1
|
Mondal M, Cao F, Conole D, Auner HW, Tate EW. Discovery of potent and selective activity-based probes (ABPs) for the deubiquitinating enzyme USP30. RSC Chem Biol 2024; 5:439-446. [PMID: 38725909 PMCID: PMC11078216 DOI: 10.1039/d4cb00029c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/07/2024] [Indexed: 05/12/2024] Open
Abstract
Ubiquitin-specific protease 30 (USP30) is a deubiquitinating enzyme (DUB) localized at the mitochondrial outer membrane and involved in PINK1/Parkin-mediated mitophagy, pexophagy, BAX/BAK-dependent apoptosis, and IKKβ-USP30-ACLY-regulated lipogenesis/tumorigenesis. A USP30 inhibitor, MTX652, has recently entered clinical trials as a potential treatment for mitochondrial dysfunction. Small molecule activity-based probes (ABPs) for DUBs have recently emerged as powerful tools for in-cell inhibitor screening and DUB activity analysis, and here, we report the first small molecule ABPs (IMP-2587 and IMP-2586) which can profile USP30 activity in cells. Target engagement studies demonstrate that IMP-2587 and IMP-2586 engage active USP30 at nanomolar concentration after only 10 min incubation time in intact cells, dependent on the presence of the USP30 catalytic cysteine. Interestingly, proteomics analyses revealed that DESI1 and DESI2, small ubiquitin-related modifier (SUMO) proteases, can also be engaged by these probes, further suggesting a novel approach to develop DESI ABPs.
Collapse
Affiliation(s)
- Milon Mondal
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Fangyuan Cao
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Daniel Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Holger W Auner
- Department of Immunology and Inflammation, Imperial College London Du Cane Road London W12 0NN UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| |
Collapse
|
2
|
van Overbeek NK, Aguirre T, van der Heden van Noort GJ, Blagoev B, Vertegaal ACO. Deciphering non-canonical ubiquitin signaling: biology and methodology. Front Mol Biosci 2024; 10:1332872. [PMID: 38414868 PMCID: PMC10897730 DOI: 10.3389/fmolb.2023.1332872] [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: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 02/29/2024] Open
Abstract
Ubiquitination is a dynamic post-translational modification that regulates virtually all cellular processes by modulating function, localization, interactions and turnover of thousands of substrates. Canonical ubiquitination involves the enzymatic cascade of E1, E2 and E3 enzymes that conjugate ubiquitin to lysine residues giving rise to monomeric ubiquitination and polymeric ubiquitination. Emerging research has established expansion of the ubiquitin code by non-canonical ubiquitination of N-termini and cysteine, serine and threonine residues. Generic methods for identifying ubiquitin substrates using mass spectrometry based proteomics often overlook non-canonical ubiquitinated substrates, suggesting that numerous undiscovered substrates of this modification exist. Moreover, there is a knowledge gap between in vitro studies and comprehensive understanding of the functional consequence of non-canonical ubiquitination in vivo. Here, we discuss the current knowledge about non-lysine ubiquitination, strategies to map the ubiquitinome and their applicability for studying non-canonical ubiquitination substrates and sites. Furthermore, we elucidate the available chemical biology toolbox and elaborate on missing links required to further unravel this less explored subsection of the ubiquitin system.
Collapse
Affiliation(s)
- Nila K. van Overbeek
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Tim Aguirre
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|
3
|
Conole D, Cao F, Am Ende CW, Xue L, Kantesaria S, Kang D, Jin J, Owen D, Lohr L, Schenone M, Majmudar JD, Tate EW. Discovery of a Potent Deubiquitinase (DUB) Small-Molecule Activity-Based Probe Enables Broad Spectrum DUB Activity Profiling in Living Cells. Angew Chem Int Ed Engl 2023; 62:e202311190. [PMID: 37779326 DOI: 10.1002/anie.202311190] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Deubiquitinases (DUBs) are a family of >100 proteases that hydrolyze isopeptide bonds linking ubiquitin to protein substrates, often leading to reduced substrate degradation through the ubiquitin proteasome system. Deregulation of DUB activity has been implicated in many diseases, including cancer, neurodegeneration and auto-inflammation, and several have been recognized as attractive targets for therapeutic intervention. Ubiquitin-derived covalent activity-based probes (ABPs) provide a powerful tool for DUB activity profiling, but their large recognition element impedes cellular permeability and presents an unmet need for small molecule ABPs which can account for regulation of DUB activity in intact cells or organisms. Here, through comprehensive chemoproteomic warhead profiling, we identify cyanopyrrolidine (CNPy) probe IMP-2373 (12) as a small molecule pan-DUB ABP to monitor DUB activity in physiologically relevant live cells. Through proteomics and targeted assays, we demonstrate that IMP-2373 quantitatively engages more than 35 DUBs across a range of non-toxic concentrations in diverse cell lines. We further demonstrate its application to quantification of changes in intracellular DUB activity during pharmacological inhibition and during MYC deregulation in a model of B cell lymphoma. IMP-2373 thus offers a complementary tool to ubiquitin ABPs to monitor dynamic DUB activity in the context of disease-relevant phenotypes.
Collapse
Affiliation(s)
- Daniel Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London, W12 0BZ, United Kingdom
- Present address: Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand
| | - Fangyuan Cao
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London, W12 0BZ, United Kingdom
| | - Christopher W Am Ende
- Pfizer Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, Connecticut, 06340, USA
| | - Liang Xue
- Pfizer Worldwide Research and Development, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts, 2139, USA
| | - Sheila Kantesaria
- Pfizer Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, Connecticut, 06340, USA
| | - Dahye Kang
- Pfizer Worldwide Research and Development, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts, 2139, USA
| | - Jun Jin
- BioDuro, No.233 North FuTe Rd., WaiGaoQiao Free Trade Zone, Shanghai, 200131, P.R. China
| | - Dafydd Owen
- Pfizer Worldwide Research and Development, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts, 2139, USA
| | - Linda Lohr
- Pfizer Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, Connecticut, 06340, USA
| | - Monica Schenone
- Pfizer Worldwide Research and Development, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts, 2139, USA
| | - Jaimeen D Majmudar
- Pfizer Worldwide Research and Development, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts, 2139, USA
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London, W12 0BZ, United Kingdom
| |
Collapse
|
4
|
Zmudzinski M, Malon O, Poręba M, Drąg M. Imaging of proteases using activity-based probes. Curr Opin Chem Biol 2023; 74:102299. [PMID: 37031620 DOI: 10.1016/j.cbpa.2023.102299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023]
Abstract
Proteases (proteolytic enzymes) are proteins that catalyze one of the most important biochemical reactions, namely the hydrolysis of the peptide bond in peptide and protein substrates. Therefore these molecular biocatalysts participate in virtually all living processes. The proper balance between intact and processed protease substrates enables to maintenance of homeostasis from a single-cell level to the whole living system. However, when the proteolytic activity is altered, this delicate balance is disturbed, which might lead to the development of a plethora of diseases. Given this, monitoring proteolytic activity is indispensable to understanding how proteases operate in disease lesions and how their altered catalytic activity might be harnessed for a better diagnosis and treatment. In this manuscript, we provide a critical review of the recent development of protease chemical probes which are small molecules that detect proteolytic activity by interacting with protease active site, individual proteases as well as complex proteolytic networks.
Collapse
Affiliation(s)
- Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wrocław, Poland
| | - Oliwia Malon
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wrocław, Poland
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wrocław, Poland.
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wrocław, Poland.
| |
Collapse
|
5
|
Rahnama A, Melvin AT. Fluorometric Characterization of DUB Activity: From Single-Enzyme Reactions to Live Intact Cells. Methods Mol Biol 2023; 2591:25-44. [PMID: 36350541 DOI: 10.1007/978-1-0716-2803-4_3] [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: 06/16/2023]
Abstract
Fluorescently tagged molecular probes capable of time- and concentration-dependent quantification of deubiquitinating enzyme (DUB) activity allow for precise characterization of both enzyme and DUB inhibitor. These probes are compatible with most plate readers allowing for rapid, facile fluorometric analysis of DUB activity. DUB activity can be measured in purified enzyme reactions, in cell lysates, or in intact cells depending upon the choice of the fluorometric probe. This chapter describes protocols and potential analysis tools to investigate DUB activity in these three scenarios.
Collapse
Affiliation(s)
- Alireza Rahnama
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA, USA.
| |
Collapse
|
6
|
Jones HBL, Heilig R, Kessler BM, Pinto-Fernández A. Activity-Based Protein Profiling (ABPP) for Cellular Deubiquitinase (DUB) and Inhibitor Profiling at Deep and High-Throughput Levels. Methods Mol Biol 2023; 2591:101-122. [PMID: 36350545 DOI: 10.1007/978-1-0716-2803-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This chapter provides detailed methodology and materials required to profile deubiquitinases (DUBs) in a cellular matrix using specific activity-based probes, with immunoblotting and mass spectrometry proteomics-based readouts. Different types of activity-based protein profiling (ABPP) for studying the potency and selectivity of DUB inhibitors are outlined here, including the standard ABPP, the deep DUBome ABPP, and the ABPP-HT (high-throughput compatible).
Collapse
Affiliation(s)
- Hannah B L Jones
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
7
|
On the Study of Deubiquitinases: Using the Right Tools for the Job. Biomolecules 2022; 12:biom12050703. [PMID: 35625630 PMCID: PMC9139131 DOI: 10.3390/biom12050703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
Deubiquitinases (DUBs) have been the subject of intense scrutiny in recent years. Many of their diverse enzymatic mechanisms are well characterized in vitro; however, our understanding of these enzymes at the cellular level lags due to the lack of quality tool reagents. DUBs play a role in seemingly every biological process and are central to many human pathologies, thus rendering them very desirable and challenging therapeutic targets. This review aims to provide researchers entering the field of ubiquitination with knowledge of the pharmacological modulators and tool molecules available to study DUBs. A focus is placed on small molecule inhibitors, ubiquitin variants (UbVs), and activity-based probes (ABPs). Leveraging these tools to uncover DUB biology at the cellular level is of particular importance and may lead to significant breakthroughs. Despite significant drug discovery efforts, only approximately 15 chemical probe-quality small molecule inhibitors have been reported, hitting just 6 of about 100 DUB targets. UbV technology is a promising approach to rapidly expand the library of known DUB inhibitors and may be used as a combinatorial platform for structure-guided drug design.
Collapse
|
8
|
Jones HBL, Heilig R, Davis S, Fischer R, Kessler BM, Pinto-Fernández A. ABPP-HT*-Deep Meets Fast for Activity-Based Profiling of Deubiquitylating Enzymes Using Advanced DIA Mass Spectrometry Methods. Int J Mol Sci 2022; 23:ijms23063263. [PMID: 35328685 PMCID: PMC8955990 DOI: 10.3390/ijms23063263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 02/01/2023] Open
Abstract
Activity-based protein profiling (ABPP) uses a combination of activity-based chemical probes with mass spectrometry (MS) to selectively characterise a particular enzyme or enzyme class. ABPP has proven invaluable for profiling enzymatic inhibitors in drug discovery. When applied to cell extracts and cells, challenging the ABP-enzyme complex formation with a small molecule can simultaneously inform on potency, selectivity, reversibility/binding affinity, permeability, and stability. ABPP can also be applied to pharmacodynamic studies to inform on cellular target engagement within specific organs when applied to in vivo models. Recently, we established separate high depth and high throughput ABPP (ABPP-HT) protocols for the profiling of deubiquitylating enzymes (DUBs). However, the combination of the two, deep and fast, in one method has been elusive. To further increase the sensitivity of the current ABPP-HT workflow, we implemented state-of-the-art data-independent acquisition (DIA) and data-dependent acquisition (DDA) MS analysis tools. Hereby, we describe an improved methodology, ABPP-HT* (enhanced high-throughput-compatible activity-based protein profiling) that in combination with DIA MS methods, allowed for the consistent profiling of 35-40 DUBs and provided a reduced number of missing values, whilst maintaining a throughput of 100 samples per day.
Collapse
Affiliation(s)
- Hannah B. L. Jones
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
| | - Simon Davis
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (B.M.K.); (A.P.-F.)
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (B.M.K.); (A.P.-F.)
| |
Collapse
|
9
|
Mondal M, Conole D, Nautiyal J, Tate EW. UCHL1 as a novel target in breast cancer: emerging insights from cell and chemical biology. Br J Cancer 2022; 126:24-33. [PMID: 34497382 PMCID: PMC8727673 DOI: 10.1038/s41416-021-01516-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/25/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022] Open
Abstract
Breast cancer has the highest incidence and death rate among cancers in women worldwide. In particular, metastatic estrogen receptor negative (ER-) breast cancer and triple-negative breast cancer (TNBC) subtypes have very limited treatment options, with low survival rates. Ubiquitin carboxyl terminal hydrolase L1 (UCHL1), a ubiquitin C-terminal hydrolase belonging to the deubiquitinase (DUB) family of enzymes, is highly expressed in these cancer types, and several key reports have revealed emerging and important roles for UCHL1 in breast cancer. However, selective and potent small-molecule UCHL1 inhibitors have been disclosed only very recently, alongside chemical biology approaches to detect regulated UHCL1 activity in cancer cells. These tools will enable novel insights into oncogenic mechanisms driven by UCHL1, and identification of substrate proteins deubiquitinated by UCHL1, with the ultimate goal of realising the potential of UCHL1 as a drug target in breast cancer.
Collapse
Affiliation(s)
- Milon Mondal
- Department of Chemistry, Imperial College London, London, UK
| | - Daniel Conole
- Department of Chemistry, Imperial College London, London, UK
| | - Jaya Nautiyal
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, London, UK.
| |
Collapse
|
10
|
McKenna SM, Fay EM, McGouran JF. Flipping the Switch: Innovations in Inducible Probes for Protein Profiling. ACS Chem Biol 2021; 16:2719-2730. [PMID: 34779621 PMCID: PMC8689647 DOI: 10.1021/acschembio.1c00572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Over the past two
decades, activity-based probes have enabled a
range of discoveries, including the characterization of new enzymes
and drug targets. However, their suitability in some labeling experiments
can be limited by nonspecific reactivity, poor membrane permeability,
or high toxicity. One method for overcoming these issues is through
the development of “inducible” activity-based probes.
These probes are added to samples in an unreactive state and require in situ transformation to their active form before labeling
can occur. In this Review, we discuss a variety of approaches to inducible
activity-based probe design, different means of probe activation,
and the advancements that have resulted from these applications. Additionally,
we highlight recent developments which may provide opportunities for
future inducible activity-based probe innovations.
Collapse
Affiliation(s)
- Sean M. McKenna
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC), Bernal Institute, Limerick V94 T9PX, Ireland
| | - Ellen M. Fay
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
| | - Joanna F. McGouran
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC), Bernal Institute, Limerick V94 T9PX, Ireland
| |
Collapse
|
11
|
Giandomenico SL, Alvarez-Castelao B, Schuman EM. Proteostatic regulation in neuronal compartments. Trends Neurosci 2021; 45:41-52. [PMID: 34489114 DOI: 10.1016/j.tins.2021.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/16/2021] [Accepted: 08/05/2021] [Indexed: 12/16/2022]
Abstract
Neurons continuously adapt to external cues and challenges, including stimulation, plasticity-inducing signals and aging. These adaptations are critical for neuronal physiology and extended survival. Proteostasis is the process by which cells adjust their protein content to achieve the specific protein repertoire necessary for cellular function. Due to their complex morphology and polarized nature, neurons possess unique proteostatic requirements. Proteostatic control in axons and dendrites must be implemented through regulation of protein synthesis and degradation in a decentralized fashion, but at the same time, it requires integration, at least in part, in the soma. Here, we discuss current understanding of neuronal proteostasis, as well as open questions and future directions requiring further exploration.
Collapse
Affiliation(s)
| | - Beatriz Alvarez-Castelao
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| |
Collapse
|
12
|
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: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [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.
Collapse
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.
| |
Collapse
|
13
|
Gui W, Davidson GA, Zhuang Z. Chemical methods for protein site-specific ubiquitination. RSC Chem Biol 2021; 2:450-467. [PMID: 34381999 PMCID: PMC8323803 DOI: 10.1039/d0cb00215a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
Ubiquitination is an important protein post-translational modification regulating many cellular processes in eukaryotes. Ubiquitination is catalyzed by a three-enzyme cascade resulting in the conjugation of the C-terminal carboxylate of ubiquitin (Ub) to the ε-amino group of a lysine residue in the acceptor protein via an isopeptide bond. In vitro enzymatic ubiquitination utilizing Ub ligases has been successfully employed to generate Ub dimers and polymers. However, limitations of the enzymatic approach exist, particularly due to the requirement of specific Ub ligase for any given target protein and the low catalytic efficiency of the Ub ligase. To achieve an in-depth understanding of the molecular mechanism of Ub signaling, new methods are needed to generate mono- and poly-ubiquitinated proteins at a specific site with defined polyubiquitin chain linkage and length. Chemical methods offer an attractive solution to the above-described challenges. In this review, we summarize the recently developed chemical methods for generating ubiquitinated proteins using synthetic and semisynthetic approaches. These new tools and approaches, as an important part of the Ub toolbox, are crucial to our understanding and exploitation of the Ub system for novel therapeutics.
Collapse
Affiliation(s)
- Weijun Gui
- Department of Chemistry and Biochemistry, University of Delaware 214A Drake Hall Newark DE 19716 USA
| | - Gregory A Davidson
- Department of Chemistry and Biochemistry, University of Delaware 214A Drake Hall Newark DE 19716 USA
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware 214A Drake Hall Newark DE 19716 USA
| |
Collapse
|
14
|
Maneiro M, De Vita E, Conole D, Kounde CS, Zhang Q, Tate EW. PROTACs, molecular glues and bifunctionals from bench to bedside: Unlocking the clinical potential of catalytic drugs. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:67-190. [PMID: 34147206 DOI: 10.1016/bs.pmch.2021.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The vast majority of currently marketed drugs rely on small molecules with an 'occupancy-driven' mechanism of action (MOA). Therefore, the efficacy of these therapeutics depends on a high degree of target engagement, which often requires high dosages and enhanced drug exposure at the target site, thus increasing the risk of off-target toxicities (Churcher, 2018 [1]). Although small molecule drugs have been successfully used as treatments for decades, tackling a variety of disease-relevant targets with a defined binding site, many relevant therapeutic targets remain challenging to drug due, for example, to lack of well-defined binding pockets or large protein-protein interaction (PPI) interfaces which resist interference (Dang et al., 2017 [2]). In the quest for alternative therapeutic approaches to address different pathologies and achieve enhanced efficacy with reduced side effects, ligand-induced targeted protein degradation (TPD) has gained the attention of many research groups both in academia and in industry in the last two decades. This therapeutic modality represents a novel paradigm compared to conventional small-molecule inhibitors. To pursue this strategy, heterobifunctional small molecule degraders, termed PROteolysis TArgeting Chimeras (PROTACs) have been devised to artificially redirect a protein of interest (POI) to the cellular protein homeostasis machinery for proteasomal degradation (Chamberlain et al., 2019 [3]). In this chapter, the development of PROTACs will first be discussed providing a historical perspective in parallel to the experimental progress made to understand this novel therapeutic modality. Furthermore, common strategies for PROTAC design, including assays and troubleshooting tips will be provided for the reader, before presenting a compendium of all PROTAC targets reported in the literature to date. Due to the recent advancement of these molecules into clinical trials, consideration of pharmacokinetics and pharmacodynamic properties will be introduced, together with the biotech landscape that has developed from the success of PROTACs. Finally, an overview of subsequent strategies for targeted protein degradation will be presented, concluding with further scientific quests triggered by the invention of PROTACs.
Collapse
Affiliation(s)
- M Maneiro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - E De Vita
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - D Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - C S Kounde
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Q Zhang
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - E W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom.
| |
Collapse
|
15
|
Gaur P, Fenteany G, Tyagi C. Mode of inhibitory binding of epigallocatechin gallate to the ubiquitin-activating enzyme Uba1 via accelerated molecular dynamics. RSC Adv 2021; 11:8264-8276. [PMID: 35423322 PMCID: PMC8695214 DOI: 10.1039/d0ra09847g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/03/2021] [Indexed: 12/19/2022] Open
Abstract
The green tea polyphenol (−)-epigallocatechin-3-gallate (EGCG) and some of its analogs potently inhibit the ubiquitin-activating enzyme Uba1. In an effort to understand the possible molecular basis of inhibitory activity of EGCG, we conducted a molecular docking and molecular dynamics simulation study. We found that EGCG and its two selected analogs, (−)-epicatechin-3-gallate (ECG) and (−)-epigallocatechin (EGC), bind favorably at two likely hot spots for small-molecule ligand binding on human Uba1. The compounds bind with energetics that mirror their experimental potency for inhibition of Uba1∼ubiquitin thioester formation. The binding of EGCG, ECG, and EGC at one of the hot spots, in particular, recapitulates the rank order of potency determined experimentally and suggests a possible mechanism for inhibition. A hinge-like conformational change of the second catalytic cysteine domain and the opposing ubiquitin-fold domain observed during accelerated molecular dynamics simulations of the EGCG-bound Uba1 complex that results in disruption of the ubiquitin-binding interfaces could explain the compounds' inhibitory activity. These results shed light on the possible molecular mechanism of EGCG and related catechins in the inhibition of Uba1. The hinge-like movement of the SCCH domain upon ligand binding closes the ubiquitin binding site and disrupts the interfaces crucial for thioester bond formation.![]()
Collapse
Affiliation(s)
- Paras Gaur
- Institute of Genetics, Biological Research Centre Temesvári krt. 62 6726 Szeged Hungary.,Doctoral School of Biology, Faculty of Sciences and Informatics, University of Szeged Közép fasor 52 Szeged 6726 Hungary
| | - Gabriel Fenteany
- Institute of Genetics, Biological Research Centre Temesvári krt. 62 6726 Szeged Hungary
| | - Chetna Tyagi
- Doctoral School of Biology, Faculty of Sciences and Informatics, University of Szeged Közép fasor 52 Szeged 6726 Hungary .,Department of Microbiology, Faculty of Science and Informatics, University of Szeged Közép fasor 52 6726 Szeged Hungary
| |
Collapse
|
16
|
Abstract
In the first decade of targeted covalent inhibition, scientists have successfully reversed the previous trend that had impeded the use of covalent inhibition in drug development. Successes in the clinic, mainly in the field of kinase inhibitors, are existing proof that safe covalent inhibitors can be designed and employed to develop effective treatments. The case of KRASG12C covalent inhibitors entering clinical trials in 2019 has been among the hottest topics discussed in drug discovery, raising expectations for the future of the field. In this perspective, an overview of the milestones hit with targeted covalent inhibitors, as well as the promise and the needs of current research, are presented. While recent results have confirmed the potential that was foreseen, many questions remain unexplored in this branch of precision medicine.
Collapse
|
17
|
Cho J, Park J, Kim EE, Song EJ. Assay Systems for Profiling Deubiquitinating Activity. Int J Mol Sci 2020; 21:E5638. [PMID: 32781716 PMCID: PMC7460613 DOI: 10.3390/ijms21165638] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023] Open
Abstract
Deubiquitinating enzymes regulate various cellular processes, particularly protein degradation, localization, and protein-protein interactions. The dysregulation of deubiquitinating enzyme (DUB) activity has been linked to several diseases; however, the function of many DUBs has not been identified. Therefore, the development of methods to assess DUB activity is important to identify novel DUBs, characterize DUB selectivity, and profile dynamic DUB substrates. Here, we review various methods of evaluating DUB activity using cell lysates or purified DUBs, as well as the types of probes used in these methods. In addition, we introduce some techniques that can deliver DUB probes into the cells and cell-permeable activity-based probes to directly visualize and quantify DUB activity in live cells. This review could contribute to the development of DUB inhibitors by providing important information on the characteristics and applications of various probes used to evaluate and detect DUB activity in vitro and in vivo.
Collapse
Affiliation(s)
- Jinhong Cho
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Jinyoung Park
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea;
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Eun Joo Song
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| |
Collapse
|
18
|
Benns HJ, Wincott CJ, Tate EW, Child MA. Activity- and reactivity-based proteomics: Recent technological advances and applications in drug discovery. Curr Opin Chem Biol 2020; 60:20-29. [PMID: 32768892 DOI: 10.1016/j.cbpa.2020.06.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
Activity-based protein profiling (ABPP) is recognized as a powerful and versatile chemoproteomic technology in drug discovery. Central to ABPP is the use of activity-based probes to report the activity of specific enzymes or reactivity of amino acid types in complex biological systems. Over the last two decades, ABPP has facilitated the identification of new drug targets and discovery of lead compounds in human and infectious disease. Furthermore, as part of a sustained global effort to illuminate the druggable proteome, the repertoire of target classes addressable with activity-based probes has vastly expanded in recent years. Here, we provide an overview of ABPP and summarise the major technological advances with an emphasis on probe development.
Collapse
Affiliation(s)
- Henry James Benns
- Department of Life Sciences, London, UK; Department of Chemistry, Imperial College London, London, UK
| | | | | | | |
Collapse
|
19
|
Panyain N, Godinat A, Lanyon-Hogg T, Lachiondo-Ortega S, Will EJ, Soudy C, Mondal M, Mason K, Elkhalifa S, Smith LM, Harrigan JA, Tate EW. Discovery of a Potent and Selective Covalent Inhibitor and Activity-Based Probe for the Deubiquitylating Enzyme UCHL1, with Antifibrotic Activity. J Am Chem Soc 2020; 142:12020-12026. [PMID: 32579346 PMCID: PMC7366380 DOI: 10.1021/jacs.0c04527] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Indexed: 12/22/2022]
Abstract
Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a deubiquitylating enzyme that is proposed as a potential therapeutic target in neurodegeneration, cancer, and liver and lung fibrosis. Herein we report the discovery of the most potent and selective UCHL1 probe (IMP-1710) to date based on a covalent inhibitor scaffold and apply this probe to identify and quantify target proteins in intact human cells. IMP-1710 stereoselectively labels the catalytic cysteine of UCHL1 at low nanomolar concentration in cells. We further demonstrate that potent and selective UCHL1 inhibitors block pro-fibrotic responses in a cellular model of idiopathic pulmonary fibrosis, supporting the potential of UCHL1 as a potential therapeutic target in fibrotic diseases.
Collapse
Affiliation(s)
- Nattawadee Panyain
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Aurélien Godinat
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Thomas Lanyon-Hogg
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Sofía Lachiondo-Ortega
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Edward J. Will
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | | | - Milon Mondal
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Katie Mason
- Mission
Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, U.K.
| | - Sarah Elkhalifa
- Mission
Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, U.K.
| | - Lisa M. Smith
- Mission
Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, U.K.
| | - Jeanine A. Harrigan
- Mission
Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, U.K.
| | - Edward W. Tate
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
- The
Francis Crick Institute, London, NW1 1AT, U.K.
| |
Collapse
|
20
|
Kleinpenning F, Steigenberger B, Wu W, Heck AJR. Fishing for newly synthesized proteins with phosphonate-handles. Nat Commun 2020; 11:3244. [PMID: 32591520 PMCID: PMC7320153 DOI: 10.1038/s41467-020-17010-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Bioorthogonal chemistry introduces affinity-labels into biomolecules with minimal disruption to the original system and is widely applicable in a range of contexts. In proteomics, immobilized metal affinity chromatography (IMAC) enables enrichment of phosphopeptides with extreme sensitivity and selectivity. Here, we adapt and combine these superb assets in a new enrichment strategy using phosphonate-handles, which we term PhosID. In this approach, click-able phosphonate-handles are introduced into proteins via 1,3-dipolar Huisgen-cycloaddition to azido-homo-alanine (AHA) and IMAC is then used to enrich exclusively for phosphonate-labeled peptides. In interferon-gamma (IFNγ) stimulated cells, PhosID enabled the identification of a large number of IFN responsive newly synthesized proteins (NSPs) whereby we monitored the differential synthesis of these proteins over time. Collectively, these data validate the excellent performance of PhosID with efficient analysis and quantification of hundreds of NSPs by single LC-MS/MS runs. We envision PhosID as an attractive and alternative tool for studying stimuli-sensitive proteome subsets. Here the authors describe PhosID, an enrichment strategy using phosphonate-handles, that combines click chemistry and IMAC-based phospho-enrichment for quantitative proteomics analysis of newly synthesized proteins.
Collapse
Affiliation(s)
- Fleur Kleinpenning
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| |
Collapse
|