1
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Imhoff RD, Rosenthal MR, Ashraf K, Bhanot P, Ng CL, Flaherty DP. Identification of covalent fragment inhibitors for Plasmodium falciparum UCHL3 with anti-malarial efficacy. Bioorg Med Chem Lett 2023; 94:129458. [PMID: 37634761 PMCID: PMC10529062 DOI: 10.1016/j.bmcl.2023.129458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/07/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Malaria continues to be a major burden on global health, responsible for 619,000 deaths in 2021. The causative agent of malaria is the eukaryotic parasite Plasmodium. Resistance to artemisinin-based combination therapies (ACTs), the current first-line treatment for malaria, has emerged in Asia, South America, and more recently Africa, where >90% of all malaria-related deaths occur. This has necessitated the identification and investigation of novel parasite proteins and pathways as antimalarial targets, including components of the ubiquitin proteasome system. Here, we investigate Plasmodium falciparum deubiquitinase ubiquitin C-terminal hydrolase L3 (PfUCHL3) as one such target. We carried out a high-throughput screen with covalent fragments and identified seven scaffolds that selectively inhibit the plasmodial UCHL3, but not human UCHL3 or the closely related human UCHL1. After assessing toxicity in human cells, we identified four promising hits and demonstrated their efficacy against asexual P. falciparum blood stages and P. berghei sporozoite stages.
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Affiliation(s)
- Ryan D Imhoff
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, United States
| | - Melissa R Rosenthal
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Kutub Ashraf
- Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, United States
| | - Purnima Bhanot
- Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, United States
| | - Caroline L Ng
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States; Global Center for Health Security, University of Nebraska Medical Center, Omaha, NE 68198, United States; Department of Biology, University of Omaha, Omaha, NE 68182, United States.
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, United States; Purdue Institute for Drug Discovery, West Lafayette, IN 47907, United States; Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN 47907, United States.
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2
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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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3
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Kao HW, Lu WL, Ho MR, Lin YF, Hsieh YJ, Ko TP, Danny Hsu ST, Wu KP. Robust Design of Effective Allosteric Activators for Rsp5 E3 Ligase Using the Machine Learning Tool ProteinMPNN. ACS Synth Biol 2023; 12:2310-2319. [PMID: 37556858 DOI: 10.1021/acssynbio.3c00042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
We used the deep learning tool ProteinMPNN to redesign ubiquitin (Ub) as a specific and functionally stimulating/enhancing binder of the Rsp5 E3 ligase. We generated 20 extensively mutated─up to 37 of 76 residues─recombinant Ub variants (UbVs), named R1 to R20, displaying well-folded structures and high thermal stabilities. These UbVs can also form stable complexes with Rsp5, as predicted using AlphaFold2. Three of the UbVs bound to Rsp5 with low micromolar affinity, with R4 and R12 effectively enhancing the Rsp5 activity six folds. AlphaFold2 predicts that R4 and R12 bind to Rsp5's exosite in an identical manner to the Rsp5-Ub template, thereby allosterically activating Rsp5-Ub thioester formation. Thus, we present a virtual solution for rapidly and cost-effectively designing UbVs as functional modulators of Ub-related enzymes.
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Affiliation(s)
- Hsi-Wen Kao
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Wei-Lin Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Fong Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Institute of Biochemical Science, National Taiwan University, Taipei 106, Taiwan
| | - Yun-Jung Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Institute of Biochemical Science, National Taiwan University, Taipei 106, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Institute of Biochemical Science, National Taiwan University, Taipei 106, Taiwan
- International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashihiroshima 739-8527, Japan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Institute of Biochemical Science, National Taiwan University, Taipei 106, Taiwan
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4
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Zmudzinski M, Malon O, Poręba M, Drąg M. Imaging of proteases using activity-based probes. Curr Opin Chem Biol 2023; 74:102299. [PMID: 37031620 DOI: 10.1016/j.cbpa.2023.102299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023]
Abstract
Proteases (proteolytic enzymes) are proteins that catalyze one of the most important biochemical reactions, namely the hydrolysis of the peptide bond in peptide and protein substrates. Therefore these molecular biocatalysts participate in virtually all living processes. The proper balance between intact and processed protease substrates enables to maintenance of homeostasis from a single-cell level to the whole living system. However, when the proteolytic activity is altered, this delicate balance is disturbed, which might lead to the development of a plethora of diseases. Given this, monitoring proteolytic activity is indispensable to understanding how proteases operate in disease lesions and how their altered catalytic activity might be harnessed for a better diagnosis and treatment. In this manuscript, we provide a critical review of the recent development of protease chemical probes which are small molecules that detect proteolytic activity by interacting with protease active site, individual proteases as well as complex proteolytic networks.
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Affiliation(s)
- Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wrocław, Poland
| | - Oliwia Malon
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wrocław, Poland
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wrocław, Poland.
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wrocław, Poland.
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Stekel Z, Sheng Y, Zhang W. The Multifaceted Role of the Ubiquitin Proteasome System in Pathogenesis and Diseases. Biomolecules 2022; 12:biom12070925. [PMID: 35883481 PMCID: PMC9313328 DOI: 10.3390/biom12070925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 02/05/2023] Open
Abstract
Ubiquitin is a small protein that is conjugated to target proteins to signal a great number of critical biological processes. Impaired ubiquitin signaling and defects in the ubiquitin proteasome system (UPS) surveillance are implicated in many human diseases, including cancer. Characterization of the physiological roles of UPS components and their regulatory mechanisms is therefore vital for the identification of therapeutic targets and the development of tools and paradigms to better understand and treat human diseases. In this Special Issue, we assembled seven original research and review articles to provide insights on the multifaceted role of the UPS in pathogenesis and disease, covering the areas of molecular and cellular mechanisms of UPS enzymes, biochemical and biophysical characterization strategies, drug development, and targeted protein degradation.
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Affiliation(s)
- Zane Stekel
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2W1, Canada;
| | - Yi Sheng
- Department of Biology, York University, Room 327B Life Science Building, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Correspondence: (Y.S.); (W.Z.)
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2W1, Canada;
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
- Correspondence: (Y.S.); (W.Z.)
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6
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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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7
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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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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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9
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Kim HR, Tagirasa R, Yoo E. Covalent Small Molecule Immunomodulators Targeting the Protease Active Site. J Med Chem 2021; 64:5291-5322. [PMID: 33904753 DOI: 10.1021/acs.jmedchem.1c00172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cells of the immune system utilize multiple proteases to regulate cell functions and orchestrate innate and adaptive immune responses. Dysregulated protease activities are implicated in many immune-related disorders; thus, protease inhibitors have been actively investigated for pharmaceutical development. Although historically considered challenging with concerns about toxicity, compounds that covalently modify the protease active site represent an important class of agents, emerging not only as chemical probes but also as approved drugs. Here, we provide an overview of technologies useful for the study of proteases with the focus on recent advances in chemoproteomic methods and screening platforms. By highlighting covalent inhibitors that have been designed to target immunomodulatory proteases, we identify opportunities for the development of small molecule immunomodulators.
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Affiliation(s)
- Hong-Rae Kim
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ravichandra Tagirasa
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Euna Yoo
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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10
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Krabill AD, Chen H, Hussain S, Hewitt CS, Imhoff RD, Muli CS, Das C, Galardy PJ, Wendt MK, Flaherty DP. Optimization and Anti-Cancer Properties of Fluoromethylketones as Covalent Inhibitors for Ubiquitin C-Terminal Hydrolase L1. Molecules 2021; 26:1227. [PMID: 33668938 PMCID: PMC7956625 DOI: 10.3390/molecules26051227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Abstract
The deubiquitinating enzyme (DUB) UCHL1 is implicated in various disease states including neurodegenerative disease and cancer. However, there is a lack of quality probe molecules to gain a better understanding on UCHL1 biology. To this end a study was carried out to fully characterize and optimize the irreversible covalent UCHL1 inhibitor VAEFMK. Structure-activity relationship studies identified modifications to improve activity versus the target and a full cellular characterization was carried out for the first time with this scaffold. The studies produced a new inhibitor, 34, with an IC50 value of 7.7 µM against UCHL1 and no observable activity versus the closest related DUB UCHL3. The molecule was also capable of selectively inhibiting UCHL1 in cells and did not demonstrate any discernible off-target toxicity. Finally, the molecule was used for initial probe studies to assess the role of UCHL1 role in proliferation of myeloma cells and migration behavior in small cell lung cancer cells making 34 a new tool to be used in the biological evaluation of UCHL1.
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Affiliation(s)
- Aaron D. Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Hao Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Sajjad Hussain
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. Guggenheim 15, Rochester, MN 55905, USA; (S.H.); (P.J.G.)
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First St. Guggenheim 15, Rochester, MN 55905, USA
| | - Chad S. Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Ryan D. Imhoff
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Christine S. Muli
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Chittaranjan Das
- Department of Chemistry, College of Science, 560 Oval Dr., West Lafayette, IN 47907, USA;
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 University St., West Lafayette, IN 47907, USA
| | - Paul J. Galardy
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. Guggenheim 15, Rochester, MN 55905, USA; (S.H.); (P.J.G.)
| | - Michael K. Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 University St., West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Ln., West Lafayette, IN 47907, USA
| | - Daniel P. Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 University St., West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Ln., West Lafayette, IN 47907, USA
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