1
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Tao H, Fang C, Xiao Y, Jin Y. The toxicity and health risk of chlorothalonil to non-target animals and humans: A systematic review. CHEMOSPHERE 2024; 358:142241. [PMID: 38705408 DOI: 10.1016/j.chemosphere.2024.142241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/17/2023] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Chlorothalonil (CTL), an organochloride fungicide applied for decades worldwide, has been found to be present in various matrixes and even accumulates in humans or other mammals through the food chain. Its high residue and diffusion in the environment have severely affected food security and public health. More and more research has considered CTL as a possible toxin to environmental non-target organisms, via influencing multiple systems such as metabolic, developmental, endocrine, genetic, and reproductive pathways. Aquatic organisms and amphibians are the most vulnerable species to CTL exposure, especially during the early period of development. Under experimental conditions, CTL can also have toxic effects on rodents and other non-target organisms. As for humans, CTL exposure is most often reported to be relevant to allergic reactions to the skin and eyes. We hope that this review will improve our understanding of the hazards and risks that CTL poses to non-target organisms and find a strategy for rational use.
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Affiliation(s)
- Huaping Tao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China; Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Chanlin Fang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China.
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2
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Deng L, Zhang C, Li B, Fu J, Zhang Z, Li S, Zhao X, Su Z, Hu C, Yu Z. Photo-induced defluorination acyl fluoride exchange as a fluorogenic photo-click reaction for photo-affinity labeling. Chem Sci 2023; 14:3630-3641. [PMID: 37006673 PMCID: PMC10056068 DOI: 10.1039/d2sc04636a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 02/24/2023] [Indexed: 02/26/2023] Open
Abstract
Photo-click chemistry has emerged as a powerful tool for revolutionizing bioconjugation technologies in pharmacological and various biomimetic applications. However, enriching the photo-click reactions to expand the bioconjugation toolkit remains challenging, especially when focusing on spatiotemporal control endowed by light activation. Herein, we describe a photo-induced defluorination acyl fluoride exchange (photo-DAFEx) as a novel type of photo-click reaction that is mediated through acyl fluorides produced by the photo-defluorination of m-trifluoromethylaniline to covalently conjugate with primary/secondary amines and thiols in an aqueous environment. (TD)-DFT calculations, together with experimental discovery, indicate that the m-NH2PhF2C(sp3)-F bond in the excited triplet state is cleaved by water molecules, which is key to inducing defluorination. Intriguingly, the benzoyl amide linkages built by this photo-click reaction exhibited a satisfactory fluorogenic performance, which allowed visualization of its formation in situ. Accordingly, this photo-controlled covalent strategy was exploited not only for the decoration of small molecules, peptide cyclization and functionalization of proteins in vitro, but also for designing photo-affinity probes targeting endogenous carbonic anhydrase II (hCA-II) in living cells.
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Affiliation(s)
- Lijun Deng
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Cefei Zhang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Baolin Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Jielin Fu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhong Zhang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Sitong Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhishan Su
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Changwei Hu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
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Abstract
Environmental agents of exposure can damage proteins, affecting protein function and cellular protein homeostasis. Specific residues are inherently chemically susceptible to damage from individual types of exposure. Amino acid content is not completely predictive of protein susceptibility, as secondary, tertiary, and quaternary structures of proteins strongly influence the reactivity of the proteome to individual exposures. Because we cannot readily predict which proteins will be affected by which chemical exposures, mass spectrometry-based proteomic strategies are necessary to determine the protein targets of environmental toxins and toxicants. This review describes the mechanisms by which environmental exposure to toxins and toxicants can damage proteins and affect their function, and emerging omic methodologies that can be used to identify the protein targets of a given agent. These methods include target identification strategies that have recently revolutionized the drug discovery field, such as activity-based protein profiling, protein footprinting, and protein stability profiling technologies. In particular, we highlight the necessity of multiple, complementary approaches to fully interrogate how protein integrity is challenged by individual exposures.
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Affiliation(s)
- Joseph C Genereux
- Department of Chemistry, University of California, Riverside, CA 92521, USA.
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4
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Němec V, Schwalm MP, Müller S, Knapp S. PROTAC degraders as chemical probes for studying target biology and target validation. Chem Soc Rev 2022; 51:7971-7993. [PMID: 36004812 DOI: 10.1039/d2cs00478j] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule degraders such as PROTACs (PROteolysis TArgeting Chimeras) have emerged as new promising pharmacological modalities and the first PROTAC drug candidates are now studied clinically. The catalytic properties of PROTACs, acting as chemical degraders of a protein of interest (POI), represent an attractive new strategy for drug development. The development and characterization of PROTACs requires an array of additional assay systems that track the degradation pathway leading ultimately to degradation of the POI, identifying critical steps for PROTAC optimization. In addition to their exciting translational potential, PROTACs represent versatile chemical tools that considerably expanded our chemical biology toolbox and significantly enlarged the proteome that can be modulated by small molecules. Similar to conventional chemical probes, PROTACs used as chemical probes in target validation require comprehensive characterization. As a consequence, PROTAC-specific quality criteria should be defined by the chemical biology community. These criteria need to comprise additional or alternative parameters compared to those for conventional occupancy-driven chemical probes, such as the maximum level of target degradation (Dmax), confirmation of a proteasome dependent degradation mechanism and, importantly, also kinetic parameters of POI degradation. The kinetic aspects are particularly relevant for PROTACs that harbor covalent binding moieties. Here, we review recent progress in the development of assay systems for PROTAC characterization and suggest a set of criteria for PROTACs as high quality chemical probes.
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Affiliation(s)
- Václav Němec
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany
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5
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Chung MK, Rappaport SM, Wheelock CE, Nguyen VK, van der Meer TP, Miller GW, Vermeulen R, Patel CJ. Utilizing a Biology-Driven Approach to Map the Exposome in Health and Disease: An Essential Investment to Drive the Next Generation of Environmental Discovery. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:85001. [PMID: 34435882 PMCID: PMC8388254 DOI: 10.1289/ehp8327] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/28/2021] [Accepted: 07/13/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Recent developments in technologies have offered opportunities to measure the exposome with unprecedented accuracy and scale. However, because most investigations have targeted only a few exposures at a time, it is hypothesized that the majority of the environmental determinants of chronic diseases remain unknown. OBJECTIVES We describe a functional exposome concept and explain how it can leverage existing bioassays and high-resolution mass spectrometry for exploratory study. We discuss how such an approach can address well-known barriers to interpret exposures and present a vision of next-generation exposomics. DISCUSSION The exposome is vast. Instead of trying to capture all exposures, we can reduce the complexity by measuring the functional exposome-the totality of the biologically active exposures relevant to disease development-through coupling biochemical receptor-binding assays with affinity purification-mass spectrometry. We claim the idea of capturing exposures with functional biomolecules opens new opportunities to solve critical problems in exposomics, including low-dose detection, unknown annotations, and complex mixtures of exposures. Although novel, biology-based measurement can make use of the existing data processing and bioinformatics pipelines. The functional exposome concept also complements conventional targeted and untargeted approaches for understanding exposure-disease relationships. CONCLUSIONS Although measurement technology has advanced, critical technological, analytical, and inferential barriers impede the detection of many environmental exposures relevant to chronic-disease etiology. Through biology-driven exposomics, it is possible to simultaneously scale up discovery of these causal environmental factors. https://doi.org/10.1289/EHP8327.
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Affiliation(s)
- Ming Kei Chung
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephen M. Rappaport
- Program in Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Craig E. Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Vy Kim Nguyen
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas P. van der Meer
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Gary W. Miller
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Roel Vermeulen
- Utrecht University & Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
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6
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Xu T, Chen L, Lim YT, Zhao H, Chen H, Chen MW, Huan T, Huang Y, Sobota RM, Fang M. System Biology-Guided Chemical Proteomics to Discover Protein Targets of Monoethylhexyl Phthalate in Regulating Cell Cycle. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1842-1851. [PMID: 33459556 DOI: 10.1021/acs.est.0c05832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical proteomics methods have been used as effective tools to identify novel protein targets for small molecules. These methods have great potential to be applied as environmental toxicants to figure out their mode of action. However, these assays usually generate dozens of possible targets, making it challenging to validate the most important one. In this study, we have integrated the cellular thermal shift assay (CETSA), quantitative proteomics, metabolomics, computer-assisted docking, and target validation methods to uncover the protein targets of monoethylhexyl phthalate (MEHP). Using the mass spectrometry implementation of CETSA (MS-CETSA), we have identified 74 possible protein targets of MEHP. The Gene Ontology (GO) enrichment integration was further conducted for the target proteins, the cellular dysregulated proteins, and the metabolites, showing that cell cycle dysregulation could be one primary change due to the MEHP-induced toxicity. Flow cytometry analysis confirmed that hepatocytes were arrested at the G1 stage due to the treatment with MEHP. Subsequently, the potential protein targets were ranked by their binding energy calculated from the computer-assisted docking with MEHP. In summary, we have demonstrated the development of interactomics workflow to simplify the redundant information from multiomics data and identified novel cell cycle regulatory protein targets (CPEB4, ANAPC5, and SPOUT1) for MEHP.
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Affiliation(s)
- Tengfei Xu
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, 637141 Singapore
| | - Liyan Chen
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673 Singapore
| | - Yan Ting Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673 Singapore
| | - Haoduo Zhao
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
| | - Hongjin Chen
- Department of Pathology in the School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211112, P. R. China
| | - Ming Wei Chen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Yichao Huang
- School of Environment, Jinan University, Guangzhou, Guangdong 511443, P. R. China
| | - Radoslaw Mikolaj Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673 Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, 637141 Singapore
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 639798 Singapore
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7
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Modification of proteins by reactive lipid oxidation products and biochemical effects of lipoxidation. Essays Biochem 2020; 64:19-31. [PMID: 31867621 DOI: 10.1042/ebc20190058] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023]
Abstract
Lipid oxidation results in the formation of many reactive products, such as small aldehydes, substituted alkenals, and cyclopentenone prostaglandins, which are all able to form covalent adducts with nucleophilic residues of proteins. This process is called lipoxidation, and the resulting adducts are called advanced lipoxidation end products (ALEs), by analogy with the formation of advanced glycoxidation end products from oxidized sugars. Modification of proteins by reactive oxidized lipids leads to structural changes such as increased β-sheet conformation, which tends to result in amyloid-like structures and oligomerization, or unfolding and aggregation. Reaction with catalytic cysteines is often responsible for the loss of enzymatic activity in lipoxidized proteins, although inhibition may also occur through conformational changes at more distant sites affecting substrate binding or regulation. On the other hand, a few proteins are activated by lipoxidation-induced oligomerization or interactions, leading to increased downstream signalling. At the cellular level, it is clear that some proteins are much more susceptible to lipoxidation than others. ALEs affect cell metabolism, protein-protein interactions, protein turnover via the proteasome, and cell viability. Evidence is building that they play roles in both physiological and pathological situations, and inhibiting ALE formation can have beneficial effects.
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8
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A quantitative thiol reactivity profiling platform to analyze redox and electrophile reactive cysteine proteomes. Nat Protoc 2020; 15:2891-2919. [PMID: 32690958 DOI: 10.1038/s41596-020-0352-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/05/2020] [Indexed: 02/08/2023]
Abstract
Cysteine is unique among all protein-coding amino acids, owing to its intrinsically high nucleophilicity. The cysteinyl thiol group can be covalently modified by a broad range of redox mechanisms or by various electrophiles derived from exogenous or endogenous sources. Measuring the response of protein cysteines to redox perturbation or electrophiles is critical for understanding the underlying mechanisms involved. Activity-based protein profiling based on thiol-reactive probes has been the method of choice for such analyses. We therefore adapted this approach and developed a new chemoproteomic platform, termed 'QTRP' (quantitative thiol reactivity profiling), that relies on the ability of a commercially available thiol-reactive probe IPM (2-iodo-N-(prop-2-yn-1-yl)acetamide) to covalently label, enrich and quantify the reactive cysteinome in cells and tissues. Here, we provide a detailed and updated workflow of QTRP that includes procedures for (i) labeling of the reactive cysteinome from cell or tissue samples (e.g., control versus treatment) with IPM, (ii) processing the protein samples into tryptic peptides and tagging the probe-modified peptides with isotopically labeled azido-biotin reagents containing a photo-cleavable linker via click chemistry reaction, (iii) capturing biotin-conjugated peptides with streptavidin beads, (iv) identifying and quantifying the photo-released peptides by mass spectrometry (MS)-based shotgun proteomics and (v) interpreting MS data by a streamlined informatic pipeline using a proteomics software, pFind 3, and an automatic post-processing algorithm. We also exemplified here how to use QTRP for mining H2O2-sensitive cysteines and for determining the intrinsic reactivity of cysteines in a complex proteome. We anticipate that this protocol should find broad applications in redox biology, chemical biology and the pharmaceutical industry. The protocol for sample preparation takes 3 d, whereas MS measurements and data analyses require 75 min and <30 min, respectively, per sample.
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9
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Ward CC, Kleinman JI, Brittain SM, Lee PS, Chung CYS, Kim K, Petri Y, Thomas JR, Tallarico JA, McKenna JM, Schirle M, Nomura DK. Covalent Ligand Screening Uncovers a RNF4 E3 Ligase Recruiter for Targeted Protein Degradation Applications. ACS Chem Biol 2019; 14:2430-2440. [PMID: 31059647 DOI: 10.1021/acschembio.8b01083] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Targeted protein degradation has arisen as a powerful strategy for drug discovery allowing the targeting of undruggable proteins for proteasomal degradation. This approach most often employs heterobifunctional degraders consisting of a protein-targeting ligand linked to an E3 ligase recruiter to ubiquitinate and mark proteins of interest for proteasomal degradation. One challenge with this approach, however, is that only a few E3 ligase recruiters currently exist for targeted protein degradation applications, despite the hundreds of known E3 ligases in the human genome. Here, we utilized activity-based protein profiling (ABPP)-based covalent ligand screening approaches to identify cysteine-reactive small-molecules that react with the E3 ubiquitin ligase RNF4 and provide chemical starting points for the design of RNF4-based degraders. The hit covalent ligand from this screen reacted with either of two zinc-coordinating cysteines in the RING domain, C132 and C135, with no effect on RNF4 activity. We further optimized the potency of this hit and incorporated this potential RNF4 recruiter into a bifunctional degrader linked to JQ1, an inhibitor of the BET family of bromodomain proteins. We demonstrate that the resulting compound CCW 28-3 is capable of degrading BRD4 in a proteasome- and RNF4-dependent manner. In this study, we have shown the feasibility of using chemoproteomics-enabled covalent ligand screening platforms to expand the scope of E3 ligase recruiters that can be exploited for targeted protein degradation applications.
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Affiliation(s)
- Carl C. Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jordan I. Kleinman
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Scott M. Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Lee
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Clive Yik Sham Chung
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Kenneth Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Yana Petri
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jason R. Thomas
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeffrey M. McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel K. Nomura
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
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10
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Chung CYS, Shin HR, Berdan CA, Ford B, Ward CC, Olzmann JA, Zoncu R, Nomura DK. Covalent targeting of the vacuolar H +-ATPase activates autophagy via mTORC1 inhibition. Nat Chem Biol 2019; 15:776-785. [PMID: 31285595 PMCID: PMC6641988 DOI: 10.1038/s41589-019-0308-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023]
Abstract
Autophagy is a lysosomal degradation pathway that eliminates aggregated proteins and damaged organelles to maintain cellular homeostasis. A major route for activating autophagy involves inhibition of the mTORC1 kinase, but current mTORC1-targeting compounds do not allow complete and selective mTORC1 blockade. Here, we have coupled screening of a covalent ligand library with activity-based protein profiling to discover EN6, a small-molecule in vivo activator of autophagy that covalently targets cysteine 277 in the ATP6V1A subunit of the lysosomal v-ATPase, which activates mTORC1 via the Rag guanosine triphosphatases. EN6-mediated ATP6V1A modification decouples the v-ATPase from the Rags, leading to inhibition of mTORC1 signaling, increased lysosomal acidification and activation of autophagy. Consistently, EN6 clears TDP-43 aggregates, a causative agent in frontotemporal dementia, in a lysosome-dependent manner. Our results provide insight into how the v-ATPase regulates mTORC1, and reveal a unique approach for enhancing cellular clearance based on covalent inhibition of lysosomal mTORC1 signaling.
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Affiliation(s)
- Clive Yik-Sham Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Hijai R Shin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - Charles A Berdan
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Breanna Ford
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA.
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA.
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11
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Wørmer GJ, Hansen BK, Palmfeldt J, Poulsen TB. A Cyclopropene Electrophile that Targets Glutathione S‐Transferase Omega‐1 in Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Gustav J. Wørmer
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Bente K. Hansen
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine—Research Unit for Molecular Medicine Aarhus University hospital Palle Juul-Jensens Boulevard 82 8200 Aarhus N Denmark
| | - Thomas B. Poulsen
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
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12
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Wørmer GJ, Hansen BK, Palmfeldt J, Poulsen TB. A Cyclopropene Electrophile that Targets Glutathione S‐Transferase Omega‐1 in Cells. Angew Chem Int Ed Engl 2019; 58:11918-11922. [DOI: 10.1002/anie.201907520] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Gustav J. Wørmer
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Bente K. Hansen
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine—Research Unit for Molecular Medicine Aarhus University hospital Palle Juul-Jensens Boulevard 82 8200 Aarhus N Denmark
| | - Thomas B. Poulsen
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
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13
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Preston GW, Phillips DH. Protein Adductomics: Analytical Developments and Applications in Human Biomonitoring. TOXICS 2019; 7:E29. [PMID: 31130613 PMCID: PMC6631498 DOI: 10.3390/toxics7020029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 02/07/2023]
Abstract
Proteins contain many sites that are subject to modification by electrophiles. Detection and characterisation of these modifications can give insights into environmental agents and endogenous processes that may be contributing factors to chronic human diseases. An untargeted approach, utilising mass spectrometry to detect modified amino acids or peptides, has been applied to blood proteins haemoglobin and albumin, focusing in particular on the N-terminal valine residue of haemoglobin and the cysteine-34 residue in albumin. Technical developments to firstly detect simultaneously multiple adducts at these sites and then subsequently to identify them are reviewed here. Recent studies in which the methods have been applied to biomonitoring human exposure to environmental toxicants are described. With advances in sensitivity, high-throughput handling of samples and robust quality control, these methods have considerable potential for identifying causes of human chronic disease and of identifying individuals at risk.
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Affiliation(s)
- George W Preston
- Environmental Research Group, Department of Analytical, Environmental and Forensic Science, School of Population Health and Environmental Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
| | - David H Phillips
- Environmental Research Group, Department of Analytical, Environmental and Forensic Science, School of Population Health and Environmental Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
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14
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Isobe Y, Kawashima Y, Ishihara T, Watanabe K, Ohara O, Arita M. Identification of Protein Targets of 12/15-Lipoxygenase-Derived Lipid Electrophiles in Mouse Peritoneal Macrophages Using Omega-Alkynyl Fatty Acid. ACS Chem Biol 2018; 13:887-893. [PMID: 29461797 DOI: 10.1021/acschembio.7b01092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The 12/15-lipoxygenase (12/15-LOX) enzyme introduces peroxyl groups, in a position-specific manner, into polyunsaturated fatty acids to form various kinds of bioactive lipid metabolites, including lipid-derived electrophiles (LDE). The resident peritoneal macrophage is the site of highest 12/15-LOX expression in the mouse. However, the role of the enzyme in the regulation of resident macrophages is not fully understood. Here, we describe a chemoproteomic method to identify the targets of enzymatically generated LDE. By treating mouse peritoneal macrophages with omega-alkynyl arachidonic acid (aAA), we identified a series of proteins adducted by LDE generated through a 12/15-LOX catalyzed reaction. Pathway analysis revealed a dramatic enrichment of proteins involved in energy metabolism and found that glycolytic flux and mitochondrial respiration were significantly affected by the expression of 12/15-LOX. Our findings thus highlight the utility of chemoproteomics using aAA for identifying intracellular targets of enzymatically generated LDE.
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Affiliation(s)
- Yosuke Isobe
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | | | - Tomoaki Ishihara
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kenji Watanabe
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | | | - Makoto Arita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Division of Physiological Chemistry and Metabolism, Keio University Faculty of Pharmacy, 1-5-30, Shibakoen, Minato-ku, Tokyo, 105-0011, Japan
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15
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Unexpected transformation of dissolved phenols to toxic dicarbonyls by hydroxyl radicals and UV light. Proc Natl Acad Sci U S A 2018; 115:2311-2316. [PMID: 29463747 PMCID: PMC5877969 DOI: 10.1073/pnas.1715821115] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Phenols are common anthropogenic and natural chemicals that contaminate drinking water sources. To reduce exposure to these compounds, hydroxyl radicals are often used as chemical oxidants during water treatment. Although this treatment process removes phenols, we have found that it unexpectedly produces toxic transformation products. We identify these products and simultaneously assess their toxicity with a technique that detects products formed when the transformation products react with amino acids and peptides. Our results highlight the potential risks of using oxidative treatment on alternative drinking water sources, such as contaminated groundwater and recycled municipal wastewater. They also suggest that these reactions produce these toxic transformation products in other situations, including in clouds and sunlit surface waters and within living cells. Water treatment systems frequently use strong oxidants or UV light to degrade chemicals that pose human health risks. Unfortunately, these treatments can result in the unintended transformation of organic contaminants into toxic products. We report an unexpected reaction through which exposure of phenolic compounds to hydroxyl radicals (•OH) or UV light results in the formation of toxic α,β-unsaturated enedials and oxoenals. We show that these transformation products damage proteins by reacting with lysine and cysteine moieties. We demonstrate that phenolic compounds react with •OH produced by the increasingly popular UV/hydrogen peroxide (H2O2) water treatment process or UV light to form toxic enedials and oxoenals. In addition to raising concerns about potential health risks of oxidative water treatment, our findings suggest the potential for formation of these toxic compounds in sunlit surface waters, atmospheric water, and living cells. For the latter, our findings may be particularly relevant to efforts to understand cellular damage caused by in vivo production of reactive oxygen species. In particular, we demonstrate that exposure of the amino acid tyrosine to •OH yields an electrophilic enedial product that undergoes cross-linking reaction with both lysine and cysteine residues.
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16
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Sun R, Shi F, Liu K, Fu L, Tian C, Yang Y, Tallman KA, Porter NA, Yang J. A Chemoproteomic Platform To Assess Bioactivation Potential of Drugs. Chem Res Toxicol 2017; 30:1797-1803. [DOI: 10.1021/acs.chemrestox.7b00183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rui Sun
- State
Key Laboratory of Proteomics, National Center for Protein Sciences,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- State
Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug
Discovery for Metabolic Disease, Center for New Drug Safety Evaluation
and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Fuguo Shi
- Department
of Pharmacology, Key Laboratory of Basic Pharmacology of Ministry
of Education and Joint International Research Laboratory of Ethnomedicine
of Ministry of Education, Zunyi Medical University, Zunyi 563003, China
| | - Keke Liu
- State
Key Laboratory of Proteomics, National Center for Protein Sciences,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Ling Fu
- State
Key Laboratory of Proteomics, National Center for Protein Sciences,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Caiping Tian
- State
Key Laboratory of Proteomics, National Center for Protein Sciences,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yong Yang
- State
Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug
Discovery for Metabolic Disease, Center for New Drug Safety Evaluation
and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Keri A. Tallman
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Ned A. Porter
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jing Yang
- State
Key Laboratory of Proteomics, National Center for Protein Sciences,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
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17
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Tian C, Sun R, Liu K, Fu L, Liu X, Zhou W, Yang Y, Yang J. Multiplexed Thiol Reactivity Profiling for Target Discovery of Electrophilic Natural Products. Cell Chem Biol 2017; 24:1416-1427.e5. [PMID: 28988947 DOI: 10.1016/j.chembiol.2017.08.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/06/2017] [Accepted: 08/30/2017] [Indexed: 02/09/2023]
Abstract
Electrophilic groups, such as Michael acceptors, expoxides, are common motifs in natural products (NPs). Electrophilic NPs can act through covalent modification of cysteinyl thiols on functional proteins, and exhibit potent cytotoxicity and anti-inflammatory/cancer activities. Here we describe a new chemoproteomic strategy, termed multiplexed thiol reactivity profiling (MTRP), and its use in target discovery of electrophilic NPs. We demonstrate the utility of MTRP by identifying cellular targets of gambogic acid, an electrophilic NP that is currently under evaluation in clinical trials as anticancer agent. Moreover, MTRP enables simultaneous comparison of seven structurally diversified α,β-unsaturated γ-lactones, which provides insights into the relative proteomic reactivity and target preference of diverse structural scaffolds coupled to a common electrophilic motif and reveals various potential druggable targets with liganded cysteines. We anticipate that this new method for thiol reactivity profiling in a multiplexed manner will find broad application in redox biology and drug discovery.
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Affiliation(s)
- Caiping Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China
| | - Rui Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China; State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Keke Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China
| | - Ling Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China
| | - Xiaoyu Liu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Wanqi Zhou
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Yong Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China.
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18
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Grossman EA, Ward CC, Spradlin JN, Bateman LA, Huffman TR, Miyamoto DK, Kleinman JI, Nomura DK. Covalent Ligand Discovery against Druggable Hotspots Targeted by Anti-cancer Natural Products. Cell Chem Biol 2017; 24:1368-1376.e4. [PMID: 28919038 DOI: 10.1016/j.chembiol.2017.08.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/10/2017] [Accepted: 08/15/2017] [Indexed: 01/30/2023]
Abstract
Many natural products that show therapeutic activities are often difficult to synthesize or isolate and have unknown targets, hindering their development as drugs. Identifying druggable hotspots targeted by covalently acting anti-cancer natural products can enable pharmacological interrogation of these sites with more synthetically tractable compounds. Here, we used chemoproteomic platforms to discover that the anti-cancer natural product withaferin A targets C377 on the regulatory subunit PPP2R1A of the tumor-suppressor protein phosphatase 2A (PP2A) complex leading to activation of PP2A activity, inactivation of AKT, and impaired breast cancer cell proliferation. We developed a more synthetically tractable cysteine-reactive covalent ligand, JNS 1-40, that selectively targets C377 of PPP2R1A to impair breast cancer signaling, proliferation, and in vivo tumor growth. Our study highlights the utility of using chemoproteomics to map druggable hotspots targeted by complex natural products and subsequently interrogating these sites with more synthetically tractable covalent ligands for cancer therapy.
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Affiliation(s)
- Elizabeth A Grossman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Carl C Ward
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Jessica N Spradlin
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Leslie A Bateman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Tucker R Huffman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - David K Miyamoto
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Jordan I Kleinman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA.
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19
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Fu L, Liu K, Sun M, Tian C, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo D, Liebler DC, Yang J. Systematic and Quantitative Assessment of Hydrogen Peroxide Reactivity With Cysteines Across Human Proteomes. Mol Cell Proteomics 2017; 16:1815-1828. [PMID: 28827280 DOI: 10.1074/mcp.ra117.000108] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Indexed: 01/23/2023] Open
Abstract
Protein cysteinyl residues are the mediators of hydrogen peroxide (H2O2)-dependent redox signaling. However, site-specific mapping of the selectivity and dynamics of these redox reactions in cells poses a major analytical challenge. Here we describe a chemoproteomic platform to systematically and quantitatively analyze the reactivity of thousands of cysteines toward H2O2 in human cells. We identified >900 H2O2-sensitive cysteines, which are defined as the H2O2-dependent redoxome. Although redox sites associated with antioxidative and metabolic functions are consistent, most of the H2O2-dependent redoxome varies dramatically between different cells. Structural analyses reveal that H2O2-sensitive cysteines are less conserved than their redox-insensitive counterparts and display distinct sequence motifs, structural features, and potential for crosstalk with lysine modifications. Notably, our chemoproteomic platform also provides an opportunity to predict oxidation-triggered protein conformational changes. The data are freely accessible as a resource at http://redox.ncpsb.org/OXID/.
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Affiliation(s)
- Ling Fu
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Keke Liu
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Mingan Sun
- §State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, China
| | - Caiping Tian
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Rui Sun
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China.,¶State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Carlos Morales Betanzos
- ‖Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Keri A Tallman
- **Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Ned A Porter
- **Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Yong Yang
- ¶State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Dianjing Guo
- §State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, China
| | - Daniel C Liebler
- ‖Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Jing Yang
- From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China;
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20
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Whitby LR, Obach RS, Simon GM, Hayward MM, Cravatt BF. Quantitative Chemical Proteomic Profiling of the in Vivo Targets of Reactive Drug Metabolites. ACS Chem Biol 2017. [PMID: 28636309 DOI: 10.1021/acschembio.7b00346] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Idiosyncratic liver toxicity represents an important problem in drug research and pharmacotherapy. Reactive drug metabolites that modify proteins are thought to be a principal factor in drug-induced liver injury. Here, we describe a quantitative chemical proteomic method to identify the targets of reactive drug metabolites in vivo. Treating mice with clickable analogues of four representative hepatotoxic drugs, we demonstrate extensive covalent binding that is confined primarily to the liver. Each drug exhibited a distinct target profile that, in certain cases, showed strong enrichment for specific metabolic pathways (e.g., lipid/sterol pathways for troglitazone). Site-specific proteomics revealed that acetaminophen reacts with high stoichiometry with several conserved, functional (seleno)cysteine residues throughout the liver proteome. Our findings thus provide an advanced experimental framework to characterize the proteomic reactivity of drug metabolites in vivo, revealing target profiles that may help to explain mechanisms and identify risk factors for drug-induced liver injury.
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Affiliation(s)
- Landon R. Whitby
- The
Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, California 92307, United States
| | - R. Scott Obach
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gabriel M. Simon
- Vividion Therapeutics, 3033 Science
Park Rd Suite D, San Diego, California 92121, United States
| | - Matthew M. Hayward
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Benjamin F. Cravatt
- The
Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, California 92307, United States
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21
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Ward CC, Kleinman JI, Nomura DK. NHS-Esters As Versatile Reactivity-Based Probes for Mapping Proteome-Wide Ligandable Hotspots. ACS Chem Biol 2017; 12:1478-1483. [PMID: 28445029 DOI: 10.1021/acschembio.7b00125] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Most of the proteome is considered undruggable, oftentimes hindering translational efforts for drug discovery. Identifying previously unknown druggable hotspots in proteins would enable strategies for pharmacologically interrogating these sites with small molecules. Activity-based protein profiling (ABPP) has arisen as a powerful chemoproteomic strategy that uses reactivity-based chemical probes to map reactive, functional, and ligandable hotspots in complex proteomes, which has enabled inhibitor discovery against various therapeutic protein targets. Here, we report an alkyne-functionalized N-hydroxysuccinimide-ester (NHS-ester) as a versatile reactivity-based probe for mapping the reactivity of a wide range of nucleophilic ligandable hotspots, including lysines, serines, threonines, and tyrosines, encompassing active sites, allosteric sites, post-translational modification sites, protein interaction sites, and previously uncharacterized potential binding sites. Surprisingly, we also show that fragment-based NHS-ester ligands can be made to confer selectivity for specific lysine hotspots on specific targets including Dpyd, Aldh2, and Gstt1. We thus put forth NHS-esters as promising reactivity-based probes and chemical scaffolds for covalent ligand discovery.
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Affiliation(s)
- Carl C. Ward
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jordan I. Kleinman
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
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22
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Roberts LS, Yan P, Bateman LA, Nomura DK. Mapping Novel Metabolic Nodes Targeted by Anti-Cancer Drugs that Impair Triple-Negative Breast Cancer Pathogenicity. ACS Chem Biol 2017; 12:1133-1140. [PMID: 28248089 DOI: 10.1021/acschembio.6b01159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Triple-negative breast cancers (TNBCs) are estrogen receptor, progesterone receptor, and HER2 receptor-negative subtypes of breast cancers that show the worst prognoses and lack targeted therapies. Here, we have coupled the screening of ∼400 anticancer agents that are under development or in the clinic with chemoproteomic and metabolomic profiling to identify novel metabolic mechanisms for agents that impair TNBC pathogenicity. We identify 20 anticancer compounds that significantly impaired cell survival across multiple types of TNBC cells. Among these 20 leads, the phytoestrogenic natural product licochalcone A was of interest, since TNBCs are unresponsive to estrogenic therapies, indicating that licochalcone A was likely acting through another target. Using chemoproteomic profiling approaches, we reveal that licochalcone A impairs TNBC pathogenicity, not through modulating estrogen receptor activity but rather through inhibiting prostaglandin reductase 1, a metabolic enzyme involved in leukotriene B4 inactivation. We also more broadly performed metabolomic profiling to map additional metabolic mechanisms of compounds that impair TNBC pathogenicity. Overlaying lipidomic profiling with drug responses, we find that deubiquitinase inhibitors cause dramatic elevations in acyl carnitine levels, which impair mitochondrial respiration and contribute to TNBC pathogenic impairments. We thus put forth two unique metabolic nodes that are targeted by drugs or drug candidates that impair TNBC pathogenicity. Our results also showcase the utility of coupling drug screens with chemoproteomic and metabolomic profiling to uncover unique metabolic drivers of TNBC pathogenicity.
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Affiliation(s)
- Lindsay S. Roberts
- Departments of Chemistry, Molecular and
Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Peter Yan
- Departments of Chemistry, Molecular and
Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Leslie A. Bateman
- Departments of Chemistry, Molecular and
Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Departments of Chemistry, Molecular and
Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
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23
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Roberts AM, Miyamoto DK, Huffman TR, Bateman LA, Ives AN, Akopian D, Heslin MJ, Contreras CM, Rape M, Skibola CF, Nomura DK. Chemoproteomic Screening of Covalent Ligands Reveals UBA5 As a Novel Pancreatic Cancer Target. ACS Chem Biol 2017; 12:899-904. [PMID: 28186401 DOI: 10.1021/acschembio.7b00020] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chemical genetic screening of small-molecule libraries has been a promising strategy for discovering unique and novel therapeutic compounds. However, identifying the targets of lead molecules that arise from these screens has remained a major bottleneck in understanding the mechanism of action of these compounds. Here, we have coupled the screening of a cysteine-reactive fragment-based covalent ligand library with an isotopic tandem orthogonal proteolysis-enabled activity-based protein profiling (isoTOP-ABPP) chemoproteomic platform to rapidly couple the discovery of lead small molecules that impair pancreatic cancer pathogenicity with the identification of druggable hotspots for potential cancer therapy. Through this coupled approach, we have discovered a covalent ligand DKM 2-93 that impairs pancreatic cancer cell survival and in vivo tumor growth through covalently modifying the catalytic cysteine of the ubiquitin-like modifier activating enzyme 5 (UBA5), thereby inhibiting its activity as a protein that activates the ubiquitin-like protein UFM1 to UFMylate proteins. We show that UBA5 is a novel pancreatic cancer therapeutic target and show DKM 2-93 as a relatively selective lead inhibitor of UBA5. Our results underscore the utility of coupling the screening of covalent ligand libraries with isoTOP-ABPP platforms for mining the proteome for druggable hotspots for cancer therapy.
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Affiliation(s)
- Allison M. Roberts
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - David K. Miyamoto
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Tucker R. Huffman
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Leslie A. Bateman
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ashley N. Ives
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - David Akopian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Martin J. Heslin
- The University of Alabama at Birmingham, Birmingham, Alabama 35233, United States
| | - Carlo M. Contreras
- The University of Alabama at Birmingham, Birmingham, Alabama 35233, United States
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Christine F. Skibola
- The University of Alabama at Birmingham, Birmingham, Alabama 35233, United States
| | - Daniel K. Nomura
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
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24
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Bateman LA, Ku WM, Heslin MJ, Contreras CM, Skibola CF, Nomura DK. Argininosuccinate Synthase 1 is a Metabolic Regulator of Colorectal Cancer Pathogenicity. ACS Chem Biol 2017; 12:905-911. [PMID: 28229591 DOI: 10.1021/acschembio.6b01158] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Like many cancer types, colorectal cancers have dysregulated metabolism that promotes their pathogenic features. In this study, we used the activity-based protein profiling chemoproteomic platform to profile cysteine-reactive metabolic enzymes that are upregulated in primary human colorectal tumors. We identified argininosuccinate synthase 1 (ASS1) as an upregulated target in primary human colorectal tumors and show that pharmacological inhibition or genetic ablation of ASS1 impairs colorectal cancer pathogenicity. Using metabolomic profiling, we show that ASS1 inhibition leads to reductions in the levels of oncogenic metabolite fumarate, leading to impairments in glycolytic metabolism that supports colorectal cancer cell pathogenicity. We show here that ASS1 inhibitors may represent a novel therapeutic approach for attenuating colorectal cancer through compromising critical metabolic and metabolite signaling pathways and demonstrate the utility of coupling chemoproteomic and metabolomic strategies to map novel metabolic regulators of cancer.
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Affiliation(s)
- Leslie A. Bateman
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | | | - Martin J. Heslin
- The University of Alabama at Birmingham, Birmingham, Alabama 35233, United States
| | - Carlo M. Contreras
- The University of Alabama at Birmingham, Birmingham, Alabama 35233, United States
| | - Christine F. Skibola
- The University of Alabama at Birmingham, Birmingham, Alabama 35233, United States
| | - Daniel K. Nomura
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
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25
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Counihan JL, Duckering M, Dalvie E, Ku WM, Bateman LA, Fisher KJ, Nomura DK. Chemoproteomic Profiling of Acetanilide Herbicides Reveals Their Role in Inhibiting Fatty Acid Oxidation. ACS Chem Biol 2017; 12:635-642. [PMID: 28094496 DOI: 10.1021/acschembio.6b01001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Acetanilide herbicides are among the most widely used pesticides in the United States, but their toxicological potential and mechanisms remain poorly understood. Here, we have used chemoproteomic platforms to map proteome-wide cysteine reactivity of acetochlor (AC), the most widely used acetanilide herbicide, in vivo in mice. We show that AC directly reacts with >20 protein targets in vivo in mouse liver, including the catalytic cysteines of several thiolase enzymes involved in mitochondrial and peroxisomal fatty acid oxidation. We show that the fatty acids that are not oxidized, due to impaired fatty acid oxidation, are instead diverted into other lipid pathways, resulting in heightened free fatty acids, triglycerides, cholesteryl esters, and other lipid species in the liver. Our findings show the utility of chemoproteomic approaches for identifying novel mechanisms of toxicity associated with environmental chemicals like acetanilide herbicides.
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Affiliation(s)
- Jessica L. Counihan
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Megan Duckering
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Esha Dalvie
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Wan-min Ku
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Leslie A. Bateman
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Karl J. Fisher
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
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26
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Henry HF, Suk WA. Sustainable exposure prevention through innovative detection and remediation technologies from the NIEHS Superfund Research Program. REVIEWS ON ENVIRONMENTAL HEALTH 2017; 32:35-44. [PMID: 28212109 PMCID: PMC7291821 DOI: 10.1515/reveh-2016-0037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 10/27/2016] [Indexed: 05/31/2023]
Abstract
Innovative devices and tools for exposure assessment and remediation play an integral role in preventing exposure to hazardous substances. New solutions for detecting and remediating organic, inorganic, and mixtures of contaminants can improve public health as a means of primary prevention. Using a public health prevention model, detection and remediation technologies contribute to primary prevention as tools to identify areas of high risk (e.g. contamination hotspots), to recognize hazards (bioassay tests), and to prevent exposure through contaminant cleanups. Primary prevention success is ultimately governed by the widespread acceptance of the prevention tool. And, in like fashion, detection and remediation technologies must convey technical and sustainability advantages to be adopted for use. Hence, sustainability - economic, environmental, and societal - drives innovation in detection and remediation technology. The National Institute of Health (NIH) National Institute of Environmental Health Sciences (NIEHS) Superfund Research Program (SRP) is mandated to advance innovative detection, remediation, and toxicity screening technology development through grants to universities and small businesses. SRP recognizes the importance of fast, accurate, robust, and advanced detection technologies that allow for portable real-time, on-site characterization, monitoring, and assessment of contaminant concentration and/or toxicity. Advances in non-targeted screening, biological-based assays, passive sampling devices (PSDs), sophisticated modeling approaches, and precision-based analytical tools are making it easier to quickly identify hazardous "hotspots" and, therefore, prevent exposures. Innovation in sustainable remediation uses a variety of approaches: in situ remediation; harnessing the natural catalytic properties of biological processes (such as bioremediation and phytotechnologies); and application of novel materials science (such as nanotechnology, advanced membranes, new carbon materials, and materials reuse). Collectively, the investment in new technologies shows promise to reduce the amount and toxicity of hazardous substances in the environment. This manuscript highlights SRP funded innovative devices and tools for exposure assessment and remediation of organic, inorganic, and mixtures of contaminants with a particular focus on sustainable technologies.
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27
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Ford B, Bateman LA, Gutierrez-Palominos L, Park R, Nomura DK. Mapping Proteome-wide Targets of Glyphosate in Mice. Cell Chem Biol 2017; 24:133-140. [PMID: 28132892 DOI: 10.1016/j.chembiol.2016.12.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/14/2016] [Accepted: 12/21/2016] [Indexed: 12/30/2022]
Abstract
Glyphosate, the active ingredient in the herbicide Roundup, is one of the most widely used pesticides in agriculture and home garden use. Whether glyphosate causes any mammalian toxicity remains highly controversial. While many studies have associated glyphosate with numerous adverse health effects, the mechanisms underlying glyphosate toxicity in mammals remain poorly understood. Here, we used activity-based protein profiling to map glyphosate targets in mice. We show that glyphosate at high doses can be metabolized in vivo to reactive metabolites such as glyoxylate and react with cysteines across many proteins in mouse liver. We show that glyoxylate inhibits liver fatty acid oxidation enzymes and glyphosate treatment in mice increases the levels of triglycerides and cholesteryl esters, likely resulting from diversion of fatty acids away from oxidation and toward other lipid pathways. Our study highlights the utility of using chemoproteomics to identify novel toxicological mechanisms of environmental chemicals such as glyphosate.
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Affiliation(s)
- Breanna Ford
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Leslie A Bateman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Leilani Gutierrez-Palominos
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Robin Park
- Integrated Proteomics Applications, Inc., 12707 High Bluff Drive Suite 200, San Diego, CA 92130, USA
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA.
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28
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Zhou Y, Li W, Wang M, Zhang X, Zhang H, Tong X, Xiao Y. Competitive profiling of celastrol targets in human cervical cancer HeLa cells via quantitative chemical proteomics. MOLECULAR BIOSYSTEMS 2017; 13:83-91. [DOI: 10.1039/c6mb00691d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We reported the proteome-wide profiling of cellular targets of celastrol in HeLa cellsviacompetitive chemoproteomics approach utilizing a cysteine-targeting activity-based probe.
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Affiliation(s)
- Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Mingli Wang
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Xixi Zhang
- University of Chinese Academy of Sciences
- Beijing 100039
- China
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
| | - Haibing Zhang
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Xiaofeng Tong
- Department of Chemistry
- East China University of Science and Technology
- Shanghai 200001
- China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
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29
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Yao X, Yin N, Faiola F. Stem cell toxicology: a powerful tool to assess pollution effects on human health. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww089] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
AbstractEnvironmental pollution is a global problem; the lack of comprehensive toxicological assessments may lead to increased health risks. To fully understand the health effects of pollution, it is paramount to implement fast, efficient and specific toxicity screening that relies on human models rather than on time-consuming, expensive and often inaccurate tests involving live animals. Human stem cell toxicology represents a valid alternative to traditional toxicity assays because it takes advantage of the ability of stem cells to differentiate into multiple cell types and tissues of the human body. Thus, this branch of toxicology provides a possibility to assess cellular, embryonic, developmental, reproductive and functional toxicity in vitro within a single system highly relevant to human physiology. In this review, we describe the development, performance and future perspectives of stem cell toxicology, with an emphasis on how it can meet the increasing challenges posed by environmental pollution in the modern world.
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Affiliation(s)
- Xinglei Yao
- Stake Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nuoya Yin
- Stake Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Francesco Faiola
- Stake Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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30
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Zaro BW, Whitby LR, Lum KM, Cravatt BF. Metabolically Labile Fumarate Esters Impart Kinetic Selectivity to Irreversible Inhibitors. J Am Chem Soc 2016; 138:15841-15844. [PMID: 27960302 DOI: 10.1021/jacs.6b10589] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Electrophilic small molecules are an important class of chemical probes and drugs that produce biological effects by irreversibly modifying proteins. Examples of electrophilic drugs include covalent kinase inhibitors that are used to treat cancer and the multiple sclerosis drug dimethyl fumarate. Optimized covalent drugs typically inactivate their protein targets rapidly in cells, but ensuing time-dependent, off-target protein modification can erode selectivity and diminish the utility of reactive small molecules as chemical probes and therapeutics. Here, we describe an approach to confer kinetic selectivity to electrophilic drugs. We show that an analogue of the covalent Bruton's tyrosine kinase (BTK) inhibitor Ibrutinib bearing a fumarate ester electrophile is vulnerable to enzymatic metabolism on a time-scale that preserves rapid and sustained BTK inhibition, while thwarting more slowly accumulating off-target reactivity in cell and animal models. These findings demonstrate that metabolically labile electrophilic groups can endow covalent drugs with kinetic selectivity to enable perturbation of proteins and biochemical pathways with greater precision.
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Affiliation(s)
- Balyn W Zaro
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Landon R Whitby
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kenneth M Lum
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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31
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Natsch A, Emter R. Reaction Chemistry to Characterize the Molecular Initiating Event in Skin Sensitization: A Journey to Be Continued. Chem Res Toxicol 2016; 30:315-331. [DOI: 10.1021/acs.chemrestox.6b00365] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andreas Natsch
- Biosciences, Givaudan Schweiz AG, Ueberlandstrasse 138, CH-8600 Duebendorf, Switzerland
| | - Roger Emter
- Biosciences, Givaudan Schweiz AG, Ueberlandstrasse 138, CH-8600 Duebendorf, Switzerland
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32
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Roberts AM, Ward CC, Nomura DK. Activity-based protein profiling for mapping and pharmacologically interrogating proteome-wide ligandable hotspots. Curr Opin Biotechnol 2016; 43:25-33. [PMID: 27568596 DOI: 10.1016/j.copbio.2016.08.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/04/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022]
Abstract
Despite the completion of human genome sequencing efforts nearly 15 years ago that brought with it the promise of genome-based discoveries that would cure human diseases, most protein targets that control human diseases have remained largely untranslated, in-part because they represent difficult protein targets to drug. In addition, many of these protein targets lack screening assays or accessible binding pockets, making the development of small-molecule modulators very challenging. Here, we discuss modern methods for activity-based protein profiling-based chemoproteomic strategies to map 'ligandable' hotspots in proteomes using activity and reactivity-based chemical probes to allow for pharmacological interrogation of these previously difficult targets. We will showcase several recent examples of how these technologies have been used to develop highly selective small-molecule inhibitors against disease-related protein targets.
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Affiliation(s)
- Allison M Roberts
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Carl C Ward
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States.
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33
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Kohnz RA, Roberts LS, DeTomaso D, Bideyan L, Yan P, Bandyopadhyay S, Goga A, Yosef N, Nomura DK. Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity. ACS Chem Biol 2016; 11:2131-9. [PMID: 27380425 PMCID: PMC4994060 DOI: 10.1021/acschembio.6b00433] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Many mechanisms have been proposed
for how heightened aerobic glycolytic
metabolism fuels cancer pathogenicity, but there are still many unexplored
pathways. Here, we have performed metabolomic profiling to map glucose
incorporation into metabolic pathways upon transformation of mammary
epithelial cells by 11 commonly mutated human oncogenes. We show that
transformation of mammary epithelial cells by oncogenic stimuli commonly
shunts glucose-derived carbons into synthesis of sialic acid, a hexosamine
pathway metabolite that is converted to CMP-sialic acid by cytidine
monophosphate N-acetylneuraminic acid synthase (CMAS)
as a precursor to glycoprotein and glycolipid sialylation. We show
that CMAS knockdown leads to elevations in intracellular sialic acid
levels, a depletion of cellular sialylation, and alterations in the
expression of many cancer-relevant genes to impair breast cancer pathogenicity.
Our study reveals the heretofore unrecognized role of sialic acid
metabolism and protein sialylation in regulating the expression of
genes that maintain breast cancer pathogenicity.
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Affiliation(s)
- Rebecca A. Kohnz
- Departments
of Chemistry, Molecular and Cell Biology, and Nutritional Sciences
and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Lindsay S. Roberts
- Departments
of Chemistry, Molecular and Cell Biology, and Nutritional Sciences
and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - David DeTomaso
- Department
of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, United States
| | - Lara Bideyan
- Departments
of Chemistry, Molecular and Cell Biology, and Nutritional Sciences
and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Peter Yan
- Departments
of Chemistry, Molecular and Cell Biology, and Nutritional Sciences
and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Sourav Bandyopadhyay
- Division
of Hematology/Oncology, Department of Cell and Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue HSW616, San Francisco, California 94143, United States
- University of California, San Francisco Helen Diller
Family Comprehensive Cancer Center, Box
0128, San Francisco, California 94143, United States
| | - Andrei Goga
- Division
of Hematology/Oncology, Department of Cell and Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue HSW616, San Francisco, California 94143, United States
- University of California, San Francisco Helen Diller
Family Comprehensive Cancer Center, Box
0128, San Francisco, California 94143, United States
| | - Nir Yosef
- Department
of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Departments
of Chemistry, Molecular and Cell Biology, and Nutritional Sciences
and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
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34
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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: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [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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35
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Mapping proteome-wide interactions of reactive chemicals using chemoproteomic platforms. Curr Opin Chem Biol 2015; 30:68-76. [PMID: 26647369 DOI: 10.1016/j.cbpa.2015.11.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 11/09/2015] [Indexed: 12/11/2022]
Abstract
A large number of pharmaceuticals, endogenous metabolites, and environmental chemicals act through covalent mechanisms with protein targets. Yet, their specific interactions with the proteome still remain poorly defined for most of these reactive chemicals. Deciphering direct protein targets of reactive small-molecules is critical in understanding their biological action, off-target effects, potential toxicological liabilities, and development of safer and more selective agents. Chemoproteomic technologies have arisen as a powerful strategy that enable the assessment of proteome-wide interactions of these irreversible agents directly in complex biological systems. We review here several chemoproteomic strategies that have facilitated our understanding of specific protein interactions of irreversibly-acting pharmaceuticals, endogenous metabolites, and environmental electrophiles to reveal novel pharmacological, biological, and toxicological mechanisms.
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