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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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3
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Jordan VN, Ordureau A, An H. Identifying E3 Ligase Substrates With Quantitative Degradation Proteomics. Chembiochem 2023; 24:e202300108. [PMID: 37166757 PMCID: PMC10548883 DOI: 10.1002/cbic.202300108] [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: 02/09/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/12/2023]
Abstract
Controlled protein degradation by the ubiquitin-proteasome pathway is critical for almost all cellular processes. E3 ubiquitin ligases are responsible for targeting proteins for ubiquitylation and subsequent proteasomal degradation with spatial and temporal precision. While studies have revealed various E3-substrate pairs involved in distinct biological processes, the complete substrate profiles of individual E3 ligases are largely unknown. Here we report a new approach to identify substrates of an E3 ligase for proteasomal degradation using unnatural amino acid incorporation pulse-chase proteomics (degradomics). Applying this approach, we determine the steady-state substrates of the C-terminal to LisH (CTLH) E3 ligase, a multi-component complex with poorly defined substrates. By comparing the proteome degradation profiles of active and inactive CTLH-expressing cells, we successfully identify previously known and new potential substrates of CTLH ligase. Altogether, degradomics can comprehensively identify degradation substrates of an E3 ligase, which can be adapted for other E3 ligases in various cellular contexts.
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Affiliation(s)
- Victoria N Jordan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alban Ordureau
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Heeseon An
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10065, USA
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5
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Shergalis AG, Marin VL, Rhee DY, Senaweera S, McCloud RL, Ronau JA, Hutchins CW, McLoughlin S, Woller KR, Warder SE, Vasudevan A, Reitsma JM. CRISPR Screen Reveals BRD2/4 Molecular Glue-like Degrader via Recruitment of DCAF16. ACS Chem Biol 2023; 18:331-339. [PMID: 36656921 DOI: 10.1021/acschembio.2c00747] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Molecular glues (MGs) are monovalent small molecules that induce an interaction between proteins (native or non-native partners) by altering the protein-protein interaction (PPI) interface toward a higher-affinity state. Enhancing the PPI between a protein and E3 ubiquitin ligase can lead to degradation of the partnering protein. Over the past decade, retrospective studies of clinical drugs identified that immunomodulatory drugs (e.g., thalidomide and analogues) and indisulam exhibit a molecular glue effect by driving the interaction between non-native substrates to CRBN and DCAF15 ligases, respectively. Ensuing reports of phenotypic screens focused on MG discovery have suggested that these molecules may be more common than initially anticipated. However, prospective discovery of MGs remains challenging. Thus, expanding the repertoire of MGs will enhance our understanding of principles for prospective design. Herein, we report the results of a CRISPR/Cas9 knockout screen of over 1000 ligases and ubiquitin proteasome system components in a BRD4 degradation assay with a JQ1-based monovalent degrader, compound 1a. We identified DCAF16, a substrate recognition component of the Cul4 ligase complex, as essential for compound activity, and we demonstrate that compound 1a drives the interaction between DCAF16 and BRD2/4 to promote target degradation. Taken together, our data suggest that compound 1a functions as an MG degrader between BRD2/4 and DCAF16 and provides a foundation for further mechanistic dissection to advance prospective MG discovery.
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Affiliation(s)
- Andrea G Shergalis
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Violeta L Marin
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - David Y Rhee
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Sameera Senaweera
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Rebecca L McCloud
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Judith A Ronau
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Charles W Hutchins
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Shaun McLoughlin
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Kevin R Woller
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Scott E Warder
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Anil Vasudevan
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Justin M Reitsma
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
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6
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Chang SL, Chan TC, Chen TJ, Yang CC, Tsai HH, Yeh CF, Lee SW, Lai HY. High SPIN4 Expression Is Linked to Advanced Nodal Status and Inferior Prognosis in Nasopharyngeal Carcinoma Patients. Life (Basel) 2021; 11:life11090912. [PMID: 34575061 PMCID: PMC8470428 DOI: 10.3390/life11090912] [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: 07/27/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 11/24/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC), characterized by the infiltration of lymphocytes, is a malignancy derived from the epithelium of the nasopharynx. Despite its sensitivity to radiation and chemotherapy, NPC has a high propensity for recurrence and metastasis. Although lymph node levels have been indicated as an independent prognostic factor for NPC, there has been no precise prognostic biomarker to predict clinical outcomes for NPC before advanced disease. In the present study, we surveyed differentially expressed genes in NPC via the next-generation sequencing (NGS)-based Oncomine database and identified the spindlin family member 4 (SPIN4) gene as the most relevant to advanced nodal status. We collected 124 tumor samples from NPC patients receiving biopsy, and the expression level of SPIN4 was evaluated by immunohistochemistry. The results showed that tumors with high SPIN4 expression were significantly correlated with advanced nodal status (p < 0.001) and advanced AJCC stages (p < 0.001). High SPIN4 expression in tumor samples was an unfavorable prognostic factor for all three endpoints at the univariate level: disease-specific survival (DSS), distal metastasis-free survival (DMeFS), and local recurrence-free survival (LRFS) (all p < 0.05). High SPIN4 expression remained independently prognostic of worse DMeFS (p = 0.049) at the multivariate level. Using bioinformatics analysis, we further found that high SPIN4 level may link tight junctions to cancer cell survival. Collectively, these results imply that high SPIN4 expression is linked to an aggressive clinical course, including advanced nodal status and poor survival in NPC patients, emphasizing the promising prognostic utility of SPIN4 expression.
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Affiliation(s)
- Shih-Lun Chang
- Department of Otolaryngology, Chi Mei Medical Center, Tainan 710, Taiwan;
- Department of Optometry, Chung Hwa University of Medical Technology, Tainan 717, Taiwan
| | - Ti-Chun Chan
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan; (T.-C.C.); (H.-H.T.)
- National Institute of Cancer Research, National Health Research Institute, Tainan 704, Taiwan
| | - Tzu-Ju Chen
- Department of Clinical Pathology, Chi Mei Medical Center, Tainan 710, Taiwan;
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Ching-Chieh Yang
- Department of Radiation Oncology, Chi Mei Medical Center, Tainan 710, Taiwan;
- Department of Pharmacy, Chia-Nan University of Pharmacy and Science, Tainan 717, Taiwan
| | - Hsin-Hwa Tsai
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan; (T.-C.C.); (H.-H.T.)
- Department of Clinical Pathology, Chi Mei Medical Center, Tainan 710, Taiwan;
| | - Cheng-Fa Yeh
- Department of Internal Medicine, Chi Mei Medical Center, Tainan 710, Taiwan;
| | - Sung-Wei Lee
- Department of Radiation Oncology, Chi Mei Medical Center, Liouying 736, Taiwan
- Correspondence: (S.-W.L.); (H.-Y.L.)
| | - Hong-Yue Lai
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan; (T.-C.C.); (H.-H.T.)
- Department of Clinical Pathology, Chi Mei Medical Center, Tainan 710, Taiwan;
- Correspondence: (S.-W.L.); (H.-Y.L.)
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