.8-MDa hexameric human CUL9-RBX1 assembly. Within one dimeric subcomplex, an E2-bound RBR domain is activated by neddylation of its own cullin domain and positioning from the adjacent CUL9-RBX1 in trans. Our data show CUL9 as unique among RBX1-bound cullins in dependence on the metazoan-specific UBE2F neddylation enzyme, while the RBR domain protects it from deneddylation. Substrates are recruited to various upstream domains, while ubiquitylation relies on both CUL9's neddylated cullin and RBR domains achieving self-assembled and chimeric cullin-RING/RBR E3 ligase activity.
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Affiliation(s)
- Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Linus V M Hopf
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany
| | - Jiale Du
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Kostrhon
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - D Tung Vu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Viola Beier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Luca Stier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany
| | - Elias M Bruss
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Yue Xiong
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Cullgen Inc., San Diego, CA, USA
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany.
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7
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Bercier P, de Thé H. History of Developing Acute Promyelocytic Leukemia Treatment and Role of Promyelocytic Leukemia Bodies. Cancers (Basel) 2024; 16:1351. [PMID: 38611029 PMCID: PMC11011038 DOI: 10.3390/cancers16071351] [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: 03/04/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The story of acute promyelocytic leukemia (APL) discovery, physiopathology, and treatment is a unique journey, transforming the most aggressive form of leukemia to the most curable. It followed an empirical route fueled by clinical breakthroughs driving major advances in biochemistry and cell biology, including the discovery of PML nuclear bodies (PML NBs) and their central role in APL physiopathology. Beyond APL, PML NBs have emerged as key players in a wide variety of biological functions, including tumor-suppression and SUMO-initiated protein degradation, underscoring their broad importance. The APL story is an example of how clinical observations led to the incremental development of the first targeted leukemia therapy. The understanding of APL pathogenesis and the basis for cure now opens new insights in the treatment of other diseases, especially other acute myeloid leukemias.
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Affiliation(s)
- Pierre Bercier
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, 75231 Paris, France;
- GenCellDis, Inserm U944, CNRS UMR7212, Université Paris Cité, 75010 Paris, France
| | - Hugues de Thé
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, 75231 Paris, France;
- GenCellDis, Inserm U944, CNRS UMR7212, Université Paris Cité, 75010 Paris, France
- Hematology Laboratory, Hôpital St Louis, AP/HP, 75010 Paris, France
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8
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Bolhuis DL, Emanuele MJ, Brown NG. Friend or foe? Reciprocal regulation between E3 ubiquitin ligases and deubiquitinases. Biochem Soc Trans 2024; 52:BST20230454. [PMID: 38414432 DOI: 10.1042/bst20230454] [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: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/29/2024]
Abstract
Protein ubiquitination is a post-translational modification that entails the covalent attachment of the small protein ubiquitin (Ub), which acts as a signal to direct protein stability, localization, or interactions. The Ub code is written by a family of enzymes called E3 Ub ligases (∼600 members in humans), which can catalyze the transfer of either a single ubiquitin or the formation of a diverse array of polyubiquitin chains. This code can be edited or erased by a different set of enzymes termed deubiquitinases (DUBs; ∼100 members in humans). While enzymes from these distinct families have seemingly opposing activities, certain E3-DUB pairings can also synergize to regulate vital cellular processes like gene expression, autophagy, innate immunity, and cell proliferation. In this review, we highlight recent studies describing Ub ligase-DUB interactions and focus on their relationships.
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Affiliation(s)
- Derek L Bolhuis
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
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9
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Düring J, Wolter M, Toplak JJ, Torres C, Dybkov O, Fokkens TJ, Bohnsack KE, Urlaub H, Steinchen W, Dienemann C, Lorenz S. Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1. Nat Struct Mol Biol 2024; 31:364-377. [PMID: 38332367 PMCID: PMC10873202 DOI: 10.1038/s41594-023-01203-4] [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: 07/31/2023] [Accepted: 12/07/2023] [Indexed: 02/10/2024]
Abstract
Ubiquitin ligases (E3s) are pivotal specificity determinants in the ubiquitin system by selecting substrates and decorating them with distinct ubiquitin signals. However, structure determination of the underlying, specific E3-substrate complexes has proven challenging owing to their transient nature. In particular, it is incompletely understood how members of the catalytic cysteine-driven class of HECT-type ligases (HECTs) position substrate proteins for modification. Here, we report a cryogenic electron microscopy (cryo-EM) structure of the full-length human HECT HACE1, along with solution-based conformational analyses by small-angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry. Structure-based functional analyses in vitro and in cells reveal that the activity of HACE1 is stringently regulated by dimerization-induced autoinhibition. The inhibition occurs at the first step of the catalytic cycle and is thus substrate-independent. We use mechanism-based chemical crosslinking to reconstitute a complex of activated, monomeric HACE1 with its major substrate, RAC1, determine its structure by cryo-EM and validate the binding mode by solution-based analyses. Our findings explain how HACE1 achieves selectivity in ubiquitinating the active, GTP-loaded state of RAC1 and establish a framework for interpreting mutational alterations of the HACE1-RAC1 interplay in disease. More broadly, this work illuminates central unexplored aspects in the architecture, conformational dynamics, regulation and specificity of full-length HECTs.
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Affiliation(s)
- Jonas Düring
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Madita Wolter
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Julia J Toplak
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Camilo Torres
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Olexandr Dybkov
- Research Group 'Bioanalytical Mass Spectrometry', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Thornton J Fokkens
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Research Group 'Bioanalytical Mass Spectrometry', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- 'Bioanalytics', Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
- 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells', University of Göttingen, Göttingen, Germany
| | - Wieland Steinchen
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sonja Lorenz
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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10
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Yoon H, Rutter JC, Li YD, Ebert BL. Induced protein degradation for therapeutics: past, present, and future. J Clin Invest 2024; 134:e175265. [PMID: 38165043 PMCID: PMC10760958 DOI: 10.1172/jci175265] [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: 01/03/2024] Open
Abstract
The concept of induced protein degradation by small molecules has emerged as a promising therapeutic strategy that is particularly effective in targeting proteins previously considered "undruggable." Thalidomide analogs, employed in the treatment of multiple myeloma, stand as prime examples. These compounds serve as molecular glues, redirecting the CRBN E3 ubiquitin ligase to degrade myeloma-dependency factors, IKZF1 and IKZF3. The clinical success of thalidomide analogs demonstrates the therapeutic potential of induced protein degradation. Beyond molecular glue degraders, several additional modalities to trigger protein degradation have been developed and are currently under clinical evaluation. These include heterobifunctional degraders, polymerization-induced degradation, ligand-dependent degradation of nuclear hormone receptors, disruption of protein interactions, and various other strategies. In this Review, we will provide a concise overview of various degradation modalities, their clinical applications, and potential future directions in the field of protein degradation.
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Affiliation(s)
- Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Justine C. Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yen-Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
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11
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Winter GE, Mayor-Ruiz C. Proximity-inducing pharmacology. Nat Chem Biol 2024; 20:13-14. [PMID: 37978259 DOI: 10.1038/s41589-023-01492-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Affiliation(s)
- Georg E Winter
- Research Center for Molecular Medicine (CeMM), Austrian Academy of Sciences, Vienna, Austria.
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona Institute of Technology (BIST), Barcelona, Spain.
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12
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Taherbhoy AM, Daniels DL. Harnessing UBR5 for targeted protein degradation of key transcriptional regulators. Trends Pharmacol Sci 2023; 44:758-761. [PMID: 37770316 DOI: 10.1016/j.tips.2023.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023]
Abstract
Targeted protein degradation (TPD) has opened the door for drugging transcriptional regulators, yet the number of proteins targeted and E3 ligases utilized remain limited. Here, we highlight UBR5 and propose multiple strategies by which this E3 ligase could be modulated to drive degradation of key transcriptional targets implicated in disease.
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Affiliation(s)
- Asad M Taherbhoy
- Foghorn Therapeutics, 500 Technology Square Suite 700, Cambridge, MA 02139, USA
| | - Danette L Daniels
- Foghorn Therapeutics, 500 Technology Square Suite 700, Cambridge, MA 02139, USA.
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13
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Dahal L, Graham TGW, Dailey GM, Heckert A, Tjian R, Darzacq X. Surprising Features of Nuclear Receptor Interaction Networks Revealed by Live Cell Single Molecule Imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.16.558083. [PMID: 37745337 PMCID: PMC10516011 DOI: 10.1101/2023.09.16.558083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Type 2 Nuclear Receptors (T2NRs) require heterodimerization with a common partner, the Retinoid X Receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and over-expression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged retinoid X receptor (RXR) and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
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Affiliation(s)
- Liza Dahal
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Thomas GW Graham
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Alec Heckert
- Eikon Therapeutics Inc., Hayward, California, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
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14
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Hehl LA, Schulman BA. To be (in a transcriptional complex) or not to be (promoting UBR5 ubiquitylation): That is an answer to how degradation controls gene expression. Mol Cell 2023; 83:2616-2618. [PMID: 37541216 DOI: 10.1016/j.molcel.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023]
Abstract
Tsai et al.1 in this issue and Mark et al.2 in Cell reveal how the E3 ligase UBR5 mediates broad regulation by selectively targeting agonist-bound nuclear hormone receptors, MYC, and other transcriptional regulators not incorporated into active gene expression complexes.
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Affiliation(s)
- Laura A Hehl
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; TUM School of Natural Sciences, Department of Chemistry, 85747 Garching, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; TUM School of Natural Sciences, Department of Chemistry, 85747 Garching, Germany.
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