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Zerfas BL, Coleman RA, Salazar-Chaparro AF, Macatangay NJ, Trader DJ. Fluorescent Probes with Unnatural Amino Acids to Monitor Proteasome Activity in Real-Time. ACS Chem Biol 2020; 15:2588-2596. [PMID: 32786259 PMCID: PMC8319958 DOI: 10.1021/acschembio.0c00634] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The proteasome is an essential protein complex that, when dysregulated, can result in various diseases in eukaryotic cells. As such, understanding the enzymatic activity of the proteasome and what can alter it is crucial to elucidating its roles in these diseases. This can be done effectively by using activity-based fluorescent substrate probes, of which there are many commercially available that target the individual protease-like subunits in the 20S CP of the proteasome. Unfortunately, these probes have not displayed appropriate characteristics for their use in live cell-based assays. In the work presented here, we have developed a set of probes which have shown improved fluorescence properties and selectivity toward the proteasome compared to other cellular proteases. By including unnatural amino acids, we have found probes which can be utilized in various applications, including monitoring the effects of small molecule stimulators of the proteasome in live cells and comparing the relative proteasome activity across different cancer cell types. In future studies, we expect the fluorescent probes presented here will serve as tools to support the discovery and characterization of small molecule modulators of proteasome activity.
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Affiliation(s)
- Breanna L. Zerfas
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Rachel A. Coleman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Andres F. Salazar-Chaparro
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Nathaniel J. Macatangay
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Darci J. Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
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2
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Osmulski PA, Karpowicz P, Jankowska E, Bohmann J, Pickering AM, Gaczyńska M. New Peptide-Based Pharmacophore Activates 20S Proteasome. Molecules 2020; 25:E1439. [PMID: 32235805 PMCID: PMC7145288 DOI: 10.3390/molecules25061439] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 02/01/2023] Open
Abstract
The proteasome is a pivotal element of controlled proteolysis, responsible for the catabolic arm of proteostasis. By inducing apoptosis, small molecule inhibitors of proteasome peptidolytic activities are successfully utilized in treatment of blood cancers. However, the clinical potential of proteasome activation remains relatively unexplored. In this work, we introduce short TAT peptides derived from HIV-1 Tat protein and modified with synthetic turn-stabilizing residues as proteasome agonists. Molecular docking and biochemical studies point to the α1/α2 pocket of the core proteasome α ring as the binding site of TAT peptides. We postulate that the TATs' pharmacophore consists of an N-terminal basic pocket-docking "activation anchor" connected via a β turn inducer to a C-terminal "specificity clamp" that binds on the proteasome α surface. By allosteric effects-including destabilization of the proteasomal gate-the compounds substantially augment activity of the core proteasome in vitro. Significantly, this activation is preserved in the lysates of cultured cells treated with the compounds. We propose that the proteasome-stimulating TAT pharmacophore provides an attractive lead for future clinical use.
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Affiliation(s)
- Paweł A. Osmulski
- Department of Molecular Medicine, UT Health San Antonio, Texas, TX 78245, USA;
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, Texas, TX 78245, USA
| | - Przemysław Karpowicz
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Elżbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Jonathan Bohmann
- Southwest Research Institute, San Antonio, Texas, TX 78238, USA;
| | - Andrew M. Pickering
- Department of Molecular Medicine, UT Health San Antonio, Texas, TX 78245, USA;
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, Texas, TX 78245, USA
- The Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, UT Health San Antonio, TX 78229, USA
| | - Maria Gaczyńska
- Department of Molecular Medicine, UT Health San Antonio, Texas, TX 78245, USA;
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, Texas, TX 78245, USA
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3
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Gaczynska M, Osmulski PA. Targeting Protein-Protein Interactions in the Ubiquitin-Proteasome Pathway. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 110:123-165. [PMID: 29412995 DOI: 10.1016/bs.apcsb.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ubiquitin-proteasome pathway (UPP) is a major venue for controlled intracellular protein degradation in Eukaryota. The machinery of several hundred proteins is involved in recognizing, tagging, transporting, and cleaving proteins, all in a highly regulated manner. Short-lived transcription factors, misfolded translation products, stress-damaged polypeptides, or worn-out long-lived proteins, all can be found among the substrates of UPP. Carefully choreographed protein-protein interactions (PPI) are involved in each step of the pathway. For many of the steps small-molecule inhibitors have been identified and often they directly or indirectly target PPI. The inhibitors may destabilize intracellular proteostasis and trigger apoptosis. So far this is the most explored option used as an anticancer strategy. Alternatively, substrate-specific polyubiquitination may be regulated for a precise intervention aimed at a particular metabolic pathway. This very attractive opportunity is moving close to clinical application. The best known drug target in UPP is the proteasome: the end point of the journey of a protein destined for degradation. The proteasome alone is a perfect object to study the mechanisms and roles of PPI on many levels. This giant protease is built from multisubunit modules and additionally utilizes a service from transient protein ligands, for example, delivering substrates. An elaborate set of PPI within the highest-order proteasome assembly is involved in substrate recognition and processing. Below we will outline PPI involved in the UPP and discuss the growing prospects for their utilization in pharmacological interventions.
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Affiliation(s)
- Maria Gaczynska
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.
| | - Pawel A Osmulski
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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Gruba N, Wysocka M, Brzezińska M, Dębowski D, Sieńczyk M, Gorodkiewicz E, Guszcz T, Czaplewski C, Rolka K, Lesner A. Bladder cancer detection using a peptide substrate of the 20S proteasome. FEBS J 2016; 283:2929-48. [PMID: 27326540 DOI: 10.1111/febs.13786] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 05/12/2016] [Accepted: 06/20/2016] [Indexed: 01/01/2023]
Abstract
The 20S catalytic core of the human 26S proteasome can be secreted from cells, and high levels of extracellular 20S proteasome have been linked to many types of cancers and autoimmune diseases. Several diagnostic approaches have been developed that detect 20S proteasome activity in plasma, but these suffer from problems with efficiency and sensitivity. In this report, we describe the optimization and synthesis of an internally quenched fluorescent substrate of the 20S proteasome, and investigate its use as a potential diagnostic test in bladder cancer. This peptide, 2-aminobenzoic acid (ABZ)-Val-Val-Ser-Tyr-Ala-Met-Gly-Tyr(3-NO2 )-NH2 , is cleaved by the chymotrypsin 20S proteasome subunit and displays an excellent specificity constant value (9.7 × 10(5) m(-1) ·s(-1) ) and a high kcat (8 s(-1) ). Using this peptide, we identified chymotrypsin-like proteasome activity in the majority of urine samples obtained from patients with bladder cancer, whereas the proteasome activity in urine samples from healthy volunteers was below the detection limit (0.5 pm). These findings were confirmed by an inhibitory study and immunochemistry methods.
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Affiliation(s)
| | | | | | | | - Marcin Sieńczyk
- Faculty of Chemistry, Wroclaw University of Technology, Poland
| | - Ewa Gorodkiewicz
- Department of Electrochemistry, Institute of Chemistry, University of Bialystok, Poland
| | - Tomasz Guszcz
- Department of Urology, J. Sniadecki Provincial Hospital of Bialystok, Poland
| | | | | | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Poland
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5
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Keita M, Kaffy J, Troufflard C, Morvan E, Crousse B, Ongeri S. (19)F NMR monitoring of the eukaryotic 20S proteasome chymotrypsin-like activity: an investigative tool for studying allosteric regulation. Org Biomol Chem 2015; 12:4576-81. [PMID: 24867821 DOI: 10.1039/c4ob00962b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The proteasome displays three distinct proteolytic activities. Currently, proteasome inhibitors are evaluated using specific fluorescent substrates for each of the individual active sites. However, the photophysical properties of the commonly used fluorophores are similar and thus, the simultaneous monitoring of the three proteolytic activities is not possible. We have developed a bimodal fluorescent fluorinated substrate as a novel tool to study the chymotrypsin-like (ChT-L) proteolytic activity and its regulation by inhibitors and by substrates of trypsin-like (T-L) and caspase-like sites (PA). We demonstrate that this substrate is reliable to evaluate the ChT-L inhibitory activity of new molecules either by fluorescence or (19)F NMR spectroscopy. We have found that the ChT-L activity is dramatically reduced in the presence of T-L and PA substrates. This work provides a proof of concept that the fluorinated substrate enables investigation of the allosteric regulation of the ChT-L activity.
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Affiliation(s)
- M Keita
- Molécules Fluorées et Chimie Médicinale, BioCIS UMR-CNRS 8076, LabEx LERMIT, Université Paris-Sud, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France.
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Kolmakov K, Hebisch E, Wolfram T, Nordwig LA, Wurm CA, Ta H, Westphal V, Belov VN, Hell SW. Far-Red Emitting Fluorescent Dyes for Optical Nanoscopy: Fluorinated Silicon-Rhodamines (SiRF Dyes) and Phosphorylated Oxazines. Chemistry 2015; 21:13344-56. [DOI: 10.1002/chem.201501394] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/16/2015] [Indexed: 12/30/2022]
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Priestman MA, Wang Q, Jernigan FE, Chowdhury R, Schmidt M, Lawrence DS. Multicolor monitoring of the proteasome's catalytic signature. ACS Chem Biol 2015; 10:433-40. [PMID: 25347733 PMCID: PMC4340355 DOI: 10.1021/cb5007322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The proteasome, a validated anticancer
target, participates in
an array of biochemical activities, which range from the proteolysis
of defective proteins to antigen presentation. We report the preparation
of biochemically and photophysically distinct green, red, and far-red
real-time sensors designed to simultaneously monitor the proteasome’s
chymotrypsin-, trypsin-, and caspase-like activities, respectively.
These sensors were employed to assess the effect of simultaneous multiple
active site catalysis on the kinetic properties of the individual
subunits. Furthermore, we have found that the catalytic signature
of the proteasome varies depending on the source, cell type, and disease
state. Trypsin-like activity is more pronounced in yeast than in mammals,
whereas chymotrypsin-like activity is the only activity detectable
in B-cells (unlike other mammalian cells). Furthermore, chymotrypsin-like
activity is more prominent in transformed B cells relative to their
counterparts from healthy donors.
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Affiliation(s)
- Melanie A. Priestman
- Department
of Chemistry, Division of Chemical Biology and Medicinal Chemistry,
and Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Qunzhao Wang
- Department
of Chemistry, Division of Chemical Biology and Medicinal Chemistry,
and Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Finith E. Jernigan
- Department
of Chemistry, Division of Chemical Biology and Medicinal Chemistry,
and Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Ruma Chowdhury
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Marion Schmidt
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - David S. Lawrence
- Department
of Chemistry, Division of Chemical Biology and Medicinal Chemistry,
and Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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8
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Wang Q, Priestman MA, Lawrence DS. Monitoring of protein arginine deiminase activity by using fluorescence quenching: multicolor visualization of citrullination. Angew Chem Int Ed Engl 2013; 52:2323-5. [PMID: 23339123 DOI: 10.1002/anie.201208464] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 12/24/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Qunzhao Wang
- Department of Chemistry, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
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9
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Wang Q, Priestman MA, Lawrence DS. Monitoring of Protein Arginine Deiminase Activity by Using Fluorescence Quenching: Multicolor Visualization of Citrullination. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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10
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Fricker LD, Gelman JS, Castro LM, Gozzo FC, Ferro ES. Peptidomic analysis of HEK293T cells: effect of the proteasome inhibitor epoxomicin on intracellular peptides. J Proteome Res 2012; 11:1981-90. [PMID: 22304392 DOI: 10.1021/pr2012076] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Peptides derived from cytosolic, mitochondrial, and nuclear proteins have been detected in extracts of animal tissues and cell lines. To test whether the proteasome is involved in their formation, HEK293T cells were treated with epoxomicin (0.2 or 2 μM) for 1 h and quantitative peptidomics analysis was performed. Altogether, 147 unique peptides were identified by mass spectrometry sequence analysis. Epoxomicin treatment decreased the levels of the majority of intracellular peptides, consistent with inhibition of the proteasome beta-2 and beta-5 subunits. Treatment with the higher concentration of epoxomicin elevated the levels of some peptides. Most of the elevated peptides resulted from cleavages at acidic residues, suggesting that epoxomicin increased the processing of proteins through the beta-1 subunit. Interestingly, some of the peptides that were elevated by the epoxomicin treatment had hydrophobic residues in P1 cleavage sites. Taken together, these findings suggest that, while the proteasome is the major source of intracellular peptides, other peptide-generating mechanisms exist. Because intracellular peptides are likely to perform intracellular functions, studies using proteasome inhibitors need to be interpreted with caution, as it is possible that the effects of these inhibitors are due to a change in the peptide levels rather than inhibition of protein degradation.
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Affiliation(s)
- Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine , Bronx, New York 10461, United States
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11
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Deu E, Verdoes M, Bogyo M. New approaches for dissecting protease functions to improve probe development and drug discovery. Nat Struct Mol Biol 2012; 19:9-16. [PMID: 22218294 DOI: 10.1038/nsmb.2203] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteases are well-established targets for pharmaceutical development because of their known enzymatic mechanism and their regulatory roles in many pathologies. However, many potent clinical lead compounds have been unsuccessful either because of a lack of specificity or because of our limited understanding of the biological roles of the targeted protease. In order to successfully develop protease inhibitors as drugs, it is necessary to understand protease functions and to expand the platform of inhibitor development beyond active site-directed design and in vitro optimization. Several newly developed technologies will enhance assessment of drug selectivity in living cells and animal models, allowing researchers to focus on compounds with high specificity and minimal side effects in vivo. In this review, we highlight advances in the development of chemical probes, proteomic methods and screening tools that we feel will help facilitate this paradigm shift in drug discovery.
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Affiliation(s)
- Edgar Deu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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12
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Pauff SM, Miller SC. Synthesis of near-IR fluorescent oxazine dyes with esterase-labile sulfonate esters. Org Lett 2011; 13:6196-9. [PMID: 22047733 DOI: 10.1021/ol202619f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Near-IR oxazine dyes are reported that contain sulfonate esters which are rapidly cleaved by esterase activity to unmask highly polar anionic sulfonates. Strategies for the synthesis of these dyes included the development of milder dye condensation conditions with improved functional compatibility and the use of an alkyl halide that allows for the introduction of esterase-labile sulfonates without the need for sulfonation of the target molecule.
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Affiliation(s)
- Steven M Pauff
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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13
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Viso A, Fernández de la Pradilla R, Tortosa M, García A, Flores A. Update 1 of: α,β-Diamino Acids: Biological Significance and Synthetic Approaches. Chem Rev 2011; 111:PR1-42. [DOI: 10.1021/cr100127y] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Alma Viso
- Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | | | - Mariola Tortosa
- Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Ana García
- Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Aida Flores
- Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
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Deu E, Yang Z, Wang F, Klemba M, Bogyo M. Use of activity-based probes to develop high throughput screening assays that can be performed in complex cell extracts. PLoS One 2010; 5:e11985. [PMID: 20700487 PMCID: PMC2916841 DOI: 10.1371/journal.pone.0011985] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 07/15/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND High throughput screening (HTS) is one of the primary tools used to identify novel enzyme inhibitors. However, its applicability is generally restricted to targets that can either be expressed recombinantly or purified in large quantities. METHODOLOGY AND PRINCIPAL FINDINGS Here, we described a method to use activity-based probes (ABPs) to identify substrates that are sufficiently selective to allow HTS in complex biological samples. Because ABPs label their target enzymes through the formation of a permanent covalent bond, we can correlate labeling of target enzymes in a complex mixture with inhibition of turnover of a substrate in that same mixture. Thus, substrate specificity can be determined and substrates with sufficiently high selectivity for HTS can be identified. In this study, we demonstrate this method by using an ABP for dipeptidyl aminopeptidases to identify (Pro-Arg)2-Rhodamine as a specific substrate for DPAP1 in Plasmodium falciparum lysates and Cathepsin C in rat liver extracts. We then used this substrate to develop highly sensitive HTS assays (Z'>0.8) that are suitable for use in screening large collections of small molecules (i.e >300,000) for inhibitors of these proteases. Finally, we demonstrate that it is possible to use broad-spectrum ABPs to identify target-specific substrates. CONCLUSIONS We believe that this approach will have value for many enzymatic systems where access to large amounts of active enzyme is problematic.
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Affiliation(s)
- Edgar Deu
- Department of Pathology, Stanford School of Medicine, Stanford, California, United States of America
| | - Zhimou Yang
- Department of Pathology, Stanford School of Medicine, Stanford, California, United States of America
| | - Flora Wang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Michael Klemba
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Matthew Bogyo
- Department of Pathology, Stanford School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, United States of America
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