1
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Sahu S, Emenike B, Beusch CM, Bagchi P, Gordon DE, Raj M. Copper(I)-nitrene platform for chemoproteomic profiling of methionine. Nat Commun 2024; 15:4243. [PMID: 38762540 PMCID: PMC11102537 DOI: 10.1038/s41467-024-48403-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 04/30/2024] [Indexed: 05/20/2024] Open
Abstract
Methionine plays a critical role in various biological and cell regulatory processes, making its chemoproteomic profiling indispensable for exploring its functions and potential in protein therapeutics. Building on the principle of rapid oxidation of methionine, we report Copper(I)-Nitrene Platform for robust, and selective labeling of methionine to generate stable sulfonyl sulfimide conjugates under physiological conditions. We demonstrate the versatility of this platform to label methionine in bioactive peptides, intact proteins (6.5-79.5 kDa), and proteins in complex cell lysate mixtures with varying payloads. We discover ligandable proteins and sites harboring hyperreactive methionine within the human proteome. Furthermore, this has been utilized to profile oxidation-sensitive methionine residues, which might increase our understanding of the protective role of methionine in diseases associated with elevated levels of reactive oxygen species. The Copper(I)-Nitrene Platform allows labeling methionine residues in live cancer cells, observing minimal cytotoxic effects and achieving dose-dependent labeling. Confocal imaging further reveals the spatial distribution of modified proteins within the cell membrane, cytoplasm, and nucleus, underscoring the platform's potential in profiling the cellular interactome.
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Affiliation(s)
- Samrat Sahu
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | | | - Christian Michel Beusch
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Pritha Bagchi
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - David Ezra Gordon
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA, USA.
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2
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Ma Y, Guo W, Mou Q, Shao X, Lyu M, Garcia V, Kong L, Lewis W, Ward C, Yang Z, Pan X, Yi SS, Lu Y. Spatial imaging of glycoRNA in single cells with ARPLA. Nat Biotechnol 2024; 42:608-616. [PMID: 37217750 PMCID: PMC10663388 DOI: 10.1038/s41587-023-01801-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
Little is known about the biological roles of glycosylated RNAs (glycoRNAs), a recently discovered class of glycosylated molecules, because of a lack of visualization methods. We report sialic acid aptamer and RNA in situ hybridization-mediated proximity ligation assay (ARPLA) to visualize glycoRNAs in single cells with high sensitivity and selectivity. The signal output of ARPLA occurs only when dual recognition of a glycan and an RNA triggers in situ ligation, followed by rolling circle amplification of a complementary DNA, which generates a fluorescent signal by binding fluorophore-labeled oligonucleotides. Using ARPLA, we detect spatial distributions of glycoRNAs on the cell surface and their colocalization with lipid rafts as well as the intracellular trafficking of glycoRNAs through SNARE protein-mediated secretory exocytosis. Studies in breast cell lines suggest that surface glycoRNA is inversely associated with tumor malignancy and metastasis. Investigation of the relationship between glycoRNAs and monocyte-endothelial cell interactions suggests that glycoRNAs may mediate cell-cell interactions during the immune response.
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Affiliation(s)
- Yuan Ma
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Weijie Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Quanbing Mou
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xiangli Shao
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Mingkuan Lyu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Valeria Garcia
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Linggen Kong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Whitney Lewis
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Carson Ward
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Zhenglin Yang
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xingxin Pan
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - S Stephen Yi
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA.
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA.
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3
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Huppertz MC, Wilhelm J, Grenier V, Schneider MW, Falt T, Porzberg N, Hausmann D, Hoffmann DC, Hai L, Tarnawski M, Pino G, Slanchev K, Kolb I, Acuna C, Fenk LM, Baier H, Hiblot J, Johnsson K. Recording physiological history of cells with chemical labeling. Science 2024; 383:890-897. [PMID: 38386755 DOI: 10.1126/science.adg0812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins that become labeled in the presence of both a specific cellular activity and a fluorescent substrate. The recording period is set by the presence of the substrate, whereas the cellular activity controls the degree of the labeling. The use of distinguishable substrates enabled the recording of successive periods of activity. We recorded protein-protein interactions, G protein-coupled receptor activation, and increases in intracellular calcium. Recordings of elevated calcium levels allowed selections of cells from heterogeneous populations for transcriptomic analysis and tracking of neuronal activities in flies and zebrafish.
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Affiliation(s)
- Magnus-Carsten Huppertz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jonas Wilhelm
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Vincent Grenier
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Martin W Schneider
- Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tjalda Falt
- Active Sensing, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Nicola Porzberg
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - David Hausmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk C Hoffmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Ling Hai
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Pino
- Chica and Heinz Schaller Foundation, Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany
| | - Krasimir Slanchev
- Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ilya Kolb
- GENIE Project Team, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Claudio Acuna
- Chica and Heinz Schaller Foundation, Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany
| | - Lisa M Fenk
- Active Sensing, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Herwig Baier
- Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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4
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Chauhan P, V R, Kumar M, Molla R, Mishra SD, Basa S, Rai V. Chemical technology principles for selective bioconjugation of proteins and antibodies. Chem Soc Rev 2024; 53:380-449. [PMID: 38095227 DOI: 10.1039/d3cs00715d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.
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Affiliation(s)
- Preeti Chauhan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Ragendu V
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Rajib Molla
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Surya Dev Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Sneha Basa
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
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5
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Lin B, Xiang L, Yuan Z, Hou Q, Ruan Y, Zhang J. ReACT (redox-activated chemical tagging) chemistry enables direct derivatization and fluorescence detection of S-adenosyl-L-homocysteine (SAH). Org Biomol Chem 2023; 21:7085-7089. [PMID: 37602780 DOI: 10.1039/d3ob01073b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
S-Adenosyl-L-homocysteine (SAH) is a universal byproduct and product inhibitor of the methyltransferase-catalyzed methylation reaction. Here based on ReACT (redox-activated chemical tagging) chemistry, direct derivatization and fluorescence measurement of SAH were achieved with features such as mild reaction conditions and simple operation.
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Affiliation(s)
- Bohong Lin
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Lingling Xiang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Zhijun Yuan
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Qi Hou
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Yaoping Ruan
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Jing Zhang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
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6
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Swenson CS, Pillai KS, Carlos AJ, Moellering RE. Spatial Chemoproteomics for Mapping the Active Proteome. Isr J Chem 2023; 63:e202200104. [PMID: 38046285 PMCID: PMC10688764 DOI: 10.1002/ijch.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Indexed: 01/06/2023]
Abstract
Functional regulation of cell signaling through dynamic changes in protein activity state as well as spatial organization represent two dynamic, complex, and conserved phenomena in biology. Seemingly separate areas of -omics method development have focused on building tools that can detect and quantify protein activity states, as well as map sub-cellular and intercellular protein organization. Integration of these efforts, through the development of chemical tools and platforms that enable detection and quantification of protein functional states with spatial resolution provide opportunities to better understand heterogeneity in the proteome within cell organelles, multi-cellular tissues, and whole organisms. This review provides an overview of and considerations for major classes of chemical proteomic probes and technologies that enable protein activity mapping from sub-cellular compartments to live animals.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Kavya Smitha Pillai
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Anthony J Carlos
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, 5735 S Ellis Dr. Chicago, IL 60637, USA
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7
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Chauhan P, V. R, Kumar M, Molla R, V. B. U, Rai V. Dis integrate (DIN) Theory Enabling Precision Engineering of Proteins. ACS CENTRAL SCIENCE 2023; 9:137-150. [PMID: 36844488 PMCID: PMC9951294 DOI: 10.1021/acscentsci.2c01455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Indexed: 06/18/2023]
Abstract
The chemical toolbox for the selective modification of proteins has witnessed immense interest in the past few years. The rapid growth of biologics and the need for precision therapeutics have fuelled this growth further. However, the broad spectrum of selectivity parameters creates a roadblock to the field's growth. Additionally, bond formation and dissociation are significantly redefined during the translation from small molecules to proteins. Understanding these principles and developing theories to deconvolute the multidimensional attributes could accelerate the area. This outlook presents a disintegrate (DIN) theory for systematically disintegrating the selectivity challenges through reversible chemical reactions. An irreversible step concludes the reaction sequence to render an integrated solution for precise protein bioconjugation. In this perspective, we highlight the key advancements, unsolved challenges, and potential opportunities.
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8
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Cotton AD, Wells JA, Seiple IB. Biotin as a Reactive Handle to Selectively Label Proteins and DNA with Small Molecules. ACS Chem Biol 2022; 17:3270-3275. [PMID: 34410115 DOI: 10.1021/acschembio.1c00252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biotin is a common functional handle for bioconjugation to proteins and DNA, but its uses are limited to protein-containing conjugation partners such as streptavidin and derivatives thereof. Recently, oxaziridine reagents were developed that selectively conjugate the thioether of methionines on the surface of proteins, a method termed redox-activated chemical tagging (ReACT). These reagents generate sulfimide linkages that range in stability depending on the solvent accessibility and substitutions on the oxaziridine. Here we show that oxaziridine reagents react rapidly with the thioether in biotin to produce sulfimide products that are stable for more than 10 d at 37 °C. This method, which we call biotin redox-activated chemical tagging (BioReACT), expands the utility of biotin labeling and enables a predictable and stable chemical conjugation to biomolecules without the need to screen for a suitable methionine conjugation site. We demonstrate the versatility of this approach by producing a fluorescently labeled antibody, an antibody-drug conjugate, and a small molecule-conjugated oligonucleotide. We anticipate that BioReACT will be useful to rapidly introduce biorthogonal handles into biomolecules using biotin, a functional group that is widespread and straightforward to install.
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Affiliation(s)
- Adam D Cotton
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco 94143, California, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco 94143, California, United States
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco 94143, California, United States.,Cardiovascular Research Institute, University of California San Francisco, San Francisco 94143, California, United States
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9
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Gonzalez-Valero A, Reeves AG, Page ACS, Moon PJ, Miller E, Coulonval K, Crossley SWM, Xie X, He D, Musacchio PZ, Christian AH, McKenna JM, Lewis RA, Fang E, Dovala D, Lu Y, McGregor LM, Schirle M, Tallarico JA, Roger PP, Toste FD, Chang CJ. An Activity-Based Oxaziridine Platform for Identifying and Developing Covalent Ligands for Functional Allosteric Methionine Sites: Redox-Dependent Inhibition of Cyclin-Dependent Kinase 4. J Am Chem Soc 2022; 144:22890-22901. [PMID: 36484997 PMCID: PMC10124963 DOI: 10.1021/jacs.2c04039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Activity-based protein profiling (ABPP) is a versatile strategy for identifying and characterizing functional protein sites and compounds for therapeutic development. However, the vast majority of ABPP methods for covalent drug discovery target highly nucleophilic amino acids such as cysteine or lysine. Here, we report a methionine-directed ABPP platform using Redox-Activated Chemical Tagging (ReACT), which leverages a biomimetic oxidative ligation strategy for selective methionine modification. Application of ReACT to oncoprotein cyclin-dependent kinase 4 (CDK4) as a representative high-value drug target identified three new ligandable methionine sites. We then synthesized a methionine-targeting covalent ligand library bearing a diverse array of heterocyclic, heteroatom, and stereochemically rich substituents. ABPP screening of this focused library identified 1oxF11 as a covalent modifier of CDK4 at an allosteric M169 site. This compound inhibited kinase activity in a dose-dependent manner on purified protein and in breast cancer cells. Further investigation of 1oxF11 found prominent cation-π and H-bonding interactions stabilizing the binding of this fragment at the M169 site. Quantitative mass-spectrometry studies validated 1oxF11 ligation of CDK4 in breast cancer cell lysates. Further biochemical analyses revealed cross-talk between M169 oxidation and T172 phosphorylation, where M169 oxidation prevented phosphorylation of the activating T172 site on CDK4 and blocked cell cycle progression. By identifying a new mechanism for allosteric methionine redox regulation on CDK4 and developing a unique modality for its therapeutic intervention, this work showcases a generalizable platform that provides a starting point for engaging in broader chemoproteomics and protein ligand discovery efforts to find and target previously undruggable methionine sites.
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Affiliation(s)
- Angel Gonzalez-Valero
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Audrey G. Reeves
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Annika C. S. Page
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Patrick J. Moon
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Edward Miller
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Katia Coulonval
- Faculté de Médecine, Institute of Interdisciplinary Research, Université Libre de Bruxelles, Campus Erasme, Brussels 1070, Belgium
| | - Steven W. M. Crossley
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Xiao Xie
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Dan He
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Patricia Z. Musacchio
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alec H. Christian
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jeffrey M. McKenna
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Richard A. Lewis
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Eric Fang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Dustin Dovala
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Yipin Lu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Lynn M. McGregor
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Pierre P. Roger
- Faculté de Médecine, Institute of Interdisciplinary Research, Université Libre de Bruxelles, Campus Erasme, Brussels 1070, Belgium
| | - F. Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
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10
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Reddy NC, Molla R, Joshi PN, T. K. S, Basu I, Kawadkar J, Kalra N, Mishra RK, Chakrabarty S, Shukla S, Rai V. Traceless cysteine-linchpin enables precision engineering of lysine in native proteins. Nat Commun 2022; 13:6038. [PMID: 36229616 PMCID: PMC9561114 DOI: 10.1038/s41467-022-33772-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
The maintenance of machinery requires its operational understanding and a toolbox for repair. The methods for the precision engineering of native proteins meet a similar requirement in biosystems. Its success hinges on the principles regulating chemical reactions with a protein. Here, we report a technology that delivers high-level control over reactivity, chemoselectivity, site-selectivity, modularity, dual-probe installation, and protein-selectivity. It utilizes cysteine-based chemoselective Linchpin-Directed site-selective Modification of lysine residue in a protein (LDMC-K). The efficiency of the end-user-friendly protocol is evident in quantitative conversions within an hour. A chemically orthogonal C-S bond-formation and bond-dissociation are essential among multiple regulatory attributes. The method offers protein selectivity by targeting a single lysine residue of a single protein in a complex biomolecular mixture. The protocol renders analytically pure single-site probe-engineered protein bioconjugate. Also, it provides access to homogeneous antibody conjugates (AFC and ADC). The LDMC-K-ADC exhibits highly selective anti-proliferative activity towards breast cancer cells.
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Affiliation(s)
- Neelesh C. Reddy
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Rajib Molla
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Pralhad Namdev Joshi
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Sajeev T. K.
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Ipsita Basu
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Jyotsna Kawadkar
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | | | - Ram Kumar Mishra
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Suman Chakrabarty
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Sanjeev Shukla
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Vishal Rai
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
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11
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He D, Feng H, Sundberg B, Yang J, Powers J, Christian AH, Wilkinson JE, Monnin C, Avizonis D, Thomas CJ, Friedman RA, Kluger MD, Hollingsworth MA, Grandgenett PM, Klute KA, Toste FD, Chang CJ, Chio IIC. Methionine oxidation activates pyruvate kinase M2 to promote pancreatic cancer metastasis. Mol Cell 2022; 82:3045-3060.e11. [PMID: 35752173 PMCID: PMC9391305 DOI: 10.1016/j.molcel.2022.06.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/06/2022] [Accepted: 06/02/2022] [Indexed: 02/07/2023]
Abstract
Cancer mortality is primarily a consequence of its metastatic spread. Here, we report that methionine sulfoxide reductase A (MSRA), which can reduce oxidized methionine residues, acts as a suppressor of pancreatic ductal adenocarcinoma (PDA) metastasis. MSRA expression is decreased in the metastatic tumors of PDA patients, whereas MSRA loss in primary PDA cells promotes migration and invasion. Chemoproteomic profiling of pancreatic organoids revealed that MSRA loss results in the selective oxidation of a methionine residue (M239) in pyruvate kinase M2 (PKM2). Moreover, M239 oxidation sustains PKM2 in an active tetrameric state to promote respiration, migration, and metastasis, whereas pharmacological activation of PKM2 increases cell migration and metastasis in vivo. These results demonstrate that methionine residues can act as reversible redox switches governing distinct signaling outcomes and that the MSRA-PKM2 axis serves as a regulatory nexus between redox biology and cancer metabolism to control tumor metastasis.
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Affiliation(s)
- Dan He
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Huijin Feng
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Belen Sundberg
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jiaxing Yang
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Justin Powers
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alec H Christian
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Cian Monnin
- Metabolomics Innovation Resource, Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Daina Avizonis
- Metabolomics Innovation Resource, Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA; Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard A Friedman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael D Kluger
- Division of Gastrointestinal & Endocrine Surgery, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Paul M Grandgenett
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kelsey A Klute
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Iok In Christine Chio
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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12
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Montgomery HR, Messina MS, Doud EA, Spokoyny AM, Maynard HD. Organometallic S-arylation Reagents for Rapid PEGylation of Biomolecules. Bioconjug Chem 2022; 33:1536-1542. [PMID: 35939764 DOI: 10.1021/acs.bioconjchem.2c00280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioconjugation techniques for biomolecule-polymer conjugation are numerous; however, slow kinetics and steric challenges generally necessitate excess reagents or long reaction times. Organometallic transformations are known to circumvent these issues; yet, harsh reaction conditions, incompatibility in aqueous media, and substrate promiscuity often limit their use in a biological context. The work reported herein demonstrates a facile and benign organometallic Au(III) S-arylation approach that enables the synthesis of poly(ethylene glycol) monomethyl ether (mPEG)-protein conjugates with high efficiency. Isolable and bench-stable 2, 5, and 10 kDa mPEG-Au(III) reagents were synthesized via oxidative addition into terminal aryl iodide substituents installed on mPEG substrates with a (Me-DalPhos)Au(I)Cl precursor. Reaction of the isolable mPEG-Au(III) oxidative addition complexes with a cysteine thiol on a biomolecule resulted in facile and selective cysteine arylation chemistry, forging covalent S-aryl linkages and affording the mPEG-biomolecule conjugates. Notably, low polymer reagent loadings were used to achieve near quantitative conversion at room temperature in 1 min due to the rapid kinetics and high chemoselectivity of this Au-based bioconjugation approach. Therefore, this work represents an important addition to the protein-polymer conjugation chemical toolbox.
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Affiliation(s)
- Hayden R Montgomery
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Marco S Messina
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Evan A Doud
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Alexander M Spokoyny
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States.,California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, United States
| | - Heather D Maynard
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States.,California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, United States
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13
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Zare F, Potenza A, Greschner AA, Gauthier MA. Consecutive Alkylation, "Click", and "Clip" Reactions for the Traceless Methionine-Based Conjugation and Release of Methionine-Containing Peptides. Biomacromolecules 2022; 23:2891-2899. [PMID: 35671380 DOI: 10.1021/acs.biomac.2c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
"Click" reactions have revolutionized research in many areas of science. However, a disadvantage of the high stability of the Click product is that identifying simple treatments for cleanly dissociating the latter under the same guiding principles, i.e., a "Clip" reaction, remains a challenge. This study demonstrates that electron-deficient alkynes, conveniently installed on methionine residues, can participate in well-known Click (nucleophilic thiol-allene addition) and subsequent Clip reactions (radical thiol-ene addition). To illustrate this concept, a variety of bioconjugates (peptide-peptide; peptide-fluorophore; peptide-polymer; and peptide-protein) were prepared. Interestingly, the Clip reaction of these bioconjugates releases the original peptides concurrent with regeneration of their unmodified methionine residue, in minutes. Moreover, the conjugates demonstrate substantial stability toward endogenous levels of reactive species in bacteria, illustrating the potential for this chemistry in the biosciences. The reaction conditions employed in the Click and Clip steps are compatible with the preservation of the integrity of biomolecules/fluorophores and involve readily accessible reagents and the natural functional groups on peptides/proteins.
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Affiliation(s)
- Fatemeh Zare
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes J3X 1S2, Canada
| | - Alessandro Potenza
- Swiss Federal Institute of Technology Zurich (ETHZ), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zurich 8092, Switzerland
| | - Andrea A Greschner
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes J3X 1S2, Canada
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes J3X 1S2, Canada.,Swiss Federal Institute of Technology Zurich (ETHZ), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zurich 8092, Switzerland
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14
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Kong Y, Zeng K, Zhang Y, Shao J, Yan J, Liao JY, Wang W, Dai X, Weng Q, Yao SQ, Zeng S, Qian L. In vivo targeted delivery of antibodies into cancer cells with pH-responsive cell-penetrating poly(disulfide)s. Chem Commun (Camb) 2022; 58:1314-1317. [PMID: 35005760 DOI: 10.1039/d1cc06840g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cell-penetrating poly(disulfide)s (CPDs) are promising vehicles for cytosolic delivery of proteins. However, currently available arginine-rich CPD has rarely been reported for systemic delivery due to its "always" positive charge. Herein, we developed pH-responsive CPDIMD that executes tumor targeting delivery via protonation of imidazole groups within the acidic tumor microenvironment.
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Affiliation(s)
- Yulong Kong
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Kui Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Ying Zhang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Jinning Shao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Jiaqi Yan
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Wenchao Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Xiaoyang Dai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Qinjie Weng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China.
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15
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A tandem activity-based sensing and labeling strategy enables imaging of transcellular hydrogen peroxide signaling. Proc Natl Acad Sci U S A 2021; 118:2018513118. [PMID: 33622793 DOI: 10.1073/pnas.2018513118] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) like hydrogen peroxide (H2O2) are transient species that have broad actions in signaling and stress, but spatioanatomical understanding of their biology remains insufficient. Here, we report a tandem activity-based sensing and labeling strategy for H2O2 imaging that enables capture and permanent recording of localized H2O2 fluxes. Peroxy Green-1 Fluoromethyl (PG1-FM) is a diffusible small-molecule probe that senses H2O2 by a boronate oxidation reaction to trigger dual release and covalent labeling of a fluorescent product, thus preserving spatial information on local H2O2 changes. This unique reagent enables visualization of transcellular redox signaling in a microglia-neuron coculture cell model, where selective activation of microglia for ROS production increases H2O2 in nearby neurons. In addition to identifying ROS-mediated cell-to-cell communication, this work provides a starting point for the design of chemical probes that can achieve high spatial fidelity by combining activity-based sensing and labeling strategies.
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16
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Abstract
Site-selective chemical bioconjugation reactions are enabling tools for the chemical biologist. Guided by a careful study of the selenomethionine (SeM) benzylation, we have refined the reaction to meet the requirements of practical protein bioconjugation. SeM is readily introduced through auxotrophic expression and exhibits unique nucleophilic properties that allow it to be selectively modified even in the presence of cysteine. The resulting benzylselenonium adduct is stable at physiological pH, is selectively labile to glutathione, and embodies a broadly tunable cleavage profile. Specifically, a 4-bromomethylphenylacetyl (BrMePAA) linker has been applied for efficient conjugation of complex organic molecules to SeM-containing proteins. This expansion of the bioconjugation toolkit has broad potential in the development of chemically enhanced proteins.
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17
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Kim J, Li BX, Huang RYC, Qiao JX, Ewing WR, MacMillan DWC. Site-Selective Functionalization of Methionine Residues via Photoredox Catalysis. J Am Chem Soc 2020; 142:21260-21266. [PMID: 33290649 DOI: 10.1021/jacs.0c09926] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bioconjugation technologies have revolutionized the practice of biology and medicine by allowing access to novel biomolecular scaffolds. New methods for residue-selective bioconjugation are highly sought to expand the toolbox for a variety of bioconjugation applications. Herein we report a site-selective methionine bioconjugation protocol that uses photoexcited lumiflavin to generate open-shell intermediates. This reduction-potential-gated strategy enables access to residues unavailable with traditional nucleophilicity-based conjugation methods. To demonstrate the versatility and robustness of this new protocol, we have modified various proteins and further utilized this functional handle to append diverse biological payloads.
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Affiliation(s)
- Junyong Kim
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Beryl X Li
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08542, United States
| | - Jennifer X Qiao
- Discovery Chemistry, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08542, United States
| | - William R Ewing
- Discovery Chemistry, Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey 08542, United States
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
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18
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Hira J, Uddin MJ, Haugland MM, Lentz CS. From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology. Molecules 2020; 25:E4949. [PMID: 33114655 PMCID: PMC7663024 DOI: 10.3390/molecules25214949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways.
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Affiliation(s)
- Jonathan Hira
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Md. Jalal Uddin
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Marius M. Haugland
- Department of Chemistry and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway;
| | - Christian S. Lentz
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
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19
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Anderson DP, Benns HJ, Tate EW, Child MA. CRISPR-TAPE: protein-centric CRISPR guide design for targeted proteome engineering. Mol Syst Biol 2020; 16:e9475. [PMID: 32485092 PMCID: PMC7266498 DOI: 10.15252/msb.20209475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/30/2022] Open
Abstract
Rational molecular engineering of proteins with CRISPR-based approaches is challenged by the gene-centric nature of gRNA design tools. To address this, we have developed CRISPR-TAPE, a protein-centric gRNA design algorithm that allows users to target specific residues, or amino acid types within proteins. gRNA outputs can be customized to support maximal efficacy of homology-directed repair for engineering purposes, removing time-consuming post hoc curation, simplifying gRNA outputs and reducing CPU times.
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Affiliation(s)
| | - Henry James Benns
- Department of Life SciencesImperial College LondonLondonUK
- Department of ChemistryImperial College LondonLondonUK
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20
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Reddy NC, Kumar M, Molla R, Rai V. Chemical methods for modification of proteins. Org Biomol Chem 2020; 18:4669-4691. [DOI: 10.1039/d0ob00857e] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The field of protein bioconjugation draws attention from stakeholders in chemistry, biology, and medicine. This review provides an overview of the present status, challenges, and opportunities for organic chemists.
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Affiliation(s)
- Neelesh C. Reddy
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Mohan Kumar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Rajib Molla
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Vishal Rai
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
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