1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Chan A, Tsourkas A. Intracellular Protein Delivery: Approaches, Challenges, and Clinical Applications. BME Front 2024; 5:0035. [PMID: 38282957 PMCID: PMC10809898 DOI: 10.34133/bmef.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024] Open
Abstract
Protein biologics are powerful therapeutic agents with diverse inhibitory and enzymatic functions. However, their clinical use has been limited to extracellular applications due to their inability to cross plasma membranes. Overcoming this physiological barrier would unlock the potential of protein drugs for the treatment of many intractable diseases. In this review, we highlight progress made toward achieving cytosolic delivery of recombinant proteins. We start by first considering intracellular protein delivery as a drug modality compared to existing Food and Drug Administration-approved drug modalities. Then, we summarize strategies that have been reported to achieve protein internalization. These techniques can be broadly classified into 3 categories: physical methods, direct protein engineering, and nanocarrier-mediated delivery. Finally, we highlight existing challenges for cytosolic protein delivery and offer an outlook for future advances.
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Affiliation(s)
| | - Andrew Tsourkas
- Department of Bioengineering,
University of Pennsylvania, Philadelphia, PA, USA
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4
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Ogawa Y, Ueda TP, Obara K, Nishimura K, Kamura T. Targeted Protein Degradation Systems: Controlling Protein Stability Using E3 Ubiquitin Ligases in Eukaryotic Species. Cells 2024; 13:175. [PMID: 38247866 PMCID: PMC10814424 DOI: 10.3390/cells13020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This review explores various methods for modulating protein stability to achieve target protein degradation, which is a crucial aspect in the study of biological processes and drug design. Thirty years have passed since the introduction of heat-inducible degron cells utilizing the N-end rule, and methods for controlling protein stability using the ubiquitin-proteasome system have moved from academia to industry. This review covers protein stability control methods, from the early days to recent advancements, and discusses the evolution of techniques in this field. This review also addresses the challenges and future directions of protein stability control techniques by tracing their development from the inception of protein stability control methods to the present day.
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Affiliation(s)
| | | | | | - Kohei Nishimura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan; (Y.O.); (T.P.U.); (K.O.)
| | - Takumi Kamura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan; (Y.O.); (T.P.U.); (K.O.)
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5
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Khramtsov YV, Ulasov AV, Lupanova TN, Slastnikova TA, Rosenkranz AA, Bunin ES, Georgiev GP, Sobolev AS. Intracellular Degradation of SARS-CoV-2 N-Protein Caused by Modular Nanotransporters Containing Anti-N-Protein Monobody and a Sequence That Recruits the Keap1 E3 Ligase. Pharmaceutics 2023; 16:4. [PMID: 38276482 PMCID: PMC10818351 DOI: 10.3390/pharmaceutics16010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
The proper viral assembly relies on both nucleic acids and structural viral proteins. Thus a biologically active agent that provides the degradation of one of these key proteins and/or destroys the viral factory could suppress viral replication efficiently. The nucleocapsid protein (N-protein) is a key protein for the SARS-CoV-2 virus. As a bioactive agent, we offer a modular nanotransporter (MNT) developed by us, which, in addition to an antibody mimetic to the N-protein, contains an amino acid sequence for the attraction of the Keap1 E3 ubiquitin ligase. This should lead to the subsequent degradation of the N-protein. We have shown that the functional properties of modules within the MNT permit its internalization into target cells, endosome escape into the cytosol, and binding to the N-protein. Using flow cytometry and western blotting, we demonstrated significant degradation of N-protein when A549 and A431 cells transfected with a plasmid coding for N-protein were incubated with the developed MNTs. The proposed MNTs open up a new approach for the treatment of viral diseases.
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Affiliation(s)
- Yuri V. Khramtsov
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.N.L.); (T.A.S.); (A.A.R.); (E.S.B.); (G.P.G.)
| | - Alexey V. Ulasov
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.N.L.); (T.A.S.); (A.A.R.); (E.S.B.); (G.P.G.)
| | - Tatiana N. Lupanova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.N.L.); (T.A.S.); (A.A.R.); (E.S.B.); (G.P.G.)
| | - Tatiana A. Slastnikova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.N.L.); (T.A.S.); (A.A.R.); (E.S.B.); (G.P.G.)
| | - Andrey A. Rosenkranz
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.N.L.); (T.A.S.); (A.A.R.); (E.S.B.); (G.P.G.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
| | - Egor S. Bunin
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.N.L.); (T.A.S.); (A.A.R.); (E.S.B.); (G.P.G.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
| | - Georgii P. Georgiev
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.N.L.); (T.A.S.); (A.A.R.); (E.S.B.); (G.P.G.)
| | - Alexander S. Sobolev
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (Y.V.K.); (A.V.U.); (T.N.L.); (T.A.S.); (A.A.R.); (E.S.B.); (G.P.G.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
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6
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Congdon EE, Ji C, Tetlow AM, Jiang Y, Sigurdsson EM. Tau-targeting therapies for Alzheimer disease: current status and future directions. Nat Rev Neurol 2023; 19:715-736. [PMID: 37875627 PMCID: PMC10965012 DOI: 10.1038/s41582-023-00883-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 10/26/2023]
Abstract
Alzheimer disease (AD) is the most common cause of dementia in older individuals. AD is characterized pathologically by amyloid-β (Aβ) plaques and tau neurofibrillary tangles in the brain, with associated loss of synapses and neurons, which eventually results in dementia. Many of the early attempts to develop treatments for AD focused on Aβ, but a lack of efficacy of these treatments in terms of slowing disease progression led to a change of strategy towards targeting of tau pathology. Given that tau shows a stronger correlation with symptom severity than does Aβ, targeting of tau is more likely to be efficacious once cognitive decline begins. Anti-tau therapies initially focused on post-translational modifications, inhibition of tau aggregation and stabilization of microtubules. However, trials of many potential drugs were discontinued because of toxicity and/or lack of efficacy. Currently, the majority of tau-targeting agents in clinical trials are immunotherapies. In this Review, we provide an update on the results from the initial immunotherapy trials and an overview of new therapeutic candidates that are in clinical development, as well as considering future directions for tau-targeting therapies.
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Affiliation(s)
- Erin E Congdon
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Changyi Ji
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Amber M Tetlow
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Yixiang Jiang
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Einar M Sigurdsson
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA.
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA.
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7
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Fletcher A, Clift D, de Vries E, Martinez Cuesta S, Malcolm T, Meghini F, Chaerkady R, Wang J, Chiang A, Weng SHS, Tart J, Wong E, Donohoe G, Rawlins P, Gordon E, Taylor JD, James L, Hunt J. A TRIM21-based bioPROTAC highlights the therapeutic benefit of HuR degradation. Nat Commun 2023; 14:7093. [PMID: 37925433 PMCID: PMC10625600 DOI: 10.1038/s41467-023-42546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 10/13/2023] [Indexed: 11/06/2023] Open
Abstract
Human antigen R (HuR) is a ubiquitously expressed RNA-binding protein, which functions as an RNA regulator. Overexpression of HuR correlates with high grade tumours and poor patient prognosis, implicating it as an attractive therapeutic target. However, an effective small molecule antagonist to HuR for clinical use remains elusive. Here, a single domain antibody (VHH) that binds HuR with low nanomolar affinity was identified and shown to inhibit HuR binding to RNA. This VHH was used to engineer a TRIM21-based biological PROTAC (bioPROTAC) that could degrade endogenous HuR. Significantly, HuR degradation reverses the tumour-promoting properties of cancer cells in vivo by altering the HuR-regulated proteome, highlighting the benefit of HuR degradation and paving the way for the development of HuR-degrading therapeutics. These observations have broader implications for degrading intractable therapeutic targets, with bioPROTACs presenting a unique opportunity to explore targeted-protein degradation through a modular approach.
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Affiliation(s)
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Emma de Vries
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | - Sergio Martinez Cuesta
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Raghothama Chaerkady
- Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Junmin Wang
- Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Abby Chiang
- Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Shao Huan Samuel Weng
- Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Jonathan Tart
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Edmond Wong
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | | | - Philip Rawlins
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Euan Gordon
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Leo James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - James Hunt
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK.
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8
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Abstract
A milestone in the field of recombinant binding molecules was achieved 30 years ago with the discovery of single-domain antibodies from which antigen-binding variable domains, better known as nanobodies (Nbs), can be derived. Being only one tenth the size of conventional antibodies, Nbs feature high affinity and specificity, while being highly stable and soluble. In addition, they display accessibility to cryptic sites, low off-target accumulation and deep tissue penetration. Efficient selection methods, such as (semi-)synthetic/naïve or immunized cDNA libraries and display technologies, have facilitated the isolation of Nbs against diverse targets, and their single-gene format enables easy functionalization and high-yield production. This Review highlights recent advances in Nb applications in various areas of biological research, including structural biology, proteomics and high-resolution and in vivo imaging. In addition, we provide insights into intracellular applications of Nbs, such as live-cell imaging, biosensors and targeted protein degradation.
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Affiliation(s)
- Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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9
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Liczmanska M, Tatham MH, Mojsa B, Eugui-Anta A, Rojas-Fernandez A, Ibrahim AFM, Hay RT. SUMO protease SENP6 protects the nucleus from hyperSUMOylation-induced laminopathy-like alterations. Cell Rep 2023; 42:112960. [PMID: 37556322 DOI: 10.1016/j.celrep.2023.112960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/22/2023] [Accepted: 07/24/2023] [Indexed: 08/11/2023] Open
Abstract
The small ubiquitin-like modifier (SUMO) protease SENP6 disassembles SUMO chains from cellular substrate proteins. We use a proteomic method to identify putative SENP6 substrates based on increased apparent molecular weight after SENP6 depletion. Proteins of the lamin family of intermediate filaments show substantially increased SUMO modification after SENP6 depletion. This is accompanied by nuclear structural changes remarkably like those associated with laminopathies. Two SUMO attachment sites on lamin A/C are close to sites of mutations in Emery-Driefuss and limb girdle muscular dystrophy. To establish a direct link between lamin SUMOylation and the observed phenotype, we developed proximity-induced SUMO modification (PISM), which fuses a lamin A/C targeting DARPin to a SUMO E3 ligase domain. This directly targets lamin A/C for SUMO conjugation and demonstrates that enhanced lamin SUMO modification recapitulates the altered nuclear structure manifest after SENP6 depletion. This shows SENP6 activity protects the nucleus against hyperSUMOylation-induced laminopathy-like alterations.
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Affiliation(s)
- Magda Liczmanska
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Michael H Tatham
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Barbara Mojsa
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ania Eugui-Anta
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alejandro Rojas-Fernandez
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Adel F M Ibrahim
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ronald T Hay
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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10
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Shen F, Dassama LMK. Opportunities and challenges of protein-based targeted protein degradation. Chem Sci 2023; 14:8433-8447. [PMID: 37592990 PMCID: PMC10430753 DOI: 10.1039/d3sc02361c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/02/2023] [Indexed: 08/19/2023] Open
Abstract
In the 20 years since the first report of a proteolysis targeting chimeric (PROTAC) molecule, targeted protein degradation (TPD) technologies have attempted to revolutionize the fields of chemical biology and biomedicine by providing exciting research opportunities and potential therapeutics. However, they primarily focus on the use of small molecules to recruit the ubiquitin proteasome system to mediate target protein degradation. This then limits protein targets to cytosolic domains with accessible and suitable small molecule binding pockets. In recent years, biologics such as proteins and nucleic acids have instead been used as binders for targeting proteins, thereby expanding the scope of TPD platforms to include secreted proteins, transmembrane proteins, and soluble but highly disordered intracellular proteins. This perspective summarizes the recent TPD platforms that utilize nanobodies, antibodies, and other proteins as binding moieties to deplete challenging targets, either through the ubiquitin proteasome system or the lysosomal degradation pathway. Importantly, the perspective also highlights opportunities and remaining challenges of current protein-based TPD technologies.
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Affiliation(s)
- Fangfang Shen
- Department of Chemistry, Sarafan ChEM-H Institute, Stanford University USA
| | - Laura M K Dassama
- Department of Chemistry, Sarafan ChEM-H Institute, Stanford University USA
- Department of Microbiology & Immunology, Stanford School of Medicine USA
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11
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Deng C, Li S, Liu Y, Bao W, Xu C, Zheng W, Wang M, Ma X. Split-Cas9-based targeted gene editing and nanobody-mediated proteolysis-targeting chimeras optogenetically coordinated regulation of Survivin to control the fate of cancer cells. Clin Transl Med 2023; 13:e1382. [PMID: 37620295 PMCID: PMC10449816 DOI: 10.1002/ctm2.1382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Precise regulation of partial critical proteins in cancer cells, such as anti-apoptotic proteins, is one of the crucial strategies for treating cancer and discovering related molecular mechanisms. Still, it is also challenging in actual research and practice. The widely used CRISPR/Cas9-based gene editing technology and proteolysis-targeting chimeras (PROTACs) have played an essential role in regulating gene expression and protein function in cells. However, the accuracy and controllability of their targeting remain necessary. METHODS Construction of UMUC-3-EGFP stable transgenic cell lines using the Sleeping Beauty system, Flow cytometry, quantitative real-time PCR, western blot, fluorescence microplate reader and fluorescence inverted microscope analysis of EGFP intensity. Characterization of Survivin inhibition was done by using Annexin V-FITC/PI apoptosis, calcein/PI/DAPI cell viability/cytotoxicity assay, cloning formation assay and scratch assay. The cell-derived xenograft (CDX) model was constructed to assess the in vivo effects of reducing Survivin expression. RESULTS Herein, we established a synergistic control platform that coordinated photoactivatable split-Cas9 targeted gene editing and light-induced protein degradation, on which the Survivin gene in the nucleus was controllably edited by blue light irradiation (named paCas9-Survivin) and simultaneously the Survivin protein in the cytoplasm was degraded precisely by a nanobody-mediated target (named paProtacL-Survivin). Meanwhile, in vitro experiments demonstrated that reducing Survivin expression could effectively promote apoptosis and decrease the proliferation and migration of bladder cancerous cells. Furthermore, the CDX model was constructed using UMUC-3 cell lines, results from animal studies indicated that both the paCas9-Survivin system and paProtacL-Survivin significantly inhibited tumour growth, with higher inhibition rates when combined. CONCLUSIONS In short, the coordinated regulatory strategies and combinable technology platforms offer clear advantages in controllability and targeting, as well as an excellent reference value and universal applicability in controlling the fate of cancer cells through multi-level regulation of key intracellular factors.
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Affiliation(s)
- Changping Deng
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiP. R. China
| | - Shihui Li
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiP. R. China
| | - Yuping Liu
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Wen Bao
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Chengnan Xu
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Wenyun Zheng
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Meiyan Wang
- Synthetic Biology and Biomedical Engineering LaboratoryBiomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory BiologyInstitute of BiomedicalSciences and School of Life SciencesEast China Normal UniversityShanghaiP. R. China
| | - Xingyuan Ma
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiP. R. China
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12
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Wang H, Zhou R, Xu F, Yang K, Zheng L, Zhao P, Shi G, Dai L, Xu C, Yu L, Li Z, Wang J, Wang J. Beyond canonical PROTAC: biological targeted protein degradation (bioTPD). Biomater Res 2023; 27:72. [PMID: 37480049 PMCID: PMC10362593 DOI: 10.1186/s40824-023-00385-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/21/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic strategy with the potential to modulate disease-associated proteins that have previously been considered undruggable, by employing the host destruction machinery. The exploration and discovery of cellular degradation pathways, including but not limited to proteasomes and lysosome pathways as well as their degraders, is an area of active research. Since the concept of proteolysis-targeting chimeras (PROTACs) was introduced in 2001, the paradigm of TPD has been greatly expanded and moved from academia to industry for clinical translation, with small-molecule TPD being particularly represented. As an indispensable part of TPD, biological TPD (bioTPD) technologies including peptide-, fusion protein-, antibody-, nucleic acid-based bioTPD and others have also emerged and undergone significant advancement in recent years, demonstrating unique and promising activities beyond those of conventional small-molecule TPD. In this review, we provide an overview of recent advances in bioTPD technologies, summarize their compositional features and potential applications, and briefly discuss their drawbacks. Moreover, we present some strategies to improve the delivery efficacy of bioTPD, addressing their challenges in further clinical development.
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Affiliation(s)
- Huifang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Runhua Zhou
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Fushan Xu
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Kongjun Yang
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Liuhai Zheng
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Pan Zhao
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Guangwei Shi
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Lingyun Dai
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Chengchao Xu
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Le Yu
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
| | - Zhijie Li
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jianhong Wang
- Shenzhen Mental Health Center, Shenzhen Kangning Hospital, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jigang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China.
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13
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Shi J, Hauschulte K, Mikicic I, Maharjan S, Arz V, Strauch T, Heidelberger JB, Schaefer JV, Dreier B, Plückthun A, Beli P, Ulrich HD, Wollscheid HP. Nuclear myosin VI maintains replication fork stability. Nat Commun 2023; 14:3787. [PMID: 37355687 PMCID: PMC10290672 DOI: 10.1038/s41467-023-39517-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 06/26/2023] Open
Abstract
The actin cytoskeleton is of fundamental importance for cellular structure and plasticity. However, abundance and function of filamentous actin in the nucleus are still controversial. Here we show that the actin-based molecular motor myosin VI contributes to the stabilization of stalled or reversed replication forks. In response to DNA replication stress, myosin VI associates with stalled replication intermediates and cooperates with the AAA ATPase Werner helicase interacting protein 1 (WRNIP1) in protecting these structures from DNA2-mediated nucleolytic attack. Using functionalized affinity probes to manipulate myosin VI levels in a compartment-specific manner, we provide evidence for the direct involvement of myosin VI in the nucleus and against a contribution of the abundant cytoplasmic pool during the replication stress response.
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Affiliation(s)
- Jie Shi
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Kristine Hauschulte
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Ivan Mikicic
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Srijana Maharjan
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Mainz Biomed N.V., Robert-Koch-Str. 50, D - 55129, Mainz, Germany
| | - Valerie Arz
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Tina Strauch
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Max Planck School Matter to Life, Jahnstr. 29, D - 69120, Heidelberg, Germany
| | - Jonas V Schaefer
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Birgit Dreier
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Andreas Plückthun
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Petra Beli
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 15, D - 55128, Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
| | - Hans-Peter Wollscheid
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
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14
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Li Z, Huang X, Li M, Chen YE, Wang Z, Liu L. A ubiquitination-mediated degradation system to target 14-3-3-binding phosphoproteins. Heliyon 2023; 9:e16318. [PMID: 37251884 PMCID: PMC10213371 DOI: 10.1016/j.heliyon.2023.e16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
The phosphorylation of 14-3-3 binding motif is involved in many cellular processes. A strategy that enables targeted degradation of 14-3-3-binding phosphoproteins (14-3-3-BPPs) for studying their functions is highly desirable for basic research. Here, we report a phosphorylation-induced, ubiquitin-proteasome-system-mediated targeted protein degradation (TPD) strategy that allows specific degradation of 14-3-3-BPPs. Specifically, by ligating a modified von Hippel-Lindau E3-ligase with an engineered 14-3-3 bait, we generated a protein chimera referred to as Targeted Degradation of 14-3-3-binding PhosphoProtein (TDPP). TDPP can serve as a universal degrader for 14-3-3-BPPs based on the specific recognition of the phosphorylation in 14-3-3 binding motifs. TDPP shows high efficiency and specificity to a difopein-EGFP reporter, general and specific 14-3-3-BPPs. TDPP can also be applied for the validation of 14-3-3-BPPs. These results strongly support TDPP as a powerful tool for 14-3-3 related research.
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Affiliation(s)
- Zhaokai Li
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Emergency Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xiaoqiang Huang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mohan Li
- Department of Geriatrics, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing 100730, China
| | - Y. Eugene Chen
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhong Wang
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liu Liu
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Jaffray EG, Tatham MH, Mojsa B, Liczmanska M, Rojas-Fernandez A, Yin Y, Ball G, Hay RT. The p97/VCP segregase is essential for arsenic-induced degradation of PML and PML-RARA. J Cell Biol 2023; 222:e202201027. [PMID: 36880596 PMCID: PMC10005898 DOI: 10.1083/jcb.202201027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 10/27/2022] [Accepted: 01/04/2023] [Indexed: 03/04/2023] Open
Abstract
Acute Promyelocytic Leukemia is caused by expression of the oncogenic Promyelocytic Leukemia (PML)-Retinoic Acid Receptor Alpha (RARA) fusion protein. Therapy with arsenic trioxide results in degradation of PML-RARA and PML and cures the disease. Modification of PML and PML-RARA with SUMO and ubiquitin precedes ubiquitin-mediated proteolysis. To identify additional components of this pathway, we performed proteomics on PML bodies. This revealed that association of p97/VCP segregase with PML bodies is increased after arsenic treatment. Pharmacological inhibition of p97 altered the number, morphology, and size of PML bodies, accumulated SUMO and ubiquitin modified PML and blocked arsenic-induced degradation of PML-RARA and PML. p97 localized to PML bodies in response to arsenic, and siRNA-mediated depletion showed that p97 cofactors UFD1 and NPLOC4 were critical for PML degradation. Thus, the UFD1-NPLOC4-p97 segregase complex is required to extract poly-ubiquitinated, poly-SUMOylated PML from PML bodies, prior to degradation by the proteasome.
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Affiliation(s)
- Ellis G. Jaffray
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael H. Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Barbara Mojsa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Magda Liczmanska
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alejandro Rojas-Fernandez
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Yili Yin
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Graeme Ball
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ronald T. Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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16
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Yong Joon Kim J, Sang Z, Xiang Y, Shen Z, Shi Y. Nanobodies: Robust miniprotein binders in biomedicine. Adv Drug Deliv Rev 2023; 195:114726. [PMID: 36754285 DOI: 10.1016/j.addr.2023.114726] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 12/30/2022] [Accepted: 02/02/2023] [Indexed: 02/10/2023]
Abstract
Variable domains of heavy chain-only antibodies (VHH), also known as nanobodies (Nbs), are monomeric antigen-binding domains derived from the camelid heavy chain-only antibodies. Nbs are characterized by small size, high target selectivity, and marked solubility and stability, which collectively facilitate high-quality drug development. In addition, Nbs are readily expressed from various expression systems, including E. coli and yeast cells. For these reasons, Nbs have emerged as preferred antibody fragments for protein engineering, disease diagnosis, and treatment. To date, two Nb-based therapies have been approved by the U.S. Food and Drug Administration (FDA). Numerous candidates spanning a wide spectrum of diseases such as cancer, immune disorders, infectious diseases, and neurodegenerative disorders are under preclinical and clinical investigation. Here, we discuss the structural features of Nbs that allow for specific, versatile, and strong target binding. We also summarize emerging technologies for identification, structural analysis, and humanization of Nbs. Our main focus is to review recent advances in using Nbs as a modular scaffold to facilitate the engineering of multivalent polymers for cutting-edge applications. Finally, we discuss remaining challenges for Nb development and envision new opportunities in Nb-based research.
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Affiliation(s)
- Jeffrey Yong Joon Kim
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA; Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhe Sang
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA
| | - Yufei Xiang
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA
| | - Zhuolun Shen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi Shi
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA.
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17
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Miao H, Liu C, Ouyang H, Zhang P, Liu Y, Zhang C, Deng C, Fu Y, Niu J, Zheng W, You F, Yang Y, Ma X. A nanobody-based molecular toolkit for ubiquitin-proteasome system explores the main role of survivin subcellular localization. Front Bioeng Biotechnol 2023; 10:952237. [PMID: 36743654 PMCID: PMC9895104 DOI: 10.3389/fbioe.2022.952237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 12/14/2022] [Indexed: 01/22/2023] Open
Abstract
Targeted protein degradation is a powerful tool for determining the function of specific proteins nowadays. Survivin is the smallest member of the inhibitor of the apoptosis protein (IAP) family. It exists in the cytoplasm and nucleus of cells, but the exact function of survivin in different subcellular locations retained unclear updates due to the lack of effective and simple technical means. In this study, we created a novel nanoantibody-based molecular toolkit, namely, the ubiquitin-proteasome system (Nb4A-Fc-T2A-TRIM21), that can target to degrade survivin localized in cytoplasmic and cell nuclear by ubiquitinating, and by which to verify the potential roles of survivin subcellular localization. Also, the results showed that the cytoplasmic survivin mainly plays an anti-apoptotic function by directly or indirectly inhibiting the caspase pathway, and the nuclear survivin mainly promotes cell proliferation and participates in the regulation of the cell cycle. In addition, the Nb4A-Fc-T2A-TRIM21 system can degrade the endogenous survivin protein in a large amount by the ubiquitin-proteasome pathway, and the system can provide theoretical support for ubiquitination degradation targeting other endogenous proteins.
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Affiliation(s)
- Hui Miao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chang Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao Ouyang
- Department of Hepatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Peiwen Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yuping Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Chen Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Changping Deng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yunhui Fu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jinping Niu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wenyun Zheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China,*Correspondence: Xingyuan Ma, ; Yi Yang, ; Wenyun Zheng,
| | - Fang You
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Yi Yang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore,*Correspondence: Xingyuan Ma, ; Yi Yang, ; Wenyun Zheng,
| | - Xingyuan Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China,*Correspondence: Xingyuan Ma, ; Yi Yang, ; Wenyun Zheng,
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18
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Yin M, Izadi M, Tenglin K, Viennet T, Zhai L, Zheng G, Arthanari H, Dassama LMK, Orkin SH. Evolution of nanobodies specific for BCL11A. Proc Natl Acad Sci U S A 2023; 120:e2218959120. [PMID: 36626555 PMCID: PMC9933118 DOI: 10.1073/pnas.2218959120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Transcription factors (TFs) control numerous genes that are directly relevant to many human disorders. However, developing specific reagents targeting TFs within intact cells is challenging due to the presence of highly disordered regions within these proteins. Intracellular antibodies offer opportunities to probe protein function and validate therapeutic targets. Here, we describe the optimization of nanobodies specific for BCL11A, a validated target for the treatment of hemoglobin disorders. We obtained first-generation nanobodies directed to a region of BCL11A comprising zinc fingers 4 to 6 (ZF456) from a synthetic yeast surface display library, and employed error-prone mutagenesis, structural determination, and molecular modeling to enhance binding affinity. Engineered nanobodies recognized ZF6 and mediated targeted protein degradation (TPD) of BCL11A protein in erythroid cells, leading to the anticipated reactivation of fetal hemoglobin (HbF) expression. Evolved nanobodies distinguished BCL11A from its close paralog BCL11B, which shares an identical DNA-binding specificity. Given the ease of manipulation of nanobodies and their exquisite specificity, nanobody-mediated TPD of TFs should be suitable for dissecting regulatory relationships of TFs and gene targets and validating therapeutic potential of proteins of interest.
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Affiliation(s)
- Maolu Yin
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Manizheh Izadi
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Karin Tenglin
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Thibault Viennet
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, MA02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, MA02215
| | - Liting Zhai
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Ge Zheng
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, MA02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, MA02215
| | - Laura M. K. Dassama
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Stuart H. Orkin
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
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19
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Shen F, Zheng G, Setegne M, Tenglin K, Izadi M, Xie H, Zhai L, Orkin SH, Dassama LMK. A Cell-Permeant Nanobody-Based Degrader That Induces Fetal Hemoglobin. ACS Cent Sci 2022; 8:1695-1703. [PMID: 36589886 PMCID: PMC9801508 DOI: 10.1021/acscentsci.2c00998] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Indexed: 06/13/2023]
Abstract
Proximity-based strategies to degrade proteins have enormous therapeutic potential in medicine, but the technologies are limited to proteins for which small molecule ligands exist. The identification of such ligands for therapeutically relevant but "undruggable" proteins remains challenging. Herein, we employed yeast surface display of synthetic nanobodies to identify a protein ligand selective for BCL11A, a critical repressor of fetal globin gene transcription. Fusion of the nanobody to a cell-permeant miniature protein and an E3 adaptor creates a degrader that depletes cellular BCL11A in differentiated primary erythroid precursor cells, thereby inducing the expression of fetal hemoglobin, a modifier of clinical severity of sickle cell disease and β-thalassemia. Our strategy provides a means of fetal hemoglobin induction through reversible, temporal modulation of BCL11A. Additionally, it establishes a new paradigm for the targeted degradation of previously intractable proteins.
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Affiliation(s)
- Fangfang Shen
- Department
of Chemistry and Sarafan ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Ge Zheng
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mekedlawit Setegne
- Department
of Chemistry and Sarafan ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Karin Tenglin
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Manizheh Izadi
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
| | - Henry Xie
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Liting Zhai
- Department
of Chemistry and Sarafan ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Stuart H. Orkin
- Dana
Farber Boston Children’s Cancer and Blood Disorders Center
and Howard Hughes Medical Institute, Boston, Massachusetts 02215, United States
- Department
of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura M. K. Dassama
- Department
of Chemistry and Sarafan ChEM-H, Stanford
University, Stanford, California 94305, United States
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20
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VanDyke D, Taylor JD, Kaeo KJ, Hunt J, Spangler JB. Biologics-based degraders - an expanding toolkit for targeted-protein degradation. Curr Opin Biotechnol 2022; 78:102807. [PMID: 36179405 PMCID: PMC9742328 DOI: 10.1016/j.copbio.2022.102807] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/14/2022]
Abstract
Targeted protein degradation (TPD) is a broadly useful proteome editing tool for biological research and therapeutic development. TPD offers several advantages over functional inhibition alone, including the ability to target previously undruggable proteins and the substantial and sustained knockout of protein activity. A variety of small molecule approaches hijack endogenous protein degradation machinery, but are limited to proteins with a cytosolic domain and suitable binding pocket. Recently, biologics-based methods have expanded the TPD toolbox by allowing access to extracellular and surface-exposed proteins and increasing target specificity. Here, we summarize recent advances in the use of biologics to deplete proteins through either the ubiquitin-proteasome system or the lysosomal degradation pathway, and discuss routes to their effective delivery as potential therapeutic interventions.
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Affiliation(s)
- Derek VanDyke
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Kyle J Kaeo
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James Hunt
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | - Jamie B Spangler
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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21
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Markússon S, Hallin EI, Bustad HJ, Raasakka A, Xu J, Muruganandam G, Loris R, Martinez A, Bramham CR, Kursula P. High-affinity anti-Arc nanobodies provide tools for structural and functional studies. PLoS One 2022; 17:e0269281. [PMID: 35671319 PMCID: PMC9173642 DOI: 10.1371/journal.pone.0269281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022] Open
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is a multidomain protein of retroviral origin with a vital role in the regulation of synaptic plasticity and memory formation in mammals. However, the mechanistic and structural basis of Arc function is poorly understood. Arc has an N-terminal domain (NTD) involved in membrane binding and a C-terminal domain (CTD) that binds postsynaptic protein ligands. In addition, the NTD and CTD both function in Arc oligomerisation, including assembly of retrovirus-like capsids involved in intercellular signalling. To obtain new tools for studies on Arc structure and function, we produced and characterised six high-affinity anti-Arc nanobodies (Nb). The CTD of rat and human Arc were both crystallised in ternary complexes with two Nbs. One Nb bound deep into the stargazin-binding pocket of Arc CTD and suggested competitive binding with Arc ligand peptides. The crystallisation of the human Arc CTD in two different conformations, accompanied by SAXS data and molecular dynamics simulations, paints a dynamic picture of the mammalian Arc CTD. The collapsed conformation closely resembles Drosophila Arc in capsids, suggesting that we have trapped a capsid-like conformation of the human Arc CTD. Our data obtained with the help of anti-Arc Nbs suggest that structural dynamics of the CTD and dimerisation of the NTD may promote the formation of capsids. Taken together, the recombinant high-affinity anti-Arc Nbs are versatile tools that can be further developed for studying mammalian Arc structure and function, as well as mechanisms of Arc capsid formation, both in vitro and in vivo. For example, the Nbs could serve as a genetically encoded tools for inhibition of endogenous Arc interactions in the study of neuronal function and plasticity.
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Affiliation(s)
| | - Erik I. Hallin
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ju Xu
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- * E-mail:
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22
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Casalino L, Talotta F, Cimmino A, Verde P. The Fra-1/AP-1 Oncoprotein: From the "Undruggable" Transcription Factor to Therapeutic Targeting. Cancers (Basel) 2022; 14:cancers14061480. [PMID: 35326630 PMCID: PMC8946526 DOI: 10.3390/cancers14061480] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
The genetic and epigenetic changes affecting transcription factors, coactivators, and chromatin modifiers are key determinants of the hallmarks of cancer. The acquired dependence on oncogenic transcriptional regulators, representing a major determinant of cancer cell vulnerability, points to transcription factors as ideal therapeutic targets. However, given the unavailability of catalytic activities or binding pockets for small-molecule inhibitors, transcription factors are generally regarded as undruggable proteins. Among components of the AP-1 complex, the FOS-family transcription factor Fra-1, encoded by FOSL1, has emerged as a prominent therapeutic target. Fra-1 is overexpressed in most solid tumors, in response to the BRAF-MAPK, Wnt-beta-catenin, Hippo-YAP, IL-6-Stat3, and other major oncogenic pathways. In vitro functional analyses, validated in onco-mouse models and corroborated by prognostic correlations, show that Fra-1-containing dimers control tumor growth and disease progression. Fra-1 participates in key mechanisms of cancer cell invasion, Epithelial-to-Mesenchymal Transition, and metastatic spreading, by driving the expression of EMT-inducing transcription factors, cytokines, and microRNAs. Here we survey various strategies aimed at inhibiting tumor growth, metastatic dissemination, and drug resistance by interfering with Fra-1 expression, stability, and transcriptional activity. We summarize several tools aimed at the design and tumor-specific delivery of Fra-1/AP-1-specific drugs. Along with RNA-based therapeutics targeting the FOSL1 gene, its mRNA, or cognate regulatory circRNAs, we will examine the exploitation of blocking peptides, small molecule inhibitors, and innovative Fra-1 protein degraders. We also consider the possible caveats concerning Fra-1 inhibition in specific therapeutic contexts. Finally, we discuss a recent suicide gene therapy-based approach, aimed at selectively killing the Fra-1-overexpressing neoplastic cells.
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Affiliation(s)
- Laura Casalino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale dele Ricerche (CNR), 80131 Naples, Italy;
- Correspondence: (L.C.); (P.V.)
| | | | - Amelia Cimmino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale dele Ricerche (CNR), 80131 Naples, Italy;
| | - Pasquale Verde
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale dele Ricerche (CNR), 80131 Naples, Italy;
- Correspondence: (L.C.); (P.V.)
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23
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Zhong Y, Chi F, Wu H, Liu Y, Xie Z, Huang W, Shi W, Qian H. Emerging targeted protein degradation tools for innovative drug discovery: From classical PROTACs to the novel and beyond. Eur J Med Chem 2022; 231:114142. [DOI: 10.1016/j.ejmech.2022.114142] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/22/2022]
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24
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Congdon EE, Jiang Y, Sigurdsson EM. Targeting tau only extracellularly is likely to be less efficacious than targeting it both intra- and extracellularly. Semin Cell Dev Biol 2021; 126:125-137. [PMID: 34896021 DOI: 10.1016/j.semcdb.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022]
Abstract
Aggregation of the tau protein is thought to be responsible for the neurodegeneration and subsequent functional impairments in diseases that are collectively named tauopathies. Alzheimer's disease is the most common tauopathy, but the group consists of over 20 different diseases, many of which have tau pathology as their primary feature. The development of tau therapies has mainly focused on preventing the formation of and/or clearing these aggregates. Of these, immunotherapies that aim to either elicit endogenous tau antibodies or deliver exogenous ones are the most common approach in clinical trials. While their mechanism of action can involve several pathways, both extra- and intracellular, pharmaceutical companies have primarily focused on antibody-mediated clearance of extracellular tau. As we have pointed out over the years, this is rather surprising because it is well known that most of pathological tau protein is found intracellularly. It has been repeatedly shown by several groups over the past decades that antibodies can enter neurons and that their cellular uptake can be enhanced by various means, particularly by altering their charge. Here, we will briefly describe the potential extra- and intracellular mechanisms involved in antibody-mediated clearance of tau pathology, discuss these in the context of recent failures of some of the tau antibody trials, and finally provide a brief overview of how the intracellular efficacy of tau antibodies can potentially be further improved by certain modifications that aim to enhance tau clearance via specific intracellular degradation pathways.
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Affiliation(s)
- Erin E Congdon
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, United States.
| | - Yixiang Jiang
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, United States
| | - Einar M Sigurdsson
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, United States; Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, United States.
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25
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Abstract
The identification of diagnostic and therapeutic targets requires a comprehensive understanding of cellular processes, for which advanced technologies in biomedical research are needed. The emergence of nanobodies (Nbs) derived from antibody fragments of camelid heavy chain-only antibodies as intracellular research tools offers new possibilities to study and modulate target antigens in living cells. Here we summarize this rapidly changing field, beginning with a brief introduction of Nbs, followed by an overview of how target-specific Nbs can be generated, and introduce the selection of intrabodies as research tools. Intrabodies, by definition, are intracellular functional Nbs that target ectopic or endogenous intracellular antigens within living cells. Such binders can be applied in various formats, e.g. as chromobodies for live cell microscopy or as biosensors to decipher complex intracellular signaling pathways. In addition, protein knockouts can be achieved by target-specific Nbs, while modulating Nbs have the potential as future therapeutics. The development of fine-tunable and switchable Nb-based systems that simultaneously provide spatial and temporal control has recently taken the application of these binders to the next level.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany.
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26
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Chen G, Kong Y, Li Y, Huang A, Wang C, Zhou S, Yang Z, Wu Y, Ren J, Ying T. A Promising Intracellular Protein-Degradation Strategy: TRIMbody-Away Technique Based on Nanobody Fragment. Biomolecules 2021; 11:biom11101512. [PMID: 34680146 PMCID: PMC8533776 DOI: 10.3390/biom11101512] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
Most recently, a technology termed TRIM-Away has allowed acute and rapid destruction of endogenous target proteins in cultured cells using specific antibodies and endogenous/exogenous tripartite motif 21 (TRIM21). However, the relatively large size of the full-size mAbs (150 kDa) results in correspondingly low tissue penetration and inaccessibility of some sterically hindered epitopes, which limits the target protein degradation. In addition, exogenous introduction of TRIM21 may cause side effects for treated cells. To tackle these limitations, we sought to replace full-size mAbs with the smaller format of antibodies, a nanobody (VHH, 15 kDa), and construct a new type of fusion protein named TRIMbody by fusing the nanobody and RBCC motif of TRIM21. Next, we introduced enhanced green fluorescent protein (EGFP) as a model substrate and generated αEGFP TRIMbody using a bispecific anti-EGFP (αEGFP) nanobody. Remarkably, inducible expression of αEGFP TRIMbody could specifically degrade intracellular EGFP in HEK293T cells in a time-dependent manner. By treating cells with inhibitors, we found that intracellular EGFP degradation by αEGFP TRIMbody relies on both ubiquitin-proteasome and autophagy-lysosome pathways. Taken together, these results suggested that TRIMbody-Away technology could be utilized to specifically degrade intracellular protein and could expand the potential applications of degrader technologies.
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Affiliation(s)
- Gang Chen
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Yu Kong
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - You Li
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Ailing Huang
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Chunyu Wang
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Shanshan Zhou
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Zhenlin Yang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China;
| | - Yanling Wu
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
- Correspondence: (Y.W.); (J.R.); (T.Y.); Tel.: +86-021-54237761 (Y.W.); +86-021-54920668 (J.R.); +86-021-54237761 (T.Y.)
| | - Jianke Ren
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (Y.W.); (J.R.); (T.Y.); Tel.: +86-021-54237761 (Y.W.); +86-021-54920668 (J.R.); +86-021-54237761 (T.Y.)
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
- Correspondence: (Y.W.); (J.R.); (T.Y.); Tel.: +86-021-54237761 (Y.W.); +86-021-54920668 (J.R.); +86-021-54237761 (T.Y.)
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27
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Benn JA, Mukadam AS, McEwan WA. Targeted protein degradation using intracellular antibodies and its application to neurodegenerative disease. Semin Cell Dev Biol 2021; 126:138-149. [PMID: 34654628 DOI: 10.1016/j.semcdb.2021.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 01/10/2023]
Abstract
Antibodies mediate the majority of their effects in the extracellular domain, or in intracellular compartments isolated from the cytosol. Under a growing list of circumstances, however, antibodies are found to gain access to the cytoplasm. Cytosolic immune complexes are bound by the atypical antibody receptor TRIM21, which mediates the rapid degradation of the immune complexes at the proteasome. These discoveries have informed the development of TRIM-Away, a technique to selectively deplete proteins using delivery of antibodies into cells. A range of related approaches that elicit selective protein degradation using intracellular constructs linking antibody fragments to degradative effector functions have also been developed. These methods hold promise for inducing the degradation of proteins as both research tools and as a novel therapeutic approach. Protein aggregates are a pathophysiological feature of neurodegenerative diseases and are considered to have a causal role in pathology. Immunotherapy is emerging as a promising route towards their selective targeting, and a role of antibodies in the cytosol has been demonstrated in cell-based assays. This review will explore the mechanisms by which therapeutic antibodies engage and eliminate intracellularly aggregated proteins. We will discuss how future developments in intracellular antibody technology may enhance the therapeutic potential of such antibody-derived therapies.
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Affiliation(s)
- Jonathan A Benn
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Cambridge, UK
| | - Aamir S Mukadam
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Cambridge, UK
| | - William A McEwan
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Cambridge, UK.
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28
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Abstract
Dramatic nuclear reorganization occurs during early development to convert terminally differentiated gametes to a totipotent zygote, which then gives rise to an embryo. Aberrant epigenome resetting severely impairs embryo development and even leads to lethality. How the epigenomes are inherited, reprogrammed, and reestablished in this critical developmental period has gradually been unveiled through the rapid development of technologies including ultrasensitive chromatin analysis methods. In this review, we summarize the latest findings on epigenetic reprogramming in gametogenesis and embryogenesis, and how it contributes to gamete maturation and parental-to-zygotic transition. Finally, we highlight the key questions that remain to be answered to fully understand chromatin regulation and nuclear reprogramming in early development.
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Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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29
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Henneberg LT, Schulman BA. Decoding the messaging of the ubiquitin system using chemical and protein probes. Cell Chem Biol 2021; 28:889-902. [PMID: 33831368 PMCID: PMC7611516 DOI: 10.1016/j.chembiol.2021.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 12/29/2022]
Abstract
Post-translational modification of proteins by ubiquitin is required for nearly all aspects of eukaryotic cell function. The numerous targets of ubiquitylation, and variety of ubiquitin modifications, are often likened to a code, where the ultimate messages are diverse responses to target ubiquitylation. E1, E2, and E3 multiprotein enzymatic assemblies modify specific targets and thus function as messengers. Recent advances in chemical and protein tools have revolutionized our ability to explore the ubiquitin system, through enabling new high-throughput screening methods, matching ubiquitylation enzymes with their cellular targets, revealing intricate allosteric mechanisms regulating ubiquitylating enzymes, facilitating structural revelation of transient assemblies determined by multivalent interactions, and providing new paradigms for inhibiting and redirecting ubiquitylation in vivo as new therapeutics. Here we discuss the development of methods that control, disrupt, and extract the flow of information across the ubiquitin system and have enabled elucidation of the underlying molecular and cellular biology.
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Affiliation(s)
- Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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30
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Bailly AP, Xirodimas DP. The HSP70 chaperone as sensor of the NEDD8 cycle upon DNA damage. Biochem Soc Trans 2021; 49:1075-83. [PMID: 34156462 DOI: 10.1042/BST20200381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Molecular chaperones are essential components of the protein quality control system and maintenance of homeostasis. Heat Shock Protein 70 (HSP70), a highly evolutionarily conserved family of chaperones is a key regulator of protein folding, oligomerisation and prevents the aggregation of misfolded proteins. HSP70 chaperone function depends on the so-called 'HSP70-cycle', where HSP70 interacts with and is released from substrates via ATP hydrolysis and the assistance of HSP70 co-factors/co-chaperones, which also provide substrate specificity. The identification of regulatory modules for HSP70 allows the elucidation of HSP70 specificity and target selectivity. Here, we discuss how the HSP70 cycle is functionally linked with the cycle of the Ubiquitin-like molecule NEDD8. Using as an example the DNA damage response, we present a model where HSP70 acts as a sensor of the NEDD8 cycle. The NEDD8 cycle acts as a regulatory module of HSP70 activity, where conversion of poly-NEDD8 chains into mono-NEDD8 upon DNA damage activates HSP70, facilitating the formation of the apoptosome and apoptosis execution.
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31
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Alabi SB, Crews CM. Major advances in targeted protein degradation: PROTACs, LYTACs, and MADTACs. J Biol Chem 2021; 296:100647. [PMID: 33839157 PMCID: PMC8131913 DOI: 10.1016/j.jbc.2021.100647] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Of late, targeted protein degradation (TPD) has surfaced as a novel and innovative chemical tool and therapeutic modality. By co-opting protein degradation pathways, TPD facilitates complete removal of the protein molecules from within or outside the cell. While the pioneering Proteolysis-Targeting Chimera (PROTAC) technology and molecular glues hijack the ubiquitin-proteasome system, newer modalities co-opt autophagy or the endo-lysosomal pathway. Using this mechanism, TPD is posited to largely expand the druggable space far beyond small-molecule inhibitors. In this review, we discuss the major advances in TPD, highlight our current understanding, and explore outstanding questions in the field.
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Affiliation(s)
- Shanique B Alabi
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA
| | - Craig M Crews
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA; Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA; Department of Chemistry, Yale University, New Haven, Connecticut, USA.
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32
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Coll-Martínez B, Delgado A, Crosas B. The Potential of Proteolytic Chimeras as Pharmacological Tools and Therapeutic Agents. Molecules 2020; 25:E5956. [PMID: 33339292 DOI: 10.3390/molecules25245956] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
The induction of protein degradation in a highly selective and efficient way by means of druggable molecules is known as targeted protein degradation (TPD). TPD emerged in the literature as a revolutionary idea: a heterobifunctional chimera with the capacity of creating an interaction between a protein of interest (POI) and a E3 ubiquitin ligase will induce a process of events in the POI, including ubiquitination, targeting to the proteasome, proteolysis and functional silencing, acting as a sort of degradative knockdown. With this programmed protein degradation, toxic and disease-causing proteins could be depleted from cells with potentially effective low drug doses. The proof-of-principle validation of this hypothesis in many studies has made the TPD strategy become a new attractive paradigm for the development of therapies for the treatment of multiple unmet diseases. Indeed, since the initial protacs (Proteolysis targeting chimeras) were posited in the 2000s, the TPD field has expanded extraordinarily, developing innovative chemistry and exploiting multiple degradation approaches. In this article, we review the breakthroughs and recent novel concepts in this highly active discipline.
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