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Gao Y, Ma M, Li W, Lei X. Chemoproteomics, A Broad Avenue to Target Deconvolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305608. [PMID: 38095542 PMCID: PMC10885659 DOI: 10.1002/advs.202305608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/29/2023] [Indexed: 12/22/2023]
Abstract
As a vital project of forward chemical genetic research, target deconvolution aims to identify the molecular targets of an active hit compound. Chemoproteomics, either with chemical probe-facilitated target enrichment or probe-free, provides a straightforward and effective approach to profile the target landscape and unravel the mechanisms of action. Canonical methods rely on chemical probes to enable target engagement, enrichment, and identification, whereas click chemistry and photoaffinity labeling techniques improve the efficiency, sensitivity, and spatial accuracy of target recognition. In comparison, recently developed probe-free methods detect protein-ligand interactions without the need to modify the ligand molecule. This review provides a comprehensive overview of different approaches and recent advancements for target identification and highlights the significance of chemoproteomics in investigating biological processes and advancing drug discovery processes.
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Affiliation(s)
- Yihui Gao
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Mingzhe Ma
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Wenyang Li
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
- Institute for Cancer ResearchShenzhen Bay LaboratoryShenzhenChina
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2
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Forrest I, Parker CG. Proteome-Wide Fragment-Based Ligand and Target Discovery. Isr J Chem 2023; 63:e202200098. [PMID: 38213795 PMCID: PMC10783656 DOI: 10.1002/ijch.202200098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/10/2023]
Abstract
Chemical probes are invaluable tools to investigate biological processes and can serve as lead molecules for the development of new therapies. However, despite their utility, only a fraction of human proteins have selective chemical probes, and more generally, our knowledge of the "chemically-tractable" proteome is limited, leaving many potential therapeutic targets unexploited. To help address these challenges, powerful chemical proteomic approaches have recently been developed to globally survey the ability of proteins to bind small molecules (i. e., ligandability) directly in native systems. In this review, we discuss the utility of such approaches, with a focus on the integration of chemoproteomic methods with fragment-based ligand discovery (FBLD), to facilitate the broad mapping of the ligandable proteome while also providing starting points for progression into lead chemical probes.
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Affiliation(s)
- Ines Forrest
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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3
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Faucher FF, Abegg D, Ipock P, Adibekian A, Lovell S, Bogyo M. Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows. Isr J Chem 2023. [DOI: 10.1002/ijch.202300020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
| | - Daniel Abegg
- Department of Chemistry University of Illinois Chicago Chicago, Illinois 60607 USA
| | - Phillip Ipock
- Department of Chemistry Stanford University Stanford 94305 CA
| | - Alexander Adibekian
- Department of Chemistry University of Illinois Chicago Chicago, Illinois 60607 USA
| | - Scott Lovell
- Department of Life Sciences University of Bath Bath BA2 7AX U.K
- Department of Pathology Stanford University School of Medicine Stanford 94305 CA
| | - Matthew Bogyo
- Department of Pathology Stanford University School of Medicine Stanford 94305 CA
- Department of Chemical and Systems Biology Stanford University School of Medicine Stanford 94305 CA
- Department of Microbiology and Immunology Stanford University School of Medicine Stanford 94305 CA
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4
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Hang HC. Benjamin F. Cravatt III – Chemical Proteomics Trailblazer. Isr J Chem 2023. [DOI: 10.1002/ijch.202200066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Howard C. Hang
- Department of Immunology and Microbiology, Scripps Research La Jolla CA 92037
- Department of Chemistry, Scripps Research La Jolla CA 92037
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5
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Firdous P, Hassan T, Farooq S, Nissar K. Applications of proteomics in cancer diagnosis. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00014-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Activity-Based Protein Profiling of Human and Plasmodium Serine Hydrolases and Interrogation of Potential Antimalarial Targets. iScience 2022; 25:104996. [PMID: 36105595 PMCID: PMC9464883 DOI: 10.1016/j.isci.2022.104996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/14/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
Malaria remains a global health issue requiring the identification of novel therapeutic targets to combat drug resistance. Metabolic serine hydrolases are druggable enzymes playing essential roles in lipid metabolism. However, very few have been investigated in malaria-causing parasites. Here, we used fluorophosphonate broad-spectrum activity-based probes and quantitative chemical proteomics to annotate and profile the activity of more than half of predicted serine hydrolases in P. falciparum across the erythrocytic cycle. Using conditional genetics, we demonstrate that the activities of four serine hydrolases, previously annotated as essential (or important) in genetic screens, are actually dispensable for parasite replication. Of importance, we also identified eight human serine hydrolases that are specifically activated at different developmental stages. Chemical inhibition of two of them blocks parasite replication. This strongly suggests that parasites co-opt the activity of host enzymes and that this opens a new drug development strategy against which the parasites are less likely to develop resistance. P. falciparum has 48 predicted metabolic SHs. Many react with the ABP, FP-N3 The activity of 25 PfSHs and 8 HsSHs was profiled throughout the asexual life cycle Catalytic mutants of 4 PfSHs (formerly held essential) had no parasite growth effect Selective inhibitors for 2 HsSHs (APEH and LPLA2) affected parasite growth
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Patel R, Santoro A, Hofer P, Tan D, Oberer M, Nelson AT, Konduri S, Siegel D, Zechner R, Saghatelian A, Kahn BB. ATGL is a biosynthetic enzyme for fatty acid esters of hydroxy fatty acids. Nature 2022; 606:968-975. [PMID: 35676490 PMCID: PMC9242854 DOI: 10.1038/s41586-022-04787-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
Branched fatty acid (FA) esters of hydroxy FAs (HFAs; FAHFAs) are recently discovered lipids that are conserved from yeast to mammals1,2. A subfamily, palmitic acid esters of hydroxy stearic acids (PAHSAs), are anti-inflammatory and anti-diabetic1,3. Humans and mice with insulin resistance have lower PAHSA levels in subcutaneous adipose tissue and serum1. PAHSA administration improves glucose tolerance and insulin sensitivity and reduces inflammation in obesity, diabetes and immune-mediated diseases1,4-7. The enzyme(s) responsible for FAHFA biosynthesis in vivo remains unknown. Here we identified adipose triglyceride lipase (ATGL, also known as patatin-like phospholipase domain containing 2 (PNPLA2)) as a candidate biosynthetic enzyme for FAHFAs using chemical biology and proteomics. We discovered that recombinant ATGL uses a transacylation reaction that esterifies an HFA with a FA from triglyceride (TG) or diglyceride to produce FAHFAs. Overexpression of wild-type, but not catalytically dead, ATGL increases FAHFA biosynthesis. Chemical inhibition of ATGL or genetic deletion of Atgl inhibits FAHFA biosynthesis and reduces the levels of FAHFA and FAHFA-TG. Levels of endogenous and nascent FAHFAs and FAHFA-TGs are 80-90 per cent lower in adipose tissue of mice in which Atgl is knocked out specifically in the adipose tissue. Increasing TG levels by upregulating diacylglycerol acyltransferase (DGAT) activity promotes FAHFA biosynthesis, and decreasing DGAT activity inhibits it, reinforcing TGs as FAHFA precursors. ATGL biosynthetic transacylase activity is present in human adipose tissue underscoring its potential clinical relevance. In summary, we discovered the first, to our knowledge, biosynthetic enzyme that catalyses the formation of the FAHFA ester bond in mammals. Whereas ATGL lipase activity is well known, our data establish a paradigm shift demonstrating that ATGL transacylase activity is biologically important.
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Affiliation(s)
- Rucha Patel
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Anna Santoro
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Peter Hofer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Dan Tan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Monika Oberer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Andrew T Nelson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, USA
| | - Srihari Konduri
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, USA
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
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8
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Keller LJ, Lakemeyer M, Bogyo M. Integration of bioinformatic and chemoproteomic tools for the study of enzyme conservation in closely related bacterial species. Methods Enzymol 2022; 664:1-22. [PMID: 35331369 DOI: 10.1016/bs.mie.2021.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Activity-based protein profiling (ABPP) is a commonly utilized technique to globally characterize the endogenous activity of multiple enzymes within a related family. While it has been used extensively to identify enzymes that are differentially active across various mammalian tissues, recent efforts have expanded this technique to studying bacteria. As ABPP is applied to diverse sets of bacterial strains found in microbial communities, there is also an increasing need for robust tools for assessing the conservation of enzymes across closely related bacterial species and strains. In this chapter, we detail the integration of gel-based ABPP with basic bioinformatic tools to enable the analysis of enzyme activity, distribution, and homology. We use as an example the family of serine hydrolases identified in the skin commensal bacterium Staphylococcus epidermidis.
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Affiliation(s)
- Laura J Keller
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, United States
| | - Markus Lakemeyer
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Matthew Bogyo
- Department of Pathology, Stanford University, Stanford, CA, United States; Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States.
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9
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Tang S, Beattie AT, Kafkova L, Petris G, Huguenin-Dezot N, Fiedler M, Freeman M, Chin JW. Mechanism-based traps enable protease and hydrolase substrate discovery. Nature 2022; 602:701-707. [PMID: 35173328 PMCID: PMC8866121 DOI: 10.1038/s41586-022-04414-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/07/2022] [Indexed: 12/28/2022]
Abstract
Hydrolase enzymes, including proteases, are encoded by 2-3% of the genes in the human genome and 14% of these enzymes are active drug targets1. However, the activities and substrate specificities of many proteases-especially those embedded in membranes-and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond2; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs. 3,4). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref. 5) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes.
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Affiliation(s)
- Shan Tang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Adam T Beattie
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Lucie Kafkova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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10
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Phospholipase Cγ2 regulates endocannabinoid and eicosanoid networks in innate immune cells. Proc Natl Acad Sci U S A 2021; 118:2112971118. [PMID: 34607960 DOI: 10.1073/pnas.2112971118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Human genetic studies have pointed to a prominent role for innate immunity and lipid pathways in immunological and neurodegenerative disorders. Our understanding of the composition and function of immunomodulatory lipid networks in innate immune cells, however, remains incomplete. Here, we show that phospholipase Cγ2 (PLCγ2 or PLCG2)-mutations in which are associated with autoinflammatory disorders and Alzheimer's disease-serves as a principal source of diacylglycerol (DAG) pools that are converted into a cascade of bioactive endocannabinoid and eicosanoid lipids by DAG lipase (DAGL) and monoacylglycerol lipase (MGLL) enzymes in innate immune cells. We show that this lipid network is tonically stimulated by disease-relevant human mutations in PLCγ2, as well as Fc receptor activation in primary human and mouse macrophages. Genetic disruption of PLCγ2 in mouse microglia suppressed DAGL/MGLL-mediated endocannabinoid-eicosanoid cross-talk and also caused widespread transcriptional and proteomic changes, including the reorganization of immune-relevant lipid pathways reflected in reductions in DAGLB and elevations in PLA2G4A. Despite these changes, Plcg2 -/- mice showed generally normal proinflammatory cytokine and chemokine responses to lipopolysaccharide treatment, instead displaying a more restricted deficit in microglial activation that included impairments in prostaglandin production and CD68 expression. Our findings enhance the understanding of PLCγ2 function in innate immune cells, delineating a role in cross-talk with endocannabinoid/eicosanoid pathways and modulation of subsets of cellular responses to inflammatory stimuli.
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11
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Kumar K, Mhetre A, Ratnaparkhi GS, Kamat SS. A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster. Biochemistry 2021; 60:1312-1324. [PMID: 33827210 PMCID: PMC7610703 DOI: 10.1021/acs.biochem.1c00171] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The serine hydrolase (SH) superfamily is, perhaps, one of the largest functional enzyme classes in all forms of life and consists of proteases, peptidases, lipases, and carboxylesterases as representative members. Consistent with the name of this superfamily, all members, without any exception to date, use a nucleophilic serine residue in the enzyme active site to perform hydrolytic-type reactions via a two-step ping-pong mechanism involving a covalent enzyme intermediate. Given the highly conserved catalytic mechanism, this superfamily has served as a classical prototype in the development of several platforms of chemical proteomics techniques, activity-based protein profiling (ABPP), to globally interrogate the functions of its different members in various native, yet complex, biological settings. While ABPP-based proteome-wide activity atlases for SH activities are available in numerous organisms, including humans, to the best of our knowledge, such an analysis for this superfamily is lacking in any insect model. To address this, we initially report a bioinformatics analysis toward the identification and categorization of nonredundant SHs in Drosophila melanogaster. Following up on this in silico analysis, leveraging discovery chemoproteomics, we identify and globally map the full complement of SH activities during various developmental stages and in different adult tissues of Drosophila. Finally, as a proof of concept of the utility of this activity atlas, we highlight sexual dimorphism in SH activities across different tissues in adult D. melanogaster, and we propose new research directions, resources, and tools that this study can provide to the fly community.
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Affiliation(s)
- Kundan Kumar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India 411008
| | - Amol Mhetre
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India 411008
| | - Girish S. Ratnaparkhi
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India 411008
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India 411008
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Szafran BN, Borazjani A, Seay CN, Carr RL, Lehner R, Kaplan BLF, Ross MK. Effects of Chlorpyrifos on Serine Hydrolase Activities, Lipid Mediators, and Immune Responses in Lungs of Neonatal and Adult Mice. Chem Res Toxicol 2021; 34:1556-1571. [PMID: 33900070 DOI: 10.1021/acs.chemrestox.0c00488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chlorpyrifos (CPF) is an organophosphate (OP) pesticide that causes acute toxicity by inhibiting acetylcholinesterase (AChE) in the nervous system. However, endocannabinoid (eCB) metabolizing enzymes in brain of neonatal rats are more sensitive than AChE to inhibition by CPF, leading to increased levels of eCBs. Because eCBs are immunomodulatory molecules, we investigated the association between eCB metabolism, lipid mediators, and immune function in adult and neonatal mice exposed to CPF. We focused on lung effects because epidemiologic studies have linked pesticide exposures to respiratory diseases. CPF was hypothesized to disrupt lung eCB metabolism and alter lung immune responses to lipopolysaccharide (LPS), and these effects would be more pronounced in neonatal mice due to an immature immune system. We first assessed the biochemical effects of CPF in adult mice (≥8 weeks old) and neonatal mice after administering CPF (2.5 mg/kg, oral) or vehicle for 7 days. Tissues were harvested 4 h after the last CPF treatment and lung microsomes from both age groups demonstrated CPF-dependent inhibition of carboxylesterases (Ces), a family of xenobiotic and lipid metabolizing enzymes, whereas AChE activity was inhibited in adult lungs only. Activity-based protein profiling (ABPP)-mass spectrometry of lung microsomes identified 31 and 32 individual serine hydrolases in neonatal lung and adult lung, respectively. Of these, Ces1c/Ces1d/Ces1b isoforms were partially inactivated by CPF in neonatal lung, whereas Ces1c/Ces1b and Ces1c/BChE were partially inactivated in adult female and male lungs, respectively, suggesting age- and sex-related differences in their sensitivity to CPF. Monoacylglycerol lipase (MAGL) and fatty acid amide hydrolase (FAAH) activities in lung were unaffected by CPF. When LPS (1.25 mg/kg, i.p.) was administered following the 7-day CPF dosing period, little to no differences in lung immune responses (cytokines and immunophenotyping) were noted between the CPF and vehicle groups. However, a CPF-dependent increase in the amounts of dendritic cells and certain lipid mediators in female lung following LPS challenge was observed. Experiments in neonatal and adult Ces1d-/- mice yielded similar results as wild type mice (WT) following CPF treatment, except that CPF augmented LPS-induced Tnfa mRNA in adult Ces1d-/- mouse lungs. This effect was associated with decreased expression of Ces1c mRNA in Ces1d-/- mice versus WT mice in the setting of LPS exposure. We conclude that CPF exposure inactivates several Ces isoforms in mouse lung and, during an inflammatory response, increases certain lipid mediators in a female-dependent manner. However, it did not cause widespread altered lung immune effects in response to an LPS challenge.
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Affiliation(s)
- Brittany N Szafran
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Abdolsamad Borazjani
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Caitlin N Seay
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Russell L Carr
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Richard Lehner
- Departments of Cell Biology and Pediatrics, Group on Molecular & Cell Biology of Lipids, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Barbara L F Kaplan
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Matthew K Ross
- Department of Comparative Biomedical Sciences, Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, United States
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13
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Electrophilic Natural Products as Drug Discovery Tools. Trends Pharmacol Sci 2021; 42:434-447. [PMID: 33902949 DOI: 10.1016/j.tips.2021.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/22/2022]
Abstract
Electrophilic natural products (ENPs) are a rich source of bioactive molecules with tremendous therapeutic potential. While their synthetic complexity may hinder their direct use as therapeutics, they represent tools for elucidation of suitable molecular targets and serve as inspiration for the design of simplified synthetic counterparts. Here, we review the recent use of various activity-based protein profiling methods to uncover molecular targets of ENPs. Beyond target identification, these examples also showcase further development of synthetic ligands from natural product starting points. Two examples demonstrate how ENPs can progress the emerging fields of targeted protein degradation and molecular glues. Though challenges still remain in the synthesis of ENP-based probes, and in their synthetic simplification, their potential for discovery of novel mechanisms of action makes it well worth the effort.
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14
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Jing Y, Montano JL, Levy M, Lopez JE, Kung PP, Richardson P, Krajewski K, Florens L, Washburn MP, Meier JL. Harnessing Ionic Selectivity in Acetyltransferase Chemoproteomic Probes. ACS Chem Biol 2021; 16:27-34. [PMID: 33373188 PMCID: PMC9093059 DOI: 10.1021/acschembio.0c00766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chemical proteomics provides a powerful strategy for the high-throughput assignment of enzyme function or inhibitor selectivity. However, identifying optimized probes for an enzyme family member of interest and differentiating signal from the background remain persistent challenges in the field. To address this obstacle, here we report a physiochemical discernment strategy for optimizing chemical proteomics based on the coenzyme A (CoA) cofactor. First, we synthesize a pair of CoA-based sepharose pulldown resins differentiated by a single negatively charged residue and find this change alters their capture properties in gel-based profiling experiments. Next, we integrate these probes with quantitative proteomics and benchmark analysis of "probe selectivity" versus traditional "competitive chemical proteomics." This reveals that the former is well-suited for the identification of optimized pulldown probes for specific enzyme family members, while the latter may have advantages in discovery applications. Finally, we apply our anionic CoA pulldown probe to evaluate the selectivity of a recently reported small molecule N-terminal acetyltransferase inhibitor. These studies further validate the use of physical discriminant strategies in chemoproteomic hit identification and demonstrate how CoA-based chemoproteomic probes can be used to evaluate the selectivity of small molecule protein acetyltransferase inhibitors, an emerging class of preclinical therapeutic agents.
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Affiliation(s)
- Yihang Jing
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jose L Montano
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Michaella Levy
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
| | - Jeffrey E Lopez
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Pei-Pei Kung
- Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, United States
| | - Paul Richardson
- Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, United States
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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15
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Casement R, Bond A, Craigon C, Ciulli A. Mechanistic and Structural Features of PROTAC Ternary Complexes. Methods Mol Biol 2021; 2365:79-113. [PMID: 34432240 DOI: 10.1007/978-1-0716-1665-9_5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The rapid and ever-growing advancements from within the field of proteolysis-targeting chimeras (PROTAC)-induced protein degradation have driven considerable development to gain a deeper understanding of their mode of action. The ternary complex formed by PROTACs with their target protein and E3 ubiquitin ligase is the key species in their substoichiometric catalytic mechanism. Here, we describe the theoretical framework that underpins ternary complexes, including a current understanding of the three-component binding model, cooperativity, hook effect and structural considerations. We discuss in detail the biophysical methods used to interrogate ternary complex formation in vitro, including X-ray crystallography, AlphaLISA, FRET, FP, ITC and SPR. Finally, we provide detailed ITC methods and discuss approaches to assess binary and ternary target engagement, target ubiquitination and degradation that can be used to obtain a more holistic understanding of the mode of action within a cellular environment.
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Affiliation(s)
- Ryan Casement
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Adam Bond
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Conner Craigon
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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16
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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] [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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17
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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] [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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Discovery of small-molecule enzyme activators by activity-based protein profiling. Nat Chem Biol 2020; 16:997-1005. [PMID: 32514184 PMCID: PMC7442688 DOI: 10.1038/s41589-020-0555-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 04/23/2020] [Indexed: 12/17/2022]
Abstract
Activity-based protein profiling (ABPP) has been used extensively to discover and optimize selective inhibitors of enzymes. Here, we show that ABPP can also be implemented to identify the converse – small-molecule enzyme activators. Using a kinetically controlled, fluorescence polarization-ABPP assay, we identify compounds that stimulate the activity of LYPLAL1 – a poorly characterized serine hydrolase with complex genetic links to human metabolic traits. We apply ABPP-guided medicinal chemistry to advance a lead into a selective LYPLAL1 activator suitable for use in vivo. Structural simulations coupled to mutational, biochemical, and biophysical analyses indicate that this compound increases LYPLAL1’s catalytic activity likely by enhancing the efficiency of the catalytic triad charge-relay system. Treatment with this LYPLAL1 activator confers beneficial effects in a mouse model of diet-induced obesity. These findings reveal a new mode of pharmacological regulation for this large enzyme family and suggest that ABPP may aid discovery of activators for additional enzyme classes.
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Keller LJ, Lentz CS, Chen YE, Metivier RJ, Weerapana E, Fischbach MA, Bogyo M. Characterization of Serine Hydrolases Across Clinical Isolates of Commensal Skin Bacteria Staphylococcus epidermidis Using Activity-Based Protein Profiling. ACS Infect Dis 2020; 6:930-938. [PMID: 32298574 DOI: 10.1021/acsinfecdis.0c00095] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The bacterial genus Staphylococcus comprises diverse species that colonize the skin as commensals but can also cause infection. Previous work identified a family of serine hydrolases termed fluorophoshonate-binding hydrolases (Fphs) in the pathogenic bacteria Staphylococcus aureus, one of which, FphB, functions as a virulence factor. Using a combination of bioinformatics and activity-based protein profiling (ABPP), we identify homologues of these enzymes in the related commensal bacteria Staphylococcus epidermidis. Two of the S. aureus Fph enzymes were not identified in S. epidermidis. Using ABPP, we identified several candidate hydrolases that were not previously identified in S. aureus that may be functionally related to the Fphs. Interestingly, the activity of the Fphs vary across clinical isolates of S. epidermidis. Biochemical characterization of the FphB homologue in S. epidermidis (SeFphB) suggests it is a functional homologue of FphB in S. aureus, but our preliminary studies suggest it may not have a role in colonization in vivo. This potential difference in biological function between the Fphs of closely related staphylococcal species may provide mechanisms for specific inhibition of S. aureus infection without perturbing commensal communities of related bacteria.
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Affiliation(s)
| | | | - Y. Erin Chen
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, California 94305, United States
- Dermatology Service, Veterans Affairs Medical Center, San Francisco, California 94121, United States
| | - Rebecca J. Metivier
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Michael A. Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, California 94305, United States
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Carvalho LAR, Almeida VT, Brito JA, Lum KM, Oliveira TF, Guedes RC, Gonçalves LM, Lucas SD, Cravatt BF, Archer M, Moreira R. 3-Oxo-β-sultam as a Sulfonylating Chemotype for Inhibition of Serine Hydrolases and Activity-Based Protein Profiling. ACS Chem Biol 2020; 15:878-883. [PMID: 32176480 DOI: 10.1021/acschembio.0c00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3-Oxo-β-sultams are four-membered ring ambident electrophiles that can react with nucleophiles either at the carbonyl carbon or at the sulfonyl sulfur atoms, and that have been reported to inhibit serine hydrolases via acylation of the active-site serine residue. We have developed a panel of 3-oxo-β-sultam inhibitors and show, through crystallographic data, that they are regioselective sulfonylating electrophiles, covalently binding to the catalytic serine of human and porcine elastases through the sulfur atom. Application of 3-oxo-β-sultam-derived activity-based probes in a human proteome revealed their potential to label disease-related serine hydrolases and proteasome subunits. Activity-based protein profiling applications of 3-oxo-β-sultams should open up new opportunities to investigate these classes of enzymes in complex proteomes and expand the toolbox of available sulfur-based covalent protein modifiers in chemical biology.
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Affiliation(s)
- Luís A. R. Carvalho
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Vanessa T. Almeida
- Biological Chemistry Division, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - José A. Brito
- Biological Chemistry Division, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Kenneth M. Lum
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Tânia F. Oliveira
- Biological Chemistry Division, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Rita C. Guedes
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Lídia M. Gonçalves
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Susana D. Lucas
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Benjamin F. Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Margarida Archer
- Biological Chemistry Division, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Rui Moreira
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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21
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High-Resolution Confocal Fluorescence Imaging of Serine Hydrolase Activity in Cryosections - Application to Glioma Brain Unveils Activity Hotspots Originating from Tumor-Associated Neutrophils. Biol Proced Online 2020; 22:6. [PMID: 32190011 PMCID: PMC7073015 DOI: 10.1186/s12575-020-00118-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Background Serine hydrolases (SHs) are a functionally diverse family of enzymes playing pivotal roles in health and disease and have emerged as important therapeutic targets in many clinical conditions. Activity-based protein profiling (ABPP) using fluorophosphonate (FP) probes has been a powerful chemoproteomic approach in studies unveiling roles of SHs in various biological systems. ABPP utilizes cell/tissue proteomes and features the FP-warhead, linked to a fluorescent reporter for in-gel fluorescence imaging or a biotin tag for streptavidin enrichment and LC-MS/MS-based target identification. Existing ABPP approaches characterize global SH activity based on mobility in gel or MS-based target identification and cannot reveal the identity of the cell-type responsible for an individual SH activity originating from complex proteomes. Results Here, by using an activity probe with broad reactivity towards the SH family, we advance the ABPP methodology to glioma brain cryosections, enabling for the first time high-resolution confocal fluorescence imaging of global SH activity in the tumor microenvironment. Tumor-associated cell types were identified by extensive immunohistochemistry on activity probe-labeled sections. Tissue-ABPP indicated heightened SH activity in glioma vs. normal brain and unveiled activity hotspots originating from tumor-associated neutrophils (TANs), rather than tumor-associated macrophages (TAMs). Thorough optimization and validation was provided by parallel gel-based ABPP combined with LC-MS/MS-based target verification. Conclusions Our study advances the ABPP methodology to tissue sections, enabling high-resolution confocal fluorescence imaging of global SH activity in anatomically preserved complex native cellular environment. To achieve global portrait of SH activity throughout the section, a probe with broad reactivity towards the SH family members was employed. As ABPP requires no a priori knowledge of the identity of the target, we envisage no imaginable reason why the presently described approach would not work for sections regardless of species and tissue source.
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22
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Parker CG, Pratt MR. Click Chemistry in Proteomic Investigations. Cell 2020; 180:605-632. [PMID: 32059777 PMCID: PMC7087397 DOI: 10.1016/j.cell.2020.01.025] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 01/20/2023]
Abstract
Despite advances in genetic and proteomic techniques, a complete portrait of the proteome and its complement of dynamic interactions and modifications remains a lofty, and as of yet, unrealized, objective. Specifically, traditional biological and analytical approaches have not been able to address key questions relating to the interactions of proteins with small molecules, including drugs, drug candidates, metabolites, or protein post-translational modifications (PTMs). Fortunately, chemists have bridged this experimental gap through the creation of bioorthogonal reactions. These reactions allow for the incorporation of chemical groups with highly selective reactivity into small molecules or protein modifications without perturbing their biological function, enabling the selective installation of an analysis tag for downstream investigations. The introduction of chemical strategies to parse and enrich subsets of the "functional" proteome has empowered mass spectrometry (MS)-based methods to delve more deeply and precisely into the biochemical state of cells and its perturbations by small molecules. In this Primer, we discuss how one of the most versatile bioorthogonal reactions, "click chemistry", has been exploited to overcome limitations of biological approaches to enable the selective marking and functional investigation of critical protein-small-molecule interactions and PTMs in native biological environments.
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Affiliation(s)
- Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Matthew R Pratt
- Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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Keller LJ, Babin BM, Lakemeyer M, Bogyo M. Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities. Curr Opin Chem Biol 2019; 54:45-53. [PMID: 31835131 DOI: 10.1016/j.cbpa.2019.10.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/09/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Activity-based protein profiling (ABPP) is a robust chemoproteomic technique that uses activity-based probes to globally measure endogenous enzymatic activity in complex proteomes. It has been utilized extensively to characterize human disease states and identify druggable targets in diverse disease conditions. ABPP has also recently found applications in microbiology. This includes using activity-based probes (ABPs) for functional studies of pathogenic bacteria as well as complex communities within a microbiome. This review will focus on recent advances in the use of ABPs to profile enzyme activity in disease models, screen for selective inhibitors of key enzymes, and develop imaging tools to better understand the host-bacterial interface.
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Affiliation(s)
- Laura J Keller
- Department of Chemical & Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Brett M Babin
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Markus Lakemeyer
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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Rajendran A, Vaidya K, Mendoza J, Bridwell-Rabb J, Kamat SS. Functional Annotation of ABHD14B, an Orphan Serine Hydrolase Enzyme. Biochemistry 2019; 59:183-196. [PMID: 31478652 DOI: 10.1021/acs.biochem.9b00703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The metabolic serine hydrolase family is, arguably, one of the largest functional enzyme classes in mammals, including humans, comprising 1-2% of the total proteome. This enzyme family uses a conserved nucleophilic serine residue in the active site to perform diverse hydrolytic reactions and consists of proteases, lipases, esterases, amidases, and transacylases, which are prototypical members of this family. In humans, this enzyme family consists of >250, of which approximately 40% members remain unannotated, in terms of both their endogenous substrates and the biological pathways that they regulate. The enzyme ABHD14B, an outlying member of this family, is also known as CCG1/TAFII250-interacting factor B, as it was found to be associated with transcription initiation factor TFIID. The crystal structure of human ABHD14B was determined more than a decade ago; however, its endogenous substrates remain elusive. In this paper, we annotate ABHD14B as a lysine deacetylase (KDAC), showing this enzyme's ability to transfer an acetyl group from a post-translationally acetylated lysine to coenzyme A (CoA), to yield acetyl-CoA, while regenerating the free amine of protein lysine residues. We validate these findings by in vitro biochemical assays using recombinantly purified human ABHD14B in conjunction with cellular studies in a mammalian cell line by knocking down ABHD14B and by identification of a putative substrate binding site. Finally, we report the development and characterization of a much-needed, exquisitely selective ABHD14B antibody, and using it, we map the cellular and tissue distribution of ABHD14B and prospective metabolic pathways that this enzyme might biologically regulate.
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Affiliation(s)
- Abinaya Rajendran
- Department of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road Pashan , Pune 411008 , Maharashtra , India
| | - Kaveri Vaidya
- Department of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road Pashan , Pune 411008 , Maharashtra , India
| | - Johnny Mendoza
- Department of Chemistry, College of Literature, Science and the Arts , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, College of Literature, Science and the Arts , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Siddhesh S Kamat
- Department of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road Pashan , Pune 411008 , Maharashtra , India
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25
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Borne AL, Huang T, McCloud RL, Pachaiyappan B, Bullock TNJ, Hsu KL. Deciphering T Cell Immunometabolism with Activity-Based Protein Profiling. Curr Top Microbiol Immunol 2019; 420:175-210. [PMID: 30128827 PMCID: PMC7134364 DOI: 10.1007/82_2018_124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
As a major sentinel of adaptive immunity, T cells seek and destroy diseased cells using antigen recognition to achieve molecular specificity. Strategies to block checkpoint inhibition of T cell activity and thus reawaken the patient's antitumor immune responses are rapidly becoming standard of care for treatment of diverse cancers. Adoptive transfer of patient T cells genetically engineered with tumor-targeting capabilities is redefining the field of personalized medicines. The diverse opportunities for exploiting T cell biology in the clinic have prompted new efforts to expand the scope of targets amenable to immuno-oncology. Given the complex spatiotemporal regulation of T cell function and fate, new technologies capable of global molecular profiling in vivo are needed to guide selection of appropriate T cell targets and subsets. In this chapter, we describe the use of activity-based protein profiling (ABPP) to illuminate different aspects of T cell metabolism and signaling as fertile starting points for investigation. We highlight the merits of ABPP methods to enable target, inhibitor, and biochemical pathway discovery of T cells in the burgeoning field of immuno-oncology.
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Affiliation(s)
- Adam L Borne
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Tao Huang
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904, USA
| | - Rebecca L McCloud
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904, USA
| | - Boobalan Pachaiyappan
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904, USA
| | - Timothy N J Bullock
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904, USA.
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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Pharmacological convergence reveals a lipid pathway that regulates C. elegans lifespan. Nat Chem Biol 2019; 15:453-462. [PMID: 30911178 PMCID: PMC6548519 DOI: 10.1038/s41589-019-0243-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
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27
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Vasudevan A, Argiriadi MA, Baranczak A, Friedman MM, Gavrilyuk J, Hobson AD, Hulce JJ, Osman S, Wilson NS. Covalent binders in drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2019; 58:1-62. [PMID: 30879472 DOI: 10.1016/bs.pmch.2018.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent modulation of protein function can have multiple utilities including therapeutics, and probes to interrogate biology. While this field is still viewed with scepticism due to the potential for (idiosyncratic) toxicities, significant strides have been made in terms of understanding how to tune electrophilicity to selectively target specific residues. Progress has also been made in harnessing the potential of covalent binders to uncover novel biology and to provide an enhanced utility as payloads for Antibody Drug Conjugates. This perspective covers the tenets and applications of covalent binders.
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Affiliation(s)
| | | | | | | | - Julia Gavrilyuk
- AbbVie Stemcentrx, LLC, South San Francisco, CA, United States
| | | | | | - Sami Osman
- AbbVie Bioresearch Center, Worcester, MA, United States
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28
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Inhibition of Protein Secretion in Escherichia coli and Sub-MIC Effects of Arylomycin Antibiotics. Antimicrob Agents Chemother 2019; 63:AAC.01253-18. [PMID: 30420476 DOI: 10.1128/aac.01253-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/04/2018] [Indexed: 12/31/2022] Open
Abstract
At sufficient concentrations, antibiotics effectively eradicate many bacterial infections. However, during therapy, bacteria are unavoidably exposed to lower antibiotic concentrations, and sub-MIC exposure can result in a wide variety of other effects, including the induction of virulence, which can complicate therapy, or horizontal gene transfer (HGT), which can accelerate the spread of resistance genes. Bacterial type I signal peptidase (SPase) is an essential protein that acts at the final step of the general secretory pathway. This pathway is required for the secretion of many proteins, including many required for virulence, and the arylomycins are a class of natural product antibiotics that target SPase. Here, we investigated the consequences of exposing Escherichia coli cultures to sub-MIC levels of an arylomycin. Using multidimensional protein identification technology mass spectrometry, we found that arylomycin treatment inhibits the proper extracytoplasmic localization of many proteins, both those that appear to be SPase substrates and several that do not. The identified proteins are involved in a broad range of extracytoplasmic processes and include a number of virulence factors. The effects of arylomycin on several processes required for virulence were then individually examined, and we found that, at even sub-MIC levels, the arylomycins potently inhibit flagellation, motility, biofilm formation, and the dissemination of antibiotic resistance via HGT. Thus, we conclude that the arylomycins represent promising novel therapeutics with the potential to eradicate infections while simultaneously reducing virulence and the dissemination of resistance.
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Clapper JR, Henry CL, Niphakis MJ, Knize AM, Coppola AR, Simon GM, Ngo N, Herbst RA, Herbst DM, Reed AW, Cisar JS, Weber OD, Viader A, Alexander JP, Cunningham ML, Jones TK, Fraser IP, Grice CA, Ezekowitz RAB, O’Neill GP, Blankman JL. Monoacylglycerol Lipase Inhibition in Human and Rodent Systems Supports Clinical Evaluation of Endocannabinoid Modulators. J Pharmacol Exp Ther 2018; 367:494-508. [DOI: 10.1124/jpet.118.252296] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/05/2018] [Indexed: 12/15/2022] Open
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30
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Janssen APA, van der Vliet D, Bakker AT, Jiang M, Grimm SH, Campiani G, Butini S, van der Stelt M. Development of a Multiplexed Activity-Based Protein Profiling Assay to Evaluate Activity of Endocannabinoid Hydrolase Inhibitors. ACS Chem Biol 2018; 13:2406-2413. [PMID: 30199617 PMCID: PMC6154214 DOI: 10.1021/acschembio.8b00534] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Endocannabinoids,
an important class of signaling lipids involved
in health and disease, are predominantly synthesized and metabolized
by enzymes of the serine hydrolase superfamily. Activity-based protein
profiling (ABPP) using fluorescent probes, such as fluorophosphonate
(FP)-TAMRA and β-lactone-based MB064, enables drug discovery
activities for serine hydrolases. FP-TAMRA and MB064 have distinct,
albeit partially overlapping, target profiles but cannot be used in
conjunction due to overlapping excitation/emission spectra. We therefore
synthesized a novel FP-probe with a green BODIPY as a fluorescent
tag and studied its labeling profile in mouse proteomes. Surprisingly,
we found that the reporter tag plays an important role in the binding
potency and selectivity of the probe. A multiplexed ABPP assay was
developed in which a probe cocktail of FP-BODIPY and MB064 visualized
most endocannabinoid serine hydrolases in mouse brain proteomes in
a single experiment. The multiplexed ABPP assay was employed to profile
endocannabinoid hydrolase inhibitor activity and selectivity in the
mouse brain.
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Affiliation(s)
| | - Daan van der Vliet
- Department of Molecular Physiology, LIC, Leiden University, Leiden, The Netherlands
| | - Alexander T. Bakker
- Department of Molecular Physiology, LIC, Leiden University, Leiden, The Netherlands
| | - Ming Jiang
- Department of Molecular Physiology, LIC, Leiden University, Leiden, The Netherlands
| | - Sebastian H. Grimm
- Department of Molecular Physiology, LIC, Leiden University, Leiden, The Netherlands
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), NatSynDrugs, University of Siena, Siena, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy (DoE 2018-2022), NatSynDrugs, University of Siena, Siena, Italy
| | - Mario van der Stelt
- Department of Molecular Physiology, LIC, Leiden University, Leiden, The Netherlands
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31
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Meng H, Ma R, Fitzgerald MC. Chemical Denaturation and Protein Precipitation Approach for Discovery and Quantitation of Protein–Drug Interactions. Anal Chem 2018; 90:9249-9255. [DOI: 10.1021/acs.analchem.8b01772] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- He Meng
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Renze Ma
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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32
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Proteomic-genomic adjustments and their confluence for elucidation of pathways and networks during liver fibrosis. Int J Biol Macromol 2018; 111:379-392. [DOI: 10.1016/j.ijbiomac.2017.12.168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/28/2017] [Accepted: 12/31/2017] [Indexed: 12/31/2022]
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33
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Arni S, de Wijn R, Garcia–Villegas R, Bitanihirwe BK, Caviezel C, Weder W, Hillinger S. A strategy to analyse activity-based profiling of tyrosine kinase substrates in OCT-embedded lung cancer tissue. Anal Biochem 2018; 547:77-83. [DOI: 10.1016/j.ab.2018.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 01/11/2023]
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34
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Abdel-Daim A, Ohura K, Imai T. A novel quantification method for serine hydrolases in cellular expression system using fluorophosphonate-biotin probe. Eur J Pharm Sci 2018; 114:267-274. [DOI: 10.1016/j.ejps.2017.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/17/2017] [Accepted: 12/18/2017] [Indexed: 12/26/2022]
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35
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Sharifzadeh S, Shirley JD, Carlson EE. Activity-Based Protein Profiling Methods to Study Bacteria: The Power of Small-Molecule Electrophiles. Curr Top Microbiol Immunol 2018; 420:23-48. [PMID: 30232601 DOI: 10.1007/82_2018_135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ABPP methods have been utilized for the last two decades as a means to investigate complex proteomes in all three domains of life. Extensive use in eukaryotes has provided a more fundamental understanding of the biological processes involved in numerous diseases and has driven drug discovery and treatment campaigns. However, the use of ABPP in prokaryotes has been less common, although it has gained more attention over the last decade. The urgent need for understanding bacteriophysiology and bacterial pathogenicity at a foundational level has never been more apparent, as the rise in antibiotic resistance has resulted in the inadequate and ineffective treatment of infections. This is not only a result of resistance to clinically used antibiotics, but also a lack of new drugs and equally as important, new drug targets. ABPP provides a means for which new, clinically relevant drug targets may be identified through gaining insight into biological processes. In this chapter, we place particular focus on the discussion of ABPP strategies that have been applied to study different classes of bacterial enzymes.
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Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA.
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36
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Ruby MA, Massart J, Hunerdosse DM, Schönke M, Correia JC, Louie SM, Ruas JL, Näslund E, Nomura DK, Zierath JR. Human Carboxylesterase 2 Reverses Obesity-Induced Diacylglycerol Accumulation and Glucose Intolerance. Cell Rep 2017; 18:636-646. [PMID: 28099843 PMCID: PMC5276805 DOI: 10.1016/j.celrep.2016.12.070] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/18/2016] [Accepted: 12/20/2016] [Indexed: 02/01/2023] Open
Abstract
Serine hydrolases are a large family of multifunctional enzymes known to influence obesity. Here, we performed activity-based protein profiling to assess the functional level of serine hydrolases in liver biopsies from lean and obese humans in order to gain mechanistic insight into the pathophysiology of metabolic disease. We identified reduced hepatic activity of carboxylesterase 2 (CES2) and arylacetamide deacetylase (AADAC) in human obesity. In primary human hepatocytes, CES2 knockdown impaired glucose storage and lipid oxidation. In mice, obesity reduced CES2, whereas adenoviral delivery of human CES2 reversed hepatic steatosis, improved glucose tolerance, and decreased inflammation. Lipidomic analysis identified a network of CES2-regulated lipids altered in human and mouse obesity. CES2 possesses triglyceride and diacylglycerol lipase activities and displayed an inverse correlation with HOMA-IR and hepatic diacylglycerol concentrations in humans. Thus, decreased CES2 is a conserved feature of obesity and plays a causative role in the pathogenesis of obesity-related metabolic disturbances. Obesity decreases hepatic activity of AADAC and CES2 in humans CES2 depletion impairs lipid and glucose metabolism in primary human hepatocytes Human CES2 expression reverses hepatic steatosis and glucose intolerance in mice CES2 controls a hepatic lipid network dysregulated in human and mouse obesity
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Affiliation(s)
- Maxwell A Ruby
- Section for Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Julie Massart
- Section for Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Devon M Hunerdosse
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Milena Schönke
- Section for Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jorge C Correia
- Molecular and Cellular Exercise Physiology Unit, Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Sharon M Louie
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jorge L Ruas
- Molecular and Cellular Exercise Physiology Unit, Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Erik Näslund
- Division of Surgery, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Juleen R Zierath
- Section for Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden.
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37
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An activity-dependent proximity ligation platform for spatially resolved quantification of active enzymes in single cells. Nat Commun 2017; 8:1775. [PMID: 29176560 PMCID: PMC5701173 DOI: 10.1038/s41467-017-01854-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/19/2017] [Indexed: 01/06/2023] Open
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. Here we report a platform that integrates family-wide chemical probes with proximity-dependent oligonucleotide amplification and imaging to quantify enzyme activity in native contexts with high spatial 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. Finally, retention of sample architecture enables interrogation of complex environments such as cellular co-culture and patient samples. ADPL should be amenable to diverse probe and protein families to detect active enzymes at scale and resolution out of reach with current methods. The interrogation of enzyme activity involves the ensemble averaging of many cells, loss of spatial relationships and is often biased to abundant proteins. Here the authors develop activity-dependent proximity ligation to quantify enzyme activity at the cellular and sub-cellular level in relevant biological contexts.
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38
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Lu M, Faull KF, Whitelegge JP, He J, Shen D, Saxton RE, Chang HR. Proteomics and Mass Spectrometry for Cancer Biomarker Discovery. Biomark Insights 2017. [DOI: 10.1177/117727190700200005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Proteomics is a rapidly advancing field not only in the field of biology but also in translational cancer research. In recent years, mass spectrometry and associated technologies have been explored to identify proteins or a set of proteins specific to a given disease, for the purpose of disease detection and diagnosis. Such biomarkers are being investigated in samples including cells, tissues, serum/plasma, and other types of body fluids. When sufficiently refined, proteomic technologies may pave the way for early detection of cancer or individualized therapy for cancer. Mass spectrometry approaches coupled with bioinformatic tools are being developed for biomarker discovery and validation. Understanding basic concepts and application of such technology by investigators in the field may accelerate the clinical application of protein biomarkers in disease management.
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Affiliation(s)
- Ming Lu
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
| | - Kym F. Faull
- The Pasarow Mass Spectrometry Laboratory, Department of Psychiatry & Biobehavioral and the Neuropsychiatric Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, Department of Psychiatry & Biobehavioral and the Neuropsychiatric Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
| | - Jianbo He
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
| | - Dejun Shen
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
| | - Romaine E. Saxton
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, Los Angeles, California
| | - Helena R. Chang
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, Los Angeles, California
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39
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Jones LH, Neubert H. Clinical chemoproteomics-Opportunities and obstacles. Sci Transl Med 2017; 9:9/386/eaaf7951. [PMID: 28424333 DOI: 10.1126/scitranslmed.aaf7951] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 03/06/2017] [Indexed: 12/19/2022]
Abstract
Chemoproteomics is the large-scale study of proteins using chemical methods. Although chemoproteomic techniques are becoming commonplace in preclinical research, few examples have found clinical utility. We explore the prospects for advancing chemoproteomics into the clinical setting to understand drug-target interactions and to identify new therapeutically relevant targets.
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Affiliation(s)
- Lyn H Jones
- Medicine Design, Pfizer, 610 Main Street, Cambridge, MA 02139, USA.
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40
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Kulkarni RA, Worth AJ, Zengeya TT, Shrimp JH, Garlick JM, Roberts AM, Montgomery DC, Sourbier C, Gibbs BK, Mesaros C, Tsai YC, Das S, Chan KC, Zhou M, Andresson T, Weissman AM, Linehan WM, Blair IA, Snyder NW, Meier JL. Discovering Targets of Non-enzymatic Acylation by Thioester Reactivity Profiling. Cell Chem Biol 2017; 24:231-242. [PMID: 28163016 DOI: 10.1016/j.chembiol.2017.01.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 01/15/2023]
Abstract
Non-enzymatic protein modification driven by thioester reactivity is thought to play a major role in the establishment of cellular lysine acylation. However, the specific protein targets of this process are largely unknown. Here we report an experimental strategy to investigate non-enzymatic acylation in cells. Specifically, we develop a chemoproteomic method that separates thioester reactivity from enzymatic utilization, allowing selective enrichment of non-enzymatic acylation targets. Applying this method to cancer cell lines identifies numerous candidate targets of non-enzymatic acylation, including several enzymes in lower glycolysis. Functional studies highlight malonyl-CoA as a reactive thioester metabolite that can modify and inhibit glycolytic enzyme activity. Finally, we show that synthetic thioesters can be used as novel reagents to probe non-enzymatic acylation in living cells. Our studies provide new insights into the targets and drivers of non-enzymatic acylation, and demonstrate the utility of reactivity-based methods to experimentally investigate this phenomenon in biology and disease.
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Affiliation(s)
- Rhushikesh A Kulkarni
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Andrew J Worth
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas T Zengeya
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Julie M Garlick
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Allison M Roberts
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Carole Sourbier
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Benjamin K Gibbs
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Clementina Mesaros
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - King C Chan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Ming Zhou
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Ian A Blair
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W Snyder
- Drexel University, A.J. Drexel Autism Institute, 3020 Market Street, Philadelphia, PA 19104, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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41
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Zhang X. Detergents: Friends not foes for high-performance membrane proteomics toward precision medicine. Proteomics 2016; 17. [PMID: 27633951 DOI: 10.1002/pmic.201600209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023]
Abstract
Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples. Frequently, expected membrane proteins and peptides are not identified by shotgun bottom-up proteomics, let alone robust quantitation. This review argues the cause of this proteomic crisis is not detergents per se, but the choice of detergents. Recently, inclusion of compatible detergents for membrane protein extraction and digestion has revealed stark improvements in both quantitative and structural proteomics. This review analyzes detergent properties behind recent proteomic advances, and proposes that rational use of detergents may reconcile outstanding membrane proteomics dilemmas, enabling ultradeep coverage and minimal artifacts for robust protein and endogenous PTM measurements. The simplicity of detergent tools confers bottom-up membrane proteomics the sophistication toward precision medicine.
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Affiliation(s)
- Xi Zhang
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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42
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Grüner BM, Schulze CJ, Yang D, Ogasawara D, Dix MM, Rogers ZN, Chuang CH, McFarland CD, Chiou SH, Brown JM, Cravatt BF, Bogyo M, Winslow MM. An in vivo multiplexed small-molecule screening platform. Nat Methods 2016; 13:883-889. [PMID: 27617390 DOI: 10.1038/nmeth.3992] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/01/2016] [Indexed: 01/04/2023]
Abstract
Phenotype-based small-molecule screening is a powerful method to identify molecules that regulate cellular functions. However, such screens are generally performed in vitro under conditions that do not necessarily model complex physiological conditions or disease states. Here, we use molecular cell barcoding to enable direct in vivo phenotypic screening of small-molecule libraries. The multiplexed nature of this approach allows rapid in vivo analysis of hundreds to thousands of compounds. Using this platform, we screened >700 covalent inhibitors directed toward hydrolases for their effect on pancreatic cancer metastatic seeding. We identified multiple hits and confirmed the relevant target of one compound as the lipase ABHD6. Pharmacological and genetic studies confirmed the role of this enzyme as a regulator of metastatic fitness. Our results highlight the applicability of this multiplexed screening platform for investigating complex processes in vivo.
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Affiliation(s)
- Barbara M Grüner
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Dian Yang
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Daisuke Ogasawara
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Melissa M Dix
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Zoë N Rogers
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Chen-Hua Chuang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Shin-Heng Chiou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - J Mark Brown
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Benjamin F Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
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43
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Kolar MJ, Kamat SS, Parsons WH, Homan EA, Maher T, Peroni OD, Syed I, Fjeld K, Molven A, Kahn BB, Cravatt BF, Saghatelian A. Branched Fatty Acid Esters of Hydroxy Fatty Acids Are Preferred Substrates of the MODY8 Protein Carboxyl Ester Lipase. Biochemistry 2016; 55:4636-41. [PMID: 27509211 DOI: 10.1021/acs.biochem.6b00565] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently discovered class of endogenous mammalian lipids, branched fatty acid esters of hydroxy fatty acids (FAHFAs), possesses anti-diabetic and anti-inflammatory activities. Here, we identified and validated carboxyl ester lipase (CEL), a pancreatic enzyme hydrolyzing cholesteryl esters and other dietary lipids, as a FAHFA hydrolase. Variants of CEL have been linked to maturity-onset diabetes of the young, type 8 (MODY8), and to chronic pancreatitis. We tested the FAHFA hydrolysis activity of the CEL MODY8 variant and found a modest increase in activity as compared with that of the normal enzyme. Together, the data suggest that CEL might break down dietary FAHFAs.
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Affiliation(s)
- Matthew J Kolar
- Peptide Biology Laboratories, Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies , La Jolla, California 92037, United States
| | - Siddhesh S Kamat
- Department of Chemical Physiology, Skaggs Institute of Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - William H Parsons
- Department of Chemical Physiology, Skaggs Institute of Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Edwin A Homan
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Tim Maher
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Odile D Peroni
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston, Massachusetts 02215, United States
| | - Ismail Syed
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston, Massachusetts 02215, United States
| | - Karianne Fjeld
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen , N-5021 Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital , N-5021 Bergen, Norway
| | - Anders Molven
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen , N-5021 Bergen, Norway.,Department of Pathology, Haukeland University Hospital , N-5021 Bergen, Norway
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston, Massachusetts 02215, United States
| | - Benjamin F Cravatt
- Department of Chemical Physiology, Skaggs Institute of Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Alan Saghatelian
- Peptide Biology Laboratories, Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies , La Jolla, California 92037, United States
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44
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Parsons WH, Kolar MJ, Kamat SS, Cognetta AB, Hulce JJ, Saez E, Kahn BB, Saghatelian A, Cravatt BF. AIG1 and ADTRP are atypical integral membrane hydrolases that degrade bioactive FAHFAs. Nat Chem Biol 2016; 12:367-372. [PMID: 27018888 PMCID: PMC4837090 DOI: 10.1038/nchembio.2051] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/05/2016] [Indexed: 12/04/2022]
Abstract
Enzyme classes may contain outlier members that share mechanistic, but not sequence or structural relatedness with more common representatives. The functional annotation of such exceptional proteins can be challenging. Here, we use activity-based profiling to discover that the poorly characterized multipass transmembrane proteins AIG1 and ADTRP are atypical hydrolytic enzymes that depend on conserved threonine and histidine residues for catalysis. Both AIG1 and ADTRP hydrolyze bioactive fatty-acid esters of hydroxy-fatty acids (FAHFAs), but not other major classes of lipids. We discover multiple cell-active, covalent inhibitors of AIG1 and show that these agents block FAHFA hydrolysis in mammalian cells. These results indicate that AIG1 and ADTRP are founding members of an evolutionarily conserved class of transmembrane threonine hydrolases involved in bioactive lipid metabolism. More generally, our findings demonstrate how chemical proteomics can excavate potential cases of convergent/parallel protein evolution that defy conventional sequence- and structure-based predictions.
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Affiliation(s)
- William H Parsons
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Matthew J Kolar
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California 92037, United States
| | - Siddhesh S Kamat
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Armand B Cognetta
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Jonathan J Hulce
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Enrique Saez
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Alan Saghatelian
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California 92037, United States
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
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45
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Viader A, Ogasawara D, Joslyn CM, Sanchez-Alavez M, Mori S, Nguyen W, Conti B, Cravatt BF. A chemical proteomic atlas of brain serine hydrolases identifies cell type-specific pathways regulating neuroinflammation. eLife 2016; 5:e12345. [PMID: 26779719 PMCID: PMC4737654 DOI: 10.7554/elife.12345] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/13/2015] [Indexed: 12/19/2022] Open
Abstract
Metabolic specialization among major brain cell types is central to nervous system function and determined in large part by the cellular distribution of enzymes. Serine hydrolases are a diverse enzyme class that plays fundamental roles in CNS metabolism and signaling. Here, we perform an activity-based proteomic analysis of primary mouse neurons, astrocytes, and microglia to furnish a global portrait of the cellular anatomy of serine hydrolases in the brain. We uncover compelling evidence for the cellular compartmentalization of key chemical transmission pathways, including the functional segregation of endocannabinoid (eCB) biosynthetic enzymes diacylglycerol lipase-alpha (DAGLα) and –beta (DAGLβ) to neurons and microglia, respectively. Disruption of DAGLβ perturbed eCB-eicosanoid crosstalk specifically in microglia and suppressed neuroinflammatory events in vivo independently of broader effects on eCB content. Mapping the cellular distribution of metabolic enzymes thus identifies pathways for regulating specialized inflammatory responses in the brain while avoiding global alterations in CNS function. DOI:http://dx.doi.org/10.7554/eLife.12345.001 The brain is made up of many types of cells. These include the neurons that transmit messages throughout the nervous system, and microglia, which act as the first line of the brain’s immune defense. The activity of both neurons and microglia can be influenced by molecules called endocannabinoids that bind to proteins on the cells’ surface. For example, endocannabinoids affect how a neuron responds to messages sent to it from a neighbouring neuron, and help microglia to regulate the inflammation of brain tissue. Enzymes called serine hydrolases play important roles in several different signaling processes in the brain, including those involving endocannabinoids. Viader et al. have now studied the activities of these enzymes – including two called DAGLα and DAGLβ – in the mouse brain using a technique called activity-based protein profiling. This revealed that DAGLα plays an important role in controlling how neurons respond to endocannabinoids, while DAGLβ performs the equivalent role in microglia. When Viader et al. shut down DAGLβ activity, this only affected endocannabinoid signaling in microglia. This also had the effect of reducing inflammation in the brain, without affecting how endocannabinoids signal in neurons. These results suggest that inhibitors of DAGLβ could offer a way to suppress inflammation in the brain, which may contribute to neuropsychiatric and neurodegenerative diseases, while preserving the normal pathways that neurons use to communicate with one another. DOI:http://dx.doi.org/10.7554/eLife.12345.002
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Affiliation(s)
- Andreu Viader
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Daisuke Ogasawara
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Christopher M Joslyn
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Manuel Sanchez-Alavez
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Simone Mori
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - William Nguyen
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Bruno Conti
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
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46
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Chen B, Ge SS, Zhao YC, Chen C, Yang S. Activity-based protein profiling: an efficient approach to study serine hydrolases and their inhibitors in mammals and microbes. RSC Adv 2016. [DOI: 10.1039/c6ra20006k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This review focuses on the identification of serine hydrolases and their inhibitors in mammals and microbes with activity-based protein profiling (ABPP).
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Affiliation(s)
- Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Yuan-Chao Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Chong Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
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47
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Chen Y, Qin W, Wang C. Chemoproteomic profiling of protein modifications by lipid-derived electrophiles. Curr Opin Chem Biol 2015; 30:37-45. [PMID: 26625013 DOI: 10.1016/j.cbpa.2015.10.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 01/21/2023]
Abstract
Lipid-derived electrophiles (LDEs) are a group of endogenous reactive metabolites generated as products of lipid peroxidation when cells are under oxidative stress. LDEs are able to covalently modify nucleophilic residues in proteins to alter their structures and activities, either resulting in irreversible functional damage or triggering aberrant signaling pathways. Traditional biochemical methods have revealed individual protein targets modified by LDEs, however, deciphering the toxicity and/or signaling roles of LDEs requires systematic studies of these modifications in a high-throughput fashion. Here we survey recent progress in developing chemical proteomic strategies to globally profile protein-LDE interactions directly from complex proteomes. These powerful chemoproteomic methods have yielded a rich inventory of proteins and residue sites that are sensitive to LDE modification, serving as valuable resources to investigate mechanisms of their cellular toxicity at the molecular level.
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Affiliation(s)
- Ying Chen
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering and Peking University, Beijing 100871, China
| | - Wei Qin
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chu Wang
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering and Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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48
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Wolf EV, Zeissler A, Verhelst SHL. Inhibitor Fingerprinting of Rhomboid Proteases by Activity-Based Protein Profiling Reveals Inhibitor Selectivity and Rhomboid Autoprocessing. ACS Chem Biol 2015. [PMID: 26218717 DOI: 10.1021/acschembio.5b00514] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rhomboid proteases were discovered almost 15 years ago and are structurally the best characterized intramembrane proteases. Apart from the general serine protease inhibitor 3,4-dichloro-isocoumarin (DCI) and a few crystal structures of the Escherichia coli rhomboid GlpG with other inhibitors, there is surprisingly little information about inhibitors of rhomboids from other species, probably because of a lack of general methods to measure inhibition against different rhomboid species. We here present activity-based protein profiling (ABPP) as a general method to screen rhomboids for their activity and inhibition. Using ABPP, we compare the inhibitory capacity of 50 small molecules against 13 different rhomboids. We find one new pan rhomboid inhibitor and several inhibitors that display selectivity. We also demonstrate that inhibition profile and sequence similarity of rhomboids are not related, which suggests that related rhomboids may be selectively inhibited. Finally, by making use of the here discovered inhibitors, we were able to show that two bacterial rhomboids autoprocess themselves in their N-terminal part.
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Affiliation(s)
- Eliane V. Wolf
- Chair
for Chemistry of Biopolymers, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Annett Zeissler
- Chair
for Chemistry of Biopolymers, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Steven H. L. Verhelst
- Chair
for Chemistry of Biopolymers, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
- Laboratory
of Chemical Biology, Department of Cellular and Molecular Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
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49
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Medina-Cleghorn D, Nomura DK. Exploring metabolic pathways and regulation through functional chemoproteomic and metabolomic platforms. ACTA ACUST UNITED AC 2015; 21:1171-84. [PMID: 25237861 DOI: 10.1016/j.chembiol.2014.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 07/15/2014] [Accepted: 07/21/2014] [Indexed: 02/07/2023]
Abstract
Genome sequencing efforts have revealed a strikingly large number of uncharacterized genes, including poorly or uncharacterized metabolic enzymes, metabolites, and metabolic networks that operate in normal physiology, and those enzymes and pathways that may be rewired under pathological conditions. Although deciphering the functions of the uncharacterized metabolic genome is a challenging prospect, it also presents an opportunity for identifying novel metabolic nodes that may be important in disease therapy. In this review, we will discuss the chemoproteomic and metabolomic platforms used in identifying, characterizing, and targeting nodal metabolic pathways important in physiology and disease, describing an integrated workflow for functional mapping of metabolic enzymes.
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Affiliation(s)
- Daniel Medina-Cleghorn
- Program in Metabolic Biology and Molecular Toxicology, Department of Nutritional Sciences and Toxicology, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Program in Metabolic Biology and Molecular Toxicology, Department of Nutritional Sciences and Toxicology, 127 Morgan Hall, Berkeley, CA 94720, USA.
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50
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Chang JW, Zuhl AM, Speers AE, Niessen S, Brown SJ, Mulvihill MM, Fan YC, Spicer TP, Southern M, Scampavia L, Fernandez-Vega V, Dix MM, Cameron MD, Hodder PS, Rosen H, Nomura DK, Kwon O, Hsu KL, Cravatt BF. Selective inhibitor of platelet-activating factor acetylhydrolases 1b2 and 1b3 that impairs cancer cell survival. ACS Chem Biol 2015; 10:925-32. [PMID: 25602368 DOI: 10.1021/cb500893q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Platelet-activating factor acetylhydrolases (PAFAHs) 1b2 and 1b3 are poorly characterized serine hydrolases that form a complex with a noncatalytic protein (1b1) to regulate brain development, spermatogenesis, and cancer pathogenesis. Determining physiological substrates and biochemical functions for the PAFAH1b complex would benefit from selective chemical probes that can perturb its activity in living systems. Here, we report a class of tetrahydropyridine reversible inhibitors of PAFAH1b2/3 discovered using a fluorescence polarization-activity-based protein profiling (fluopol-ABPP) screen of the NIH 300,000+ compound library. The most potent of these agents, P11, exhibited IC50 values of ∼40 and 900 nM for PAFAH1b2 and 1b3, respectively. We confirm selective inhibition of PAFAH1b2/3 in cancer cells by P11 using an ABPP protocol adapted for in situ analysis of reversible inhibitors and show that this compound impairs tumor cell survival, supporting a role for PAFAH1b2/3 in cancer.
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Affiliation(s)
| | | | | | | | | | - Melinda M. Mulvihill
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Yi Chiao Fan
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | | | | | | | | | | | | | | | | | - Daniel K. Nomura
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Ohyun Kwon
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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