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Bai Q, Wang M, Wang K, Liu J, Qu F, Lin H. CuPc-Fe@BSA nanocomposite: Intracellular acid-sensitive aggregation for enhanced sonodynamic and chemo-therapy. J Colloid Interface Sci 2024; 671:577-588. [PMID: 38820842 DOI: 10.1016/j.jcis.2024.05.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/02/2024]
Abstract
Due to their rigid π-conjugated macrocyclic structure, organic sonosensitizers face significant aggregation in physiological conditions, hindering the production of reactive oxygen species (ROS). An acid-sensitive nanoassembly was developed to address this issue and enhance sonodynamic therapy (SDT) and emission. Initially, copper phthalocyanine (CuPc) was activated using a H2SO4-assisted hydrothermal method to introduce multiple functional groups (-COOH, -OH, and -SO3H), disrupting strong π-π stacking and promoting ROS generation and emission. Subsequently, negatively charged CuPc-SO4 was incorporated into bovine serum albumin (BSA) to form CuPc-Fe@BSA nanoparticles (10 nm) with Fe3+ ions serving as linkers. In acidic conditions, protonation of CuPc-SO4 and BSA weakened the interactions, leading to Fe3+ release and nanostructure dissociation. Protonated CuPc-SO4 tended to self-aggregate into nanorods. This acidity-sensitive aggregation is vital for achieving specific accumulation within the tumor microenvironment (TME), thereby enhancing retention and SDT efficacy. Prior to this, the nanocomposites demonstrated cycling stability under neutral conditions. Additionally, the released Fe ions exhibited mimicry of glutathione peroxidase and peroxidase activity for chemotherapy (CDT). The synergistic effect of SDT and CDT increased intracellular oxidative stress, causing mitochondrial injury and ferroptosis. Furthermore, the combined therapy induced immunogenic cell death (ICD), effectively activating anticancer immune responses and suppressing metastasis and recurrence.
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Affiliation(s)
- Qingchen Bai
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Miao Wang
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Kai Wang
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Molecular Imaging Research Center (MIRC), Harbin Medical University, Harbin 150028, China; Department of Nuclear Medicine, the Fourth Hospital of Harbin Medical University, Harbin 150028, China.
| | - Jingwei Liu
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin 150025, China.
| | - Fengyu Qu
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin 150025, China
| | - Huiming Lin
- Key Laboratory of Photochemical Biomaterials and Energy Storage Materials, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin 150025, China; Laboratory for Photon and Electronic Bandgap Materials, Ministry of Education, Harbin Normal University, Harbin 150025, China.
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2
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 PMCID: PMC11088880 DOI: 10.1042/bcj20230284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M. Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K. Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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3
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Keijzer N, Priyanka A, Stijf-Bultsma Y, Fish A, Gersch M, Sixma TK. Variety in the USP deubiquitinase catalytic mechanism. Life Sci Alliance 2024; 7:e202302533. [PMID: 38355287 PMCID: PMC10867860 DOI: 10.26508/lsa.202302533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The ubiquitin-specific protease (USP) family of deubiquitinases (DUBs) controls cellular ubiquitin-dependent signaling events. This generates therapeutic potential, with active-site inhibitors in preclinical and clinical studies. Understanding of the USP active site is primarily guided by USP7 data, where the catalytic triad consists of cysteine, histidine, and a third residue (third critical residue), which polarizes the histidine through a hydrogen bond. A conserved aspartate (fourth critical residue) is directly adjacent to this third critical residue. Although both critical residues accommodate catalysis in USP2, these residues have not been comprehensively investigated in other USPs. Here, we quantitatively investigate their roles in five USPs. Although USP7 relies on the third critical residue for catalysis, this residue is dispensable in USP1, USP15, USP40, and USP48, where the fourth critical residue is vital instead. Furthermore, these residues vary in importance for nucleophilic attack. The diverging catalytic mechanisms of USP1 and USP7 are independent of substrate and retained in cells for USP1. This unexpected variety of catalytic mechanisms in this well-conserved protein family may generate opportunities for selective targeting of individual USPs.
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Affiliation(s)
- Niels Keijzer
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anu Priyanka
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Yvette Stijf-Bultsma
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Alexander Fish
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Malte Gersch
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Titia K Sixma
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
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4
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Campos Alonso M, Knobeloch KP. In the moonlight: non-catalytic functions of ubiquitin and ubiquitin-like proteases. Front Mol Biosci 2024; 11:1349509. [PMID: 38455765 PMCID: PMC10919355 DOI: 10.3389/fmolb.2024.1349509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024] Open
Abstract
Proteases that cleave ubiquitin or ubiquitin-like proteins (UBLs) are critical players in maintaining the homeostasis of the organism. Concordantly, their dysregulation has been directly linked to various diseases, including cancer, neurodegeneration, developmental aberrations, cardiac disorders and inflammation. Given their potential as novel therapeutic targets, it is essential to fully understand their mechanisms of action. Traditionally, observed effects resulting from deficiencies in deubiquitinases (DUBs) and UBL proteases have often been attributed to the misregulation of substrate modification by ubiquitin or UBLs. Therefore, much research has focused on understanding the catalytic activities of these proteins. However, this view has overlooked the possibility that DUBs and UBL proteases might also have significant non-catalytic functions, which are more prevalent than previously believed and urgently require further investigation. Moreover, multiple examples have shown that either selective loss of only the protease activity or complete absence of these proteins can have different functional and physiological consequences. Furthermore, DUBs and UBL proteases have been shown to often contain domains or binding motifs that not only modulate their catalytic activity but can also mediate entirely different functions. This review aims to shed light on the non-catalytic, moonlighting functions of DUBs and UBL proteases, which extend beyond the hydrolysis of ubiquitin and UBL chains and are just beginning to emerge.
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Affiliation(s)
- Marta Campos Alonso
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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5
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Gan J, Pinto-Fernández A, Flierman D, Akkermans JJLL, O’Brien DP, Greenwood H, Scott HC, Fritz G, Knobeloch KP, Neefjes J, van Dam H, Ovaa H, Ploegh HL, Kessler BM, Geurink PP, Sapmaz A. USP16 is an ISG15 cross-reactive deubiquitinase that targets pro-ISG15 and ISGylated proteins involved in metabolism. Proc Natl Acad Sci U S A 2023; 120:e2315163120. [PMID: 38055744 PMCID: PMC10722975 DOI: 10.1073/pnas.2315163120] [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: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023] Open
Abstract
Interferon-induced ubiquitin (Ub)-like modifier ISG15 covalently modifies host and viral proteins to restrict viral infections. Its function is counteracted by the canonical deISGylase USP18 or Ub-specific protease 18. Notwithstanding indications for the existence of other ISG15 cross-reactive proteases, these remain to be identified. Here, we identify deubiquitinase USP16 as an ISG15 cross-reactive protease by means of ISG15 activity-based profiling. Recombinant USP16 cleaved pro-ISG15 and ISG15 isopeptide-linked model substrates in vitro, as well as ISGylated substrates from cell lysates. Moreover, interferon-induced stimulation of ISGylation was increased by depletion of USP16. The USP16-dependent ISG15 interactome indicated that the deISGylating function of USP16 may regulate metabolic pathways. Targeted enzymes include malate dehydrogenase, cytoplasmic superoxide dismutase 1, fructose-bisphosphate aldolase A, and cytoplasmic glutamic-oxaloacetic transaminase 1. USP16 may thus contribute to the regulation of a subset of metabolism-related proteins during type-I interferon responses.
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Affiliation(s)
- Jin Gan
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA02115
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Dennis Flierman
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Jimmy J. L. L. Akkermans
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Leiden2333 ZC, The Netherlands
| | - Darragh P. O’Brien
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Helene Greenwood
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Hannah Claire Scott
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Günter Fritz
- Department of Cellular Microbiology, University of Hohenheim, Stuttgart70599, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, Department of Molecular Genetics, University of Freiburg, Freiburg79106, Germany
- Centre for Integrative Biological Signalling Studies, Department of Molecular Genetics, University of Freiburg, Freiburg79104, Germany
| | - Jacques Neefjes
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Leiden2333 ZC, The Netherlands
| | - Hans van Dam
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Hidde L. Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA02115
| | - Benedikt M. Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Paul P. Geurink
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Aysegul Sapmaz
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
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6
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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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