1
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Coukos JS, Lee CW, Pillai KS, Shah H, Moellering RE. PARK7 Catalyzes Stereospecific Detoxification of Methylglyoxal Consistent with Glyoxalase and Not Deglycase Function. Biochemistry 2023; 62:3126-3133. [PMID: 37884446 PMCID: PMC10634309 DOI: 10.1021/acs.biochem.3c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023]
Abstract
The protein PARK7 (also known as DJ-1) has been implicated in several diseases, with the most notable being Parkinson's disease. While several molecular and cellular roles have been ascribed to DJ-1, there is no real consensus on what its true cellular functions are and how the loss of DJ-1 function may contribute to the pathogenesis of Parkinson's disease. Recent reports have implicated DJ-1 in the detoxification of several reactive metabolites that are produced during glycolytic metabolism, with the most notable being the α-oxoaldehyde species methylglyoxal. While it is generally agreed that DJ-1 is able to metabolize methylglyoxal to lactate, the mechanism by which it does so is hotly debated with potential implications for cellular function. In this work, we provide definitive evidence that recombinant DJ-1 produced in human cells prevents the stable glycation of other proteins through the conversion of methylglyoxal or a related alkynyl dicarbonyl probe to their corresponding α-hydroxy carboxylic acid products. This protective action of DJ-1 does not require a physical interaction with a target protein, providing direct evidence for a glutathione-free glyoxalase and not a deglycase mechanism of methylglyoxal detoxification. Stereospecific liquid chromatography-mass spectrometry (LC-MS) measurements further uncovered the existence of nonenzymatic production of racemic lactate from MGO under physiological buffer conditions, whereas incubation with DJ-1 predominantly produces l-lactate. Collectively, these studies provide direct support for the stereospecific conversion of MGO to l-lactate by DJ-1 in solution with negligible or no contribution of direct protein deglycation.
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Affiliation(s)
- John S. Coukos
- Department
of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, United States
| | - Chris W. Lee
- Department
of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, United States
| | - Kavya S. Pillai
- Department
of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, United States
| | - Hardik Shah
- University
of Chicago Medicine Comprehensive Cancer Center Metabolomics Platform, The University of Chicago, 900 E. 57th Street, Chicago, Illinois 60637, United States
| | - Raymond E. Moellering
- Department
of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, United States
- University
of Chicago Medicine Comprehensive Cancer Center Metabolomics Platform, The University of Chicago, 900 E. 57th Street, Chicago, Illinois 60637, United States
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2
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Stein BD, Ferrarone JR, Gardner EE, Chang JW, Wu D, Hollstein PE, Liang RJ, Yuan M, Chen Q, Coukos JS, Sindelar M, Ngo B, Gross SS, Shaw RJ, Zhang C, Asara JM, Moellering RE, Varmus H, Cantley LC. LKB1-Dependent Regulation of TPI1 Creates a Divergent Metabolic Liability between Human and Mouse Lung Adenocarcinoma. Cancer Discov 2023; 13:1002-1025. [PMID: 36715544 PMCID: PMC10068449 DOI: 10.1158/2159-8290.cd-22-0805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/14/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
KRAS is the most frequently mutated oncogene in human lung adenocarcinomas (hLUAD), and activating mutations frequently co-occur with loss-of-function mutations in TP53 or STK11/LKB1. However, mutation of all three genes is rarely observed in hLUAD, even though engineered comutation is highly aggressive in mouse lung adenocarcinoma (mLUAD). Here, we provide a mechanistic explanation for this difference by uncovering an evolutionary divergence in the regulation of triosephosphate isomerase (TPI1). In hLUAD, TPI1 activity is regulated via phosphorylation at Ser21 by the salt inducible kinases (SIK) in an LKB1-dependent manner, modulating flux between the completion of glycolysis and production of glycerol lipids. In mice, Ser21 of TPI1 is a Cys residue that can be oxidized to alter TPI1 activity without a need for SIKs or LKB1. Our findings suggest this metabolic flexibility is critical in rapidly growing cells with KRAS and TP53 mutations, explaining why the loss of LKB1 creates a liability in these tumors. SIGNIFICANCE Utilizing phosphoproteomics and metabolomics in genetically engineered human cell lines and genetically engineered mouse models (GEMM), we uncover an evolutionary divergence in metabolic regulation within a clinically relevant genotype of human LUAD with therapeutic implications. Our data provide a cautionary example of the limits of GEMMs as tools to study human diseases such as cancers. This article is highlighted in the In This Issue feature, p. 799.
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Affiliation(s)
- Benjamin D. Stein
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - John R. Ferrarone
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Eric E. Gardner
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Jae Won Chang
- Department of Chemistry, University of Chicago, Chicago, Illinois
| | - David Wu
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Pablo E. Hollstein
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Roger J. Liang
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Min Yuan
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medicine, New York, New York
| | - John S. Coukos
- Department of Chemistry, University of Chicago, Chicago, Illinois
| | - Miriam Sindelar
- Department of Pharmacology, Weill Cornell Medicine, New York, New York
| | - Bryan Ngo
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Steven S. Gross
- Department of Pharmacology, Weill Cornell Medicine, New York, New York
| | - Reuben J. Shaw
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Chen Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - John M. Asara
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Harold Varmus
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Lewis C. Cantley
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, New York
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
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3
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Swenson CS, Pillai KS, Carlos AJ, Moellering RE. Spatial Chemoproteomics for Mapping the Active Proteome. Isr J Chem 2023; 63:e202200104. [PMID: 38046285 PMCID: PMC10688764 DOI: 10.1002/ijch.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Indexed: 01/06/2023]
Abstract
Functional regulation of cell signaling through dynamic changes in protein activity state as well as spatial organization represent two dynamic, complex, and conserved phenomena in biology. Seemingly separate areas of -omics method development have focused on building tools that can detect and quantify protein activity states, as well as map sub-cellular and intercellular protein organization. Integration of these efforts, through the development of chemical tools and platforms that enable detection and quantification of protein functional states with spatial resolution provide opportunities to better understand heterogeneity in the proteome within cell organelles, multi-cellular tissues, and whole organisms. This review provides an overview of and considerations for major classes of chemical proteomic probes and technologies that enable protein activity mapping from sub-cellular compartments to live animals.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Kavya Smitha Pillai
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Anthony J Carlos
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
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4
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Coukos JS, Lee CW, Pillai KS, Liu KJ, Moellering RE. Widespread, Reversible Cysteine Modification by Methylglyoxal Regulates Metabolic Enzyme Function. ACS Chem Biol 2023; 18:91-101. [PMID: 36562291 PMCID: PMC9872086 DOI: 10.1021/acschembio.2c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
Methylglyoxal (MGO), a reactive metabolite byproduct of glucose metabolism, is known to form a variety of posttranslational modifications (PTMs) on nucleophilic amino acids. For example, cysteine, the most nucleophilic proteinogenic amino acid, forms reversible hemithioacetal and stable mercaptomethylimidazole adducts with MGO. The high reactivity of cysteine toward MGO and the rate of formation of such modifications provide the opportunity for mechanisms by which proteins and pathways might rapidly sense and respond to alterations in levels of MGO. This indirect measure of alterations in glycolytic flux would thereby allow disparate cellular processes to dynamically respond to changes in nutrient availability and utilization. Here we report the use of quantitative LC-MS/MS-based chemoproteomic profiling approaches with a cysteine-reactive probe to map the proteome-wide landscape of MGO modification of cysteine residues. This approach led to the identification of many sites of potential functional regulation by MGO. We further characterized the role that such modifications have in a catalytic cysteine residue in a key metabolic enzyme and the resulting effects on cellular metabolism.
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Affiliation(s)
- John S. Coukos
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, United States
| | - Chris W. Lee
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, United States
| | - Kavya S. Pillai
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, United States
| | - Kimberly J. Liu
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, United States
| | - Raymond E. Moellering
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, United States
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5
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Nguyen LC, Renner DM, Silva D, Yang D, Parenti N, Medina KM, Nicolaescu V, Gula H, Drayman N, Valdespino A, Mohamed A, Dann C, Wannemo K, Robinson-Mailman L, Gonzalez A, Stock L, Cao M, Qiao Z, Moellering RE, Tay S, Randall G, Beers MF, Rosner MR, Oakes SA, Weiss SR. SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells. bioRxiv 2022:2021.12.30.474519. [PMID: 35821981 PMCID: PMC9275661 DOI: 10.1101/2021.12.30.474519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed over 6 million individuals worldwide and continues to spread in countries where vaccines are not yet widely available, or its citizens are hesitant to become vaccinated. Therefore, it is critical to unravel the molecular mechanisms that allow SARS-CoV-2 and other coronaviruses to infect and overtake the host machinery of human cells. Coronavirus replication triggers endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR), a key host cell pathway widely believed essential for viral replication. We examined the master UPR sensor IRE1α kinase/RNase and its downstream transcription factor effector XBP1s, which is processed through an IRE1α-mediated mRNA splicing event, in human lung-derived cells infected with betacoronaviruses. We found human respiratory coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome coronavirus (MERS-CoV), and murine coronavirus (MHV) all induce ER stress and strongly trigger the kinase and RNase activities of IRE1α as well as XBP1 splicing. In contrast, SARS-CoV-2 only partially activates IRE1α through autophosphorylation, but its RNase activity fails to splice XBP1. Moreover, while IRE1α was dispensable for replication in human cells for all coronaviruses tested, it was required for maximal expression of genes associated with several key cellular functions, including the interferon signaling pathway, during SARS-CoV-2 infection. Our data suggest that SARS-CoV-2 actively inhibits the RNase of autophosphorylated IRE1α, perhaps as a strategy to eliminate detection by the host immune system. IMPORTANCE SARS-CoV-2 is the third lethal respiratory coronavirus after MERS-CoV and SARS-CoV to emerge this century, causing millions of deaths world-wide. Other common coronaviruses such as HCoV-OC43 cause less severe respiratory disease. Thus, it is imperative to understand the similarities and differences among these viruses in how each interacts with host cells. We focused here on the inositol-requiring enzyme 1α (IRE1α) pathway, part of the host unfolded protein response to virus-induced stress. We found that while MERS-CoV and HCoV-OC43 fully activate the IRE1α kinase and RNase activities, SARS-CoV-2 only partially activates IRE1α, promoting its kinase activity but not RNase activity. Based on IRE1α-dependent gene expression changes during infection, we propose that SARS-CoV-2 prevents IRE1α RNase activation as a strategy to limit detection by the host immune system.
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Affiliation(s)
- Long C. Nguyen
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, U.S.A
| | - David M. Renner
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Diane Silva
- Department of Pathology, University of Chicago, Chicago, IL 60637, U.S.A
| | - Dongbo Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, U.S.A
| | - Nicholas Parenti
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kaeri M. Medina
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vlad Nicolaescu
- Department of Microbiology, University of Chicago, Chicago, IL 60637, U.S.A
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Haley Gula
- Department of Microbiology, University of Chicago, Chicago, IL 60637, U.S.A
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Nir Drayman
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Andrea Valdespino
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, U.S.A
| | - Adil Mohamed
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Christopher Dann
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, U.S.A
| | - Kristin Wannemo
- Department of Pathology, University of Chicago, Chicago, IL 60637, U.S.A
| | | | - Alan Gonzalez
- Department of Pathology, University of Chicago, Chicago, IL 60637, U.S.A
| | - Letícia Stock
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, U.S.A
| | - Mengrui Cao
- Department of Pathology, University of Chicago, Chicago, IL 60637, U.S.A
| | - Zeyu Qiao
- Department of Chemistry, University of Chicago, Chicago, IL 60637, U.S.A
| | | | - Savas Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Glenn Randall
- Department of Microbiology, University of Chicago, Chicago, IL 60637, U.S.A
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael F. Beers
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marsha Rich Rosner
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, U.S.A
| | - Scott A. Oakes
- Department of Pathology, University of Chicago, Chicago, IL 60637, U.S.A
| | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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6
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Coukos JS, Moellering RE. Methylglyoxal Forms Diverse Mercaptomethylimidazole Crosslinks with Thiol and Guanidine Pairs in Endogenous Metabolites and Proteins. ACS Chem Biol 2021; 16:2453-2461. [PMID: 34581579 PMCID: PMC8609522 DOI: 10.1021/acschembio.1c00553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methylglyoxal (MGO) is a reactive byproduct formed by several metabolic precursors, the most notable being triosephosphates in glycolysis. While many MGO-mediated adducts have been described, the reactivity and specific biomolecular targets of MGO remain incompletely mapped. Based on our recent discovery that MGO can form stable mercaptomethylimidazole crosslinks between cysteine and arginine (MICA) in proteins, we hypothesized that MGO may participate in myriad reactions with biologically relevant guanidines and thiols in proteins, metabolites, and perhaps other biomolecules. Herein, we performed steady-state and kinetic analyses of MGO reactivity with several model thiols, guanidines, and biguanide drugs to establish the plausible and prevalent adducts formed by MGO in proteins, peptides, and abundant cellular metabolites. We identified several novel, stable MICA metabolites that form in vitro and in cells, as well as a novel intermolecular post-translational MICA modification of surface cysteines in proteins. These data confirm that kinetic trapping of free MGO by thiols occurs rapidly and can decrease formation of more stable imidazolone (MG-H1) arginine adducts. However, reversible hemithioacetal adducts can go on to form stable MICA modifications in an inter- and intramolecular fashion with abundant or proximal guanidines, respectively. Finally, we discovered that intracellular MICA-glutathione metabolites are recognized and exported by the efflux pump MRP1, providing a parallel and perhaps complementary pathway for MGO detoxification working alongside the glyoxalase pathway. These data provide new insights into the plausible reactions involving MGO in cells and tissues, as well as several new molecular species in proteins and metabolites for further study.
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Affiliation(s)
- John S. Coukos
- Department of Chemistry, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Raymond E. Moellering
- Department of Chemistry, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
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7
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Chang JW, Bhuiyan M, Tsai H, Zhang HJ, Li G, Fathi S, McCutcheon DC, Leoni L, Freifelder R, Chen C, Moellering RE. In Vivo Imaging of the Tumor‐Associated Enzyme NCEH1 with a Covalent PET Probe. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jae Won Chang
- Department of Chemistry The University of Chicago 929 E. 57th St. Chicago IL 60637 USA
- Current address: Department of Pharmacology and Chemical Biology, Hematology and Medical Oncology Winship Cancer Institute Emory University 1510 Clifton Rd NE Atlanta GA 30322 USA
| | - Mohammed Bhuiyan
- Department of Radiology The University of Chicago 5735 S. Ellis Ave Chicago IL 60637 USA
| | - Hsiu‐Ming Tsai
- Integrated Small Animal Imaging Research Resource The University of Chicago 5735 S. Ellis Ave Chicago IL 60637 USA
| | - Hannah J. Zhang
- Integrated Small Animal Imaging Research Resource The University of Chicago 5735 S. Ellis Ave Chicago IL 60637 USA
- Department of Radiology The University of Chicago 5735 S. Ellis Ave Chicago IL 60637 USA
| | - Gang Li
- Department of Chemistry The University of Chicago 929 E. 57th St. Chicago IL 60637 USA
| | - Shaghayegh Fathi
- Department of Chemistry The University of Chicago 929 E. 57th St. Chicago IL 60637 USA
| | - David C. McCutcheon
- Department of Chemistry The University of Chicago 929 E. 57th St. Chicago IL 60637 USA
| | - Lara Leoni
- Integrated Small Animal Imaging Research Resource The University of Chicago 5735 S. Ellis Ave Chicago IL 60637 USA
| | - Richard Freifelder
- Department of Radiology The University of Chicago 5735 S. Ellis Ave Chicago IL 60637 USA
| | - Chin‐Tu Chen
- Integrated Small Animal Imaging Research Resource The University of Chicago 5735 S. Ellis Ave Chicago IL 60637 USA
- Department of Radiology The University of Chicago 5735 S. Ellis Ave Chicago IL 60637 USA
| | - Raymond E. Moellering
- Department of Chemistry The University of Chicago 929 E. 57th St. Chicago IL 60637 USA
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8
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Chang JW, Bhuiyan M, Tsai HM, Zhang HJ, Li G, Fathi S, McCutcheon DC, Leoni L, Freifelder R, Chen CT, Moellering RE. In Vivo Imaging of the Tumor-Associated Enzyme NCEH1 with a Covalent PET Probe. Angew Chem Int Ed Engl 2020; 59:15161-15165. [PMID: 32415874 DOI: 10.1002/anie.202004762] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Indexed: 12/14/2022]
Abstract
Herein, we report the development of an 18 F-labeled, activity-based small-molecule probe targeting the cancer-associated serine hydrolase NCEH1. We undertook a focused medicinal chemistry campaign to simultaneously preserve potent and specific NCEH1 labeling in live cells and animals, while permitting facile 18 F radionuclide incorporation required for PET imaging. The resulting molecule, [18 F]JW199, labels active NCEH1 in live cells at nanomolar concentrations and greater than 1000-fold selectivity relative to other serine hydrolases. [18 F]JW199 displays rapid, NCEH1-dependent accumulation in mouse tissues. Finally, we demonstrate that [18 F]JW199 labels aggressive cancer tumor cells in vivo, which uncovered localized NCEH1 activity at the leading edge of triple-negative breast cancer tumors, suggesting roles for NCEH1 in tumor aggressiveness and metastasis.
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Affiliation(s)
- Jae Won Chang
- Department of Chemistry, The University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA.,Current address: Department of Pharmacology and Chemical Biology, Hematology and Medical Oncology, Winship Cancer Institute, Emory University, 1510 Clifton Rd NE, Atlanta, GA, 30322, USA
| | - Mohammed Bhuiyan
- Department of Radiology, The University of Chicago, 5735 S. Ellis Ave, Chicago, IL, 60637, USA
| | - Hsiu-Ming Tsai
- Integrated Small Animal Imaging Research Resource, The University of Chicago, 5735 S. Ellis Ave, Chicago, IL, 60637, USA
| | - Hannah J Zhang
- Integrated Small Animal Imaging Research Resource, The University of Chicago, 5735 S. Ellis Ave, Chicago, IL, 60637, USA.,Department of Radiology, The University of Chicago, 5735 S. Ellis Ave, Chicago, IL, 60637, USA
| | - Gang Li
- Department of Chemistry, The University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
| | - Shaghayegh Fathi
- Department of Chemistry, The University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
| | - David C McCutcheon
- Department of Chemistry, The University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
| | - Lara Leoni
- Integrated Small Animal Imaging Research Resource, The University of Chicago, 5735 S. Ellis Ave, Chicago, IL, 60637, USA
| | - Richard Freifelder
- Department of Radiology, The University of Chicago, 5735 S. Ellis Ave, Chicago, IL, 60637, USA
| | - Chin-Tu Chen
- Integrated Small Animal Imaging Research Resource, The University of Chicago, 5735 S. Ellis Ave, Chicago, IL, 60637, USA.,Department of Radiology, The University of Chicago, 5735 S. Ellis Ave, Chicago, IL, 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, The University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
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9
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Moellering RE. Editorial Overview: Tracking the ties that bind: Emerging technologies to profile biomolecular interactions in native environments. Curr Opin Chem Biol 2020; 54:A1-A4. [PMID: 32245537 DOI: 10.1016/j.cbpa.2020.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Raymond E Moellering
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA; Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA.
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10
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Abstract
In this issue of Cell Chemical Biology, Cook et al. (2019) report a new small-molecule activator that enhances osteogenesis and skeletal regeneration in developmental and adult animal models, respectively. This discovery has therapeutic potential for healing following traumatic bone injury, as well as bone remodeling in response to osteoporosis.
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Affiliation(s)
- Jae Won Chang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA; Institute for Genomics and Systems Biology, University of Chicago, IL 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA; Institute for Genomics and Systems Biology, University of Chicago, IL 60637, USA.
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11
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Huang JX, Coukos JS, Moellering RE. Interaction profiling methods to map protein and pathway targets of bioactive ligands. Curr Opin Chem Biol 2020; 54:76-84. [PMID: 32146330 DOI: 10.1016/j.cbpa.2020.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/17/2020] [Accepted: 02/05/2020] [Indexed: 01/08/2023]
Abstract
Recent advances in -omic profiling technologies have ushered in an era where we no longer want to merely measure the presence or absence of a biomolecule of interest, but instead hope to understand its function and interactions within larger signaling networks. Here, we review several emerging proteomic technologies capable of detecting protein interaction networks in live cells and their integration to draft holistic maps of proteins that respond to diverse stimuli, including bioactive small molecules. Moreover, we provide a conceptual framework to combine so-called 'top-down' and 'bottom-up' interaction profiling methods and ensuing proteomic profiles to directly identify binding targets of small molecule ligands, as well as for unbiased discovery of proteins and pathways that may be directly bound or influenced by those first responders. The integrated, interaction-based profiling methods discussed here have the potential to provide a unique and dynamic view into cellular signaling networks for both basic and translational biological studies.
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Affiliation(s)
- Jun X Huang
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - John S Coukos
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA.
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12
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McCutcheon DC, Lee G, Carlos A, Montgomery JE, Moellering RE. Photoproximity Profiling of Protein-Protein Interactions in Cells. J Am Chem Soc 2019; 142:146-153. [PMID: 31820968 DOI: 10.1021/jacs.9b06528] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We report a novel photoproximity protein interaction (PhotoPPI) profiling method to map protein-protein interactions in vitro and in live cells. This approach utilizes a bioorthogonal, multifunctional chemical probe that can be targeted to a genetically encoded protein of interest (POI) through a modular SNAP-Tag/benzylguanine covalent interaction. A first generation photoproximity probe, PP1, responds to 365 nm light to simultaneously cleave a central nitroveratryl linker and a peripheral diazirine group, resulting in diffusion of a highly reactive carbene nucleophile away from the POI. We demonstrate facile probe loading, and subsequent interaction- and light-dependent proximal labeling of a model protein-protein interaction (PPI) in vitro. Integration of the PhotoPPI workflow with quantitative LC-MS/MS enabled unbiased interaction mapping for the redox regulated sensor protein, KEAP1, for the first time in live cells. We validated known and novel interactions between KEAP1 and the proteins PGAM5 and HK2, among others, under basal cellular conditions. By contrast, comparison of PhotoPPI profiles in cells experiencing metabolic or redox stress confirmed that KEAP1 sheds many basal interactions and becomes associated with known lysosomal trafficking and proteolytic proteins like SQSTM1, CTSD, and LGMN. Together, these data establish PhotoPPI as a method capable of tracking the dynamic subcellular and protein interaction "social network" of a redox-sensitive protein in cells with high temporal resolution.
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13
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Montgomery JE, Donnelly JA, Fanning SW, Speltz TE, Shangguan X, Coukos JS, Greene GL, Moellering RE. Versatile Peptide Macrocyclization with Diels-Alder Cycloadditions. J Am Chem Soc 2019; 141:16374-16381. [PMID: 31523967 DOI: 10.1021/jacs.9b07578] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Macrocyclization can improve bioactive peptide ligands through preorganization of molecular topology, leading to improvement of pharmacologic properties like binding affinity, cell permeability, and metabolic stability. Here we demonstrate that Diels-Alder [4 + 2] cycloadditions can be harnessed for peptide macrocyclization and stabilization within a range of peptide scaffolds and chemical environments. Diels-Alder cyclization of diverse diene-dienophile reactive pairs proceeds rapidly, in high yield and with tunable stereochemical preferences on solid-phase or in aqueous solution. This reaction can be applied alone or in concert with other stabilization chemistries, such as ring-closing olefin metathesis, to stabilize loop, turn, and α-helical secondary structural motifs. NMR and molecular dynamics studies of model loop peptides confirmed preferential formation of endo cycloadduct stereochemistry, imparting significant structural rigidity to the peptide backbone that resulted in augmented protease resistance and increased biological activity of a Diels-Alder cyclized (DAC) RGD peptide. Separately, we demonstrated the stabilization of DAC α-helical peptides derived from the ERα-binding protein SRC2. We solved a 2.25 Å cocrystal structure of one DAC helical peptide bound to ERα, which unequivocally corroborated endo stereochemistry of the resulting Diels-Alder adduct, and confirmed that the unique architecture of stabilizing motifs formed with this chemistry can directly contribute to target binding. These data establish Diels-Alder cyclization as a versatile approach to stabilize diverse protein structural motifs under a range of chemical environments.
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14
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Huang JX, Lee G, Cavanaugh KE, Chang JW, Gardel ML, Moellering RE. High throughput discovery of functional protein modifications by Hotspot Thermal Profiling. Nat Methods 2019; 16:894-901. [PMID: 31384043 PMCID: PMC7238970 DOI: 10.1038/s41592-019-0499-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/21/2019] [Indexed: 12/29/2022]
Abstract
Mass spectrometry has revolutionized the ability to study posttranslationally modified proteoforms from biologic samples, yet we still lack methods to systematically predict, or even prioritize, which modification sites may perturb protein function. Here we describe a proteomic method to detect the effects of site-specific protein phosphorylation on the thermal stability of thousands of native proteins in live cells. This massively parallel biophysical assay unveiled shifts in overall protein stability in response to site-specific phosphorylation sites, as well as trends related to protein function and structure. This method can detect both intrinsic changes to protein structure as well as extrinsic changes to protein-protein, and protein-metabolite interactions resulting from the diminutive introduction of a phosphate onto large proteins. Finally, we show that functional “hotspot” protein modification sites can be discovered and prioritized for study in a high-throughput and unbiased fashion. This approach is applicable to diverse organisms, cell types and posttranslational modifications.
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Affiliation(s)
- Jun X Huang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Gihoon Lee
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Kate E Cavanaugh
- Department of Physics, The University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,James Franck Institute, The University of Chicago, Chicago, IL, USA
| | - Jae W Chang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Margaret L Gardel
- Department of Physics, The University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,James Franck Institute, The University of Chicago, Chicago, IL, USA
| | - Raymond E Moellering
- Department of Chemistry, The University of Chicago, Chicago, IL, USA. .,Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
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15
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Li G, Moellering RE. Abstract 1142: An activity-dependent proximity ligation platform for spatially resolved and multiplexed quantifications of active enzymes in single cells. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Integration of chemical probes into proteomic workflows enables the interrogation of protein activity, rather than abundance. Current methods limit the biological contexts that can be addressed due to sample homogenization, signal-averaging, and bias toward abundant proteins. To expand the application scope of chemical proteomics and explore the cellular heterogeneity on enzyme activities, we developed a new platform that integrates family-wide chemical probes with proximity-dependent oligonucleotide amplification and imaging to quantify enzyme activity in native contexts with high spatial and single cell resolution. Application of this method, activity-dependent proximity ligation (ADPL), to serine hydrolase and cysteine protease enzymes enables quantification of differential enzyme activity resulting from endogenous changes in localization and expression. In a competitive format, small molecule target engagement with endogenous proteins in live cells can be quantified. Retention of sample architecture enables interrogation of complex environments such as cellular co-culture and patient samples. We also successfully applied ADPL in xenograft tissue sample, exhibiting the application prospect in primary patient tissue. Additionally, implementation of barcoded antibody-oligo direct conjugation enabled multiplexed readout of active enzymes within and between enzyme families, providing the possibility of simultaneous biomarker detection. Together, this work supports ADPL should be amenable to diverse and multiplexed protein families to detect active enzymes at scale and resolution out of reach with current methods.
Citation Format: Gang Li, Raymond E. Moellering. An activity-dependent proximity ligation platform for spatially resolved and multiplexed quantifications of active enzymes in single cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1142.
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Affiliation(s)
- Gang Li
- The University of Chicago, Chicago, IL
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16
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Li G, Moellering RE. A Concise, Modular Antibody-Oligonucleotide Conjugation Strategy Based on Disuccinimidyl Ester Activation Chemistry. Chembiochem 2019; 20:1599-1605. [PMID: 30767357 DOI: 10.1002/cbic.201900027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 12/17/2022]
Abstract
The synthesis of antibody-oligonucleotide conjugates has enabled the development of highly sensitive bioassays for specific epitopes in the laboratory and clinic. Most synthetic schemes to generate these hybrid molecules require expensive reagents, significant quantities of input antibody, and multistep purification routes; thus limiting widespread application. Herein a facile and robust conjugation strategy is reported that involves "plug-and-play" antibody conjugation with succinimidyl-functionalized oligonucleotides, which are high yielding and compatible for use directly after buffer exchange. The succinimidyl-linked oligonucleotides are synthesized with 5'-amine-modified oligonucleotides and disuccinimidyl suberate (DSS), both of which are inexpensive and commercially available. Direct incubation of the resulting stable succinimidyl- oligonucleotide conjugates with commercial antibodies yields conjugates ready for use after benchtop buffer exchange. It is demonstrated that the resulting oligonucleotide-antibody and oligonucleotide-streptavidin conjugates retain potent and specific binding in activity-dependent proximity ligation imaging, and proximity ligation-mediated qPCR detection of endogenous proteins in native cellular contexts down to picogram levels of whole proteome. This DSS conjugation strategy should be widely applicable in the synthesis of protein-oligonucleotide conjugates.
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Affiliation(s)
- Gang Li
- Department of Chemistry, University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
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17
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Eckert MA, Coscia F, Chryplewicz A, Chang JW, Hernandez KM, Pan S, Tienda SM, Nahotko DA, Li G, Blaženović I, Lastra RR, Curtis M, Yamada SD, Perets R, McGregor SM, Andrade J, Fiehn O, Moellering RE, Mann M, Lengyel E. Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts. Nature 2019; 569:723-728. [PMID: 31043742 PMCID: PMC6690743 DOI: 10.1038/s41586-019-1173-8] [Citation(s) in RCA: 270] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 03/27/2019] [Indexed: 12/23/2022]
Abstract
High-grade serous carcinoma has a poor prognosis, owing primarily to its early dissemination throughout the abdominal cavity. Genomic and proteomic approaches have provided snapshots of the proteogenomics of ovarian cancer1,2, but a systematic examination of both the tumour and stromal compartments is critical in understanding ovarian cancer metastasis. Here we develop a label-free proteomic workflow to analyse as few as 5,000 formalin-fixed, paraffin-embedded cells microdissected from each compartment. The tumour proteome was stable during progression from in situ lesions to metastatic disease; however, the metastasis-associated stroma was characterized by a highly conserved proteomic signature, prominently including the methyltransferase nicotinamide N-methyltransferase (NNMT) and several of the proteins that it regulates. Stromal NNMT expression was necessary and sufficient for functional aspects of the cancer-associated fibroblast (CAF) phenotype, including the expression of CAF markers and the secretion of cytokines and oncogenic extracellular matrix. Stromal NNMT expression supported ovarian cancer migration, proliferation and in vivo growth and metastasis. Expression of NNMT in CAFs led to depletion of S-adenosyl methionine and reduction in histone methylation associated with widespread gene expression changes in the tumour stroma. This work supports the use of ultra-low-input proteomics to identify candidate drivers of disease phenotypes. NNMT is a central, metabolic regulator of CAF differentiation and cancer progression in the stroma that may be therapeutically targeted.
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Affiliation(s)
- Mark A Eckert
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Fabian Coscia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Agnieszka Chryplewicz
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Jae Won Chang
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Kyle M Hernandez
- Center for Research Informatics, University of Chicago, Chicago, IL, USA
| | - Shawn Pan
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Samantha M Tienda
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Dominik A Nahotko
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Gang Li
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Ivana Blaženović
- West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA, USA
| | - Ricardo R Lastra
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Marion Curtis
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - S Diane Yamada
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Ruth Perets
- Division of Oncology, Clinical Research Institute at Rambam, Rambam Health Care Campus, Haifa, Israel
| | | | - Jorge Andrade
- Center for Research Informatics, University of Chicago, Chicago, IL, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA, USA
| | | | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA.
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18
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Eckert MA, Coscia F, Chryplewicz AA, Chang JW, Hernandez KM, Pan S, Tienda SM, Nahotko DA, Li G, Blaženović I, Lastra RR, Curtis M, Yamada SD, Perets R, McGregor S, Andrade J, Fiehn O, Moellering RE, Mann M, Lengyel E. Metabolic reprogramming of the stromal epigenome in ovarian cancer metastasis. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.lb240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mark A Eckert
- Obstetrics & Gynecology/Section of Gynecologic OncologyUniversity of ChicagoChicagoIL
| | - Fabian Coscia
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | | | | | | | - Shawn Pan
- Obstetrics & Gynecology/Section of Gynecologic OncologyUniversity of ChicagoChicagoIL
| | - Samantha M Tienda
- Obstetrics & Gynecology/Section of Gynecologic OncologyUniversity of ChicagoChicagoIL
| | - Dominik A Nahotko
- Obstetrics & Gynecology/Section of Gynecologic OncologyUniversity of ChicagoChicagoIL
| | - Gang Li
- ChemistryUniversity of ChicagoChicagoIL
| | - Ivana Blaženović
- West Coast Metabolomics Center, University of California, DavisDavisCA
| | | | - Marion Curtis
- Obstetrics & Gynecology/Section of Gynecologic OncologyUniversity of ChicagoChicagoIL
| | - S. Diane Yamada
- Obstetrics & Gynecology/Section of Gynecologic OncologyUniversity of ChicagoChicagoIL
| | - Ruth Perets
- Division of OncologyRambam Health Care CampusHaifaIsrael
| | | | - Jorge Andrade
- Center for Research InformaticsUniversity of ChicagoChicagoIL
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, DavisDavisCA
| | | | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Ernst Lengyel
- Obstetrics & Gynecology/Section of Gynecologic OncologyUniversity of ChicagoChicagoIL
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19
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Chang JW, Montgomery JE, Lee G, Moellering RE. Chemoproteomic Profiling of Phosphoaspartate Modifications in Prokaryotes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jae Won Chang
- Department of Chemistry, Institute for Genomics and Systems Biology; The University of Chicago; 929 E. 57th Street Chicago IL 60637 USA
| | - Jeffrey E. Montgomery
- Department of Chemistry, Institute for Genomics and Systems Biology; The University of Chicago; 929 E. 57th Street Chicago IL 60637 USA
| | - Gihoon Lee
- Department of Chemistry, Institute for Genomics and Systems Biology; The University of Chicago; 929 E. 57th Street Chicago IL 60637 USA
| | - Raymond E. Moellering
- Department of Chemistry, Institute for Genomics and Systems Biology; The University of Chicago; 929 E. 57th Street Chicago IL 60637 USA
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20
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Chang JW, Montgomery JE, Lee G, Moellering RE. Chemoproteomic Profiling of Phosphoaspartate Modifications in Prokaryotes. Angew Chem Int Ed Engl 2018; 57:15712-15716. [PMID: 30231186 DOI: 10.1002/anie.201809059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/17/2018] [Indexed: 11/11/2022]
Abstract
Phosphorylation at aspartic acid residues represents an abundant and critical post-translational modification (PTM) in prokaryotes. In contrast to most characterized PTMs, such as phosphorylation at serine or threonine, the phosphoaspartate moiety is intrinsically labile, and therefore incompatible with common proteomic profiling methods. Herein, we report a nucleophilic, desthiobiotin-containing hydroxylamine (DBHA) chemical probe that covalently labels modified aspartic acid residues in native proteomes. DBHA treatment coupled with LC-MS/MS analysis enabled detection of known phosphoaspartate modifications, as well as novel aspartic acid sites in the E. coli proteome. Coupled with isotopic labelling, DBHA-dependent proteomic profiling also permitted global quantification of changes in endogenous protein modification status, as demonstrated with the detection of increased E. coli OmpR phosphorylation, but not abundance, in response to changes in osmolarity.
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Affiliation(s)
- Jae Won Chang
- Department of Chemistry, Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Jeffrey E Montgomery
- Department of Chemistry, Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Gihoon Lee
- Department of Chemistry, Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, Institute for Genomics and Systems Biology, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
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21
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Bollong MJ, Lee G, Coukos JS, Yun H, Zambaldo C, Chang JW, Chin EN, Ahmad I, Chatterjee AK, Lairson LL, Schultz PG, Moellering RE. A metabolite-derived protein modification integrates glycolysis with KEAP1-NRF2 signalling. Nature 2018; 562:600-604. [PMID: 30323285 PMCID: PMC6444936 DOI: 10.1038/s41586-018-0622-0] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 08/21/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Michael J Bollong
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Gihoon Lee
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - John S Coukos
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Hwayoung Yun
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.,College of Pharmacy, Pusan National University, Busan, South Korea
| | - Claudio Zambaldo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Jae Won Chang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Emily N Chin
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Insha Ahmad
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Arnab K Chatterjee
- California Institute for Biomedical Research (Calibr), La Jolla, CA, USA
| | - Luke L Lairson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,California Institute for Biomedical Research (Calibr), La Jolla, CA, USA.
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,California Institute for Biomedical Research (Calibr), La Jolla, CA, USA.
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
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22
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Yang H, Swartz AM, Park HJ, Srivastava P, Ellis-Guardiola K, Upp DM, Lee G, Belsare K, Gu Y, Zhang C, Moellering RE, Lewis JC. Evolving artificial metalloenzymes via random mutagenesis. Nat Chem 2018; 10:318-324. [PMID: 29461523 PMCID: PMC5891097 DOI: 10.1038/nchem.2927] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 11/30/2017] [Indexed: 01/18/2023]
Abstract
Random mutagenesis has the potential to optimize the efficiency and selectivity of protein catalysts without requiring detailed knowledge of protein structure; however, introducing synthetic metal cofactors complicates the expression and screening of enzyme libraries, and activity arising from free cofactor must be eliminated. Here we report an efficient platform to create and screen libraries of artificial metalloenzymes (ArMs) via random mutagenesis, which we use to evolve highly selective dirhodium cyclopropanases. Error-prone PCR and combinatorial codon mutagenesis enabled multiplexed analysis of random mutations, including at sites distal to the putative ArM active site that are difficult to identify using targeted mutagenesis approaches. Variants that exhibited significantly improved selectivity for each of the cyclopropane product enantiomers were identified, and higher activity than previously reported ArM cyclopropanases obtained via targeted mutagenesis was also observed. This improved selectivity carried over to other dirhodium-catalysed transformations, including N-H, S-H and Si-H insertion, demonstrating that ArMs evolved for one reaction can serve as starting points to evolve catalysts for others.
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Affiliation(s)
- Hao Yang
- Merck Research Laboratories, 126 E. Lincoln Avenue, Rahway, New Jersey 07065, USA
| | - Alan M Swartz
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - Hyun June Park
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | | | - Ken Ellis-Guardiola
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - David M Upp
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - Gihoon Lee
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Ketaki Belsare
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - Yifan Gu
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
| | - Chen Zhang
- Provivi, Inc., 1701 Colorado Avenue, Santa Monica, California 90404, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, USA
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23
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KleinJan A, Tindemans I, Montgomery JE, Lukkes M, de Bruijn MJW, van Nimwegen M, Bergen I, Moellering RE, Hoogsteden HC, Boon L, Amsen D, Hendriks RW. The Notch pathway inhibitor stapled α-helical peptide derived from mastermind-like 1 (SAHM1) abrogates the hallmarks of allergic asthma. J Allergy Clin Immunol 2017; 142:76-85.e8. [PMID: 29111218 DOI: 10.1016/j.jaci.2017.08.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 07/12/2017] [Accepted: 08/24/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND The Notch signaling pathway has been implicated in the pathogenesis of allergic airway inflammation. Targeting the active Notch transactivation complex by using the cell-permeable, hydrocarbon-stapled synthetic peptide stapled α-helical peptide derived from mastermind-like 1 (SAHM1) resulted in genome-wide suppression of Notch-activated genes in leukemic cells and other models. However, the efficacy of SAHM1 in allergic asthma models has remained unexplored. OBJECTIVE We aimed to investigate the therapeutic efficacy of SAHM1 in a house dust mite (HDM)-driven asthma model. METHODS Topical therapeutic intervention with SAHM1 or a control peptide was performed during sensitization, challenge, or both with HDM in mice. Airway inflammation was assessed by using multicolor flow cytometry, and bronchial hyperreactivity was studied. Additionally, SAHM1 therapy was investigated in mice with established allergic airway inflammation and in a model in which we neutralized IFN-γ during HDM challenge to support the TH2 response and exacerbate asthma. RESULTS SAHM1 treatment during the challenge phase led to a marked reduction of eosinophil and T cell numbers in bronchoalveolar lavage fluid compared with those in diluent-treated or control peptide-treated mice. Likewise, T-cell cytokine content and bronchial hyperreactivity were reduced. SAHM1 treatment dampened TH2 inflammation during ongoing HDM challenge and enhanced recovery after established asthma. Additionally, in the presence of anti-IFN-γ antibodies, SAHM1 downregulated expression of the key TH2 transcription factor GATA3 and intracellular IL-4 in bronchoalveolar lavage fluid T cells, but expression of the TH17 transcription factor retinoic acid-related orphan receptor γt or intracellular IL-17 was not affected. SAHM1 therapy also reduced serum IgE levels. CONCLUSIONS Therapeutic intervention of Notch signaling by SAHM1 inhibits allergic airway inflammation in mice and is therefore an interesting new topical treatment opportunity in asthmatic patients.
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Affiliation(s)
- Alex KleinJan
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands.
| | - Irma Tindemans
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Jeffrey E Montgomery
- Department of Chemistry, University of Chicago, Chicago, Ill; Institute for Genomics and Systems Biology, University of Chicago, Chicago, Ill
| | - Melanie Lukkes
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | | | - Menno van Nimwegen
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Ingrid Bergen
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, Chicago, Ill; Institute for Genomics and Systems Biology, University of Chicago, Chicago, Ill
| | - Henk C Hoogsteden
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Louis Boon
- Epirus Biopharmaceuticals Netherlands, Utrecht, The Netherlands
| | | | - R W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
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Abstract
Metabolomic profiling studies aim to provide a comprehensive, quantitative, and dynamic portrait of the endogenous metabolites in a biological system. While contemporary technologies permit routine profiling of many metabolites, intrinsically labile metabolites are often improperly measured or omitted from studies due to unwanted chemical transformations that occur during sample preparation or mass spectrometric analysis. The primary glycolytic metabolite 1,3-bisphosphoglyceric acid (1,3-BPG) typifies this class of metabolites, and, despite its central position in metabolism, has largely eluded analysis in profiling studies. Here we take advantage of the reactive acylphosphate group in 1,3-BPG to chemically trap the metabolite with hydroxylamine during metabolite isolation, enabling quantitative analysis by targeted LC-MS/MS. This approach is compatible with complex cellular metabolome, permits specific detection of the reactive (1,3-) instead of nonreactive (2,3-) BPG isomer, and has enabled direct analysis of dynamic 1,3-BPG levels resulting from perturbations to glucose processing. These studies confirmed that standard metabolomic methods misrepresent cellular 1,3-BPG levels in response to altered glucose metabolism and underscore the potential for chemical trapping to be used for other classes of reactive metabolites.
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Affiliation(s)
- Jae Won Chang
- Department of Chemistry and ‡Institute for Genomics and Systems Biology, University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Gihoon Lee
- Department of Chemistry and ‡Institute for Genomics and Systems Biology, University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - John S Coukos
- Department of Chemistry and ‡Institute for Genomics and Systems Biology, University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Raymond E Moellering
- Department of Chemistry and ‡Institute for Genomics and Systems Biology, University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
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25
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Chu Q, Moellering RE, Hilinski GJ, Kim YW, Grossmann TN, Yeh JTH, Verdine GL. Towards understanding cell penetration by stapled peptides. Med Chem Commun 2015. [DOI: 10.1039/c4md00131a] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A systematic study on cell penetration by stapled peptides.
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Affiliation(s)
- Qian Chu
- Department of Stem Cell & Regenerative Biology
- Harvard University
- Cambridge
- USA
- Chemistry & Chemical Biology
| | - Raymond E. Moellering
- Department of Stem Cell & Regenerative Biology
- Harvard University
- Cambridge
- USA
- Chemistry & Chemical Biology
| | - Gerard J. Hilinski
- Department of Stem Cell & Regenerative Biology
- Harvard University
- Cambridge
- USA
- Chemistry & Chemical Biology
| | - Young-Woo Kim
- Department of Stem Cell & Regenerative Biology
- Harvard University
- Cambridge
- USA
- Chemistry & Chemical Biology
| | - Tom N. Grossmann
- Department of Stem Cell & Regenerative Biology
- Harvard University
- Cambridge
- USA
- Chemistry & Chemical Biology
| | - Johannes T.-H. Yeh
- Department of Stem Cell & Regenerative Biology
- Harvard University
- Cambridge
- USA
- Chemistry & Chemical Biology
| | - Gregory L. Verdine
- Department of Stem Cell & Regenerative Biology
- Harvard University
- Cambridge
- USA
- Chemistry & Chemical Biology
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26
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Abstract
The posttranslational modification of proteins and their regulation by metabolites represent conserved mechanisms in biology. At the confluence of these two processes, we report that the primary glycolytic intermediate 1,3-bisphosphoglycerate (1,3-BPG) reacts with select lysine residues in proteins to form 3-phosphoglyceryl-lysine (pgK). This reaction, which does not require enzyme catalysis, but rather exploits the electrophilicity of 1,3-BPG, was found by proteomic profiling to be enriched on diverse classes of proteins and prominently in or around the active sites of glycolytic enzymes. pgK modifications inhibit glycolytic enzymes and, in cells exposed to high glucose, accumulate on these enzymes to create a potential feedback mechanism that contributes to the buildup and redirection of glycolytic intermediates to alternate biosynthetic pathways.
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Affiliation(s)
- Raymond E Moellering
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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27
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Moellering RE, Cravatt BF. How chemoproteomics can enable drug discovery and development. ACTA ACUST UNITED AC 2012; 19:11-22. [PMID: 22284350 DOI: 10.1016/j.chembiol.2012.01.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 12/29/2011] [Accepted: 01/03/2012] [Indexed: 12/15/2022]
Abstract
Creating first-in-class medications to treat human disease is an extremely challenging endeavor. While genome sequencing and genetics are making direct connections between mutations and human disorders at an unprecedented rate, matching molecular targets with a suitable therapeutic indication must ultimately be achieved by pharmacology. Here, we discuss how the integration of chemical proteomic platforms (such as activity-based protein profiling) into the earliest stages of the drug discovery process has the potential to greatly expand the scope of proteins that can be pharmacologically evaluated in living systems, and, through doing so, promote the identification and prioritization of new therapeutic targets.
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Affiliation(s)
- Raymond E Moellering
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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28
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Chang JW, Moellering RE, Cravatt BF. An activity-based imaging probe for the integral membrane hydrolase KIAA1363. Angew Chem Int Ed Engl 2011; 51:966-70. [PMID: 22162147 DOI: 10.1002/anie.201107236] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Jae Won Chang
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Moellering RE, Cornejo M, Davis TN, Bianco CD, Aster JC, Blacklow SC, Kung AL, Gilliland DG, Verdine GL, Bradner JE. Erratum: Direct inhibition of the NOTCH transcription factor complex. Nature 2010. [DOI: 10.1038/nature08660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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