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Till NA, Ramanathan M, Bertozzi CR. Induced proximity at the cell surface. Nat Biotechnol 2025; 43:702-711. [PMID: 40140559 DOI: 10.1038/s41587-025-02592-1] [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: 09/13/2024] [Accepted: 02/17/2025] [Indexed: 03/28/2025]
Abstract
Molecular proximity is a governing principle of biology that is essential to normal and disease-related biochemical pathways. At the cell surface, protein-protein proximity regulates receptor activation, inhibition and protein recycling and degradation. Induced proximity is a molecular engineering principle in which bifunctional molecules are designed to bring two protein targets into close contact, inducing a desired biological outcome. Researchers use this engineering principle for therapeutic purposes and to interrogate fundamental biological mechanisms. This Review focuses on the use of induced proximity at the cell surface for diverse applications, such as targeted protein degradation, receptor inhibition and activating intracellular signaling cascades. We see a rich future for proximity-based modulation of cell surface protein activity both in basic and translational science.
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Affiliation(s)
- Nicholas A Till
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Muthukumar Ramanathan
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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2
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Hinterndorfer M, Spiteri VA, Ciulli A, Winter GE. Targeted protein degradation for cancer therapy. Nat Rev Cancer 2025:10.1038/s41568-025-00817-8. [PMID: 40281114 DOI: 10.1038/s41568-025-00817-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2025] [Indexed: 04/29/2025]
Abstract
Targeted protein degradation (TPD) aims at reprogramming the target specificity of the ubiquitin-proteasome system, the major cellular protein disposal machinery, to induce selective ubiquitination and degradation of therapeutically relevant proteins. Since its conception over 20 years ago, TPD has gained a lot of attention mainly due to improvements in the design of bifunctional proteolysis targeting chimeras (PROTACs) and understanding the mechanisms underlying molecular glue degraders. Today, PROTACs are on the verge of a first clinical approval and recent structural and mechanistic insights combined with technological leaps promise to unlock the rational design of protein degraders, following the lead of lenalidomide and related clinically approved analogues. At the same time, the TPD universe is expanding at a record speed with the discovery of novel modalities beyond molecular glue degraders and PROTACs. Here we review the recent progress in the field, focusing on newly discovered degrader modalities, the current state of clinical degrader candidates for cancer therapy and upcoming design approaches.
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Affiliation(s)
- Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Valentina A Spiteri
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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3
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Hage A, Janes M, Best SM. A No-Brainer! The Therapeutic Potential of TRIM Proteins in Viral and Central Nervous System Diseases. Viruses 2025; 17:562. [PMID: 40285004 PMCID: PMC12031127 DOI: 10.3390/v17040562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2025] [Revised: 04/11/2025] [Accepted: 04/12/2025] [Indexed: 04/29/2025] Open
Abstract
Tripartite motif (TRIM) proteins comprise an important class of E3 ubiquitin ligases that regulate numerous biological processes including protein expression, cellular signaling pathways, and innate immunity. This ubiquitous participation in fundamental aspects of biology has made TRIM proteins a focus of study in many fields and has illuminated the negative impact they exert when functioning improperly. Disruption of TRIM function has been linked to the success of various pathogens and separately to the occurrence and development of several neurodegenerative diseases, making TRIM proteins an appealing candidate to study for novel therapeutic approaches. Here, we review the current findings on TRIM proteins that demonstrate their analogous properties in the distinct fields of viral infection and central nervous system (CNS) disorders. We also examine recent advancements in drug development and targeted protein degradation as potential strategies for TRIM-mediated therapeutic treatments and discuss the implications these technologies have on future research directions.
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Affiliation(s)
- Adam Hage
- Innate Immunity and Pathogenesis Section, Laboratory of Neurological Infections and Immunity, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; (M.J.); (S.M.B.)
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4
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Ou L, Setegne MT, Elliot J, Shen F, Dassama LMK. Protein-Based Degraders: From Chemical Biology Tools to Neo-Therapeutics. Chem Rev 2025; 125:2120-2183. [PMID: 39818743 PMCID: PMC11870016 DOI: 10.1021/acs.chemrev.4c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 12/26/2024] [Accepted: 12/30/2024] [Indexed: 01/19/2025]
Abstract
The nascent field of targeted protein degradation (TPD) could revolutionize biomedicine due to the ability of degrader molecules to selectively modulate disease-relevant proteins. A key limitation to the broad application of TPD is its dependence on small-molecule ligands to target proteins of interest. This leaves unstructured proteins or those lacking defined cavities for small-molecule binding out of the scope of many TPD technologies. The use of proteins, peptides, and nucleic acids (otherwise known as "biologics") as the protein-targeting moieties in degraders addresses this limitation. In the following sections, we provide a comprehensive and critical review of studies that have used proteins and peptides to mediate the degradation and hence the functional control of otherwise challenging disease-relevant protein targets. We describe existing platforms for protein/peptide-based ligand identification and the drug delivery systems that might be exploited for the delivery of biologic-based degraders. Throughout the Review, we underscore the successes, challenges, and opportunities of using protein-based degraders as chemical biology tools to spur discoveries, elucidate mechanisms, and act as a new therapeutic modality.
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Affiliation(s)
- Lisha Ou
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Sarafan
ChEM-H Institute, Stanford University, Stanford, California 94305, United States
| | - Mekedlawit T. Setegne
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Sarafan
ChEM-H Institute, Stanford University, Stanford, California 94305, United States
| | - Jeandele Elliot
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Fangfang Shen
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Laura M. K. Dassama
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Sarafan
ChEM-H Institute, Stanford University, Stanford, California 94305, United States
- Department
of Microbiology & Immunology, Stanford
School of Medicine, Stanford, California 94305, United States
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5
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Zhang D, Duque-Jimenez J, Facchinetti F, Brixi G, Rhee K, Feng WW, Jänne PA, Zhou X. Transferrin receptor targeting chimeras for membrane protein degradation. Nature 2025; 638:787-795. [PMID: 39322661 PMCID: PMC11839386 DOI: 10.1038/s41586-024-07947-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/14/2024] [Indexed: 09/27/2024]
Abstract
Cancer cells require high levels of iron for rapid proliferation, leading to significant upregulation of cell-surface transferrin receptor 1 (TfR1), which mediates iron uptake by binding to the iron-carrying protein transferrin1-3. Leveraging this phenomenon and the fast endocytosis rate of TfR1 (refs. 4,5), we developed transferrin receptor targeting chimeras (TransTACs), a heterobispecific antibody modality for membrane protein degradation. TransTACs are engineered to drive rapid co-internalization of a target protein of interest and TfR1 from the cell surface, and to enable target protein entry into the lysosomal degradation pathway. We show that TransTACs can efficiently degrade a diverse range of single-pass, multi-pass, native or synthetic membrane proteins, including epidermal growth factor receptor, programmed cell death 1 ligand 1, cluster of differentiation 20 and chimeric antigen receptor. In example applications, TransTACs enabled the reversible control of human primary chimeric antigen receptor T cells and the targeting of drug-resistant epidermal growth factor receptor-driven lung cancer with the exon 19 deletion/T790M/C797S mutations in a mouse xenograft model. TransTACs represent a promising new family of bifunctional antibodies for precise manipulation of membrane proteins and targeted cancer therapy.
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Affiliation(s)
- Dingpeng Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Francesco Facchinetti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Kaitlin Rhee
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - William W Feng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xin Zhou
- 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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6
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Zhou Z, Huang Z, Tang Y, Zhu Y, Li J. Modulating membrane-bound enzyme activity with chemical stimuli. Eur J Med Chem 2024; 280:116964. [PMID: 39406113 DOI: 10.1016/j.ejmech.2024.116964] [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: 03/17/2024] [Revised: 10/10/2024] [Accepted: 10/11/2024] [Indexed: 11/25/2024]
Abstract
Membrane-bound enzymes play pivotal roles in various cellular processes, making their activity regulation essential for cellular homeostasis and signaling transduction. Given that dysregulation of membrane-bound enzymes involved in various disease, controlling enzyme activity offers valuable avenues for designing targeted therapies and novel pharmaceutical interventions. This review explores chemical stimuli-responsive strategies for modulating the activity of these enzymes, employing diverse stimuli such as small molecules, proteins, nucleic acids, and bifunctional molecules to either inhibit or enhance their catalytic function. We systematically delineate the mechanisms underlying enzyme activity regulation, including substrate binding site blockade, conformational changes, and local concentration of enzymes and substrates. Furthermore, based on some examples, we elucidate the binding modalities between stimuli and enzymes, along with potential modes of regulation, and discuss their potential medical applications and future prospects. This review underscores the significance of understanding and manipulating enzyme activity on the cell membrane for advancing biomedical research and therapeutic development.
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Affiliation(s)
- Zhilan Zhou
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China; Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Zening Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| | - Yiyuan Tang
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yingdi Zhu
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Juan Li
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China.
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Korona B, Itzhaki LS. How to target membrane proteins for degradation: Bringing GPCRs into the TPD fold. J Biol Chem 2024; 300:107926. [PMID: 39454955 PMCID: PMC11626814 DOI: 10.1016/j.jbc.2024.107926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 09/30/2024] [Accepted: 10/02/2024] [Indexed: 10/28/2024] Open
Abstract
We are now in the middle of a so-called "fourth wave" of drug innovation: multispecific medicines aimed at diseases and targets previously thought to be "undruggable"; by inducing proximity between two or more proteins, for example, a target and an effector that do not naturally interact, such modalities have potential far beyond the scope of conventional drugs. In particular, targeted protein degradation (TPD) strategies to destroy disease-associated proteins have emerged as an exciting pipeline in drug discovery. Most efforts are focused on intracellular proteins, whereas membrane proteins have been less thoroughly explored despite the fact that they comprise roughly a quarter of the human proteome with G-protein coupled receptors (GPCRs) notably dysregulated in many diseases. Here, we discuss the opportunities and challenges of developing degraders for membrane proteins with a focus on GPCRs. We provide an overview of different TPD platforms in the context of membrane-tethered targets, and we present recent degradation technologies highlighting their potential application to GPCRs.
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Affiliation(s)
- Boguslawa Korona
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom.
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom.
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8
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Wang C, Hou Y, Zak J, Zheng Q, McCord KA, Wu M, Zhang D, Chung S, Shi Y, Ye J, Zhao Y, Hajjar S, Wilson IA, Paulson JC, Teijaro JR, Zhou X, Sharpless KB, Macauley MS, Wu P. Reshaping the tumor microenvironment by degrading glycoimmune checkpoints Siglec-7 and -9. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.11.617879. [PMID: 39416090 PMCID: PMC11483058 DOI: 10.1101/2024.10.11.617879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Cancer treatment has been rapidly transformed by the development of immune checkpoint inhibitors targeting CTLA-4 and PD-1/PD-L1. However, many patients fail to respond, especially those with an immunosuppressive tumor microenvironment (TME), suggesting the existence of additional immune checkpoints that act through orthogonal mechanisms. Sialic acid-binding immunoglobulin-like lectin (Siglec)-7 and -9 are newly designated glycoimmune checkpoints that are abundantly expressed by tumor-infiltrating myeloid cells. We discovered that T cells express only basal levels of Siglec transcripts; instead, they acquire Siglec-7 and -9 from interacting myeloid cells in the TME via trogocytosis, which impairs their activation and effector function. Mechanistically, Siglec-7 and -9 suppress T cell activity by dephosphorylating T cell receptor (TCR)-related signaling cascades. Using sulfur fluoride exchange (SuFEx) click chemistry, we developed a ligand that binds to Siglec-7 and -9 with high-affinity and exclusive specificity. Using this ligand, we constructed a Siglec-7/9 degrader that targets membrane Siglec-7 and -9 to the lysosome for degradation. Administration of this degrader induced efficient Siglec degradation in both T cells and myeloid cells in the TME. We found that Siglec-7/9 degradation has a negligible effect on macrophage phagocytosis, but significantly enhances T cell anti-tumor immunity. The degrader, particularly when combined with anti-CTLA-4, enhanced macrophage antigen presentation, reshaped the TME, and resulted in long-lasting T cell memory and excellent tumor control in multiple murine tumor models. These findings underscore the need to consider exogenous checkpoints acquired by T cells in the TME when selecting specific checkpoint blockade therapy to enhance T cell immunity.
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Affiliation(s)
- Chao Wang
- Department of Molecular and Cellular Biology, The Scripps Research Institute, California, United States
- Department of Chemistry, The Scripps Research Institute, California, United States
| | - Yingqin Hou
- Department of Molecular and Cellular Biology, The Scripps Research Institute, California, United States
| | - Jaroslav Zak
- Department of Immunology and Microbiology, The Scripps Research Institute, California, United States
| | - Qinheng Zheng
- Department of Chemistry, The Scripps Research Institute, California, United States
| | | | - Mengyao Wu
- Department of Molecular and Cellular Biology, The Scripps Research Institute, California, United States
- Department of Oncology, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Ding Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, California, United States
| | - Shereen Chung
- Department of Molecular and Cellular Biology, The Scripps Research Institute, California, United States
| | - Yujie Shi
- Department of Molecular and Cellular Biology, The Scripps Research Institute, California, United States
| | - Jinfeng Ye
- Department of Molecular and Cellular Biology, The Scripps Research Institute, California, United States
| | - Yunlong Zhao
- Department of Immunology, Center of Excellence for Pediatric Immuno-Oncology, St. Jude Children’s Research Hospital, Tennessee, United States
| | - Stephanie Hajjar
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, and Harvard Medical School, Boston, United States
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, California, United States
| | - James C. Paulson
- Department of Molecular Medicine, The Scripps Research Institute, California, United States
| | - John R. Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, California, United States
| | - Xu Zhou
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, and Harvard Medical School, Boston, United States
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, California, United States
| | - Matthew S. Macauley
- Department of Chemistry, University of Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Canada
| | - Peng Wu
- Department of Molecular and Cellular Biology, The Scripps Research Institute, California, United States
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9
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Crook ZR, Sevilla GP, Young P, Girard EJ, Phi TD, Howard ML, Price J, Olson JM, Nairn NW. CYpHER: catalytic extracellular targeted protein degradation with high potency and durable effect. Nat Commun 2024; 15:8731. [PMID: 39384759 PMCID: PMC11464628 DOI: 10.1038/s41467-024-52975-2] [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] [Accepted: 09/27/2024] [Indexed: 10/11/2024] Open
Abstract
Many disease-causing proteins have multiple pathogenic mechanisms, and conventional inhibitors struggle to reliably disrupt more than one. Targeted protein degradation (TPD) can eliminate the protein, and thus all its functions, by directing a cell's protein turnover machinery towards it. Two established strategies either engage catalytic E3 ligases or drive uptake towards the endolysosomal pathway. Here we describe CYpHER (CatalYtic pH-dependent Endolysosomal delivery with Recycling) technology with potency and durability from a catalytic mechanism that shares the specificity and straightforward modular design of endolysosomal uptake. By bestowing pH-dependent release on the target engager and using the rapid-cycling transferrin receptor as the uptake receptor, CYpHER induces endolysosomal delivery of surface and extracellular targets while re-using drug, potentially yielding increased potency and reduced off-target tissue exposure risks. The TfR-based approach allows targeting to tumors that overexpress this receptor and offers the potential for transport to the CNS. CYpHER function was demonstrated in vitro with EGFR and PD-L1, and in vivo with EGFR in a model of EGFR-driven non-small cell lung cancer.
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Affiliation(s)
- Zachary R Crook
- Cyclera Therapeutics Inc, Seattle, WA, 98115, USA
- Blaze Bioscience Inc, Seattle, WA, 98109, USA
- Clinical Research Division, Fred Hutchinson Research Center, Seattle, WA, 98109, USA
| | - Gregory P Sevilla
- Cyclera Therapeutics Inc, Seattle, WA, 98115, USA
- Blaze Bioscience Inc, Seattle, WA, 98109, USA
- Clinical Research Division, Fred Hutchinson Research Center, Seattle, WA, 98109, USA
| | | | - Emily J Girard
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, 98105, USA
| | | | | | - Jason Price
- Clinical Research Division, Fred Hutchinson Research Center, Seattle, WA, 98109, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Research Center, Seattle, WA, 98109, USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, 98105, USA
| | - Natalie W Nairn
- Cyclera Therapeutics Inc, Seattle, WA, 98115, USA.
- Blaze Bioscience Inc, Seattle, WA, 98109, USA.
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10
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Niehrs C, Seidl C, Lee H. An "R-spondin code" for multimodal signaling ON-OFF states. Bioessays 2024; 46:e2400144. [PMID: 39180250 DOI: 10.1002/bies.202400144] [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: 06/14/2024] [Revised: 08/02/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
R-spondins (RSPOs) are a family of secreted proteins and stem cell growth factors that are potent co-activators of Wnt signaling. Recently, RSPO2 and RSPO3 were shown to be multifunctional, not only amplifying Wnt- but also binding BMP- and FGF receptors to downregulate signaling. The common mechanism underlying these diverse functions is that RSPO2 and RSPO3 act as "endocytosers" that link transmembrane proteins to ZNRF3/RNF43 E3 ligases and trigger target internalization. Thus, RSPOs are natural protein targeting chimeras for cell surface proteins. Conducting data mining and cell surface binding assays we report additional candidate RSPO targets, including SMO, PTC1,2, LGI1, ROBO4, and PTPR(F/S). We propose that there is an "R-spondin code" that imparts combinatorial signaling ON-OFF states of multiple growth factors. This code involves the modular RSPO domains, notably distinct motifs in the divergent RSPO-TSP1 domains to mediate target interaction and internalization. The RSPO code offers a novel framework for the understanding how diverse signaling pathways may be coordinately regulated in development and disease.
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Affiliation(s)
- Christof Niehrs
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Carina Seidl
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Hyeyoon Lee
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
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11
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Castagna D, Gourdet B, Hjerpe R, MacFaul P, Novak A, Revol G, Rochette E, Jordan A. To homeostasis and beyond! Recent advances in the medicinal chemistry of heterobifunctional derivatives. PROGRESS IN MEDICINAL CHEMISTRY 2024; 63:61-160. [PMID: 39370242 DOI: 10.1016/bs.pmch.2024.07.002] [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: 10/08/2024]
Abstract
The field of induced proximity therapeutics has expanded dramatically over the past 3 years, and heterobifunctional derivatives continue to form a significant component of the activities in this field. Here, we review recent advances in the field from the perspective of the medicinal chemist, with a particular focus upon informative case studies, alongside a review of emerging topics such as Direct-To-Biology (D2B) methodology and utilities for heterobifunctional compounds beyond E3 ligase mediated degradation. We also include a critical evaluation of the latest thinking around the optimisation of physicochemical and pharmacokinetic attributes of these beyond Role of Five molecules, to deliver appropriate therapeutic exposure in vivo.
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Affiliation(s)
| | | | | | | | | | | | | | - Allan Jordan
- Sygnature Discovery, Nottingham, United Kingdom; Sygnature Discovery, Macclesfield, United Kingdom.
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12
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Boonsawat P, Asadollahi R, Niedrist D, Steindl K, Begemann A, Joset P, Bhoj EJ, Li D, Zackai E, Vetro A, Barba C, Guerrini R, Whalen S, Keren B, Khan A, Jing D, Palomares Bralo M, Rikeros Orozco E, Hao Q, Schlott Kristiansen B, Zheng B, Donnelly D, Clowes V, Zweier M, Papik M, Siegel G, Sabatino V, Mocera M, Horn AHC, Sticht H, Rauch A. Deleterious ZNRF3 germline variants cause neurodevelopmental disorders with mirror brain phenotypes via domain-specific effects on Wnt/β-catenin signaling. Am J Hum Genet 2024; 111:1994-2011. [PMID: 39168120 PMCID: PMC11393693 DOI: 10.1016/j.ajhg.2024.07.016] [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: 04/29/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 08/23/2024] Open
Abstract
Zinc and RING finger 3 (ZNRF3) is a negative-feedback regulator of Wnt/β-catenin signaling, which plays an important role in human brain development. Although somatically frequently mutated in cancer, germline variants in ZNRF3 have not been established as causative for neurodevelopmental disorders (NDDs). We identified 12 individuals with ZNRF3 variants and various phenotypes via GeneMatcher/Decipher and evaluated genotype-phenotype correlation. We performed structural modeling and representative deleterious and control variants were assessed using in vitro transcriptional reporter assays with and without Wnt-ligand Wnt3a and/or Wnt-potentiator R-spondin (RSPO). Eight individuals harbored de novo missense variants and presented with NDD. We found missense variants associated with macrocephalic NDD to cluster in the RING ligase domain. Structural modeling predicted disruption of the ubiquitin ligase function likely compromising Wnt receptor turnover. Accordingly, the functional assays showed enhanced Wnt/β-catenin signaling for these variants in a dominant negative manner. Contrarily, an individual with microcephalic NDD harbored a missense variant in the RSPO-binding domain predicted to disrupt binding affinity to RSPO and showed attenuated Wnt/β-catenin signaling in the same assays. Additionally, four individuals harbored de novo truncating or de novo or inherited large in-frame deletion variants with non-NDD phenotypes, including heart, adrenal, or nephrotic problems. In contrast to NDD-associated missense variants, the effects on Wnt/β-catenin signaling were comparable between the truncating variant and the empty vector and between benign variants and the wild type. In summary, we provide evidence for mirror brain size phenotypes caused by distinct pathomechanisms in Wnt/β-catenin signaling through protein domain-specific deleterious ZNRF3 germline missense variants.
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Affiliation(s)
| | - Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland; Faculty of Engineering and Science, University of Greenwich London, Medway Campus, Chatham Maritime ME4 4TB, UK
| | - Dunja Niedrist
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Pascal Joset
- Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Annalisa Vetro
- Neuroscience Department, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Carmen Barba
- Neuroscience Department, Meyer Children's Hospital IRCCS, Florence, Italy; University of Florence, Florence, Italy
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Sandra Whalen
- Unité Fonctionnelle de Génétique Odellin, Hôpital Armand Trousseau, Paris, France
| | - Boris Keren
- Département de Génétique, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Amjad Khan
- Faculty of Science, Department of Biological Science (Zoology), University of Lakki Marwat, Khyber Pakhtunkhwa 28420, Pakistan
| | - Duan Jing
- Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - María Palomares Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Unidad de Trastornos Del Neurodesarrollo, Hospital Universitario La Paz, Madrid, Spain
| | - Emi Rikeros Orozco
- Instituto de Genética Médica y Molecular (INGEMM), Unidad de Trastornos Del Neurodesarrollo, Hospital Universitario La Paz, Madrid, Spain
| | - Qin Hao
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Deirdre Donnelly
- Northern Ireland Regional Genetics Centre, Belfast Health & Social Care Trust, Belfast, Northern Ireland
| | - Virginia Clowes
- Thames Regional Genetics Service, North West University Healthcare NHS Trust, London, UK
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Michael Papik
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Gabriele Siegel
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Valeria Sabatino
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Martina Mocera
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anselm H C Horn
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland; Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland; Pediatric University Hospital Zurich, Zurich, Switzerland.
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13
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Oslund RC, Holland PM, Lesley SA, Fadeyi OO. Therapeutic potential of cis-targeting bispecific antibodies. Cell Chem Biol 2024; 31:1473-1489. [PMID: 39111317 DOI: 10.1016/j.chembiol.2024.07.004] [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: 12/14/2023] [Revised: 05/13/2024] [Accepted: 07/12/2024] [Indexed: 08/18/2024]
Abstract
The growing clinical success of bispecific antibodies (bsAbs) has led to rapid interest in leveraging dual targeting in order to generate novel modes of therapeutic action beyond mono-targeting approaches. While bsAbs that bind targets on two different cells (trans-targeting) are showing promise in the clinic, the co-targeting of two proteins on the same cell surface through cis-targeting bsAbs (cis-bsAbs) is an emerging strategy to elicit new functionalities. This includes the ability to induce proximity, enhance binding to a target, increase target/cell selectivity, and/or co-modulate function on the cell surface with the goal of altering, reversing, or eradicating abnormal cellular activity that contributes to disease. In this review, we focus on the impact of cis-bsAbs in the clinic, their emerging applications, and untangle the intricacies of improving bsAb discovery and development.
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14
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Post Y, Lu C, Fletcher RB, Yeh WC, Nguyen H, Lee SJ, Li Y. Design principles and therapeutic applications of novel synthetic WNT signaling agonists. iScience 2024; 27:109938. [PMID: 38832011 PMCID: PMC11145361 DOI: 10.1016/j.isci.2024.109938] [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: 06/05/2024] Open
Abstract
Wingless-related integration site or Wingless and Int-1 or Wingless-Int (WNT) signaling is crucial for embryonic development, and adult tissue homeostasis and regeneration, through its essential roles in cell fate, patterning, and stem cell regulation. The biophysical characteristics of WNT ligands have hindered efforts to interrogate ligand activity in vivo and prevented their development as therapeutics. Recent breakthroughs have enabled the generation of synthetic WNT signaling molecules that possess characteristics of natural ligands and potently activate the pathway, while also providing distinct advantages for therapeutic development and manufacturing. This review provides a detailed discussion of the protein engineering of these molecular platforms for WNT signaling agonism. We discuss the importance of WNT signaling in several organs and share insights from the initial application of these new classes of molecules in vitro and in vivo. These molecules offer a unique opportunity to enhance our understanding of how WNT signaling agonism promotes tissue repair, enabling targeted development of tailored therapeutics.
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Affiliation(s)
- Yorick Post
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA 94080, USA
| | - Chenggang Lu
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA 94080, USA
| | - Russell B. Fletcher
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA 94080, USA
| | - Wen-Chen Yeh
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA 94080, USA
| | - Huy Nguyen
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA 94080, USA
| | - Sung-Jin Lee
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA 94080, USA
| | - Yang Li
- Surrozen, Inc., 171 Oyster Point Blvd, Suite 400, South San Francisco, CA 94080, USA
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15
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Sampathkumar P, Jung H, Chen H, Zhang Z, Suen N, Yang Y, Huang Z, Lopez T, Benisch R, Lee SJ, Ye J, Yeh WC, Li Y. Targeted protein degradation systems to enhance Wnt signaling. eLife 2024; 13:RP93908. [PMID: 38847394 PMCID: PMC11161174 DOI: 10.7554/elife.93908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024] Open
Abstract
Molecules that facilitate targeted protein degradation (TPD) offer great promise as novel therapeutics. The human hepatic lectin asialoglycoprotein receptor (ASGR) is selectively expressed on hepatocytes. We have previously engineered an anti-ASGR1 antibody-mutant RSPO2 (RSPO2RA) fusion protein (called SWEETS) to drive tissue-specific degradation of ZNRF3/RNF43 E3 ubiquitin ligases, which achieved hepatocyte-specific enhanced Wnt signaling, proliferation, and restored liver function in mouse models, and an antibody-RSPO2RA fusion molecule is currently in human clinical trials. In the current study, we identified two new ASGR1- and ASGR1/2-specific antibodies, 8M24 and 8G8. High-resolution crystal structures of ASGR1:8M24 and ASGR2:8G8 complexes revealed that these antibodies bind to distinct epitopes on opposing sides of ASGR, away from the substrate-binding site. Both antibodies enhanced Wnt activity when assembled as SWEETS molecules with RSPO2RA through specific effects sequestering E3 ligases. In addition, 8M24-RSPO2RA and 8G8-RSPO2RA efficiently downregulate ASGR1 through TPD mechanisms. These results demonstrate the possibility of combining different therapeutic effects and degradation mechanisms in a single molecule.
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Affiliation(s)
| | | | - Hui Chen
- Surrozen, IncSouth San FranciscoUnited States
| | | | | | - Yiran Yang
- Surrozen, IncSouth San FranciscoUnited States
| | - Zhong Huang
- Surrozen, IncSouth San FranciscoUnited States
| | - Tom Lopez
- Surrozen, IncSouth San FranciscoUnited States
| | | | | | - Jay Ye
- Surrozen, IncSouth San FranciscoUnited States
| | | | - Yang Li
- Surrozen, IncSouth San FranciscoUnited States
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16
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Crook ZR, Sevilla GP, Young P, Girard EJ, Phi TD, Howard M, Price J, Olson JM, Nairn NW. CYpHER: Catalytic extracellular targeted protein degradation with high potency and durable effect. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.21.581471. [PMID: 38712232 PMCID: PMC11071310 DOI: 10.1101/2024.02.21.581471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Many disease-causing proteins have multiple pathogenic mechanisms, and conventional inhibitors struggle to reliably disrupt more than one. Targeted protein degradation (TPD) can eliminate the protein, and thus all its functions, by directing a cell's protein turnover machinery towards it. Two established strategies either engage catalytic E3 ligases or drive uptake towards the endolysosomal pathway. Here we describe CYpHER (CatalYtic pH-dependent Endolysosomal delivery with Recycling) technology with potency and durability from a novel catalytic mechanism that shares the specificity and straightforward modular design of endolysosomal uptake. By bestowing pH-dependent release on the target engager and using the rapid-cycling transferrin receptor as the uptake receptor, CYpHER induces endolysosomal target delivery while re-using drug, potentially yielding increased potency and reduced off-target tissue exposure risks. The TfR-based approach allows targeting to tumors that overexpress this receptor and offers the potential for transport to the CNS. CYpHER function was demonstrated in vitro with EGFR and PD-L1, and in vivo with EGFR in a model of EGFR-driven non-small cell lung cancer.
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Affiliation(s)
- Zachary R. Crook
- Cyclera Therapeutics Inc, Seattle, WA 98115, USA. Present address of Z.R.C., G.P.S., and N.W.N
- Blaze Bioscience Inc., Seattle, WA 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Gregory P. Sevilla
- Cyclera Therapeutics Inc, Seattle, WA 98115, USA. Present address of Z.R.C., G.P.S., and N.W.N
- Blaze Bioscience Inc., Seattle, WA 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Emily J. Girard
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98105, USA. Present address of E.J.G. and J.M.O
| | | | | | - Jason Price
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98105, USA. Present address of E.J.G. and J.M.O
| | - James M. Olson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98105, USA. Present address of E.J.G. and J.M.O
| | - Natalie W. Nairn
- Cyclera Therapeutics Inc, Seattle, WA 98115, USA. Present address of Z.R.C., G.P.S., and N.W.N
- Blaze Bioscience Inc., Seattle, WA 98109, USA
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17
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Klein C, Brinkmann U, Reichert JM, Kontermann RE. The present and future of bispecific antibodies for cancer therapy. Nat Rev Drug Discov 2024; 23:301-319. [PMID: 38448606 DOI: 10.1038/s41573-024-00896-6] [Citation(s) in RCA: 116] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2024] [Indexed: 03/08/2024]
Abstract
Bispecific antibodies (bsAbs) enable novel mechanisms of action and/or therapeutic applications that cannot be achieved using conventional IgG-based antibodies. Consequently, development of these molecules has garnered substantial interest in the past decade and, as of the end of 2023, 14 bsAbs have been approved: 11 for the treatment of cancer and 3 for non-oncology indications. bsAbs are available in different formats, address different targets and mediate anticancer function via different molecular mechanisms. Here, we provide an overview of recent developments in the field of bsAbs for cancer therapy. We focus on bsAbs that are approved or in clinical development, including bsAb-mediated dual modulators of signalling pathways, tumour-targeted receptor agonists, bsAb-drug conjugates, bispecific T cell, natural killer cell and innate immune cell engagers, and bispecific checkpoint inhibitors and co-stimulators. Finally, we provide an outlook into next-generation bsAbs in earlier stages of development, including trispecifics, bsAb prodrugs, bsAbs that induce degradation of tumour targets and bsAbs acting as cytokine mimetics.
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Affiliation(s)
- Christian Klein
- Roche Pharma Research and Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland.
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | | | - Roland E Kontermann
- Institute of Cell Biology and Immunology, University Stuttgart, Stuttgart, Germany.
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18
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Yang JL, Yamada-Hunter SA, Labanieh L, Sotillo E, Cheah JS, Roberts DS, Mackall CL, Bertozzi CR, Ting AY. Directed evolution of genetically encoded LYTACs for cell-mediated delivery. Proc Natl Acad Sci U S A 2024; 121:e2320053121. [PMID: 38513100 PMCID: PMC10990137 DOI: 10.1073/pnas.2320053121] [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: 11/15/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
Lysosome-targeting chimeras (LYTACs) are a promising therapeutic modality to drive the degradation of extracellular proteins. However, early versions of LYTAC contain synthetic glycopeptides that cannot be genetically encoded. Here, we present our designs for a fully genetically encodable LYTAC (GELYTAC), making our tool compatible with integration into therapeutic cells for targeted delivery at diseased sites. To achieve this, we replaced the glycopeptide portion of LYTACs with the protein insulin-like growth factor 2 (IGF2). After showing initial efficacy with wild-type IGF2, we increased the potency of GELYTAC using directed evolution. Subsequently, we demonstrated that our engineered GELYTAC construct not only secretes from HEK293T cells but also from human primary T-cells to drive the uptake of various targets into receiver cells. Immune cells engineered to secrete GELYTAC thus represent a promising avenue for spatially selective targeted protein degradation.
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Affiliation(s)
- Jonathan Lee Yang
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Sean A. Yamada-Hunter
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Parker Institute for Cancer Immunotherapy, San Francisco, CA94305
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Bioengineering, Stanford University, Stanford, CA94305
| | - Joleen S. Cheah
- Department of Biology, Stanford University, Stanford, CA94305
| | - David S. Roberts
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Crystal L. Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
- Parker Institute for Cancer Immunotherapy, San Francisco, CA94305
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
| | - Alice Y. Ting
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biology, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA94158
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19
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Shi Y, Bashian EE, Hou Y, Wu P. Chemical immunology: Recent advances in tool development and applications. Cell Chem Biol 2024; 31:S2451-9456(24)00080-1. [PMID: 38508196 PMCID: PMC11393185 DOI: 10.1016/j.chembiol.2024.02.006] [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: 09/01/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
Immunology was one of the first biological fields to embrace chemical approaches. The development of new chemical approaches and techniques has provided immunologists with an impressive arsenal of tools to address challenges once considered insurmountable. This review focuses on advances at the interface of chemistry and immunobiology over the past two decades that have not only opened new avenues in basic immunological research, but also revolutionized drug development for the treatment of cancer and autoimmune diseases. These include chemical approaches to understand and manipulate antigen presentation and the T cell priming process, to facilitate immune cell trafficking and regulate immune cell functions, and therapeutic applications of chemical approaches to disease control and treatment.
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Affiliation(s)
- Yujie Shi
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eleanor E Bashian
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yingqin Hou
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peng Wu
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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20
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Nalawansha DA, Mangano K, den Besten W, Potts PR. TAC-tics for Leveraging Proximity Biology in Drug Discovery. Chembiochem 2024; 25:e202300712. [PMID: 38015747 DOI: 10.1002/cbic.202300712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
Chemically induced proximity (CIP) refers to co-opting naturally occurring biological pathways using synthetic molecules to recruit neosubstrates that are not normally encountered or to enhance the affinity of naturally occurring interactions. Leveraging proximity biology through CIPs has become a rapidly evolving field and has garnered considerable interest in basic research and drug discovery. PROteolysis TArgeting Chimera (PROTAC) is a well-established CIP modality that induces the proximity between a target protein and an E3 ubiquitin ligase, causing target protein degradation via the ubiquitin-proteasome system. Inspired by PROTACs, several other induced proximity modalities have emerged to modulate both proteins and RNA over recent years. In this review, we summarize the critical advances and opportunities in the field, focusing on protein degraders, RNA degraders and non-degrader modalities such as post-translational modification (PTM) and protein-protein interaction (PPI) modulators. We envision that these emerging proximity-based drug modalities will be valuable resources for both biological research and therapeutic discovery in the future.
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Affiliation(s)
| | - Kyle Mangano
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Willem den Besten
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
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21
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Wells JA, Kumru K. Extracellular targeted protein degradation: an emerging modality for drug discovery. Nat Rev Drug Discov 2024; 23:126-140. [PMID: 38062152 DOI: 10.1038/s41573-023-00833-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2023] [Indexed: 02/08/2024]
Abstract
Targeted protein degradation (TPD) has emerged in the past decade as a major new drug modality to remove intracellular proteins with bispecific small molecules that recruit the protein of interest (POI) to an E3 ligase for degradation in the proteasome. Unlike classic occupancy-based drugs, intracellular TPD (iTPD) eliminates the target and works catalytically, and so can be more effective and sustained, with lower dose requirements. Recently, this approach has been expanded to the extracellular proteome, including both secreted and membrane proteins. Extracellular targeted protein degradation (eTPD) uses bispecific antibodies, conjugates or small molecules to degrade extracellular POIs by trafficking them to the lysosome for degradation. Here, we focus on recent advances in eTPD, covering degrader systems, targets, molecular designs and parameters to advance them. Now almost any protein, intracellular or extracellular, is addressable in principle with TPD.
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Affiliation(s)
- James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
| | - Kaan Kumru
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
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22
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Rhee K, Zhou X. Two in one: the emerging concept of bifunctional antibodies. Curr Opin Biotechnol 2024; 85:103050. [PMID: 38142645 PMCID: PMC10922881 DOI: 10.1016/j.copbio.2023.103050] [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: 02/19/2023] [Revised: 11/16/2023] [Accepted: 11/26/2023] [Indexed: 12/26/2023]
Abstract
Therapeutic antibodies have become indispensable for treating a wide range of diseases, and their significance in drug discovery has expanded considerably over the past few decades. Bifunctional antibodies are now emerging as a promising new drug modality to address previously unmet needs in antibody therapeutics. Distinct from traditional antibodies that operate through an 'occupancy-based' inhibition mechanism, these innovative molecules recruit the protein of interest to a 'biological effector,' initiating specific downstream consequences such as targeted protein degradation or posttranslational modifications. In this review, we emphasize the potential of bifunctional antibodies to tackle diverse biomedical challenges.
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Affiliation(s)
- Kaitlin Rhee
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Xin Zhou
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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23
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Mukai K, Cost R, Zhang XS, Condiff E, Cotton J, Liu X, Boudanova E, Niebel B, Piepenhagen P, Cai X, Park A, Zhou Q. Targeted protein degradation through site-specific antibody conjugation with mannose 6-phosphate glycan. MAbs 2024; 16:2415333. [PMID: 39434219 PMCID: PMC11497922 DOI: 10.1080/19420862.2024.2415333] [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: 04/16/2024] [Revised: 10/03/2024] [Accepted: 10/07/2024] [Indexed: 10/23/2024] Open
Abstract
Recent developments in targeted protein degradation have provided great opportunities to eliminating extracellular protein targets using potential therapies with unique mechanisms of action and pharmacology. Among them, Lysosome-Targeting Chimeras (LYTACs) acting through mannose 6-phosphate receptor (M6PR) have been shown to facilitate degradation of several soluble and membrane-associated proteins in lysosomes with high efficiency. Herein we have developed a novel site-specific antibody conjugation approach to generate antibody mannose 6-phosphate (M6P) conjugates. The method uses a high affinity synthetic M6P glycan, bisM6P, that is coupled to an Fc-engineered antibody NNAS. This mutant without any effector function was generated by switching the native glycosylation site from position 297 to 298 converting non-sialylated structures to highly sialylated N-glycans. The sialic acid of the glycans attached to Asn298 in the engineered antibody was selectively conjugated to bisM6P without chemoenzymatic modification, which is often used for site-specific antibody conjugation through glycans. The conjugate is mainly homogeneous by analysis using mass spectrometry, typically with one or two glycans coupled. The M6P-conjugated antibody against a protein of interest (POI) efficiently internalized targeted soluble proteins, such as human tumor necrosis factor (TNF), in both cancer cell lines and human immune cells, through the endo-lysosomal pathway as demonstrated by confocal microscopy and flow cytometry. TNF in cell culture media was significantly depleted after the cells were incubated with the M6P-conjugated antibody. TNF internalization is mediated through M6PR, and it is correlated well with cell surface expression of cation-independent M6PR (CI-MPR) in immune cells. A significant amount of CI-MPR remains on the cell surface, while internalized TNF is degraded in lysosomes. Thus, the antibody-M6P conjugate is highly efficient in inducing internalization and subsequent lysosome-mediated protein degradation. Our platform provides a unique method for producing biologics-based degraders that may be used to treat diseases through event-driven pharmacology, thereby addressing unmet medical needs.
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Affiliation(s)
- Kaori Mukai
- Immunology & Inflammation Research, Sanofi, Cambridge, MA, USA
| | - Robert Cost
- Large Molecules Research, Sanofi, Cambridge, MA, USA
| | - Xin Sheen Zhang
- Translational In Vivo Models Research, Sanofi, Cambridge, MA, USA
| | - Emily Condiff
- Translational In Vivo Models Research, Sanofi, Cambridge, MA, USA
| | | | - Xiaohua Liu
- Large Molecules Research, Sanofi, Cambridge, MA, USA
| | | | - Björn Niebel
- Large Molecules Research, Sanofi R&D Ghent, Ghent, Belgium
| | | | - Xinming Cai
- Immunology & Inflammation Research, Sanofi, Cambridge, MA, USA
| | - Anna Park
- Large Molecules Research, Sanofi, Cambridge, MA, USA
| | - Qun Zhou
- Large Molecules Research, Sanofi, Cambridge, MA, USA
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24
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Yang JL, Yamada-Hunter SA, Labanieh L, Sotillo E, Cheah JS, Roberts DS, Mackall CL, Ting AY, Bertozzi CR. Directed Evolution of Genetically Encoded LYTACs for Cell-Mediated Delivery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567117. [PMID: 38014030 PMCID: PMC10680704 DOI: 10.1101/2023.11.14.567117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Lysosome-targeting chimeras (LYTACs) are a promising therapeutic modality to drive the degradation of extracellular proteins. However, early versions of LYTAC contain synthetic glycopeptides that cannot be genetically encoded. Here we present our designs for a fully genetically encodable LYTAC (GELYTAC), making our tool compatible with integration into therapeutic cells for targeted delivery at diseased sites. To achieve this, we replaced the glycopeptide portion of LYTACs with the protein insulin like growth factor 2 (IGF2). After showing initial efficacy with wild type IGF2, we increased the potency of GELYTAC using directed evolution. Subsequently, we demonstrated that our engineered GELYTAC construct not only secretes from HEK293T cells but also from human primary T-cells to drive the uptake of various targets into receiver cells. Immune cells engineered to secrete GELYTAC thus represent a promising avenue for spatially-selective targeted protein degradation.
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Affiliation(s)
- Jonathan Lee Yang
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Sean A. Yamada-Hunter
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Louai Labanieh
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elena Sotillo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joleen S. Cheah
- Departments of Biology, and Genetics Stanford University, Stanford, CA 94305, USA
| | - David S. Roberts
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Crystal L. Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94305, USA
| | - Alice Y. Ting
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Departments of Biology, and Genetics Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
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