1
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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.
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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
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2
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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.
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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
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3
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Zhao Z, O’Dea R, Wendrich K, Kazi N, Gersch M. Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases. J Am Chem Soc 2023; 145:20801-20812. [PMID: 37712884 PMCID: PMC10540217 DOI: 10.1021/jacs.3c04062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 09/16/2023]
Abstract
Post-translational modifications with ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are regulated by isopeptidases termed deubiquitinases (DUBs) and Ubl proteases. Here, we describe a mild chemical method for the preparation of fluorescence polarization substrates for these enzymes that is based on the activation of C-terminal Ub/Ubl hydrazides to acyl azides and their subsequent functionalization to isopeptides. The procedure is complemented by native purification routes and thus circumvents the previous need for desulfurization and refolding. Its broad applicability was demonstrated by the generation of fully cleavable substrates for Ub, SUMO1, SUMO2, NEDD8, ISG15, and Fubi. We employed these reagents for the investigation of substrate specificities of human UCHL3, USPL1, USP2, USP7, USP16, USP18, and USP36. Pronounced selectivity of USPL1 for SUMO2/3 over SUMO1 was observed, which we rationalize with crystal structures and biochemical assays, revealing a SUMO paralogue specificity mechanism distinct from SENP family deSUMOylases. Moreover, we investigated the recently identified Fubi proteases USP16 and USP36 and found both to act as bona fide deFubiylases, harboring catalytic activity against isopeptide-linked Fubi. Surprisingly, we also noticed the activity of both enzymes toward ISG15, previously not identified in chemoproteomics, which makes USP16 and USP36 the first human DUBs with specific isopeptidase activity toward three distinct modifiers. The methods described here for the preparation of isopeptide-linked, fully folded substrates will aid in the characterization of further DUBs/Ubl proteases. More broadly, our findings highlight possible limitations associated with fluorogenic substrates and Ubl activity-based probes and stress the importance of isopeptide-containing reagents for validating isopeptidase activities and quantifying substrate specificities.
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Affiliation(s)
- Zhou Zhao
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Rachel O’Dea
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Kim Wendrich
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Nafizul Kazi
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Malte Gersch
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
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4
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Forrest I, Parker CG. Proteome-Wide Fragment-Based Ligand and Target Discovery. Isr J Chem 2023; 63:e202200098. [PMID: 38213795 PMCID: PMC10783656 DOI: 10.1002/ijch.202200098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/10/2023]
Abstract
Chemical probes are invaluable tools to investigate biological processes and can serve as lead molecules for the development of new therapies. However, despite their utility, only a fraction of human proteins have selective chemical probes, and more generally, our knowledge of the "chemically-tractable" proteome is limited, leaving many potential therapeutic targets unexploited. To help address these challenges, powerful chemical proteomic approaches have recently been developed to globally survey the ability of proteins to bind small molecules (i. e., ligandability) directly in native systems. In this review, we discuss the utility of such approaches, with a focus on the integration of chemoproteomic methods with fragment-based ligand discovery (FBLD), to facilitate the broad mapping of the ligandable proteome while also providing starting points for progression into lead chemical probes.
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Affiliation(s)
- Ines Forrest
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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5
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Chan WC, Liu X, Magin RS, Girardi NM, Ficarro SB, Hu W, Tarazona Guzman MI, Starnbach CA, Felix A, Adelmant G, Varca AC, Hu B, Bratt AS, DaSilva E, Schauer NJ, Jaen Maisonet I, Dolen EK, Ayala AX, Marto JA, Buhrlage SJ. Accelerating inhibitor discovery for deubiquitinating enzymes. Nat Commun 2023; 14:686. [PMID: 36754960 PMCID: PMC9908924 DOI: 10.1038/s41467-023-36246-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) are an emerging drug target class of ~100 proteases that cleave ubiquitin from protein substrates to regulate many cellular processes. A lack of selective chemical probes impedes pharmacologic interrogation of this important gene family. DUBs engage their cognate ligands through a myriad of interactions. We embrace this structural complexity to tailor a chemical diversification strategy for a DUB-focused covalent library. Pairing our library with activity-based protein profiling as a high-density primary screen, we identify selective hits against 23 endogenous DUBs spanning four subfamilies. Optimization of an azetidine hit yields a probe for the understudied DUB VCPIP1 with nanomolar potency and in-family selectivity. Our success in identifying good chemical starting points as well as structure-activity relationships across the gene family from a modest but purpose-build library challenges current paradigms that emphasize ultrahigh throughput in vitro or virtual screens against an ever-increasing scope of chemical space.
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Affiliation(s)
- Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Robert S Magin
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nicholas M Girardi
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wanyi Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Maria I Tarazona Guzman
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Cara A Starnbach
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Alejandra Felix
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Guillaume Adelmant
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anthony C Varca
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bin Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ariana S Bratt
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ethan DaSilva
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nathan J Schauer
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Isabella Jaen Maisonet
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emma K Dolen
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anthony X Ayala
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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6
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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).
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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.
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7
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Rothweiler EM, Huber KVM. Global Assessment of Drug Target Engagement and Selectivity of Covalent Cysteine-Reactive Inhibitors Using Alkyne-Functionalized Probes. Methods Mol Biol 2023; 2706:191-200. [PMID: 37558950 DOI: 10.1007/978-1-0716-3397-7_14] [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: 08/11/2023]
Abstract
Covalent inhibitors are emerging as a promising therapeutic means for efficient and sustained targeting of key disease-driving proteins. As for classic non-covalent inhibitors, understanding target engagement and selectivity is essential for determining optimal dosing and limiting potential on- or off-target toxicity. Here, we present a complementary activity-based protein profiling (ABPP) strategy for unbiased proteome-wide profiling of cysteine-reactive inhibitors based on two orthogonal approaches. We illustrate the use of clickable alkyne probes for in-gel fluorescence and mass spectrometry studies using a series of therapeutic XPO1 inhibitors as an example.
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Affiliation(s)
- Elisabeth M Rothweiler
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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8
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de Jesus Salazar-Estrada I, Kamath KS, Liu F. Precision Targeting of Endogenous Epidermal Growth Factor Receptor (EGFR) by Structurally Aligned Dual-Modifier Labeling. ACS Pharmacol Transl Sci 2022; 5:859-871. [PMID: 36268127 PMCID: PMC9578136 DOI: 10.1021/acsptsci.2c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Indexed: 11/28/2022]
Abstract
Covalent modification of endogenous proteins by chemical probes is used for proteome-wide profiling of cellular protein function and drug discovery. However, probe selectivity in the complex cellular environment is a challenge, and new probes with better target selectivity are continuously needed. On the basis of the success of monocovalent activity-based and reactivity-based probes, an approach of structurally aligned dual-modifier labeling (SADL) was investigated here on its potential in improving target precision. Two reactive groups, based on the acrylamide and NHS ester chemistry, were linked with structural alignment to be under the same anilinoquinazoline ligand-directive for targeting the epidermal growth factor receptor (EGFR) protein kinase as the model system for proteome-wide profiling. The SADL approach was compared with its monocovalent precursors in a label-free MaxLFQ workflow using MDA-MB-468 triple negative breast cancer cells. The dual-modifier probe consistently showed labeling of EGFR with improved precision over both monocovalent precursors under various controls. The workflow also labeled endogenous USP34 and PKMYT1 with high selectivity. Precision labeling with two covalent modifiers under a common ligand directive may broaden protein identification opportunities in the native environment to complement genetic and antibody-based approaches for elucidating biological or disease mechanisms, as well as accelerating drug target discovery.
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Affiliation(s)
| | | | - Fei Liu
- School
of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
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9
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Bailly C, Vergoten G. Binding of Vialinin A and p-Terphenyl Derivatives to Ubiquitin-Specific Protease 4 (USP4): A Molecular Docking Study. Molecules 2022; 27:molecules27185909. [PMID: 36144645 PMCID: PMC9505430 DOI: 10.3390/molecules27185909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
The para-terphenyl derivative vialinin A (Vi-A), isolated from Thelephora fungi, has been characterized as a potent inhibitor of the ubiquitin-specific protease 4 (USP4). Blockade of USP4 contributes to the anti-inflammatory and anticancer properties of the natural product. We have investigated the interaction of Vi-A with USP4 by molecular modeling, to locate the binding site (around residue V98 within the domain in USP segment) and to identify the binding process and interaction contacts. From this model, a series of 32 p-terphenyl compounds were tested as potential USP4 binders, mainly in the vialinin, terrestrin and telephantin series. We identified 11 compounds presenting a satisfactory USP4 binding capacity, including two fungal products, vialinin B and aurantiotinin A, with a more favorable empirical energy of USP4 interaction (ΔE) than the reference product Vi-A. The rare p-terphenyl aurantiotinin A, isolated from the basidiomycete T. aurantiotincta, emerged as a remarkable USP4 binder. Structure-binding relationships have been identified and discussed, to guide the future design of USP4 inhibitors based on the p-terphenyl skeleton. The docking study should help the identification of other protease inhibitors from fungus.
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Affiliation(s)
- Christian Bailly
- OncoWitan, Consulting Scientific Office, 59290 Lille (Wasquehal), France
- Correspondence:
| | - Gérard Vergoten
- Institut de Chimie Pharmaceutique Albert Lespagnol, Faculté de Pharmacie, University of Lille, Inserm, INFINITE-U1286, 3 rue du Professeur Laguesse, BP-83, 59006 Lille, France
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10
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Ubiquitin-Specific Protease 6 n-Terminal-like Protein (USP6NL) and the Epidermal Growth Factor Receptor (EGFR) Signaling Axis Regulates Ubiquitin-Mediated DNA Repair and Temozolomide-Resistance in Glioblastoma. Biomedicines 2022; 10:biomedicines10071531. [PMID: 35884836 PMCID: PMC9312792 DOI: 10.3390/biomedicines10071531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most malignant glioma, with a 30–60% epidermal growth factor receptor (EGFR) mutation. This mutation is associated with unrestricted cell growth and increases the possibility of cancer invasion. Patients with EGFR-mutated GBM often develop resistance to the available treatment modalities and higher recurrence rates. The drug resistance observed is associated with multiple genetic or epigenetic factors. The ubiquitin-specific protease 6 N-terminal-like protein (USP6NL) is a GTPase-activating protein that functions as a deubiquitinating enzyme and regulates endocytosis and signal transduction. It is highly expressed in many cancer types and may promote the growth and proliferation of cancer cells. We hypothesized that USP6NL affects GBM chemoresistance and tumorigenesis, and that its inhibition may be a novel therapeutic strategy for GBM treatment. The USP6NL level, together with EGFR expression in human GBM tissue samples and cell lines associated with therapy resistance, tumor growth, and cancer invasion, were investigated. Its pivotal roles and potential mechanism in modulating tumor growth, and the key mechanism associated with therapy resistance of GBM cells, were studied, both in vitro and in vivo. Herein, we found that deubiquitinase USP6NL and growth factor receptor EGFR were strongly associated with the oncogenicity and resistance of GBM, both in vitro and in vivo, toward temozolomide, as evidenced by enhanced migration, invasion, and acquisition of a highly invasive and drug-resistant phenotype by the GBM cells. Furthermore, abrogation of USP6NL reversed the properties of GBM cells and resensitized them toward temozolomide by enhancing autophagy and reducing the DNA damage repair response. Our results provide novel insights into the probable mechanism through which USP6NL/EGFR signaling might suppress the anticancer therapeutic response, induce cancer invasiveness, and facilitate reduced sensitivity to temozolomide treatment in GBM in an autolysosome-dependent manner. Therefore, controlling the USP6NL may offer an alternative, but efficient, therapeutic strategy for targeting and eradicating otherwise resistant and recurrent phenotypes of aggressive GBM cells.
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11
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Panyain N, Godinat A, Thawani AR, Lachiondo-Ortega S, Mason K, Elkhalifa S, Smith LM, Harrigan JA, Tate EW. Activity-based protein profiling reveals deubiquitinase and aldehyde dehydrogenase targets of a cyanopyrrolidine probe. RSC Med Chem 2021; 12:1935-1943. [PMID: 34820624 PMCID: PMC8597422 DOI: 10.1039/d1md00218j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/11/2021] [Indexed: 11/21/2022] Open
Abstract
Ubiquitin carboxy-terminal hydrolase L1 (UCHL1), a deubiquitinating enzyme (DUB), is a potential drug target in various cancers, and liver and lung fibrosis. However, bona fide functions and substrates of UCHL1 remain poorly understood. Herein, we report the characterization of UCHL1 covalent inhibitor MT16-001 based on a thiazole cyanopyrrolidine scaffold. In combination with chemical proteomics, a closely related activity-based probe (MT16-205) was used to generate a comprehensive quantitative profile for on- and off-targets at endogenous cellular abundance. Both compounds are selective for UCHL1 over other DUBs in intact cells but also engage a range of other targets with good selectivity over the wider proteome, including aldehyde dehydrogenases, redox-sensitive Parkinson's disease related protein PARK7, and glutamine amidotransferase. Taken together, these results underline the importance of robust profiling of activity-based probes as chemical tools and highlight the cyanopyrrolidine warhead as a versatile platform for liganding diverse classes of protein with reactive cysteine residues which can be used for further inhibitor screening, and as a starting point for inhibitor development.
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Affiliation(s)
- Nattawadee Panyain
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
| | - Aurélien Godinat
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
| | - Aditya Raymond Thawani
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
| | - Sofía Lachiondo-Ortega
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
| | - Katie Mason
- Mission Therapeutics Ltd, The Glenn Berge Building, Babraham Research Campus Babraham Cambridge CB22 3FH UK
| | - Sarah Elkhalifa
- Mission Therapeutics Ltd, The Glenn Berge Building, Babraham Research Campus Babraham Cambridge CB22 3FH UK
| | - Lisa M Smith
- Mission Therapeutics Ltd, The Glenn Berge Building, Babraham Research Campus Babraham Cambridge CB22 3FH UK
| | - Jeanine A Harrigan
- Mission Therapeutics Ltd, The Glenn Berge Building, Babraham Research Campus Babraham Cambridge CB22 3FH UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
- The Francis Crick Institute London NW1 1AT UK
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12
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Yao T, Xu X, Huang R. Recent Advances about the Applications of Click Reaction in Chemical Proteomics. Molecules 2021; 26:5368. [PMID: 34500797 PMCID: PMC8434046 DOI: 10.3390/molecules26175368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022] Open
Abstract
Despite significant advances in biological and analytical approaches, a comprehensive portrait of the proteome and its dynamic interactions and modifications remains a challenging goal. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to elucidate protein composition, distribution, and relevant physiological and pharmacological functions. Click chemistry focuses on the development of new combinatorial chemical methods for carbon heteroatom bond (C-X-C) synthesis, which have been utilized extensively in the field of chemical proteomics. Click reactions have various advantages including high yield, harmless by-products, and simple reaction conditions, upon which the molecular diversity can be easily and effectively obtained. This paper reviews the application of click chemistry in proteomics from four aspects: (1) activity-based protein profiling, (2) enzyme-inhibitors screening, (3) protein labeling and modifications, and (4) hybrid monolithic column in proteomic analysis.
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Affiliation(s)
- Tingting Yao
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China;
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaowei Xu
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
| | - Rong Huang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China;
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13
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Do HA, Baek KH. Cellular functions regulated by deubiquitinating enzymes in neurodegenerative diseases. Ageing Res Rev 2021; 69:101367. [PMID: 34023421 DOI: 10.1016/j.arr.2021.101367] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022]
Abstract
Neurodegenerative diseases are one of the most common diseases in mankind. Although there are reports of several candidates that cause neurodegenerative diseases, the exact mechanism of pathogenesis is poorly understood. The ubiquitin-proteasome system (UPS) is an important posttranslational modification for protein degradation and control of homeostasis. Enzymes such as E1, E2, E3 ligases, and deubiquitinating enzymes (DUBs) participating in UPS, regulate disease-inducing proteins by controlling the degree of ubiquitination. Therefore, the development of treatments targeting enzymes for degenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS), is emerging as an attractive perspective. In particular, as DUBs are able to regulate one or more degenerative disease-related proteins, the potential as a therapeutic target is even more evident. DUBs influence the regulation of toxic proteins that cause neurodegenerative diseases by not only their removal, but also by regulating signals associated with mitophagy, autophagy, and endoplasmic reticulum-associated degradation (ERAD). In this review, we analyze not only the cellular processes of DUBs, which control neurodegenerative disease-inducing proteins, but also their potentials as a therapeutic agent for neurodegenerative diseases.
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14
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Martin JG, Ward JA, Feyertag F, Zhang L, Couvertier S, Guckian K, Huber KVM, Johnson DS. Chemoproteomic Profiling of Covalent XPO1 Inhibitors to Assess Target Engagement and Selectivity. Chembiochem 2021; 22:2116-2123. [PMID: 33887086 DOI: 10.1002/cbic.202100038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/19/2021] [Indexed: 11/11/2022]
Abstract
Selinexor, a covalent XPO1 inhibitor, is approved in the USA in combination with dexamethasone for penta-refractory multiple myeloma. Additional XPO1 covalent inhibitors are currently in clinical trials for multiple diseases including hematologic malignancies, solid tumor malignancies, glioblastoma multiforme (GBM), and amyotrophic lateral sclerosis (ALS). It is important to measure the target engagement and selectivity of covalent inhibitors to understand the degree of engagement needed for efficacy, while avoiding both mechanism-based and off-target toxicity. Herein, we report clickable probes based on the XPO1 inhibitors selinexor and eltanexor for the labeling of XPO1 in live cells to assess target engagement and selectivity. We used mass spectrometry-based chemoproteomic workflows to profile the proteome-wide selectivity of selinexor and eltanexor and show that they are highly selective for XPO1. Thermal profiling analysis of selinexor further offers an orthogonal approach to measure XPO1 engagement in live cells. We believe these probes and assays will serve as useful tools to further interrogate the biology of XPO1 and its inhibition in cellular and in vivo systems.
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Affiliation(s)
- Jeffrey G Martin
- Biogen, Chemical Biology & Proteomics 225 Binney Street, Cambridge, MA 02142, USA
| | - Jennifer A Ward
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Felix Feyertag
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Lu Zhang
- Biogen, Chemical Biology & Proteomics 225 Binney Street, Cambridge, MA 02142, USA
| | - Shalise Couvertier
- Biogen, Chemical Biology & Proteomics 225 Binney Street, Cambridge, MA 02142, USA
| | - Kevin Guckian
- Biogen, Medicinal Chemistry 225 Binney Street, Cambridge, MA 02142, USA
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Douglas S Johnson
- Biogen, Chemical Biology & Proteomics 225 Binney Street, Cambridge, MA 02142, USA
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15
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Fang H, Peng B, Ong SY, Wu Q, Li L, Yao SQ. Recent advances in activity-based probes (ABPs) and affinity-based probes (A fBPs) for profiling of enzymes. Chem Sci 2021; 12:8288-8310. [PMID: 34221311 PMCID: PMC8221178 DOI: 10.1039/d1sc01359a] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a technique that uses highly selective active-site targeted chemical probes to label and monitor the state of proteins. ABPP integrates the strengths of both chemical and biological disciplines. By utilizing chemically synthesized or modified bioactive molecules, ABPP is able to reveal complex physiological and pathological enzyme-substrate interactions at molecular and cellular levels. It is also able to provide critical information of the catalytic activity changes of enzymes, annotate new functions of enzymes, discover new substrates of enzymes, and allow real-time monitoring of the cellular location of enzymes. Based on the mechanism of probe-enzyme interaction, two types of probes that have been used in ABPP are activity-based probes (ABPs) and affinity-based probes (AfBPs). This review highlights the recent advances in the use of ABPs and AfBPs, and summarizes their design strategies (based on inhibitors and substrates) and detection approaches.
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Affiliation(s)
- Haixiao Fang
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 P. R. China
| | - Sing Yee Ong
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
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16
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Cordova D, Benner EA, Clark DA, Bolgunas SP, Lahm GP, Gutteridge S, Rhoades DF, Wu L, Sopa JS, Rauh JJ, Barry JD. Pyrrole-2 carboxamides - A novel class of insect ryanodine receptor activators. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 174:104798. [PMID: 33838722 DOI: 10.1016/j.pestbp.2021.104798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
The ryanodine receptor (RyR) is an intracellular calcium channel critical to the regulation of insect muscle contraction and the target site of diamide insecticides such as chlorantraniliprole, cyantraniliprole and flubendiamide. To-date, diamides are the only known class of synthetic molecules with high potency against insect RyRs. Target-based screening of an informer library led to discovery of a novel class of RyR activators, pyrrole-2-carboxamides. Efforts to optimize receptor activity resulted in analogs with potency comparable to that of commercial diamides when tested against RyR of the fruit fly, Drosophila melanogaster. Surprisingly, testing of pyrrole-2-carboxamides in whole-insect screens showed poor insecticidal activity, which is partially attributed to differential selectivity among insect receptors and rapid detoxification. Among various lepidopteran species field resistance to diamide insecticides has been well documented and in many cases has been attributed to a single point mutation, G4946E, of the RyR gene. As with diamide insecticides, the G4946E mutation confers greatly reduced sensitivity to pyrrole-2-carboxamides. This, coupled with findings from radioligand binding studies, indicates a shared binding domain between anthranilic diamides and pyrrole-2-carboxamides.
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Affiliation(s)
- Daniel Cordova
- FMC, Agricultural Solutions Discovery Biology, Stine Research Center, 1090 Elkton Road, Newark, DE 19711, USA.
| | - Eric A Benner
- FMC, Agricultural Solutions Discovery Biology, Stine Research Center, 1090 Elkton Road, Newark, DE 19711, USA
| | - David A Clark
- FMC, Agricultural Solutions Discovery Biology, Stine Research Center, 1090 Elkton Road, Newark, DE 19711, USA
| | - Stephen P Bolgunas
- FMC, Agricultural Solutions Discovery Biology, Stine Research Center, 1090 Elkton Road, Newark, DE 19711, USA
| | - George P Lahm
- FMC, Agricultural Solutions Discovery Biology, Stine Research Center, 1090 Elkton Road, Newark, DE 19711, USA
| | - Steven Gutteridge
- FMC, Agricultural Solutions Discovery Biology, Stine Research Center, 1090 Elkton Road, Newark, DE 19711, USA
| | - Daniel F Rhoades
- FMC, Agricultural Solutions Discovery Biology, Stine Research Center, 1090 Elkton Road, Newark, DE 19711, USA
| | - Lihong Wu
- FMC, Agricultural Solutions Discovery Biology, Stine Research Center, 1090 Elkton Road, Newark, DE 19711, USA
| | - Jeffrey S Sopa
- ThermoFisher Scientific, 105 Pearl Wyn Lane, Rising Sun, MD 21911, United States of America
| | - James J Rauh
- 49 Ravens Rd. Winthrop, WA 98862, United States of America
| | - James D Barry
- FMC, Agricultural Solutions Discovery Biology, Stine Research Center, 1090 Elkton Road, Newark, DE 19711, USA
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17
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Qiao Y, Yu G, Leeuwon SZ, Liu WR. Site-Specific Conversion of Cysteine in a Protein to Dehydroalanine Using 2-Nitro-5-thiocyanatobenzoic Acid. Molecules 2021; 26:2619. [PMID: 33947165 PMCID: PMC8125731 DOI: 10.3390/molecules26092619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/21/2023] Open
Abstract
Dehydroalanine exists natively in certain proteins and can also be chemically made from the protein cysteine. As a strong Michael acceptor, dehydroalanine in proteins has been explored to undergo reactions with different thiolate reagents for making close analogues of post-translational modifications (PTMs), including a variety of lysine PTMs. The chemical reagent 2-nitro-5-thiocyanatobenzoic acid (NTCB) selectively modifies cysteine to form S-cyano-cysteine, in which the S-Cβ bond is highly polarized. We explored the labile nature of this bond for triggering E2 elimination to generate dehydroalanine. Our results indicated that when cysteine is at the flexible C-terminal end of a protein, the dehydroalanine formation is highly effective. We produced ubiquitin and ubiquitin-like proteins with a C-terminal dehydroalanine residue with high yields. When cysteine is located at an internal region of a protein, the efficiency of the reaction varies with mainly hydrolysis products observed. Dehydroalanine in proteins such as ubiquitin and ubiquitin-like proteins can serve as probes for studying pathways involving ubiquitin and ubiquitin-like proteins and it is also a starting point to generate proteins with many PTM analogues; therefore, we believe that this NTCB-triggered dehydroalanine formation method will find broad applications in studying ubiquitin and ubiquitin-like protein pathways and the functional annotation of many PTMs in proteins such as histones.
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Affiliation(s)
- Yuchen Qiao
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
| | - Ge Yu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
| | - Sunshine Z. Leeuwon
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
- Molecular & Cellular Medicine Department, College of Medicine, Texas A&M University, College Station, TX 77843, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
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18
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Kim HR, Tagirasa R, Yoo E. Covalent Small Molecule Immunomodulators Targeting the Protease Active Site. J Med Chem 2021; 64:5291-5322. [PMID: 33904753 DOI: 10.1021/acs.jmedchem.1c00172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cells of the immune system utilize multiple proteases to regulate cell functions and orchestrate innate and adaptive immune responses. Dysregulated protease activities are implicated in many immune-related disorders; thus, protease inhibitors have been actively investigated for pharmaceutical development. Although historically considered challenging with concerns about toxicity, compounds that covalently modify the protease active site represent an important class of agents, emerging not only as chemical probes but also as approved drugs. Here, we provide an overview of technologies useful for the study of proteases with the focus on recent advances in chemoproteomic methods and screening platforms. By highlighting covalent inhibitors that have been designed to target immunomodulatory proteases, we identify opportunities for the development of small molecule immunomodulators.
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Affiliation(s)
- Hong-Rae Kim
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ravichandra Tagirasa
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Euna Yoo
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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19
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Kooij R, Liu S, Sapmaz A, Xin BT, Janssen GMC, van Veelen PA, Ovaa H, Dijke PT, Geurink PP. Small-Molecule Activity-Based Probe for Monitoring Ubiquitin C-Terminal Hydrolase L1 (UCHL1) Activity in Live Cells and Zebrafish Embryos. J Am Chem Soc 2020; 142:16825-16841. [PMID: 32886496 PMCID: PMC7530896 DOI: 10.1021/jacs.0c07726] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Many reagents have emerged to study
the function of specific enzymes in vitro. On the
other hand, target specific reagents are
scarce or need improvement, allowing investigations of the function
of individual enzymes in their native cellular context. Here we report
the development of a target-selective fluorescent small-molecule activity-based
DUB probe that is active in live cells and an in vivo animal model. The probe labels active ubiquitin carboxy-terminal
hydrolase L1 (UCHL1), also known as neuron-specific protein PGP9.5
(PGP9.5) and Parkinson disease 5 (PARK5), a DUB active in neurons
that constitutes 1 to 2% of the total brain protein. UCHL1 variants
have been linked with neurodegenerative disorders Parkinson’s
and Alzheimer’s diseases. In addition, high levels of UCHL1
also correlate often with cancer and especially metastasis. The function
of UCHL1 activity or its role in cancer and neurodegenerative disease
is poorly understood and few UCHL1-specific activity tools exist.
We show that the reagents reported here are specific to UCHL1 over
all other DUBs detectable by competitive activity-based protein profiling
and by mass spectrometry. Our cell-penetrable probe, which contains
a cyanimide reactive moiety, binds to the active-site cysteine residue
of UCHL1 in an activity-dependent manner. Its use is demonstrated
by the fluorescent labeling of active UCHL1 both in vitro and in live cells. We furthermore show that this probe can selectively
and spatiotemporally report UCHL1 activity during the development
of zebrafish embryos. Our results indicate that our probe has potential
applications as a diagnostic tool for diseases with perturbed UCHL1
activity.
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Affiliation(s)
- Raymond Kooij
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Sijia Liu
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Bo-Tao Xin
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Peter Ten Dijke
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Paul P Geurink
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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20
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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.
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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
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21
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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.
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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.
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22
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Ward JA, Pinto-Fernandez A, Cornelissen L, Bonham S, Díaz-Sáez L, Riant O, Huber KVM, Kessler BM, Feron O, Tate EW. Re-Evaluating the Mechanism of Action of α,β-Unsaturated Carbonyl DUB Inhibitors b-AP15 and VLX1570: A Paradigmatic Example of Unspecific Protein Cross-linking with Michael Acceptor Motif-Containing Drugs. J Med Chem 2020; 63:3756-3762. [PMID: 32109059 PMCID: PMC7152998 DOI: 10.1021/acs.jmedchem.0c00144] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Deubiquitinating
enzymes (DUBs) are a growing target class across
multiple disease states, with several inhibitors now reported. b-AP15
and VLX1570 are two structurally related USP14/UCH-37 inhibitors.
Through a proteomic approach, we demonstrate that these compounds
target a diverse range of proteins, resulting in the formation of
higher molecular weight (MW) complexes. Activity-based proteome profiling
identified CIAPIN1 as a submicromolar covalent target of VLX1570,
and further analysis demonstrated that high MW complex formation leads
to aggregation of CIAPIN1 in intact cells. Our results suggest that
in addition to DUB inhibition, these compounds induce nonspecific
protein aggregation, providing molecular explanation for general cellular
toxicity.
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Affiliation(s)
- Jennifer A Ward
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.,Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London W12 0BZ, U.K
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.,Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, 57 Avenue Hippocrate B1.57.04, Brussels B-1200, Belgium
| | - Loïc Cornelissen
- Institute of Condensed Matter and Nanosciences, MOST Division, Place Louis Pasteur, UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Laura Díaz-Sáez
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Olivier Riant
- Institute of Condensed Matter and Nanosciences, MOST Division, Place Louis Pasteur, UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Olivier Feron
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, 57 Avenue Hippocrate B1.57.04, Brussels B-1200, Belgium
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London W12 0BZ, U.K
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23
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Krabill AD, Chen H, Hussain S, Feng C, Abdullah A, Das C, Aryal UK, Post CB, Wendt MK, Galardy PJ, Flaherty DP. Ubiquitin C-Terminal Hydrolase L1: Biochemical and Cellular Characterization of a Covalent Cyanopyrrolidine-Based Inhibitor. Chembiochem 2020; 21:712-722. [PMID: 31449350 PMCID: PMC7042063 DOI: 10.1002/cbic.201900434] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Indexed: 11/09/2022]
Abstract
The deubiquitinase (DUB) ubiquitin C-terminal hydrolase L1 (UCHL1) is expressed primarily in the central nervous system under normal physiological conditions. However, UCHL1 is overexpressed in various aggressive forms of cancer with strong evidence supporting UCHL1 as an oncogene in lung, glioma, and blood cancers. In particular, the level of UCHL1 expression in these cancers correlates with increased invasiveness and metastatic behavior, as well as poor patient prognosis. Although UCHL1 is considered an oncogene with potential as a therapeutic target, there remains a significant lack of useful small-molecule probes to pharmacologically validate in vivo targeting of the enzyme. Herein, we describe the characterization of a new covalent cyanopyrrolidine-based UCHL1 inhibitory scaffold in biochemical and cellular studies to better understand the utility of this inhibitor in elucidating the role of UCHL1 in cancer biology.
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Affiliation(s)
- Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - Hao Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - Sajjad Hussain
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. SW, Guggenheim 15, Rochester, MN, 55905, USA
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First St. SW, Guggenheim 15, Rochester, MN, 55905, USA
| | - Chao Feng
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - Ammara Abdullah
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, College of Science, Purdue University, 560 Oval, West Lafayette, IN, 47907, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Biosciences Center, Purdue University, 1275 3rd St., West Lafayette, IN, 47907, USA
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, 915 W State St., West Lafayette, IN, 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Dr., West Lafayette, IN, 47907, USA
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 S University St., West Lafayette, IN, 47907, USA
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Dr., West Lafayette, IN, 47907, USA
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 S University St., West Lafayette, IN, 47907, USA
| | - Paul J Galardy
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. SW, Guggenheim 15, Rochester, MN, 55905, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Dr., West Lafayette, IN, 47907, USA
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 S University St., West Lafayette, IN, 47907, USA
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24
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Parker CG, Pratt MR. Click Chemistry in Proteomic Investigations. Cell 2020; 180:605-632. [PMID: 32059777 PMCID: PMC7087397 DOI: 10.1016/j.cell.2020.01.025] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 01/20/2023]
Abstract
Despite advances in genetic and proteomic techniques, a complete portrait of the proteome and its complement of dynamic interactions and modifications remains a lofty, and as of yet, unrealized, objective. Specifically, traditional biological and analytical approaches have not been able to address key questions relating to the interactions of proteins with small molecules, including drugs, drug candidates, metabolites, or protein post-translational modifications (PTMs). Fortunately, chemists have bridged this experimental gap through the creation of bioorthogonal reactions. These reactions allow for the incorporation of chemical groups with highly selective reactivity into small molecules or protein modifications without perturbing their biological function, enabling the selective installation of an analysis tag for downstream investigations. The introduction of chemical strategies to parse and enrich subsets of the "functional" proteome has empowered mass spectrometry (MS)-based methods to delve more deeply and precisely into the biochemical state of cells and its perturbations by small molecules. In this Primer, we discuss how one of the most versatile bioorthogonal reactions, "click chemistry", has been exploited to overcome limitations of biological approaches to enable the selective marking and functional investigation of critical protein-small-molecule interactions and PTMs in native biological environments.
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Affiliation(s)
- Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Matthew R Pratt
- Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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25
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Gui W, Paudel P, Zhuang Z. Activity-Based Ubiquitin Probes for Investigation of Deubiquitinases. COMPREHENSIVE NATURAL PRODUCTS III 2020. [PMCID: PMC7157470 DOI: 10.1016/b978-0-12-409547-2.14672-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ubiquitination is emerging as an important post-translational modification (PTM) for numerous cellular functions including protein degradation, DNA damage repair and tolerance, and cell cycle progression. Compared with other small-molecule modifiers found in phosphorylation, acetylation and glycosylation, ubiquitin is a small protein modifier that exists as either a single ubiquitin or a polyubiquitin chain. Furthermore, the polyubiquitin chains are formed via various linkages imparting an additional layer of specificity in cellular signaling. In order to adequately study ubiquitin signaling and particularly deubiquitination, a number of ubiquitin activity-based probes (ABPs) were developed and utilized in understanding the deubiquitinase (DUBs) function. Here, we focus on the current state of the DUB ABP development and their application in understanding DUB function and specificity for polyubiquitin chains and ubiquitinated proteins.
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26
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Conole D, Mondal M, Majmudar JD, Tate EW. Recent Developments in Cell Permeable Deubiquitinating Enzyme Activity-Based Probes. Front Chem 2019; 7:876. [PMID: 31921788 PMCID: PMC6930156 DOI: 10.3389/fchem.2019.00876] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/04/2019] [Indexed: 01/25/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) function to remove or cleave ubiquitin from post-translationally modified protein substrates. There are about 100 known DUBs in the proteome, and their dysregulation has been implicated a number of disease states, but the specific function of many subclass members remains poorly understood. Activity-based probes (ABPs) react covalently with an active site residue to report on specific enzyme activity, and thus represent a powerful method to evaluate cellular and physiological enzyme function and dynamics. Ubiquitin-based ABPs, such as HA-Ub-VME, an epitope-tagged ubiquitin carrying a C-terminal reactive warhead, are the leading tool for "DUBome" activity profiling. However, these probes are generally cell membrane impermeable, limiting their use to isolated enzymes or lysates. Development of cell-permeable ABPs would allow engagement of DUB enzymes directly within the context of an intact live cell or organism, refining our understanding of physiological and pathological function, and greatly enhancing opportunities for translational research, including target engagement, imaging and biomarker discovery. This mini-review discusses recent developments in small molecule activity-based probes that target DUBs in live cells, and the unique applications of cell-permeable DUB activity-based probes vs. their traditional ubiquitin-based counterparts.
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Affiliation(s)
- Daniel Conole
- Department of Chemistry, Imperial College London, London, United Kingdom
| | - Milon Mondal
- Department of Chemistry, Imperial College London, London, United Kingdom
| | | | - Edward W. Tate
- Department of Chemistry, Imperial College London, London, United Kingdom
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27
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Schauer NJ, Magin RS, Liu X, Doherty LM, Buhrlage SJ. Advances in Discovering Deubiquitinating Enzyme (DUB) Inhibitors. J Med Chem 2019; 63:2731-2750. [DOI: 10.1021/acs.jmedchem.9b01138] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nathan J. Schauer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Robert S. Magin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xiaoxi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura M. Doherty
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sara J. Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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28
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Pinto-Fernández A, Davis S, Schofield AB, Scott HC, Zhang P, Salah E, Mathea S, Charles PD, Damianou A, Bond G, Fischer R, Kessler BM. Comprehensive Landscape of Active Deubiquitinating Enzymes Profiled by Advanced Chemoproteomics. Front Chem 2019; 7:592. [PMID: 31555637 PMCID: PMC6727631 DOI: 10.3389/fchem.2019.00592] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
Enzymes that bind and process ubiquitin, a small 76-amino-acid protein, have been recognized as pharmacological targets in oncology, immunological disorders, and neurodegeneration. Mass spectrometry technology has now reached the capacity to cover the proteome with enough depth to interrogate entire biochemical pathways including those that contain DUBs and E3 ligase substrates. We have recently characterized the breast cancer cell (MCF7) deep proteome by detecting and quantifying ~10,000 proteins, and within this data set, we can detect endogenous expression of 65 deubiquitylating enzymes (DUBs), whereas matching transcriptomics detected 78 DUB mRNAs. Since enzyme activity provides another meaningful layer of information in addition to the expression levels, we have combined advanced mass spectrometry technology, pre-fractionation, and more potent/selective ubiquitin active-site probes with propargylic-based electrophiles to profile 74 DUBs including distinguishable isoforms for 5 DUBs in MCF7 crude extract material. Competition experiments with cysteine alkylating agents and pan-DUB inhibitors combined with probe labeling revealed the proportion of active cellular DUBs directly engaged with probes by label-free quantitative (LFQ) mass spectrometry. This demonstrated that USP13, 39, and 40 are non-reactive to probe, indicating restricted enzymatic activity under these cellular conditions. Our extended chemoproteomics workflow increases depth of covering the active DUBome, including isoform-specific resolution, and provides the framework for more comprehensive cell-based small-molecule DUB selectivity profiling.
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Affiliation(s)
- Adán Pinto-Fernández
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Davis
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Abigail B Schofield
- University of Oxford, Oxford, United Kingdom.,Christ Church, University of Oxford, Oxford, United Kingdom
| | - Hannah C Scott
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ping Zhang
- University of Oxford, Oxford, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Eidarus Salah
- University of Oxford, Oxford, United Kingdom.,Department of Chemistry, University of Oxford, Oxford, United Kingdom.,Structural Genomics Consortium (United Kingdom), Oxford, United Kingdom
| | - Sebastian Mathea
- Structural Genomics Consortium (United Kingdom), Oxford, United Kingdom.,Institute of Pharmaceutical Chemistry, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Philip D Charles
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andreas Damianou
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gareth Bond
- University of Oxford, Oxford, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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29
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Sun K, He SB, Yao YZ, Qu JG, Xie R, Ma YQ, Zong MH, Chen JX. Tre2 (USP6NL) promotes colorectal cancer cell proliferation via Wnt/β-catenin pathway. Cancer Cell Int 2019; 19:102. [PMID: 31015802 PMCID: PMC6469084 DOI: 10.1186/s12935-019-0823-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/09/2019] [Indexed: 12/25/2022] Open
Abstract
Background Most colorectal cancer (CRC) patients are diagnosed at an advanced or metastatic stage with poor prognosis. Ubiquitin-specific protease 6 N-terminal-like protein (USP6NL) with high expression in CRC tissues regulates CRC cell proliferation via Wnt/β-catenin pathway. We hypothesized that USP6NL impacts CRC growth and inhibition of USP6NL may be a novel treatment strategy to improve CRC therapy. Methods USP6NL level in human CRC tissues and its association with tumor growth and metastasis were examined. Its roles and potential mechanisms in regulating tumor growth were studied by genetic and pharmacological manipulation of CRC cells in vitro and in vivo. Results Herein, we found that USP6NL was up-regulated in tumorous tissues of CRC patients. Our data suggested that knockdown of USP6NL in human CRC cell lines (HCT116 and LOVO cells) inhibited cell proliferation, induced G0/G1 cell cycle arrest, and prevented the tumorigenicity of HCT116 cells in nude mice, and which was associated with the prevention of Wnt/β-catenin pathway. On the contrary, USP6NL overexpression in human CRC cells (SW480) showed the opposite result. Our data suggested that the promoted cell proliferation, G1/S cell cycle progression, and the enhanced expression of β-catenin Cyclin D1 and C-myc while reduced P27 induced by the overexpression of USP6NL were significantly reversed by additional treatment of XAV939, indicating that activating Wnt/β-catenin pathway was the mechanism, by which USP6NL exerted carcinogenesis in CRC in vitro. Besides, our data suggested that knockdown of USP6NL increased the ubiquitination of β-catenin, indicating that USP6NL may serve as a deubiquitinase that regulated β-catenin accumulation in this process. Furthermore, 10058-F4 down-regulated USP6NL, inhibited CRC cell proliferation and induced cell cycle arrest. The result demonstrated a possible feedback loop between USP6NL, β-catenin and C-myc in regulating CRC cell growth. Conclusion USP6NL was an oncogene in CRC, and it may be a potential target for the treatment of CRC.
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Affiliation(s)
- Kang Sun
- 1Department of General Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001 People's Republic of China
| | - Song-Bing He
- 2Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006 People's Republic of China
| | - Yi-Zhou Yao
- 2Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006 People's Republic of China
| | - Jian-Guo Qu
- 1Department of General Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001 People's Republic of China
| | - Rong Xie
- 1Department of General Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001 People's Republic of China
| | - Yu-Qiao Ma
- 1Department of General Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001 People's Republic of China
| | - Ming-Hui Zong
- 3School of Medicine, Jiangsu University, Zhenjiang, 212013 People's Republic of China
| | - Ji-Xiang Chen
- 1Department of General Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001 People's Republic of China
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30
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Gui W, Ott CA, Yang K, Chung JS, Shen S, Zhuang Z. Cell-Permeable Activity-Based Ubiquitin Probes Enable Intracellular Profiling of Human Deubiquitinases. J Am Chem Soc 2018; 140:12424-12433. [PMID: 30240200 DOI: 10.1021/jacs.8b05147] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Advancement in our knowledge of deubiquitinases (DUBs) and their biological functions requires biochemical tools permitting interrogation of DUB activities under physiologically relevant conditions. Activity-based DUB probes (DUB ABPs) have been widely used in investigating the function and activity of DUBs. However, most ubiquitin (Ub)-based DUB ABPs are not cell-permeable, limiting their utility to purified proteins and cell lysates. Lysis of cells usually leads to dilution of the cytoplasm and disruption of the normal cellular organization, which may alter the activity of many DUBs and DUB complexes. Here, we report a new class of cell-permeable DUB ABPs that enable intracellular DUB profiling. We used a semisynthetic approach to generate modular ubiquitin-based DUB probes containing a reactive warhead for covalent trapping of DUBs with a catalytic cysteine. We employed cell-penetrating peptides (CPPs), particualrly cyclic polyarginine (cR10), to deliver the DUB ABPs into cells, as confirmed using live-cell fluorescence microscopy and DUB ABPs containing a fluorophore at the C-terminus of Ub. In comparison to TAT, enhanced intacellular delivery was observed through conjugation of a cyclic polyarginine (cR10) to the N-terminus of ubiquitin via a disulfide linkage. Using the new cell-permeable DUB ABPs, we carried out DUB profiling in intact HeLa cells, and identified active DUBs using immunocapture and label-free quantitative mass spectrometry. Additionally, we demonstrated that the cell-permeable DUB ABPs can be used in assessing the inhibition of DUBs by small-molecule inhibitors in intact cells. Our results indicate that cell-permeable DUB ABPs hold great promise in providing a better understanding of the cellular functions of DUBs and advancing drug discovery efforts targeting human DUBs.
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Affiliation(s)
- Weijun Gui
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , Delaware 19716 , United States
| | - Christine A Ott
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , Delaware 19716 , United States
| | - Kun Yang
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , Delaware 19716 , United States
| | - Jedidiah S Chung
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , Delaware 19716 , United States
| | - Siqi Shen
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , Delaware 19716 , United States
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , Delaware 19716 , United States
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31
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Mulder MPC, Merkx R, Witting KF, Hameed DS, El Atmioui D, Lelieveld L, Liebelt F, Neefjes J, Berlin I, Vertegaal ACO, Ovaa H. Total Chemical Synthesis of SUMO and SUMO-Based Probes for Profiling the Activity of SUMO-Specific Proteases. Angew Chem Int Ed Engl 2018; 57:8958-8962. [PMID: 29771001 PMCID: PMC6055820 DOI: 10.1002/anie.201803483] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/09/2018] [Indexed: 12/31/2022]
Abstract
SUMO is a post-translational modifier critical for cell cycle progression and genome stability that plays a role in tumorigenesis, thus rendering SUMO-specific enzymes potential pharmacological targets. However, the systematic generation of tools for the activity profiling of SUMO-specific enzymes has proven challenging. We developed a diversifiable synthetic platform for SUMO-based probes by using a direct linear synthesis method, which permits N- and C-terminal labelling to incorporate dyes and reactive warheads, respectively. In this manner, activity-based probes (ABPs) for SUMO-1, SUMO-2, and SUMO-3-specific proteases were generated and validated in cells using gel-based assays and confocal microscopy. We further expanded our toolbox with the synthesis of a K11-linked diSUMO-2 probe to study the proteolytic cleavage of SUMO chains. Together, these ABPs demonstrate the versatility and specificity of our synthetic SUMO platform for in vitro and in vivo characterization of the SUMO protease family.
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Affiliation(s)
- Monique P C Mulder
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Remco Merkx
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Current address: Medicines Evaluation Board, Graadt van Roggenweg 500, 3531, AH, Utrecht, The Netherlands
| | - Katharina F Witting
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Dharjath S Hameed
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Dris El Atmioui
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Lindsey Lelieveld
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Current address: Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300, RA, Leiden, The Netherlands
| | - Frauke Liebelt
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Jacques Neefjes
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
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32
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Mulder MPC, Merkx R, Witting KF, Hameed DS, El Atmioui D, Lelieveld L, Liebelt F, Neefjes J, Berlin I, Vertegaal ACO, Ovaa H. Total Chemical Synthesis of SUMO and SUMO-Based Probes for Profiling the Activity of SUMO-Specific Proteases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803483] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Monique P. C. Mulder
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Remco Merkx
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Current address: Medicines Evaluation Board; Graadt van Roggenweg 500 3531 AH Utrecht The Netherlands
| | - Katharina F. Witting
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Dharjath S. Hameed
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Dris El Atmioui
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Lindsey Lelieveld
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Current address: Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Frauke Liebelt
- Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Jacques Neefjes
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Ilana Berlin
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Huib Ovaa
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
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33
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Lead discovery and chemical biology approaches targeting the ubiquitin proteasome system. Bioorg Med Chem Lett 2017; 27:4589-4596. [DOI: 10.1016/j.bmcl.2017.08.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 12/26/2022]
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34
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Mass spectrometry techniques for studying the ubiquitin system. Biochem Soc Trans 2017; 45:1137-1148. [PMID: 28939693 DOI: 10.1042/bst20170091] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/07/2017] [Accepted: 08/10/2017] [Indexed: 11/17/2022]
Abstract
Post-translational control of proteins through covalent attachment of ubiquitin plays important roles in all eukaryotic cell functions. The ubiquitin system in humans consists of 2 E1, 35 E2 and >600 E3 ubiquitin ligases as well as hundreds of deubiquitylases, which reverse ubiquitin attachment. Moreover, there are hundreds of proteins with ubiquitin-binding domains that bind one of the eight possible polyubiquitin chains. Dysfunction of the ubiquitin system is associated with many diseases such as cancer, autoimmunity and neurodegeneration, demonstrating the importance of ubiquitylation. Therefore, enzymes of the ubiquitin system are considered highly attractive drug targets. In recent years, mass spectrometry (MS)-based techniques have become increasingly important in the deciphering of the ubiquitin system. This short review addresses the state-of-the-art MS techniques for the identification of ubiquitylated proteins and their ubiquitylation sites. We also discuss the identification and quantitation of ubiquitin chain topologies and highlight how the activity of enzymes in the ubiquitin pathway can be measured. Finally, we present current MS tools that can be used for drug discovery in the ubiquitin space.
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de Jong A, Witting K, Kooij R, Flierman D, Ovaa H. Release of Enzymatically Active Deubiquitinating Enzymes upon Reversible Capture by Disulfide Ubiquitin Reagents. Angew Chem Int Ed Engl 2017; 56:12967-12970. [PMID: 28841265 PMCID: PMC5656918 DOI: 10.1002/anie.201706738] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Indexed: 01/21/2023]
Abstract
Deubiquitinating enzymes (DUBs) catalyze the cleavage of ubiquitin from target proteins. Ubiquitin is post‐translationally attached to proteins and serves as an important regulatory signal for key cellular processes. In this study, novel activity‐based probes to study DUBs were synthesized that comprise a ubiquitin moiety and a novel disulfide warhead at the C‐terminus. These reagents can bind DUBs covalently by forming a disulfide bridge between the active‐site cysteine residue and the ubiquitin‐based probe. As disulfide bridges can be broken by the addition of a reducing agent, these novel ubiquitin reagents can be used to capture and subsequently release catalytically active DUBs, whereas existing capturing agents bind irreversibly. These novel reagents allow for the study of these enzymes in their active state under various conditions.
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Affiliation(s)
- Annemieke de Jong
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Katharina Witting
- Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.,Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Raymond Kooij
- Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.,Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Dennis Flierman
- Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.,Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Huib Ovaa
- Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.,Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
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36
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de Jong A, Witting K, Kooij R, Flierman D, Ovaa H. Release of Enzymatically Active Deubiquitinating Enzymes upon Reversible Capture by Disulfide Ubiquitin Reagents. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Annemieke de Jong
- Department of Cell Biology; The Netherlands Cancer Institute; Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Katharina Witting
- Department of Chemical Immunology; Leiden University Medical Center; Einthovenweg 20 2333 ZC Leiden The Netherlands
- Department of Cell Biology; The Netherlands Cancer Institute; Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Raymond Kooij
- Department of Chemical Immunology; Leiden University Medical Center; Einthovenweg 20 2333 ZC Leiden The Netherlands
- Department of Cell Biology; The Netherlands Cancer Institute; Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Dennis Flierman
- Department of Chemical Immunology; Leiden University Medical Center; Einthovenweg 20 2333 ZC Leiden The Netherlands
- Department of Cell Biology; The Netherlands Cancer Institute; Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Huib Ovaa
- Department of Chemical Immunology; Leiden University Medical Center; Einthovenweg 20 2333 ZC Leiden The Netherlands
- Department of Cell Biology; The Netherlands Cancer Institute; Plesmanlaan 121 1066 CX Amsterdam The Netherlands
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37
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Wong YK, Zhang J, Hua ZC, Lin Q, Shen HM, Wang J. Recent advances in quantitative and chemical proteomics for autophagy studies. Autophagy 2017; 13:1472-1486. [PMID: 28820289 DOI: 10.1080/15548627.2017.1313944] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process. In this review, we attempted to provide an overview of principles and techniques relevant to the application of quantitative and chemical proteomics methods to autophagy, and outline the current landscape as well as future outlook of these methods in autophagy research.
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Affiliation(s)
- Yin-Kwan Wong
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore
| | - Jianbin Zhang
- b Department of Oncology, Clinical Research Institute , Zhejiang Provincial People's Hospital , Hangzhou , China
| | - Zi-Chun Hua
- c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
| | - Qingsong Lin
- d Department of Biological Sciences , National University of Singapore , Singapore
| | - Han-Ming Shen
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,e NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore , Singapore
| | - Jigang Wang
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
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38
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Hewings DS, Flygare JA, Bogyo M, Wertz IE. Activity-based probes for the ubiquitin conjugation-deconjugation machinery: new chemistries, new tools, and new insights. FEBS J 2017; 284:1555-1576. [PMID: 28196299 PMCID: PMC7163952 DOI: 10.1111/febs.14039] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/21/2017] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
The reversible post‐translational modification of proteins by ubiquitin and ubiquitin‐like proteins regulates almost all cellular processes, by affecting protein degradation, localization, and complex formation. Deubiquitinases (DUBs) are proteases that remove ubiquitin modifications or cleave ubiquitin chains. Most DUBs are cysteine proteases, which makes them well suited for study by activity‐based probes. These DUB probes report on deubiquitinase activity by reacting covalently with the active site in an enzyme‐catalyzed manner. They have proven to be important tools to study DUB selectivity and proteolytic activity in different settings, to identify novel DUBs, and to characterize deubiquitinase inhibitors. Inspired by the efficacy of activity‐based probes for DUBs, several groups have recently reported probes for the ubiquitin conjugation machinery (E1, E2, and E3 enzymes). Many of these enzymes, while not proteases, also posses active site cysteine residues and can be targeted by covalent probes. In this review, we will discuss how features of the probe (cysteine‐reactive group, recognition element, and reporter tag) affect reactivity and suitability for certain experimental applications. We will also review the diverse applications of the current probes, and discuss the need for new probe types to study emerging aspects of ubiquitin biology.
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Affiliation(s)
- David S Hewings
- Discovery Chemistry, Genentech, South San Francisco, CA, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA.,Department of Pathology, Stanford University School of Medicine, CA, USA
| | - John A Flygare
- Discovery Chemistry, Genentech, South San Francisco, CA, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, CA, USA
| | - Ingrid E Wertz
- Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA
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