1
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Zou M, Zhou H, Gu L, Zhang J, Fang L. Therapeutic Target Identification and Drug Discovery Driven by Chemical Proteomics. BIOLOGY 2024; 13:555. [PMID: 39194493 DOI: 10.3390/biology13080555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/07/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024]
Abstract
Throughout the human lifespan, from conception to the end of life, small molecules have an intrinsic relationship with numerous physiological processes. The investigation into small-molecule targets holds significant implications for pharmacological discovery. The determination of the action sites of small molecules provide clarity into the pharmacodynamics and toxicological mechanisms of small-molecule drugs, assisting in the elucidation of drug off-target effects and resistance mechanisms. Consequently, innovative methods to study small-molecule targets have proliferated in recent years, with chemical proteomics standing out as a vanguard development in chemical biology in the post-genomic age. Chemical proteomics can non-selectively identify unknown targets of compounds within complex biological matrices, with both probe and non-probe modalities enabling effective target identification. This review attempts to summarize methods and illustrative examples of small-molecule target identification via chemical proteomics. It delves deeply into the interactions between small molecules and human biology to provide pivotal directions and strategies for the discovery and comprehension of novel pharmaceuticals, as well as to improve the evaluation of drug safety.
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Affiliation(s)
- Mingjie Zou
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Haiyuan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Letian Gu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Jingzi Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Lei Fang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
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2
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Lou J, Ancajas CF, Zhou Y, Lane NS, Reynolds TB, Best MD. Probing Glycerolipid Metabolism using a Caged Clickable Glycerol-3-Phosphate Probe. Chembiochem 2024:e202300853. [PMID: 38705850 DOI: 10.1002/cbic.202300853] [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: 12/19/2023] [Revised: 04/25/2024] [Accepted: 05/05/2024] [Indexed: 05/07/2024]
Abstract
In this study, we present the probe SATE-G3P-N3 as a novel tool for metabolic labeling of glycerolipids (GLs) to investigate lipid metabolism in yeast cells. By introducing a clickable azide handle onto the glycerol backbone, this probe enables general labeling of glycerolipids. Additionally, this probe contains a caged phosphate moiety at the glycerol sn-3 position to not only facilitate probe uptake by masking negative charge but also to bypass the phosphorylation step crucial for initiating phospholipid synthesis, thereby enhancing phospholipid labeling. The metabolic labeling activity of the probe was thoroughly assessed through cellular fluorescence microscopy, mass spectrometry (MS), and thin-layer chromatography (TLC) experiments. Fluorescence microscopy analysis demonstrated successful incorporation of the probe into yeast cells, with labeling predominantly localized at the plasma membrane. LCMS analysis confirmed metabolic labeling of various phospholipid species (PC, PS, PA, PI, and PG) and neutral lipids (MAG, DAG, and TAG), and GL labeling was corroborated by TLC. These results showcased the potential of the SATE-G3P-N3 probe in studying GL metabolism, offering a versatile and valuable approach to explore the intricate dynamics of lipids in yeast cells.
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Affiliation(s)
- Jinchao Lou
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Christelle F Ancajas
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Yue Zhou
- Department of Microbiology, University of Tennessee, Knoxville, 1311 Cumberland Avenue, Knoxville, TN, 337996, USA
| | - Nicolas S Lane
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, 1311 Cumberland Avenue, Knoxville, TN, 337996, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
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3
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Huang W, Laughlin ST. Cell-selective bioorthogonal labeling. Cell Chem Biol 2024; 31:409-427. [PMID: 37837964 DOI: 10.1016/j.chembiol.2023.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/25/2023] [Accepted: 09/19/2023] [Indexed: 10/16/2023]
Abstract
In classic bioorthogonal labeling experiments, the cell's biosynthetic machinery incorporates bioorthogonal tags, creating tagged biomolecules that are subsequently reacted with a corresponding bioorthogonal partner. This two-step approach labels biomolecules throughout the organism indiscriminate of cell type, which can produce background in applications focused on specific cell populations. In this review, we cover advances in bioorthogonal chemistry that enable targeting of bioorthogonal labeling to a desired cell type. Such cell-selective bioorthogonal labeling is achieved in one of three ways. The first approach restricts labeling to specific cells by cell-selective expression of engineered enzymes that enable the bioorthogonal tag's incorporation. The second approach preferentially localizes the bioorthogonal reagents to the desired cell types to restrict their uptake to the desired cells. Finally, the third approach cages the reactivity of the bioorthogonal reagents, allowing activation of the reaction in specific cells by uncaging the reagents selectively in those cell populations.
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Affiliation(s)
- Wei Huang
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Scott T Laughlin
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA.
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4
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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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5
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Zhang Q, Kuang G, Wang L, Duan P, Sun W, Ye F. Designing Bioorthogonal Reactions for Biomedical Applications. RESEARCH (WASHINGTON, D.C.) 2023; 6:0251. [PMID: 38107023 PMCID: PMC10723801 DOI: 10.34133/research.0251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 12/19/2023]
Abstract
Bioorthogonal reactions are a class of chemical reactions that can be carried out in living organisms without interfering with other reactions, possessing high yield, high selectivity, and high efficiency. Since the first proposal of the conception by Professor Carolyn Bertozzi in 2003, bioorthogonal chemistry has attracted great attention and has been quickly developed. As an important chemical biology tool, bioorthogonal reactions have been applied broadly in biomedicine, including bio-labeling, nucleic acid functionalization, drug discovery, drug activation, synthesis of antibody-drug conjugates, and proteolysis-targeting chimeras. Given this, we summarized the basic knowledge, development history, research status, and prospects of bioorthogonal reactions and their biomedical applications. The main purpose of this paper is to furnish an overview of the intriguing bioorthogonal reactions in a variety of biomedical applications and to provide guidance for the design of novel reactions to enrich bioorthogonal chemistry toolkits.
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Affiliation(s)
- Qingfei Zhang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
| | - Gaizhen Kuang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Li Wang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Ping Duan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Weijian Sun
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Fangfu Ye
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
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6
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Chowdhury A, Chatterjee S, Kushwaha A, Nanda S, Dhilip Kumar TJ, Bandyopadhyay A. Sulfonyl Diazaborine 'Click' Chemistry Enables Rapid and Efficient Bioorthogonal Labeling. Chemistry 2023; 29:e202300393. [PMID: 37155600 DOI: 10.1002/chem.202300393] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
Finding an ideal bioorthogonal reaction that responds to a wide range of biological queries and applications is of great interest in biomedical applications. Rapid diazaborine (DAB) formation in water by the reactions of ortho-carbonyl phenylboronic acid with α-nucleophiles is an attractive conjugation module. Nevertheless, these conjugation reactions demand to satisfy stringent criteria for bioorthogonal applications. Here we show that widely used sulfonyl hydrazide (SHz) offers a stable DAB conjugate by combining with ortho-carbonyl phenylboronic acid at physiological pH, competent for an optimal biorthogonal reaction. Remarkably, the reaction conversion is quantitative and rapid (k2 >103 M-1 s-1 ) at low micromolar concentrations, and it preserves comparable efficacy in a complex biological milieu. DFT calculations support that SHz facilitates DAB formation via the most stable hydrazone intermediate and the lowest energy transition state compared to other biocompatible α-nucleophiles. This conjugation is extremely efficient on living cell surfaces, enabling compelling pretargeted imaging and peptide delivery. We anticipate this work will permit addressing a wide range of cell biology queries and drug discovery platforms exploiting commercially available sulfonyl hydrazide fluorophores and derivatives.
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Affiliation(s)
- Arnab Chowdhury
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India
| | - Saurav Chatterjee
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India
| | - Apoorv Kushwaha
- Quantum Dynamics Laboratory, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India
| | - Sidhanta Nanda
- Immunology Lab, Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India
| | - T J Dhilip Kumar
- Quantum Dynamics Laboratory, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India
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7
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Ancajas CF, Carr AJ, Lou J, Sagar R, Zhou Y, Reynolds TB, Best MD. Harnessing Clickable Acylated Glycerol Probes as Chemical Tools for Tracking Glycerolipid Metabolism. Chemistry 2023; 29:e202300417. [PMID: 37085958 PMCID: PMC10498425 DOI: 10.1002/chem.202300417] [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: 02/08/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 04/23/2023]
Abstract
We report the use of clickable monoacylglycerol (MAG) analogs as probes for the labeling of glycerolipids during lipid metabolism. Incorporation of azide tags onto the glycerol region was pursued to develop probes that would label glycerolipids, in which the click tag would not be removed through processes including acyl chain and headgroup remodeling. Analysis of clickable MAG probes containing acyl chains of different length resulted in widely variable cell imaging and cytotoxicity profiles. Based on these results, we focused on a probe bearing a short acyl chain (C4 -MAG-N3 ) that was found to infiltrate natural lipid biosynthetic pathways to produce click-tagged versions of both neutral and phospholipid products. Alternatively, strategic blocking of the glycerol sn-3 position in probe C4 -MEG-N3 served to deactivate phospholipid tagging and focus labeling on neutral lipids. This work shows that lipid metabolic labeling profiles can be tuned based on probe structures and provides valuable tools for evaluating alterations to lipid metabolism in cells.
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Affiliation(s)
- Christelle F Ancajas
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Adam J Carr
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Jinchao Lou
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Ruhani Sagar
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Yue Zhou
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN, 37996, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN, 37996, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
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8
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Ancajas CF, Alam S, Alves DS, Zhou Y, Wadsworth NM, Cassilly CD, Ricks TJ, Carr AJ, Reynolds TB, Barrera FN, Best MD. Cellular Labeling of Phosphatidylserine Using Clickable Serine Probes. ACS Chem Biol 2023; 18:377-384. [PMID: 36745020 DOI: 10.1021/acschembio.2c00813] [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: 02/07/2023]
Abstract
Phosphatidylserine (PS) is a key lipid that plays important roles in disease-related biological processes, and therefore, the means to track PS in live cells are invaluable. Herein, we describe the metabolic labeling of PS in Saccharomyces cerevisiae cells using analogues of serine, a PS precursor, derivatized with azide moieties at either the amino (N-l-SerN3) or carbonyl (C-l-SerN3) groups. The conservative click tag modification enabled these compounds to infiltrate normal lipid biosynthetic pathways, thereby producing tagged PS molecules as supported by mass spectrometry studies, thin-layer chromatography (TLC) analysis, and further derivatization with fluorescent reporters via click chemistry to enable imaging in yeast cells. This approach shows strong prospects for elucidating the complex biosynthetic and trafficking pathways involving PS.
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Affiliation(s)
- Christelle F Ancajas
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Shahrina Alam
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Yue Zhou
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Nicholas M Wadsworth
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Chelsi D Cassilly
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Tanei J Ricks
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Adam J Carr
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Michael D Best
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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Shanbhag K, Sharma K, Kamat SS. Photoreactive bioorthogonal lipid probes and their applications in mammalian biology. RSC Chem Biol 2023; 4:37-46. [PMID: 36685253 PMCID: PMC9811504 DOI: 10.1039/d2cb00174h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
Lipids are an important class of biological molecules that possess many critical physiological functions, which enable the optimal survival of all organisms, including humans. While the role of lipids in the formation of biological cellular membranes and as a source of energy is fairly well understood, the cellular signalling pathways that lipids modulate in mammals are, in comparison, poorly characterized mechanistically and/or largely unknown. In an effort to dissect these mammalian cellular pathways regulated by signalling lipids and map hitherto unknown protein-lipid interactions, the last two decades have seen tremendous progress in the development of multifunctional lipid probes that, in conjunction with well-established bioorthogonal chemistries and chemoproteomics platforms, has almost exponentially expanded our knowledge in this field. In this review, we focus on the various photoreactive bioorthogonal lipid probes described in the literature, and briefly summarize the different photo-crosslinking groups and bioorthogonal chemistries used by them. Furthermore, we report specific case examples of such photoreactive bioorthogonal lipid probes, and discuss the new biological pathways and insights that have emerged from their use through chemoproteomics in mammalian cells. Finally, we highlight the challenges associated with the use of lipid probes in biological systems, and highlight their importance in the discovery and mechanistic understanding of lipid signalling pathways in the years to come.
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Affiliation(s)
- Karthik Shanbhag
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan Pune 411008 Maharashtra India
| | - Kavita Sharma
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan Pune 411008 Maharashtra India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan Pune 411008 Maharashtra India
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10
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Zhao X, Yang X, Hang HC. Chemoproteomic Analysis of Microbiota Metabolite-Protein Targets and Mechanisms. Biochemistry 2022; 61:2822-2834. [PMID: 34989554 PMCID: PMC9256862 DOI: 10.1021/acs.biochem.1c00758] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The microbiota have emerged as an important factor in host physiology, disease, and response to therapy. These diverse microbes (bacteria, virus, fungi, and protists) encode unique functions and metabolites that regulate intraspecies and interspecies interactions. While the mechanisms of some microbiota species and metabolites have been elucidated, the diversity and abundance of different microbiota species and their associated pathways suggest many more metabolites and mechanisms of action remain to be discovered. In this Perspective, we highlight how the advances in chemical proteomics have provided new opportunities to elucidate the molecular targets of specific microbiota metabolites and reveal new mechanisms of action. The continued development of specific microbiota metabolite reporters and more precise proteomic methods should reveal new microbiota mechanisms of action, therapeutic targets, and biomarkers for a variety of human diseases.
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11
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Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJC, Overkleeft HS, van der Stelt M, van Kasteren SI. Live-Cell Imaging of Sterculic Acid-a Naturally Occurring 1,2-Cyclopropene Fatty Acid-by Bioorthogonal Reaction with Turn-On Tetrazine-Fluorophore Conjugates. Angew Chem Int Ed Engl 2022; 61:e202207640. [PMID: 35838324 PMCID: PMC9546306 DOI: 10.1002/anie.202207640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Indexed: 12/25/2022]
Abstract
In the field of lipid research, bioorthogonal chemistry has made the study of lipid uptake and processing in living systems possible, whilst minimising biological properties arising from detectable pendant groups. To allow the study of unsaturated free fatty acids in live cells, we here report the use of sterculic acid, a 1,2-cyclopropene-containing oleic acid analogue, as a bioorthogonal probe. We show that this lipid can be readily taken up by dendritic cells without toxic side effects, and that it can subsequently be visualised using an inverse electron-demand Diels-Alder reaction with quenched tetrazine-fluorophore conjugates. In addition, the lipid can be used to identify changes in protein oleoylation after immune cell activation. Finally, this reaction can be integrated into a multiplexed bioorthogonal reaction workflow by combining it with two sequential copper-catalysed Huisgen ligation reactions. This allows for the study of multiple biomolecules in the cell simultaneously by multimodal confocal imaging.
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Affiliation(s)
- Kristine Bertheussen
- Department of Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Merel van de Plassche
- Department of Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Thomas Bakkum
- Department of Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Berend Gagestein
- Department of Molecular PhysiologyLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Iakovia Ttofi
- Department of Molecular PhysiologyLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Alexi J. C. Sarris
- Department of Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Department of Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Mario van der Stelt
- Department of Molecular PhysiologyLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Sander I. van Kasteren
- Department of Bio-Organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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12
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Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJ, Overkleeft HS, van der Stelt M, van Kasteren SI. Live‐Cell Imaging of Sterculic Acid – a Naturally Occurring 1,2‐Cyclopropene Fatty Acid – by Bioorthogonal Reaction with Turn‐On Tetrazine‐Fluorophore Conjugates. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kristine Bertheussen
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | | | - Thomas Bakkum
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Berend Gagestein
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Iakovia Ttofi
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Alexi J.C. Sarris
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Herman S. Overkleeft
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Mario van der Stelt
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Sander Izaak van Kasteren
- Leiden University Leiden Institute of Chemistry Gorlaeus LaboratoryEinsteinweg 55 2333 CC Leiden NETHERLANDS
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13
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Mondal J, Sivaramakrishna A. Functionalized Triazines and Tetrazines: Synthesis and Applications. Top Curr Chem (Cham) 2022; 380:34. [PMID: 35737142 DOI: 10.1007/s41061-022-00385-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/13/2022] [Indexed: 12/19/2022]
Abstract
The molecules possessing triazine and tetrazine moieties belong to a special class of heterocyclic compounds. Both triazines and tetrazines are building blocks and have provided a new dimension to the design of biologically important organic molecules. Several of their derivatives with fine-tuned electronic properties have been identified as multifunctional, adaptable, switchable, remarkably antifungal, anticancer, antiviral, antitumor, cardiotonic, anti-HIV, analgesic, anti-protozoal, etc. The objective of this review is to comprehensively describe the recent developments in synthesis, coordination properties, and various applications of triazine and tetrazine molecules. The rich literature demonstrates various synthetic routes for a variety of triazines and tetrazines through microwave-assisted, solid-phase, metal-based, [4+2] cycloaddition, and multicomponent one-pot reactions. Synthetic approaches contain linear, angular, and fused triazine and tetrazine heterocycles through a combinatorial method. Notably, the triazines and tetrazines undergo a variety of organic transformations, including electrophilic addition, coupling, nucleophilic displacement, and intramolecular cyclization. The mechanistic aspects of these heterocycles are discussed in a detailed way. The bioorthogonal application of these polyazines with various strained alkenes and alkynes provides a new prospect for investigations in chemical biology. This review systematically encapsulates the recent developments and challenges in the synthesis and possible potential applications of various triazine and tetrazine systems.
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Affiliation(s)
- Joydip Mondal
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632 014, India
| | - Akella Sivaramakrishna
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632 014, India.
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14
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Zhang X, Gao J, Tang Y, Yu J, Liew SS, Qiao C, Cao Y, Liu G, Fan H, Xia Y, Tian J, Pu K, Wang Z. Bioorthogonally activatable cyanine dye with torsion-induced disaggregation for in vivo tumor imaging. Nat Commun 2022; 13:3513. [PMID: 35717407 PMCID: PMC9206667 DOI: 10.1038/s41467-022-31136-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/27/2022] [Indexed: 11/17/2022] Open
Abstract
Advancement of bioorthogonal chemistry in molecular optical imaging lies in expanding the repertoire of fluorophores that can undergo fluorescence signal changes upon bioorthogonal ligation. However, most available bioorthogonally activatable fluorophores only emit shallow tissue-penetrating visible light via an intramolecular charge transfer mechanism. Herein, we report a serendipitous "torsion-induced disaggregation (TIDA)" phenomenon in the design of near-infrared (NIR) tetrazine (Tz)-based cyanine probe. The TIDA of the cyanine is triggered upon Tz-transcyclooctene ligation, converting its heptamethine chain from S-trans to S-cis conformation. Thus, after bioorthogonal reaction, the tendency of the resulting cyanine towards aggregation is reduced, leading to TIDA-induced fluorescence enhancement response. This Tz-cyanine probe sensitively delineates the tumor in living mice as early as 5 min post intravenous injection. As such, this work discovers a design mechanism for the construction of bioorthogonally activatable NIR fluorophores and opens up opportunities to further exploit bioorthogonal chemistry in in vivo imaging.
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Affiliation(s)
- Xianghan Zhang
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
- Academy of Advanced Interdisciplinary Research, Xidian University, Xi'an, Shaanxi, 710071, China
| | - Jingkai Gao
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Yingdi Tang
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Jie Yu
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Si Si Liew
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Chaoqiang Qiao
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Yutian Cao
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Guohuan Liu
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Hongyu Fan
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Yuqiong Xia
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Jie Tian
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine, Beihang University, Beijing, 100191, China.
| | - Kanyi Pu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore.
| | - Zhongliang Wang
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China.
- Academy of Advanced Interdisciplinary Research, Xidian University, Xi'an, Shaanxi, 710071, China.
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15
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Madeo G, Savojardo C, Luigi Martelli P, Casadio R. SVMyr: a web server detecting co- and post-translational myristoylation in proteins. J Mol Biol 2022; 434:167605. [DOI: 10.1016/j.jmb.2022.167605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/31/2022] [Accepted: 04/19/2022] [Indexed: 12/31/2022]
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16
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17
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Click chemistry-enabled CRISPR screening reveals GSK3 as a regulator of PLD signaling. Proc Natl Acad Sci U S A 2021; 118:2025265118. [PMID: 34810254 DOI: 10.1073/pnas.2025265118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 12/20/2022] Open
Abstract
Enzymes that produce second messengers are highly regulated. Revealing the mechanisms underlying such regulation is critical to understanding both how cells achieve specific signaling outcomes and return to homeostasis following a particular stimulus. Pooled genome-wide CRISPR screens are powerful unbiased approaches to elucidate regulatory networks, their principal limitation being the choice of phenotype selection. Here, we merge advances in bioorthogonal fluorescent labeling and CRISPR screening technologies to discover regulators of phospholipase D (PLD) signaling, which generates the potent lipid second messenger phosphatidic acid. Our results reveal glycogen synthase kinase 3 as a positive regulator of protein kinase C and PLD signaling. More generally, this work demonstrates how bioorthogonal, activity-based fluorescent tagging can expand the power of CRISPR screening to uncover mechanisms regulating specific enzyme-driven signaling pathways in mammalian cells.
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18
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Kang D, Cheung ST, Kim J. Bioorthogonal Hydroamination of Push-Pull-Activated Linear Alkynes. Angew Chem Int Ed Engl 2021; 60:16947-16952. [PMID: 34019705 DOI: 10.1002/anie.202104863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/16/2021] [Indexed: 01/14/2023]
Abstract
A bioorthogonal reaction between N,N-dialkylhydroxylamines and push-pull-activated halogenated alkynes is described. We explore the use of rehybridization effects in activating alkynes, and we show that electronic effects, when competing stereoelectronic and inductive factors are properly balanced, sufficiently activate a linear alkyne in the uncatalyzed conjugative retro-Cope elimination reaction while adequately protecting it against cellular nucleophiles. This design preserves the low steric profile of an alkyne and pairs it with a comparably unobtrusive hydroxylamine. The kinetics are on par with those of the fastest strain-promoted azide-alkyne cycloaddition reactions, the products regioselectively formed, the components sufficiently stable and easily installed, and the reaction suitable for cellular labeling.
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Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sheldon T Cheung
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
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19
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Kang D, Cheung ST, Kim J. Bioorthogonal Hydroamination of Push–Pull‐Activated Linear Alkynes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dahye Kang
- Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA
| | - Sheldon T. Cheung
- Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA
| | - Justin Kim
- Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA
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20
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Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
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Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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21
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Kang D, Kim J. Bioorthogonal Retro-Cope Elimination Reaction of N, N-Dialkylhydroxylamines and Strained Alkynes. J Am Chem Soc 2021; 143:5616-5621. [PMID: 33829777 DOI: 10.1021/jacs.1c00885] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A bioorthogonal reaction between N,N-dialkylhydroxylamines and cyclooctynes is described. This reaction features a highly regioselective transformation between small, easily functionalizable reaction components with second-order rate constants reaching 84 M-1 s-1. The reaction is orthogonal to the inverse-electron demand Diels-Alder reactions between tetrazine and strained alkenes, and its components exhibit exquisite stability and chemoselectivity in cell lysate. This retro-Cope elimination reaction introduces a new member to the bioorthogonal reaction compendium outside the prolific class of cycloaddition reactions.
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Affiliation(s)
- Dahye Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Justin Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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22
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Pseudopeptide Amyloid Aggregation Inhibitors: In Silico, Single Molecule and Cell Viability Studies. Int J Mol Sci 2021; 22:ijms22031051. [PMID: 33494369 PMCID: PMC7865305 DOI: 10.3390/ijms22031051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Neurodegeneration in Alzheimer's disease (AD) is defined by pathology featuring amyloid-β (Aβ) deposition in the brain. Aβ monomers themselves are generally considered to be nontoxic, but misfold into β-sheets and aggregate to form neurotoxic oligomers. One suggested strategy to treat AD is to prevent the formation of toxic oligomers. The SG inhibitors are a class of pseudopeptides designed and optimized using molecular dynamics (MD) simulations for affinity to Aβ and experimentally validated for their ability to inhibit amyloid-amyloid binding using single molecule force spectroscopy (SMFS). In this work, we provide a review of our previous MD and SMFS studies of these inhibitors and present new cell viability studies that demonstrate their neuroprotective effects against Aβ(1-42) oligomers using mouse hippocampal-derived HT22 cells. Two of the tested SG inhibitors, predicted to bind Aβ in anti-parallel orientation, demonstrated neuroprotection against Aβ(1-42). A third inhibitor, predicted to bind parallel to Aβ, was not neuroprotective. Myristoylation of SG inhibitors, intended to enhance delivery across the blood-brain barrier (BBB), resulted in cytotoxicity. This is the first use of HT22 cells for the study of peptide aggregation inhibitors. Overall, this work will inform the future development of peptide aggregation inhibitors against Aβ toxicity.
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23
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Hu Y, Roberts JM, Kilgore HR, Lani ASM, Raines RT, Schomaker JM. Triple, Mutually Orthogonal Bioorthogonal Pairs through the Design of Electronically Activated Sulfamate-Containing Cycloalkynes. J Am Chem Soc 2020; 142:18826-18835. [PMID: 33085477 PMCID: PMC7891878 DOI: 10.1021/jacs.0c06725] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds that are capable of fast and predictable reactions. The ability to easily modify S-, N-, and O-containing cyclooctynes (SNO-OCTs) enables electronic tuning of various SNO-OCTs to influence their cycloaddition rates with Type I-III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems. Significant reaction rate enhancements of a difluorinated SNO-OCT derivative, as compared to the parent scaffold, were noted, with the second-order rate constant in cycloadditions with diazoacetamides exceeding 5.13 M-1 s-1. Computational and experimental studies were employed to inform the design of triple ligation systems that encompass three orthogonal reactivities. Finally, polar SNO-OCTs are rapidly internalized by mammalian cells and remain functional in the cytosol for live-cell labeling, highlighting their potential for diverse in vitro and in vivo applications.
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Affiliation(s)
- Yun Hu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Jessica M. Roberts
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Henry R. Kilgore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amirah S. Mat Lani
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jennifer M. Schomaker
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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24
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Yang F, Wang C. Profiling of post-translational modifications by chemical and computational proteomics. Chem Commun (Camb) 2020; 56:13506-13519. [PMID: 33084662 DOI: 10.1039/d0cc05447j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational modifications (PTMs) diversify the molecular structures of proteins and play essential roles in regulating their functions. Abnormal PTM status has been linked to a variety of developmental disorders and human diseases, highlighting the importance of studying PTMs in understanding physiological processes and discovering novel nodes and links with therapeutic intervention potential. Classical biochemical methods are suitable for studying PTMs on individual proteins; however, global profiling of PTMs in proteomes remains a challenging task. In this feature article, we start with a brief review of the traditional affinity-based strategies and shift the emphasis to summarizing recent progress in the development and application of chemical and computational proteomic strategies to delineate the global landscapes of functional PTMs. Finally, we discuss current challenges in PTM detection and provide future perspectives on how the field can be further advanced.
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Affiliation(s)
- Fan Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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25
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Ancajas CF, Ricks TJ, Best MD. Metabolic labeling of glycerophospholipids via clickable analogs derivatized at the lipid headgroup. Chem Phys Lipids 2020; 232:104971. [PMID: 32898510 PMCID: PMC7606648 DOI: 10.1016/j.chemphyslip.2020.104971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/01/2020] [Indexed: 02/09/2023]
Abstract
Metabolic labeling, in which substrate analogs containing diminutive tags can infiltrate biosynthetic pathways and generate labeled products in cells, has led to dramatic advancements in the means by which complex biomolecules can be detected and biological processes can be elucidated. Within this realm, metabolic labeling of lipid products, particularly in a manner that is headgroup-specific, brings about a number of technical challenges including the complexity of lipid metabolic pathways as well as the simplicity of biosynthetic precursors to headgroup functionality. As such, only a handful of strategies for metabolic labeling of lipids have thus far been reported. However, these approaches provide enticing examples of how strategic modifications to substrate structures, particularly by introducing clickable moieties, can enable the hijacking of lipid biosynthesis. Furthermore, early work in this field has led to an explosion in diverse applications by which these techniques have been exploited to answer key biological questions or detect and track various lipid-containing biological entities. In this article, we review these efforts and emphasize recent advancements in the development and application of lipid metabolic labeling strategies.
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Affiliation(s)
- Christelle F Ancajas
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Tanei J Ricks
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA.
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26
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Yuan M, Chen X, Sun Y, Jiang L, Xia Z, Ye K, Jiang H, Yang B, Ying M, Cao J, He Q. ZDHHC12-mediated claudin-3 S-palmitoylation determines ovarian cancer progression. Acta Pharm Sin B 2020; 10:1426-1439. [PMID: 32963941 PMCID: PMC7488353 DOI: 10.1016/j.apsb.2020.03.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
The membrane protein claudin-3 (CLDN3) is critical for the formation and maintenance of tight junction and its high expression has been implicated in dictating malignant progression in various cancers. However, the post-translational modification of CLDN3 and its biological function remains poorly understood. Here, we report that CLDN3 is positively correlated with ovarian cancer progression both in vitro and in vivo. Of interest, CLDN3 undergoes S-palmitoylation on three juxtamembrane cysteine residues, which contribute to the accurate plasma membrane localization and protein stability of CLDN3. Moreover, the deprivation of S-palmitoylation in CLDN3 significantly abolishes its tumorigenic promotion effect in ovarian cancer cells. By utilizing the co-immunoprecipitation assay, we further identify ZDHHC12 as a CLDN3-targating palmitoyltransferase from 23 ZDHHC family proteins. Furthermore, the knockdown of ZDHHC12 also significantly inhibits CLDN3 accurate membrane localization, protein stability and ovarian cancer cells tumorigenesis. Thus, our work reveals S-palmitoylation as a novel regulatory mechanism that modulates CLDN3 function, which implies that targeting ZDHHC12-mediated CLDN3 S-palmitoylation might be a potential strategy for ovarian cancer therapy.
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Affiliation(s)
- Meng Yuan
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaobing Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yitang Sun
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Li Jiang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhongni Xia
- Tongde Hospital of Zhejiang Province, Hangzhou 310012, China
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Hong Jiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 100098, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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27
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Affiliation(s)
- Christin Bednarek
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Ilona Wehl
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Nicole Jung
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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28
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Wang L, Zhang J, Zhao J, Yu P, Wang S, Hu H, Wang R. Recent synthesis of functionalized s-tetrazines and their application in ligation reactions under physiological conditions: a concise overview. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2020. [DOI: 10.1080/01614940.2020.1726009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Li Wang
- Huazhong University of Science and Technology Wuhan City, China
| | - Jingwen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizhong Zhao
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Yu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongmei Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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29
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Tsukidate T, Li Q, Hang HC. Targeted and proteome-wide analysis of metabolite-protein interactions. Curr Opin Chem Biol 2020; 54:19-27. [PMID: 31790852 PMCID: PMC7131882 DOI: 10.1016/j.cbpa.2019.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/09/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022]
Abstract
Understanding the molecular mechanisms of endogenous and environmental metabolites is crucial for basic biology and drug discovery. With the genome, proteome, and metabolome of many organisms being readily available, researchers now have the opportunity to dissect how key metabolites regulate complex cellular pathways in vivo. Nonetheless, characterizing the specific and functional protein targets of key metabolites associated with specific cellular phenotypes remains a major challenge. Innovations in chemical biology are now poised to address this fundamental limitation in physiology and disease. In this review, we highlight recent advances in chemoproteomics for targeted and proteome-wide analysis of metabolite-protein interactions that have enabled the discovery of unpredicted metabolite-protein interactions and facilitated the development of new small molecule therapeutics.
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Affiliation(s)
- Taku Tsukidate
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, 10065, United States
| | - Qiang Li
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, 10065, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, 10065, United States.
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30
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Abstract
Bioorthogonal chemistry has offered an invaluable reactivity-based tool to chemical biology owing to its exquisite specificity in tagging a diverse set of biomolecules in their native environment. Despite tremendous progress in the field over the past decade, designing a suitable bioorthogonal chemical probe to investigate a given biological system remains a challenge. In this Perspective, we put forward a series of fitness factors that can be used to assess the performance of bioorthogonal chemical probes. The consideration of these criteria should encourage continuous innovation in bioorthogonal probe development as well as enhance the quality of biological data.
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Affiliation(s)
- Yulin Tian
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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31
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Inoue N, Onoda A, Hayashi T. Site-Specific Modification of Proteins through N-Terminal Azide Labeling and a Chelation-Assisted CuAAC Reaction. Bioconjug Chem 2019; 30:2427-2434. [DOI: 10.1021/acs.bioconjchem.9b00515] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Nozomu Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Akira Onoda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
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32
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Saleh AM, Wilding KM, Calve S, Bundy BC, Kinzer-Ursem TL. Non-canonical amino acid labeling in proteomics and biotechnology. J Biol Eng 2019; 13:43. [PMID: 31139251 PMCID: PMC6529998 DOI: 10.1186/s13036-019-0166-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/11/2019] [Indexed: 02/03/2023] Open
Abstract
Metabolic labeling of proteins with non-canonical amino acids (ncAAs) provides unique bioorthogonal chemical groups during de novo synthesis by taking advantage of both endogenous and heterologous protein synthesis machineries. Labeled proteins can then be selectively conjugated to fluorophores, affinity reagents, peptides, polymers, nanoparticles or surfaces for a wide variety of downstream applications in proteomics and biotechnology. In this review, we focus on techniques in which proteins are residue- and site-specifically labeled with ncAAs containing bioorthogonal handles. These ncAA-labeled proteins are: readily enriched from cells and tissues for identification via mass spectrometry-based proteomic analysis; selectively purified for downstream biotechnology applications; or labeled with fluorophores for in situ analysis. To facilitate the wider use of these techniques, we provide decision trees to help guide the design of future experiments. It is expected that the use of ncAA labeling will continue to expand into new application areas where spatial and temporal analysis of proteome dynamics and engineering new chemistries and new function into proteins are desired.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Kristen M. Wilding
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
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33
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Ejendal KFK, Fraseur JG, Kinzer-Ursem TL. Protein Labeling and Bioconjugation Using N-Myristoyltransferase. Methods Mol Biol 2019; 2033:149-165. [PMID: 31332753 DOI: 10.1007/978-1-4939-9654-4_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Methods that allow for labeling of proteins cotranslationally within protein expression systems have had wide-ranging applications in health, engineering, and medicine. Bioorthogonal chemistries that allow for conjugation of proteins or biomolecules of interest to substrates (fluorophores, gold nanoparticles, polymers, etc.) in living cells without prior enrichment or purification have likewise enabled advances in technology to study and engineer cellular and biomolecular systems. At the intersection of these, chemoenzymatic labeling of proteins at specific sites of interest and their subsequent selective bioconjugation to substrates without prior purification has dramatically streamlined workflows that allow proteins to reside in the native expression volumes as long as possible prior to conjugation, be readily isolated upon conjugation, and remain functionally active after conjugation. Here we present methods and protocols to express and label proteins of interest at the N-terminus with azide derivatives of myristic acid, a small, soluble, 14-carbon fatty acid, and conjugate the labeled protein to fluorophores and gold nanoparticle substrates. These methods can be extended to label proteins with other myristoyl derivatives and to conjugation to other solid or polymeric substrates of interest.
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Affiliation(s)
- Karin F K Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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34
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Sibbersen C, Schou Oxvig AM, Bisgaard Olesen S, Nielsen CB, Galligan JJ, Jørgensen KA, Palmfeldt J, Johannsen M. Profiling of Methylglyoxal Blood Metabolism and Advanced Glycation End-Product Proteome Using a Chemical Probe. ACS Chem Biol 2018; 13:3294-3305. [PMID: 30508371 DOI: 10.1021/acschembio.8b00732] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Methylglyoxal (MG) is quantitatively the most important precursor to advanced glycation end-products (AGEs), and evidence is accumulating that it is also a causally linked to diabetes and aging related diseases. Living systems primarily reside on the glyoxalase system to detoxify MG into benign d-lactate. The flux to either glycation or detoxification, accordingly, is a key parameter for how well a system handles the ubiquitous glyoxal burden. Furthermore, insight into proteins and in particular their individual modification sites are central to understanding the involvement of MG and AGE in diabetes and aging related diseases. Here, we present a simple method to simultaneously monitor the flux of MG both to d-lactate and to protein AGE formation in a biological sample by employing an alkyne-labeled methylglyoxal probe. We apply the method to blood and plasma to demonstrate the impact of blood cell glyoxalase activity on plasma protein AGE formation. We move on to isolate proteins modified by the MG probe and accordingly can present the first general inventory of more than 100 proteins and 300 binding sites of the methylglyoxal probe on plasma as well as erythrocytic proteins. Some of the data could be validated against a number of in vivo and in vitro targets for advanced glycation previously known from the literature; the majority of proteins and specific sites however were previously unknown and may guide future research into MG and AGE to elucidate how these are functionally linked to diabetic disease and aging.
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Affiliation(s)
- Christian Sibbersen
- Department of Forensic Medicine, Aarhus University, Aarhus 8200, Denmark
- Department of Chemistry, Aarhus University, Aarhus 8000, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus 8000, Denmark
| | - Anne-Mette Schou Oxvig
- Department of Forensic Medicine, Aarhus University, Aarhus 8200, Denmark
- Department of Chemistry, Aarhus University, Aarhus 8000, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus 8000, Denmark
| | - Sarah Bisgaard Olesen
- Department of Forensic Medicine, Aarhus University, Aarhus 8200, Denmark
- Department of Chemistry, Aarhus University, Aarhus 8000, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus 8000, Denmark
| | | | - James J. Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | | | - Johan Palmfeldt
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus 8000, Denmark
| | - Mogens Johannsen
- Department of Forensic Medicine, Aarhus University, Aarhus 8200, Denmark
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35
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Akgun B, Hall DG. Boronic Acids as Bioorthogonal Probes for Site‐Selective Labeling of Proteins. Angew Chem Int Ed Engl 2018; 57:13028-13044. [DOI: 10.1002/anie.201712611] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/23/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Dennis G. Hall
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
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36
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Bao X, Xiong Y, Li X, Li XD. A chemical reporter facilitates the detection and identification of lysine HMGylation on histones. Chem Sci 2018; 9:7797-7801. [PMID: 30429988 PMCID: PMC6194501 DOI: 10.1039/c8sc02483a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/21/2018] [Indexed: 01/19/2023] Open
Abstract
Chemical reporter, HMGAM-yne, facilitates the detection and identification of lysine HMGylation on histones.
Lysine 3-hydroxyl-3-methylglutarylation (HMG-K) is a newly identified PTM that can occur non-enzymatically in mitochondria. However, the substrate scope of this new PTM remains insufficiently explored, which has greatly hindered the progress in interpreting its regulatory mechanisms and cellular functions. Here, we report the development of an alkyne-functionalized chemical reporter (HMGAM-yne), for the detection and identification of cellular HMGylated proteins. HMGAM-yne is cell-permeable and metabolically incorporated into proteins in living cells. Subsequent biorthogonal conjugation enables fluorescence visualization and identification of the protein substrates of HMG-K. Using HMGAM-yne, we also identified Sirt5 as an ‘eraser’ that regulates HMGylation in cells. In addition to the known mitochondrial HMG-K proteins, HMGAM-yne facilitates the discovery of multiple nuclear proteins, including histones, as novel substrates of lysine HMGylation.
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Affiliation(s)
- Xiucong Bao
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
| | - Ying Xiong
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
| | - Xin Li
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
| | - Xiang David Li
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
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37
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Akgun B, Hall DG. Boronsäuren als bioorthogonale Sonden für zentrenselektives Protein‐Labeling. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712611] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
| | - Dennis G. Hall
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
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38
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Bakkum T, van Leeuwen T, Sarris AJC, van Elsland DM, Poulcharidis D, Overkleeft HS, van Kasteren SI. Quantification of Bioorthogonal Stability in Immune Phagocytes Using Flow Cytometry Reveals Rapid Degradation of Strained Alkynes. ACS Chem Biol 2018; 13:1173-1179. [PMID: 29693370 PMCID: PMC5962927 DOI: 10.1021/acschembio.8b00355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
One of the areas
in which bioorthogonal chemistry—chemistry
performed inside a cell or organism—has become of pivotal importance
is in the study of host–pathogen interactions. The incorporation
of bioorthogonal groups into the cell wall or proteome of intracellular
pathogens has allowed study within the endolysosomal system. However,
for the approach to be successful, the incorporated bioorthogonal
groups must be stable to chemical conditions found within these organelles,
which are some of the harshest found in metazoans: the groups are
exposed to oxidizing species, acidic conditions, and reactive thiols.
Here we present an assay that allows the assessment of the stability
of bioorthogonal groups within host cell phagosomes. Using a flow
cytometry-based assay, we have quantified the relative label stability
inside dendritic cell phagosomes of strained and unstrained alkynes.
We show that groups that were shown to be stable in other systems
were degraded by as much as 79% after maturation of the phagosome.
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Affiliation(s)
- Thomas Bakkum
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Tyrza van Leeuwen
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexi J. C. Sarris
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Daphne M. van Elsland
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Dimitrios Poulcharidis
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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39
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Oliveira BL, Guo Z, Bernardes GJL. Inverse electron demand Diels-Alder reactions in chemical biology. Chem Soc Rev 2018; 46:4895-4950. [PMID: 28660957 DOI: 10.1039/c7cs00184c] [Citation(s) in RCA: 655] [Impact Index Per Article: 109.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.
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Affiliation(s)
- B L Oliveira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Z Guo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - G J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, 1649-028, Portugal.
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40
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An P, Lewandowski TM, Lin Q. Design and Synthesis of a BODIPY-Tetrazole Based "Off-On" in-Cell Fluorescence Reporter of Hydrogen Peroxide. Chembiochem 2018; 19:1326-1333. [PMID: 29385317 DOI: 10.1002/cbic.201700656] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Indexed: 12/21/2022]
Abstract
BODIPY-linked bithiophene-tetrazoles were designed and synthesized for bioorthogonal photoclick reactions in vitro and in vivo. The reactivity of these tetrazoles toward dimethyl fumarate was found to depend on the BODIPY attachment site, with the meta-linked BODIPY-tetrazole being the most reactive. The resulting pyrazoline cycloadduct showed drastically reduced BODIPY fluorescence. However, BODIPY fluorescence recovered after treatment with hydrogen peroxide. This turn-on effect was attributed to conversion from the pyrazoline to a pyrazole. Finally, we showed that this unique BODIPY-tetrazole off-on fluorescence probe can be used to detect hydrogen peroxide inside HeLa cells.
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Affiliation(s)
- Peng An
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, 14260-3000, USA
| | - Tracey M Lewandowski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, 14260-3000, USA
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41
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Howes SC, Koning RI, Koster AJ. Correlative microscopy for structural microbiology. Curr Opin Microbiol 2018; 43:132-138. [PMID: 29414444 DOI: 10.1016/j.mib.2018.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/12/2018] [Accepted: 01/14/2018] [Indexed: 10/18/2022]
Abstract
Understanding how microbes utilize their environment is aided by visualizing them in their natural context at high resolution. Correlative imaging enables efficient targeting and identification of labelled viral and bacterial components by light microscopy combined with high resolution imaging by electron microscopy. Advances in genetic and bioorthogonal labelling, improved workflows for targeting and image correlation, and large-scale data collection are increasing the applicability of correlative imaging methods. Furthermore, developments in mass spectroscopy and soft X-ray imaging are expanding the correlative imaging modalities available. Investigating the structure and organization of microbes within their host by combined imaging methods provides important insights into mechanisms of infection and disease which cannot be obtained by other techniques.
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Affiliation(s)
- Stuart C Howes
- Leiden University Medical Centre, Department of Molecular Cell Biology, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Roman I Koning
- Leiden University Medical Centre, Department of Molecular Cell Biology, PO Box 9600, 2300 RC Leiden, The Netherlands; Netherlands Centre for Electron Nanoscopy, Institute of Biology, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Abraham J Koster
- Leiden University Medical Centre, Department of Molecular Cell Biology, PO Box 9600, 2300 RC Leiden, The Netherlands; Netherlands Centre for Electron Nanoscopy, Institute of Biology, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
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42
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Favre C, de Cremoux L, Badaut J, Friscourt F. Sydnone Reporters for Highly Fluorogenic Copper-Free Click Ligations. J Org Chem 2018; 83:2058-2066. [DOI: 10.1021/acs.joc.7b03004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Camille Favre
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
| | - Lucie de Cremoux
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
| | - Jerome Badaut
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
- Basic
Science Department, Loma Linda University, Loma Linda, California 92350, United States
| | - Frédéric Friscourt
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France
- Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, CNRS UMR5287, Bordeaux, France
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43
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Coleman DT, Gray AL, Kridel SJ, Cardelli JA. Palmitoylation regulates the intracellular trafficking and stability of c-Met. Oncotarget 2018; 7:32664-77. [PMID: 27081699 PMCID: PMC5078042 DOI: 10.18632/oncotarget.8706] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/28/2016] [Indexed: 01/08/2023] Open
Abstract
c-Met is a receptor tyrosine kinase whose activity can promote both mitogenic and motogenic phenotypes involved in tissue development and cancer progression. Herein, we report the first evidence that c-Met is palmitoylated and that palmitoylation facilitates its trafficking and stability. Inhibition of palmitoylation reduced the expression of c-Met in multiple cancer cell lines post-transcriptionally. Using surface biotinylation, confocal microscopy, and metabolic labeling we determined that inhibition of palmitoylation reduces the stability of newly synthesized c-Met and causes accumulation at the Golgi. Acyl-biotin exchange and click chemistry-based palmitate labeling indicated the c-Met β-chain is palmitoylated, and site-directed mutagenesis revealed two likely cysteine palmitoylation sites. Moreover, by monitoring palmitoylation kinetics during the biosynthesis and trafficking of c-Met, we revealed that stable palmitoylation occurs in the endoplasmic reticulum prior to cleavage of the 170 kDa c-Met precursor to the mature 140 kDa form. Our data suggest palmitoylation is required for egress from the Golgi for transport to the plasma membrane. These findings introduce palmitoylation as a critical modification of c-Met, providing a novel therapeutic target for c-Met-driven cancers.
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Affiliation(s)
- David T Coleman
- Department of Microbiology and Immunology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Alana L Gray
- Department of Microbiology and Immunology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Steven J Kridel
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 25157, USA
| | - James A Cardelli
- Department of Microbiology and Immunology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
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44
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Peng T, Hang HC. Chemical Proteomic Profiling of Protein Fatty-Acylation in Microbial Pathogens. Curr Top Microbiol Immunol 2018; 420:93-110. [PMID: 30128826 DOI: 10.1007/82_2018_126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein fatty-acylation describes the covalent modification of protein with fatty acids during or after translation. Chemical proteomic profiling methods have provided new opportunities to explore protein fatty-acylation in microbial pathogens. Recent studies suggest that protein fatty-acylation is essential to survival and pathogenesis of eukaryotic pathogens such as parasites and fungi. Moreover, fatty-acylation in host cells can be exploited or manipulated by pathogenic bacteria. Herein, we first review the prevalent classes of fatty-acylation in microbial pathogens and the chemical proteomic profiling methods for their global analysis. We then summarize recent fatty-acylation profiling studies performed in eukaryotic pathogens and during bacterial infections, highlighting how they contribute to functional characterization of fatty-acylation under these contexts.
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Affiliation(s)
- Tao Peng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, 10065, USA.
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45
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Gao X, Hannoush RN. A Decade of Click Chemistry in Protein Palmitoylation: Impact on Discovery and New Biology. Cell Chem Biol 2017; 25:236-246. [PMID: 29290622 DOI: 10.1016/j.chembiol.2017.12.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/10/2017] [Accepted: 11/30/2017] [Indexed: 12/17/2022]
Abstract
Protein palmitoylation plays diverse roles in regulating the trafficking, stability, and activity of cellular proteins. The advent of click chemistry has propelled the field of protein palmitoylation forward by providing specific, sensitive, rapid, and easy-to-handle methods for studying protein palmitoylation. This year marks the 10th anniversary since the first click chemistry-based fatty acid probes for detecting protein lipid modifications were reported. The goal of this review is to highlight key biological advancements in the field of protein palmitoylation during the past 10 years. In particular, we discuss the impact of click chemistry on enabling protein palmitoylation proteomics methods, uncovering novel lipid modifications on proteins and elucidating their functions, as well as the development of non-radioactive biochemical and enzymatic assays. In addition, this review provides context for building and exploring new research avenues in protein palmitoylation through the use of clickable fatty acid probes.
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.
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46
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Percher A, Thinon E, Hang H. Mass-Tag Labeling Using Acyl-PEG Exchange for the Determination of Endogenous Protein S-Fatty Acylation. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2017; 89:14.17.1-14.17.11. [PMID: 28762493 DOI: 10.1002/cpps.36] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The covalent coupling of fatty acids to proteins provides an important mechanism of regulation in cells. In eukaryotes, cysteine fatty acylation (S-fatty acylation) has been shown to be critical for protein function in a variety of cellular pathways as well as microbial pathogenesis. While methods developed over the past decade have improved the detection and profiling of S-fatty acylation, these are hampered in their ability to characterize endogenous protein S-fatty acylation levels under physiological conditions. Furthermore, understanding the contribution of specific sites and levels of S-fatty acylation remains a major challenge. To evaluate S-fatty acylation of endogenous proteins as well as to determine the number of S-fatty acylation events, we developed the acyl-PEG exchange (APE) that utilizes cysteine-specific chemistry to exchange S-fatty acylation sites with mass-tags of defined size, which can be readily observed by western blotting. APE provides a readily accessible approach to investigate endogenous S-fatty acylation from any sample source, with high sensitivity and broad applicability that complements the current toolbox of methods for thioester-based post-translational modifications. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Avital Percher
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York
| | - Emmanuelle Thinon
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York
| | - Howard Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York
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Poulcharidis D, Belfor K, Kros A, van Kasteren SI. A flow cytometry assay to quantify intercellular exchange of membrane components. Chem Sci 2017; 8:5585-5590. [PMID: 28970937 PMCID: PMC5618768 DOI: 10.1039/c7sc00260b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/20/2017] [Indexed: 12/12/2022] Open
Abstract
Membrane-compound exchange is vital for cell-to-cell communication, yet quantification of this process is difficult. Here we present a method using flow cytometry in combination with bioorthogonal and fluorescent labelling techniques to quantify the amount of exchange of cholesterol and sialylated compounds between cells. We demonstrate that direct cell-cell contact is the likely mechanism of sterol-exchange and show that by manipulating the contact time between cells using complementary coiled-coil peptides results in an enhanced exchange rate of membrane components between cells.
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Affiliation(s)
- Dimitrios Poulcharidis
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Division of Supramolecular and Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Kimberley Belfor
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
| | - Alexander Kros
- Division of Supramolecular and Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Sander I van Kasteren
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
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48
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Ji X, Ji K, Chittavong V, Aghoghovbia RE, Zhu M, Wang B. Click and Fluoresce: A Bioorthogonally Activated Smart Probe for Wash-Free Fluorescent Labeling of Biomolecules. J Org Chem 2017; 82:1471-1476. [PMID: 28067514 DOI: 10.1021/acs.joc.6b02654] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bioorthogonally activated smart probes greatly facilitate the selective labeling of biomolecules in living system. Herein, we described a novel type of smart probes with tunable reaction rates, high fluorescence turn-on ratio, and easy access. The practicality of such probes was demonstrated by selective labeling of lipid and hCAII in Hela cells.
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Affiliation(s)
- Xingyue Ji
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Kaili Ji
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Vayou Chittavong
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Robert E Aghoghovbia
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Mengyuan Zhu
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30303 United States
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49
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Ravasco JMJM, Monteiro CM, Trindade AF. Cyclopropenes: a new tool for the study of biological systems. Org Chem Front 2017. [DOI: 10.1039/c7qo00054e] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyclopropenes have become an important mini-tag tool in chemical biology, participating in fast inverse electron demand Diels–Alder and photoclick reactions in biological settings.
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Affiliation(s)
- João M. J. M. Ravasco
- Instituto de Investigação do Medicamento (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- 1649-003 Lisboa
- Portugal
| | - Carlos M. Monteiro
- Instituto de Investigação do Medicamento (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- 1649-003 Lisboa
- Portugal
| | - Alexandre F. Trindade
- Instituto de Investigação do Medicamento (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- 1649-003 Lisboa
- Portugal
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50
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STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live Cells. Methods Mol Biol 2017; 1663:65-78. [PMID: 28924659 DOI: 10.1007/978-1-4939-7265-4_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Long time-lapse super-resolution imaging in live cells requires a labeling strategy that combines a bright, photostable fluorophore with a high-density localization probe. Lipids are ideal high-density localization probes, as they are >100 times more abundant than most membrane-bound proteins and simultaneously demark the boundaries of cellular organelles. Here, we describe Cer-SiR, a two-component, high-density lipid probe that is exceptionally photostable. Cer-SiR is generated in cells via a bioorthogonal reaction of two components: a ceramide lipid tagged with trans-cyclooctene (Cer-TCO) and a reactive, photostable Si-rhodamine dye (SiR-Tz). These components assemble within the Golgi apparatus of live cells to form Cer-SiR. Cer-SiR is benign to cellular function, localizes within the Golgi at a high density, and is sufficiently photostable to enable visualization of Golgi structure and dynamics by 3D confocal or long time-lapse STED microscopy.
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