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Li K, Hou Y, Han J, Lv C, Liu W, Du J, Sun W, Fan J, Peng X. A non-peptide-based fluorescent probe capable of sensitively visualizing asparagine endopeptidase. Chem Commun (Camb) 2024; 60:3031-3034. [PMID: 38391081 DOI: 10.1039/d3cc05419e] [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: 02/24/2024]
Abstract
The non-peptide-based fluorescent probe QMC11 is capable of specifically targeting asparagine endopeptidase (AEP) and imaging cellular endogenous AEP. The motion of the probe can be restricted by AEP to activate fluorescence while keeping a low background signal.
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Affiliation(s)
- Kang Li
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Yanxian Hou
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Jinliang Han
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Chengyuan Lv
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Wenkai Liu
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Jianjun Du
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Jiangli Fan
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
- Ningbo Institute of Dalian University of Technology, Ningbo 315016, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
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Swenson CS, Pillai KS, Carlos AJ, Moellering RE. Spatial Chemoproteomics for Mapping the Active Proteome. Isr J Chem 2023; 63:e202200104. [PMID: 38046285 PMCID: PMC10688764 DOI: 10.1002/ijch.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Indexed: 01/06/2023]
Abstract
Functional regulation of cell signaling through dynamic changes in protein activity state as well as spatial organization represent two dynamic, complex, and conserved phenomena in biology. Seemingly separate areas of -omics method development have focused on building tools that can detect and quantify protein activity states, as well as map sub-cellular and intercellular protein organization. Integration of these efforts, through the development of chemical tools and platforms that enable detection and quantification of protein functional states with spatial resolution provide opportunities to better understand heterogeneity in the proteome within cell organelles, multi-cellular tissues, and whole organisms. This review provides an overview of and considerations for major classes of chemical proteomic probes and technologies that enable protein activity mapping from sub-cellular compartments to live animals.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Kavya Smitha Pillai
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Anthony J Carlos
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
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The Asparaginyl Endopeptidase Legumain: An Emerging Therapeutic Target and Potential Biomarker for Alzheimer’s Disease. Int J Mol Sci 2022; 23:ijms231810223. [PMID: 36142134 PMCID: PMC9499314 DOI: 10.3390/ijms231810223] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
Alzheimer’s disease (AD) is incurable dementia closely associated with aging. Most cases of AD are sporadic, and very few are inherited; the pathogenesis of sporadic AD is complex and remains to be elucidated. The asparaginyl endopeptidase (AEP) or legumain is the only recognized cysteine protease that specifically hydrolyzes peptide bonds after asparagine residues in mammals. The expression level of AEPs in healthy brains is far lower than that of peripheral organs. Recently, growing evidence has indicated that aging may upregulate and overactivate brain AEPs. The overactivation of AEPs drives the onset of AD through cleaving tau and amyloid precursor proteins (APP), and SET, an inhibitor of protein phosphatase 2A (PP2A). The AEP-mediated cleavage of these peptides enhances amyloidosis, promotes tau hyperphosphorylation, and ultimately induces neurodegeneration and cognitive impairment. Upregulated AEPs and related deleterious reactions constitute upstream events of amyloid/tau toxicity in the brain, and represent early pathological changes in AD. Thus, upregulated AEPs are an emerging drug target for disease modification and a potential biomarker for predicting preclinical AD. However, the presence of the blood–brain barrier greatly hinders establishing body-fluid-based methods to measure brain AEPs. Research on AEP-activity-based imaging probes and our recent work suggest that the live brain imaging of AEPs could be used to evaluate its predictive efficacy as an AD biomarker. To advance translational research in this area, AEP imaging probes applicable to human brain and AEP inhibitors with good druggability are urgently needed.
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Walker E, Linders DGJ, Abenojar E, Wang X, Hazelbag HM, Straver ME, Bijlstra OD, March TL, Vahrmeijer AL, Exner A, Bogyo M, Basilion JP, Straight B. Formulation of a Thermosensitive Imaging Hydrogel for Topical Application and Rapid Visualization of Tumor Margins in the Surgical Cavity. Cancers (Basel) 2022; 14:cancers14143459. [PMID: 35884520 PMCID: PMC9323389 DOI: 10.3390/cancers14143459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 01/07/2023] Open
Abstract
Simple Summary We have developed a formulation for an innovative, quenched, cathepsin-targeted, fluorescent molecular probe to enhance resection quality for several solid-tumor cancers. Unlike other formulations for imaging probes or tracers in development and entering the clinic, which require systemic administration hours before the procedure, this current formulation is applied topically into the surgical cavity immediately after a standard of care resection. Within minutes of application, the probe activates in the presence of residual cancer in the surgical wound and provides a strong fluorescent signal that precisely delineates any remaining cancer, enabling a more complete resection. Utilization of this imaging gel formulation for topical application to detect breast cancer in the surgical cavity during surgery has the potential to reduce re-excisions, with consequent savings in healthcare costs and enhancement in patient quality of life. Abstract Background: Tumor-positive surgical margins during primary breast cancer (BCa) surgery are associated with a two-fold increase in the risk of local recurrence when compared with tumor-negative margins. Pathological microscopic evaluation of the samples only assesses about 1/10 of 1% of the entire volume of the removed BCa specimens, leading to margin under-sampling and potential local recurrence in patients with pathologically clean margins, i.e., false negative margins. In the case of tumor-positive margins, patients need to undergo re-excision and/or radiation therapy, resulting in increases in complications, morbidity, and healthcare costs. Development of a simple real-time imaging technique to identify residual BCa in the surgical cavity rapidly and precisely could significantly improve the quality of care. Methods: A small-molecule, fluorescently quenched protease-substrate probe, AKRO-QC-ICG, was tested as part of a thermosensitive imaging gel formulated for topical application and imaging of the BCa surgical cavity. Results: More than forty formulations of gel mixtures were investigated to enable easy fluid application and subsequent solidification once applied, preventing dripping and pooling in the surgical cavity. The final formulation was tested using human BCa orthotopic implants in nude and NSG patient-derived xenografts (PDX) mice. This formulation of Pluronic F-127/DMSO/AKRO-QC-ICG imaging gel was found to be a good solvent for the probe, with a desirable thermo-reversible solid–gel transition and mechanical strength for distribution of AKRO-QC-ICG on the surfaces of tissue. It demonstrated excellent ability to detect BCa tissue after 10 min exposure, with a high signal-to-noise ratio both in mouse xenografts and freshly excised human lumpectomy tissue. The in vivo efficacy of the AKRO-QC-ICG imaging gel to detect BCa revealed the levels of sensitivity/specificity = 0.92/1 in 12 nude mice, which was corroborated with the sensitivity/specificity = 0.94/1 in 10 PDX mice. Conclusions: Utilization of Pluronic F-127/DMSO/AKRO-QC-ICG imaging gel for topical application to detect BCa in the surgical cavity during surgery has the potential to reduce re-excisions, with consequent savings in healthcare costs and enhancement in patient quality of life.
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Affiliation(s)
- Ethan Walker
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA; (E.W.); (X.W.); (A.E.); (J.P.B.)
| | - Daan G. J. Linders
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (D.G.J.L.); (O.D.B.); (A.L.V.)
| | - Eric Abenojar
- Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Xinning Wang
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA; (E.W.); (X.W.); (A.E.); (J.P.B.)
| | - Hans Marten Hazelbag
- Department of Pathology, Haaglanden Medical Center, 2512 VA The Hague, The Netherlands;
| | - Marieke E. Straver
- Department of Surgery, Haaglanden Medical Center, 2512 VA The Hague, The Netherlands;
| | - Okker D. Bijlstra
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (D.G.J.L.); (O.D.B.); (A.L.V.)
| | - Taryn L. March
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
| | - Alexander L. Vahrmeijer
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (D.G.J.L.); (O.D.B.); (A.L.V.)
| | - Agata Exner
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA; (E.W.); (X.W.); (A.E.); (J.P.B.)
- Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Matthew Bogyo
- Department of Pathology, Stanford University, Stanford, CA 94305, USA;
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - James P. Basilion
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA; (E.W.); (X.W.); (A.E.); (J.P.B.)
- Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA;
- Akrotome Imaging Inc., Charlotte, NC 28205, USA
| | - Brian Straight
- Akrotome Imaging Inc., Charlotte, NC 28205, USA
- Correspondence: ; Tel.: +1-216-983-3264
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Fundamentals and developments in fluorescence-guided cancer surgery. Nat Rev Clin Oncol 2022; 19:9-22. [PMID: 34493858 DOI: 10.1038/s41571-021-00548-3] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Fluorescence-guided surgery using tumour-targeted imaging agents has emerged over the past decade as a promising and effective method of intraoperative cancer detection. An impressive number of fluorescently labelled antibodies, peptides, particles and other molecules related to cancer hallmarks have been developed for the illumination of target lesions. New approaches are being implemented to translate these imaging agents into the clinic, although only a few have made it past early-phase clinical trials. For this translational process to succeed, target selection, imaging agents and their related detection systems and clinical implementation have to operate in perfect harmony to enable real-time intraoperative visualization that can benefit patients. Herein, we review key aspects of this imaging cascade and focus on imaging approaches and methods that have helped to shed new light onto the field of intraoperative fluorescence-guided cancer surgery with the singular goal of improving patient outcomes.
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Wang SS, Liu ZK, Liu JJ, Cheng Q, Wang YX, Liu Y, Ni WW, Chen HZ, Song M. Imaging asparaginyl endopeptidase (AEP) in the live brain as a biomarker for Alzheimer's disease. J Nanobiotechnology 2021; 19:249. [PMID: 34412639 PMCID: PMC8375181 DOI: 10.1186/s12951-021-00988-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/05/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Discovery of early-stage biomarkers is a long-sought goal of Alzheimer's disease (AD) diagnosis. Age is the greatest risk factor for most AD and accumulating evidence suggests that age-dependent elevation of asparaginyl endopeptidase (AEP) in the brain may represent a new biological marker for predicting AD. However, this speculation remains to be explored with an appropriate assay method because mammalian AEP exists in many organs and the level of AEP in body fluid isn't proportional to its concentration in brain parenchyma. To this end, we here modified gold nanoparticle (AuNPs) into an AEP-responsive imaging probe and choose transgenic APPswe/PS1dE9 (APP/PS1) mice as an animal model of AD. Our aim is to determine whether imaging of brain AEP can be used to predict AD pathology. RESULTS This AEP-responsive imaging probe AuNPs-Cy5.5-A&C consisted of two particles, AuNPs-Cy5.5-AK and AuNPs-Cy5.5-CABT, which were respectively modified with Ala-Ala-Asn-Cys-Lys (AK) and 2-cyano-6-aminobenzothiazole (CABT). We showed that AuNPs-Cy5.5-A&C could be selectively activated by AEP to aggregate and emit strong fluorescence. Moreover, AuNPs-Cy5.5-A&C displayed a general applicability in various cell lines and its florescence intensity correlated well with AEP activity in these cells. In the brain of APP/PS1 transgenic mice , AEP activity was increased at an early disease stage of AD that precedes formation of senile plaques and cognitive impairment. Pharmacological inhibition of AEP with δ-secretase inhibitor 11 (10 mg kg-1, p.o.) reduced production of β-amyloid (Aβ) and ameliorated memory loss. Therefore, elevation of AEP is an early sign of AD onset. Finally, we showed that live animal imaging with this AEP-responsive probe could monitor the up-regulated AEP in the brain of APP/PS1 mice. CONCLUSIONS The current work provided a proof of concept that assessment of brain AEP activity by in vivo imaging assay is a potential biomarker for early diagnosis of AD.
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Affiliation(s)
- Shan-Shan Wang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Zi-Kai Liu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Jing-Jing Liu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Qing Cheng
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Yan-Xia Wang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Yan Liu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Wen-Wen Ni
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Hong-Zhuan Chen
- Institute of Interdisciplinary Integrative Biomedical Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201210, China.
| | - Mingke Song
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
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Fang H, Peng B, Ong SY, Wu Q, Li L, Yao SQ. Recent advances in activity-based probes (ABPs) and affinity-based probes (A fBPs) for profiling of enzymes. Chem Sci 2021; 12:8288-8310. [PMID: 34221311 PMCID: PMC8221178 DOI: 10.1039/d1sc01359a] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a technique that uses highly selective active-site targeted chemical probes to label and monitor the state of proteins. ABPP integrates the strengths of both chemical and biological disciplines. By utilizing chemically synthesized or modified bioactive molecules, ABPP is able to reveal complex physiological and pathological enzyme-substrate interactions at molecular and cellular levels. It is also able to provide critical information of the catalytic activity changes of enzymes, annotate new functions of enzymes, discover new substrates of enzymes, and allow real-time monitoring of the cellular location of enzymes. Based on the mechanism of probe-enzyme interaction, two types of probes that have been used in ABPP are activity-based probes (ABPs) and affinity-based probes (AfBPs). This review highlights the recent advances in the use of ABPs and AfBPs, and summarizes their design strategies (based on inhibitors and substrates) and detection approaches.
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Affiliation(s)
- Haixiao Fang
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 P. R. China
| | - Sing Yee Ong
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
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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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Vizovisek M, Ristanovic D, Menghini S, Christiansen MG, Schuerle S. The Tumor Proteolytic Landscape: A Challenging Frontier in Cancer Diagnosis and Therapy. Int J Mol Sci 2021; 22:ijms22052514. [PMID: 33802262 PMCID: PMC7958950 DOI: 10.3390/ijms22052514] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
In recent decades, dysregulation of proteases and atypical proteolysis have become increasingly recognized as important hallmarks of cancer, driving community-wide efforts to explore the proteolytic landscape of oncologic disease. With more than 100 proteases currently associated with different aspects of cancer development and progression, there is a clear impetus to harness their potential in the context of oncology. Advances in the protease field have yielded technologies enabling sensitive protease detection in various settings, paving the way towards diagnostic profiling of disease-related protease activity patterns. Methods including activity-based probes and substrates, antibodies, and various nanosystems that generate reporter signals, i.e., for PET or MRI, after interaction with the target protease have shown potential for clinical translation. Nevertheless, these technologies are costly, not easily multiplexed, and require advanced imaging technologies. While the current clinical applications of protease-responsive technologies in oncologic settings are still limited, emerging technologies and protease sensors are poised to enable comprehensive exploration of the tumor proteolytic landscape as a diagnostic and therapeutic frontier. This review aims to give an overview of the most relevant classes of proteases as indicators for tumor diagnosis, current approaches to detect and monitor their activity in vivo, and associated therapeutic applications.
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Benns HJ, Wincott CJ, Tate EW, Child MA. Activity- and reactivity-based proteomics: Recent technological advances and applications in drug discovery. Curr Opin Chem Biol 2020; 60:20-29. [PMID: 32768892 DOI: 10.1016/j.cbpa.2020.06.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
Activity-based protein profiling (ABPP) is recognized as a powerful and versatile chemoproteomic technology in drug discovery. Central to ABPP is the use of activity-based probes to report the activity of specific enzymes or reactivity of amino acid types in complex biological systems. Over the last two decades, ABPP has facilitated the identification of new drug targets and discovery of lead compounds in human and infectious disease. Furthermore, as part of a sustained global effort to illuminate the druggable proteome, the repertoire of target classes addressable with activity-based probes has vastly expanded in recent years. Here, we provide an overview of ABPP and summarise the major technological advances with an emphasis on probe development.
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Affiliation(s)
- Henry James Benns
- Department of Life Sciences, London, UK; Department of Chemistry, Imperial College London, London, UK
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Poreba M. Recent advances in the development of legumain-selective chemical probes and peptide prodrugs. Biol Chem 2020; 400:1529-1550. [PMID: 31021817 DOI: 10.1515/hsz-2019-0135] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
Abstract
Legumain, which is also known as vacuolar processing enzyme (VPE) or asparaginyl endopeptidase (AEP), is a cysteine protease that was first discovered and characterized in the leguminous seeds of the moth bean in the early 1990s. Later, this enzyme was also detected in higher organisms, including eukaryotes. This pH-dependent protease displays the highest activity in acidic endolysosomal compartments; however, legumain also displays nuclear, cytosolic and extracellular activity when stabilized by other proteins or intramolecular complexes. Based on the results from over 25 years of research, this protease is involved in multiple cellular events, including protein degradation and antigen presentation. Moreover, when dysregulated, this protease contributes to the progression of several diseases, with cancer being the well-studied example. Research on legumain biology was undoubtedly facilitated by the use of small molecule chemical tools. Therefore, in this review, I present the historical perspectives and most current strategies for the development of small molecule substrates, inhibitors and activity-based probes for legumain. These tools are of paramount importance in elucidating the roles of legumain in multiple biological processes. Finally, as this enzyme appears to be a promising molecular target for anticancer therapies, the development of legumain-activated prodrugs is also described.
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Affiliation(s)
- Marcin Poreba
- Department of Bioorganic Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
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12
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Design of a New Peptide Substrate Probe of the Putative Biomarker Legumain with Potential Application in Prostate Cancer Diagnosis Ex Vivo. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09994-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractThe lysosomal endoprotease legumain (asparaginyl endoprotease) has been proposed as a putative biomarker in prostate tumours, in which the enzyme is markedly overexpressed. Overexpression, coupled with highly selective specificity for cleavage of substrates at the C-terminus of asparagine (Asn) residues, make legumain an attractive biochemical target for potential diagnosis, prognosis and treatment. We report the design, synthesis, characterisation and preliminary evaluation of a new rhodamine-B (Rho-B)-labelled legumain peptide substrate probe5[Rho-Pro-Ala-Asn-PEG-AQ(4-OH)] and its selective targeting to lysosomes in PC3 prostate cancer cells. Probe5was efficiently activated by recombinant human legumain to afford the high quantum yield reporter fluorophore tripeptide4b(Rho-Pro-Ala-Asn-OH) with concomitant release of intense fluorescence. Furthermore, probe5was activated upon incubation with homogenates derived from fresh-frozen tissue material of prostatectomy specimens. Probe5represents a new viable biochemical tool for probing the activity of legumain with the potential to be used in ex vivo diagnostics in the cancer pathology laboratory.
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Johnson SM, Dempsey C, Parker C, Mironov A, Bradley H, Saha V. Acute lymphoblastic leukaemia cells produce large extracellular vesicles containing organelles and an active cytoskeleton. J Extracell Vesicles 2017; 6:1294339. [PMID: 28386390 PMCID: PMC5373679 DOI: 10.1080/20013078.2017.1294339] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 01/26/2016] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles have been described in non-paracrine cellular interactions in cancer. We report a similar phenomenon in B-cell precursor (BCP) acute lymphoblastic leukaemia (ALL). Using advanced microscopy and high throughput screening, we further characterise a subset of large vesicles (LEVs) identified in cell lines, murine models of human BCP-ALL and clinical samples. Primary ALL blasts and cell lines released heterogeneous anucleate vesicles <6 micron into extracellular fluids. Larger LEVs were enclosed in continuous membranes, contained intact organelles and demonstrated an organised cytoskeleton. An excess of circulating CD19-positive LEVs were observed in diagnostic samples and isolated from mice engrafted with BCP-ALL primary cells. LEVs exhibited dynamic shape change in vitro and were internalised by other leukaemic cell lines leading to phenotypic transformation analogous to the cell of origin. In patient-derived xenografts, LEVs were released by primary ALL cells into extracellular spaces and internalised by murine mesenchymal cells in vivo. Collectively these data highlight the heterogeneity but accessibility of LEVs in clinical samples and their potential to provide a unique insight into the biology of the cell of origin and to their development as novel biomarkers to aid diagnosis and improve therapeutic outcomes.
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Affiliation(s)
- Suzanne M Johnson
- Children's Cancer Group, Division of Molecular and Clinical Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester , Manchester , UK
| | - Clare Dempsey
- Children's Cancer Group, Division of Molecular and Clinical Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester , Manchester , UK
| | - Catriona Parker
- Children's Cancer Group, Division of Molecular and Clinical Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester , Manchester , UK
| | - Aleksandr Mironov
- Children's Cancer Group, Division of Molecular and Clinical Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester , Manchester , UK
| | - Helen Bradley
- Faculty of Biology, Medicine and Health, CRUK Manchester Institute, University of Manchester , Manchester , UK
| | - Vaskar Saha
- Children's Cancer Group, Division of Molecular and Clinical Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Tata Translational Cancer Research Centre, Tata Medical Center, Kolkata, India
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14
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Walker E, Mann M, Honda K, Vidimos A, Schluchter MD, Straight B, Bogyo M, Popkin D, Basilion JP. Rapid visualization of nonmelanoma skin cancer. J Am Acad Dermatol 2017; 76:209-216.e9. [PMID: 27876303 PMCID: PMC5341746 DOI: 10.1016/j.jaad.2016.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Mohs micrographic surgery examines all margins of the resected sample and has a 99% cure rate. However, many nonmelanoma skin cancers (NMSCs) are not readily amenable to Mohs micrographic surgery. This defines an unmet clinical need to assess the completeness of non-Mohs micrographic surgery resections during surgery to prevent re-excision/recurrence. OBJECTIVE We sought to examine the utility of quenched activity-based probe imaging to discriminate cancerous versus normal-appearing skin tissue. METHODS The quenched activity-based probe GB119 was applied to NMSC excised from 68 patients. We validated activation of the probe for hematoxylin-eosin-confirmed cancerous tissue versus normal-appearing skin tissue. RESULTS Topical application of the probe differentiated basal cell carcinoma and squamous cell carcinoma from normal-appearing skin with overall estimated sensitivity and specificity of 0.989 (95% confidence interval 0.940-1.00) and 0.894 (95% confidence interval 0.769-0.965), respectively. Probe activation accurately defined peripheral margins of NMSC as compared with conventional hematoxylin-eosin-based pathology. LIMITATIONS This study only examined NMSC debulking excision specimens. The sensitivity and specificity for this approach using final NMSC excision margins will be clinically important. CONCLUSIONS These findings merit further studies to determine whether quenched activity-based probe technology may enable cost-effective increased cure rates for patients with NMSC by reducing re-excision and recurrence rates with a rapid and easily interpretable technological advance.
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Affiliation(s)
- Ethan Walker
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Margaret Mann
- Department of Dermatology, University Hospital, Cleveland, Ohio
| | - Kord Honda
- Department of Dermatology, University Hospital, Cleveland, Ohio
| | - Allison Vidimos
- Department of Dermatology, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Mark D Schluchter
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | | | - Matthew Bogyo
- Department of Pathology, Stanford University, Stanford, California; Department of Microbiology and Immunology, Stanford University, Stanford, California
| | - Daniel Popkin
- Department of Dermatology, University Hospital, Cleveland, Ohio
| | - James P Basilion
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio; Department of Radiology, Case Western Reserve University, Cleveland, Ohio; National Foundation for Cancer Research Center for Molecular Imaging, Case Western Reserve University, Cleveland, Ohio.
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15
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Srp J, Nussbaumerová M, Horn M, Mareš M. Digestive proteolysis in the Colorado potato beetle, Leptinotarsa decemlineata: Activity-based profiling and imaging of a multipeptidase network. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 78:1-11. [PMID: 27539253 DOI: 10.1016/j.ibmb.2016.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
The Colorado potato beetle (CPB), Leptinotarsa decemlineata, is a major pest of potato plants, and its digestive system is a promising target for development of pest control strategies. This work focuses on functional proteomic analysis of the digestive proteolytic enzymes expressed in the CPB gut. We identified a set of peptidases using imaging with specific activity-based probes and activity profiling with selective substrates and inhibitors. The secreted luminal peptidases were classified as: (i) endopeptidases of cathepsin D, cathepsin L, and trypsin types and (ii) exopeptidases with aminopeptidase (cathepsin H), carboxypeptidase (serine carboxypeptidase, prolyl carboxypeptidase), and carboxydipeptidase (cathepsin B) activities. The proteolytic arsenal also includes non-luminal peptidases with prolyl oligopeptidase and metalloaminopeptidase activities. Our results indicate that the CPB gut employs a multienzyme network of peptidases with complementary specificities to efficiently degrade ingested proteins. This proteolytic system functions in both CPB larvae and adults and is controlled mainly by cysteine and aspartic peptidases and supported by serine and metallopeptidases. The component enzymes identified here are potential targets for inhibitors with tailored specificities that could be engineered into potato plants to confer resistance to CPB.
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Affiliation(s)
- Jaroslav Srp
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 166 10, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 128 40, Czech Republic
| | - Martina Nussbaumerová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 166 10, Czech Republic
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 166 10, Czech Republic
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 166 10, Czech Republic.
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16
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Counter Selection Substrate Library Strategy for Developing Specific Protease Substrates and Probes. Cell Chem Biol 2016; 23:1023-35. [PMID: 27478158 DOI: 10.1016/j.chembiol.2016.05.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/11/2016] [Accepted: 05/30/2016] [Indexed: 01/29/2023]
Abstract
Legumain (AEP) is a lysosomal cysteine protease that was first characterized in leguminous seeds and later discovered in higher eukaryotes. AEP upregulation is linked to a number of diseases including inflammation, arteriosclerosis, and tumorigenesis. Thus this protease is an excellent molecular target for the development of new chemical markers. We deployed a hybrid combinatorial substrate library (HyCoSuL) approach to obtain P1-Asp fluorogenic substrates and biotin-labeled inhibitors that targeted legumain. Since this approach led to probes that were also recognized by caspases, we introduced a Counter Selection Substrate Library (CoSeSuL) approach that biases the peptidic scaffold against caspases, thus delivering highly selective legumain probes. The selectivity of these tools was validated using M38L and HEK293 cells. We also propose that the CoSeSuL methodology can be considered as a general principle in the design of selective probes for other protease families where selectivity is difficult to achieve by conventional sequence-based profiling.
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17
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Salvesen GS, Hempel A, Coll NS. Protease signaling in animal and plant-regulated cell death. FEBS J 2016; 283:2577-98. [PMID: 26648190 PMCID: PMC5606204 DOI: 10.1111/febs.13616] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/23/2015] [Accepted: 11/30/2015] [Indexed: 12/26/2022]
Abstract
This review aims to highlight the proteases required for regulated cell death mechanisms in animals and plants. The aim is to be incisive, and not inclusive of all the animal proteases that have been implicated in various publications. The review also aims to focus on instances when several publications from disparate groups have demonstrated the involvement of an animal protease, and also when there is substantial biochemical, mechanistic and genetic evidence. In doing so, the literature can be culled to a handful of proteases, covering most of the known regulated cell death mechanisms: apoptosis, regulated necrosis, necroptosis, pyroptosis and NETosis in animals. In plants, the literature is younger and not as extensive as for mammals, although the molecular drivers of vacuolar death, necrosis and the hypersensitive response in plants are becoming clearer. Each of these death mechanisms has at least one proteolytic component that plays a major role in controlling the pathway, and sometimes they combine in networks to regulate cell death/survival decision nodes. Some similarities are found among animal and plant cell death proteases but, overall, the pathways that they govern are kingdom-specific with very little overlap.
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Affiliation(s)
- Guy S. Salvesen
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Anne Hempel
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nuria Sanchez Coll
- Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra 08193, Barcelona, Spain
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18
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Mackay M, Pérez-López AM, Bradley M, Lilienkampf A. Eliminating caspase-7 and cathepsin B cross-reactivity on fluorogenic caspase-3 substrates. MOLECULAR BIOSYSTEMS 2016; 12:693-6. [PMID: 26726961 PMCID: PMC4763880 DOI: 10.1039/c5mb00730e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/07/2015] [Indexed: 12/11/2022]
Abstract
11 FRET-based fluorogenic substrates were constructed using the pentapeptide template Asp-Glu-X2-Asp-X1', and evaluated with caspase-3, caspase-7 and cathepsin B. The sequence Asp-Glu-Pro-Asp-Ser was able to selectively quantify caspase-3 activity in vitro without notable caspase-7 and cathepsin B cross-reactivity, while exhibiting low μM KM values and good catalytic efficiencies (7.0-16.9 μM(-1) min(-1)).
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Affiliation(s)
- Martha Mackay
- EaStCHEM, School of Chemistry, University of Edinburgh, West Mains Road, EH9 3FJ Edinburgh, UK.
| | - Ana M Pérez-López
- EaStCHEM, School of Chemistry, University of Edinburgh, West Mains Road, EH9 3FJ Edinburgh, UK.
| | - Mark Bradley
- EaStCHEM, School of Chemistry, University of Edinburgh, West Mains Road, EH9 3FJ Edinburgh, UK.
| | - Annamaria Lilienkampf
- EaStCHEM, School of Chemistry, University of Edinburgh, West Mains Road, EH9 3FJ Edinburgh, UK.
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19
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Shaulov-Rotem Y, Merquiol E, Weiss-Sadan T, Moshel O, Salpeter S, Shabat D, Kaschani F, Kaiser M, Blum G. A novel quenched fluorescent activity-based probe reveals caspase-3 activity in the endoplasmic reticulum during apoptosis. Chem Sci 2015; 7:1322-1337. [PMID: 29910890 PMCID: PMC5975724 DOI: 10.1039/c5sc03207e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/07/2015] [Indexed: 01/03/2023] Open
Abstract
A selective quenched activity-based probe detects caspase-3 activity in the endoplasmic reticulum of cancerous cells during apoptosis.
The caspases are a family of cysteine proteases that are key regulators of apoptosis and their activity may thus serve as a good marker to monitor cell death. We have developed a quenched fluorescent activity-based probe (qABP) that is selective for caspase-3 activity and emits a fluorescent signal after covalently modifying its target. The probe has a wide range of potential applications, e.g. in real-time imaging, FACS analysis or biochemical quantification of caspase activity in intact cells. Application of the probe allowed us to monitor caspase-3 activation after chemotherapy-treatment and to distinguish between apoptosis sensitive and resistant cells. Moreover, it enabled real-time high-resolution visualization of active caspase-3 during apoptosis. This led to the surprising finding that in cancerous cells active caspase-3 is not only found at the familiar cellular locations but also in mitochondria and the endoplasmic reticulum. Thus, our novel covalent probe allows high spatial and temporal resolution imaging of caspase-3 activation and may thus be used as an effective tool to study molecular mechanisms of programmed cell death in healthy and disease states.
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Affiliation(s)
- Yulia Shaulov-Rotem
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Emmanuelle Merquiol
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Tommy Weiss-Sadan
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Ofra Moshel
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Seth Salpeter
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Doron Shabat
- School of Chemistry , Faculty of Exact Sciences , Tel-Aviv University , Tel Aviv , 69978 , Israel
| | - Farnusch Kaschani
- Department of Chemical Biology , University of Duisburg-Essen , Center for Medical Biotechnology , Faculty of Biology , 45117 Essen , Germany
| | - Markus Kaiser
- Department of Chemical Biology , University of Duisburg-Essen , Center for Medical Biotechnology , Faculty of Biology , 45117 Essen , Germany
| | - Galia Blum
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
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20
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Structure and function of legumain in health and disease. Biochimie 2015; 122:126-50. [PMID: 26403494 DOI: 10.1016/j.biochi.2015.09.022] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/18/2015] [Indexed: 12/27/2022]
Abstract
The last years have seen a steady increase in our understanding of legumain biology that is driven from two largely uncoupled research arenas, the mammalian and the plant legumain field. Research on legumain, which is also referred to as asparaginyl endopeptidase (AEP) or vacuolar processing enzyme (VPE), is slivered, however. Here we summarise recent important findings and put them into a common perspective. Legumain is usually associated with its cysteine endopeptidase activity in lysosomes where it contributes to antigen processing for class II MHC presentation. However, newly recognized functions disperse previously assumed boundaries with respect to their cellular compartmentalisation and enzymatic activities. Legumain is also found extracellularly and even translocates to the cytosol and the nucleus, with seemingly incompatible pH and redox potential. These different milieus translate into changes of legumain's molecular properties, including its (auto-)activation, conformational stability and enzymatic functions. Contrasting its endopeptidase activity, legumain can develop a carboxypeptidase activity which remains stable at neutral pH. Moreover, legumain features a peptide ligase activity, with intriguing mechanistic peculiarities in plant and human isoforms. In pathological settings, such as cancer or Alzheimer's disease, the proper association of legumain activities with the corresponding cellular compartments is breached. Legumain's increasingly recognized physiological and pathological roles also indicate future research opportunities in this vibrant field.
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21
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Lu H, Chandrasekar B, Oeljeklaus J, Misas-Villamil JC, Wang Z, Shindo T, Bogyo M, Kaiser M, van der Hoorn RAL. Subfamily-Specific Fluorescent Probes for Cysteine Proteases Display Dynamic Protease Activities during Seed Germination. PLANT PHYSIOLOGY 2015; 168:1462-75. [PMID: 26048883 PMCID: PMC4528725 DOI: 10.1104/pp.114.254466] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 05/27/2015] [Indexed: 05/20/2023]
Abstract
Cysteine proteases are an important class of enzymes implicated in both developmental and defense-related programmed cell death and other biological processes in plants. Because there are dozens of cysteine proteases that are posttranslationally regulated by processing, environmental conditions, and inhibitors, new methodologies are required to study these pivotal enzymes individually. Here, we introduce fluorescence activity-based probes that specifically target three distinct cysteine protease subfamilies: aleurain-like proteases, cathepsin B-like proteases, and vacuolar processing enzymes. We applied protease activity profiling with these new probes on Arabidopsis (Arabidopsis thaliana) protease knockout lines and agroinfiltrated leaves to identify the probe targets and on other plant species to demonstrate their broad applicability. These probes revealed that most commercially available protease inhibitors target unexpected proteases in plants. When applied on germinating seeds, these probes reveal dynamic activities of aleurain-like proteases, cathepsin B-like proteases, and vacuolar processing enzymes, coinciding with the remobilization of seed storage proteins.
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Affiliation(s)
- Haibin Lu
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (H.L., B.C., J.C.M.-V., R.A.L.v.d.H.);Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (H.L., B.C., J.C.M.-V., T.S., R.A.L.v.d.H.);Center for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany (J.O., Z.W., M.K.); andDepartment of Pathology, Stanford School for Medicine, Stanford, California 94305-5324 (M.B.)
| | - Balakumaran Chandrasekar
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (H.L., B.C., J.C.M.-V., R.A.L.v.d.H.);Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (H.L., B.C., J.C.M.-V., T.S., R.A.L.v.d.H.);Center for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany (J.O., Z.W., M.K.); andDepartment of Pathology, Stanford School for Medicine, Stanford, California 94305-5324 (M.B.)
| | - Julian Oeljeklaus
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (H.L., B.C., J.C.M.-V., R.A.L.v.d.H.);Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (H.L., B.C., J.C.M.-V., T.S., R.A.L.v.d.H.);Center for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany (J.O., Z.W., M.K.); andDepartment of Pathology, Stanford School for Medicine, Stanford, California 94305-5324 (M.B.)
| | - Johana C Misas-Villamil
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (H.L., B.C., J.C.M.-V., R.A.L.v.d.H.);Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (H.L., B.C., J.C.M.-V., T.S., R.A.L.v.d.H.);Center for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany (J.O., Z.W., M.K.); andDepartment of Pathology, Stanford School for Medicine, Stanford, California 94305-5324 (M.B.)
| | - Zheming Wang
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (H.L., B.C., J.C.M.-V., R.A.L.v.d.H.);Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (H.L., B.C., J.C.M.-V., T.S., R.A.L.v.d.H.);Center for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany (J.O., Z.W., M.K.); andDepartment of Pathology, Stanford School for Medicine, Stanford, California 94305-5324 (M.B.)
| | - Takayuki Shindo
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (H.L., B.C., J.C.M.-V., R.A.L.v.d.H.);Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (H.L., B.C., J.C.M.-V., T.S., R.A.L.v.d.H.);Center for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany (J.O., Z.W., M.K.); andDepartment of Pathology, Stanford School for Medicine, Stanford, California 94305-5324 (M.B.)
| | - Matthew Bogyo
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (H.L., B.C., J.C.M.-V., R.A.L.v.d.H.);Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (H.L., B.C., J.C.M.-V., T.S., R.A.L.v.d.H.);Center for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany (J.O., Z.W., M.K.); andDepartment of Pathology, Stanford School for Medicine, Stanford, California 94305-5324 (M.B.)
| | - Markus Kaiser
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (H.L., B.C., J.C.M.-V., R.A.L.v.d.H.);Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (H.L., B.C., J.C.M.-V., T.S., R.A.L.v.d.H.);Center for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany (J.O., Z.W., M.K.); andDepartment of Pathology, Stanford School for Medicine, Stanford, California 94305-5324 (M.B.)
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (H.L., B.C., J.C.M.-V., R.A.L.v.d.H.);Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (H.L., B.C., J.C.M.-V., T.S., R.A.L.v.d.H.);Center for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany (J.O., Z.W., M.K.); andDepartment of Pathology, Stanford School for Medicine, Stanford, California 94305-5324 (M.B.)
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22
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Yang P, Liu K. Activity-based protein profiling: recent advances in probe development and applications. Chembiochem 2015; 16:712-24. [PMID: 25652106 DOI: 10.1002/cbic.201402582] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/08/2022]
Abstract
The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.
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Affiliation(s)
- Pengyu Yang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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23
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Radulović ŽM, Kim TK, Porter LM, Sze SH, Lewis L, Mulenga A. A 24-48 h fed Amblyomma americanum tick saliva immuno-proteome. BMC Genomics 2014; 15:518. [PMID: 24962723 PMCID: PMC4099483 DOI: 10.1186/1471-2164-15-518] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/12/2014] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Multiple tick saliva proteins, the majority of which are unknown, confer tick resistance in repeatedly infested animals. The objective of this study was to identify the 24-48 h fed Amblyomma americanum tick saliva immuno-proteome. The 24-48 h tick-feeding phase is critical to tick parasitism as it precedes important events in tick biology, blood meal feeding and disease agent transmission. Fed male, 24 and 96 h fed female phage display cDNA expression libraries were biopanned using rabbit antibodies to 24 and 48 h fed A. americanum female tick saliva proteins. Biopanned immuno-cDNA libraries were subjected to next generation sequencing, de novo assembly, and bioinformatic analysis. RESULTS More than 800 transcripts that code for 24-48 h fed A. americanum immuno-proteins are described. Of the 895 immuno-proteins, 52% (464/895) were provisionally identified based on matches in GenBank. Of these, ~19% (86/464) show high level of identity to other tick hypothetical proteins, and the rest include putative proteases (serine, cysteine, leukotriene A-4 hydrolase, carboxypeptidases, and metalloproteases), protease inhibitors (serine and cysteine protease inhibitors, tick carboxypeptidase inhibitor), and transporters and/or ligand binding proteins (histamine binding/lipocalin, fatty acid binding, calreticulin, hemelipoprotein, IgG binding protein, ferritin, insulin-like growth factor binding proteins, and evasin). Others include enzymes (glutathione transferase, cytochrome oxidase, protein disulfide isomerase), ribosomal proteins, and those of miscellaneous functions (histamine release factor, selenoproteins, tetraspanin, defensin, heat shock proteins). CONCLUSIONS Data here demonstrate that A. americanum secretes a complex cocktail of immunogenic tick saliva proteins during the first 24-48 h of feeding. Of significance, previously validated immunogenic tick saliva proteins including AV422 protein, calreticulin, histamine release factor, histamine binding/lipocalins, selenoproteins, and paramyosin were identified in this screen, supporting the specificity of the approach in this study. While descriptive, this study opens opportunities for in-depth tick feeding physiology studies.
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Affiliation(s)
- Željko M Radulović
- />Department of Entomology, AgriLife Research, Texas A & M University, 2475 TAMU, College Station, TX77843 USA
| | - Tae K Kim
- />Department of Entomology, AgriLife Research, Texas A & M University, 2475 TAMU, College Station, TX77843 USA
| | - Lindsay M Porter
- />Department of Entomology, AgriLife Research, Texas A & M University, 2475 TAMU, College Station, TX77843 USA
| | - Sing-Hoi Sze
- />Department of Computer Sciences and Engineering, Texas A & M University, College Station, TX77843 USA
- />Department of Biochemistry & Biophysics, Texas A & M University, College Station, TX77843 USA
| | - Lauren Lewis
- />Department of Entomology, AgriLife Research, Texas A & M University, 2475 TAMU, College Station, TX77843 USA
| | - Albert Mulenga
- />Department of Entomology, AgriLife Research, Texas A & M University, 2475 TAMU, College Station, TX77843 USA
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24
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Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling. Proc Natl Acad Sci U S A 2014; 111:2518-23. [PMID: 24550277 DOI: 10.1073/pnas.1318548111] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The exploration of protease substrate specificity is generally restricted to naturally occurring amino acids, limiting the degree of conformational space that can be surveyed. We substantially enhanced this by incorporating 102 unnatural amino acids to explore the S1-S4 pockets of human neutrophil elastase. This approach provides hybrid natural and unnatural amino acid sequences, and thus we termed it the Hybrid Combinatorial Substrate Library. Library results were validated by the synthesis of individual tetrapeptide substrates, with the optimal substrate demonstrating more than three orders of magnitude higher catalytic efficiency than commonly used substrates of elastase. This optimal substrate was converted to an activity-based probe that demonstrated high selectivity and revealed the specific presence of active elastase during the process of neutrophil extracellular trap formation. We propose that this approach can be successfully used for any type of endopeptidase to deliver high activity and selectivity in substrates and probes.
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25
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Misas-Villamil JC, Toenges G, Kolodziejek I, Sadaghiani AM, Kaschani F, Colby T, Bogyo M, van der Hoorn RAL. Activity profiling of vacuolar processing enzymes reveals a role for VPE during oomycete infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:689-700. [PMID: 23134548 DOI: 10.1111/tpj.12062] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/24/2012] [Indexed: 05/23/2023]
Abstract
Vacuolar processing enzymes (VPEs) are important cysteine proteases that are implicated in the maturation of seed storage proteins, and programmed cell death during plant-microbe interactions and development. Here, we introduce a specific, cell-permeable, activity-based probe for VPEs. This probe is highly specific for all four Arabidopsis VPEs, and labeling is activity-dependent, as illustrated by sensitivity for inhibitors, pH and reducing agents. We show that the probe can be used for in vivo imaging and displays multiple active isoforms of VPEs in various tissues and in both monocot and dicot plant species. Thus, VPE activity profiling is a robust, simple and powerful tool for plant research for a wide range of applications. Using VPE activity profiling, we discovered that VPE activity is increased during infection with the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa). The enhanced VPE activity is host-derived and EDS1-independent. Sporulation of Hpa is reduced on vpe mutant plants, demonstrating a role for VPE during compatible interactions that is presumably independent of programmed cell death. Our data indicate that, as an obligate biotroph, Hpa takes advantage of increased VPE activity in the host, e.g. to mediate protein turnover and nutrient release.
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Affiliation(s)
- Johana C Misas-Villamil
- Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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26
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Edgington LE, Verdoes M, Ortega A, Withana NP, Lee J, Syed S, Bachmann MH, Blum G, Bogyo M. Functional imaging of legumain in cancer using a new quenched activity-based probe. J Am Chem Soc 2012; 135:174-82. [PMID: 23215039 DOI: 10.1021/ja307083b] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Legumain is a lysosomal cysteine protease whose biological function remains poorly defined. Legumain activity is up-regulated in most human cancers and inflammatory diseases most likely as the result of high expression in populations of activated macrophages. Within the tumor microenvironment, legumain activity is thought to promote tumorigenesis. To obtain a greater understanding of the role of legumain activity during cancer progression and inflammation, we developed an activity-based probe that becomes fluorescent only upon binding active legumain. This probe is highly selective for legumain, even in the context of whole cells and tissues, and is also a more effective label of legumain than previously reported probes. Here we present the synthesis and application of our probe to the analysis of legumain activity in primary macrophages and in two mouse models of cancer. We find that legumain activity is highly correlated with macrophage activation and furthermore that it is an ideal marker for primary tumor inflammation and early stage metastatic lesions.
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Affiliation(s)
- Laura E Edgington
- Cancer Biology Program, Department of Pathology, Stanford School of Medicine, 300 Pasteur Drive, Stanford, California 94305-5324, United States
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27
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Albrow VE, Ponder EL, Fasci D, Békés M, Deu E, Salvesen GS, Bogyo M. Development of small molecule inhibitors and probes of human SUMO deconjugating proteases. ACTA ACUST UNITED AC 2011; 18:722-32. [PMID: 21700208 DOI: 10.1016/j.chembiol.2011.05.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 05/17/2011] [Accepted: 05/20/2011] [Indexed: 11/28/2022]
Abstract
Sentrin specific proteases (SENPs) are responsible for activating and deconjugating SUMO (Small Ubiquitin like MOdifier) from target proteins. It remains difficult to study this posttranslational modification due to the lack of reagents that can be used to block the removal of SUMO from substrates. Here, we describe the identification of small molecule SENP inhibitors and active site probes containing aza-epoxide and acyloxymethyl ketone (AOMK) reactive groups. Both classes of compounds are effective inhibitors of hSENPs 1, 2, 5, and 7 while only the AOMKs efficiently inhibit hSENP6. Unlike previous reported peptide vinyl sulfones, these compounds covalently labeled the active site cysteine of multiple recombinantly expressed SENP proteases and the AOMK probe showed selective labeling of these SENPs when added to complex protein mixtures. The AOMK compound therefore represents promising new reagents to study the process of SUMO deconjugation.
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Affiliation(s)
- Victoria E Albrow
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
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28
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Leyva MJ, Degiacomo F, Kaltenbach LS, Holcomb J, Zhang N, Gafni J, Park H, Lo DC, Salvesen GS, Ellerby LM, Ellman JA. Identification and evaluation of small molecule pan-caspase inhibitors in Huntington's disease models. ACTA ACUST UNITED AC 2011; 17:1189-200. [PMID: 21095569 DOI: 10.1016/j.chembiol.2010.08.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 08/30/2010] [Accepted: 08/31/2010] [Indexed: 11/29/2022]
Abstract
Huntington's Disease (HD) is characterized by a mutation in the huntingtin (Htt) gene encoding an expansion of glutamine repeats on the N terminus of the Htt protein. Numerous studies have identified Htt proteolysis as a critical pathological event in HD postmortem human tissue and mouse HD models, and proteases known as caspases have emerged as attractive HD therapeutic targets. We report the use of the substrate activity screening method against caspase-3 and -6 to identify three novel, pan-caspase inhibitors that block proteolysis of Htt at caspase-3 and -6 cleavage sites. In HD models these irreversible inhibitors suppressed Hdh(111Q/111Q)-mediated toxicity and rescued rat striatal and cortical neurons from cell death. In this study, the identified nonpeptidic caspase inhibitors were used to confirm the role of caspase-mediated Htt proteolysis in HD. These results further implicate caspases as promising targets for HD therapeutic development.
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Affiliation(s)
- Melissa J Leyva
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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29
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Lee J, Bogyo M. Development of near-infrared fluorophore (NIRF)-labeled activity-based probes for in vivo imaging of legumain. ACS Chem Biol 2010; 5:233-43. [PMID: 20017516 DOI: 10.1021/cb900232a] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asparaginyl endopeptidase, or legumain, is a lysosomal cysteine protease that was originally identified in plants and later found to be involved in antigen presentation in higher eukaryotes. Legumain is also up-regulated in a number of human cancers, and recent studies suggest that it may play important functional roles in the process of tumorigenesis. However, detailed functional studies in relevant animal models of human disease have been hindered by the lack of suitably selective small molecule inhibitors and imaging reagents. Here we present the design, optimization, and in vivo application of fluorescently labeled activity-based probes (ABPs) for legumain. We demonstrate that optimized aza-peptidyl Asn epoxides are highly selective and potent inhibitors that can be readily converted into near-infrared fluorophore-labeled ABPs for whole body, noninvasive imaging applications. We show that these probes specifically label legumain in various normal tissues as well as in solid tumors when applied in vivo. Interestingly, addition of cell-penetrating peptides to the probes enhanced cellular uptake but resulted in increased cross-reactivity toward other lysosomal proteases as the result of their accumulation in lysosomes. Overall, we find that aza-peptidyl Asn ABPs are valuable new tools for the future study of legumain function in more complex models of human disease.
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Affiliation(s)
- Jiyoun Lee
- Departments of Pathology and Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Dr., Stanford, California 94305-5324
| | - Matthew Bogyo
- Departments of Pathology and Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Dr., Stanford, California 94305-5324
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30
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Horn M, Nussbaumerová M, Sanda M, Kovárová Z, Srba J, Franta Z, Sojka D, Bogyo M, Caffrey CR, Kopácek P, Mares M. Hemoglobin digestion in blood-feeding ticks: mapping a multipeptidase pathway by functional proteomics. ACTA ACUST UNITED AC 2010; 16:1053-63. [PMID: 19875079 DOI: 10.1016/j.chembiol.2009.09.009] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/20/2009] [Accepted: 09/03/2009] [Indexed: 11/25/2022]
Abstract
Hemoglobin digestion is an essential process for blood-feeding parasites. Using chemical tools, we deconvoluted the intracellular hemoglobinolytic cascade in the tick Ixodes ricinus, a vector of Lyme disease and tick-borne encephalitis. In tick gut tissue, a network of peptidases was demonstrated through imaging with specific activity-based probes and activity profiling with peptidic substrates and inhibitors. This peptidase network is induced upon blood feeding and degrades hemoglobin at acidic pH. Selective inhibitors were applied to dissect the roles of the individual peptidases and to determine the peptidase-specific cleavage map of the hemoglobin molecule. The degradation pathway is initiated by endopeptidases of aspartic and cysteine class (cathepsin D supported by cathepsin L and legumain) and is continued by cysteine amino- and carboxy-dipeptidases (cathepsins C and B). The identified enzymes are potential targets to developing novel anti-tick vaccines.
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Affiliation(s)
- Martin Horn
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Praha, Czech Republic
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31
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Noninvasive optical imaging of apoptosis by caspase-targeted activity-based probes. Nat Med 2009; 15:967-73. [PMID: 19597506 DOI: 10.1038/nm.1938] [Citation(s) in RCA: 233] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 02/03/2009] [Indexed: 11/08/2022]
Abstract
Imaging agents that enable direct visualization and quantification of apoptosis in vivo have great potential value for monitoring chemotherapeutic response as well as for early diagnosis and disease monitoring. We describe here the development of fluorescently labeled activity-based probes (ABPs) that covalently label active caspases in vivo. We used these probes to monitor apoptosis in the thymi of mice treated with dexamethasone as well as in tumor-bearing mice treated with the apoptosis-inducing monoclonal antibody Apomab (Genentech). Caspase ABPs provided direct readouts of the kinetics of apoptosis in live mice, whole organs and tissue extracts. The probes produced a maximum fluorescent signal that could be monitored noninvasively and that coincided with the peak in caspase activity, as measured by gel analysis. Overall, these studies demonstrate that caspase-specific ABPs have the potential to be used for noninvasive imaging of apoptosis in both preclinical and clinical settings.
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32
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Patel N, Krishnan S, Offman MN, Krol M, Moss CX, Leighton C, van Delft FW, Holland M, Liu J, Alexander S, Dempsey C, Ariffin H, Essink M, Eden TO, Watts C, Bates PA, Saha V. A dyad of lymphoblastic lysosomal cysteine proteases degrades the antileukemic drug L-asparaginase. J Clin Invest 2009; 119:1964-73. [PMID: 19509471 PMCID: PMC2701869 DOI: 10.1172/jci37977] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 04/08/2009] [Indexed: 01/23/2023] Open
Abstract
l-Asparaginase is a key therapeutic agent for treatment of childhood acute lymphoblastic leukemia (ALL). There is wide individual variation in pharmacokinetics, and little is known about its metabolism. The mechanisms of therapeutic failure with l-asparaginase remain speculative. Here, we now report that 2 lysosomal cysteine proteases present in lymphoblasts are able to degrade l-asparaginase. Cathepsin B (CTSB), which is produced constitutively by normal and leukemic cells, degraded asparaginase produced by Escherichia coli (ASNase) and Erwinia chrysanthemi. Asparaginyl endopeptidase (AEP), which is overexpressed predominantly in high-risk subsets of ALL, specifically degraded ASNase. AEP thereby destroys ASNase activity and may also potentiate antigen processing, leading to allergic reactions. Using AEP-mediated cleavage sequences, we modeled the effects of the protease on ASNase and created a number of recombinant ASNase products. The N24 residue on the flexible active loop was identified as the primary AEP cleavage site. Sole modification at this site rendered ASNase resistant to AEP cleavage and suggested a key role for the flexible active loop in determining ASNase activity. We therefore propose what we believe to be a novel mechanism of drug resistance to ASNase. Our results may help to identify alternative therapeutic strategies with the potential of further improving outcome in childhood ALL.
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Affiliation(s)
- Naina Patel
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Shekhar Krishnan
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Marc N. Offman
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Marcin Krol
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Catherine X. Moss
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Carly Leighton
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Frederik W. van Delft
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Mark Holland
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - JiZhong Liu
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Seema Alexander
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Clare Dempsey
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Hany Ariffin
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Monika Essink
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Tim O.B. Eden
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Colin Watts
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Paul A. Bates
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
| | - Vaskar Saha
- Cancer Research UK Children’s Cancer Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, London, United Kingdom.
Division of Cell Biology and Immunology, School of Life Sciences Research Biocentre, University of Dundee, Dundee, United Kingdom.
Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia.
Medac GmbH, Wedel, Germany.
Paediatric and Adolescent Oncology Unit, Christie Hospital, Manchester, United Kingdom
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33
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Fonović M, Bogyo M. Activity-based probes as a tool for functional proteomic analysis of proteases. Expert Rev Proteomics 2009; 5:721-30. [PMID: 18937562 DOI: 10.1586/14789450.5.5.721] [Citation(s) in RCA: 188] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Traditional proteomics methodology allows global analysis of protein abundance but does not provide information on the regulation of protein activity. Proteases, in particular, are known for their multilayered post-translational activity regulation that can lead to a significant difference between protease abundance levels and their enzyme activity. To address these issues, the field of activity-based proteomics has been established in order to characterize protein activity and monitor the functional regulation of enzymes in complex proteomes. In this review, we present structural features of activity-based probes for proteases and discuss their applications in proteomic profiling of various catalytic classes of proteases.
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Affiliation(s)
- Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, JoZef Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia.
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34
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Raghavan A, Charron G, Flexner J, Hang HC. Chemical probes for profiling fatty acid-associated proteins in living cells. Bioorg Med Chem Lett 2008; 18:5982-6. [DOI: 10.1016/j.bmcl.2008.09.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 09/22/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022]
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35
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Cravatt BF, Wright AT, Kozarich JW. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu Rev Biochem 2008; 77:383-414. [PMID: 18366325 DOI: 10.1146/annurev.biochem.75.101304.124125] [Citation(s) in RCA: 933] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome sequencing projects have provided researchers with a complete inventory of the predicted proteins produced by eukaryotic and prokaryotic organisms. Assignment of functions to these proteins represents one of the principal challenges for the field of proteomics. Activity-based protein profiling (ABPP) has emerged as a powerful chemical proteomic strategy to characterize enzyme function directly in native biological systems on a global scale. Here, we review the basic technology of ABPP, the enzyme classes addressable by this method, and the biological discoveries attributable to its application.
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Affiliation(s)
- Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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36
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Götz MG, James KE, Hansell E, Dvořák J, Seshaadri A, Sojka D, Kopáček P, McKerrow JH, Caffrey CR, Powers JC. Aza-peptidyl Michael Acceptors. A New Class of Potent and Selective Inhibitors of Asparaginyl Endopeptidases (Legumains) from Evolutionarily Diverse Pathogens. J Med Chem 2008; 51:2816-32. [DOI: 10.1021/jm701311r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Marion G. Götz
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
| | - Karen Ellis James
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
| | - Elizabeth Hansell
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
| | - Jan Dvořák
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
| | - Amritha Seshaadri
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
| | - Daniel Sojka
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
| | - Petr Kopáček
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
| | - James H. McKerrow
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
| | - Conor R. Caffrey
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
| | - James C. Powers
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Sandler Center for Basic Research in Parasitic Diseases, Byers Hall, University of California San Francisco, San Francisco, California 94158, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic, and Department of Chemistry, Whitman College, 345 Boyer Avenue, Walla
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37
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Verdoes M, Hillaert U, Florea BI, Sae-Heng M, Risseeuw MDP, Filippov DV, van der Marel GA, Overkleeft HS. Acetylene functionalized BODIPY dyes and their application in the synthesis of activity based proteasome probes. Bioorg Med Chem Lett 2007; 17:6169-71. [PMID: 17888658 DOI: 10.1016/j.bmcl.2007.09.025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 09/03/2007] [Accepted: 09/05/2007] [Indexed: 01/26/2023]
Abstract
The synthesis of three acetylene functionalized BODIPY dyes is described. These dyes are used to fluorescently modify an azido functionalized epoxomicin analogue employing the Huisgen 1,3-dipolar cycloaddition, resulting in a panel of fluorescent epoxomicin derived proteasome probes.
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Affiliation(s)
- Martijn Verdoes
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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