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Nemmara VV, Tilvawala R, Salinger AJ, Miller L, Nguyen SH, Weerapana E, Thompson PR. Citrullination Inactivates Nicotinamide- N-methyltransferase. ACS Chem Biol 2018; 13:2663-2672. [PMID: 30044909 DOI: 10.1021/acschembio.8b00578] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nicotinamide- N-methyltransferase (NNMT) catalyzes the irreversible methylation of nicotinamide (NAM) to form N-methyl nicotinamide using S-adenosyl methionine as a methyl donor. NNMT is implicated in several chronic disease conditions, including cancers, kidney disease, cardiovascular disease, and Parkinson's disease. Although phosphorylation of NNMT in gastric tumors is reported, the functional effects of this post-translational modification has not been investigated. We previously reported that citrullination of NNMT by Protein Arginine Deiminases abolished its methyltransferase activity. Herein, we investigate the mechanism of inactivation. Using tandem mass spectrometry, we identified three sites of citrullination in NNMT. With this information in hand, we used a combination of site-directed mutagenesis, kinetics, and circular dichoism experiments to demonstrate that citrullination of R132 leads to a structural perturbation that ultimately promotes NNMT inactivation.
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Affiliation(s)
- Venkatesh V. Nemmara
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ronak Tilvawala
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ari J. Salinger
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Lacey Miller
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Son Hong Nguyen
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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52
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Cravatt BF, Hsu KL, Weerapana E. How to Target Viral and Bacterial Effector Proteins Interfering with Ubiquitin Signaling. Curr Top Microbiol Immunol 2018; 420:111-130. [PMID: 30178261 PMCID: PMC7120092 DOI: 10.1007/82_2018_134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ubiquitination is a frequently occurring and very diverse posttranslational modification influencing a wide scope of cellular processes. Ubiquitin (Ub) has the unique ability to form eight different lysine-linked polymeric chains, mixed chains and engages with ubiquitin-like (Ubl) molecules. The distinct signals evoked by specific enzymes play a crucial role in, for instance, proteasome-mediated protein degradation, cell cycle regulation, and DNA damage responses. Due to the large variety of cellular functions that this posttranslational modification influences, the enzymes that construct such Ub modifications, and subsequently controle and degrade these signals, is enormous. In this chapter, we will discuss the current state-of-the-art of activity-based probes, reporter substrates, and other relevant tools based on Ub as recognition element, to study the enzymes involved in the complex system of ubiquitination.
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Affiliation(s)
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA USA
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53
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Gao J, Yang F, Che J, Han Y, Wang Y, Chen N, Bak DW, Lai S, Xie X, Weerapana E, Wang C. Selenium-Encoded Isotopic Signature Targeted Profiling. ACS Cent Sci 2018; 4:960-970. [PMID: 30159393 PMCID: PMC6107865 DOI: 10.1021/acscentsci.8b00112] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Indexed: 05/09/2023]
Abstract
Selenium (Se), as an essential trace element, plays crucial roles in many organisms including humans. The biological functions of selenium are mainly mediated by selenoproteins, a unique class of selenium-containing proteins in which selenium is inserted in the form of selenocysteine. Due to their low abundance and uneven tissue distribution, detection of selenoproteins within proteomes is very challenging, and therefore functional studies of these proteins are limited. In this study, we developed a computational method, named as selenium-encoded isotopic signature targeted profiling (SESTAR), which utilizes the distinct natural isotopic distribution of selenium to assist detection of trace selenium-containing signals from shotgun-proteomic data. SESTAR can detect femtomole quantities of synthetic selenopeptides in a benchmark test and dramatically improved detection of native selenoproteins from tissue proteomes in a targeted profiling mode. By applying SESTAR to screen publicly available datasets from Human Proteome Map, we provide a comprehensive picture of selenoprotein distributions in human primary hematopoietic cells and tissues. We further demonstrated that SESTAR can aid chemical-proteomic strategies to identify additional selenoprotein targets of RSL3, a canonical inducer of cell ferroptosis. We believe SESTAR not only serves as a powerful tool for global profiling of native selenoproteomes, but can also work seamlessly with chemical-proteomic profiling strategies to enhance identification of target proteins, post-translational modifications, or protein-protein interactions.
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Affiliation(s)
- Jinjun Gao
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fan Yang
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Jinteng Che
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu Han
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Yankun Wang
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Nan Chen
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Daniel W. Bak
- Department
of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Shuchang Lai
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao Xie
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Eranthie Weerapana
- Department
of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chu Wang
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- E-mail:
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54
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Lentz CS, Sheldon JR, Crawford LA, Cooper R, Garland M, Amieva MR, Weerapana E, Skaar EP, Bogyo M. Identification of a S. aureus virulence factor by activity-based protein profiling (ABPP). Nat Chem Biol 2018; 14:609-617. [PMID: 29769740 PMCID: PMC6202179 DOI: 10.1038/s41589-018-0060-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/27/2018] [Indexed: 12/22/2022]
Abstract
Serine hydrolases play diverse roles in regulating host-pathogen interactions in a number of organisms, yet few have been characterized in the human pathogen Staphylococcus aureus. Here we describe a chemical proteomic screen that identified ten previously uncharacterized S. aureus serine hydrolases that mostly lack human homologs. We termed these enzymes fluorophosphonate-binding hydrolases (FphA-J). One hydrolase, FphB, can process short fatty acid esters, exhibits increased activity in response to host cell factors, is located predominantly on the bacterial cell surface in a subset of cells, and is concentrated in the division septum. Genetic disruption of fphB confirmed that the enzyme is dispensable for bacterial growth in culture but crucial for establishing infection in distinct sites in vivo. A selective small molecule inhibitor of FphB effectively reduced infectivity in vivo, suggesting that it may be a viable therapeutic target for the treatment or management of Staphylococcus infections.
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Affiliation(s)
- Christian S Lentz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jessica R Sheldon
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa A Crawford
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Rachel Cooper
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Megan Garland
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Manuel R Amieva
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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55
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Weerapana E. Chemical‐proteomic strategies to investigate reactive cysteines. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.476.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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56
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Cole KS, Grandjean JMD, Chen K, Witt CH, O'Day J, Shoulders MD, Wiseman RL, Weerapana E. Characterization of an A-Site Selective Protein Disulfide Isomerase A1 Inhibitor. Biochemistry 2018. [PMID: 29521097 DOI: 10.1021/acs.biochem.8b00178] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein disulfide isomerase A1 (PDIA1) is an endoplasmic reticulum (ER)-localized thiol-disulfide oxidoreductase that is an important folding catalyst for secretory pathway proteins. PDIA1 contains two active-site domains (a and a'), each containing a Cys-Gly-His-Cys (CGHC) active-site motif. The two active-site domains share 37% sequence identity and function independently to perform disulfide-bond reduction, oxidation, and isomerization. Numerous inhibitors for PDIA1 have been reported, yet the selectivity of these inhibitors toward the a and a' sites is poorly characterized. Here, we identify a potent and selective PDIA1 inhibitor, KSC-34, with 30-fold selectivity for the a site over the a' site. KSC-34 displays time-dependent inhibition of PDIA1 reductase activity in vitro with a kinact/ KI of 9.66 × 103 M-1 s-1 and is selective for PDIA1 over other members of the PDI family, and other cellular cysteine-containing proteins. We provide the first cellular characterization of an a-site selective PDIA1 inhibitor and demonstrate that KSC-34 has minimal sustained effects on the cellular unfolded protein response, indicating that a-site inhibition does not induce global protein folding-associated ER stress. KSC-34 treatment significantly decreases the rate of secretion of a destabilized, amyloidogenic antibody light chain, thereby minimizing pathogenic amyloidogenic extracellular proteins that rely on high PDIA1 activity for proper folding and secretion. Given the poor understanding of the contribution of each PDIA1 active site to the (patho)physiological functions of PDIA1, site selective inhibitors like KSC-34 provide useful tools for delineating the pathological role and therapeutic potential of PDIA1.
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Affiliation(s)
- Kyle S Cole
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Julia M D Grandjean
- Department of Molecular Medicine , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Kenny Chen
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Collin H Witt
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Johanna O'Day
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Matthew D Shoulders
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - R Luke Wiseman
- Department of Molecular Medicine , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Eranthie Weerapana
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
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57
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Nemmara VV, Subramanian V, Muth A, Mondal S, Salinger AJ, Maurais AJ, Tilvawala R, Weerapana E, Thompson PR. The Development of Benzimidazole-Based Clickable Probes for the Efficient Labeling of Cellular Protein Arginine Deiminases (PADs). ACS Chem Biol 2018; 13:712-722. [PMID: 29341591 DOI: 10.1021/acschembio.7b00957] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Citrullination is the post-translational hydrolysis of peptidyl-arginines to form peptidyl-citrulline, a reaction that is catalyzed by the protein arginine deiminases (PADs), a family of calcium-regulated enzymes. Aberrantly increased protein citrullination is associated with a slew of autoimmune diseases (e.g., rheumatoid arthritis (RA), multiple sclerosis, lupus, and ulcerative colitis) and certain cancers. Given the clear link between increased PAD activity and human disease, the PADs are therapeutically relevant targets. Herein, we report the development of next generation cell permeable and "clickable" probes (BB-Cl-Yne and BB-F-Yne) for covalent labeling of the PADs both in vitro and in cell-based systems. Using advanced chemoproteomic technologies, we also report the off targets of both BB-Cl-Yne and BB-F-Yne. The probes are highly specific for the PADs, with relatively few off targets, especially BB-F-Yne, suggesting the preferential use of the fluoroacetamidine warhead in next generation irreversible PAD inhibitors. Notably, these compounds can be used in a variety of modalities, including the identification of off targets of the parent compounds and as activity-based protein profiling probes in target engagement assays to demonstrate the efficacy of PAD inhibitors.
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Affiliation(s)
- Venkatesh V. Nemmara
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Venkataraman Subramanian
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Aaron Muth
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Santanu Mondal
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ari J. Salinger
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Aaron J. Maurais
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Ronak Tilvawala
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
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58
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Abstract
Cysteine residues on proteins serve a variety of catalytic and regulatory functions due to the high nucleophilicity and redox activity of the thiol group. Quantitative proteomic platforms for profiling cysteine reactivity can provide valuable information related to the post-translational modification state and inhibitor occupancy of functional cysteine residues within a complex proteome. Cysteine-reactivity profiling typically monitors changes in the extent of cysteine labeling by cysteine-reactive chemical probes, such as iodoacetamide (IA)-alkyne. To enable accurate measurements of cysteine reactivity changes, isotopic labels are introduced into the two proteomes of interest using either isotopically tagged proteomes (SILAC) or cleavable linkers (isoTOP-ABPP) that are installed using copper-catalyzed azide-alkyne cycloaddition (CuAAC). Here we provide an alternative strategy for isotopic tagging of two proteomes for cysteine-reactivity profiling by developing IA-light and IA-heavy, a pair of isotopically labeled iodoacetamide-alkyne probes. These probes can be utilized for proteome samples that are not amenable to SILAC labeling and are facile to synthesize, especially when compared to the isotopically tagged cleavable linkers. We confirm the quantitative accuracy of IA-light and IA-heavy by assessing cysteine reactivity in a purified thioredoxin protein, as well as globally within a complex proteome where IA-light treatment generates mass-spectrometry identification of 992 cysteine residues. Importantly, these isotopically tagged probes can also be utilized for quantifying the percentage of cysteine modification within a single sample. Preliminary data supports the use of these tags to quantify the stoichiometry of TCEP-susceptible cysteine oxidation events in cell lysates.
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Affiliation(s)
- Masahiro Abo
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Chun Li
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Eranthie Weerapana
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
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59
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Gorelenkova Miller O, Cole KS, Emerson CC, Allimuthu D, Golczak M, Stewart PL, Weerapana E, Adams DJ, Mieyal JJ. Novel chloroacetamido compound CWR-J02 is an anti-inflammatory glutaredoxin-1 inhibitor. PLoS One 2017; 12:e0187991. [PMID: 29155853 PMCID: PMC5695812 DOI: 10.1371/journal.pone.0187991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022] Open
Abstract
Glutaredoxin (Grx1) is a ubiquitously expressed thiol-disulfide oxidoreductase that specifically catalyzes reduction of S-glutathionylated substrates. Grx1 is known to be a key regulator of pro-inflammatory signaling, and Grx1 silencing inhibits inflammation in inflammatory disease models. Therefore, we anticipate that inhibition of Grx1 could be an anti-inflammatory therapeutic strategy. We used a rapid screening approach to test 504 novel electrophilic compounds for inhibition of Grx1, which has a highly reactive active-site cysteine residue (pKa 3.5). From this chemical library a chloroacetamido compound, CWR-J02, was identified as a potential lead compound to be characterized. CWR-J02 inhibited isolated Grx1 with an IC50 value of 32 μM in the presence of 1 mM glutathione. Mass spectrometric analysis documented preferential adduction of CWR-J02 to the active site Cys-22 of Grx1, and molecular dynamics simulation identified a potential non-covalent binding site. Treatment of the BV2 microglial cell line with CWR-J02 led to inhibition of intracellular Grx1 activity with an IC50 value (37 μM). CWR-J02 treatment decreased lipopolysaccharide-induced inflammatory gene transcription in the microglial cells in a parallel concentration-dependent manner, documenting the anti-inflammatory potential of CWR-J02. Exploiting the alkyne moiety of CWR-J02, we used click chemistry to link biotin azide to CWR-J02-adducted proteins, isolating them with streptavidin beads. Tandem mass spectrometric analysis identified many CWR-J02-reactive proteins, including Grx1 and several mediators of inflammatory activation. Taken together, these data identify CWR-J02 as an intracellularly effective Grx1 inhibitor that may elicit its anti-inflammatory action in a synergistic manner by also disabling other pro-inflammatory mediators. The CWR-J02 molecule provides a starting point for developing more selective Grx1 inhibitors and anti-inflammatory agents for therapeutic development.
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Affiliation(s)
- Olga Gorelenkova Miller
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Kyle S. Cole
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Corey C. Emerson
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Dharmaraja Allimuthu
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Marcin Golczak
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Phoebe L. Stewart
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Drew J. Adams
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - John J. Mieyal
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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60
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Bechtel TJ, Weerapana E. From structure to redox: The diverse functional roles of disulfides and implications in disease. Proteomics 2017; 17. [PMID: 28044432 DOI: 10.1002/pmic.201600391] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/02/2016] [Accepted: 12/28/2016] [Indexed: 12/16/2022]
Abstract
This review provides a comprehensive overview of the functional roles of disulfide bonds and their relevance to human disease. The critical roles of disulfide bonds in protein structure stabilization and redox regulation of protein activity are addressed. Disulfide bonds are essential to the structural stability of many proteins within the secretory pathway and can exist as intramolecular or inter-domain disulfides. The proper formation of these bonds often relies on folding chaperones and oxidases such as members of the protein disulfide isomerase (PDI) family. Many of the PDI family members catalyze disulfide-bond formation, reduction, and isomerization through redox-active disulfides and perturbed PDI activity is characteristic of carcinomas and neurodegenerative diseases. In addition to catalytic function in oxidoreductases, redox-active disulfides are also found on a diverse array of cellular proteins and act to regulate protein activity and localization in response to oxidative changes in the local environment. These redox-active disulfides are either dynamic intramolecular protein disulfides or mixed disulfides with small-molecule thiols generating glutathionylation and cysteinylation adducts. The oxidation and reduction of redox-active disulfides are mediated by cellular reactive oxygen species and activity of reductases, such as glutaredoxin and thioredoxin. Dysregulation of cellular redox conditions and resulting changes in mixed disulfide formation are directly linked to diseases such as cardiovascular disease and Parkinson's disease.
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Affiliation(s)
- Tyler J Bechtel
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
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61
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Abstract
Glutathione S-transferase Pi (GSTP1) mediates cellular defense against reactive electrophiles. Here, we report LAS17, a dichlorotriazine-containing compound that irreversibly inhibits GSTP1 and is selective for GSTP1 within cellular proteomes. Mass spectrometry and mutational studies identified Y108 as the site of modification, providing a unique mode of GSTP1 inhibition.
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Affiliation(s)
- L A Crawford
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - E Weerapana
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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62
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Casás-Selves M, Zhang AX, Dowling JE, Hallén S, Kawatkar A, Pace NJ, Denz CR, Pontz T, Garahdaghi F, Cao Q, Sabirsh A, Thakur K, O'Connell N, Hu J, Cornella-Taracido I, Weerapana E, Zinda M, Goodnow RA, Castaldi MP. Target Deconvolution Efforts on Wnt Pathway Screen Reveal Dual Modulation of Oxidative Phosphorylation and SERCA2. ChemMedChem 2017; 12:917-924. [PMID: 28371485 DOI: 10.1002/cmdc.201700028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/09/2017] [Indexed: 11/12/2022]
Abstract
Wnt signaling is critical for development, cell proliferation and differentiation, and mutations in this pathway resulting in constitutive signaling have been implicated in various cancers. A pathway screen using a Wnt-dependent reporter identified a chemical series based on a 1,2,3-thiadiazole-5-carboxamide (TDZ) core with sub-micromolar potency. Herein we report a comprehensive mechanism-of-action deconvolution study toward identifying the efficacy target(s) and biological implication of this chemical series involving bottom-up quantitative chemoproteomics, cell biology, and biochemical methods. Through observing the effects of our probes on metabolism and performing confirmatory cellular and biochemical assays, we found that this chemical series inhibits ATP synthesis by uncoupling the mitochondrial potential. Affinity chemoproteomics experiments identified sarco(endo)plasmic reticulum Ca2+ -dependent ATPase (SERCA2) as a binding partner of the TDZ series, and subsequent validation studies suggest that the TDZ series can act as ionophores through SERCA2 toward Wnt pathway inhibition.
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Affiliation(s)
- Matias Casás-Selves
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA.,Present address: Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Andrew X Zhang
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - James E Dowling
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Stefan Hallén
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Discovery Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Aarti Kawatkar
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Nicholas J Pace
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
| | - Christopher R Denz
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Timothy Pontz
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Farzin Garahdaghi
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA.,Present address: Synageva BioPharma Corp., 33 Hayden Avenue, Lexington, MA, 02421, USA
| | - Qing Cao
- Discovery Sciences-Computational Chemistry, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA.,Present address: Ra Pharmaceuticals, Inc., 87 Cambridge Park Drive, Cambridge, MA, 02140, USA
| | - Alan Sabirsh
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Discovery Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Kumar Thakur
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Nichole O'Connell
- Discovery Sciences-Structure and Biophysics, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA.,Present address: Nurix, Inc., 1700 Owens Street, Suite 290, San Francisco, CA, 94158, USA
| | - Jun Hu
- Discovery Sciences-Structure and Biophysics, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA.,Present address: Shire, 300 Shire Way, Lexington, MA, 02421, USA
| | - Iván Cornella-Taracido
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA.,Present address: Discovery Chemistry, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | | | - Michael Zinda
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Robert A Goodnow
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA.,Present address: Pharmaron, 303 Wyman Street, Room 322, Waltham, MA, 02451, USA
| | - M Paola Castaldi
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
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Casás-Selves M, Zhang AX, Dowling JE, Hallén S, Kawatkar A, Pace NJ, Denz CR, Pontz T, Garahdaghi F, Cao Q, Sabirsh A, Thakur K, O'Connell N, Hu J, Cornella-Taracido I, Weerapana E, Zinda M, Goodnow RA, Castaldi MP. Cover Picture: Target Deconvolution Efforts on Wnt Pathway Screen Reveal Dual Modulation of Oxidative Phosphorylation and SERCA2 (ChemMedChem 12/2017). ChemMedChem 2017. [DOI: 10.1002/cmdc.201700341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matias Casás-Selves
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
- Present address: Drug Discovery Program, Ontario Institute for Cancer Research; 661 University Avenue, Suite 510 Toronto ON M5G 0A3 Canada
| | - Andrew X. Zhang
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
| | - James E. Dowling
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
| | - Stefan Hallén
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Discovery Unit, AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Sweden
| | - Aarti Kawatkar
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
| | - Nicholas J. Pace
- Department of Chemistry; Boston College; Chestnut Hill MA 02467 USA
| | - Christopher R. Denz
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
| | - Timothy Pontz
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
| | - Farzin Garahdaghi
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
- Present address: Synageva BioPharma Corp.; 33 Hayden Avenue Lexington MA 02421 USA
| | - Qing Cao
- Discovery Sciences-Computational Chemistry, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
- Present address: Ra Pharmaceuticals, Inc.; 87 Cambridge Park Drive Cambridge MA 02140 USA
| | - Alan Sabirsh
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Discovery Unit, AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Sweden
| | - Kumar Thakur
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
| | - Nichole O'Connell
- Discovery Sciences-Structure and Biophysics, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
- Present address: Nurix, Inc.; 1700 Owens Street, Suite 290 San Francisco CA 94158 USA
| | - Jun Hu
- Discovery Sciences-Structure and Biophysics, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
- Present address: Shire; 300 Shire Way Lexington MA 02421 USA
| | - Iván Cornella-Taracido
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
- Present address: Discovery Chemistry, Merck Research Laboratories; 33 Avenue Louis Pasteur Boston MA 02115 USA
| | | | - Michael Zinda
- Oncology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
| | - Robert A. Goodnow
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
- Present address: Pharmaron; 303 Wyman Street, Room 322 Waltham MA 02451 USA
| | - M. Paola Castaldi
- Discovery Sciences-Chemical Biology, Innovative Medicines and Early Discovery Unit, AstraZeneca; 35 Gatehouse Drive Waltham MA 02451 USA
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64
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Sun B, Dwivedi N, Bechtel TJ, Paulsen JL, Muth A, Bawadekar M, Li G, Thompson PR, Shelef MA, Schiffer CA, Weerapana E, Ho IC. Citrullination of NF-κB p65 promotes its nuclear localization and TLR-induced expression of IL-1β and TNFα. Sci Immunol 2017; 2:2/12/eaal3062. [PMID: 28783661 DOI: 10.1126/sciimmunol.aal3062] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 03/12/2017] [Accepted: 05/09/2017] [Indexed: 12/16/2022]
Abstract
Many citrullinated proteins are known autoantigens in rheumatoid arthritis, a disease mediated by inflammatory cytokines, such as tumor necrosis factor-α (TNFα). Citrullinated proteins are generated by converting peptidylarginine to peptidylcitrulline, a process catalyzed by the peptidylarginine deiminases (PADs), including PAD1 to PAD4 and PAD6. Several major risk factors for rheumatoid arthritis are associated with heightened citrullination. However, the physiological role of citrullination in immune cells is poorly understood. We report that suppression of PAD activity attenuates Toll-like receptor-induced expression of interleukin-1β (IL-1β) and TNFα by neutrophils in vivo and in vitro but not their global transcription activity. Mechanistically, PAD4 directly citrullinates nuclear factor κB (NF-κB) p65 and enhances the interaction of p65 with importin α3, which brings p65 into the nucleus. The citrullination-enhanced interaction of p65 with importin α3 and its nuclear translocation and transcriptional activity can be attributed to citrullination of four arginine residues located in the Rel homology domain of p65. Furthermore, a rheumatoid arthritis-prone variant of PAD4, carrying three missense mutations, is more efficient in interacting with p65 and enhancing NF-κB activity. Together, these data not only demonstrate a critical role of citrullination in an NF-κB-dependent expression of IL-1β and TNFα but also provide a molecular mechanism by which heightened citrullination propagates inflammation in rheumatoid arthritis. Accordingly, attenuating p65-mediated production of IL-1β and TNFα by blocking the citrullination of p65 has great therapeutic potential in rheumatoid arthritis.
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Affiliation(s)
- Bo Sun
- Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Nishant Dwivedi
- Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Tyler J Bechtel
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Janet L Paulsen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Aaron Muth
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mandar Bawadekar
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gang Li
- Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Miriam A Shelef
- Department of Medicine, University of Wisconsin-Madison and William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - I-Cheng Ho
- Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA. .,Harvard Medical School, Boston, MA 02115, USA
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65
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Quinti L, Dayalan Naidu S, Träger U, Chen X, Kegel-Gleason K, Llères D, Connolly C, Chopra V, Low C, Moniot S, Sapp E, Tousley AR, Vodicka P, Van Kanegan MJ, Kaltenbach LS, Crawford LA, Fuszard M, Higgins M, Miller JRC, Farmer RE, Potluri V, Samajdar S, Meisel L, Zhang N, Snyder A, Stein R, Hersch SM, Ellerby LM, Weerapana E, Schwarzschild MA, Steegborn C, Leavitt BR, Degterev A, Tabrizi SJ, Lo DC, DiFiglia M, Thompson LM, Dinkova-Kostova AT, Kazantsev AG. KEAP1-modifying small molecule reveals muted NRF2 signaling responses in neural stem cells from Huntington's disease patients. Proc Natl Acad Sci U S A 2017; 114:E4676-E4685. [PMID: 28533375 PMCID: PMC5468652 DOI: 10.1073/pnas.1614943114] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The activity of the transcription factor nuclear factor-erythroid 2 p45-derived factor 2 (NRF2) is orchestrated and amplified through enhanced transcription of antioxidant and antiinflammatory target genes. The present study has characterized a triazole-containing inducer of NRF2 and elucidated the mechanism by which this molecule activates NRF2 signaling. In a highly selective manner, the compound covalently modifies a critical stress-sensor cysteine (C151) of the E3 ligase substrate adaptor protein Kelch-like ECH-associated protein 1 (KEAP1), the primary negative regulator of NRF2. We further used this inducer to probe the functional consequences of selective activation of NRF2 signaling in Huntington's disease (HD) mouse and human model systems. Surprisingly, we discovered a muted NRF2 activation response in human HD neural stem cells, which was restored by genetic correction of the disease-causing mutation. In contrast, selective activation of NRF2 signaling potently repressed the release of the proinflammatory cytokine IL-6 in primary mouse HD and WT microglia and astrocytes. Moreover, in primary monocytes from HD patients and healthy subjects, NRF2 induction repressed expression of the proinflammatory cytokines IL-1, IL-6, IL-8, and TNFα. Together, our results demonstrate a multifaceted protective potential of NRF2 signaling in key cell types relevant to HD pathology.
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Affiliation(s)
- Luisa Quinti
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | - Sharadha Dayalan Naidu
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - Ulrike Träger
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
| | - Xiqun Chen
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | - Kimberly Kegel-Gleason
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | - David Llères
- Institute of Molecular Genetics of Montpellier, F-34293 Montpellier, France
| | - Colúm Connolly
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Vanita Chopra
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | - Cho Low
- Department of Developmental, Molecular and Chemical Biology, Tufts University, Boston, MA 02111
| | - Sébastien Moniot
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | - Adelaide R Tousley
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | - Petr Vodicka
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | - Michael J Van Kanegan
- Center for Drug Discovery, Duke University Medical Center, Durham, NC 27710
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710
| | - Linda S Kaltenbach
- Center for Drug Discovery, Duke University Medical Center, Durham, NC 27710
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710
| | - Lisa A Crawford
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467
| | - Matthew Fuszard
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Maureen Higgins
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - James R C Miller
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
| | - Ruth E Farmer
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Vijay Potluri
- Department of Medicinal Chemistry, Aurigene Discovery Technologies Limited, Bangalore 560 100, India
| | - Susanta Samajdar
- Department of Medicinal Chemistry, Aurigene Discovery Technologies Limited, Bangalore 560 100, India
| | - Lisa Meisel
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Ningzhe Zhang
- Buck Institute for Research on Aging, Novato, CA 94945
| | - Andrew Snyder
- Targanox, Cambridge Research Laboratories, Cambridge, MA 02139
| | - Ross Stein
- Targanox, Cambridge Research Laboratories, Cambridge, MA 02139
| | - Steven M Hersch
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | | | | | - Michael A Schwarzschild
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Alexei Degterev
- Department of Developmental, Molecular and Chemical Biology, Tufts University, Boston, MA 02111
| | - Sarah J Tabrizi
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
| | - Donald C Lo
- Center for Drug Discovery, Duke University Medical Center, Durham, NC 27710
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114
| | - Leslie M Thompson
- Department of Biological Chemistry, University of California, Irvine, CA 92697
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Albena T Dinkova-Kostova
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Aleksey G Kazantsev
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114;
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66
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Abstract
The mitochondria are dynamic organelles that regulate oxidative metabolism and mediate cellular redox homeostasis. Proteins within the mitochondria are exposed to large fluxes in the surrounding redox environment. In particular, cysteine residues within mitochondrial proteins sense and respond to these redox changes through oxidative modifications of the cysteine thiol group. These oxidative modifications result in a loss in cysteine reactivity, which can be monitored using cysteine-reactive chemical probes and quantitative mass spectrometry (MS). Analysis of cell lysates treated with cysteine-reactive probes enable the identification of hundreds of cysteine residues, however, the mitochondrial proteome is poorly represented (<10% of identified peptides), due to the low abundance of mitochondrial proteins and suppression of mitochondrial peptide MS signals by highly abundant cytosolic peptides. Here, we apply a mitochondrial isolation and purification protocol to substantially increase coverage of the mitochondrial cysteine proteome. Over 1500 cysteine residues from ∼450 mitochondrial proteins were identified, thereby enabling interrogation of an unprecedented number of mitochondrial cysteines. Specifically, these mitochondrial cysteines were ranked by reactivity to identify hyper-reactive cysteines with potential catalytic and regulatory functional roles. Furthermore, analyses of mitochondria exposed to nitrosative stress revealed previously uncharacterized sites of protein S-nitrosation on mitochondrial proteins. Together, the mitochondrial cysteine enrichment strategy presented herein enables detailed characterization of protein modifications that occur within the mitochondria during (patho)physiological fluxes in the redox environment.
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Affiliation(s)
- Daniel W. Bak
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Mattia D. Pizzagalli
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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67
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Lawson AP, Bak DW, Shannon DA, Long MJC, Vijaykumar T, Yu R, Oualid FE, Weerapana E, Hedstrom L. Identification of deubiquitinase targets of isothiocyanates using SILAC-assisted quantitative mass spectrometry. Oncotarget 2017; 8:51296-51316. [PMID: 28881649 PMCID: PMC5584250 DOI: 10.18632/oncotarget.17261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 03/22/2017] [Indexed: 01/14/2023] Open
Abstract
Cruciferous vegetables such as broccoli and kale have well documented chemopreventative and anticancer effects that are attributed to the presence of isothiocyanates (ITCs). ITCs modulate the levels of many oncogenic proteins, but the molecular mechanisms of ITC action are not understood. We previously reported that phenethyl isothiocyanate (PEITC) inhibits two deubiquitinases (DUBs), USP9x and UCH37. DUBs regulate many cellular processes and DUB dysregulation is linked to the pathogenesis of human diseases including cancer, neurodegeneration, and inflammation. Using SILAC assisted quantitative mass spectrometry, here we identify 9 new PEITC-DUB targets: USP1, USP3, USP10, USP11, USP16, USP22, USP40, USP48 and VCPIP1. Seven of these PEITC-sensitive DUBs have well-recognized roles in DNA repair or chromatin remodeling. PEITC both inhibits USP1 and increases its ubiquitination and degradation, thus decreasing USP1 activity by two mechanisms. The loss of USP1 activity increases the level of mono-ubiquitinated DNA clamp PCNA, impairing DNA repair. Both the inhibition/degradation of USP1 and the increase in mono-ubiquitinated PCNA are new activities for PEITC that can explain the previously recognized ability of ITCs to enhance cancer cell sensitivity to cisplatin treatment. Our work also demonstrates that PEITC reduces the mono-ubiquityl histones H2A and H2B. Understanding the mechanism of action of ITCs should facilitate their use as therapeutic agents.
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Affiliation(s)
- Ann P Lawson
- Department of Biology, Brandeis University, Waltham, MA 02453-9110, USA
| | - Daniel W Bak
- Department of Chemistry, Merkert Center, Boston College, Chestnut Hill, MA 02467-3860, USA
| | - D Alexander Shannon
- Department of Chemistry, Merkert Center, Boston College, Chestnut Hill, MA 02467-3860, USA
| | - Marcus J C Long
- Graduate Program in Biochemistry and Biophysics, Brandeis University, Waltham, MA 02453-9110, USA.,Current address: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Tushara Vijaykumar
- Graduate Program in Molecular and Cellular Biology, Brandeis University, Waltham, MA 02453-9110, USA.,Current address: Sanofi Genzyme, Framingham, MA 01701, USA
| | - Runhan Yu
- Department of Chemistry, Brandeis University, Waltham, MA 02453-9110, USA
| | | | - Eranthie Weerapana
- Department of Chemistry, Merkert Center, Boston College, Chestnut Hill, MA 02467-3860, USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, Waltham, MA 02453-9110, USA.,Department of Chemistry, Brandeis University, Waltham, MA 02453-9110, USA
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68
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Weerapana E. Taking AKTion on HNEs. Nat Chem Biol 2017; 13:244-245. [DOI: 10.1038/nchembio.2311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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69
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Abstract
Cysteine residues on proteins serve diverse functional roles in catalysis and regulation and are susceptible to numerous posttranslational modifications. Methods to monitor the reactivity of cysteines within the context of a complex proteome have facilitated the identification and functional characterization of cysteine residues on disparate proteins. Here, we describe the use of a cysteine-reactive iodoacetamide probe coupled to isotopically labeled, cleavable linkers to identify and quantify cysteine-reactivity changes from two biological samples.
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Affiliation(s)
- Yu Qian
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA.
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70
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Abo M, Bak DW, Weerapana E. Optimization of Caged Electrophiles for Improved Monitoring of Cysteine Reactivity in Living Cells. Chembiochem 2016; 18:81-84. [PMID: 27813293 DOI: 10.1002/cbic.201600524] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 11/07/2022]
Abstract
Cysteine residues play critical roles in protein function and are susceptible to numerous post-translational modifications (PTMs) that serve to modulate the activity and localization of diverse proteins. Many of these PTMs are highly transient and labile, thus necessitating methods to study these modifications directly within the context of living cells. We previously reported a caged electrophilic probe, CBK1, that can be activated by UV for temporally controlled covalent modification of cysteine residues in living cells. To improve upon the number of cysteine residues identified in cellular cysteine-profiling studies, the reactivity and uncaging efficiency of a panel of caged electrophiles were explored. We identified an optimized caged electrophilic probe, CIK4, that affords significantly improved coverage of cellular cysteine residues. The broader proteome coverage afforded by CIK4 renders it a useful tool for the biological investigation of cysteine-reactivity changes and PTMs directly within living cells and highlights design elements that are critical to optimizing photoactivatable chemical probes for cellular labeling.
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Affiliation(s)
- Masahiro Abo
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
| | - Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
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71
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Martell J, Seo Y, Bak DW, Kingsley SF, Tissenbaum HA, Weerapana E. Global Cysteine-Reactivity Profiling during Impaired Insulin/IGF-1 Signaling in C. elegans Identifies Uncharacterized Mediators of Longevity. Cell Chem Biol 2016; 23:955-66. [PMID: 27499530 DOI: 10.1016/j.chembiol.2016.06.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 12/11/2022]
Abstract
In the nematode Caenorhabditis elegans, inactivating mutations in the insulin/IGF-1 receptor, DAF-2, result in a 2-fold increase in lifespan mediated by DAF-16, a FOXO-family transcription factor. Downstream protein activities that directly regulate longevity during impaired insulin/IGF-1 signaling (IIS) are poorly characterized. Here, we use global cysteine-reactivity profiling to identify protein activity changes during impaired IIS. Upon confirming that cysteine reactivity is a good predictor of functionality in C. elegans, we profiled cysteine-reactivity changes between daf-2 and daf-16;daf-2 mutants, and identified 40 proteins that display a >2-fold change. Subsequent RNAi-mediated knockdown studies revealed that lbp-3 and K02D7.1 knockdown caused significant increases in lifespan and dauer formation. The proteins encoded by these two genes, LBP-3 and K02D7.1, are implicated in intracellular fatty acid transport and purine metabolism, respectively. These studies demonstrate that cysteine-reactivity profiling can be complementary to abundance-based transcriptomic and proteomic studies, serving to identify uncharacterized mediators of C. elegans longevity.
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Affiliation(s)
- Julianne Martell
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Yonghak Seo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Samuel F Kingsley
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Heidi A Tissenbaum
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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72
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Samarasinghe KTG, Munkanatta Godage DNP, Zhou Y, Ndombera FT, Weerapana E, Ahn YH. A clickable glutathione approach for identification of protein glutathionylation in response to glucose metabolism. Mol Biosyst 2016; 12:2471-80. [PMID: 27216279 PMCID: PMC4955733 DOI: 10.1039/c6mb00175k] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Glucose metabolism and mitochondrial function are closely interconnected with cellular redox-homeostasis. Although glucose starvation, which mimics ischemic conditions or insufficient vascularization, is known to perturb redox-homeostasis, global and individual protein glutathionylation in response to glucose metabolism or mitochondrial activity remains largely unknown. In this report, we use our clickable glutathione approach, which forms clickable glutathione (azido-glutathione) by using a mutant of glutathione synthetase (GS M4), for detection and identification of protein glutathionylation in response to glucose starvation. We found that protein glutathionylation is readily induced in HEK293 cells in response to low glucose concentrations when mitochondrial reactive oxygen species (ROS) are elevated in cells, and glucose is the major determinant for inducing reversible glutathionylation. Proteomic and biochemical analysis identified over 1300 proteins, including SMYD2, PP2Cα, and catalase. We further showed that PP2Cα is glutathionylated at C314 in a C-terminal domain, and PP2Cα C314 glutathionylation disrupts the interaction with mGluR3, an important glutamate receptor associated with synaptic plasticity.
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Affiliation(s)
| | | | - Yani Zhou
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Fidelis T Ndombera
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Eranthie Weerapana
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Young-Hoon Ahn
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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73
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Zhou Y, Wynia-Smith SL, Couvertier SM, Kalous KS, Marletta MA, Smith BC, Weerapana E. Chemoproteomic Strategy to Quantitatively Monitor Transnitrosation Uncovers Functionally Relevant S-Nitrosation Sites on Cathepsin D and HADH2. Cell Chem Biol 2016; 23:727-37. [PMID: 27291402 DOI: 10.1016/j.chembiol.2016.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/22/2016] [Accepted: 05/05/2016] [Indexed: 10/25/2022]
Abstract
S-Nitrosoglutathione (GSNO) is an endogenous transnitrosation donor involved in S-nitrosation of a variety of cellular proteins, thereby regulating diverse protein functions. Quantitative proteomic methods are necessary to establish which cysteine residues are most sensitive to GSNO-mediated transnitrosation. Here, a competitive cysteine-reactivity profiling strategy was implemented to quantitatively measure the sensitivity of >600 cysteine residues to transnitrosation by GSNO. This platform identified a subset of cysteine residues with a high propensity for GSNO-mediated transnitrosation. Functional characterization of previously unannotated S-nitrosation sites revealed that S-nitrosation of a cysteine residue distal to the 3-hydroxyacyl-CoA dehydrogenase type 2 (HADH2) active site impaired catalytic activity. Similarly, S-nitrosation of a non-catalytic cysteine residue in the lysosomal aspartyl protease cathepsin D (CTSD) inhibited proteolytic activation. Together, these studies revealed two previously uncharacterized cysteine residues that regulate protein function, and established a chemical-proteomic platform with capabilities to determine substrate specificity of other cellular transnitrosation agents.
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Affiliation(s)
- Yani Zhou
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Sarah L Wynia-Smith
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Kelsey S Kalous
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael A Marletta
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Brian C Smith
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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74
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Hatzios SK, Abel S, Martell J, Hubbard T, Sasabe J, Munera D, Clark L, Bachovchin DA, Qadri F, Ryan ET, Davis BM, Weerapana E, Waldor MK. Erratum: Chemoproteomic profiling of host and pathogen enzymes active in cholera. Nat Chem Biol 2016; 12:466. [DOI: 10.1038/nchembio0616-466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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75
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Jones LH, Weerapana E. Protein labelling. Mol Biosyst 2016; 12:1725-7. [PMID: 27215194 DOI: 10.1039/c6mb90019d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Professor Eranthie Weerapana and Professor Lyn Jones introduce this Protein Labelling themed issue.
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Affiliation(s)
- Lyn H Jones
- Worldwide Medicinal Chemistry, Pfizer, 610 Main Street, Cambridge, MA, USA.
| | - Eranthie Weerapana
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA.
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76
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Louie SM, Grossman EA, Crawford LA, Ding L, Camarda R, Huffman TR, Miyamoto DK, Goga A, Weerapana E, Nomura DK. GSTP1 Is a Driver of Triple-Negative Breast Cancer Cell Metabolism and Pathogenicity. Cell Chem Biol 2016; 23:567-578. [PMID: 27185638 DOI: 10.1016/j.chembiol.2016.03.017] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/18/2016] [Accepted: 03/20/2016] [Indexed: 01/08/2023]
Abstract
Breast cancers possess fundamentally altered metabolism that fuels their pathogenicity. While many metabolic drivers of breast cancers have been identified, the metabolic pathways that mediate breast cancer malignancy and poor prognosis are less well understood. Here, we used a reactivity-based chemoproteomic platform to profile metabolic enzymes that are enriched in breast cancer cell types linked to poor prognosis, including triple-negative breast cancer (TNBC) cells and breast cancer cells that have undergone an epithelial-mesenchymal transition-like state of heightened malignancy. We identified glutathione S-transferase Pi 1 (GSTP1) as a novel TNBC target that controls cancer pathogenicity by regulating glycolytic and lipid metabolism, energetics, and oncogenic signaling pathways through a protein interaction that activates glyceraldehyde-3-phosphate dehydrogenase activity. We show that genetic or pharmacological inactivation of GSTP1 impairs cell survival and tumorigenesis in TNBC cells. We put forth GSTP1 inhibitors as a novel therapeutic strategy for combatting TNBCs through impairing key cancer metabolism and signaling pathways.
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Affiliation(s)
- Sharon M Louie
- Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth A Grossman
- Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lisa A Crawford
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Lucky Ding
- Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roman Camarda
- Department of Cell and Tissue Biology and Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tucker R Huffman
- Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David K Miyamoto
- Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrei Goga
- Department of Cell and Tissue Biology and Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Daniel K Nomura
- Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA.
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77
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Sanman LE, Qian Y, Eisele NA, Ng TM, van der Linden WA, Monack DM, Weerapana E, Bogyo M. Disruption of glycolytic flux is a signal for inflammasome signaling and pyroptotic cell death. eLife 2016; 5:e13663. [PMID: 27011353 PMCID: PMC4846378 DOI: 10.7554/elife.13663] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/23/2016] [Indexed: 12/20/2022] Open
Abstract
When innate immune cells such as macrophages are challenged with environmental stresses or infection by pathogens, they trigger the rapid assembly of multi-protein complexes called inflammasomes that are responsible for initiating pro-inflammatory responses and a form of cell death termed pyroptosis. We describe here the identification of an intracellular trigger of NLRP3-mediated inflammatory signaling, IL-1β production and pyroptosis in primed murine bone marrow-derived macrophages that is mediated by the disruption of glycolytic flux. This signal results from a drop of NADH levels and induction of mitochondrial ROS production and can be rescued by addition of products that restore NADH production. This signal is also important for host-cell response to the intracellular pathogen Salmonella typhimurium, which can disrupt metabolism by uptake of host-cell glucose. These results reveal an important inflammatory signaling network used by immune cells to sense metabolic dysfunction or infection by intracellular pathogens. DOI:http://dx.doi.org/10.7554/eLife.13663.001 Cells of the innate immune system, such as macrophages, are the body’s first line of defense against infection. Macrophages can sense a wide variety of danger signals associated with the presence of infectious microbes, and some of these signals cause macrophages to form protein complexes called inflammasomes inside the cell. Inflammasomes produce molecules that stimulate inflammation and trigger the death of the macrophage. This attracts other immune cells to the infection site to help combat the source of danger. Inflammasome complexes form around an activated receptor molecule called NLRP3. NLRP3 is activated by a range of danger signals, including those produced by Salmonella bacteria. However, the sequence of events that leads to NLRP3 activation is still not well understood. Sanman et al. have now identified a small molecule that unexpectedly causes the formation of inflammasomes via NLRP3 and so triggers the death of macrophages. Further investigation revealed that this molecule disrupts glycolysis, a process macrophages use to produce energy. The energy imbalance caused by disrupting glycolysis triggers a stress response in macrophages, which ultimately activates the NLRP3 receptor and hence the inflammasome. Sanman et al. then found that Salmonella bacteria also activate the inflammasome by disrupting glycolysis when they invade macrophages. This occurs because the bacteria use up the macrophage’s supply of glycolysis precursor molecules. Replenishing the macrophage with products of glycolysis restored partial energy production and prevented the inflammasome from being activated. Overall, Sanman et al. have identified a previously unknown trigger of inflammation and cell death in macrophages whereby cells can respond to infectious bacteria by sensing a change in energy levels. A next step will be to define the signaling molecules that activate NLRP3 to trigger the construction of the inflammasome. Sanman et al. also hope to uncover other infections and diseases where changes in energy balance might trigger inflammation and cell death. DOI:http://dx.doi.org/10.7554/eLife.13663.002
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Affiliation(s)
- Laura E Sanman
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Yu Qian
- Department of Chemistry, Boston College, Chestnut Hill, United States
| | - Nicholas A Eisele
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Tessie M Ng
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | | | - Denise M Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | | | - Matthew Bogyo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States.,Department of Pathology, Stanford University School of Medicine, Stanford, United States
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78
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Saghatelian A, Nomura DK, Weerapana E. Editorial overview: Omics: The maturation of chemical biology. Curr Opin Chem Biol 2016; 30:v-vi. [DOI: 10.1016/j.cbpa.2015.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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79
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Lewallen DM, Bicker KL, Subramanian V, Clancy KW, Slade DJ, Martell J, Dreyton CJ, Sokolove J, Weerapana E, Thompson PR. Chemical Proteomic Platform To Identify Citrullinated Proteins. ACS Chem Biol 2015; 10:2520-8. [PMID: 26360112 PMCID: PMC4729336 DOI: 10.1021/acschembio.5b00438] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Anti-citrullinated protein antibodies (ACPAs) are a hallmark of rheumatoid arthritis (RA) and are routinely used for disease diagnosis. Protein citrullination is also increased in cancer and other autoimmune disorders, suggesting that citrullinated proteins may serve as biomarkers for diseases beyond RA. To identify these citrullinated proteins, we developed biotin-conjugated phenylglyoxal (biotin-PG). Using this probe and our platform technology, we identified >50 intracellular citrullinated proteins. More than 20 of these are involved in RNA splicing, suggesting, for the first time, that citrullination modulates RNA biology. Overall, this chemical proteomic platform will play a key role in furthering our understanding of protein citrullination in rheumatoid arthritis and potentially a wider spectrum of inflammatory diseases.
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Affiliation(s)
| | | | - Venkataraman Subramanian
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Kathleen W. Clancy
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | | | - Julianne Martell
- Department
of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Christina J. Dreyton
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jeremy Sokolove
- Division
of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Eranthie Weerapana
- Department
of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul R. Thompson
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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80
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Lawson AP, Long MJC, Coffey RT, Qian Y, Weerapana E, El Oualid F, Hedstrom L. Naturally Occurring Isothiocyanates Exert Anticancer Effects by Inhibiting Deubiquitinating Enzymes. Cancer Res 2015; 75:5130-5142. [PMID: 26542215 DOI: 10.1158/0008-5472.can-15-1544] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/31/2015] [Indexed: 01/09/2023]
Abstract
The anticancer properties of cruciferous vegetables are well known and attributed to an abundance of isothiocyanates such as benzyl isothiocyanate (BITC) and phenethyl isothiocyanate (PEITC). While many potential targets of isothiocyanates have been proposed, a full understanding of the mechanisms underlying their anticancer activity has remained elusive. Here we report that BITC and PEITC effectively inhibit deubiquitinating enzymes (DUB), including the enzymes USP9x and UCH37, which are associated with tumorigenesis, at physiologically relevant concentrations and time scales. USP9x protects the antiapoptotic protein Mcl-1 from degradation, and cells dependent on Mcl-1 were especially sensitive to BITC and PEITC. These isothiocyanates increased Mcl-1 ubiquitination and either isothiocyanate treatment, or RNAi-mediated silencing of USP9x decreased Mcl-1 levels, consistent with the notion that USP9x is a primary target of isothiocyanate activity. These isothiocyanates also increased ubiquitination of the oncogenic fusion protein Bcr-Abl, resulting in degradation under low isothiocyanate concentrations and aggregation under high isothiocyanate concentrations. USP9x inhibition paralleled the decrease in Bcr-Abl levels induced by isothiocyanate treatment, and USP9x silencing was sufficient to decrease Bcr-Abl levels, further suggesting that Bcr-Abl is a USP9x substrate. Overall, our findings suggest that USP9x targeting is critical to the mechanism underpinning the well-established anticancer activity of isothiocyanate. We propose that the isothiocyanate-induced inhibition of DUBs may also explain how isothiocyanates affect inflammatory and DNA repair processes, thus offering a unifying theme in understanding the function and useful application of isothiocyanates to treat cancer as well as a variety of other pathologic conditions.
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Affiliation(s)
- Ann P Lawson
- Department of Biology, Brandeis University, MS009, 415 South Street, Waltham, MA 02453-9110 USA
| | - Marcus J C Long
- Graduate Program in Biochemistry and Biophysics, Brandeis University, MS009, 415 South Street, Waltham, MA 02453-9110 USA
| | - Rory T Coffey
- Department of Biology, Brandeis University, MS009, 415 South Street, Waltham, MA 02453-9110 USA.,Graduate Program in Molecular and Cellular Biology, Brandeis University, MS008, 415 South St., Waltham MA 02453-9110
| | - Yu Qian
- Department of Chemistry, Merkert Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467-3860 USA
| | - Eranthie Weerapana
- Department of Chemistry, Merkert Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467-3860 USA
| | | | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, MS009, 415 South Street, Waltham, MA 02453-9110 USA.,Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453-9110 USA
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81
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Affiliation(s)
- Masahiro Abo
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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82
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Cole K, Banerjee R, Pace N, Weerapana E. Synthesis and Characterization of Triazine‐based Chemical Probes. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.721.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyle Cole
- ChemistryBoston CollegeChestnut HillMAUnited States
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83
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Lawson A, Long M, Qian Y, Coffey R, Weerapana E, El Oualid F, Hedstrom L. Another Reason to Eat Your Broccoli: Naturally Occurring Isothiocyanates Inhibit Deubiquitinating Enzymes. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.897.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ann Lawson
- Department of BiologyBrandeis UniversityWalthamMassachusettsUnited States
| | - Marcus Long
- Graduate Program in Biochemistry and Biophysics Brandeis UniversityWalthamMassachusettsUnited States
| | - Yu Qian
- Department of ChemistryMerket CenterBoston CollegeChestnut HillMassachusettsUnited States
| | - Rory Coffey
- Department of BiologyBrandeis UniversityWalthamMassachusettsUnited States
| | - Eranthie Weerapana
- Department of ChemistryMerket CenterBoston CollegeChestnut HillMassachusettsUnited States
| | | | - Lizbeth Hedstrom
- Department of BiologyBrandeis UniversityWalthamMassachusettsUnited States
- Department of ChemistryBrandeis UniversityWalthamMassachusettsUnited States
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84
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Weerapana E. A Chemical‐Proteomic Platform to Investigate Cysteine S‐Nitrosation. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.370.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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85
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Abo M, Weerapana E. Development of A Caged Cysteine‐Reactive Probe for Characterizing Physiological Reactivity of Cysteine. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.723.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Masahiro Abo
- Department of ChemistryBoston CollegeChestnut HillMAUnited States
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86
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Couvertier S, Weerapana E. Investigating cysteine‐mediated protein activities in complex proteomes. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.567.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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87
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Shannon DA, Weerapana E. Covalent protein modification: the current landscape of residue-specific electrophiles. Curr Opin Chem Biol 2015; 24:18-26. [DOI: 10.1016/j.cbpa.2014.10.021] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 10/24/2014] [Accepted: 10/27/2014] [Indexed: 12/11/2022]
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88
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Abstract
This review represents a novel look at the many sources, cysteine targets, and signaling processes of ROS in the mitochondria.
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Affiliation(s)
- D. W. Bak
- Department of Chemistry
- Merkert Chemistry Center
- Boston College
- Massachusetts 02467
- USA
| | - E. Weerapana
- Department of Chemistry
- Merkert Chemistry Center
- Boston College
- Massachusetts 02467
- USA
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89
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Wei Y, Stec B, Redfield AG, Weerapana E, Roberts MF. Phospholipid-binding sites of phosphatase and tensin homolog (PTEN): exploring the mechanism of phosphatidylinositol 4,5-bisphosphate activation. J Biol Chem 2014; 290:1592-606. [PMID: 25429968 DOI: 10.1074/jbc.m114.588590] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The lipid phosphatase activity of the tumor suppressor phosphatase and tensin homolog (PTEN) is enhanced by the presence of its biological product, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This enhancement is suggested to occur via the product binding to the N-terminal region of the protein. PTEN effects on short-chain phosphoinositide (31)P linewidths and on the full field dependence of the spin-lattice relaxation rate (measured by high resolution field cycling (31)P NMR using spin-labeled protein) are combined with enzyme kinetics with the same short-chain phospholipids to characterize where PI(4,5)P2 binds on the protein. The results are used to model a discrete site for a PI(4,5)P2 molecule close to, but distinct from, the active site of PTEN. This PI(4,5)P2 site uses Arg-47 and Lys-13 as phosphate ligands, explaining why PTEN R47G and K13E can no longer be activated by that phosphoinositide. Placing a PI(4,5)P2 near the substrate site allows for proper orientation of the enzyme on interfaces and should facilitate processive catalysis.
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Affiliation(s)
- Yang Wei
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
| | - Boguslaw Stec
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
| | - Alfred G Redfield
- the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
| | - Eranthie Weerapana
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
| | - Mary F Roberts
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
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90
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Couvertier SM, Zhou Y, Weerapana E. Chemical-proteomic strategies to investigate cysteine posttranslational modifications. Biochim Biophys Acta 2014; 1844:2315-30. [PMID: 25291386 DOI: 10.1016/j.bbapap.2014.09.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 01/10/2023]
Abstract
The unique combination of nucleophilicity and redox-sensitivity that is characteristic of cysteine residues results in a variety of posttranslational modifications (PTMs), including oxidation, nitrosation, glutathionylation, prenylation, palmitoylation and Michael adducts with lipid-derived electrophiles (LDEs). These PTMs regulate the activity of diverse protein families by modulating the reactivity of cysteine nucleophiles within active sites of enzymes, and governing protein localization between soluble and membrane-bound forms. Many of these modifications are highly labile, sensitive to small changes in the environment, and dynamic, rendering it difficult to detect these modified species within a complex proteome. Several chemical-proteomic platforms have evolved to study these modifications and enable a better understanding of the diversity of proteins that are regulated by cysteine PTMs. These platforms include: (1) chemical probes to selectively tag PTM-modified cysteines; (2) differential labeling platforms that selectively reveal and tag PTM-modified cysteines; (3) lipid, isoprene and LDE derivatives containing bioorthogonal handles; and (4) cysteine-reactivity profiling to identify PTM-induced decreases in cysteine nucleophilicity. Here, we will provide an overview of these existing chemical-proteomic strategies and their effectiveness at identifying PTM-modified cysteine residues within native biological systems.
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Affiliation(s)
| | - Yani Zhou
- Boston College, Chestnut Hill, MA 02467, USA
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91
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Zhuang J, Kuo CH, Chou LY, Liu DY, Weerapana E, Tsung CK. Optimized metal-organic-framework nanospheres for drug delivery: evaluation of small-molecule encapsulation. ACS Nano 2014; 8:2812-9. [PMID: 24506773 DOI: 10.1021/nn406590q] [Citation(s) in RCA: 521] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We have developed a general synthetic route to encapsulate small molecules in monodisperse zeolitic imid-azolate framework-8 (ZIF-8) nanospheres for drug delivery. Electron microscopy, powder X-ray diffraction, and elemental analysis show that the small-molecule-encapsulated ZIF-8 nanospheres are uniform 70 nm particles with single-crystalline structure. Several small molecules, including fluorescein and the anticancer drug camptothecin, were encapsulated inside of the ZIF-8 framework. Evaluation of fluorescein-encapsulated ZIF-8 nanospheres in the MCF-7 breast cancer cell line demonstrated cell internalization and minimal cytotoxicity. The 70 nm particle size facilitates cellular uptake, and the pH-responsive dissociation of the ZIF-8 framework likely results in endosomal release of the small-molecule cargo, thereby rendering the ZIF-8 scaffold an ideal drug delivery vehicle. To confirm this, we demonstrate that camptothecin encapsulated ZIF-8 particles show enhanced cell death, indicative of internalization and intracellular release of the drug. To demonstrate the versatility of this ZIF-8 system, iron oxide nanoparticles were also encapsulated into the ZIF-8 nanospheres, thereby endowing magnetic features to these nanospheres.
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Affiliation(s)
- Jia Zhuang
- Department of Chemistry, Merkert Chemistry Center, Boston College , Chestnut Hill, Massachusetts 02467, United States
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92
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Shannon DA, Banerjee R, Webster ER, Bak DW, Wang C, Weerapana E. Investigating the proteome reactivity and selectivity of aryl halides. J Am Chem Soc 2014; 136:3330-3. [PMID: 24548313 DOI: 10.1021/ja4116204] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein-reactive electrophiles are critical to chemical proteomic applications including activity-based protein profiling, site-selective protein modification, and covalent inhibitor development. Here, we explore the protein reactivity of a panel of aryl halides that function through a nucleophilic aromatic substitution (S(N)Ar) mechanism. We show that the reactivity of these electrophiles can be finely tuned by varying the substituents on the aryl ring. We identify p-chloro- and fluoronitrobenzenes and dichlorotriazines as covalent protein modifiers at low micromolar concentrations. Interestingly, investigating the site of labeling of these electrophiles within complex proteomes identified p-chloronitrobenzene as highly cysteine selective, whereas the dichlorotriazine favored reactivity with lysines. These studies illustrate the diverse reactivity and amino-acid selectivity of aryl halides and enable the future application of this class of electrophiles in chemical proteomics.
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Affiliation(s)
- D Alexander Shannon
- Department of Chemistry, Merkert Chemistry Center , Boston College, Chestnut Hill, Massachusetts 02467, United States
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93
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Martell J, Weerapana E. Applications of copper-catalyzed click chemistry in activity-based protein profiling. Molecules 2014; 19:1378-93. [PMID: 24473203 PMCID: PMC6270908 DOI: 10.3390/molecules19021378] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/09/2014] [Accepted: 01/17/2014] [Indexed: 12/24/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a chemical proteomic technique that enables the interrogation of protein activity directly within complex proteomes. Given the dominant role of posttranslational modifications in regulating protein function in vivo, ABPP provides a direct readout of activity that is not attained through traditional proteomic methods. ABPP relies on the design of covalent binding probes that either target a specific enzyme or a class of enzymes with related function. These covalent warheads are coupled to either fluorophores or biotin groups for visualization and enrichment of these active proteins. The advent of bioorthogonal chemistries, in particular, the copper (I)-catalyzed azide-alkyne cycloaddition (CuAAC), has benefitted the field of ABPP by achieving the following: (1) replacing bulky reporter groups with smaller alkyne or azide groups to promote cell permeability; (2) adding modularity to the system such that a single probe can be diversified with a variety of reporter groups without the need to develop new synthetic routes; and (3) enabling the conjugation of complex linkers to facilitate quantitative proteomic analyses. Here, we summarize recent examples of CuAAC in ABPP that serve to illustrate the contribution of bioorthogonal chemistry to advancing discoveries in this field.
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Affiliation(s)
- Julianne Martell
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.
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94
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Abstract
Zinc ions (Zn(2+)) play vital catalytic, structural, and regulatory roles in protein function and are commonly chelated to cysteine residues within the protein framework. Current methods to identify Zn(2+)-binding cysteines rely on computational studies based on known Zn(2+)-chelating motifs, as well as high-resolution structural data. These available approaches preclude the global identification of putative Zn(2+)-chelating cysteines, particularly on poorly characterized proteins in the proteome. Herein, we describe an experimental platform that identifies metal-binding cysteines on the basis of their reduced nucleophilicity upon treatment with metal ions. As validation of our platform, we utilize a peptide-based cysteine-reactive probe to show that the known Zn(2+)-chelating cysteine in sorbitol dehydrogenase (SORD) demonstrates an expected loss in nucleophilicity in the presence of Zn(2+) ions and a gain in nucleophilicity upon treatment with a Zn(2+) chelator. We also identified the active-site cysteine in glutathione S-transferase omega-1 (GSTO1) as a potential Zn(2+)-chelation site, albeit with lower metal affinity relative to SORD. Treatment of recombinant GSTO1 with Zn(2+) ions results in a dose-dependent decrease in GSTO1 activity. Furthermore, we apply a promiscuous cysteine-reactive probe to globally identify putative Zn(2+)-binding cysteines across ∼900 cysteines in the human proteome. This proteomic study identified several well-characterized Zn(2+)-binding proteins, as well as numerous uncharacterized proteins from functionally distinct classes. This platform is highly versatile and provides an experimental tool that complements existing computational and structural methods to identify metal-binding cysteine residues.
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Affiliation(s)
- Nicholas J. Pace
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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95
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Schwaid AG, Shannon DA, Ma J, Slavoff SA, Levin JZ, Weerapana E, Saghatlian A. Correction to “Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames. J Am Chem Soc 2014. [DOI: 10.1021/ja412027d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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96
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Abstract
Tri-substituted 4-aminopiperidine provides a modular and versatile scaffold for the generation of cysteine-reactive probes for diverse proteins.
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97
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Wang C, Weerapana E, Blewett MM, Cravatt BF. A chemoproteomic platform to quantitatively map targets of lipid-derived electrophiles. Nat Methods 2013; 11:79-85. [PMID: 24292485 PMCID: PMC3901407 DOI: 10.1038/nmeth.2759] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 10/11/2013] [Indexed: 02/07/2023]
Abstract
Cells produce electrophilic products with the potential to modify and affect the function of proteins. Chemoproteomic methods have provided a means to qualitatively inventory proteins targeted by endogenous electrophiles; however, ascertaining the potency and specificity of these reactions to identify the most sensitive sites in the proteome to electrophilic modification requires more quantitative methods. Here, we describe a competitive activity-based profiling method for quantifying the reactivity of electrophilic compounds against 1000+ cysteines in parallel in the human proteome. Using this approach, we identify a select set of proteins that constitute “hot spots” for modification by various lipid-derived electrophiles, including the oxidative stress product 4-hydroxynonenal (HNE). We show that one of these proteins, ZAK kinase, is labeled by HNE on a conserved, active site-proximal cysteine, resulting in enzyme inhibition to create a negative feedback mechanism that can suppress the activation of JNK pathways by oxidative stress.
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Affiliation(s)
- Chu Wang
- 1] The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Eranthie Weerapana
- 1] The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Megan M Blewett
- 1] The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Benjamin F Cravatt
- 1] The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
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98
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Shannon DA, Weerapana E. Orphan PTMs: Rare, yet functionally important modifications of cysteine. Biopolymers 2013; 101:156-64. [DOI: 10.1002/bip.22252] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/01/2013] [Indexed: 12/16/2022]
Affiliation(s)
- D. Alexander Shannon
- Department of Chemistry; Merkert Chemistry Center, Boston College; Chestnut Hill MA 02467
| | - Eranthie Weerapana
- Department of Chemistry; Merkert Chemistry Center, Boston College; Chestnut Hill MA 02467
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99
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Schwaid AG, Shannon DA, Ma J, Slavoff SA, Levin JZ, Weerapana E, Saghatelian A. Chemoproteomic discovery of cysteine-containing human short open reading frames. J Am Chem Soc 2013; 135:16750-3. [PMID: 24152191 PMCID: PMC3868496 DOI: 10.1021/ja406606j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The application of ribosome profiling and mass spectrometry technologies has recently revealed that the human proteome is larger than previously appreciated. Short open reading frames (sORFs), which are difficult to identify using traditional gene-finding algorithms, constitute a significant fraction of unknown protein-coding genes. Thus, experimental approaches to identify sORFs provide invaluable insight into the protein-coding potential of genomes. Here, we report an affinity-based approach to enrich and identify cysteine-containing human sORF-encoded polypeptides (ccSEPs) from cells. This approach revealed 16 novel ccSEPs, each derived from an uncharacterized sORF, demonstrating its potential for discovering new genes. We validated expression of a SEP from its endogenous RNA, and demonstrated the specificity of our labeling approach using synthetic SEP. The discovery of additional human SEPs and their conservation indicate the potential importance of these molecules in biology.
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Affiliation(s)
- Adam G. Schwaid
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - D. Alexander Shannon
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Jiao Ma
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Sarah A. Slavoff
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Joshua Z. Levin
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Eranthie Weerapana
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
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100
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Gu C, Shannon DA, Colby T, Wang Z, Shabab M, Kumari S, Villamor JG, McLaughlin CJ, Weerapana E, Kaiser M, Cravatt BF, van der Hoorn RAL. Chemical proteomics with sulfonyl fluoride probes reveals selective labeling of functional tyrosines in glutathione transferases. ACTA ACUST UNITED AC 2013; 20:541-8. [PMID: 23601643 DOI: 10.1016/j.chembiol.2013.01.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 01/07/2013] [Accepted: 01/12/2013] [Indexed: 01/16/2023]
Abstract
Chemical probes have great potential for identifying functional residues in proteins in crude proteomes. Here we studied labeling sites of chemical probes based on sulfonyl fluorides (SFs) on plant and animal proteomes. Besides serine proteases and many other proteins, SF-based probes label Tyr residues in glutathione transferases (GSTs). The labeled GSTs represent four different GST classes that share less than 30% sequence identity. The targeted Tyr residues are located at similar positions in the promiscuous substrate binding site and are essential for GST function. The high selectivity of SF-based probes for functional Tyr residues in GSTs illustrates how these probes can be used for functional studies of GSTs and other proteins in crude proteomes.
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Affiliation(s)
- Christian Gu
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany
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