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Mamun MAA, Bakunts AG, Chernorudskiy AL. Targeted degradation of extracellular proteins: state of the art and diversity of degrader designs. J Hematol Oncol 2025; 18:52. [PMID: 40307925 PMCID: PMC12044797 DOI: 10.1186/s13045-025-01703-4] [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: 01/28/2025] [Accepted: 04/13/2025] [Indexed: 05/02/2025] Open
Abstract
Selective elimination of proteins associated with the pathogenesis of diseases is an emerging therapeutic modality with distinct advantages over traditional inhibitor-based approaches. This strategy, called targeted protein degradation (TPD), is based on hijacking the cellular proteolytic machinery using chimeric degrader molecules that physically link the target protein of interest with the degradation effectors. The TPD era began with the development of PROteolysis TAtrgeting Chimeras (PROTACs) in 2001, with various methods and applications currently available. Classical PROTAC molecules are heterobifunctional chimeras linking target proteins with E3 ubiquitin ligases. This induced interaction leads to the ubiquitylation of the target protein, which is needed for its recognition and subsequent degradation by the cellular proteasomes. However, this technology is limited to intracellular proteins since the effectors involved (E3 ubiquitin ligases and proteasomes) are located in the cytosol. The related methods for selective destruction of proteins present in the extracellular space have only emerged recently and are collectively termed extracellular TPD (eTPD). The prototypic eTPD technology utilizes LYsosomal TArgeting Chimeras (LYTACs) that link extracellular target proteins (secreted or membrane-associated) to lysosome-targeting receptors (LTRs) on the cell surface. The resulting complex is then internalized by endocytosis and trafficked to lysosomes, where the target protein is degraded. The successful elimination of various extracellular proteins via LYTACs and related approaches has been reported, including several important targets in oncology that drive tumor growth and dissemination. This review summarizes current progress in the eTPD field and focuses primarily on the respective technological developments. It discusses the design principles and diversity of degrader molecules and the landscape of available targets and effectors that can be employed for eTPD. Finally, it emphasizes current open questions, challenges, and perspectives of this technological platform to promote the expansion of the eTPD toolkit and further development of its therapeutic applications.
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Affiliation(s)
- M A A Mamun
- School of Medicine, Taizhou University, Taizhou, Zhejiang, 318000, People's Republic of China
| | - Anush G Bakunts
- Division of Genetics and Cell Biology, Vita-Salute San Raffaele University, Milan, 20132, Italy
| | - Alexander L Chernorudskiy
- School of Medicine, Taizhou University, Taizhou, Zhejiang, 318000, People's Republic of China.
- Department of Biochemistry and Molecular Pharmacology, Mario Negri Institute for Pharmacological Research, Milan, 20156, Italy.
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2
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Sung Y, Choi Y, Kim ES, Ryu JH, Kwon IC. Receptor-ligand interactions for optimized endocytosis in targeted therapies. J Control Release 2025; 380:524-538. [PMID: 39875075 DOI: 10.1016/j.jconrel.2025.01.060] [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: 09/28/2024] [Revised: 01/14/2025] [Accepted: 01/21/2025] [Indexed: 01/30/2025]
Abstract
Receptor-mediated endocytosis plays a crucial role in the success of numerous therapies and remains central to advancing drug development. This process begins with ligand binding to specific receptors, triggering the internalization and intracellular trafficking of receptor-ligand complexes. These complexes are subsequently directed into distinct routes, either toward lysosomal degradation or recycling to the cell surface, with implications for therapeutic outcomes. This review examines receptor-ligand interactions as key modulators of endocytosis, emphasizing their role in shaping therapeutic design and efficacy. Advances in selecting receptor-ligand pairs and engineering ligands with optimized properties have enabled precise control over internalization, endosomal sorting, and trafficking, providing tailored solutions for diverse therapeutic applications. Leveraging these insights, strategies such as RNA-based therapies, antibody-drug conjugates (ADCs), and targeted protein degradation (TPD) platforms have been refined to selectively avoid or promote lysosomal degradation, thereby enhancing therapeutic efficacy. By bridging fundamental mechanisms of receptor-mediated endocytosis with innovative therapeutic approaches, this review offers a framework for advancing precision medicine.
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Affiliation(s)
- Yejin Sung
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Youngjin Choi
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Eun Sun Kim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Korea University College of Medicine, Seoul 20841, Republic of Korea
| | - Ju Hee Ryu
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea.
| | - Ick Chan Kwon
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea.
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3
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Pan Y, Xiang Q, Deng K, Anwar MI, Wang L, Wang Y, Liang Q, Shen L, Yang J, Hou Z, Shen W. Engineering IGF2 for Lysosome-targeting chimeras development to target drug-resistant membrane proteins in tumor therapy. Protein Sci 2025; 34:e70051. [PMID: 39969096 PMCID: PMC11837023 DOI: 10.1002/pro.70051] [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: 03/26/2024] [Revised: 01/14/2025] [Accepted: 01/19/2025] [Indexed: 02/20/2025]
Abstract
Lysosome-targeting chimeras (LYTACs) represent a promising approach for the targeted degradation of membrane proteins. Currently, two primary methods for LYTAC development involve chemically modified antibodies and wild-type insulin-like growth factor 2 (IGF2) fusion proteins (iLYTACs). However, LYTACs necessitate intricate chemical modification processes, while wild-type IGF2 in iLYTAC technology binds to IGF1R, potentially triggering carcinogenesis. To tackle this challenge, we introduce specific IGF2R-binding lysosomal targeting chimeras (sLYTACs), a novel technology utilizing engineered IGF2 mutant fusion antibodies for the degradation of endogenous membrane proteins. Diverging from iLYTACs, sLYTACs exhibit selective binding to IGF2R with increased affinity, significantly bolstering the anti-proliferative impact on drug-resistant tumor cells both in vitro and in vivo. By effectively degrading third-generation tyrosine kinase inhibitor-resistant EGFR mutants, masking binding epitope HER2, and concurrently targeting compensatory receptors interacting with these proteins, sLYTACs show great promise in drug development to overcome bypass signaling and combat drug resistance in tumors.
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Affiliation(s)
- Yanchao Pan
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
| | - Qing Xiang
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
| | - Kai Deng
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
| | | | - Leiming Wang
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
| | - Yuan Wang
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
| | - Qiulian Liang
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
| | - Lirou Shen
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
| | - Jing Yang
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
| | - Zhongyu Hou
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
| | - Weijun Shen
- Translational Research CenterShenzhen Bay LaboratoryShenzhenChina
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4
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Huang B, Abedi M, Ahn G, Coventry B, Sappington I, Tang C, Wang R, Schlichthaerle T, Zhang JZ, Wang Y, Goreshnik I, Chiu CW, Chazin-Gray A, Chan S, Gerben S, Murray A, Wang S, O'Neill J, Yi L, Yeh R, Misquith A, Wolf A, Tomasovic LM, Piraner DI, Duran Gonzalez MJ, Bennett NR, Venkatesh P, Ahlrichs M, Dobbins C, Yang W, Wang X, Sahtoe DD, Vafeados D, Mout R, Shivaei S, Cao L, Carter L, Stewart L, Spangler JB, Roybal KT, Greisen PJ, Li X, Bernardes GJL, Bertozzi CR, Baker D. Designed endocytosis-inducing proteins degrade targets and amplify signals. Nature 2025; 638:796-804. [PMID: 39322662 PMCID: PMC11839401 DOI: 10.1038/s41586-024-07948-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/13/2024] [Indexed: 09/27/2024]
Abstract
Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by endogenous ligands. Therapeutic approaches such as lysosome-targeting chimaeras1,2 (LYTACs) and cytokine receptor-targeting chimeras3 (KineTACs) have used this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. Although powerful, these approaches can be limited by competition with native ligands and requirements for chemical modification that limit genetic encodability and can complicate manufacturing, and, more generally, there may be no native ligands that stimulate endocytosis through a given receptor. Here we describe computational design approaches for endocytosis-triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for insulin-like growth factor 2 receptor (IGF2R) and asialoglycoprotein receptor (ASGPR), sortilin and transferrin receptors, and show that fusing these tags to soluble or transmembrane target protein binders leads to lysosomal trafficking and target degradation. As these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. EndoTag fusion to a PD-L1 antibody considerably increases efficacy in a mouse tumour model compared to antibody alone. The modularity and genetic encodability of EndoTags enables AND gate control for higher-specificity targeted degradation, and the localized secretion of degraders from engineered cells. By promoting endocytosis, EndoTag fusion increases signalling through an engineered ligand-receptor system by nearly 100-fold. EndoTags have considerable therapeutic potential as targeted degradation inducers, signalling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody-drug and antibody-RNA conjugates.
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Affiliation(s)
- Buwei Huang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Mohamad Abedi
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Green Ahn
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Isaac Sappington
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Cong Tang
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Rong Wang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas Schlichthaerle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yujia Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Ching Wen Chiu
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Adam Chazin-Gray
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Stacey Gerben
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Analisa Murray
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Shunzhi Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Li Yi
- Novo Nordisk, Måløv, Denmark
| | | | | | | | - Luke M Tomasovic
- Departments of Biomedical Engineering and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan I Piraner
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Maria J Duran Gonzalez
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Nathaniel R Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinru Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Dionne Vafeados
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Rubul Mout
- Harvard Medical School, Harvard University, Boston, MA, USA
| | - Shirin Shivaei
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Longxing Cao
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Kole T Roybal
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | | | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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5
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Bohnsack RN, Misra SK, Liu J, Ishihara-Aoki M, Pereckas M, Aoki K, Ren G, Sharp JS, Dahms NM. Lysosomal enzyme binding to the cation-independent mannose 6-phosphate receptor is regulated allosterically by insulin-like growth factor 2. Sci Rep 2024; 14:26875. [PMID: 39505925 PMCID: PMC11541866 DOI: 10.1038/s41598-024-75300-9] [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: 05/20/2024] [Accepted: 10/03/2024] [Indexed: 11/08/2024] Open
Abstract
The cation-independent mannose 6-phosphate receptor (CI-MPR) is clinically significant in the treatment of patients with lysosomal storage diseases because it functions in the biogenesis of lysosomes by transporting mannose 6-phosphate (M6P)-containing lysosomal enzymes to endosomal compartments. CI-MPR is multifunctional and modulates embryonic growth and fetal size by downregulating circulating levels of the peptide hormone insulin-like growth factor 2 (IGF2). The extracellular region of CI-MPR comprises 15 homologous domains with binding sites for M6P-containing ligands located in domains 3, 5, 9, and 15, whereas IGF2 interacts with residues in domain 11. How a particular ligand affects the receptor's conformation or its ability to bind other ligands remains poorly understood. To address these questions, we purified a soluble form of the receptor from newborn calf serum, carried out glycoproteomics to define the N-glycans at its 19 potential glycosylation sites, probed its ability to bind lysosomal enzymes in the presence and absence of IGF2 using surface plasmon resonance, and assessed its conformation in the presence and absence of IGF2 by negative-staining electron microscopy and hydroxyl radical protein footprinting studies. Together, our findings support the hypothesis that IGF2 acts as an allosteric inhibitor of lysosomal enzyme binding by inducing global conformational changes of CI-MPR.
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Affiliation(s)
- Richard N Bohnsack
- Department of Biochemistry, Medical College of Wisconsin, 8701 W. Watertown Plank Rd., Milwaukee, WI, 53226, USA
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, 38677, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mayumi Ishihara-Aoki
- Translational Metabolomics Shared Resource, Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Michaela Pereckas
- Department of Biochemistry, Medical College of Wisconsin, 8701 W. Watertown Plank Rd., Milwaukee, WI, 53226, USA
| | - Kazuhiro Aoki
- Translational Metabolomics Shared Resource, Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, 38677, USA
- Department of Chemistry and Biochemistry, University of Mississippi, Oxford, MS, 38677, USA
| | - Nancy M Dahms
- Department of Biochemistry, Medical College of Wisconsin, 8701 W. Watertown Plank Rd., Milwaukee, WI, 53226, USA.
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6
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Bonini S, Winter D. Two-Step Enrichment Facilitates Background Reduction for Proteomic Analysis of Lysosomes. J Proteome Res 2024; 23:3393-3403. [PMID: 38967832 DOI: 10.1021/acs.jproteome.4c00053] [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] [Indexed: 07/06/2024]
Abstract
Lysosomes constitute the main degradative compartment of most mammalian cells and are involved in various cellular functions. Most of them are catalyzed by lysosomal proteins, which typically are low abundant, complicating their analysis by mass spectrometry-based proteomics. To increase analytical performance and to enable profiling of lysosomal content, lysosomes are often enriched. Two approaches have gained popularity in recent years, namely, superparamagnetic iron oxide nanoparticles (SPIONs) and immunoprecipitation from cells overexpressing a 3xHA-tagged version of TMEM192 (TMEM-IP). The effect of these approaches on the lysosomal proteome has not been investigated to date. We addressed this topic through a combination of both techniques and proteomic analysis of lysosome-enriched fractions. For SPIONs treatment, we identified altered cellular iron homeostasis and moderate changes of the lysosomal proteome. For overexpression of TMEM192, we observed more pronounced effects in lysosomal protein expression, especially for lysosomal membrane proteins and those involved in protein trafficking. Furthermore, we established a combined strategy based on the sequential enrichment of lysosomes with SPIONs and TMEM-IP. This enabled increased purity of lysosome-enriched fractions and, through TMEM-IP-based lysosome enrichment from SPIONs flow-through and eluate fractions, additional insights into the properties of individual approaches. All data are available via ProteomeXchange with PXD048696.
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Affiliation(s)
- Sara Bonini
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn 53115, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn 53115, Germany
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7
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Hämälistö S, Del Valle Batalla F, Yuseff MI, Mattila PK. Endolysosomal vesicles at the center of B cell activation. J Cell Biol 2024; 223:e202307047. [PMID: 38305771 PMCID: PMC10837082 DOI: 10.1083/jcb.202307047] [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: 07/14/2023] [Revised: 12/22/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
The endolysosomal system specializes in degrading cellular components and is crucial to maintaining homeostasis and adapting rapidly to metabolic and environmental cues. Cells of the immune system exploit this network to process antigens or promote cell death by secreting lysosome-related vesicles. In B lymphocytes, lysosomes are harnessed to facilitate the extraction of antigens and to promote their processing into peptides for presentation to T cells, critical steps to mount protective high-affinity antibody responses. Intriguingly, lysosomal vesicles are now considered important signaling units within cells and also display secretory functions by releasing their content to the extracellular space. In this review, we focus on how B cells use pathways involved in the intracellular trafficking, secretion, and function of endolysosomes to promote adaptive immune responses. A basic understanding of such mechanisms poses an interesting frontier for the development of therapeutic strategies in the context of cancer and autoimmune diseases.
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Affiliation(s)
- Saara Hämälistö
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
- Cancer Research Unit and FICAN West Cancer Centre Laboratory, Turku, Finland
| | - Felipe Del Valle Batalla
- Laboratory of Immune Cell Biology, Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Isabel Yuseff
- Laboratory of Immune Cell Biology, Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pieta K. Mattila
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
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8
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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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9
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Huang B, Abedi M, Ahn G, Coventry B, Sappington I, Wang R, Schlichthaerle T, Zhang JZ, Wang Y, Goreshnik I, Chiu CW, Chazin-Gray A, Chan S, Gerben S, Murray A, Wang S, O'Neill J, Yeh R, Misquith A, Wolf A, Tomasovic LM, Piraner DI, Gonzalez MJD, Bennett NR, Venkatesh P, Satoe D, Ahlrichs M, Dobbins C, Yang W, Wang X, Vafeados D, Mout R, Shivaei S, Cao L, Carter L, Stewart L, Spangler JB, Bernardes GJL, Roybal KT, Greisen P, Li X, Bertozzi C, Baker D. Designed Endocytosis-Triggering Proteins mediate Targeted Degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553321. [PMID: 37781607 PMCID: PMC10541094 DOI: 10.1101/2023.08.19.553321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by interaction with endogenous ligands. Therapeutic approaches such as LYTAC1,2 and KineTAC3, have taken advantage of this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. While powerful, these approaches can be limited by possible competition with the endogenous ligand(s), the requirement in some cases for chemical modification that limits genetic encodability and can complicate manufacturing, and more generally, there may not be natural ligands which stimulate endocytosis through a given receptor. Here we describe general protein design approaches for designing endocytosis triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for the IGF-2R, ASGPR, Sortillin, and Transferrin receptors, and show that fusing these tags to proteins which bind to soluble or transmembrane protein leads to lysosomal trafficking and target degradation; as these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. The modularity and genetic encodability of EndoTags enables AND gate control for higher specificity targeted degradation, and the localized secretion of degraders from engineered cells. The tunability and modularity of our genetically encodable EndoTags should contribute to deciphering the relationship between receptor engagement and cellular trafficking, and they have considerable therapeutic potential as targeted degradation inducers, signaling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody drug and RNA conjugates.
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Affiliation(s)
- Buwei Huang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Mohamad Abedi
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Green Ahn
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Isaac Sappington
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Rong Wang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas Schlichthaerle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yujia Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Ching Wen Chiu
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Adam Chazin-Gray
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Stacey Gerben
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Analisa Murray
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Shunzhi Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Luke M Tomasovic
- Departments of Biomedical Engineering and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan I Piraner
- Department of Microbiology and Immunology, University of California San Francisco
| | | | - Nathaniel R Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Danny Satoe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinru Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dionne Vafeados
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Rubul Mout
- Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - Shirin Shivaei
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Longxing Cao
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jamie B Spangler
- Departments of Biomedical Engineering and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gonçalo J L Bernardes
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Kole T Roybal
- Department of Microbiology and Immunology, University of California San Francisco
| | | | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carolyn Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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10
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Potalitsyn P, Mrázková L, Selicharová I, Tencerová M, Ferenčáková M, Chrudinová M, Turnovská T, Brzozowski AM, Marek A, Kaminský J, Jiráček J, Žáková L. Non-glycosylated IGF2 prohormones are more mitogenic than native IGF2. Commun Biol 2023; 6:863. [PMID: 37598269 PMCID: PMC10439913 DOI: 10.1038/s42003-023-05239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 08/10/2023] [Indexed: 08/21/2023] Open
Abstract
Insulin-like Growth Factor-2 (IGF2) is important for the regulation of human embryonic growth and development, and for adults' physiology. Incorrect processing of the IGF2 precursor, pro-IGF2(156), leads to the formation of two IGF2 proforms, big-IGF2(87) and big-IGF2(104). Unprocessed and mainly non-glycosylated IGF2 proforms are found at abnormally high levels in certain diseases, but their mode of action is still unclear. Here, we found that pro-IGF2(156) has the lowest ability to form its inactivating complexes with IGF-Binding Proteins and has higher proliferative properties in cells than IGF2 and other IGF prohormones. We also showed that big-IGF2(104) has a seven-fold higher binding affinity for the IGF2 receptor than IGF2, and that pro-IGF2(87) binds and activates specific receptors and stimulates cell growth similarly to the mature IGF2. The properties of these pro-IGF2 forms, especially of pro-IGF2(156) and big-IGF2(104), indicate them as hormones that may be associated with human diseases related to the accumulation of IGF-2 proforms in the circulation.
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Affiliation(s)
- Pavlo Potalitsyn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 116 10, Prague 6, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, 12800, Prague 2, Czech Republic
| | - Lucie Mrázková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 116 10, Prague 6, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, 12800, Prague 2, Czech Republic
| | - Irena Selicharová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 116 10, Prague 6, Czech Republic
| | - Michaela Tencerová
- Institute of Physiology, Czech Academy of Sciences, Vídeňská 1083, Prague 4, Czech Republic
| | - Michaela Ferenčáková
- Institute of Physiology, Czech Academy of Sciences, Vídeňská 1083, Prague 4, Czech Republic
| | - Martina Chrudinová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 116 10, Prague 6, Czech Republic
| | - Tereza Turnovská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 116 10, Prague 6, Czech Republic
| | - Andrzej Marek Brzozowski
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 116 10, Prague 6, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 116 10, Prague 6, Czech Republic
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 116 10, Prague 6, Czech Republic.
| | - Lenka Žáková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 116 10, Prague 6, Czech Republic.
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11
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Vimercati A, Tannorella P, Orlandini E, Calzari L, Moro M, Guzzetti S, Selicorni A, Crippa M, Larizza L, Bonati MT, Russo S. Case report: atypical Silver-Russell syndrome patient with hand dystonia: the valuable support of the consensus statement to the wide syndromic spectrum. Front Genet 2023; 14:1198821. [PMID: 37529781 PMCID: PMC10387531 DOI: 10.3389/fgene.2023.1198821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/19/2023] [Indexed: 08/03/2023] Open
Abstract
The amount of Insulin Growth Factor 2 (IGF2) controls the rate of embryonal and postnatal growth. The IGF2 and adjacent H19 are the imprinted genes of the telomeric cluster in the 11p15 chromosomal region regulated by differentially methylated regions (DMRs) or imprinting centers (ICs): H19/IGF2:IG-DMR (IC1). Dysregulation due to IC1 Loss-of-Methylation (LoM) or Gain-of-Methyaltion (GoM) causes Silver-Russell syndrome (SRS) or Beckwith-Wiedemann syndrome (BWS) disorders associated with growth retardation or overgrowth, respectively. Specific features define each of the two syndromes, but isolated asymmetry is a common cardinal feature, which is considered sufficient for a diagnosis in the BWS spectrum. Here, we report the case of a girl with right body asymmetry, which suggested BWS spectrum. Later, BWS/SRS molecular analysis identified IC1_LoM revealing the discrepant diagnosis of SRS. A clinical re-evaluation identified a relative macrocephaly and previously unidentified growth rate at lower limits of normal at birth, feeding difficulties, and asymmetry. Interestingly, and never previously described in IC1_LoM SRS patients, since the age of 16, she has developed hand-writer's cramps, depression, and bipolar disorder. Trio-WES identified a VPS16 heterozygous variant [NM_022575.4:c.2185C>G:p.Leu729Val] inherited from her healthy mother. VPS16 is involved in the endolysosomal system, and its dysregulation is linked to autosomal dominant dystonia with incomplete penetrance and variable expressivity. IGF2 involvement in the lysosomal pathway led us to speculate that the neurological phenotype of the proband might be triggered by the concurrent IGF2 deficit and VPS16 alteration.
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Affiliation(s)
- Alessandro Vimercati
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Pierpaola Tannorella
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Eleonora Orlandini
- Specialty School of Pediatrics, Alma Mater University of Bologna, Bologna, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Mirella Moro
- Department of Endocrine and Metabolic Diseases and Lab of Endocrine and Metabolic Research, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Sara Guzzetti
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | | | - Milena Crippa
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Lidia Larizza
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Maria Teresa Bonati
- Unit of Medical Genetics, Institute for Maternal and Child Health Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Burlo Garofalo, Trieste, Italy
| | - Silvia Russo
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milano, Italy
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12
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Li R, Heuer J, Kuckhoff T, Landfester K, Ferguson CTJ. pH-Triggered Recovery of Organic Polymer Photocatalytic Particles for the Production of High Value Compounds and Enhanced Recyclability. Angew Chem Int Ed Engl 2023; 62:e202217652. [PMID: 36749562 DOI: 10.1002/anie.202217652] [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: 11/30/2022] [Revised: 01/23/2023] [Accepted: 02/07/2023] [Indexed: 02/08/2023]
Abstract
Pseudo-homogeneous polymeric photocatalysts are an emerging class of highly efficient and tunable photocatalytic materials, where the photocatalytic centers are easily accessible. The creation of highly efficient photocatalytic materials that can be rapidly separated and recovered is one of the critical challenges in photocatalytic chemistry. Here, we describe pH-responsive photocatalytic nanoparticles that are active and well-dispersed under acidic conditions but aggregate instantly upon elevation of pH, enabling easy recovery. These responsive photocatalytic polymers can be used in various photocatalytic transformations, including CrVI reduction and photoredox alkylation of indole derivative. Notably, the cationic nature of the photocatalyst accelerates reaction rate of an anionic substrate compared to uncharged species. These photocatalytic particles could be readily recycled allowing multiple successive photocatalytic reactions with no clear loss in activity.
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Affiliation(s)
- Rong Li
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Julian Heuer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Thomas Kuckhoff
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Calum T J Ferguson
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
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13
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Abstract
Single-pass transmembrane receptors (SPTMRs) represent a diverse group of integral membrane proteins that are involved in many essential cellular processes, including signal transduction, cell adhesion, and transmembrane transport of materials. Dysregulation of the SPTMRs is linked with many human diseases. Despite extensive efforts in past decades, the mechanisms of action of the SPTMRs remain incompletely understood. One major hurdle is the lack of structures of the full-length SPTMRs in different functional states. Such structural information is difficult to obtain by traditional structural biology methods such as X-ray crystallography and nuclear magnetic resonance (NMR). The recent rapid development of single-particle cryo-electron microscopy (cryo-EM) has led to an exponential surge in the number of high-resolution structures of integral membrane proteins, including SPTMRs. Cryo-EM structures of SPTMRs solved in the past few years have tremendously improved our understanding of how SPTMRs function. In this review, we will highlight these progresses in the structural studies of SPTMRs by single-particle cryo-EM, analyze important structural details of each protein involved, and discuss their implications on the underlying mechanisms. Finally, we also briefly discuss remaining challenges and exciting opportunities in the field.
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Affiliation(s)
- Kai Cai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
| | - Xuewu Zhang
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xuewu Zhang, Department of pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Xiao-chen Bai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xiao-chen Bai, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA;
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14
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Wirchnianski AS, Wec AZ, Nyakatura EK, Herbert AS, Slough MM, Kuehne AI, Mittler E, Jangra RK, Teruya J, Dye JM, Lai JR, Chandran K. Two Distinct Lysosomal Targeting Strategies Afford Trojan Horse Antibodies With Pan-Filovirus Activity. Front Immunol 2021; 12:729851. [PMID: 34721393 PMCID: PMC8551868 DOI: 10.3389/fimmu.2021.729851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple agents in the family Filoviridae (filoviruses) are associated with sporadic human outbreaks of highly lethal disease, while others, including several recently identified agents, possess strong zoonotic potential. Although viral glycoprotein (GP)-specific monoclonal antibodies have demonstrated therapeutic utility against filovirus disease, currently FDA-approved molecules lack antiviral breadth. The development of broadly neutralizing antibodies has been challenged by the high sequence divergence among filovirus GPs and the complex GP proteolytic cleavage cascade that accompanies filovirus entry. Despite this variability in the antigenic surface of GP, all filoviruses share a site of vulnerability-the binding site for the universal filovirus entry receptor, Niemann-Pick C1 (NPC1). Unfortunately, this site is shielded in extracellular GP and only uncovered by proteolytic cleavage by host proteases in late endosomes and lysosomes, which are generally inaccessible to antibodies. To overcome this obstacle, we previously developed a 'Trojan horse' therapeutic approach in which engineered bispecific antibodies (bsAbs) coopt viral particles to deliver GP:NPC1 interaction-blocking antibodies to their endo/lysosomal sites of action. This approach afforded broad protection against members of the genus Ebolavirus but could not neutralize more divergent filoviruses. Here, we describe next-generation Trojan horse bsAbs that target the endo/lysosomal GP:NPC1 interface with pan-filovirus breadth by exploiting the conserved and widely expressed host cation-independent mannose-6-phosphate receptor for intracellular delivery. Our work highlights a new avenue for the development of single therapeutics protecting against all known and newly emerging filoviruses.
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Affiliation(s)
- Ariel S. Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Anna Z. Wec
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Elisabeth K. Nyakatura
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Andrew S. Herbert
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
- The Geneva Foundation, Tacoma, WA, United States
| | - Megan M. Slough
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ana I. Kuehne
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Eva Mittler
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Rohit K. Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Jonathan Teruya
- Antibody Discovery and Research group, Mapp Biopharmaceutical, San Diego, CA, United States
| | - John M. Dye
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
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15
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Roles of interstitial fluid pH and weak organic acids in development and amelioration of insulin resistance. Biochem Soc Trans 2021; 49:715-726. [PMID: 33769491 DOI: 10.1042/bst20200667] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/20/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is one of the most common lifestyle-related diseases (metabolic disorders) due to hyperphagia and/or hypokinesia. Hyperglycemia is the most well-known symptom occurring in T2DM patients. Insulin resistance is also one of the most important symptoms, however, it is still unclear how insulin resistance develops in T2DM. Detailed understanding of the pathogenesis primarily causing insulin resistance is essential for developing new therapies for T2DM. Insulin receptors are located at the plasma membrane of the insulin-targeted cells such as myocytes, adipocytes, etc., and insulin binds to the extracellular site of its receptor facing the interstitial fluid. Thus, changes in interstitial fluid microenvironments, specially pH, affect the insulin-binding affinity to its receptor. The most well-known clinical condition regarding pH is systemic acidosis (arterial blood pH < 7.35) frequently observed in severe T2DM associated with insulin resistance. Because the insulin-binding site of its receptor faces the interstitial fluid, we should recognize the interstitial fluid pH value, one of the most important factors influencing the insulin-binding affinity. It is notable that the interstitial fluid pH is unstable compared with the arterial blood pH even under conditions that the arterial blood pH stays within the normal range, 7.35-7.45. This review article introduces molecular mechanisms on unstable interstitial fluid pH value influencing the insulin action via changes in insulin-binding affinity and ameliorating actions of weak organic acids on insulin resistance via their characteristics as bases after absorption into the body even with sour taste at the tongue.
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16
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Gully BS, Venugopal H, Fulcher AJ, Fu Z, Li J, Deuss FA, Llerena C, Heath WR, Lahoud MH, Caminschi I, Rossjohn J, Berry R. The cryo-EM structure of the endocytic receptor DEC-205. J Biol Chem 2020; 296:100127. [PMID: 33257321 PMCID: PMC7948739 DOI: 10.1074/jbc.ra120.016451] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 11/06/2022] Open
Abstract
DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine oligonucleotides, a motif often seen in bacterial or viral DNA. However, despite growing biological and clinical significance, little is known about the structural arrangement of this receptor or any of its family members. Here, we describe the 3.2 Å cryo-EM structure of human DEC-205, thereby illuminating the structure of the mannose receptor protein family. The DEC-205 monomer forms a compact structure comprising two intercalated rings of C-type lectin-like domains, where the N-terminal cysteine-rich and fibronectin domains reside at the central intersection. We establish a pH-dependent oligomerization pathway forming tetrameric DEC-205 using solution-based techniques and ultimately solved the 4.9 Å cryo-EM structure of the DEC-205 tetramer to identify the unfurling of the second lectin ring which enables tetramer formation. Furthermore, we suggest the relevance of this oligomerization pathway within a cellular setting, whereby cytosine-guanosine binding appeared to disrupt this cell-surface oligomer. Accordingly, we provide insight into the structure and oligomeric assembly of the DEC-205 receptor.
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Affiliation(s)
- Benjamin S Gully
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Melbourne, Victoria, Australia
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, Victoria, Australia
| | - Zhihui Fu
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jessica Li
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Felix A Deuss
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Carmen Llerena
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - William R Heath
- Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Parkville, Victoria, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Mireille H Lahoud
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Irina Caminschi
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom.
| | - Richard Berry
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.
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17
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Olson LJ, Misra SK, Ishihara M, Battaile KP, Grant OC, Sood A, Woods RJ, Kim JJP, Tiemeyer M, Ren G, Sharp JS, Dahms NM. Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor. Commun Biol 2020; 3:498. [PMID: 32908216 PMCID: PMC7481795 DOI: 10.1038/s42003-020-01211-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/11/2020] [Indexed: 01/09/2023] Open
Abstract
The cation-independent mannose 6-phosphate receptor (CI-MPR, IGF2 receptor or CD222), is a multifunctional glycoprotein required for normal development. Through the receptor's ability to bind unrelated extracellular and intracellular ligands, it participates in numerous functions including protein trafficking, lysosomal biogenesis, and regulation of cell growth. Clinically, endogenous CI-MPR delivers infused recombinant enzymes to lysosomes in the treatment of lysosomal storage diseases. Although four of the 15 domains comprising CI-MPR's extracellular region bind phosphorylated glycans on lysosomal enzymes, knowledge of how CI-MPR interacts with ~60 different lysosomal enzymes is limited. Here, we show by electron microscopy and hydroxyl radical protein footprinting that the N-terminal region of CI-MPR undergoes dynamic conformational changes as a consequence of ligand binding and different pH conditions. These data, coupled with X-ray crystallography, surface plasmon resonance and molecular modeling, allow us to propose a model explaining how high-affinity carbohydrate binding is achieved through allosteric domain cooperativity.
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Affiliation(s)
- Linda J Olson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, 38677, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, IL, USA
- New York Structural Biology Center, New York City, NY, 10027, USA
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Amika Sood
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Jung-Ja P Kim
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, 38677, USA
| | - Nancy M Dahms
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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Bochel AJ, Williams C, McCoy AJ, Hoppe HJ, Winter AJ, Nicholls RD, Harlos K, Jones EY, Berger I, Hassan AB, Crump MP. Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7-11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9. Structure 2020; 28:1300-1312.e5. [PMID: 32877646 DOI: 10.1016/j.str.2020.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/13/2020] [Accepted: 08/07/2020] [Indexed: 11/29/2022]
Abstract
The cation-independent mannose 6-phosphate (M6P)/Insulin-like growth factor-2 receptor (CI-MPR/IGF2R) is an ∼300 kDa transmembrane protein responsible for trafficking M6P-tagged lysosomal hydrolases and internalizing IGF2. The extracellular region of the CI-MPR has 15 homologous domains, including M6P-binding domains (D) 3, 5, 9, and 15 and IGF2-binding domain 11. We have focused on solving the first structures of human D7-10 within two multi-domain constructs, D9-10 and D7-11, and provide the first high-resolution description of the high-affinity M6P-binding D9. Moreover, D9 stabilizes a well-defined hub formed by D7-11 whereby two penta-domains intertwine to form a dimeric helical-type coil via an N-glycan bridge on D9. Remarkably the D7-11 structure matches an IGF2-bound state of the receptor, suggesting this may be an intrinsically stable conformation at neutral pH. Interdomain clusters of histidine and proline residues may impart receptor rigidity and play a role in structural transitions at low pH.
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Affiliation(s)
- Alice J Bochel
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK
| | - Christopher Williams
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK; BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Airlie J McCoy
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Hans-Jürgen Hoppe
- Tumour Growth Control Group, Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; dAInomics Ltd, 66 High Street, Bassingbourn Royston SG8 5LF, UK
| | - Ashley J Winter
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK
| | - Ryan D Nicholls
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK
| | - Karl Harlos
- Cancer Research UK Receptor Structure Research Group, Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - E Yvonne Jones
- Cancer Research UK Receptor Structure Research Group, Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Imre Berger
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - A Bassim Hassan
- Tumour Growth Control Group, Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
| | - Matthew P Crump
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK; BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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Wang R, Long T, Hassan A, Wang J, Sun Y, Xie XS, Li X. Cryo-EM structures of intact V-ATPase from bovine brain. Nat Commun 2020; 11:3921. [PMID: 32764564 PMCID: PMC7414150 DOI: 10.1038/s41467-020-17762-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022] Open
Abstract
The vacuolar-type H+-ATPases (V-ATPase) hydrolyze ATP to pump protons across the plasma or intracellular membrane, secreting acids to the lumen or acidifying intracellular compartments. It has been implicated in tumor metastasis, renal tubular acidosis, and osteoporosis. Here, we report two cryo-EM structures of the intact V-ATPase from bovine brain with all the subunits including the subunit H, which is essential for ATPase activity. Two type-I transmembrane proteins, Ac45 and (pro)renin receptor, along with subunit c", constitute the core of the c-ring. Three different conformations of A/B heterodimers suggest a mechanism for ATP hydrolysis that triggers a rotation of subunits DF, inducing spinning of subunit d with respect to the entire c-ring. Moreover, many lipid molecules have been observed in the Vo domain to mediate the interactions between subunit c, c", (pro)renin receptor, and Ac45. These two structures reveal unique features of mammalian V-ATPase and suggest a mechanism of V1-Vo torque transmission.
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Affiliation(s)
- Rong Wang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tao Long
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Abdirahman Hassan
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jin Wang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yingyuan Sun
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiao-Song Xie
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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