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Zhang R, Zheng Y, Xiang F, Zhou J. Inducing or enhancing protein-protein interaction to develop drugs: Molecular glues with various biological activity. Eur J Med Chem 2024; 277:116756. [PMID: 39191033 DOI: 10.1016/j.ejmech.2024.116756] [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: 05/24/2024] [Revised: 07/15/2024] [Accepted: 08/01/2024] [Indexed: 08/29/2024]
Abstract
Over the past two decades, molecular glues (MGs) have gradually attracted the attention of the pharmaceutical community with the advent of MG degraders such as IMiDs and indisulam. Such molecules degrade the target protein by promoting the interaction between the target protein and E3 ligase. In addition, as a chemical inducer, MGs promote the dimerization of homologous proteins and heterologous proteins to form ternary complexes, which have great prospects in regulating biological activities. This review focuses on the application of MGs in the field of drug development including protein-protein interaction (PPI) stability and protein degradation. We thoroughly analyze the structure of various MGs and the interactions between MGs and various biologically active molecules, thus providing new perspectives for the development of PPI stabilizers and new degraders.
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Affiliation(s)
- Rongyu Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China
| | - Yirong Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China
| | - Fengjiao Xiang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China.
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2
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Tan X, Huang Z, Pei H, Jia Z, Zheng J. Molecular glue-mediated targeted protein degradation: A novel strategy in small-molecule drug development. iScience 2024; 27:110712. [PMID: 39297173 PMCID: PMC11409024 DOI: 10.1016/j.isci.2024.110712] [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] [Indexed: 09/21/2024] Open
Abstract
Small-molecule drugs are effective and thus most widely used. However, their applications are limited by their reliance on active high-affinity binding sites, restricting their target options. A breakthrough approach involves molecular glues, a novel class of small-molecule compounds capable of inducing protein-protein interactions (PPIs). This opens avenues to target conventionally undruggable proteins, overcoming limitations seen in conventional small-molecule drugs. Molecular glues play a key role in targeted protein degradation (TPD) techniques, including ubiquitin-proteasome system-based approaches such as proteolysis targeting chimeras (PROTACs) and molecular glue degraders and recently emergent lysosome system-based techniques like molecular degraders of extracellular proteins through the asialoglycoprotein receptors (MoDE-As) and macroautophagy degradation targeting chimeras (MADTACs). These techniques enable an innovative targeted degradation strategy for prolonged inhibition of pathology-associated proteins. This review provides an overview of them, emphasizing the clinical potential of molecular glues and guiding the development of molecular-glue-mediated TPD techniques.
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Affiliation(s)
- Xueqiang Tan
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zuyi Huang
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hairun Pei
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing Technology & Business University, Beijing 100048, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Jimin Zheng
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
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3
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Jang JH, Kim JY, Lee TJ. Recent advances in anticancer mechanisms of molecular glue degraders: focus on RBM39-dgrading synthetic sulfonamide such as indisulam, E7820, tasisulam, and chloroquinoxaline sulfonamide. Genes Genomics 2024:10.1007/s13258-024-01565-z. [PMID: 39271535 DOI: 10.1007/s13258-024-01565-z] [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: 08/11/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024]
Abstract
Synthetic sulfonamide anticancer drugs, including E7820, indisulam, tasisulam, and chloroquinoxaline sulfonamide, exhibit diverse mechanisms of action and therapeutic potential, functioning as molecular glue degraders. E7820 targets RBM39, affecting RNA splicing and angiogenesis by suppressing integrin α2. Phase I studies have demonstrated some stability in advanced solid malignancies; however, further efficacy studies are required. Indisulam causes G1 cell cycle arrest and delays the G1/S transition by modulating splicing through RBM39 degradation via DCAF15. Despite its limited initial efficacy, it shows promise in combination therapies, particularly for hematopoietic malignancies and gliomas. Tasisulam inhibits VEGF signaling, suppresses angiogenesis, and induces apoptosis. Although early trials indicated broad activity, safety concerns have halted its development. Chloroquinoxaline sulfonamide, initially investigated for cell cycle arrest and topoisomerase II inhibition, was discontinued owing to its limited efficacy and toxicity, despite promising initial results. Recent studies revealed the structural interaction of E7820 with DCAF15 and RBM39, although phase II trials on myeloid malignancies have shown limited efficacy. Indisulam is effective against glioblastoma and neuroblastoma, with potential synergy in combination therapies and metabolic disruption. Recent research on tasisulam reveals its potential in cancer therapy by targeting RBM39 degradation through DCAF15-mediated pathways. Understanding these mechanisms could lead to new treatments that affect alternative splicing and improve cancer therapies Overall, although these drugs exhibit promising mechanisms of action, further research is required to optimize their clinical efficacy and safety.
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Affiliation(s)
- Ji Hoon Jang
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-gu, Daegu, 42415, Republic of Korea
| | - Joo-Young Kim
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-gu, Daegu, 42415, Republic of Korea
| | - Tae-Jin Lee
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-gu, Daegu, 42415, Republic of Korea.
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4
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Winter GE. Extrapolating Lessons from Targeted Protein Degradation to Other Proximity-Inducing Drugs. ACS Chem Biol 2024. [PMID: 39264973 DOI: 10.1021/acschembio.4c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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5
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Serebrenik YV, Mani D, Maujean T, Burslem GM, Shalem O. Pooled endogenous protein tagging and recruitment for systematic profiling of protein function. CELL GENOMICS 2024:100651. [PMID: 39255790 DOI: 10.1016/j.xgen.2024.100651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/28/2024] [Accepted: 08/12/2024] [Indexed: 09/12/2024]
Abstract
The emerging field of induced proximity therapeutics, which involves designing molecules to bring together an effector and target protein-typically to induce target degradation-is rapidly advancing. However, its progress is constrained by the lack of scalable and unbiased tools to explore effector-target protein interactions. We combine pooled endogenous gene tagging using a ligand-binding domain with generic small-molecule-based recruitment to screen for induction of protein proximity. We apply this methodology to identify effectors for degradation in two orthogonal screens: using fluorescence to monitor target levels and a cellular growth that depends on the degradation of an essential protein. Our screens revealed new effector proteins for degradation, including previously established examples, and converged on members of the C-terminal-to-LisH (CTLH) complex. We introduce a platform for pooled induction of endogenous protein-protein interactions to expand our toolset of effector proteins for protein degradation and other forms of induced proximity.
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Affiliation(s)
- Yevgeniy V Serebrenik
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Deepak Mani
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Timothé Maujean
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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6
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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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7
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Raina K, Forbes CD, Stronk R, Rappi JP, Eastman KJ, Zaware N, Yu X, Li H, Bhardwaj A, Gerritz SW, Forgione M, Hundt A, King MP, Posner ZM, Correia AD, McGovern A, Puleo DE, Chenard R, Mousseau JJ, Vergara JI, Garvin E, Macaluso J, Martin M, Bassoli K, Jones K, Garcia M, Howard K, Yaggi M, Smith LM, Chen JM, Mayfield AB, De Leon CA, Hines J, Kayser-Bricker KJ, Crews CM. Regulated induced proximity targeting chimeras-RIPTACs-A heterobifunctional small molecule strategy for cancer selective therapies. Cell Chem Biol 2024; 31:1490-1502.e42. [PMID: 39116881 PMCID: PMC11371387 DOI: 10.1016/j.chembiol.2024.07.005] [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: 03/20/2024] [Revised: 05/30/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024]
Abstract
We describe a protein proximity inducing therapeutic modality called Regulated Induced Proximity Targeting Chimeras or RIPTACs: heterobifunctional small molecules that elicit a stable ternary complex between a target protein (TP) selectively expressed in tumor cells and a pan-expressed protein essential for cell survival. The resulting co-operative protein-protein interaction (PPI) abrogates the function of the essential protein, thus leading to death selectively in cells expressing the TP. This approach leverages differentially expressed intracellular proteins as novel cancer targets, with the advantage of not requiring the target to be a disease driver. In this chemical biology study, we design RIPTACs that incorporate a ligand against a model TP connected via a linker to effector ligands such as JQ1 (BRD4) or BI2536 (PLK1) or CDK inhibitors such as TMX3013 or dinaciclib. RIPTACs accumulate selectively in cells expressing the HaloTag-FKBP target, form co-operative intracellular ternary complexes, and induce an anti-proliferative response in target-expressing cells.
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Affiliation(s)
- Kanak Raina
- Halda Therapeutics OpCo Inc, New Haven, CT, USA
| | | | | | | | | | | | - Xinheng Yu
- Halda Therapeutics OpCo Inc, New Haven, CT, USA
| | - Hao Li
- Halda Therapeutics OpCo Inc, New Haven, CT, USA
| | | | | | | | | | | | | | | | | | | | | | | | - J Ignacio Vergara
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA
| | | | | | | | | | - Kelli Jones
- Halda Therapeutics OpCo Inc, New Haven, CT, USA
| | | | | | | | | | | | - Andrew B Mayfield
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA
| | - Cesar A De Leon
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA
| | - John Hines
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Craig M Crews
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA; Department of Pharmacology, Yale University, New Haven, CT, USA; Department of Chemistry, Yale University, New Haven, CT, USA.
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8
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Sonkin D, Thomas A, Teicher BA. Cancer treatments: Past, present, and future. Cancer Genet 2024; 286-287:18-24. [PMID: 38909530 PMCID: PMC11338712 DOI: 10.1016/j.cancergen.2024.06.002] [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: 03/25/2024] [Revised: 05/21/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
There is a rich history of cancer treatments which provides a number of important lessons for present and future cancer therapies. We outline this history by looking in the past, reviewing the current landscape of cancer treatments, and by glancing at the potential future cancer therapies.
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Affiliation(s)
- Dmitriy Sonkin
- National Cancer Institute, Division of Cancer Treatment and Diagnosis, Rockville, MD 20850, USA.
| | - Anish Thomas
- National Cancer Institute, Center for Cancer Research, Bethesda, MD 20892, USA
| | - Beverly A Teicher
- National Cancer Institute, Division of Cancer Treatment and Diagnosis, Rockville, MD 20850, USA
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9
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Agarwal P, Reid DL, Amiji M. CNS delivery of targeted protein degraders. J Control Release 2024; 372:661-673. [PMID: 38936742 DOI: 10.1016/j.jconrel.2024.06.057] [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: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
Heterobifunctional small molecule degraders are a subset of targeted protein degraders (TPDs), consisting of two ligands joined by a linker to induce proteasomal degradation of a target protein. As compared to traditional small molecules these compounds generally demonstrate inflated physicochemical properties, which may require innovative formulation strategies to enable their delivery and exert pharmacodynamic effect. The blood brain barrier (BBB) serves an essential function in human physiology, but its presence requires advanced approaches for treating central nervous system (CNS) diseases. By integrating emerging modalities like TPDs with conventional concepts of drug delivery, novel strategies to overcome the BBB can be developed. Amongst the available routes, lipid and polymer-based long-acting delivery seems to be the most amenable to TPDs, due to their ability to encapsulate lipophilic cargo and potential to be functionalized for targeted delivery. Another key consideration will be understanding E3 ligase expression in the different regions of the brain. Discovery of new brain or CNS disease specific E3 ligases could help overcome some of the barriers currently associated with CNS delivery of TPDs. This review discusses the current strategies that exist to overcome and improve therapeutic delivery of TPDs to the CNS.
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Affiliation(s)
- Prashant Agarwal
- Drug Product Technologies, Process Development, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, United States of America; Department of Chemical Engineering, College of Engineering, Northeastern University, 360 Huntington Ave, Boston, MA 02115, United States of America
| | - Darren L Reid
- Drug Product Technologies, Process Development, Amgen, Inc., 360 Binney St, Cambridge, MA 02142, United States of America
| | - Mansoor Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, 360 Huntington Ave, Boston, MA 02115, United States of America; Department of Chemical Engineering, College of Engineering, Northeastern University, 360 Huntington Ave, Boston, MA 02115, United States of America.
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10
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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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11
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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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12
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Lim M, Cong TD, Orr LM, Toriki ES, Kile AC, Papatzimas JW, Lee E, Lin Y, Nomura DK. DCAF16-Based Covalent Handle for the Rational Design of Monovalent Degraders. ACS CENTRAL SCIENCE 2024; 10:1318-1331. [PMID: 39071058 PMCID: PMC11273451 DOI: 10.1021/acscentsci.4c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 07/30/2024]
Abstract
Targeted protein degradation with monovalent molecular glue degraders is a powerful therapeutic modality for eliminating disease causing proteins. However, rational design of molecular glue degraders remains challenging. In this study, we sought to identify a transplantable and linker-less covalent handle that could be appended onto the exit vector of various protein-targeting ligands to induce the degradation of their respective targets. Using the BET family inhibitor JQ1 as a testbed, we synthesized and screened a series of covalent JQ1 analogs and identified a vinylsulfonyl piperazine handle that led to the potent and selective degradation of BRD4 in cells. Through chemoproteomic profiling, we identified DCAF16 as the E3 ligase responsible for BRD4 degradation-an E3 ligase substrate receptor that has been previously covalently targeted for molecular glue-based degradation of BRD4. Interestingly, we demonstrated that this covalent handle can be transplanted across a diverse array of protein-targeting ligands spanning many different protein classes to induce the degradation of CDK4, the androgen receptor, BTK, SMARCA2/4, and BCR-ABL/c-ABL. Our study reveals a DCAF16-based covalent degradative and linker-less chemical handle that can be attached to protein-targeting ligands to induce the degradation of several different classes of protein targets.
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Affiliation(s)
- Melissa Lim
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94720, United States
| | - Thang Do Cong
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94720, United States
| | - Lauren M. Orr
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94720, United States
| | - Ethan S. Toriki
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94720, United States
| | - Andrew C. Kile
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Biomedical Research, Emeryville, California 94608, United States
| | - James W. Papatzimas
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Biomedical Research, Emeryville, California 94608, United States
| | - Elijah Lee
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94720, United States
| | - Yihan Lin
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94720, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, California 94720, United States
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13
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Chen YF, Rahman A, Sax JL, Atala Pleshinger MJ, Friedrich RM, Adams DJ. C646 degrades Exportin-1 to modulate p300 chromatin occupancy and function. Cell Chem Biol 2024; 31:1363-1372.e8. [PMID: 38917791 PMCID: PMC11268802 DOI: 10.1016/j.chembiol.2024.05.016] [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: 11/10/2023] [Revised: 03/13/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
Molecular glues can induce proximity between a target protein and ubiquitin ligases to induce target degradation, but strategies for their discovery remain limited. We screened 3,200 bioactive small molecules and identified that C646 requires neddylation-dependent protein degradation to induce cytotoxicity. Although the histone acetyltransferase p300 is the canonical target of C646, we provide extensive evidence that C646 directly targets and degrades Exportin-1 (XPO1). Multiple cellular phenotypes induced by C646 were abrogated in cells expressing the known XPO1C528S drug-resistance allele. While XPO1 catalyzes nuclear-to-cytoplasmic transport of many cargo proteins, it also directly binds chromatin. We demonstrate that p300 and XPO1 co-occupy hundreds of chromatin loci. Degrading XPO1 using C646 or the known XPO1 modulator S109 diminishes the chromatin occupancy of both XPO1 and p300, enabling direct targeting of XPO1 to phenocopy p300 inhibition. This work highlights the utility of drug-resistant alleles and further validates XPO1 as a targetable regulator of chromatin state.
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Affiliation(s)
- Yi Fan Chen
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Atikur Rahman
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Joel L Sax
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Matthew J Atala Pleshinger
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ryan M Friedrich
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Drew J Adams
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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14
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Tin G, Cigler M, Hinterndorfer M, Dong KD, Imrichova H, Gygi SP, Winter GE. Discovery of a DCAF11-dependent cyanoacrylamide-containing covalent degrader of BET-proteins. Bioorg Med Chem Lett 2024; 107:129779. [PMID: 38729317 DOI: 10.1016/j.bmcl.2024.129779] [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: 01/18/2024] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Targeted protein degradation is mediated by small molecules that induce or stabilize protein-protein interactions between targets and the ubiquitin-proteasome machinery. Currently, there remains a need to expand the repertoire of viable E3 ligases available for hijacking. Notably, covalent chemistry has been employed to engage a handful of E3 ligases, including DCAF11. Here, we disclose a covalent PROTAC that enables DCAF11-dependent degradation, featuring a cyanoacrylamide warhead. Our findings underscore DCAF11 as an interesting candidate with a capacity to accommodate diverse electrophilic chemistries compatible with targeted protein degradation.
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Affiliation(s)
- Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kevin D Dong
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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15
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Reboud-Ravaux M. [Protein induced proximity and targeted degradations by new degraders: concepts, developments, challenges for clinical applications]. Biol Aujourdhui 2024; 218:41-54. [PMID: 39007776 DOI: 10.1051/jbio/2024007] [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: 04/10/2024] [Indexed: 07/16/2024]
Abstract
The review is focused on recent drug discovery advances based on targeted protein degradation strategies. This new area of research has exploded leading to the development of potential drugs useful in a large variety of human diseases. They first target disease relevant proteins difficult to counteract with other classical strategies and extend now to aggregates, organelles, nucleic acids or lipidic droplets. These degraders engaged either the ubiquitin-proteasome system for PROTACs and molecular glues (first generation), or the lysosomal system via endosome-lysosome degradation (LYTACs) and autophagy-lysosome degradation (ATTEC, AUTAC, AUTOTAC) (following generations of degraders). PROTACs have expanded from the orthodox heterobifunctional ones to new derivatives such as homo-PROTACs, pro-PROTACs, CLIPTACs, HaloPROTACs, PHOTOTACs, Bac-PROTACs, AbTACs, ARN-PROTACs. The small molecular-weight molecular glues induce the formation of new ternary complexes which implicate the targeted protein and an ubiquitin ligase E3 allowing the protein ubiquinitation followed by its proteasomal degradation. Lysosomal degraders (LYTAC, ATTEC, AUTAC, AUTOTAC) specifically recognize extracellular and membrane proteins or dysfunctional organelles and transport them into lysosomes where they are degraded. They overcome the limitations observed with proteasomal degradations induced by PROTAC and molecular glues and demonstrate their potential to treat human diseases, especially neurodegenerative ones. Pharmaceutical companies are engaged at the world level to develop these new potential drugs targeting cancers, immuno-inflammatory and neurodegenerative diseases as well as a variety of other ones. Efficiency and risks for these novel therapeutic strategies are discussed.
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Affiliation(s)
- Michèle Reboud-Ravaux
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, 7 quai Saint-Bernard, 75252 Paris, France
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16
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Bell LE, Bardelle C, Packer MJ, Kastl J, Holdgate GA, Davies G. Characterisation of high throughput screening outputs for small molecule degrader discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100162. [PMID: 38797285 DOI: 10.1016/j.slasd.2024.100162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
Targeted protein degradation is an important mechanism carried out by the cellular machinery, one that is gaining momentum as an exploitable strategy for the development of drug-like compounds. Molecules which are able to induce proximity between elusive therapeutic targets of interest and E3 ligases which subsequently leads to proteasomal degradation of the target are beginning to decrease the percentage of the human proteome described as undruggable. Therefore, having the ability to screen for, and understand the mechanism of, such molecules is becoming an increasingly attractive scientific focus. We have established a number of cascade experiments including cell-based assays and orthogonal triage steps to provide annotation to the selectivity and mechanism of action for compounds identified as putative degraders from a primary high throughput screen against a high value oncology target. We will describe our current position, using PROTACs as proof-of-concept, on the analysis of these novel outputs and highlight challenges encountered.
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Affiliation(s)
- Lillie E Bell
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Catherine Bardelle
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | | | - Johanna Kastl
- Assay.Works GmbH, Am Biopark 11, Regensburg, Germany
| | - Geoffrey A Holdgate
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK.
| | - Gareth Davies
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
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17
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Vickery HR, Virta JM, Konstantinidou M, Arkin MR. Development of a NanoBRET assay for evaluation of 14-3-3σ molecular glues. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100165. [PMID: 38797286 DOI: 10.1016/j.slasd.2024.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
We report the development of a 384-well formatted NanoBRET assay to characterize molecular glues of 14-3-3/client interactions in living cells. The seven isoforms of 14-3-3 are dimeric hub proteins with diverse roles including transcription factor regulation and signal transduction. 14-3-3 interacts with hundreds of client proteins to regulate their function and is therefore an ideal therapeutic target when client selectivity can be achieved. We have developed the NanoBRET system for three 14-3-3σ client proteins CRAF, TAZ, and estrogen receptor α (ERα), which represent three specific binding modes. We have measured stabilization of 14-3-3σ/client complexes by molecular glues with EC50 values between 100 nM and 1 μM in cells, which align with the EC50 values calculated by fluorescence anisotropy in vitro. Developing this NanoBRET system for the hub protein 14-3-3σ allows for a streamlined approach, bypassing multiple optimization steps in the assay development process for other 14-3-3σ clients. The NanoBRET system allows for an assessment of PPI stabilization in a more physiologically relevant, cell-based environment using full-length proteins. The method is applicable to diverse protein-protein interactions (PPIs) and offers a robust platform to explore libraries of compounds for both PPI stabilizers and inhibitors.
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Affiliation(s)
- Holly R Vickery
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Johanna M Virta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA.
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18
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Cao S. Lessons from natural molecular glue degraders. Biochem Soc Trans 2024; 52:1191-1197. [PMID: 38864421 DOI: 10.1042/bst20230836] [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: 03/06/2024] [Revised: 04/25/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]
Abstract
Molecular glue (MG) degraders include plant hormones and therapeutic drugs and have become a hot topic in drug discovery. Unlike bivalent proteolysis targeting chimeras (PROTACs), monovalent MGs can trigger the degradation of non-ligandable proteins by enhancing their interaction with E3 ubiquitin ligases. Here, I analyze the characteristics of natural MG degraders, contrast them with synthetic ones, and provide a rationale for optimizing MGs. In natural MG-based degradation systems, a stable complex is only formed when all three partners (MG, E3 ligase, and substrate) are present, while the affinities between any two components are either weak or undetectable. After the substrate is degraded, the MG will dissociate from its receptor (E3 ligase) due to their low micromolar affinity. In contrast, synthetic MGs, such as immunomodulatory drugs (IMiDs) and CR8, are potent inhibitors of their receptors by blocking the CRBN-native substrate interaction or by occupying the active site of CDK12. Inspired by nature, the affinities of IMiDs to CRBN can be reduced to make those compounds degraders without the E3-inhibitory activity, therefore, minimizing the interference with the physiological substrates of CRBN. Similarly, the CR8-CDK interaction can be weakened to uncouple the degrader function from the kinase inhibition. To mimic natural examples and reduce side effects, future development of MG degraders that lack the inhibitory activity should be considered.
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Affiliation(s)
- Shiyun Cao
- Department of Pharmacology, University of Washington, Seattle, WA, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, U.S.A
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19
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Kagiou C, Cisneros JA, Farnung J, Liwocha J, Offensperger F, Dong K, Yang K, Tin G, Horstmann CS, Hinterndorfer M, Paulo JA, Scholes NS, Sanchez Avila J, Fellner M, Andersch F, Hannich JT, Zuber J, Kubicek S, Gygi SP, Schulman BA, Winter GE. Alkylamine-tethered molecules recruit FBXO22 for targeted protein degradation. Nat Commun 2024; 15:5409. [PMID: 38926334 PMCID: PMC11208438 DOI: 10.1038/s41467-024-49739-3] [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: 01/29/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Targeted protein degradation (TPD) relies on small molecules to recruit proteins to E3 ligases to induce their ubiquitylation and degradation by the proteasome. Only a few of the approximately 600 human E3 ligases are currently amenable to this strategy. This limits the actionable target space and clinical opportunities and thus establishes the necessity to expand to additional ligases. Here we identify and characterize SP3N, a specific degrader of the prolyl isomerase FKBP12. SP3N features a minimal design, where a known FKBP12 ligand is appended with a flexible alkylamine tail that conveys degradation properties. We found that SP3N is a precursor and that the alkylamine is metabolized to an active aldehyde species that recruits the SCFFBXO22 ligase for FKBP12 degradation. Target engagement occurs via covalent adduction of Cys326 in the FBXO22 C-terminal domain, which is critical for ternary complex formation, ubiquitylation and degradation. This mechanism is conserved for two recently reported alkylamine-based degraders of NSD2 and XIAP, thus establishing alkylamine tethering and covalent hijacking of FBXO22 as a generalizable TPD strategy.
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Affiliation(s)
- Chrysanthi Kagiou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Jose A Cisneros
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Jakob Farnung
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Fabian Offensperger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Kevin Dong
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ka Yang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Christina S Horstmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Natalie S Scholes
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Juan Sanchez Avila
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Michaela Fellner
- Research Institute of Molecular Pathology, Vienna BioCenter, 1030, Vienna, Austria
| | - Florian Andersch
- Research Institute of Molecular Pathology, Vienna BioCenter, 1030, Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, 1030, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
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20
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Cigler M, Imrichova H, Frommelt F, Caramelle L, Depta L, Rukavina A, Kagiou C, Hannich JT, Mayor-Ruiz C, Superti-Furga G, Sievers S, Forrester A, Laraia L, Waldmann H, Winter GE. Orpinolide disrupts a leukemic dependency on cholesterol transport by inhibiting OSBP. Nat Chem Biol 2024:10.1038/s41589-024-01614-4. [PMID: 38907113 DOI: 10.1038/s41589-024-01614-4] [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: 03/27/2023] [Accepted: 04/10/2024] [Indexed: 06/23/2024]
Abstract
Metabolic alterations in cancer precipitate in associated dependencies that can be therapeutically exploited. To meet this goal, natural product-inspired small molecules can provide a resource of invaluable chemotypes. Here, we identify orpinolide, a synthetic withanolide analog with pronounced antileukemic properties, via orthogonal chemical screening. Through multiomics profiling and genome-scale CRISPR-Cas9 screens, we identify that orpinolide disrupts Golgi homeostasis via a mechanism that requires active phosphatidylinositol 4-phosphate signaling at the endoplasmic reticulum-Golgi membrane interface. Thermal proteome profiling and genetic validation studies reveal the oxysterol-binding protein OSBP as the direct and phenotypically relevant target of orpinolide. Collectively, these data reaffirm sterol transport as a therapeutically actionable dependency in leukemia and motivate ensuing translational investigation via the probe-like compound orpinolide.
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Affiliation(s)
- Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lucie Caramelle
- Unit of Research of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Laura Depta
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Chrysanthi Kagiou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- IRB Barcelona-Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Sonja Sievers
- Department of Chemical Biology, Max-Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Alison Forrester
- Unit of Research of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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21
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Robinson SA, Co JA, Banik SM. Molecular glues and induced proximity: An evolution of tools and discovery. Cell Chem Biol 2024; 31:1089-1100. [PMID: 38688281 DOI: 10.1016/j.chembiol.2024.04.001] [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: 07/25/2023] [Revised: 01/23/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
Small molecule molecular glues can nucleate protein complexes and rewire interactomes. Molecular glues are widely used as probes for understanding functional proximity at a systems level, and the potential to instigate event-driven pharmacology has motivated their application as therapeutics. Despite advantages such as cell permeability and the potential for low off-target activity, glues are still rare when compared to canonical inhibitors in therapeutic development. Their often simple structure and specific ability to reshape protein-protein interactions pose several challenges for widespread, designer applications. Molecular glue discovery and design campaigns can find inspiration from the fields of synthetic biology and biophysics to mine chemical libraries for glue-like molecules.
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Affiliation(s)
| | | | - Steven Mark Banik
- Department of Chemistry, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
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22
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Konstantinidou M, Arkin MR. Molecular glues for protein-protein interactions: Progressing toward a new dream. Cell Chem Biol 2024; 31:1064-1088. [PMID: 38701786 PMCID: PMC11193649 DOI: 10.1016/j.chembiol.2024.04.002] [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: 01/04/2024] [Revised: 03/08/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
The modulation of protein-protein interactions with small molecules is one of the most rapidly developing areas in drug discovery. In this review, we discuss advances over the past decade (2014-2023) focusing on molecular glues (MGs)-monovalent small molecules that induce proximity, either by stabilizing native interactions or by inducing neomorphic interactions. We include both serendipitous and rational discoveries and describe the different approaches that were used to identify them. We classify the compounds in three main categories: degradative MGs, non-degradative MGs or PPI stabilizers, and MGs that induce self-association. Diverse, illustrative examples with structural data are described in detail, emphasizing the elements of molecular recognition and cooperative binding at the interface that are fundamental for a MG mechanism of action.
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Affiliation(s)
- Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA.
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23
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Wang B, Cao S, Zheng N. Emerging strategies for prospective discovery of molecular glue degraders. Curr Opin Struct Biol 2024; 86:102811. [PMID: 38598983 DOI: 10.1016/j.sbi.2024.102811] [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: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/12/2024]
Abstract
Molecular glue (MG) degraders are monovalent small molecule compounds that co-opt E3 ubiquitin ligases to target neo-substrates for proteasomal degradation. Here, we provide a concise review of recent advances in rational MG discovery, which are categorized into two major strategies, ligand modification and de novo discovery. We also highlight the structural mechanisms underlying the formation of MG-enabled ternary complexes and their thermodynamic properties. Finally, we summarize the broader category of proximity inducers including MGs, proteolysis-targeting chimeras (PROTACs), peptides, and viral proteins. MGs are specified as a unique class of proximity inducers with chemical simplicity and a requirement of pre-existing weak protein-protein interactions. We propose that leveraging the weak basal interaction provides a starting point to prospectively develop MGs to degrade high-value therapeutic targets.
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Affiliation(s)
- Baiyun Wang
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Shiyun Cao
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Ning Zheng
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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24
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Chen Y, Xue H, Jin J. Applications of protein ubiquitylation and deubiquitylation in drug discovery. J Biol Chem 2024; 300:107264. [PMID: 38582446 PMCID: PMC11087986 DOI: 10.1016/j.jbc.2024.107264] [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: 07/09/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024] Open
Abstract
The ubiquitin (Ub)-proteasome system (UPS) is the major machinery mediating specific protein turnover in eukaryotic cells. By ubiquitylating unwanted, damaged, or harmful proteins and driving their degradation, UPS is involved in many important cellular processes. Several new UPS-based technologies, including molecular glue degraders and PROTACs (proteolysis-targeting chimeras) to promote protein degradation, and DUBTACs (deubiquitinase-targeting chimeras) to increase protein stability, have been developed. By specifically inducing the interactions between different Ub ligases and targeted proteins that are not otherwise related, molecular glue degraders and PROTACs degrade targeted proteins via the UPS; in contrast, by inducing the proximity of targeted proteins to deubiquitinases, DUBTACs are created to clear degradable poly-Ub chains to stabilize targeted proteins. In this review, we summarize the recent research progress in molecular glue degraders, PROTACs, and DUBTACs and their applications. We discuss immunomodulatory drugs, sulfonamides, cyclin-dependent kinase-targeting molecular glue degraders, and new development of PROTACs. We also introduce the principle of DUBTAC and its applications. Finally, we propose a few future directions of these three technologies related to targeted protein homeostasis.
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Affiliation(s)
- Yilin Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Haoan Xue
- Life Sciences Institute, Zhejiang University, Hangzhou, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Jianping Jin
- Life Sciences Institute, Zhejiang University, Hangzhou, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China; Cancer Center, Zhejiang University, Hangzhou, China.
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25
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Reicher A, Reiniš J, Ciobanu M, Růžička P, Malik M, Siklos M, Kartysh V, Tomek T, Koren A, Rendeiro AF, Kubicek S. Pooled multicolour tagging for visualizing subcellular protein dynamics. Nat Cell Biol 2024; 26:745-756. [PMID: 38641660 PMCID: PMC11098740 DOI: 10.1038/s41556-024-01407-w] [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: 07/25/2023] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
Imaging-based methods are widely used for studying the subcellular localization of proteins in living cells. While routine for individual proteins, global monitoring of protein dynamics following perturbation typically relies on arrayed panels of fluorescently tagged cell lines, limiting throughput and scalability. Here, we describe a strategy that combines high-throughput microscopy, computer vision and machine learning to detect perturbation-induced changes in multicolour tagged visual proteomics cell (vpCell) pools. We use genome-wide and cancer-focused intron-targeting sgRNA libraries to generate vpCell pools and a large, arrayed collection of clones each expressing two different endogenously tagged fluorescent proteins. Individual clones can be identified in vpCell pools by image analysis using the localization patterns and expression level of the tagged proteins as visual barcodes, enabling simultaneous live-cell monitoring of large sets of proteins. To demonstrate broad applicability and scale, we test the effects of antiproliferative compounds on a pool with cancer-related proteins, on which we identify widespread protein localization changes and new inhibitors of the nuclear import/export machinery. The time-resolved characterization of changes in subcellular localization and abundance of proteins upon perturbation in a pooled format highlights the power of the vpCell approach for drug discovery and mechanism-of-action studies.
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Affiliation(s)
- Andreas Reicher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jiří Reiniš
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Maria Ciobanu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Pavel Růžička
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Monika Malik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Kartysh
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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26
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Liang G, Cao W, Tang D, Zhang H, Yu Y, Ding J, Karges J, Xiao H. Nanomedomics. ACS NANO 2024; 18:10979-11024. [PMID: 38635910 DOI: 10.1021/acsnano.3c11154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Nanomaterials have attractive physicochemical properties. A variety of nanomaterials such as inorganic, lipid, polymers, and protein nanoparticles have been widely developed for nanomedicine via chemical conjugation or physical encapsulation of bioactive molecules. Superior to traditional drugs, nanomedicines offer high biocompatibility, good water solubility, long blood circulation times, and tumor-targeting properties. Capitalizing on this, several nanoformulations have already been clinically approved and many others are currently being studied in clinical trials. Despite their undoubtful success, the molecular mechanism of action of the vast majority of nanomedicines remains poorly understood. To tackle this limitation, herein, this review critically discusses the strategy of applying multiomics analysis to study the mechanism of action of nanomedicines, named nanomedomics, including advantages, applications, and future directions. A comprehensive understanding of the molecular mechanism could provide valuable insight and therefore foster the development and clinical translation of nanomedicines.
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Affiliation(s)
- Ganghao Liang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wanqing Cao
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, P. R. China
| | - Dongsheng Tang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hanchen Zhang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yingjie Yu
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, P. R. China
| | - Johannes Karges
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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27
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Offensperger F, Tin G, Duran-Frigola M, Hahn E, Dobner S, Ende CWA, Strohbach JW, Rukavina A, Brennsteiner V, Ogilvie K, Marella N, Kladnik K, Ciuffa R, Majmudar JD, Field SD, Bensimon A, Ferrari L, Ferrada E, Ng A, Zhang Z, Degliesposti G, Boeszoermenyi A, Martens S, Stanton R, Müller AC, Hannich JT, Hepworth D, Superti-Furga G, Kubicek S, Schenone M, Winter GE. Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells. Science 2024; 384:eadk5864. [PMID: 38662832 DOI: 10.1126/science.adk5864] [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: 08/31/2023] [Accepted: 03/22/2024] [Indexed: 05/04/2024]
Abstract
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advanced fragment-based ligand discovery toward cellular systems, but throughput limitations have stymied the scalable identification of fragment-protein interactions. We report proteome-wide maps of protein-binding propensity for 407 structurally diverse small-molecule fragments. We verified that identified interactions can be advanced to active chemical probes of E3 ubiquitin ligases, transporters, and kinases. Integrating machine learning binary classifiers further enabled interpretable predictions of fragment behavior in cells. The resulting resource of fragment-protein interactions and predictive models will help to elucidate principles of molecular recognition and expedite ligand discovery efforts for hitherto undrugged proteins.
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Affiliation(s)
- Fabian Offensperger
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gary Tin
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Miquel Duran-Frigola
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Ersilia Open Source Initiative, Cambridge CB1 3DE, UK
| | - Elisa Hahn
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sarah Dobner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Andrea Rukavina
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincenth Brennsteiner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Kevin Ogilvie
- Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Nara Marella
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katharina Kladnik
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Rodolfo Ciuffa
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Luca Ferrari
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Evandro Ferrada
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Amanda Ng
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Zhechun Zhang
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - Gianluca Degliesposti
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andras Boeszoermenyi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Robert Stanton
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - André C Müller
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - J Thomas Hannich
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Georg E Winter
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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28
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An J, Zhang X. Crbn-based molecular Glues: Breakthroughs and perspectives. Bioorg Med Chem 2024; 104:117683. [PMID: 38552596 DOI: 10.1016/j.bmc.2024.117683] [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: 12/11/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/20/2024]
Abstract
CRBN is a substrate receptor for the Cullin Ring E3 ubiquitin ligase 4 (CRL4) complex. It has been observed that CRBN can be exploited by small molecules to facilitate the recruitment and ubiquitination of non-natural CRL4 substrates, resulting in the degradation of neosubstrate through the ubiquitin-proteasome system. This phenomenon, known as molecular glue-induced protein degradation, has emerged as an innovative therapeutic approach in contrast to traditional small-molecule drugs. One key advantage of molecular glues, in comparison to conventional small-molecule drugs adhering to Lipinski's Rule of Five, is their ability to operate without the necessity for specific binding pockets on target proteins. This unique characteristic empowers molecular glues to interact with conventionally intractable protein targets, such as transcription factors and scaffold proteins. The ability to induce the degradation of these previously elusive targets by hijacking the ubiquitin-proteasome system presents a promising avenue for the treatment of recalcitrant diseases. Nevertheless, the rational design of molecular glues remains a formidable challenge due to the limited understanding of their mechanisms and actions. This review offers an overview of recent advances and breakthroughs in the field of CRBN-based molecular glues, while also exploring the prospects for a systematic approach to designing these compounds.
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Affiliation(s)
- Juzeng An
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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29
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Carter TR, Milosevich N, Dada L, Shaum JB, Barry Sharpless K, Kitamura S, Erb MA. SuFEx-based chemical diversification for the systematic discovery of CRBN molecular glues. Bioorg Med Chem 2024; 104:117699. [PMID: 38608634 PMCID: PMC11195152 DOI: 10.1016/j.bmc.2024.117699] [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: 01/30/2024] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
Molecular glues are small molecules that stabilize protein-protein interactions, enabling new molecular pharmacologies, such as targeted protein degradation. They offer advantages over proteolysis targeting chimeras (PROTACs), which present challenges associated with the size and properties of heterobifunctional constructions, but glues lack the rational design principles analogous to PROTACs. One notable exception is the ability to alter the structure of Cereblon (CRBN)-based molecular glues and redirect their activity toward new neo-substrate proteins. We took a focused approach toward modifying the CRBN ligand, 5'-amino lenalidomide, to alter its neo-substrate specificity using high-throughput chemical diversification by parallelized sulfur(VI)-fluoride exchange (SuFEx) transformations. We synthesized over 3,000 analogs of 5'-amino lenalidomide using this approach and screened the crude products using a phenotypic screen for cell viability, identifying dozens of analogs with differentiated activity. We characterized four compounds that degrade G-to-S phase transition 1 (GSPT1) protein, providing a proof-of-concept model for SuFEx-based discovery of CRBN molecular glues.
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Affiliation(s)
- Trever R Carter
- Department of Chemistry, The Scripps Research Institute, United States
| | | | - Lucas Dada
- Department of Biochemistry, Albert Einstein College of Medicine, United States
| | - James B Shaum
- Department of Chemistry, The Scripps Research Institute, United States
| | - K Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, United States
| | - Seiya Kitamura
- Department of Chemistry, The Scripps Research Institute, United States; Department of Biochemistry, Albert Einstein College of Medicine, United States
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, United States
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30
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Sun X, Zhou Y, Wang Z, Peng M, Wei X, Xie Y, Wen C, Liu J, Ye M. Biomolecular Condensates Decipher Molecular Codes of Cell Fate: From Biophysical Fundamentals to Therapeutic Practices. Int J Mol Sci 2024; 25:4127. [PMID: 38612940 PMCID: PMC11012904 DOI: 10.3390/ijms25074127] [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: 02/29/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Cell fate is precisely modulated by complex but well-tuned molecular signaling networks, whose spatial and temporal dysregulation commonly leads to hazardous diseases. Biomolecular condensates (BCs), as a newly emerging type of biophysical assemblies, decipher the molecular codes bridging molecular behaviors, signaling axes, and clinical prognosis. Particularly, physical traits of BCs play an important role; however, a panoramic view from this perspective toward clinical practices remains lacking. In this review, we describe the most typical five physical traits of BCs, and comprehensively summarize their roles in molecular signaling axes and corresponding major determinants. Moreover, establishing the recent observed contribution of condensate physics on clinical therapeutics, we illustrate next-generation medical strategies by targeting condensate physics. Finally, the challenges and opportunities for future medical development along with the rapid scientific and technological advances are highlighted.
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Affiliation(s)
- Xing Sun
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Yangyang Zhou
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Zhiyan Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Menglan Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Xianhua Wei
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Yifang Xie
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Chengcai Wen
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Jing Liu
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
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31
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Kaushik A, Parashar S, Ambasta RK, Kumar P. Ubiquitin E3 ligases assisted technologies in protein degradation: Sharing pathways in neurodegenerative disorders and cancer. Ageing Res Rev 2024; 96:102279. [PMID: 38521359 DOI: 10.1016/j.arr.2024.102279] [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: 01/10/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
E3 ligases, essential components of the ubiquitin-proteasome-mediated protein degradation system, play a critical role in cellular regulation. By covalently attaching ubiquitin (Ub) molecules to target proteins, these ligases mark them for degradation, influencing various bioprocesses. With over 600 E3 ligases identified, there is a growing realization of their potential as therapeutic candidates for addressing proteinopathies in cancer and neurodegenerative disorders (NDDs). Recent research has highlighted the need to delve deeper into the intricate roles of E3 ligases as nexus points in the pathogenesis of both cancer and NDDs. Their dysregulation is emerging as a common thread linking these seemingly disparate diseases, necessitating a comprehensive understanding of their molecular intricacies. Herein, we have discussed (i) the fundamental mechanisms through which different types of E3 ligases actively participate in selective protein degradation in cancer and NDDs, followed by an examination of common E3 ligases playing pivotal roles in both situations, emphasising common players. Moving to, (ii) the functional domains and motifs of E3 ligases involved in ubiquitination, we have explored their interactions with specific substrates in NDDs and cancer. Additionally, (iii) we have explored techniques like PROTAC, molecular glues, and other state-of-the-art methods for hijacking neurotoxic and oncoproteins. Lastly, (iv) we have provided insights into ongoing clinical trials, offering a glimpse into the evolving landscape of E3-based therapeutics for cancer and NDDs. Unravelling the intricate network of E3 ligase-mediated regulation holds the key to unlocking targeted therapies that address the specific molecular signatures of individual patients, heralding a new era in personalized medicines.
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Affiliation(s)
- Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Somya Parashar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University-Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India.
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32
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Garber K. The glue degraders. Nat Biotechnol 2024; 42:546-550. [PMID: 38448663 DOI: 10.1038/s41587-024-02164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
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33
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Lemaitre T, Cornu M, Schwalen F, Since M, Kieffer C, Voisin-Chiret AS. Molecular glue degraders: exciting opportunities for novel drug discovery. Expert Opin Drug Discov 2024; 19:433-449. [PMID: 38240114 DOI: 10.1080/17460441.2024.2306845] [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: 10/06/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Molecular Glue Degraders (MGDs) is a concept that refers to a class of compounds that facilitate the interaction between two proteins or molecules within a cell. These compounds act as bridge that enhances specific Protein-Protein Interactions (PPIs). Over the past decade, this technology has gained attention as a potential strategy to target proteins that were traditionally considered undruggable using small molecules. AREAS COVERED This review presents the concept of cellular homeostasis and the balance between protein synthesis and protein degradation. The concept of protein degradation is concerned with molecular glues, which form part of the broader field of Targeted Protein Degradation (TPD). Next, pharmacochemical strategies for the rational design of MGDs are detailed and illustrated by examples of Ligand-Based (LBDD), Structure-Based (SBDD) and Fragment-Based Drug Design (FBDD). EXPERT OPINION Expanding the scope of what can be effectively targeted in the development of treatments for diseases that are incurable or resistant to conventional therapies offers new therapeutic options. The treatment of microbial infections and neurodegenerative diseases is a major societal challenge, and the discovery of MGDs appears to be a promising avenue. Combining different approaches to discover and exploit a variety of innovative therapeutic agents will create opportunities to treat diseases that are still incurable.
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Affiliation(s)
| | - Marie Cornu
- Normandie University, UNICAEN, CERMN, Caen, France
| | - Florian Schwalen
- Normandie University, UNICAEN, CERMN, Caen, France
- Department of Pharmacy, Caen University Hospital, Caen, France
| | - Marc Since
- Normandie University, UNICAEN, CERMN, Caen, France
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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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Barbosa BMG, Sfyaki A, Rafael S, José-Duran F, Pous J, Sánchez-Zarzalejo C, Perez-Lopez C, Vilanova M, Cigler M, Gay M, Vilaseca M, Winter GE, Riera A, Mayor-Ruiz C. Discovery and Mechanistic Elucidation of NQO1-Bioactivatable Small Molecules That Overcome Resistance to Degraders. Angew Chem Int Ed Engl 2024; 63:e202316730. [PMID: 38153885 DOI: 10.1002/anie.202316730] [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: 11/05/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 12/30/2023]
Abstract
Degraders hold the promise to efficiently inactivate previously intractable disease-relevant targets. Unlike traditional inhibitors, degraders act substoichiometrically and rely on the hijacked proteolysis machinery, which can also act as an entry point for resistance. To fully harness the potential of targeted protein degradation, it is crucial to comprehend resistance mechanisms and formulate effective strategies to overcome them. We conducted a chemical screening to identify synthetic lethal vulnerabilities of cancer cells that exhibit widespread resistance to degraders. Comparative profiling followed by tailored optimization delivered the small molecule RBS-10, which shows preferential cytotoxicity against cells pan-resistant to degraders. Multiomics deconvolution of the mechanism of action revealed that RBS-10 acts as a prodrug bioactivated by the oxidoreductase enzyme NQO1, which is highly overexpressed in our resistance models. Collectively, our work informs on NQO1 as an actionable vulnerability to overcome resistance to degraders and as a biomarker to selectively exploit bioactivatable prodrugs in cancer.
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Affiliation(s)
- Bárbara M G Barbosa
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Aikaterini Sfyaki
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Sergi Rafael
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Ferran José-Duran
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Carolina Sánchez-Zarzalejo
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Carles Perez-Lopez
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Mar Vilanova
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Marko Cigler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090, Vienna, Austria
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Georg E Winter
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090, Vienna, Austria
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Secció Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
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Hsia O, Hinterndorfer M, Cowan AD, Iso K, Ishida T, Sundaramoorthy R, Nakasone MA, Imrichova H, Schätz C, Rukavina A, Husnjak K, Wegner M, Correa-Sáez A, Craigon C, Casement R, Maniaci C, Testa A, Kaulich M, Dikic I, Winter GE, Ciulli A. Targeted protein degradation via intramolecular bivalent glues. Nature 2024; 627:204-211. [PMID: 38383787 PMCID: PMC10917667 DOI: 10.1038/s41586-024-07089-6] [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: 02/18/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Targeted protein degradation is a pharmacological modality that is based on the induced proximity of an E3 ubiquitin ligase and a target protein to promote target ubiquitination and proteasomal degradation. This has been achieved either via proteolysis-targeting chimeras (PROTACs)-bifunctional compounds composed of two separate moieties that individually bind the target and E3 ligase, or via molecular glues that monovalently bind either the ligase or the target1-4. Here, using orthogonal genetic screening, biophysical characterization and structural reconstitution, we investigate the mechanism of action of bifunctional degraders of BRD2 and BRD4, termed intramolecular bivalent glues (IBGs), and find that instead of connecting target and ligase in trans as PROTACs do, they simultaneously engage and connect two adjacent domains of the target protein in cis. This conformational change 'glues' BRD4 to the E3 ligases DCAF11 or DCAF16, leveraging intrinsic target-ligase affinities that do not translate to BRD4 degradation in the absence of compound. Structural insights into the ternary BRD4-IBG1-DCAF16 complex guided the rational design of improved degraders of low picomolar potency. We thus introduce a new modality in targeted protein degradation, which works by bridging protein domains in cis to enhance surface complementarity with E3 ligases for productive ubiquitination and degradation.
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Affiliation(s)
- Oliver Hsia
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Angus D Cowan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Kentaro Iso
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Tsukuba Research Laboratory, Eisai Co., Ibaraki, Japan
| | - Tasuku Ishida
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Tsukuba Research Laboratory, Eisai Co., Ibaraki, Japan
| | | | - Mark A Nakasone
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Caroline Schätz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Koraljka Husnjak
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Martin Wegner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alejandro Correa-Sáez
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Conner Craigon
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ryan Casement
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chiara Maniaci
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Andrea Testa
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Amphista Therapeutics, Cambridge, UK
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
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Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
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Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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Liang X, Ren H, Han F, Liang R, Zhao J, Liu H. The new direction of drug development: Degradation of undruggable targets through targeting chimera technology. Med Res Rev 2024; 44:632-685. [PMID: 37983964 DOI: 10.1002/med.21992] [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: 11/30/2022] [Revised: 06/13/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Imbalances in protein and noncoding RNA levels in vivo lead to the occurrence of many diseases. In addition to the use of small molecule inhibitors and agonists to restore these imbalances, recently emerged targeted degradation technologies provide a new direction for disease treatment. Targeted degradation technology directly degrades target proteins or RNA by utilizing the inherent degradation pathways, thereby eliminating the functions of pathogenic proteins (or RNA) to treat diseases. Compared with traditional therapies, targeted degradation technology which avoids the principle of traditional inhibitor occupation drive, has higher efficiency and selectivity, and widely expands the range of drug targets. It is one of the most promising and hottest areas for future drug development. Herein, we systematically introduced the in vivo degradation systems applied to degrader design: ubiquitin-proteasome system, lysosomal degradation system, and RNA degradation system. We summarized the development progress, structural characteristics, and limitations of novel chimeric design technologies based on different degradation systems. In addition, due to the lack of clear ligand-binding pockets, about 80% of disease-associated proteins cannot be effectively intervened with through traditional therapies. We deeply elucidated how to use targeted degradation technology to discover and design molecules for representative undruggable targets including transcription factors, small GTPases, and phosphatases. Overall, this review provides a comprehensive and systematic overview of targeted degradation technology-related research advances and a new guidance for the chimeric design of undruggable targets.
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Affiliation(s)
- Xuewu Liang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hairu Ren
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Fengyang Han
- School of Pharmacy, Fudan University, Shanghai, China
| | - Renwen Liang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jiayan Zhao
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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Tao L, Xia X, Kong S, Wang T, Fan F, Wang W. Natural pentacyclic triterpenoid from Pristimerin sensitizes p53-deficient tumor to PARP inhibitor by ubiquitination of Chk1. Pharmacol Res 2024; 201:107091. [PMID: 38316371 DOI: 10.1016/j.phrs.2024.107091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Inhibition of checkpoint kinase 1 (Chk1) has shown to overcome resistance to poly (ADP-ribose) polymerase (PARP) inhibitors and expand the clinical utility of PARP inhibitors in a broad range of human cancers. Pristimerin, a naturally occurring pentacyclic triterpenoid, has been the focus of intensive studies for its anticancer potential. However, it is not yet known whether low dose of pristimerin can be combined with PARP inhibitors by targeting Chk1 signaling pathway. In this study, we investigated the efficacy, safety and molecular mechanisms of the synergistic effect produced by the combination olaparib and pristimerin in TP53-deficient and BRCA-proficient cell models. As a result, an increased expression of Chk1 was correlated with TP53 mutation, and pristimerin preferentially sensitized p53-defective cells to olaparib. The combination of olaparib and pristimerin resulted in a more pronounced abrogation of DNA synthesis and induction of DNA double-strand breaks (DSBs). Moreover, pristimerin disrupted the constitutional levels of Chk1 and DSB repair activities. Mechanistically, pristimerin promoted K48-linked polyubiquitination and proteasomal degradation of Chk1 while not affecting its kinase domain and activity. Importantly, combinatorial therapy led to a higher rate of tumor growth inhibition without apparent hematological toxicities. In addition, pristimerin suppressed olaparib-induced upregulation of Chk1 and enhanced olaparib-induced DSB marker γΗ2ΑΧ in vivo. Taken together, inhibition of Chk1 by pristimerin has been observed to induce DNA repair deficiency, which may expand the application of olaparib in BRCA-proficient cancers harboring TP53 mutations. Thus, pristimerin can be combined for PARP inhibitor-based therapy.
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Affiliation(s)
- Li Tao
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Xiangyu Xia
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shujing Kong
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Tingye Wang
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Fangtian Fan
- Anhui Engineering Technology Research Center of Biochemical Pharmaceuticals, School of Pharmacy, Bengbu Medical College, Bengbu, Anhui 233003, China
| | - Weimin Wang
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China; Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yixing, Jiangsu 214200, China.
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Menendez JA, Cuyàs E, Encinar JA, Vander Steen T, Verdura S, Llop‐Hernández À, López J, Serrano‐Hervás E, Osuna S, Martin‐Castillo B, Lupu R. Fatty acid synthase (FASN) signalome: A molecular guide for precision oncology. Mol Oncol 2024; 18:479-516. [PMID: 38158755 PMCID: PMC10920094 DOI: 10.1002/1878-0261.13582] [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: 10/02/2023] [Revised: 10/27/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024] Open
Abstract
The initial excitement generated more than two decades ago by the discovery of drugs targeting fatty acid synthase (FASN)-catalyzed de novo lipogenesis for cancer therapy was short-lived. However, the advent of the first clinical-grade FASN inhibitor (TVB-2640; denifanstat), which is currently being studied in various phase II trials, and the exciting advances in understanding the FASN signalome are fueling a renewed interest in FASN-targeted strategies for the treatment and prevention of cancer. Here, we provide a detailed overview of how FASN can drive phenotypic plasticity and cell fate decisions, mitochondrial regulation of cell death, immune escape and organ-specific metastatic potential. We then present a variety of FASN-targeted therapeutic approaches that address the major challenges facing FASN therapy. These include limitations of current FASN inhibitors and the lack of precision tools to maximize the therapeutic potential of FASN inhibitors in the clinic. Rethinking the role of FASN as a signal transducer in cancer pathogenesis may provide molecularly driven strategies to optimize FASN as a long-awaited target for cancer therapeutics.
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Affiliation(s)
- Javier A. Menendez
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Elisabet Cuyàs
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Jose Antonio Encinar
- Institute of Research, Development and Innovation in Biotechnology of Elche (IDiBE) and Molecular and Cell Biology Institute (IBMC)Miguel Hernández University (UMH)ElcheSpain
| | - Travis Vander Steen
- Division of Experimental Pathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
- Mayo Clinic Cancer CenterRochesterMNUSA
- Department of Biochemistry and Molecular Biology LaboratoryMayo Clinic LaboratoryRochesterMNUSA
| | - Sara Verdura
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Àngela Llop‐Hernández
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Júlia López
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Eila Serrano‐Hervás
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaGironaSpain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaGironaSpain
- ICREABarcelonaSpain
| | - Begoña Martin‐Castillo
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
- Unit of Clinical ResearchCatalan Institute of OncologyGironaSpain
| | - Ruth Lupu
- Division of Experimental Pathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
- Mayo Clinic Cancer CenterRochesterMNUSA
- Department of Biochemistry and Molecular Biology LaboratoryMayo Clinic LaboratoryRochesterMNUSA
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Setia N, Almuqdadi HTA, Abid M. Journey of Von Hippel-Lindau (VHL) E3 ligase in PROTACs design: From VHL ligands to VHL-based degraders. Eur J Med Chem 2024; 265:116041. [PMID: 38199162 DOI: 10.1016/j.ejmech.2023.116041] [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: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The scientific community has shown considerable interest in proteolysis-targeting chimeras (PROTACs) in the last decade, indicating their remarkable potential as a means of achieving targeted protein degradation (TPD). Not only are PROTACs seen as valuable tools in molecular biology but their emergence as a modality for drug discovery has also garnered significant attention. PROTACs bind to E3 ligases and target proteins through respective ligands connected via a linker to induce proteasome-mediated protein degradation. The discovery of small molecule ligands for E3 ligases has led to the prevalent use of various E3 ligases in PROTAC design. Furthermore, the incorporation of different types of linkers has proven beneficial in enhancing the efficacy of PROTACs. By far more than 3300 PROTACs have been reported in the literature. Notably, Von Hippel-Lindau (VHL)-based PROTACs have surfaced as a propitious strategy for targeting proteins, even encompassing those that were previously considered non-druggable. VHL is extensively utilized as an E3 ligase in the advancement of PROTACs owing to its widespread expression in various tissues and well-documented binders. Here, we review the discovery of VHL ligands, the types of linkers employed to develop VHL-based PROTACs, and their subsequent modulation to design advanced non-conventional degraders to target various disease-causing proteins. Furthermore, we provide an overview of other E3 ligases recruited in the field of PROTAC technology.
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Affiliation(s)
- Nisha Setia
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | | | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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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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Zheng M, Zhang XY, Chen W, Xia F, Yang H, Yuan K, Yang P. Molecules inducing specific cyclin-dependent kinase degradation and their possible use in cancer therapy. Future Med Chem 2024; 16:369-388. [PMID: 38288571 DOI: 10.4155/fmc-2023-0259] [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: 09/01/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Cyclin-dependent kinases (CDKs) play an important role in the regulation of cell proliferation, and many CDK inhibitors were developed. However, pan-CDK inhibitors failed to be approved due to intolerant toxicity or low efficacy and the use of selective CDK4/6 inhibitors is limited by resistance. Protein degraders have the potential to increase selectivity, efficacy and overcome resistance, which provides a novel strategy for regulating CDKs. In this review, we summarized the function of CDKs in regulating the cell cycle and transcription, and introduced the representative CDK inhibitors. Then we made a detailed introduction about four types of CDKs degraders, including their action mechanisms, research status and application prospects, which could help the development of novel CDKs degraders.
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Affiliation(s)
- Mingming Zheng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiao-Yu Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Weijiao Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Fei Xia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Huanaoyu Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China
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44
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Szewczyk SM, Verma I, Edwards JT, Weiss DR, Chekler ELP. Trends in Neosubstrate Degradation by Cereblon-Based Molecular Glues and the Development of Novel Multiparameter Optimization Scores. J Med Chem 2024; 67:1327-1335. [PMID: 38170610 DOI: 10.1021/acs.jmedchem.3c01872] [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: 01/05/2024]
Abstract
Molecular glues enable the degradation of previously "undruggable" proteins via the recruitment of cereblon (CRBN) to the target. One major challenge in designing CRBN E3 ligase modulating compounds (CELMoDs) is the selectivity profile toward neosubstrates, proteins recruited by CRBN E3 ligase agents for degradation. Common neosubstrates include Aiolos, Ikaros, GSPT1, CK1α, and SALL4. Unlike achieving potency and selectivity for traditional small molecule inhibitors, reducing the degradation of these neosubstrates is complicated by the ternary nature of the complex formed between the protein, CRBN, and CELMoD. The standard guiding principles of medicinal chemistry, such as enforcing hydrogen bond formation, are less predictive of degradation efficiency and selectivity. Disclosed is an analysis of our glutarimide CELMoD library to identify interpretable chemical features correlated to selectivity profiles and general cytotoxicity. Included is a simple multiparameter optimization function using only three parameters to predict whether molecules will have undesired neosubstrate activity.
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Affiliation(s)
| | - Isha Verma
- Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Jacob T Edwards
- Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Dahlia R Weiss
- Bristol Myers Squibb, Redwood City, California 94063, United States
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45
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Thomas K, Bouguenina H, Miller DSJ, Sialana FJ, Hayhow TG, Choudhary JS, Rossanese OW, Bellenie BR. Degradation by Design: New Cyclin K Degraders from Old CDK Inhibitors. ACS Chem Biol 2024; 19:173-184. [PMID: 38193430 PMCID: PMC10804372 DOI: 10.1021/acschembio.3c00616] [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: 10/06/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024]
Abstract
Small molecules that induce protein degradation hold the potential to overcome several limitations of the currently available inhibitors. Monovalent or molecular glue degraders, in particular, enable the benefits of protein degradation without the disadvantages of high molecular weight and the resulting challenge in drug development that are associated with bivalent molecules like Proteolysis Targeting Chimeras. One key challenge in designing monovalent degraders is how to build in the degrader activity─how can we convert an inhibitor into a degrader? If degradation activity requires very specific molecular features, it will be difficult to find new degraders and challenging to optimize those degraders toward drugs. Herein, we demonstrate that an unexpectedly wide range of modifications to the degradation-inducing group of the cyclin K degrader CR8 are tolerated, including both aromatic and nonaromatic groups. We used these findings to convert the pan-CDK inhibitors dinaciclib and AT-7519 to Cyclin K degraders, leading to a novel dinaciclib-based compound with improved degradation activity compared to CR8 and confirm the mechanism of degradation. These results suggest that general design principles can be generated for the development and optimization of monovalent degraders.
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Affiliation(s)
- Katie
L. Thomas
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Habib Bouguenina
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Daniel S. J. Miller
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Fernando J. Sialana
- Functional
Proteomics Group, The Institute of Cancer
Research, London SW3 6JB, U.K.
| | - Thomas G. Hayhow
- Oncology
R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, U.K.
| | - Jyoti S. Choudhary
- Functional
Proteomics Group, The Institute of Cancer
Research, London SW3 6JB, U.K.
| | - Olivia W. Rossanese
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Benjamin R. Bellenie
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
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46
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Kuchukulla RR, Hwang I, Kim SH, Kye Y, Park N, Cha H, Moon S, Chung HW, Lee C, Kong G, Hur W. Identification of a novel potent CDK inhibitor degrading cyclinK with a superb activity to reverse trastuzumab-resistance in HER2-positive breast cancer in vivo. Eur J Med Chem 2024; 264:116014. [PMID: 38061230 DOI: 10.1016/j.ejmech.2023.116014] [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: 09/21/2023] [Revised: 11/19/2023] [Accepted: 11/26/2023] [Indexed: 12/30/2023]
Abstract
CDK12 is overexpressed in HER2-positive breast cancers and promotes tumorigenesis and trastuzumab resistance. Thus CDK12 is a good therapeutic target for the HER2-positive breast tumors resistant to trastuzumab. We previously reported a novel purine-based CDK inhibitor with an ability to degrade cyclinK. Herein, we further explored and synthesized new derivatives, and identified a new potent pan-CDK inhibitor degrading cyclinK (32e). Compound 32e potently inhibited CDK12/cyclinK with IC50 = 3 nM, and suppressed the growth of the both trastuzumab-sensitive and trastuzumab-resistant HER2-positive breast cancer cell lines (GI50's = 9-21 nM), which is superior to a potent, clinical pan-CDK inhibitor dinaciclib. Moreover, 32e (10, 20 mg/kg, ip, twice a week) showed a dose-dependent inhibition of tumor growth and a more dramatic anti-cancer effect than dinaciclib in mouse in vivo orthotopic breast cancer model of trastuzumab-resistant HCC1954 cells. Kinome-wide inhibition profiling revealed that 32e at 1 μM exhibits a decent selectivity toward CDK-family kinases including CDK12 over other wildtype protein kinases. Quantitative global proteomic analysis of 32e-treated HCC1954 cells demonstrated that 32e also showed a decent selectivity in degrading cyclinK over other cyclins. Compound 32e could be developed as a drug for intractable trastuzumab-resistant HER2-positive breast cancers. Our current study would provide a useful insight in designing potent cyclinK degraders.
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Affiliation(s)
- Ratnakar Reddy Kuchukulla
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Injeoung Hwang
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea; Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Suhn Hyung Kim
- Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Younghyeon Kye
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Narae Park
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyungheedaero, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Heary Cha
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Sojeong Moon
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Hwan Won Chung
- Computational Science Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Cheolju Lee
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Gu Kong
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea; Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea; Department of Pathology, Hanyang University College of Medicine, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Wooyoung Hur
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea; Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea.
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47
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Jiang W, Jiang Y, Luo Y, Qiao W, Yang T. Facilitating the development of molecular glues: Opportunities from serendipity and rational design. Eur J Med Chem 2024; 263:115950. [PMID: 37984298 DOI: 10.1016/j.ejmech.2023.115950] [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: 08/28/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
Molecular glues can specifically induce interactions between two or more proteins to modulate biological functions and have been proven to be a powerful therapeutic modality in drug discovery. It plays a variety of vital roles in several biological processes, such as complex stabilization, interactome modulation and transporter inhibition, thus enabling challenging therapeutic targets to be druggable. Most known molecular glues were identified serendipitously, such as IMiDs, auxin, and rapamycin. In recent years, more rational strategies were explored with the development of chemical biology and a deep understanding of the interaction between molecular glues and proteins, which led to the rational discovery of several molecular glues. Thus, in this review, we aim to highlight the discovery strategies of molecular glues from three aspects: serendipitous discovery, screening methods and rational design principles. We expect that this review will provide a reasonable reference and insights for the discovery of molecular glues.
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Affiliation(s)
- Weiqing Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunhan Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Cardiovascular Surgery Research Laboratory, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Youfu Luo
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
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48
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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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49
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Schmitz M, Kaltheuner IH, Anand K, Düster R, Moecking J, Monastyrskyi A, Duckett DR, Roush WR, Geyer M. The reversible inhibitor SR-4835 binds Cdk12/cyclin K in a noncanonical G-loop conformation. J Biol Chem 2024; 300:105501. [PMID: 38016516 PMCID: PMC10767194 DOI: 10.1016/j.jbc.2023.105501] [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: 07/18/2023] [Revised: 10/23/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023] Open
Abstract
Inhibition of cyclin-dependent kinases (CDKs) has evolved as an emerging anticancer strategy. In addition to the cell cycle-regulating CDKs, the transcriptional kinases Cdk12 and Cdk13 have become the focus of interest as they mediate a variety of functions, including the transition from transcription initiation to elongation and termination, precursor mRNA splicing, and intronic polyadenylation. Here, we determine the crystal structure of the small molecular inhibitor SR-4835 bound to the Cdk12/cyclin K complex at 2.68 Å resolution. The compound's benzimidazole moiety is embedded in a unique hydrogen bond network mediated by the kinase hinge region with flanking hydroxy groups of the Y815 and D819 side chains. Whereas the SR-4835 head group targets the adenine-binding pocket, the kinase's glycine-rich loop is shifted down toward the activation loop. Additionally, the αC-helix adopts an inward conformation, and the phosphorylated T-loop threonine interacts with all three canonical arginines, a hallmark of CDK activation that is altered in Cdk12 and Cdk13. Dose-response inhibition measurements with recombinant CMGC kinases show that SR-4835 is highly specific for Cdk12 and Cdk13 following a 10-fold lower potency for Cdk10. Whereas other CDK-targeting compounds exhibit tighter binding affinities and higher potencies for kinase inhibition, SR-4835 can be considered a selective transcription elongation antagonist. Our results provide the basis for a rational improvement of SR-4835 toward Cdk12 inhibition and a gain in selectivity over other transcription regulating CDKs.
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Affiliation(s)
| | | | - Kanchan Anand
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Robert Düster
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Jonas Moecking
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | | | - Derek R Duckett
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida, USA
| | - William R Roush
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany.
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50
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Kozicka Z, Suchyta DJ, Focht V, Kempf G, Petzold G, Jentzsch M, Zou C, Di Genua C, Donovan KA, Coomar S, Cigler M, Mayor-Ruiz C, Schmid-Burgk JL, Häussinger D, Winter GE, Fischer ES, Słabicki M, Gillingham D, Ebert BL, Thomä NH. Design principles for cyclin K molecular glue degraders. Nat Chem Biol 2024; 20:93-102. [PMID: 37679459 PMCID: PMC10746543 DOI: 10.1038/s41589-023-01409-z] [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: 12/01/2022] [Accepted: 07/24/2023] [Indexed: 09/09/2023]
Abstract
Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12-cyclin K to the DDB1-CUL4-RBX1 E3 ligase. Here, to investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure-activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.
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Affiliation(s)
- Zuzanna Kozicka
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Biology, University of Basel, Basel, Switzerland
| | - Dakota J Suchyta
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Vivian Focht
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Petzold
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Monte Rosa Therapeutics, Basel, Switzerland
| | - Marius Jentzsch
- Institute of Clinical Chemistry and Clinical Pharmacology, University and University Hospital Bonn, Bonn, Germany
| | - Charles Zou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Yale University, New Haven, CT, USA
| | - Cristina Di Genua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- VantAI, New York, NY, USA
| | - Katherine A Donovan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Seemon Coomar
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- IRB Barcelona-Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jonathan L Schmid-Burgk
- Institute of Clinical Chemistry and Clinical Pharmacology, University and University Hospital Bonn, Bonn, Germany
| | | | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Eric S Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, 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
| | | | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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