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Liang CT, Roscow O, Zhang W. Generation and Characterization of Engineered Ubiquitin Variants to Modulate the Ubiquitin Signaling Cascade. Cold Spring Harb Protoc 2024; 2024:107784. [PMID: 36997275 DOI: 10.1101/pdb.over107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The ubiquitin signaling cascade plays a crucial role in human cells. Consistent with this, malfunction of ubiquitination and deubiquitination is implicated in the initiation and progression of numerous human diseases, including cancer. Therefore, the development of potent and specific modulators of ubiquitin signal transduction has been at the forefront of drug development. In the past decade, a structure-based combinatorial protein-engineering approach has been used to generate ubiquitin variants (UbVs) as protein-based modulators of multiple components in the ubiquitin-proteasome system. Here, we review the design and generation of phage-displayed UbV libraries, including the processes of binder selection and library improvement. We also provide a comprehensive overview of the general in vitro and cellular methodologies involved in characterizing UbV binders. Finally, we describe two recent applications of UbVs for developing molecules with therapeutic potential.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Olivia Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre, Toronto, Ontario M5G1M1, Canada
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2
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Spano D, Catara G. Targeting the Ubiquitin-Proteasome System and Recent Advances in Cancer Therapy. Cells 2023; 13:29. [PMID: 38201233 PMCID: PMC10778545 DOI: 10.3390/cells13010029] [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: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Ubiquitination is a reversible post-translational modification based on the chemical addition of ubiquitin to proteins with regulatory effects on various signaling pathways. Ubiquitination can alter the molecular functions of tagged substrates with respect to protein turnover, biological activity, subcellular localization or protein-protein interaction. As a result, a wide variety of cellular processes are under ubiquitination-mediated control, contributing to the maintenance of cellular homeostasis. It follows that the dysregulation of ubiquitination reactions plays a relevant role in the pathogenic states of human diseases such as neurodegenerative diseases, immune-related pathologies and cancer. In recent decades, the enzymes of the ubiquitin-proteasome system (UPS), including E3 ubiquitin ligases and deubiquitinases (DUBs), have attracted attention as novel druggable targets for the development of new anticancer therapeutic approaches. This perspective article summarizes the peculiarities shared by the enzymes involved in the ubiquitination reaction which, when deregulated, can lead to tumorigenesis. Accordingly, an overview of the main pharmacological interventions based on targeting the UPS that are in clinical use or still in clinical trials is provided, also highlighting the limitations of the therapeutic efficacy of these approaches. Therefore, various attempts to circumvent drug resistance and side effects as well as UPS-related emerging technologies in anticancer therapeutics are discussed.
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Affiliation(s)
- Daniela Spano
- Institute for Endocrinology and Experimental Oncology “G. Salvatore”, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuliana Catara
- Institute of Biochemistry and Cell Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
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3
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Pereira TO, Abbasi M, Arrais JP. Enhancing reinforcement learning for de novo molecular design applying self-attention mechanisms. Brief Bioinform 2023; 24:bbad368. [PMID: 37903414 DOI: 10.1093/bib/bbad368] [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: 07/05/2023] [Revised: 09/04/2023] [Accepted: 09/26/2023] [Indexed: 11/01/2023] Open
Abstract
The drug discovery process can be significantly improved by applying deep reinforcement learning (RL) methods that learn to generate compounds with desired pharmacological properties. Nevertheless, RL-based methods typically condense the evaluation of sampled compounds into a single scalar value, making it difficult for the generative agent to learn the optimal policy. This work combines self-attention mechanisms and RL to generate promising molecules. The idea is to evaluate the relative significance of each atom and functional group in their interaction with the target, and to utilize this information for optimizing the Generator. Therefore, the framework for de novo drug design is composed of a Generator that samples new compounds combined with a Transformer-encoder and a biological affinity Predictor that evaluate the generated structures. Moreover, it takes the advantage of the knowledge encapsulated in the Transformer's attention weights to evaluate each token individually. We compared the performance of two output prediction strategies for the Transformer: standard and masked language model (MLM). The results show that the MLM Transformer is more effective in optimizing the Generator compared with the state-of-the-art works. Additionally, the evaluation models identified the most important regions of each molecule for the biological interaction with the target. As a case study, we generated synthesizable hit compounds that can be putative inhibitors of the enzyme ubiquitin-specific protein 7 (USP7).
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Affiliation(s)
- Tiago O Pereira
- Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, Univ Coimbra, Coimbra, Portugal
| | - Maryam Abbasi
- Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, Univ Coimbra, Coimbra, Portugal
| | - Joel P Arrais
- Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, Univ Coimbra, Coimbra, Portugal
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4
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Liu Q, Mallette E, Zheng H, Zhang W. Development of an OTUD1 ubiquitin variant inhibitor. Biochem J 2023; 480:1317-1330. [PMID: 37589489 DOI: 10.1042/bcj20230119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/18/2023]
Abstract
OTUD1 (Ovarian tumor domain-containing deubiquitinase 1) is a member of the OTU domain-containing deubiquitinase family of enzymes involved in immunoregulation and tumorigenesis pathways. OTUD1 consists of three distinct regions: an unstructured N-terminal region, an OTU-fold catalytic domain, and a ubiquitin-interacting motif (UIM) containing region. Enhanced enzymatic activity and a strong preference for K63-linked substrates are imparted by the UIM containing region. We used phage display with a ubiquitin variant (UbV) library to identify binders for OTUD1 lacking the unstructured N-terminal region (OTUD1OTU + UIM) in an attempt to identify inhibitors bridging the catalytic domain and the UIM containing region. Two UbVs were identified (UbVOD.1 and UbVOD.2) with high affinity and specificity for OTUD1. Of the UbVs identified, UbVOD.1 inhibited OTUD1 activity towards mono-Ub and K63-linked di-Ub substrates in vitro with single-digit nanomolar IC50 and potently inhibited deubiquitinase activity with poly-Ub chains of other linkages. In vivo expression of UbVOD.1 alone was unstable, however as a di-UbV, global deubiquitination and deubiquitinase activity with the OTUD1 substrate RIPK1 were inhibited. Herein we describe the development of molecular tools for exploring the activity of OTUD1 in a cellular context, towards protein-based therapeutics.
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Affiliation(s)
- Qi Liu
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph N1G 2W1, Canada
| | - Evan Mallette
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph N1G 2W1, Canada
| | - Hui Zheng
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, Jiangsu 215123, China
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph N1G 2W1, Canada
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
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5
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Tang JQ, Marchand MM, Veggiani G. Ubiquitin Engineering for Interrogating the Ubiquitin-Proteasome System and Novel Therapeutic Strategies. Cells 2023; 12:2117. [PMID: 37626927 PMCID: PMC10453149 DOI: 10.3390/cells12162117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Protein turnover, a highly regulated process governed by the ubiquitin-proteasome system (UPS), is essential for maintaining cellular homeostasis. Dysregulation of the UPS has been implicated in various diseases, including viral infections and cancer, making the proteins in the UPS attractive targets for therapeutic intervention. However, the functional and structural redundancies of UPS enzymes present challenges in identifying precise drug targets and achieving target selectivity. Consequently, only 26S proteasome inhibitors have successfully advanced to clinical use thus far. To overcome these obstacles, engineered peptides and proteins, particularly engineered ubiquitin, have emerged as promising alternatives. In this review, we examine the impact of engineered ubiquitin on UPS and non-UPS proteins, as well as on viral enzymes. Furthermore, we explore their potential to guide the development of small molecules targeting novel surfaces, thereby expanding the range of druggable targets.
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Affiliation(s)
- Jason Q. Tang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Mary M. Marchand
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- Division of Biotechnology and Molecular Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
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Zhu J, Kong W, Huang L, Bi S, Jiao X, Zhu S. Identification of immunotherapy and chemotherapy-related molecular subtypes in colon cancer by integrated multi-omics data analysis. Front Immunol 2023; 14:1142609. [PMID: 37020539 PMCID: PMC10067602 DOI: 10.3389/fimmu.2023.1142609] [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: 01/11/2023] [Accepted: 02/27/2023] [Indexed: 03/22/2023] Open
Abstract
BackgroundColon cancer is a highly heterogeneous disease, and identifying molecular subtypes can provide insights into deregulated pathways within tumor subsets, which may lead to personalized treatment options. However, most prognostic models are based on single-pathway genes.MethodsIn this study, we aimed to identify three clinically relevant subtypes of colon cancer based on multiple signaling pathways-related genes. Integrative multi-omics analysis was used to explain the biological processes contributing to colon cancer aggressiveness, recurrence, and progression. Machine learning methods were employed to identify the subtypes and provide medication guidance for distinct subtypes using the L1000 platform. We developed a robust prognostic model (MKPC score) based on gene pairs and validated it in one internal test set and three external test sets. Risk-related genes were extracted and verified by qPCR.ResultsThree clinically relevant subtypes of colon cancer were identified based on multiple signaling pathways-related genes, which had significantly different survival state (Log-Rank test, p<0.05). Integrative multi-omics analysis revealed biological processes contributing to colon cancer aggressiveness, recurrence, and progression. The developed MKPC score, based on gene pairs, was robust in predicting prognosis state (Log-Rank test, p<0.05), and risk-related genes were successfully verified by qPCR (t test, p<0.05). An easy-to-use web tool was created for risk scoring and therapy stratification in colon cancer patients, and the practical nomogram can be extended to other cancer types.ConclusionIn conclusion, our study identified three clinically relevant subtypes of colon cancer and developed a robust prognostic model based on gene pairs. The developed web tool is a valuable resource for researchers and clinicians in risk scoring and therapy stratification in colon cancer patients, and the practical nomogram can be extended to other cancer types.
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Affiliation(s)
- Jie Zhu
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Weikaixin Kong
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
- Gastrointestinal Surgery Department, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- *Correspondence: Sujie Zhu, ; Weikaixin Kong, ; Xuelong Jiao,
| | - Liting Huang
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Suzhen Bi
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Xuelong Jiao
- Gastrointestinal Surgery Department, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- *Correspondence: Sujie Zhu, ; Weikaixin Kong, ; Xuelong Jiao,
| | - Sujie Zhu
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- *Correspondence: Sujie Zhu, ; Weikaixin Kong, ; Xuelong Jiao,
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Ye Z, Chen J, Huang P, Xuan Z, Zheng S. Ubiquitin-specific peptidase 10, a deubiquitinating enzyme: Assessing its role in tumor prognosis and immune response. Front Oncol 2022; 12:990195. [PMID: 36248971 PMCID: PMC9554417 DOI: 10.3389/fonc.2022.990195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin-specific peptidase 10 (USP10) is a member of the ubiquitin-specific protease family that removes the ubiquitin chain from ubiquitin-conjugated protein substrates. We performed a literature search to evaluate the structure and biological activity of USP10, summarize its role in tumorigenesis and tumor progression, and discuss how USP10 may act as a tumor suppressor or a tumor-promoting gene depending on its mechanism of action. Subsequently, we elaborated further on these results through bioinformatics analysis. We demonstrated that abnormal expression of USP10 is related to tumorigenesis in various types of cancer, including liver, lung, ovarian, breast, prostate, and gastric cancers and acute myeloid leukemia. Meanwhile, in certain cancers, increased USP10 expression is associated with tumor suppression. USP10 was downregulated in kidney renal clear cell carcinoma (KIRC) and associated with reduced overall survival in patients with KIRC. In contrast, USP10 upregulation was associated with poor prognosis in head and neck squamous cell carcinoma (HNSC). In addition, we elucidated the novel role of USP10 in the regulation of tumor immunity in KIRC and HNSC through bioinformatics analysis. We identified several signaling pathways to be significantly associated with USP10 expression, such as ferroptosis, PI3K/AKT/mTOR, TGF-β, and G2/M checkpoint. In summary, this review outlines the role of USP10 in various forms of cancer, discusses the relevance of USP10 inhibitors in anti-tumor therapies, and highlights the potential function of USP10 in regulating the immune responses of tumors.
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Affiliation(s)
- Ziqi Ye
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Chen
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ping Huang
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
| | - Zixue Xuan
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
- *Correspondence: Zixue Xuan, ; Shuilian Zheng,
| | - Shuilian Zheng
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
- *Correspondence: Zixue Xuan, ; Shuilian Zheng,
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8
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Oliveira RI, Guedes RA, Salvador JAR. Highlights in USP7 inhibitors for cancer treatment. Front Chem 2022; 10:1005727. [PMID: 36186590 PMCID: PMC9520255 DOI: 10.3389/fchem.2022.1005727] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Ubiquitin-specific protease 7 (USP7) is a member of one of the most largely studied families of deubiquitylating enzymes. It plays a key role modulating the levels of multiple proteins, including tumor suppressors, transcription factors, epigenetic modulators, DNA repair proteins, and regulators of the immune response. The abnormal expression of USP7 is found in various malignant tumors and a high expression signature generally indicates poor tumor prognosis. This suggests USP7 as a promising prognostic and druggable target for cancer therapy. Nonetheless, no approved drugs targeting USP7 have already entered clinical trials. Therefore, the development of potent and selective USP7 inhibitors still requires intensive research and development efforts before the pre-clinical benefits translate into the clinic. This mini review systematically summarizes the role of USP7 as a drug target for cancer therapeutics, as well as the scaffolds, activities, and binding modes of some of the most representative small molecule USP7 inhibitors reported in the scientific literature. To wind up, development challenges and potential combination therapies using USP7 inhibitors for less tractable tumors are also disclosed.
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Affiliation(s)
- Rita I. Oliveira
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Romina A. Guedes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- *Correspondence: Jorge A. R. Salvador,
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McClary WD, Catala A, Zhang W, Gamboni F, Dzieciatkowska M, Sidhu SS, D'Alessandro A, Catalano CE. A Designer Nanoparticle Platform for Controlled Intracellular Delivery of Bioactive Macromolecules: Inhibition of Ubiquitin-Specific Protease 7 in Breast Cancer Cells. ACS Chem Biol 2022; 17:1853-1865. [PMID: 35796308 DOI: 10.1021/acschembio.2c00256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological therapeutics represent an increasing and critical component of newly approved drugs; however, the inability to deliver biologics intracellularly in a controlled manner remains a major limitation. We have developed a semi-synthetic, tunable phage-like particle (PLP) platform derived from bacteriophage λ. The shell surface can be decorated with small-molecule, biological and synthetic moieties, alone or in combination and in defined ratios. Here, we demonstrate that the platform can be used to deliver biological macromolecules intracellularly and in a controlled manner. Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme that has been widely recognized as an ideal target for the treatment of a variety of cancers. Recently, UbV.7.2, a novel biologic derived from the ubiquitin scaffold, was developed for inhibition of USP7, but issues remain in achieving efficient and controlled intracellular delivery of the biologic. We have shown that decoration of PLPs with trastuzumab (Trz), a HER2-targeted therapeutic used in the treatment of various cancers, results in specific targeting and uptake of Trz-PLPs into HER2-overexpressing breast cancer cells. By simultaneously decorating PLPs with Trz and UbV.7.2, we now show that these particles are also internalized by HER2-positive cells, thus providing a means for intracellular delivery of the biologic in a controlled fashion. Internalized particles retain USP7 inhibition activity of UbV.7.2 and alter the metabolic and proteomic landscapes of these cells. This study demonstrates that the λ "designer nanoparticles" represent a powerful system for the intracellular delivery of biologics in a defined dose.
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Affiliation(s)
- Wynton D McClary
- The Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Alexis Catala
- The Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G2W1, Canada.,Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Fabia Gamboni
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Sachdev S Sidhu
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G2W1, Canada.,Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States.,Department of Medicine - Division of Hematology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Carlos E Catalano
- The Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045, United States
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Zhao J, Guo J, Wang Y, Ma Q, Shi Y, Cheng F, Lu Q, Fu W, Ouyang G, Zhang J, Xu Q, Hu X. Research Progress of DUB Enzyme in Hepatocellular Carcinoma. Front Oncol 2022; 12:920287. [PMID: 35875077 PMCID: PMC9303014 DOI: 10.3389/fonc.2022.920287] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
According to GLOBOCAN 2021 cancer incidence and mortality statistics compiled by the International Agency for Research on Cancer, hepatocellular carcinoma (HCC) is the most common malignancy in the human liver and one of the leading causes of cancer death worldwide. Although there have been great advances in the treatment of HCC, such as regofenib, sorafenib, and lomvatinib, which have been developed and approved for the clinical treatment of advanced or metastatic HCC. However, they only prolong survival by a few months, and patients with advanced liver cancer are susceptible to tumor invasion metastasis and drug resistance. Ubiquitination modification is a type of post-translational modification of proteins. It can affect the physiological activity of cells by regulating the localization, stability and activity of proteins, such as: gene transcription, DNA damage signaling and other pathways. The reversible process of ubiquitination is called de-ubiquitination: it is the process of re-releasing ubiquitinated substrates with the participation of de-ubiquitinases (DUBs) and other active substances. There is growing evidence that many dysregulations of DUBs are associated with tumorigenesis. Although dysregulation of deuquitinase function is often found in HCC and other cancers, The mechanisms of action of many DUBs in HCC have not been elucidated. In this review, we focused on several deubiquitinases (DUBs) associated with hepatocellular carcinoma, including their structure, function, and relationship to hepatocellular carcinoma. hepatocellular carcinoma was highlighted, as well as the latest research reports. Among them, we focus on the USP family and OTU family which are more studied in the HCC. In addition, we discussed the prospects and significance of targeting DUBs as a new strategy for the treatment of hepatocellular carcinoma. It also briefly summarizes the research progress of some DUB-related small molecule inhibitors and their clinical application significance as a treatment for HCC in the future.
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Affiliation(s)
- Jie Zhao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jinhui Guo
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Yanan Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiancheng Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu Shi
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Feng Cheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiliang Lu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Wen Fu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | | | - Ji Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiuran Xu
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoge Hu, ; Qiuran Xu,
| | - Xiaoge Hu
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical CollegeHangzhou, China
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoge Hu, ; Qiuran Xu,
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11
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On the Study of Deubiquitinases: Using the Right Tools for the Job. Biomolecules 2022; 12:biom12050703. [PMID: 35625630 PMCID: PMC9139131 DOI: 10.3390/biom12050703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
Deubiquitinases (DUBs) have been the subject of intense scrutiny in recent years. Many of their diverse enzymatic mechanisms are well characterized in vitro; however, our understanding of these enzymes at the cellular level lags due to the lack of quality tool reagents. DUBs play a role in seemingly every biological process and are central to many human pathologies, thus rendering them very desirable and challenging therapeutic targets. This review aims to provide researchers entering the field of ubiquitination with knowledge of the pharmacological modulators and tool molecules available to study DUBs. A focus is placed on small molecule inhibitors, ubiquitin variants (UbVs), and activity-based probes (ABPs). Leveraging these tools to uncover DUB biology at the cellular level is of particular importance and may lead to significant breakthroughs. Despite significant drug discovery efforts, only approximately 15 chemical probe-quality small molecule inhibitors have been reported, hitting just 6 of about 100 DUB targets. UbV technology is a promising approach to rapidly expand the library of known DUB inhibitors and may be used as a combinatorial platform for structure-guided drug design.
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12
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Tao L, Liu X, Jiang X, Zhang K, Wang Y, Li X, Jiang S, Han T. USP10 as a Potential Therapeutic Target in Human Cancers. Genes (Basel) 2022; 13:genes13050831. [PMID: 35627217 PMCID: PMC9142050 DOI: 10.3390/genes13050831] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 12/04/2022] Open
Abstract
Deubiquitination is a major form of post-translational protein modification involved in the regulation of protein homeostasis and various cellular processes. Deubiquitinating enzymes (DUBs), comprising about five subfamily members, are key players in deubiquitination. USP10 is a USP-family DUB featuring the classic USP domain, which performs deubiquitination. Emerging evidence has demonstrated that USP10 is a double-edged sword in human cancers. However, the precise molecular mechanisms underlying its different effects in tumorigenesis remain elusive. A possible reason is dependence on the cell context. In this review, we summarize the downstream substrates and upstream regulators of USP10 as well as its dual role as an oncogene and tumor suppressor in various human cancers. Furthermore, we summarize multiple pharmacological USP10 inhibitors, including small-molecule inhibitors, such as spautin-1, and traditional Chinese medicines. Taken together, the development of specific and efficient USP10 inhibitors based on USP10’s oncogenic role and for different cancer types could be a promising therapeutic strategy.
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Affiliation(s)
- Li Tao
- The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China;
| | - Xiao Liu
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China; (X.L.); (X.J.); (K.Z.); (Y.W.)
| | - Xinya Jiang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China; (X.L.); (X.J.); (K.Z.); (Y.W.)
| | - Kun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China; (X.L.); (X.J.); (K.Z.); (Y.W.)
| | - Yijing Wang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China; (X.L.); (X.J.); (K.Z.); (Y.W.)
| | - Xiumin Li
- Henan Key Laboratory of Tumor Molecular Therapy Medicine, Xinxiang Medical University, Xinxiang 453003, China;
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Jining Medical University, Jining 272000, China
- Correspondence: (S.J.); (T.H.)
| | - Tao Han
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China; (X.L.); (X.J.); (K.Z.); (Y.W.)
- Henan Key Laboratory of Tumor Molecular Therapy Medicine, Xinxiang Medical University, Xinxiang 453003, China;
- Correspondence: (S.J.); (T.H.)
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13
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Veggiani G, Yates BP, Martyn GD, Manczyk N, Singer AU, Kurinov I, Sicheri F, Sidhu SS. Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs. ACS Chem Biol 2022; 17:941-956. [PMID: 35385646 PMCID: PMC9305627 DOI: 10.1021/acschembio.2c00089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ubiquitin (Ub)-binding domains embedded in intracellular proteins act as readers of the complex Ub code and contribute to regulation of numerous eukaryotic processes. Ub-interacting motifs (UIMs) are short α-helical modular recognition elements whose role in controlling proteostasis and signal transduction has been poorly investigated. Moreover, impaired or aberrant activity of UIM-containing proteins has been implicated in numerous diseases, but targeting modular recognition elements in proteins remains a major challenge. To overcome this limitation, we developed Ub variants (UbVs) that bind to 42 UIMs in the human proteome with high affinity and specificity. Structural analysis of a UbV:UIM complex revealed the molecular determinants of enhanced affinity and specificity. Furthermore, we showed that a UbV targeting a UIM in the cancer-associated Ub-specific protease 28 potently inhibited catalytic activity. Our work demonstrates the versatility of UbVs to target short α-helical Ub receptors with high affinity and specificity. Moreover, the UbVs provide a toolkit to investigate the role of UIMs in regulating and transducing Ub signals and establish a general strategy for the systematic development of probes for Ub-binding domains.
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Affiliation(s)
- Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Bradley P. Yates
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Gregory D. Martyn
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Alex U. Singer
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, NE-CAT, Cornell University, Argonne, Illinois 60439, United States
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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14
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Hewitt CS, Das C, Flaherty DP. Rational Development and Characterization of a Ubiquitin Variant with Selectivity for Ubiquitin C-Terminal Hydrolase L3. Biomolecules 2022; 12:biom12010062. [PMID: 35053210 PMCID: PMC8773573 DOI: 10.3390/biom12010062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 01/12/2023] Open
Abstract
There is currently a lack of reliable methods and strategies to probe the deubiquitinating enzyme UCHL3. Current small molecules reported for this purpose display reduced potency and selectivity in cellular assays. To bridge this gap and provide an alternative approach to probe UCHL3, our group has carried out the rational design of ubiquitin-variant activity-based probes with selectivity for UCHL3 over the closely related UCHL1 and other DUBs. The approach successfully produced a triple-mutant ubiquitin variant activity-based probe, UbVQ40V/T66K/V70F-PRG, that was ultimately 20,000-fold more selective for UCHL3 over UCHL1 when assessed by rate of inactivation assays. This same variant was shown to selectively form covalent adducts with UCHL3 in MDA-MB-231 breast cancer cells and no reactivity toward other DUBs expressed. Overall, this study demonstrates the feasibility of the approach and also provides insight into how this approach may be applied to other DUB targets.
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Affiliation(s)
- Chad S. Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA;
| | - Chittaranjan Das
- Department of Chemistry, College of Science, Purdue University, West Lafayette, IN 47907, USA;
| | - Daniel P. Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA;
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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15
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A Panel of Engineered Ubiquitin Variants Targeting the Family of Domains Found in Ubiquitin Specific Proteases (DUSPs). J Mol Biol 2021; 433:167300. [PMID: 34666042 DOI: 10.1016/j.jmb.2021.167300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/16/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022]
Abstract
Domains found in ubiquitin specific proteases (DUSPs) occur in seven members of the ubiquitin specific protease (USP) family. DUSPs are defined by a distinct structural fold but their functions remain largely unknown, although studies with USP4 suggest that its DUSP enhances deubiquitination activity. We used phage-displayed libraries of ubiquitin variants (UbVs) to derive protein-based tools to target DUSP family members with high affinity and specificity. We designed a UbV library based on insights from the structure of a previously identified UbV bound to the DUSP of USP15. The new library yielded 33 unique UbVs that bound to DUSPs from five different USPs (USP4, USP11, USP15, USP20 and USP33). For each USP, we were able to identify at least one DUSP that bound with high affinity and absolute specificity relative to the other DUSPs. We showed that UbVs targeting the DUSPs of USP15, USP11 and USP20 inhibited the catalytic activity of the enzyme, despite the fact that the DUSP is located outside of the catalytic domain. These findings provide an alternative means of inhibiting USP activity by targeting DUSPs, and this mechanism could be potentially extended other DUSP-containing USPs.
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16
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Guo Y, Liu Q, Mallette E, Caba C, Hou F, Fux J, LaPlante G, Dong A, Zhang Q, Zheng H, Tong Y, Zhang W. Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1. J Biol Chem 2021; 297:101107. [PMID: 34425109 PMCID: PMC8449267 DOI: 10.1016/j.jbc.2021.101107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 01/23/2023] Open
Abstract
Ubiquitination is a crucial posttranslational protein modification involved in a myriad of biological pathways. This modification is reversed by deubiquitinases (DUBs) that deconjugate the single ubiquitin (Ub) moiety or poly-Ub chains from substrates. In the past decade, tremendous efforts have been focused on targeting DUBs for drug discovery. However, most chemical compounds with inhibitory activity for DUBs suffer from mild potency and low selectivity. To overcome these obstacles, we developed a phage display-based protein engineering strategy for generating Ub variant (UbV) inhibitors, which was previously successfully applied to the Ub-specific protease (USP) family of cysteine proteases. In this work, we leveraged the UbV platform to selectively target STAMBP, a member of the JAB1/MPN/MOV34 (JAMM) metalloprotease family of DUB enzymes. We identified two UbVs (UbVSP.1 and UbVSP.3) that bind to STAMBP with high affinity but differ in their selectivity for the closely related paralog STAMBPL1. We determined the STAMBPL1-UbVSP.1 complex structure by X-ray crystallography, revealing hotspots of the JAMM-UbV interaction. Finally, we show that UbVSP.1 and UbVSP.3 are potent inhibitors of STAMBP isopeptidase activity, far exceeding the reported small-molecule inhibitor BC-1471. This work demonstrates that UbV technology is suitable to develop molecules as tools to target metalloproteases, which can be used to further understand the cellular function of JAMM family DUBs.
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Affiliation(s)
- Yusong Guo
- Fisheries College, Guangdong Ocean University, Guangdong, China; Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Qi Liu
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Canada
| | - Evan Mallette
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Canada
| | - Cody Caba
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| | - Feng Hou
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Julia Fux
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Canada
| | - Gabriel LaPlante
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Qi Zhang
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Hui Zheng
- Jiangsu Key Laboratory of Infection and Immunity, International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Yufeng Tong
- Structural Genomics Consortium, University of Toronto, Toronto, Canada; Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada.
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Canada; CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, Toronto, Canada.
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17
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Zhou XJ, Li R, Liu X, Qu YQ. Advances in deubiquitinating enzymes in lung adenocarcinoma. J Cancer 2021; 12:5573-5582. [PMID: 34405018 PMCID: PMC8364634 DOI: 10.7150/jca.56532] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 07/09/2021] [Indexed: 12/25/2022] Open
Abstract
The process of ubiquitination and deubiquitination is widely present in the human body's protein reactions and plays versatile roles in multiple diseases. Deubiquitinating enzymes (DUBs) are significant regulators of this process, which cleave the ubiquitin (Ub) moiety from various substrates and maintain protein stability. Lung adenocarcinoma (LUAD) is the most common type of non-small cell lung cancer (NSCLC) and remains refractory to treatment. To elucidate the mechanism of LUAD and advance new therapeutic targets, we review the latest research progress on DUBs in LUAD. We summarize the biological capabilities of these DUBs and further highlight those DUBs that may serve as anticancer target candidates for precision treatment. We also discuss deubiquitinase inhibitors, which are expected to play a role in targeted LUAD therapy.
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Affiliation(s)
- Xi-Jia Zhou
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University (Jinan 250012, China)
| | - Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University (Jinan 250012, China)
| | - Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University (Jinan 250012, China)
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University (Jinan 250012, China)
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18
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Armstrong LA, Lange SM, Dee Cesare V, Matthews SP, Nirujogi RS, Cole I, Hope A, Cunningham F, Toth R, Mukherjee R, Bojkova D, Gruber F, Gray D, Wyatt PG, Cinatl J, Dikic I, Davies P, Kulathu Y. Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. PLoS One 2021; 16:e0253364. [PMID: 34270554 PMCID: PMC8284666 DOI: 10.1371/journal.pone.0253364] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Of the 16 non-structural proteins (Nsps) encoded by SARS CoV-2, Nsp3 is the largest and plays important roles in the viral life cycle. Being a large, multidomain, transmembrane protein, Nsp3 has been the most challenging Nsp to characterize. Encoded within Nsp3 is the papain-like protease domain (PLpro) that cleaves not only the viral polypeptide but also K48-linked polyubiquitin and the ubiquitin-like modifier, ISG15, from host cell proteins. We here compare the interactors of PLpro and Nsp3 and find a largely overlapping interactome. Intriguingly, we find that near full length Nsp3 is a more active protease compared to the minimal catalytic domain of PLpro. Using a MALDI-TOF based assay, we screen 1971 approved clinical compounds and identify five compounds that inhibit PLpro with IC50s in the low micromolar range but showed cross reactivity with other human deubiquitinases and had no significant antiviral activity in cellular SARS-CoV-2 infection assays. We therefore looked for alternative methods to block PLpro activity and engineered competitive nanobodies that bind to PLpro at the substrate binding site with nanomolar affinity thus inhibiting the enzyme. Our work highlights the importance of studying Nsp3 and provides tools and valuable insights to investigate Nsp3 biology during the viral infection cycle.
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Affiliation(s)
- Lee A. Armstrong
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Sven M. Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Virginia Dee Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Stephen P. Matthews
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Raja Sekhar Nirujogi
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Isobel Cole
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Anthony Hope
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Fraser Cunningham
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Rachel Toth
- MRC Reagents and Services, University of Dundee, Dundee, Scotland, United Kingdom
| | - Rukmini Mukherjee
- Institute of Biochemistry II, Goethe University Frankfurt Medical Faculty, University Hospital, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Denisa Bojkova
- Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Franz Gruber
- National Phenotypic Screening Centre, University of Dundee, Dundee, Scotland, United Kingdom
| | - David Gray
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Paul G. Wyatt
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Jindrich Cinatl
- Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University Frankfurt Medical Faculty, University Hospital, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
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19
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LaPlante G, Zhang W. Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors. Cancers (Basel) 2021; 13:3079. [PMID: 34203106 PMCID: PMC8235664 DOI: 10.3390/cancers13123079] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/14/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is a critical regulator of cellular protein levels and activity. It is, therefore, not surprising that its dysregulation is implicated in numerous human diseases, including many types of cancer. Moreover, since cancer cells exhibit increased rates of protein turnover, their heightened dependence on the UPS makes it an attractive target for inhibition via targeted therapeutics. Indeed, the clinical application of proteasome inhibitors in treatment of multiple myeloma has been very successful, stimulating the development of small-molecule inhibitors targeting other UPS components. On the other hand, while the discovery of potent and selective chemical compounds can be both challenging and time consuming, the area of targeted protein degradation through utilization of the UPS machinery has seen promising developments in recent years. The repertoire of proteolysis-targeting chimeras (PROTACs), which employ E3 ligases for the degradation of cancer-related proteins via the proteasome, continues to grow. In this review, we will provide a thorough overview of small-molecule UPS inhibitors and highlight advancements in the development of targeted protein degradation strategies for cancer therapeutics.
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Affiliation(s)
- Gabriel LaPlante
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1G2W1, Canada;
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1G2W1, Canada;
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre West Tower, 661 University Avenue, Toronto, ON M5G1M1, Canada
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20
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Liang CT, Roscow OMA, Zhang W. Recent developments in engineering protein-protein interactions using phage display. Protein Eng Des Sel 2021; 34:6297171. [PMID: 34117768 DOI: 10.1093/protein/gzab014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Targeted inhibition of misregulated protein-protein interactions (PPIs) has been a promising area of investigation in drug discovery and development for human diseases. However, many constraints remain, including shallow binding surfaces and dynamic conformation changes upon interaction. A particularly challenging aspect is the undesirable off-target effects caused by inherent structural similarity among the protein families. To tackle this problem, phage display has been used to engineer PPIs for high-specificity binders with improved binding affinity and greatly reduced undesirable interactions with closely related proteins. Although general steps of phage display are standardized, library design is highly variable depending on experimental contexts. Here in this review, we examined recent advances in the structure-based combinatorial library design and the advantages and limitations of different approaches. The strategies described here can be explored for other protein-protein interactions and aid in designing new libraries or improving on previous libraries.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Olivia M A Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada.,CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre West Tower, 661 University Avenue, Toronto, Ontario M5G1M1, Canada
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21
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Targeting the Ubiquitin Signaling Cascade in Tumor Microenvironment for Cancer Therapy. Int J Mol Sci 2021; 22:ijms22020791. [PMID: 33466790 PMCID: PMC7830467 DOI: 10.3390/ijms22020791] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Tumor microenvironments are composed of a myriad of elements, both cellular (immune cells, cancer-associated fibroblasts, mesenchymal stem cells, etc.) and non-cellular (extracellular matrix, cytokines, growth factors, etc.), which collectively provide a permissive environment enabling tumor progression. In this review, we focused on the regulation of tumor microenvironment through ubiquitination. Ubiquitination is a reversible protein post-translational modification that regulates various key biological processes, whereby ubiquitin is attached to substrates through a catalytic cascade coordinated by multiple enzymes, including E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes and E3 ubiquitin ligases. In contrast, ubiquitin can be removed by deubiquitinases in the process of deubiquitination. Here, we discuss the roles of E3 ligases and deubiquitinases as modulators of both cellular and non-cellular components in tumor microenvironment, providing potential therapeutic targets for cancer therapy. Finally, we introduced several emerging technologies that can be utilized to develop effective therapeutic agents for targeting tumor microenvironment.
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22
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Xu L, Wang J, Yuan X, Yang S, Xu X, Li K, He Y, Wei L, Zhang J, Tian Y. IU1 suppresses proliferation of cervical cancer cells through MDM2 degradation. Int J Biol Sci 2020; 16:2951-2963. [PMID: 33061808 PMCID: PMC7545697 DOI: 10.7150/ijbs.47999] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/02/2020] [Indexed: 02/02/2023] Open
Abstract
Previous studies have demonstrated that the antitumor potential of IU1 (a pharmacological compound), which was mediated by selective inhibition of proteasome-associated deubiquitinase ubiquitin-specific protease 14 (USP14). However, the underlying molecular mechanisms remain elusive. It has been well established that mdm2 (Murine double minute 2) gene was amplified and/or overexpressed in a variety of human neoplasms, including cervical cancer. Furthermore, MDM2 is critical to cervical cancer development and progression. Relatively studies have reported that USP15 and USP7 stabilized MDM2 protein levels by removing its ubiquitin chain. In the current study, we studied the cell proliferation status after IU1 treatment and the USP14-MDM2 protein interaction in cervical cancer cells. This study experimentally revealed that IU1 treatment reduced MDM2 protein expression in HeLa cervical cancer cells, along with the activation of autophagy-lysosomal protein degradation and promotion of ubiquitin-proteasome system (UPS) function, thereby blocked G0/G1 to S phase transition, decreased cell growth and triggered cell apoptosis. Thus, these results indicate that IU1 treatment simultaneously targets two major intracellular protein degradation systems, ubiquitin-proteasome and autophagy-lysosome systems, which leads to MDM2 degradation and contributes to the antitumor effect of IU1.
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Affiliation(s)
- Liu Xu
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Jing Wang
- Department of Pathology, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiaoning Yuan
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Shuhua Yang
- Department of Human Anatomy, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xiaolong Xu
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Kai Li
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yanqi He
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Lei Wei
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Jingwei Zhang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan, Hubei 430071, P.R. China
| | - Yihao Tian
- Department of Human Anatomy, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
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23
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LeBlanc N, Mallette E, Zhang W. Targeted modulation of E3 ligases using engineered ubiquitin variants. FEBS J 2020; 288:2143-2165. [PMID: 32867007 DOI: 10.1111/febs.15536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
Ubiquitination plays an essential role in signal transduction to regulate most if not all cellular processes. Among the enzymes that are involved in the ubiquitin (Ub) signaling cascade, tremendous efforts have been focused on elucidating the roles of E3 Ub ligases as they determine the complexity and specificity of ubiquitination. Not surprisingly, the malfunction of E3 ligases is directly implicated in many human diseases, including cancer. Therefore, there is an urgent need to develop potent and specific molecules to modulate E3 ligase activity as intracellular probes for target validation and as pharmacological agents in preclinical research. Unfortunately, the progress has been hampered by the dynamic regulation mechanisms for different types of E3 ligases. Here, we summarize the progress of using protein engineering to develop Ub variant (UbV) inhibitors for all major families of E3 ligases and UbV activators for homologous with E6-associated protein C terminus E3s and homodimeric RING E3s. We believe that this provides a general strategy and a valuable toolkit for the research community to inhibit or activate E3 ligases and these synthetic molecules have important implications in exploring protein degradation for drug discovery.
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Affiliation(s)
- Nicole LeBlanc
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| | - Evan Mallette
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada.,CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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24
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Hewitt CS, Krabill AD, Das C, Flaherty DP. Development of Ubiquitin Variants with Selectivity for Ubiquitin C-Terminal Hydrolase Deubiquitinases. Biochemistry 2020; 59:3447-3462. [PMID: 32865982 DOI: 10.1021/acs.biochem.9b01076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ubiquitin (Ub) is a highly conserved protein that is covalently attached to substrate proteins as a post-translational modification to regulate signaling pathways such as proteasomal degradation and cell cycle/transcriptional regulation in the eukaryotic cellular environment. Ub signaling is regulated by the homeostasis of substrate protein ubiquitination/deubiquitination by E3 ligases and deubiquitinating enzymes (DUBs) in healthy eukaryotic systems. One such DUB, ubiquitin C-terminal hydrolase L1 (UCHL1), is endogenously expressed in the central nervous system under normal physiological conditions, but overexpression and/or mutation has been linked to various cancers and neurodegenerative diseases. The lack of UCHL1 probing strategies suggests development of a selective Ub variant (UbV) for probing UCHL1's role in these disease states would be beneficial. We describe a computational design approach to investigate UbVs that lend selectivity, both binding and inhibition, to UCHL1 over the close structural homologue UCHL3 and members of other DUB families. A number of UbVs, mainly those containing Thr9 mutations, displayed appreciable binding and inhibition selectivity for UCHL1 over UCHL3, compared to wild-type Ub in in vitro assays. By appending reactive electrophiles to the C-terminus of the UbVs, we created the first activity-based probe (ABP) with demonstrated reaction selectivity for UCH family DUBs over other families in cell lysates. Further kinetic analysis of covalent inhibition by the UbV-ABP with UCHL1 and UCHL3 offers insight into the future design of UCHL1 selective UbV-ABP. These studies serve as a proof of concept of the viability of the in silico design of ubiquitin variants for UCH family DUBs as a step toward the development of macromolecular UCHL1 inhibitors.
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Affiliation(s)
- Chad S Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Chittaranjan Das
- Department of Chemistry, College of Science, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
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25
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Gjonaj L, Sapmaz A, Flierman D, Janssen GMC, van Veelen PA, Ovaa H. Development of a DUB-selective fluorogenic substrate. Chem Sci 2019; 10:10290-10296. [PMID: 32110315 PMCID: PMC6988746 DOI: 10.1039/c9sc02226k] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/28/2019] [Indexed: 12/21/2022] Open
Abstract
Developing USP16-selective ubiquitin-based reagents to study USP16 and its related biology.
Ubiquitination is a post-translational modification that is involved in a plethora of cellular processes. Target proteins can be specifically modified with a single ubiquitin (Ub) molecule or with complex chains. In recent years, research has focused on deubiquitinating enzymes (DUBs) as potential therapeutic candidates in various diseases. USP16 is an emerging target due to its involvement in mitosis and stem cell self-renewal. Generally, activity-based probes (ABPs) used to study DUBs are based on the ubiquitin scaffold, thus lacking target selectivity. To overcome this issue, we designed a Ub-based activity probe bearing specific mutations to achieve selectivity for USP16, by combining structural modelling and analysis and mutational calculation predictions. We develop a fluorogenic substrate, the first of its kind, that is processed exclusively by USP16, which allows us to monitor USP16 activity in complex samples.
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Affiliation(s)
- Lorina Gjonaj
- 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 .
| | - Dennis Flierman
- Oncode Institute , Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC , Leiden , The Netherlands .
| | - George M C Janssen
- Centre for Proteomics and Metabolomics , Leiden University Medical Center , Albinusdreef 2 , 2333 ZA , Leiden , The Netherlands
| | - Peter A van Veelen
- Centre for Proteomics and Metabolomics , Leiden University Medical Center , Albinusdreef 2 , 2333 ZA , Leiden , The Netherlands
| | - Huib Ovaa
- Oncode Institute , Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC , Leiden , The Netherlands .
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26
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27
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Gabrielsen M, Buetow L, Kowalczyk D, Zhang W, Sidhu SS, Huang DT. Identification and Characterization of Mutations in Ubiquitin Required for Non-covalent Dimer Formation. Structure 2019; 27:1452-1459.e4. [PMID: 31303481 PMCID: PMC6720194 DOI: 10.1016/j.str.2019.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 05/29/2019] [Accepted: 06/21/2019] [Indexed: 11/26/2022]
Abstract
Ubiquitin (Ub) is a small protein that post-translationally modifies a variety of substrates in eukaryotic cells to modulate substrate function. The ability of Ub to interact with numerous protein domains makes Ub an attractive scaffold for engineering ubiquitin variants (UbVs) with high target specificity. Previously, we identified a UbV that formed a non-covalent stable dimer via a β-strand exchange, and in the current work we identified and characterized the minimal substitutions in the primary sequence of Ub required to form a higher ordered complex. Using solution angle scattering and X-ray crystallography, we show that a single substitution of residue Gly10 to either Ala or Val is sufficient to convert Ub from a monomer to a dimer. We also investigate contributions to dimer formation by the residues in the surrounding sequence. These results can be used to develop next-generation phage-display libraries of UbVs to engineer new interfaces for protein recognition.
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Affiliation(s)
- Mads Gabrielsen
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lori Buetow
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Dominika Kowalczyk
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.
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28
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Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site. Proc Natl Acad Sci U S A 2019; 116:17280-17289. [PMID: 31350353 DOI: 10.1073/pnas.1902889116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub's C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at "exosites." However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.
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29
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Balancing the Photoreceptor Proteome: Proteostasis Network Therapeutics for Inherited Retinal Disease. Genes (Basel) 2019; 10:genes10080557. [PMID: 31344897 PMCID: PMC6722924 DOI: 10.3390/genes10080557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
The light sensing outer segments of photoreceptors (PRs) are renewed every ten days due to their high photoactivity, especially of the cones during daytime vision. This demands a tremendous amount of energy, as well as a high turnover of their main biosynthetic compounds, membranes, and proteins. Therefore, a refined proteostasis network (PN), regulating the protein balance, is crucial for PR viability. In many inherited retinal diseases (IRDs) this balance is disrupted leading to protein accumulation in the inner segment and eventually the death of PRs. Various studies have been focusing on therapeutically targeting the different branches of the PR PN to restore the protein balance and ultimately to treat inherited blindness. This review first describes the different branches of the PN in detail. Subsequently, insights are provided on how therapeutic compounds directed against the different PN branches might slow down or even arrest the appalling, progressive blinding conditions. These insights are supported by findings of PN modulators in other research disciplines.
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30
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Zhang W, Sidhu SS. Generating Intracellular Modulators of E3 Ligases and Deubiquitinases from Phage-Displayed Ubiquitin Variant Libraries. Methods Mol Biol 2019; 1844:101-119. [PMID: 30242706 DOI: 10.1007/978-1-4939-8706-1_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ubiquitination is a posttranslational protein modification pathway regulating diverse cellular processes that are implicated in numerous human diseases. However, targeting the enzymes in the ubiquitination cascade potently and selectively remains a major challenge. Recently we devised a methodology to generate ubiquitin-based modulators for E3 ligases and deubiquitinases, enzymes that control the specificity of protein ubiquitination and deubiquitination, respectively. Here, we describe methods to generate libraries of ubiquitin variants and perform phage display selections to isolate high-affinity binders for target proteins. Importantly, the strategy introduced here can be applied to other small protein domains mediating protein-protein interactions to engineer tools for target validation and potential therapeutic development.
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Affiliation(s)
- Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada. .,Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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31
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Zhong M, Lee GM, Sijbesma E, Ottmann C, Arkin MR. Modulating protein-protein interaction networks in protein homeostasis. Curr Opin Chem Biol 2019; 50:55-65. [PMID: 30913483 DOI: 10.1016/j.cbpa.2019.02.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 12/12/2022]
Abstract
Protein-protein interactions (PPIs) occur in complex networks. These networks are highly dependent on cellular context and can be extensively altered in disease states such as cancer and viral infection. In recent years, there has been significant progress in developing inhibitors that target individual PPIs either orthosterically (at the interface) or allosterically. These molecules can now be used as tools to dissect PPI networks. Here, we review recent examples that highlight the use of small molecules and engineered proteins to probe PPIs within the complex networks that regulate protein homeostasis. Researchers have discovered multiple mechanisms to modulate PPIs involved in host/viral interactions, deubiquitinases, the ATPase p97/VCP, and HSP70 chaperones. However, few studies have evaluated the effect of such modulators on the target's network or have compared the biological implications of different modulation strategies. Such studies will have an important impact on next generation therapeutics.
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Affiliation(s)
- Mengqi Zhong
- Department of Pharmaceutical Chemistry and the Small Molecule Discovery Center, University of California, San Francisco, CA, USA
| | - Gregory M Lee
- Department of Pharmaceutical Chemistry and the Small Molecule Discovery Center, University of California, San Francisco, CA, USA
| | - Eline Sijbesma
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Christian Ottmann
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and the Small Molecule Discovery Center, University of California, San Francisco, CA, USA.
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32
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The ubiquitin interacting motifs of USP37 act on the proximal Ub of a di-Ub chain to enhance catalytic efficiency. Sci Rep 2019; 9:4119. [PMID: 30858488 PMCID: PMC6412040 DOI: 10.1038/s41598-019-40815-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/14/2019] [Indexed: 02/08/2023] Open
Abstract
USP37 is a deubiquitinase (DUB) with roles in the regulation of DNA damage repair and the cohesion of sister chromatids during mitosis. USP37 contains a unique insert of three ubiquitin interacting motifs (UIMs) within its catalytic DUB domain. We investigated the role of the three UIMs in the ability of USP37 to cleave di-ubiquitin chains. We found that the third UIM of USP37 recognizes the proximal ubiquitin moiety of K48 di-Ub to potentiate cleavage activity and posit that this mechanism of action may be generalizable to other chain types. In the case of K48-linked ubiquitin chains this potentiation stemmed largely from a dramatic increase in catalytic rate (kcat). We also developed and characterized three ubiquitin variant (UbV) inhibitors that selectively engage distinct binding sites in USP37. In addition to validating the deduced functional roles of the three UIMs in catalysis, the UbVs highlight a novel and effective means to selectively inhibit members of the difficult to drug DUB family.
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33
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Veggiani G, Gerpe MCR, Sidhu SS, Zhang W. Emerging drug development technologies targeting ubiquitination for cancer therapeutics. Pharmacol Ther 2019; 199:139-154. [PMID: 30851297 PMCID: PMC7112620 DOI: 10.1016/j.pharmthera.2019.03.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Development of effective cancer therapeutic strategies relies on our ability to interfere with cellular processes that are dysregulated in tumors. Given the essential role of the ubiquitin proteasome system (UPS) in regulating a myriad of cellular processes, it is not surprising that malfunction of UPS components is implicated in numerous human diseases, including many types of cancer. The clinical success of proteasome inhibitors in treating multiple myeloma has further stimulated enthusiasm for targeting UPS proteins for pharmacological intervention in cancer treatment, particularly in the precision medicine era. Unfortunately, despite tremendous efforts, the paucity of potent and selective UPS inhibitors has severely hampered attempts to exploit the UPS for therapeutic benefits. To tackle this problem, many groups have been working on technology advancement to rapidly and effectively screen for potent and specific UPS modulators as intracellular probes or early-phase therapeutic agents. Here, we review several emerging technologies for developing chemical- and protein-based molecules to manipulate UPS enzymatic activity, with the aim of providing an overview of strategies available to target ubiquitination for cancer therapy.
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Affiliation(s)
- Gianluca Veggiani
- The Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - María Carla Rosales Gerpe
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E., Guelph, Ontario N1G2W1, Canada
| | - Sachdev S Sidhu
- The Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada.
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E., Guelph, Ontario N1G2W1, Canada.
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34
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USP7: Structure, substrate specificity, and inhibition. DNA Repair (Amst) 2019; 76:30-39. [PMID: 30807924 DOI: 10.1016/j.dnarep.2019.02.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/07/2019] [Indexed: 12/24/2022]
Abstract
Turnover of cellular proteins is regulated by Ubiquitin Proteasome System (UPS). Components of this pathway, including the proteasome, ubiquitinating enzymes and deubiquitinating enzymes, are highly specialized and tightly regulated. In this mini-review we focus on the de-ubiquitinating enzyme USP7, and summarize latest advances in understanding its structure, substrate specificity and relevance to human cancers. There is increasing interest in UPS components as targets for cancer therapy and here we also overview the recent progress in the development of small molecule inhibitors that target USP7.
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35
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Pascoe N, Seetharaman A, Teyra J, Manczyk N, Satori MA, Tjandra D, Makhnevych T, Schwerdtfeger C, Brasher BB, Moffat J, Costanzo M, Boone C, Sicheri F, Sidhu SS. Yeast Two-Hybrid Analysis for Ubiquitin Variant Inhibitors of Human Deubiquitinases. J Mol Biol 2019; 431:1160-1171. [PMID: 30763569 DOI: 10.1016/j.jmb.2019.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/01/2019] [Accepted: 02/06/2019] [Indexed: 11/20/2022]
Abstract
We applied a yeast-two-hybrid (Y2H) analysis to screen for ubiquitin variant (UbV) inhibitors of a human deubiquitinase (DUB), ubiquitin-specific protease 2 (USP2). The Y2H screen used USP2 as the bait and a prey library consisting of UbVs randomized at four specific positions, which were known to interact with USP2 from phage display analysis. The screen yielded numerous UbVs that bound to USP2 both as a Y2H interaction in vivo and as purified proteins in vitro. The Y2H-derived UbVs inhibited the catalytic activity of USP2 in vitro with nanomolar-range potencies, and they bound and inhibited USP2 in human cells. Mutational and structural analysis showed that potent and selective inhibition could be achieved by just two substitutions in a UbV, which exhibited improved hydrophobic and hydrophilic contacts compared to the wild-type ubiquitin interaction with USP2. Our results establish Y2H as an effective platform for the development of UbV inhibitors of DUBs in vivo, providing an alternative strategy for the analysis of DUBs that are recalcitrant to phage display and other in vitro methods.
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Affiliation(s)
- Natasha Pascoe
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Ashwin Seetharaman
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Joan Teyra
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Maria Augusta Satori
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Donna Tjandra
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Taras Makhnevych
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | | | - Bradley B Brasher
- Boston Biochem, a Bio-Techne Brand 840 Memorial Drive, Cambridge, MA 02139, USA
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON, M5G1Z8, Canada
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON, M5G1Z8, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON, M5G1Z8, Canada
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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36
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Teyra J, Singer AU, Schmitges FW, Jaynes P, Kit Leng Lui S, Polyak MJ, Fodil N, Krieger JR, Tong J, Schwerdtfeger C, Brasher BB, Ceccarelli DFJ, Moffat J, Sicheri F, Moran MF, Gros P, Eichhorn PJA, Lenter M, Boehmelt G, Sidhu SS. Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Structure 2019; 27:590-605.e5. [PMID: 30713027 DOI: 10.1016/j.str.2019.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/23/2018] [Accepted: 12/31/2018] [Indexed: 12/12/2022]
Abstract
The multi-domain deubiquitinase USP15 regulates diverse eukaryotic processes and has been implicated in numerous diseases. We developed ubiquitin variants (UbVs) that targeted either the catalytic domain or each of three adaptor domains in USP15, including the N-terminal DUSP domain. We also designed a linear dimer (diUbV), which targeted the DUSP and catalytic domains, and exhibited enhanced specificity and more potent inhibition of catalytic activity than either UbV alone. In cells, the UbVs inhibited the deubiquitination of two USP15 substrates, SMURF2 and TRIM25, and the diUbV inhibited the effects of USP15 on the transforming growth factor β pathway. Structural analyses revealed that three distinct UbVs bound to the catalytic domain and locked the active site in a closed, inactive conformation, and one UbV formed an unusual strand-swapped dimer and bound two DUSP domains simultaneously. These inhibitors will enable the study of USP15 function in oncology, neurology, immunology, and inflammation.
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Affiliation(s)
- Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Alex U Singer
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frank W Schmitges
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sarah Kit Leng Lui
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Maria J Polyak
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Nassima Fodil
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Jonathan R Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jiefei Tong
- Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | | | - Bradley B Brasher
- Boston Biochem, a Bio-Techne Brand, 840 Memorial Drive, Cambridge, MA 02139, USA
| | - Derek F J Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael F Moran
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Pieter J A Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Martin Lenter
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | | | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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37
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Gjonaj L, Sapmaz A, González-Prieto R, Vertegaal ACO, Flierman D, Ovaa H. USP7: combining tools towards selectivity. Chem Commun (Camb) 2019; 55:5075-5078. [PMID: 30972393 DOI: 10.1039/c9cc00969h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Active-site directed probes based on the ubiquitin scaffold have been successfully applied as tools to determine the levels of active deubiquitinating enzymes (DUBs). Here, we show the development of a Ub-based reagent selective for the DUB USP7. This concept can be applied for the generation of other new selective reagents.
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Affiliation(s)
- Lorina Gjonaj
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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38
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Yeasmin Khusbu F, Chen FZ, Chen HC. Targeting ubiquitin specific protease 7 in cancer: A deubiquitinase with great prospects. Cell Biochem Funct 2018; 36:244-254. [PMID: 29781103 DOI: 10.1002/cbf.3336] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/21/2018] [Accepted: 04/23/2018] [Indexed: 12/20/2022]
Abstract
Deubiquitinase (DUB)-mediated cleavage of ubiquitin chain balances ubiquitination and deubiquitination for determining protein fate. USP7 is one of the best characterized DUBs and functionally important. Numerous proteins have been identified as potential substrates and binding partners of USP7; those play crucial roles in diverse array of cellular and biological processes including tumour suppression, cell cycle, DNA repair, chromatin remodelling, and epigenetic regulation. This review aims at summarizing the current knowledge of this wide association of USP7 with many cellular processes that enlightens the possibility of abnormal USP7 activity in promoting oncogenesis and the importance of identification of specific inhibitors.
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Affiliation(s)
- Farjana Yeasmin Khusbu
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Fang-Zhi Chen
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Han-Chun Chen
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
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39
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Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sibbet GJ, Smith BO, Zhang W, Sidhu SS, Huang DT. A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants. Mol Cell 2017; 68:456-470.e10. [PMID: 29053960 PMCID: PMC5655547 DOI: 10.1016/j.molcel.2017.09.027] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/09/2017] [Accepted: 09/20/2017] [Indexed: 10/26/2022]
Abstract
RING and U-box E3 ubiquitin ligases regulate diverse eukaryotic processes and have been implicated in numerous diseases, but targeting these enzymes remains a major challenge. We report the development of three ubiquitin variants (UbVs), each binding selectively to the RING or U-box domain of a distinct E3 ligase: monomeric UBE4B, phosphorylated active CBL, or dimeric XIAP. Structural and biochemical analyses revealed that UbVs specifically inhibited the activity of UBE4B or phosphorylated CBL by blocking the E2∼Ub binding site. Surprisingly, the UbV selective for dimeric XIAP formed a dimer to stimulate E3 activity by stabilizing the closed E2∼Ub conformation. We further verified the inhibitory and stimulatory functions of UbVs in cells. Our work provides a general strategy to inhibit or activate RING/U-box E3 ligases and provides a resource for the research community to modulate these enzymes.
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Affiliation(s)
- Mads Gabrielsen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lori Buetow
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Mark A Nakasone
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Syed Feroj Ahmed
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Gary J Sibbet
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Brian O Smith
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada.
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada.
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK.
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40
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Kumari N, Jaynes PW, Saei A, Iyengar PV, Richard JLC, Eichhorn PJA. The roles of ubiquitin modifying enzymes in neoplastic disease. Biochim Biophys Acta Rev Cancer 2017; 1868:456-483. [PMID: 28923280 DOI: 10.1016/j.bbcan.2017.09.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/22/2022]
Abstract
The initial experiments performed by Rose, Hershko, and Ciechanover describing the identification of a specific degradation signal in short-lived proteins paved the way to the discovery of the ubiquitin mediated regulation of numerous physiological functions required for cellular homeostasis. Since their discovery of ubiquitin and ubiquitin function over 30years ago it has become wholly apparent that ubiquitin and their respective ubiquitin modifying enzymes are key players in tumorigenesis. The human genome encodes approximately 600 putative E3 ligases and 80 deubiquitinating enzymes and in the majority of cases these enzymes exhibit specificity in sustaining either pro-tumorigenic or tumour repressive responses. In this review, we highlight the known oncogenic and tumour suppressive effects of ubiquitin modifying enzymes in cancer relevant pathways with specific focus on PI3K, MAPK, TGFβ, WNT, and YAP pathways. Moreover, we discuss the capacity of targeting DUBs as a novel anticancer therapeutic strategy.
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Affiliation(s)
- Nishi Kumari
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Patrick William Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Azad Saei
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore; Genome Institute of Singapore, A*STAR, Singapore
| | | | | | - Pieter Johan Adam Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.
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