1
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Nicolau I, Hădade ND, Matache M, Funeriu DP. Synthetic Approaches of Epoxysuccinate Chemical Probes. Chembiochem 2023; 24:e202300157. [PMID: 37096389 DOI: 10.1002/cbic.202300157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 04/26/2023]
Abstract
Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.
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Affiliation(s)
- Ioana Nicolau
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Niculina D Hădade
- Babes-Bolyai University, Faculty of Chemistry and Chemical Engineering, Supramolecular and Organometallic Chemistry Centre, 11 Arany Janos Street, 400028, Cluj-Napoca, Romania
| | - Mihaela Matache
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Daniel P Funeriu
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
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2
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Bhuiyan AI, Rathod P, Ghoshal S, Dana D, Das T, Li G, Dickson AA, Rafi F, Subramaniam GS, Fath KR, Paroly S, Chang EJ, Pathak SK. Clickable, selective, and cell-permeable activity-based probe of human cathepsin B - Minimalistic approach for enhanced selectivity. Bioorg Chem 2021; 117:105463. [PMID: 34753058 DOI: 10.1016/j.bioorg.2021.105463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/28/2021] [Indexed: 01/13/2023]
Abstract
Human cathepsin B is a cysteine-dependent protease whose roles in both normal and diseased cellular states remain yet to be fully delineated. This is primarily due to overlapping substrate specificities and lack of unambiguously annotated physiological functions. In this work, a selective, cell-permeable, clickable and tagless small molecule cathepsin B probe, KDA-1, is developed and kinetically characterized. KDA-1 selectively targets active site Cys25 residue of cathepsin B for labeling and can detect active cellular cathepsin B in proteomes derived from live human MDA-MB-231 breast cancer cells and HEK293 cells. It is anticipated that KDA-1 probe will find suitable applications in functional proteomics involving human cathepsin B enzyme.
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Affiliation(s)
- Ashif I Bhuiyan
- Queens College of The City University of New York, Chemistry and Biochemistry Department, 65-30 Kissena Blvd, Flushing, NY 11367, USA; Chemistry Doctoral Program, The Graduate Center of The City University of New York, 365 5th Ave, New York, NY 10016, USA
| | - Pratikkumar Rathod
- Laguardia Community College, 31-10 Thomson Ave, Long Island City, NY 11101, USA
| | - Sarbani Ghoshal
- Department of Biological Sc. and Geology, QCC-CUNY, Bayside, NY, USA
| | - Dibyendu Dana
- Queens College of The City University of New York, Chemistry and Biochemistry Department, 65-30 Kissena Blvd, Flushing, NY 11367, USA
| | - Tuhin Das
- Queens College of The City University of New York, Chemistry and Biochemistry Department, 65-30 Kissena Blvd, Flushing, NY 11367, USA
| | - Guoshen Li
- Queens College of The City University of New York, Chemistry and Biochemistry Department, 65-30 Kissena Blvd, Flushing, NY 11367, USA
| | - Anna A Dickson
- Queens College of The City University of New York, Chemistry and Biochemistry Department, 65-30 Kissena Blvd, Flushing, NY 11367, USA
| | - Faiza Rafi
- Bard High School Early College Queens, 30-20 Thomson Avenue, Long Island City, NY 11101, USA
| | - Gopal S Subramaniam
- Queens College of The City University of New York, Chemistry and Biochemistry Department, 65-30 Kissena Blvd, Flushing, NY 11367, USA
| | - Karl R Fath
- Queens College of The City University of New York, Department of Biology, 65-30 Kissena Blvd, Flushing, NY 11367, USA; Biochemistry Doctoral Program, The Graduate Center of The City University of New York, 365 5th Ave, New York, NY 10016, USA
| | - Suneeta Paroly
- Bard High School Early College Queens, 30-20 Thomson Avenue, Long Island City, NY 11101, USA
| | - Emmanuel J Chang
- Biochemistry Doctoral Program, The Graduate Center of The City University of New York, 365 5th Ave, New York, NY 10016, USA; York College of the City University of New York, Department of Chemistry, 94-20 Guy R. Brewer Blvd, Jamaica, NY 11451, USA; Chemistry Doctoral Program, The Graduate Center of The City University of New York, 365 5th Ave, New York, NY 10016, USA
| | - Sanjai K Pathak
- Queens College of The City University of New York, Chemistry and Biochemistry Department, 65-30 Kissena Blvd, Flushing, NY 11367, USA; Biochemistry Doctoral Program, The Graduate Center of The City University of New York, 365 5th Ave, New York, NY 10016, USA; Chemistry Doctoral Program, The Graduate Center of The City University of New York, 365 5th Ave, New York, NY 10016, USA.
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3
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Burton NR, Kim P, Backus KM. Photoaffinity labelling strategies for mapping the small molecule-protein interactome. Org Biomol Chem 2021; 19:7792-7809. [PMID: 34549230 PMCID: PMC8489259 DOI: 10.1039/d1ob01353j] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nearly all FDA approved drugs and bioactive small molecules exert their effects by binding to and modulating proteins. Consequently, understanding how small molecules interact with proteins at an molecular level is a central challenge of modern chemical biology and drug development. Complementary to structure-guided approaches, chemoproteomics has emerged as a method capable of high-throughput identification of proteins covalently bound by small molecules. To profile noncovalent interactions, established chemoproteomic workflows typically incorporate photoreactive moieties into small molecule probes, which enable trapping of small molecule-protein interactions (SMPIs). This strategy, termed photoaffinity labelling (PAL), has been utilized to profile an array of small molecule interactions, including for drugs, lipids, metabolites, and cofactors. Herein we describe the discovery of photocrosslinking chemistries, including a comparison of the strengths and limitations of implementation of each chemotype in chemoproteomic workflows. In addition, we highlight key examples where photoaffinity labelling has enabled target deconvolution and interaction site mapping.
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Affiliation(s)
- Nikolas R Burton
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
| | - Phillip Kim
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M Backus
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
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4
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Abstract
Cysteine cathepsins are proteases critical in physiopathological processes and show potential as targets or biomarkers for diseases and medical conditions. The 11 members of the cathepsin family are redundant in some cases but remarkably independent of others, demanding the development of both pan-cathepsin targeting tools as well as probes that are selective for specific cathepsins with little off-target activity. This review addresses the diverse design strategies that have been employed to accomplish this tailored selectivity among cysteine cathepsin targets and the imaging modalities incorporated. The power of these diverse tools is contextualized by briefly highlighting the nature of a few prominent cysteine cathepsins, their involvement in select diseases, and the application of cathepsin imaging probes in research spanning basic biochemical studies to clinical applications.
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Affiliation(s)
- Kelton A Schleyer
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Dr, Gainesville, FL 32610, USA.
| | - Lina Cui
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Dr, Gainesville, FL 32610, USA.
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Verhelst SHL, Bonger KM, Willems LI. Bioorthogonal Reactions in Activity-Based Protein Profiling. Molecules 2020; 25:E5994. [PMID: 33352858 PMCID: PMC7765892 DOI: 10.3390/molecules25245994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.
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Affiliation(s)
- Steven H. L. Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, Box 802, 3000 Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Kimberly M. Bonger
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Lianne I. Willems
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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6
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Szulc-Dąbrowska L, Bossowska-Nowicka M, Struzik J, Toka FN. Cathepsins in Bacteria-Macrophage Interaction: Defenders or Victims of Circumstance? Front Cell Infect Microbiol 2020; 10:601072. [PMID: 33344265 PMCID: PMC7746538 DOI: 10.3389/fcimb.2020.601072] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
Macrophages are the first encounters of invading bacteria and are responsible for engulfing and digesting pathogens through phagocytosis leading to initiation of the innate inflammatory response. Intracellular digestion occurs through a close relationship between phagocytic/endocytic and lysosomal pathways, in which proteolytic enzymes, such as cathepsins, are involved. The presence of cathepsins in the endo-lysosomal compartment permits direct interaction with and killing of bacteria, and may contribute to processing of bacterial antigens for presentation, an event necessary for the induction of antibacterial adaptive immune response. Therefore, it is not surprising that bacteria can control the expression and proteolytic activity of cathepsins, including their inhibitors – cystatins, to favor their own intracellular survival in macrophages. In this review, we summarize recent developments in defining the role of cathepsins in bacteria-macrophage interaction and describe important strategies engaged by bacteria to manipulate cathepsin expression and activity in macrophages. Particularly, we focus on specific bacterial species due to their clinical relevance to humans and animal health, i.e., Mycobacterium, Mycoplasma, Staphylococcus, Streptococcus, Salmonella, Shigella, Francisella, Chlamydia, Listeria, Brucella, Helicobacter, Neisseria, and other genera.
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Affiliation(s)
- Lidia Szulc-Dąbrowska
- Division of Immunology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-Szkoła Główna Gospodarstwa Wejskiego, Warsaw, Poland
| | - Magdalena Bossowska-Nowicka
- Division of Immunology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-Szkoła Główna Gospodarstwa Wejskiego, Warsaw, Poland
| | - Justyna Struzik
- Division of Immunology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-Szkoła Główna Gospodarstwa Wejskiego, Warsaw, Poland
| | - Felix N Toka
- Division of Immunology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-Szkoła Główna Gospodarstwa Wejskiego, Warsaw, Poland.,Center for Integrative Mammalian Research, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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7
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Affiliation(s)
- Christin Bednarek
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Ilona Wehl
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Nicole Jung
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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8
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Deng H, Lei Q, Wu Y, He Y, Li W. Activity-based protein profiling: Recent advances in medicinal chemistry. Eur J Med Chem 2020; 191:112151. [PMID: 32109778 DOI: 10.1016/j.ejmech.2020.112151] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 02/05/2023]
Abstract
Activity-based protein profiling (ABPP) has become an emerging chemical proteomic approach to illustrate the interaction mechanisms between compounds and proteins. This approach has combined organic synthesis, biochemistry, cell biology, biophysics and bioinformatics to accelerate the process of drug discovery in target identification and validation, as well as in the stage of lead discovery and optimization. This review will summarize new developments and applications of ABPP in medicinal chemistry. Here, we mainly described the design principles of activity-base probes (ABPs) and general workflows of ABPP approach. Moreover, we discussed various basic and advanced ABPP strategies and their applications in medicinal chemistry, including competitive and comparative ABPP, two-step ABPP, fluorescence polarization ABPP (FluoPol-ABPP) and ABPs for visualization. In conclusion, this review will give a general overview of the applications of ABPP as a powerful and efficient technique in medicinal chemistry.
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Affiliation(s)
- Hui Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Qian Lei
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yangping Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yang He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
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9
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Functional screenings reveal different requirements for host microRNAs in Salmonella and Shigella infection. Nat Microbiol 2019; 5:192-205. [DOI: 10.1038/s41564-019-0614-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022]
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10
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Dual pH/Activity Probes Expand the Cathepsin Toolkit. Cell Chem Biol 2019; 23:891-2. [PMID: 27541194 DOI: 10.1016/j.chembiol.2016.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In a recent issue of Cell Chemical Biology, Sanman et al. (2016) describe novel activity-based probes that simultaneously report cathepsin activity and pH. Using these bifunctional probes, the authors find that the intracellular bacterial pathogen Salmonella typhimurium induces dynamic alterations in the pH of cathepsin-containing organelles in both infected and bystander cells.
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11
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Target identification reveals protein arginine methyltransferase 1 is a potential target of phenyl vinyl sulfone and its derivatives. Biosci Rep 2018. [PMID: 29540535 PMCID: PMC5968187 DOI: 10.1042/bsr20171717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Phenyl vinyl sulfone (PVS) and phenyl vinyl sulfonate (PVSN) inactivate protein tyrosine phosphatases (PTPs) by mimicking the phosphotyrosine structure and providing a Michael addition acceptor for the active-site cysteine residue of PTPs, thus forming covalent adducts between PVS (or PVSN) and PTPs. We developed a specific antiserum against PVS. This antiserum can be used in general antibody-based assays such as immunoblotting, immunofluorescence staining, and immunoprecipitation. Target identification through immunoprecipitation and mass spectrometry analysis reveals potential targets of PVS, mostly proteins with reactive cysteine residues or low-pKa cysteine residues that are prone to reversible redox modifications. Target identification of PVSN has been conducted because the anti-PVS antiserum can also recognize PVSN. Among the targets, protein arginine methyltransferase 1 (PRMT1), inosine-5'-monophosphate dehydrogenase 1, vimentin, and glutathione reductase (GR) were further confirmed by immunoprecipitation followed by immunoblotting. In addition, PVSN and Bay11-7082 inhibited GR activity, and PVS, PVSN, and Bay 11-7082 inhibited PRMT1 activity in in vitro assays. In addition, treatment of PVSN, Bay11-7082, or Bay 11-7085 in cultured HeLa cells can cause the quick decline in the levels of protein asymmetric dimethylarginine. These results indicate that the similar moiety among PVS, PVSN, Bay 11-7082, and Bay 11-7085 can be the key structure of lead compounds of PRMT1. Therefore, we expect to use this approach in the identification of potential targets of other covalent drugs.
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12
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Ono S, Nakai T, Kuroda H, Miyatake R, Horino Y, Abe H, Umezaki M, Oyama H. Site-selective chemical modification of chymotrypsin using peptidyl derivatives bearing optically active diphenyl 1-amino-2-phenylethylphosphonate: Stereochemical effect of the diphenyl phosphonate moiety. Biopolymers 2016; 106:521-30. [PMID: 26615968 DOI: 10.1002/bip.22790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 01/24/2023]
Abstract
Diphenyl (α-aminoalkyl)phosphonates act as mechanism-based inhibitors against serine proteases by forming a covalent bond with the hydroxy group of the active center Ser residue. Because the covalent bond was found to be broken and replaced by 2-pyridinaldoxime methiodide (2PAM), we employed a peptidyl derivative bearing diphenyl 1-amino-2-phenylethylphosphonate moiety (Phe(p) (OPh)2 ) to target the active site of chymotrypsin and to selectively anchor to Lys175 in the vicinity of the active site. Previously, it was reported that the configuration of the α-carbon of phosphorus in diphenyl (α-aminoalkyl)phosphonates affects the inactivation reaction of serine proteases, i.e., the (R)-enantiomeric diphenyl phosphonate is comparable to l-amino acids and it effectively reacts with serine proteases, whereas the (S)-enantiomeric form does not. In this study, we evaluated the stereochemical effect of the phosphonate moiety on the selective chemical modification. Epimeric dipeptidyl derivatives, Ala-(R or S)-Phe(p) (OPh)2 , were prepared by separation with RP-HPLC. A tripeptidyl (R)-epimer (Ala-Ala-(R)-Phe(p) (OPh)2 ) exhibited a more potent inactivation ability against chymotrypsin than the (S)-epimer. The enzyme inactivated by the (R)-epimer was more effectively reactivated with 2PAM than the enzyme inactivated by the (S)-epimer. Finally, N-succinimidyl (NHS) active ester derivatives, NHS-Suc-Ala-Ala- (R or S)-Phe(p) (OPh)2 , were prepared, and we evaluated their action when modifying Lys175 in chymotrypsin. We demonstrated that the epimeric NHS derivative that possessed the diphenyl phosphonate moiety with the (R)-configuration effectively modified Lys175 in chymotrypsin, whereas that with the (S)-configuration did not. These results demonstrate the utility of peptidyl derivatives that bear an optically active diphenyl phosphonate moiety as affinity labeling probes in protein bioconjugation. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 521-530, 2016.
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Affiliation(s)
- Shin Ono
- Genome Biotechnology Laboratory, Kanazawa Institute of Technology, Hakusan, 924-0838, Japan
| | - Takahiko Nakai
- Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan
| | - Hirofumi Kuroda
- Department of General Education, Ishikawa National College of Technology, Ishikawa, 929-0392, Japan
| | - Ryuta Miyatake
- Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan
| | - Yoshikazu Horino
- Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan
| | - Hitoshi Abe
- Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan
| | - Masahito Umezaki
- Institute of Natural Medicine, University of Toyama, Toyama, 930-0194, Japan
| | - Hiroshi Oyama
- Faculty of Science and Engineering, Setsunan University, Osaka, 572-8508, Japan
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Sanman LE, van der Linden WA, Verdoes M, Bogyo M. Bifunctional Probes of Cathepsin Protease Activity and pH Reveal Alterations in Endolysosomal pH during Bacterial Infection. Cell Chem Biol 2016; 23:793-804. [PMID: 27427229 DOI: 10.1016/j.chembiol.2016.05.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/05/2016] [Accepted: 05/24/2016] [Indexed: 12/21/2022]
Abstract
Cysteine cathepsins are lysosomal proteases involved in regulation of both normal cellular processes and disease. Biochemical studies with peptide substrates indicate that cathepsins have optimal activity at acidic pH and highly attenuated activity at neutral pH. In contrast, there is mounting evidence that cathepsins have biological roles in environments that have non-acidic pH. To further define the specific pH environments where cathepsins act, we designed bifunctional activity-based probes (ABPs) that allow simultaneous analysis of cathepsin protease activity and pH. We use these probes to analyze the steady-state environment of cathepsin activity in macrophages and to measure dynamic changes in activity and pH upon stimulation. We show that Salmonella typhimurium induces a change in lysosomal pH that ultimately impairs cathepsin activity in both infected cells and a fraction of bystander cells, highlighting a mechanism by which Salmonella can simultaneously flourish within host cells and alter the behavior of nearby uninfected cells.
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Affiliation(s)
- Laura E Sanman
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Martijn Verdoes
- Department of Tumor Immunology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Matthew Bogyo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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14
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Brewer TF, Garcia FJ, Onak CS, Carroll KS, Chang CJ. Chemical approaches to discovery and study of sources and targets of hydrogen peroxide redox signaling through NADPH oxidase proteins. Annu Rev Biochem 2015; 84:765-90. [PMID: 26034893 DOI: 10.1146/annurev-biochem-060614-034018] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hydrogen peroxide (H2O2) is a prime member of the reactive oxygen species (ROS) family of molecules produced during normal cell function and in response to various stimuli, but if left unchecked, it can inflict oxidative damage on all types of biological macromolecules and lead to cell death. In this context, a major source of H2O2 for redox signaling purposes is the NADPH oxidase (Nox) family of enzymes, which were classically studied for their roles in phagocytic immune response but have now been found to exist in virtually all mammalian cell types in various isoforms with distinct tissue and subcellular localizations. Downstream of this tightly regulated ROS generation, site-specific, reversible covalent modification of proteins, particularly oxidation of cysteine thiols to sulfenic acids, represents a prominent posttranslational modification akin to phosphorylation as an emerging molecular mechanism for transforming an oxidant signal into a dynamic biological response. We review two complementary types of chemical tools that enable (a) specific detection of H2O2 generated at its sources and (b) mapping of sulfenic acid posttranslational modification targets that mediate its signaling functions, which can be used to study this important chemical signal in biological systems.
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15
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Hütten M, Geukes M, Misas-Villamil JC, van der Hoorn RAL, Grundler FMW, Siddique S. Activity profiling reveals changes in the diversity and activity of proteins in Arabidopsis roots in response to nematode infection. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 97:36-43. [PMID: 26408809 DOI: 10.1016/j.plaphy.2015.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 08/27/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Abstract
Cyst nematodes are obligate, sedentary endoparasites with a highly specialised biology and a huge economic impact in agriculture. Successful parasitism involves morphological and physiological modifications of the host cells which lead to the formation of specialised syncytial feeding structures in roots. The development of the syncytium is aided by a cocktail of nematode effectors that manipulate the host plant activities in a complex network of interactions through post-translational modifications. Traditional transcriptomic and proteomic approaches cannot display this functional proteomic information. Activity-based protein profiling (ABPP) is a powerful technology that can be used to investigate the activity of the proteome through activity-based probes. To better understand the functional proteomics of syncytium, ABPP was conducted on syncytia induced by the beet cyst nematode Heterodera schachtii in Arabidopsis roots. Our results demonstrated that the activity of several enzymes is differentially regulated in the syncytium compared to the control roots. Among those specifically activated in the syncytium are a putative S-formyl-glutathione hydrolase (SFGH), a putative methylesterase (MES) and two unidentified enzymes. In contrast, the activities of vacuolar processing enzymes (VPEs) are specifically suppressed in the syncytium. Competition labelling, quantitative gene expression and T-DNA knock-out mutants were used to further characterise the roles of the differentially regulated enzymes during plant-nematode interaction. In conclusion, our study will open the door to generate a comprehensive and integrated view of the host-pathogen warfare that results in the formation of long-term feeding sites for pathogens.
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Affiliation(s)
- Marion Hütten
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany.
| | - Melanie Geukes
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany.
| | - Johana C Misas-Villamil
- Plant Chemetics Lab, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany; Botanical Institute and Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany.
| | - Renier A L van der Hoorn
- Plant Chemetics Lab, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany; Plant Chemetics Lab, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3UB Oxford, UK.
| | - Florian M W Grundler
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany.
| | - Shahid Siddique
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany.
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16
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Detection of protease activity in cells and animals. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:130-42. [PMID: 25960278 DOI: 10.1016/j.bbapap.2015.04.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/21/2015] [Accepted: 04/28/2015] [Indexed: 01/05/2023]
Abstract
Proteases are involved in a wide variety of biologically and medically important events. They are entangled in a complex network of processes that regulate their activity, which makes their study intriguing, but challenging. For comprehensive understanding of protease biology and effective drug discovery, it is therefore essential to study proteases in models that are close to their complex native environments such as live cells or whole organisms. Protease activity can be detected by reporter substrates and activity-based probes, but not all of these reagents are suitable for intracellular or in vivo use. This review focuses on the detection of proteases in cells and in vivo. We summarize the use of probes and substrates as molecular tools, discuss strategies to deliver these tools inside cells, and describe sophisticated read-out techniques such as mass spectrometry and various imaging applications. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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17
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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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18
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Abstract
Eukaryotic and prokaryotic organisms possess huge numbers of uncharacterized enzymes. Selective inhibitors offer powerful probes for assigning functions to enzymes in native biological systems. Here, we discuss how the chemical proteomic platform activity-based protein profiling (ABPP) can be implemented to discover selective and in vivo-active inhibitors for enzymes. We further describe how these inhibitors have been used to delineate the biochemical and cellular functions of enzymes, leading to the discovery of metabolic and signaling pathways that make important contributions to human physiology and disease. These studies demonstrate the value of selective chemical probes as drivers of biological inquiry.
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Affiliation(s)
- Micah J Niphakis
- The Skaggs Institute for Chemical Biology and the Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037;
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19
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Wang ZPA, Tian CL, Zheng JS. The recent developments and applications of the traceless-Staudinger reaction in chemical biology study. RSC Adv 2015. [DOI: 10.1039/c5ra21496c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bioorthogonal reactions are one of the most important topics in chemical biology. Traceless-Staudinger reaction/ligation has been investigated and widely applied in life science. Herein, the current developments, mechanism studies, and biological applications are summarized.
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Affiliation(s)
- Zhi-Peng A. Wang
- High Magnetic Field Laboratory
- Chinese Academy of Sciences
- Hefei 230031
- China
- Department of Chemistry
| | - Chang-Lin Tian
- High Magnetic Field Laboratory
- Chinese Academy of Sciences
- Hefei 230031
- China
| | - Ji-Shen Zheng
- High Magnetic Field Laboratory
- Chinese Academy of Sciences
- Hefei 230031
- China
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20
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Edem PE, Czorny S, Valliant JF. Synthesis and Evaluation of Radioiodinated Acyloxymethyl Ketones as Activity-Based Probes for Cathepsin B. J Med Chem 2014; 57:9564-77. [PMID: 25360988 DOI: 10.1021/jm501357r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Patricia E. Edem
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Shannon Czorny
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - John F. Valliant
- Department of Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
- Centre for Probe Development and Commercialization, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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21
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Tan Y, Kagan JC. A cross-disciplinary perspective on the innate immune responses to bacterial lipopolysaccharide. Mol Cell 2014; 54:212-23. [PMID: 24766885 DOI: 10.1016/j.molcel.2014.03.012] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The study of innate immunity to bacteria has focused heavily on the mechanisms by which mammalian cells detect lipopolysaccharide (LPS), the conserved surface component of Gram-negative bacteria. While Toll-like receptor 4 (TLR4) is responsible for all the host transcriptional responses to LPS, recent discoveries have revealed the existence of several TLR4-independent responses to LPS. These discoveries not only broaden our view of the means by which mammalian cells interact with bacteria, but they also highlight new selective pressures that may have promoted the evolution of bacterial immune evasion strategies. In this review, we highlight past and recent discoveries on host LPS sensing mechanisms and discuss bacterial countermeasures that promote infection. By looking at both sides of the host-pathogen interaction equation, we hope to provide comprehensive insights into host defense mechanisms and bacterial pathogenesis.
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Affiliation(s)
- Yunhao Tan
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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22
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Wiedner SD, Anderson LN, Sadler NC, Chrisler WB, Kodali VK, Smith RD, Wright AT. Organelle-Specific Activity-Based Protein Profiling in Living Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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23
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Wiedner SD, Anderson LN, Sadler NC, Chrisler WB, Kodali VK, Smith RD, Wright AT. Organelle-specific activity-based protein profiling in living cells. Angew Chem Int Ed Engl 2014; 53:2919-22. [PMID: 24505022 DOI: 10.1002/anie.201309135] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/26/2013] [Indexed: 12/26/2022]
Abstract
A multimodal activity-based probe for targeting acidic organelles was developed to measure subcellular native enzymatic activity in cells by fluorescence microscopy and mass spectrometry. A cathepsin-reactive warhead conjugated to a weakly basic amine and a clickable alkyne, for subsequent appendage of a fluorophore or biotin reporter tag, accumulated in lysosomes as observed by structured illumination microscopy (SIM) in J774 mouse macrophage cells. Analysis of in vivo labeled J774 cells by mass spectrometry showed that the probe was very selective for cathepsins B and Z, two lysosomal cysteine proteases. Analysis of starvation-induced autophagy, a catabolic pathway involving lysosomes, showed a large increase in the number of tagged proteins and an increase in cathepsin activity. The organelle-targeting of activity-based probes holds great promise for the characterization of enzyme activities in the myriad diseases linked to specific subcellular locations, particularly the lysosome.
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Affiliation(s)
- Susan D Wiedner
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
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24
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Quesne MG, Ward RA, de Visser SP. Cysteine protease inhibition by nitrile-based inhibitors: a computational study. Front Chem 2013; 1:39. [PMID: 24790966 PMCID: PMC3982517 DOI: 10.3389/fchem.2013.00039] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 12/15/2013] [Indexed: 12/31/2022] Open
Abstract
Cysteine protease enzymes are important for human physiology and catalyze key protein degradation pathways. These enzymes react via a nucleophilic reaction mechanism that involves a cysteine residue and the proton of a proximal histidine. Particularly efficient inhibitors of these enzymes are nitrile-based, however, the details of the catalytic reaction mechanism currently are poorly understood. To gain further insight into the inhibition of these molecules, we have performed a combined density functional theory and quantum mechanics/molecular mechanics study on the reaction of a nitrile-based inhibitor with the enzyme active site amino acids. We show here that small perturbations to the inhibitor structure can have dramatic effects on the catalysis and inhibition processes. Thus, we investigated a range of inhibitor templates and show that specific structural changes reduce the inhibitory efficiency by several orders of magnitude. Moreover, as the reaction takes place on a polar surface, we find strong differences between the DFT and QM/MM calculated energetics. In particular, the DFT model led to dramatic distortions from the starting structure and the convergence to a structure that would not fit the enzyme active site. In the subsequent QM/MM study we investigated the use of mechanical vs. electronic embedding on the kinetics, thermodynamics and geometries along the reaction mechanism. We find minor effects on the kinetics of the reaction but large geometric and thermodynamics differences as a result of inclusion of electronic embedding corrections. The work here highlights the importance of model choice in the investigation of this biochemical reaction mechanism.
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Affiliation(s)
- Matthew G Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester Manchester, UK
| | | | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester Manchester, UK
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25
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Yang Y, Yang X, Verhelst SHL. Comparative analysis of click chemistry mediated activity-based protein profiling in cell lysates. Molecules 2013; 18:12599-608. [PMID: 24126377 PMCID: PMC6270401 DOI: 10.3390/molecules181012599] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/07/2013] [Accepted: 09/26/2013] [Indexed: 12/14/2022] Open
Abstract
Activity-based protein profiling uses chemical probes that covalently attach to active enzyme targets. Probes with conventional tags have disadvantages, such as limited cell permeability or steric hindrance around the reactive group. A tandem labeling strategy with click chemistry is now widely used to study enzyme targets in situ and in vivo. Herein, the probes are reacted in live cells, whereas the ensuing detection by click chemistry takes place in cell lysates. We here make a comparison of the efficiency of the activity-based tandem labeling strategy by using Cu(I)-catalyzed and strain-promoted click chemistry, different ligands and different lysis conditions.
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Affiliation(s)
- Yinliang Yang
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.
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26
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Puri AW, Bogyo M. Applications of small molecule probes in dissecting mechanisms of bacterial virulence and host responses. Biochemistry 2013; 52:5985-96. [PMID: 23937332 DOI: 10.1021/bi400854d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Elucidating the molecular and biochemical details of bacterial infections can be challenging because of the many complex interactions that exist between a pathogen and its host. Consequently, many tools have been developed to aid the study of bacterial pathogenesis. Small molecules are a valuable complement to traditional genetic techniques because they can be used to rapidly perturb genetically intractable systems and to monitor post-translationally regulated processes. Activity-based probes are a subset of small molecules that covalently label an enzyme of interest based on its catalytic mechanism. These tools allow monitoring of enzyme activation within the context of a native biological system and can be used to dissect the biochemical details of enzyme function. This review describes the development and application of activity-based probes for examining aspects of bacterial infection on both sides of the host-pathogen interface.
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Affiliation(s)
- Aaron W Puri
- Department of Chemical and Systems Biology, ‡Department of Microbiology and Immunology, and §Department of Pathology, Stanford University School of Medicine , 300 Pasteur Drive, Stanford, California 94305, United States
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27
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Ono S, Murai J, Nakai T, Kuroda H, Horino Y, Yoshimura T, Oyama H, Umezaki M. Site-selective Chemical Modification of Chymotrypsin Using a Peptidyl Diphenyl 1-Amino-2-phenylethylphosphonate Derivative. CHEM LETT 2013. [DOI: 10.1246/cl.130244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shin Ono
- Graduate School of Science and Engineering, University of Toyama
| | - Junya Murai
- Graduate School of Science and Engineering, University of Toyama
| | - Takahiko Nakai
- Graduate School of Science and Engineering, University of Toyama
| | | | - Yoshikazu Horino
- Graduate School of Science and Engineering, University of Toyama
| | | | - Hiroshi Oyama
- Faculty of Science and Engineering, Setsunan University
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28
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Paulsen C, Carroll KS. Cysteine-mediated redox signaling: chemistry, biology, and tools for discovery. Chem Rev 2013; 113:4633-79. [PMID: 23514336 PMCID: PMC4303468 DOI: 10.1021/cr300163e] [Citation(s) in RCA: 790] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Candice
E. Paulsen
- Department of Chemistry, The Scripps Research
Institute, Jupiter, Florida, 33458, United States
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research
Institute, Jupiter, Florida, 33458, United States
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29
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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30
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Yang Y, Verhelst SHL. Cleavable trifunctional biotin reagents for protein labelling, capture and release. Chem Commun (Camb) 2013; 49:5366-8. [DOI: 10.1039/c3cc42076k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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McGourty K, Thurston TL, Matthews SA, Pinaud L, Mota LJ, Holden DW. Salmonella inhibits retrograde trafficking of mannose-6-phosphate receptors and lysosome function. Science 2012; 338:963-7. [PMID: 23162002 DOI: 10.1126/science.1227037] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Salmonella enterica is an intracellular bacterial pathogen that replicates within membrane-bound vacuoles through the action of effector proteins translocated into host cells. Salmonella vacuoles have characteristics of lysosomes but are reduced in hydrolytic enzymes transported by mannose-6-phosphate receptors (MPRs). We found that the effector SifA subverted Rab9-dependent retrograde trafficking of MPRs, thereby attenuating lysosome function. This required binding of SifA to its host cell target SKIP/PLEKHM2. Furthermore, SKIP regulated retrograde trafficking of MPRs in noninfected cells. Translocated SifA formed a stable complex with SKIP and Rab9 in infected cells. Sequestration of Rab9 by SifA-SKIP accounted for the effect of SifA on MPR transport and lysosome function. Growth of Salmonella increased in cells with reduced lysosomal activity and decreased in cells with higher lysosomal activity. These results suggest that Salmonella vacuoles undergo fusion with lysosomes whose potency has been reduced by SifA.
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Affiliation(s)
- Kieran McGourty
- Section of Microbiology, Centre for Molecular Microbiology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
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32
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Fan F, Nie S, Dammer EB, Duong DM, Pan D, Ping L, Zhai L, Wu J, Hong X, Qin L, Xu P, Zhang YH. Protein Profiling of Active Cysteine Cathepsins in Living Cells Using an Activity-Based Probe Containing a Cell-Penetrating Peptide. J Proteome Res 2012; 11:5763-72. [DOI: 10.1021/pr300575u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Fengkai Fan
- Britton Chance Center for Biomedical
Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology (HUST),
Wuhan, China
- Key Laboratory of Biomedical
Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan,
China
| | - Si Nie
- Britton Chance Center for Biomedical
Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology (HUST),
Wuhan, China
- Key Laboratory of Biomedical
Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan,
China
| | - Eric B. Dammer
- Department of Human Genetics,
and Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, United States
| | - Duc M. Duong
- Department of Human Genetics,
and Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, United States
| | - Deng Pan
- Britton Chance Center for Biomedical
Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology (HUST),
Wuhan, China
- Key Laboratory of Biomedical
Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan,
China
| | - Lingyan Ping
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- Department of Biochemistry,
School of Medicine, Wuhan University, Wuhan,
China
| | - Linhui Zhai
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- Key Laboratory of Combinatorial
Biosynthesis and Drug Discovery, Wuhan University, Ministry of Education, and Wuhan University School of Pharmaceutical
Sciences, Wuhan, China
| | - Junzhu Wu
- Department of Biochemistry,
School of Medicine, Wuhan University, Wuhan,
China
| | - Xuechuan Hong
- Key Laboratory of Combinatorial
Biosynthesis and Drug Discovery, Wuhan University, Ministry of Education, and Wuhan University School of Pharmaceutical
Sciences, Wuhan, China
| | - Lingsong Qin
- Britton Chance Center for Biomedical
Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology (HUST),
Wuhan, China
- Key Laboratory of Biomedical
Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan,
China
| | - Ping Xu
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- Key Laboratory of Combinatorial
Biosynthesis and Drug Discovery, Wuhan University, Ministry of Education, and Wuhan University School of Pharmaceutical
Sciences, Wuhan, China
| | - Yu-Hui Zhang
- Britton Chance Center for Biomedical
Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology (HUST),
Wuhan, China
- Key Laboratory of Biomedical
Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan,
China
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33
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Yang Y, Hahne H, Kuster B, Verhelst SHL. A simple and effective cleavable linker for chemical proteomics applications. Mol Cell Proteomics 2012; 12:237-44. [PMID: 23028061 DOI: 10.1074/mcp.m112.021014] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The study of metabolically labeled or probe-modified proteins is an important area in chemical proteomics. Isolation and purification of the protein targets is a necessary step before MS identification. The biotin-streptavidin system is widely used in this process, but the harsh denaturing conditions also release natively biotinylated proteins and non-selectively bound proteins. A cleavable linker strategy is a promising approach for solving this problem. Though several cleavable linkers have been developed and tested, an efficient, easily synthesized, and inexpensive cleavable linker is a desirable addition to the proteomics toolbox. Here, we describe the chemical proteomics application of a vicinal diol cleavable linker. Through easy-to-handle chemistry we incorporate this linker into an activity-based probe and a biotin alkyne tag amenable for bioorthogonal ligation. With these reagents, background protein identifications are significantly reduced relative to standard on-bead digestion.
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Affiliation(s)
- Yinliang Yang
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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34
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Shannon DA, Gu C, McLaughlin CJ, Kaiser M, van der Hoorn RAL, Weerapana E. Sulfonyl fluoride analogues as activity-based probes for serine proteases. Chembiochem 2012; 13:2327-30. [PMID: 23008217 DOI: 10.1002/cbic.201200531] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Indexed: 12/21/2022]
Abstract
Enriched with fluoride: To expand on the available tools to interrogate proteases, we explored sulfonyl fluorides as activity-based probes. An alkyne-tagged sulfonyl fluoride covalently modifies members of the S1 family of serine proteases. By applying click chemistry, avidin enrichment and mass spectrometry, we can enrich and identify active endogenous serine proteases from a complex proteome.
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35
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Serim S, Haedke U, Verhelst SHL. Activity-based probes for the study of proteases: recent advances and developments. ChemMedChem 2012; 7:1146-59. [PMID: 22431376 DOI: 10.1002/cmdc.201200057] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/28/2012] [Indexed: 11/11/2022]
Abstract
Proteases are important targets for the treatment of human disease. Several protease inhibitors have failed in clinical trials due to a lack of in vivo specificity, indicating the need for studies of protease function and inhibition in complex, disease-related models. The tight post-translational regulation of protease activity complicates protease analysis by traditional proteomics methods. Activity-based protein profiling is a powerful technique that can resolve this issue. It uses small-molecule tools-activity-based probes-to label and analyze active enzymes in lysates, cells, and whole animals. Over the last twelve years, a wide variety of protease activity-based probes have been developed. These synthetic efforts have enabled techniques ranging from real-time in vivo imaging of protease activity to high-throughput screening of uncharacterized proteases. This Review introduces the general principles of activity-based protein profiling and describes the recent advancements in probe design and analysis techniques, which have increased the knowledge of protease biology and will aid future protease drug discovery.
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Affiliation(s)
- Sevnur Serim
- Center for Integrated Protein Science Munich (CIPS(M)), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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36
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van Berkel SS, van Eldijk MB, van Hest JCM. Staudinger ligation as a method for bioconjugation. Angew Chem Int Ed Engl 2011; 50:8806-27. [PMID: 21887733 DOI: 10.1002/anie.201008102] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 11/11/2022]
Abstract
In 1919 the German chemist Hermann Staudinger was the first to describe the reaction between an azide and a phosphine. It was not until recently, however, that Bertozzi and co-workers recognized the potential of this reaction as a method for bioconjugation and transformed it into the so-called Staudinger ligation. The bio-orthogonal character of both the azide and the phosphine functions has resulted in the Staudinger ligation finding numerous applications in various complex biological systems. For example, the Staudinger ligation has been utilized to label glycans, lipids, DNA, and proteins. Moreover, the Staudinger ligation has been used as a synthetic method to construct glycopeptides, microarrays, and functional biopolymers. In the emerging field of bio-orthogonal ligation strategies, the Staudinger ligation has set a high standard to which most of the new techniques are often compared. This Review summarizes recent developments and new applications of the Staudinger ligation.
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Affiliation(s)
- Sander S van Berkel
- Department of Bioorganic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
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37
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van Berkel SS, van Eldijk MB, van Hest JCM. Staudinger-Ligation als Methode zur Biokonjugation. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008102] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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Johnson CM, Monzingo AF, Ke Z, Yoon DW, Linsky TW, Guo H, Robertus JD, Fast W. On the mechanism of dimethylarginine dimethylaminohydrolase inactivation by 4-halopyridines. J Am Chem Soc 2011; 133:10951-9. [PMID: 21630706 PMCID: PMC3135753 DOI: 10.1021/ja2033684] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules capable of selective covalent protein modification are of significant interest for the development of biological probes and therapeutics. We recently reported that 2-methyl-4-bromopyridine is a quiescent affinity label for the nitric oxide controlling enzyme dimethylarginine dimethylaminohydrolase (DDAH) (Johnson, C. M.; Linsky, T. W.; Yoon, D. W.; Person, M. D.; Fast, W. J. Am. Chem. Soc. 2011, 133, 1553-1562). Discovery of this novel protein modifier raised the possibility that the 4-halopyridine motif may be suitable for wider application. Therefore, the inactivation mechanism of the related compound 2-hydroxymethyl-4-chloropyridine is probed here in more detail. Solution studies support an inactivation mechanism in which the active site Asp66 residue stabilizes the pyridinium form of the inactivator, which has enhanced reactivity toward the active site Cys, resulting in covalent bond formation, loss of the halide, and irreversible inactivation. A 2.18 Å resolution X-ray crystal structure of the inactivated complex elucidates the orientation of the inactivator and its covalent attachment to the active site Cys, but the structural model does not show an interaction between the inactivator and Asp66. Molecular modeling is used to investigate inactivator binding, reaction, and also a final pyridinium deprotonation step that accounts for the apparent differences between the solution-based and structural studies with respect to the role of Asp66. This work integrates multiple approaches to elucidate the inactivation mechanism of a novel 4-halopyridine "warhead," emphasizing the strategy of using pyridinium formation as a "switch" to enhance reactivity when bound to the target protein.
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Affiliation(s)
| | | | | | | | | | - Hua Guo
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
| | - Jon D. Robertus
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
| | - Walter Fast
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
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Abstract
Cathepsin X is a lysosomal cysteine protease that functions as a carboxypeptidase with broad substrate specificity. Cathepsin X was discovered only recently, and its physiological roles are still not well understood. A number of studies suggest that cathepsin X may be involved in a variety of biological processes, including cancer, aging and degenerative conditions of the brain, inflammation, and cellular communication. Here we present the synthesis and characterization of several activity-based probes (ABPs) that target active cathepsin X. These ABPs were used to label cathepsin X in complex lysates, whole cells, and in vivo. Furthermore, we have developed a method for selectively labeling and visualizing active cathepsin X in vitro and in vivo. Overall, the probes developed in this study are valuable tools for the study of cathepsin X function.
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Affiliation(s)
- Margot G. Paulick
- Departments of †Pathology and ‡Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Dr. Stanford, California 94305-5324, United States
| | - Matthew Bogyo
- Departments of †Pathology and ‡Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Dr. Stanford, California 94305-5324, United States
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40
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Schilling CI, Jung N, Biskup M, Schepers U, Bräse S. Bioconjugation via azide–Staudinger ligation: an overview. Chem Soc Rev 2011; 40:4840-71. [DOI: 10.1039/c0cs00123f] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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41
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Krysiak J, Breinbauer R. Activity-based protein profiling for natural product target discovery. Top Curr Chem (Cham) 2011; 324:43-84. [PMID: 22025071 DOI: 10.1007/128_2011_289] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Natural products represent an important treasure box of biologically active molecules, from which many drug candidates have been sourced. The identification of the target proteins addressed by these natural products is a foremost goal for which new techniques are required. Activity-based protein profiling (ABPP), exploiting protein-reactive functional groups present in many natural products, offers unseen opportunities in this respect. This review article describes the current status of this field. Many examples are given for the annotation of biological target proteins of natural products containing epoxides, lactones, lactams, Michael acceptors, and other electrophilic groups. In addition, the development of probe molecules identified from biomimetic natural product libraries is discussed.
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Affiliation(s)
- Joanna Krysiak
- Institute of Organic Chemistry, Graz University of Technology, Austria
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42
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Böttcher T, Pitscheider M, Sieber SA. Natural products and their biological targets: proteomic and metabolomic labeling strategies. Angew Chem Int Ed Engl 2010; 49:2680-98. [PMID: 20333627 DOI: 10.1002/anie.200905352] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Activity-based protein profiling (ABPP) has matured into a standard method for the fast, sensitive, and selective identification of enzyme activity and inhibitors in proteomes. By using natural product based probes, the targets of many uncharacterized molecules can be easily identified in complex proteomes, and their exact function and mechanism of action understood. Natural products and their derivatives can also serve as pharmaceutical lead structures that impede essential components in the cell and their effects can be studied in biological assays. Since the complex regulatory processes in a cell go beyond mere transcription, translation, and activation, it is imperative to also identify the products of the active proteome--the metabolites and binding partners of individual enzymes and proteins. Therefore, methods by which the chemically complex metabolome can be characterized are necessary. A series of interesting approaches have become available in recent years that enable the global investigation of enzyme-metabolite pairs.
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Affiliation(s)
- Thomas Böttcher
- Center for Integrated Protein Science Munich CiPSM, Department of Chemistry and Biochemistry, Technische Universität Munich, Lichtenbergstrasse 4, 85747 Garching, Germany
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43
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Barker CA, Farha MA, Brown ED. Chemical Genomic Approaches to Study Model Microbes. ACTA ACUST UNITED AC 2010; 17:624-32. [DOI: 10.1016/j.chembiol.2010.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 05/05/2010] [Accepted: 05/06/2010] [Indexed: 12/15/2022]
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44
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Böttcher T, Pitscheider M, Sieber S. Naturstoffe und ihre biologischen Angriffsziele: proteomische und metabolomische Markierungsstrategien. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905352] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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45
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Dang THT, Riva LDL, Fagan RP, Storck EM, Heal WP, Janoir C, Fairweather NF, Tate EW. Chemical probes of surface layer biogenesis in Clostridium difficile. ACS Chem Biol 2010; 5:279-85. [PMID: 20067320 DOI: 10.1021/cb9002859] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Clostridium difficile, a leading cause of hospital-acquired infection, possesses a dense surface layer (S-layer) that mediates host-pathogen interactions. The key structural components of the S-layer result from proteolytic cleavage of a precursor protein, SlpA, into high- and low-molecular-weight components. Here we report the discovery and optimization of the first inhibitors of this process in live bacteria and their application for probing S-layer processing. We also describe the design and in vivo application of activity-based probes that identify the protein Cwp84 as the cysteine protease that mediates SlpA cleavage. This work provides novel chemical tools for the analysis of S-layer biogenesis and for the potential identification of novel drug targets within clostridia and related bacterial pathogens.
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Affiliation(s)
| | - Lucia de la Riva
- Department of Chemistry
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| | - Robert P. Fagan
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| | | | | | - Claire Janoir
- EA 4043, Université Paris-Sud 11, Faculté de Pharmacie, 92296 Châtenay-Malabry, France
| | - Neil F. Fairweather
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
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46
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Pratt MR, Sekedat MD, Chiang KP, Muir TW. Direct measurement of cathepsin B activity in the cytosol of apoptotic cells by an activity-based probe. ACTA ACUST UNITED AC 2010; 16:1001-12. [PMID: 19778728 DOI: 10.1016/j.chembiol.2009.07.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/26/2009] [Accepted: 07/23/2009] [Indexed: 12/22/2022]
Abstract
Cells control their own death through a program termed apoptosis, which is indispensable for development and homeostasis in all metazoans. Lysosomal cysteine proteases are not normally thought of as participating in apoptosis; however, recent reports have shown that the cathepsin proteases can be released from the lysosome during apoptosis, where they can participate in cell death. We report here the development of an activity-based probe that, under optimized conditions, reports on cathepsin B activity only in apoptotic cells by reading out the release of cathepsin B from the lysosomes. Biochemical characterization of apoptosis in cells from cathepsin B null mice shows delayed and suboptimal activation of caspases. Our data further supports a role for cathepsin B in the cytosol as a positive regulator of a cell death feed-forward loop and provides a chemical tool for future investigations.
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Affiliation(s)
- Matthew R Pratt
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, NY 10065, USA.
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47
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Leonard SE, Reddie KG, Carroll KS. Mining the thiol proteome for sulfenic acid modifications reveals new targets for oxidation in cells. ACS Chem Biol 2009; 4:783-99. [PMID: 19645509 DOI: 10.1021/cb900105q] [Citation(s) in RCA: 234] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Oxidation of cysteine to sulfenic acid has emerged as a biologically relevant post-translational modification with particular importance in redox-mediated signal transduction; however, the identity of modified proteins remains largely unknown. We recently reported DAz-1, a cell-permeable chemical probe capable of detecting sulfenic acid modified proteins directly in living cells. Here we describe DAz-2, an analogue of DAz-1 that exhibits significantly improved potency in vitro and in cells. Application of this new probe for global analysis of the sulfenome in a tumor cell line identifies most known sulfenic acid modified proteins: 14 in total, plus more than 175 new candidates, with further testing confirming oxidation in several candidates. The newly identified proteins have roles in signal transduction, DNA repair, metabolism, protein synthesis, redox homeostasis, nuclear transport, vesicle trafficking, and ER quality control. Cross-comparison of these results with those from disulfide, S-glutathionylation, and S-nitrosylation proteomes reveals moderate overlap, suggesting fundamental differences in the chemical and biological basis for target specificity. The combination of selective chemical enrichment and live-cell compatibility makes DAz-2 a powerful new tool with the potential to reveal new regulatory mechanisms in signaling pathways and identify new therapeutic targets.
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Affiliation(s)
| | | | - Kate S. Carroll
- Chemical Biology Graduate Program
- Life Sciences Institute
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2216
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48
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Sletten E, Bertozzi C. Bioorthogonale Chemie - oder: in einem Meer aus Funktionalität nach Selektivität fischen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900942] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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49
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Puri AW, Bogyo M. Using small molecules to dissect mechanisms of microbial pathogenesis. ACS Chem Biol 2009; 4:603-16. [PMID: 19606820 DOI: 10.1021/cb9001409] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the ways in which pathogens invade and neutralize their hosts is of great interest from both an academic and a clinical perspective. However, in many cases genetic tools are unavailable or insufficient to fully characterize the detailed mechanisms of pathogenesis. Small molecule approaches are particularly powerful due to their ability to modulate specific biological functions in a highly controlled manner and their potential to broadly target conserved processes across species. Recently, two approaches that make use of small molecules, activity-based protein profiling and high-throughput phenotypic screening, have begun to find applications in the study of pathways involved in pathogenesis. In this Review we highlight ways in which these techniques have been applied to examine bacterial and parasitic pathogenesis and discuss possible ways in which these efforts can be expanded in the near future.
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Affiliation(s)
| | - Matthew Bogyo
- Chemical and Systems Biology
- Pathology
- Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Dr., Stanford, California 94305
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50
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Yu B, Qin Z, Wijewickrama GT, Edirisinghe P, Bolton JL, Thatcher GRJ. Comparative methods for analysis of protein covalent modification by electrophilic quinoids formed from xenobiotics. Bioconjug Chem 2009; 20:728-41. [PMID: 19301905 DOI: 10.1021/bc800435m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Conjugation of biotin and fluorophore tags is useful for assaying covalent protein modification. Oxidative bioactivation of selective estrogen receptor modulators (SERMs) yields reactive quinoid electrophiles that covalently modify proteins, and bioactivation is associated with carcinogenic and chemopreventive effects. Identification of the protein targets of electrophilic metabolites is of general importance for xenobiotics. Four methodologies using SERM derivatized biotin/fluorophore tags were compared for purification and quantification: (1) covert oxidatively activated tags (COATags; SERM conjugated to biotin); (2) dansylTags (SERM conjugated to fluorophore); and azidoTags (SERM azide derivatives) in a two-step conjugation to biotin, using either (3) Staudinger ligation or (4) click chemistry. All synthetic derivatives retained the estrogen receptor ligand characteristics of the parent SERMs. Model proteins with bioactivation by tyrosinase in buffer or cell lysates and liver proteins with in situ bioactivation in rat primary hepatocytes were studied by immunoassay and fluorescence. Comparison showed that the azidoTag/Staudinger method was sensitive but nonspecific, the azidoTag/click methodology had low sensitivity, and the dansylTag methodology failed to detect modified proteins in hepatocytes. The COATag methodology was judged superior, detecting 5 ng of modified protein in vitro and identifying protein targets in hepatocytes. In metabolism studies in rat liver microsomes, the azide group was metabolically labile, which was a contributing factor in not selecting the azidoTag methodology in the oxidative environments required for bioactivation. For study of the protein targets of electrophilic metabolites formed by in situ oxidative bioactivation, the COATag is both sensitive and specific and does not appear to suffer from poor cell permeability.
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Affiliation(s)
- Bolan Yu
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 60612, USA
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