1
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Jiang Y, Zhang X, Nie H, Fan J, Di S, Fu H, Zhang X, Wang L, Tang C. Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping. Nat Commun 2024; 15:6060. [PMID: 39025860 PMCID: PMC11258254 DOI: 10.1038/s41467-024-50315-y] [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: 03/07/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
While photo-cross-linking (PXL) with alkyl diazirines can provide stringent distance restraints and offer insights into protein structures, unambiguous identification of cross-linked residues hinders data interpretation to the same level that has been achieved with chemical cross-linking (CXL). We address this challenge by developing an in-line system with systematic modulation of light intensity and irradiation time, which allows for a quantitative evaluation of diazirine photolysis and photo-reaction mechanism. Our results reveal a two-step pathway with mainly sequential generation of diazo and carbene intermediates. Diazo intermediate preferentially targets buried polar residues, many of which are inaccessible with known CXL probes for their limited reactivity. Moreover, we demonstrate that tuning light intensity and duration enhances selectivity towards polar residues by biasing diazo-mediated cross-linking reactions over carbene ones. This mechanistic dissection unlocks the full potential of PXL, paving the way for accurate distance mapping against protein structures and ultimately, unveiling protein dynamic behaviors.
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Affiliation(s)
- Yida Jiang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xinghe Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Honggang Nie
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jianxiong Fan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shuangshuang Di
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hui Fu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiu Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Lijuan Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Center for Quantitative Biology, PKU-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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2
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Nakashima T, Iwanabe T, Tanimoto H, Tomohiro T. Fluorescent Labeling of a Target Protein with an Alkyl Diazirine Photocrosslinker Bearing a Cinnamate Moiety. Chem Asian J 2024:e202400288. [PMID: 38641560 DOI: 10.1002/asia.202400288] [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: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/21/2024]
Abstract
A novel fluorogenic alkyl diazirine photocrosslinker bearing an o-hydroxycinnamate moiety has been developed for identification of the targets of bioactive molecules. The o-hydroxycinnamate moiety can be converted to the corresponding 7-hydroxycoumarin derivative, which should be created on the interacting site within the photocaptured target protein. The label yield and fluorescence intensity have been immensely improved in comparison with our previous aromatic crosslinkers to facilitate target identification in small quantities.
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Affiliation(s)
- Taikai Nakashima
- Laboratory of Biorecognition Chemistry, Faculty of Pharmaceutical Sciences, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Takumi Iwanabe
- Laboratory of Biorecognition Chemistry, Faculty of Pharmaceutical Sciences, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Hiroki Tanimoto
- Laboratory of Biorecognition Chemistry, Faculty of Pharmaceutical Sciences, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Takenori Tomohiro
- Laboratory of Biorecognition Chemistry, Faculty of Pharmaceutical Sciences, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
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3
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De León González FV, Boddington ME, Kofsky JM, Prindl MI, Capicciotti CJ. Glyco-Engineering Cell Surfaces by Exo-Enzymatic Installation of GlcNAz and LacNAz Motifs. ACS Chem Biol 2024; 19:629-640. [PMID: 38394345 DOI: 10.1021/acschembio.3c00542] [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: 02/25/2024]
Abstract
Exo-enzymatic glyco-engineering of cell-surface glycoconjugates enables the selective display of well-defined glyco-motifs bearing bioorthogonal functional groups, which can be used to study glycans and their interactions with glycan-binding proteins. In recent years, strategies to edit cellular glycans by installing monosaccharides and their derivatives using glycosyltransferase enzymes have rapidly expanded. However, analogous methods to introduce chemical reporter-functionalized type 2 LacNAc motifs have not been reported. Herein, we report the chemo-enzymatic synthesis of unnatural UDP-GlcNAc and UDP-GalNAc nucleotide-sugars bearing azide, alkyne, and diazirine functionalities on the C2-acetamido group using the mutant uridylyltransferase AGX1F383A. The unnatural UDP-GlcNAc derivatives were examined as substrates for the human GlcNAc-transferase B3GNT2, where it was found that modified donors were tolerated for transfer, albeit to a lesser extent than the natural UDP-GlcNAc substrate. When the GlcNAc derivatives were examined as acceptor substrates for the human Gal-transferase B4GalT1, all derivatives were well tolerated and the enzyme could successfully form derivatized LacNAcs. B3GNT2 was also used to exo-enzymatically install GlcNAc and unnatural GlcNAc derivatives on cell-surface glycans. GlcNAc- or GlcNAz-engineered cells were further extended by B4GalT1 and UDP-Gal, producing LacNAc- or LacNAz-engineered cells. Our proof-of-concept glyco-engineering labeling strategy is amenable to different cell types and our work expands the exo-enzymatic glycan editing toolbox to selectively introduce unnatural type 2 LacNAc motifs.
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Affiliation(s)
| | - Marie E Boddington
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Joshua M Kofsky
- Department of Chemistry, Queen's University, Kingston K7L 2S8, Canada
| | - Martha I Prindl
- Department of Chemistry, Queen's University, Kingston K7L 2S8, Canada
| | - Chantelle J Capicciotti
- Department of Chemistry, Queen's University, Kingston K7L 2S8, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
- Department of Surgery, Queen's University, Kingston K7L 2V7, Canada
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4
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Zheng X, Li Y, Cui T, Yang J, Meng X, Wang H, Chen L, He J, Chen N, Meng L, Ding L, Xie R. Traceless Protein-Selective Glycan Labeling and Chemical Modification. J Am Chem Soc 2023; 145:23670-23680. [PMID: 37857274 DOI: 10.1021/jacs.3c07889] [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: 10/21/2023]
Abstract
Executing glycan editing at a molecular level not only is pivotal for the elucidation of complicated mechanisms involved in glycan-relevant biological processes but also provides a promising solution to potentiate disease therapy. However, the precision control of glycan modification or glyco-editing on a selected glycoprotein is by far a grand challenge. Of note is to preserve the intact cellular glycan landscape, which is preserved after editing events are completed. We report herein a versatile, traceless glycan modification methodology for customizing the glycoforms of targeted proteins (subtypes), by orchestrating chemical- and photoregulation in a protein-selective glycoenzymatic system. This method relies on a three-module, ligand-photocleavable linker-glycoenzyme (L-P-G) conjugate. We demonstrated that RGD- or synthetic carbohydrate ligand-containing conjugates (RPG and SPG) would not activate until after the ligand-receptor interaction is accomplished (chemical regulation). RPG and SPG can both release the glycoenzyme upon photoillumination (photoregulation). The adjustable glycoenzyme activity, combined with ligand recognition selectivity, minimizes unnecessary glycan editing perturbation, and photolytic cleavage enables precise temporal control of editing events. An altered target protein turnover and dimerization were observed in our system, emphasizing the significance of preserving the native physiological niche of a particular protein when precise modification on the carbohydrate epitope occurs.
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Affiliation(s)
- Xiaocui Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yiran Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing Yang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiangfeng Meng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haiqi Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Liusheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jian He
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Nan Chen
- ChinaChomiX Biotech (Nanjing) Co., Ltd., Nanjing 210061, China
| | - Liying Meng
- Department of Medical Experimental Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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5
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Vilen Z, Reeves AE, Huang ML. (Glycan Binding) Activity‐Based Protein Profiling in Cells Enabled by Mass Spectrometry‐Based Proteomics. Isr J Chem 2023; 63. [PMID: 37131487 PMCID: PMC10150848 DOI: 10.1002/ijch.202200097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The presence of glycan modifications at the cell surface and other locales positions them as key regulators of cell recognition and function. However, due to the complexity of glycosylation, the annotation of which proteins bear glycan modifications, which glycan patterns are present, and which proteins are capable of binding glycans is incomplete. Inspired by activity-based protein profiling to enrich for proteins in cells based on select characteristics, these endeavors have been greatly advanced by the development of appropriate glycan-binding and glycan-based probes. Here, we provide context for these three problems and describe how the capability of molecules to interact with glycans has enabled the assignment of proteins with specific glycan modifications or of proteins that bind glycans. Furthermore, we discuss how the integration of these probes with high resolution mass spectrometry-based technologies has greatly advanced glycoscience.
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Affiliation(s)
- Zak Vilen
- Skaggs Graduate School of Chemical and Biological Sciences Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- Department of Molecular Medicine Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037, USA
| | - Abigail E. Reeves
- Skaggs Graduate School of Chemical and Biological Sciences Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- Department of Molecular Medicine Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037, USA
| | - Mia L. Huang
- Skaggs Graduate School of Chemical and Biological Sciences Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- Department of Molecular Medicine Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037, USA
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6
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Meyer CF, Seath CP, Knutson SD, Lu W, Rabinowitz JD, MacMillan DWC. Photoproximity Labeling of Sialylated Glycoproteins (GlycoMap) Reveals Sialylation-Dependent Regulation of Ion Transport. J Am Chem Soc 2022; 144:23633-23641. [PMID: 36525649 PMCID: PMC10782853 DOI: 10.1021/jacs.2c11094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sialylation, the addition of sialic acid to glycans, is a crucial post-translational modification of proteins, contributing to neurodevelopment, oncogenesis, and immune response. In cancer, sialylation is dramatically upregulated. Yet, the functional biochemical consequences of sialylation remain mysterious. Here, we establish a μMap proximity labeling platform that utilizes metabolically inserted azidosialic acid to introduce iridium-based photocatalysts on sialylated cell-surface glycoproteins as a means to profile local microenvironments across the sialylated proteome. In comparative experiments between primary cervical cells and a cancerous cell line (HeLa), we identify key differences in both the global sialome and proximal proteins, including solute carrier proteins that regulate metabolite and ion transport. In particular, we show that cell-surface interactions between receptors trafficking ethanolamine and zinc are sialylation-dependent and impact intracellular metabolite levels. These results establish a μMap method for interrogating proteoglycan function and support a role for sialylated glycoproteins in regulating cell-surface transporters.
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Affiliation(s)
- Claudio F. Meyer
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ciaran P. Seath
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Steve D. Knutson
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Wenyun Lu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Ludwig Institute for Cancer Research, Princeton University, Princeton, New Jersey, 08544, United States
| | - David W. C. MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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7
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Yarravarapu N, Konada RSR, Darabedian N, Pedowitz NJ, Krishnamurthy SN, Pratt MR, Kohler JJ. Exo-Enzymatic Addition of Diazirine-Modified Sialic Acid to Cell Surfaces Enables Photocrosslinking of Glycoproteins. Bioconjug Chem 2022; 33:781-787. [PMID: 35437982 DOI: 10.1021/acs.bioconjchem.2c00037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycan binding often mediates extracellular macromolecular recognition events. Accurate characterization of these binding interactions can be difficult because of dissociation and scrambling that occur during purification and analysis steps. Use of photocrosslinking methods has been pursued to covalently capture glycan-dependent interactions in situ; however, use of metabolic glycan engineering methods to incorporate photocrosslinking sugar analogs is limited to certain cell types. Here, we report an exo-enzymatic labeling method to add a diazirine-modified sialic acid (SiaDAz) to cell surface glycoconjugates. The method involves the chemoenzymatic synthesis of diazirine-modified CMP-sialic acid (CMP-SiaDAz), followed by sialyltransferase-catalyzed addition of SiaDAz to desialylated cell surfaces. Cell surface SiaDAzylation is compatible with multiple cell types and is facilitated by endogenous extracellular sialyltransferase activity present in Daudi B cells. This method for extracellular addition of α2-6-linked SiaDAz enables UV-induced crosslinking of CD22, demonstrating the utility for covalent capture of glycan-mediated binding interactions.
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Affiliation(s)
| | | | | | | | | | | | - Jennifer J Kohler
- Department of Biochemistry, UT Southwestern, Dallas, Texas 75390, United States
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8
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Babulic JL, Capicciotti CJ. Exo-Enzymatic Cell-Surface Glycan Labeling for Capturing Glycan–Protein Interactions through Photo-Cross-Linking. Bioconjug Chem 2022; 33:773-780. [DOI: 10.1021/acs.bioconjchem.2c00043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jonathan L. Babulic
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Chantelle J. Capicciotti
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
- Department of Chemistry, and Department of Surgery, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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9
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Tachrim ZP, Wang L, Murai Y, Hashimoto M. New Trends in Diaziridine Formation and Transformation (a Review). Molecules 2021; 26:4496. [PMID: 34361648 PMCID: PMC8348119 DOI: 10.3390/molecules26154496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 01/18/2023] Open
Abstract
This review focuses on diaziridine, a high strained three-membered heterocycle with two nitrogen atoms that plays an important role as one of the most important precursors of diazirine photoaffinity probes, as well as their formation and transformation. Recent research trends can be grouped into three categories, based on whether they have examined non-substituted, N-monosubstituted, or N,N-disubstituted diaziridines. The discussion expands on the conventional methods for recent applications, the current spread of studies, and the unconventional synthesis approaches arising over the last decade of publications.
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Affiliation(s)
- Zetryana Puteri Tachrim
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (L.W.); (Y.M.)
- Research Center for Chemistry, Indonesian Institute of Sciences, Kawasan Puspiptek, Serpong, South Tangerang 15314, Banten, Indonesia
| | - Lei Wang
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (L.W.); (Y.M.)
- State Key Laboratory of Fine Chemicals, Department of Pharmacy, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Yuta Murai
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (L.W.); (Y.M.)
- Frontier Research Center for Post-Genome Science and Technology, Faculty of Advanced Life Science, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo 001-0021, Japan
| | - Makoto Hashimoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (L.W.); (Y.M.)
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10
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Yu H, Gadi MR, Bai Y, Zhang L, Li L, Yin J, Wang PG, Chen X. Chemoenzymatic Total Synthesis of GM3 Gangliosides Containing Different Sialic Acid Forms and Various Fatty Acyl Chains. J Org Chem 2021; 86:8672-8682. [PMID: 34152144 DOI: 10.1021/acs.joc.1c00450] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Gangliosides are sialic acid-containing glycosphingolipids that have been found in the cell membranes of all vertebrates. Their important biological functions are contributed by both the glycan and the ceramide lipid components. GM3 is a major ganglioside and a precursor for many other more complex gangliosides. To obtain structurally diverse GM3 gangliosides containing various sialic acid forms and different fatty acyl chains in low cost, an improved process was developed to chemically synthesize lactosyl sphingosine from an inexpensive l-serine derivative. It was then used to obtain GM3 sphingosines from diverse modified sialic acid precursors by an efficient one-pot multienzyme sialylation system containing Pasteurella multocida sialyltransferase 3 (PmST3) with in situ generation of sugar nucleotides. A highly effective chemical acylation and facile C18-cartridge purification process was then used to install fatty acyl chains of varying lengths and different modifications. The chemoenzymatic method represents a powerful total synthetic strategy to access a library of structurally defined GM3 gangliosides to explore their functions.
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Affiliation(s)
- Hai Yu
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Madhusudhan Reddy Gadi
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yuanyuan Bai
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Libo Zhang
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Lei Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jun Yin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Peng G Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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11
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Zhang Z, Ortega D, Rush A, Blankenship LR, Cheng ZJ, Moore RE, Tran MLN, Sandoval LG, Aboulhosn K, Watanabe S, Cortez KS, Perlman DH, Semmelhack MF, Miller Conrad LC. Antibiotic Adjuvant Activity Revealed in a Photoaffinity Approach to Determine the Molecular Target of Antipyocyanin Compounds. ACS Infect Dis 2021; 7:535-543. [PMID: 33587590 DOI: 10.1021/acsinfecdis.0c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Infections with Pseudomonas aeruginosa are a looming threat to public health. New treatment strategies are needed to combat this pathogen, for example, by blocking the production of virulence factors like pyocyanin. A photoaffinity analogue of an antipyocyanin compound was developed to interrogate the inhibitor's molecular mechanism of action. While we sought to develop antivirulence inhibitors, the proteomics results suggested that the compounds had antibiotic adjuvant activity. Unexpectedly, we found that these compounds amplify the bactericidal activity of colistin, a well-characterized antibiotic, suggesting they may represent a first-in-class antibiotic adjuvant therapy. Analogues have the potential not only to widen the therapeutic index of cationic antimicrobial peptides like colistin, but also to be effective against colistin-resistant strains, strengthening our arsenal to combat P. aeruginosa infections.
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Affiliation(s)
- Zinan Zhang
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Dominic Ortega
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
| | - Anthony Rush
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, California 94305, United States
| | - Lauren R. Blankenship
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
| | - Zi Jun Cheng
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
| | - Rebecca E. Moore
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
| | - Minh L. N. Tran
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
| | - Lucero G. Sandoval
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
| | - Kareem Aboulhosn
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
| | - Seiichiro Watanabe
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
| | - Kendra S. Cortez
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
| | - David H. Perlman
- Princeton Proteomics and Mass Spectrometry Center, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Martin F. Semmelhack
- Department of Chemistry, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Laura C. Miller Conrad
- Department of Chemistry, San José State University, 1 Washington Square, San Jose, California 95192, United States
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12
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Congdon MD, Gildersleeve JC. Enhanced Binding and Reduced Immunogenicity of Glycoconjugates Prepared via Solid-State Photoactivation of Aliphatic Diazirine Carbohydrates. Bioconjug Chem 2020; 32:133-142. [PMID: 33325683 DOI: 10.1021/acs.bioconjchem.0c00555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological conjugation is an important tool employed for many basic research and clinical applications. While useful, common methods of biological conjugation suffer from a variety of limitations, such as (a) requiring the presence of specific surface-exposed residues, such as lysines or cysteines, (b) reducing protein activity, and/or (c) reducing protein stability and solubility. Use of photoreactive moieties including diazirines, azides, and benzophenones provide an alternative, mild approach to conjugation. Upon irradiation with UV and visible light, these functionalities generate highly reactive carbenes, nitrenes, and radical intermediates. Many of these will couple to proteins in a non-amino-acid-specific manner. The main hurdle for photoactivated biological conjugation is very low yield. In this study, we developed a solid-state method to increase conjugation efficiency of diazirine-containing carbohydrates to proteins. Using this methodology, we produced multivalent carbohydrate-protein conjugates with unaltered protein charge and secondary structure. Compared to carbohydrate conjugates prepared with amide linkages to lysine residues using standard NHS conjugation, the photoreactive prepared conjugates displayed up to 100-fold improved binding to lectins and diminished immunogenicity in mice. These results indicate that photoreactive bioconjugation could be especially useful for in vivo applications, such as lectin targeting, where high binding affinity and low immunogenicity are desired.
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Affiliation(s)
- Molly D Congdon
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Jeffrey C Gildersleeve
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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13
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Metabolic glycan labelling for cancer-targeted therapy. Nat Chem 2020; 12:1102-1114. [PMID: 33219365 DOI: 10.1038/s41557-020-00587-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 10/19/2020] [Indexed: 12/19/2022]
Abstract
Metabolic glycoengineering with unnatural sugars provides a powerful tool to label cell membranes with chemical tags for subsequent targeted conjugation of molecular cargos via efficient chemistries. This technology has been widely explored for cancer labelling and targeting. However, as this metabolic labelling process can occur in both cancerous and normal cells, cancer-selective labelling needs to be achieved to develop cancer-targeted therapies. Unnatural sugars can be either rationally designed to enable preferential labelling of cancer cells, or specifically delivered to cancerous tissues. In this Review Article, we will discuss the progress to date in design and delivery of unnatural sugars for metabolic labelling of tumour cells and subsequent development of tumour-targeted therapy. Metabolic cell labelling for cancer immunotherapy will also be discussed. Finally, we will provide a perspective on future directions of metabolic labelling of cancer and immune cells for the development of potent, clinically translatable cancer therapies.
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14
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Papakyriakou A, Cencetti F, Puliti E, Morelli L, Tricomi J, Bruni P, Compostella F, Richichi B. Glycans Meet Sphingolipids: Structure-Based Design of Glycan Containing Analogues of a Sphingosine Kinase Inhibitor. ACS Med Chem Lett 2020; 11:913-920. [PMID: 32435405 PMCID: PMC7236250 DOI: 10.1021/acsmedchemlett.9b00665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/30/2020] [Indexed: 01/23/2023] Open
Abstract
Sphingosine 1-phosphate (S1P) is a bioactive lipid mediator associated with diverse homeostatic and signaling roles. Enhanced biosynthesis of S1P, mediated by the sphingosine kinase isozymes (SK1 and SK2), is implicated in several pathophysiological conditions and diseases, including skeletal muscle fibrosis, inflammation, multiple sclerosis, and cancer. Therefore, therapeutic approaches that control S1P production have focused on the development of SK1/2 inhibitors. In this framework, we designed a series of natural monosaccharide-based compounds to enhance anchoring of the known SK1 inhibitor PF-543 at the polar head of the J-shaped substrate-binding channel. Herein, we describe the structure-based design and synthesis of new glycan-containing PF-543 analogues and we demonstrate their efficiency in a TGFβ1-induced pro-fibrotic assay.
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Affiliation(s)
- Athanasios Papakyriakou
- Institute
of Biosciences & Applications, National
Centre for Scientific Research “Demokritos”, GR-15341 Agia Paraskevi, Athens, Greece
| | - Francesca Cencetti
- Department
of Experimental and Clinical Biomedical Sciences, University of Florence, Viale GB Morgagni 50, 50134 Firenze, Italy
| | - Elisa Puliti
- Department
of Experimental and Clinical Biomedical Sciences, University of Florence, Viale GB Morgagni 50, 50134 Firenze, Italy
| | - Laura Morelli
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Via Saldini 50, 20133 Milano, Italy
| | - Jacopo Tricomi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy)
| | - Paola Bruni
- Department
of Experimental and Clinical Biomedical Sciences, University of Florence, Viale GB Morgagni 50, 50134 Firenze, Italy
| | - Federica Compostella
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Via Saldini 50, 20133 Milano, Italy
- Federica Compostella,
| | - Barbara Richichi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, FI, Italy)
- Barbara Richichi,
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15
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Chambers SA, Townsend SD. Bioorthogonal human milk oligosaccharide probes for antimicrobial target identification within Streptococcus agalactiae. Carbohydr Res 2019; 488:107895. [PMID: 31901817 DOI: 10.1016/j.carres.2019.107895] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Abstract
Human milk oligosaccharides (HMOs) are a structurally diverse class of carbohydrates that possess strong antibacterial activity against Streptococcus agalactiae (Group B Strep, GBS). This work highlights the design, synthesis, and retained biological activity of several HMO bioorthogonal probes within GBS, a first in class advance. The use of such probes will assist in identifying HMO-protein interactions within GBS and may be broadly applicable in researching HMO cellular targets within a variety of biological systems. Finally, this strategy is highly amenable to other oligosaccharide scaffolds, requiring minimal synthetic transformations and chemical perturbation.
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Affiliation(s)
- Schuyler A Chambers
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Science Center, Nashville, TN, 37235, United States
| | - Steven D Townsend
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Science Center, Nashville, TN, 37235, United States.
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16
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Liu G, Jia L, Xing G. Probing Sialidases or Siglecs with Sialic Acid Analogues, Clusters and Precursors. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Guang‐jian Liu
- College of ChemistryBeijing Normal University Beijing 100875 P.R. China
| | - Li‐yan Jia
- College of ChemistryBeijing Normal University Beijing 100875 P.R. China
| | - Guo‐wen Xing
- College of ChemistryBeijing Normal University Beijing 100875 P.R. China
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17
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Wu H, Kohler J. Photocrosslinking probes for capture of carbohydrate interactions. Curr Opin Chem Biol 2019; 53:173-182. [PMID: 31706134 DOI: 10.1016/j.cbpa.2019.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023]
Abstract
Glycan-mediated interactions are essential in many biological processes and regulate a wide variety of cellular functions. However, characterizing these interactions is difficult because glycan biosynthesis is not template driven and because carbohydrate recognition events are usually of low affinity and transient. Photocrosslinking carbohydrate probes can form a covalent bond with molecules in close proximity on UV irradiation and are capable of capturing interactions between glycans and glycan-binding proteins in situ. Because of these advantages, multiple photocrosslinking carbohydrate probes have been designed and applied to study the biological functions of glycans. This review will discuss recent advances in the development of novel photocrosslinking functional groups and the design of photocrosslinking probes to detect interactions mediated by glycolipids, peptidoglycan, and multivalent carbohydrate ligands. These probes have demonstrated the potential to address some of the major challenges in the study of glycan-mediated interactions in both model systems and in more complex biological settings.
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Affiliation(s)
- Han Wu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer Kohler
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA. http://
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18
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Purcell SC, Godula K. Synthetic glycoscapes: addressing the structural and functional complexity of the glycocalyx. Interface Focus 2019; 9:20180080. [PMID: 30842878 PMCID: PMC6388016 DOI: 10.1098/rsfs.2018.0080] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2019] [Indexed: 12/11/2022] Open
Abstract
The glycocalyx is an information-dense network of biomacromolecules extensively modified through glycosylation that populates the cellular boundary. The glycocalyx regulates biological events ranging from cellular protection and adhesion to signalling and differentiation. Owing to the characteristically weak interactions between individual glycans and their protein binding partners, multivalency of glycan presentation is required for the high-avidity interactions needed to trigger cellular responses. As such, biological recognition at the glycocalyx interface is determined by both the structure of glycans that are present as well as their spatial distribution. While genetic and biochemical approaches have proven powerful in controlling glycan composition, modulating the three-dimensional complexity of the cell-surface 'glycoscape' at the sub-micrometre scale remains a considerable challenge in the field. This focused review highlights recent advances in glycocalyx engineering using synthetic nanoscale glycomaterials, which allows for controlled de novo assembly of complexity with precision not accessible with traditional molecular biology tools. We discuss several exciting new studies in the field that demonstrate the power of precision glycocalyx editing in living cells in revealing and controlling the complex mechanisms by which the glycocalyx regulates biological processes.
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Affiliation(s)
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA
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19
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Sethi A, Wands AM, Mettlen M, Krishnamurthy S, Wu H, Kohler JJ. Cell type and receptor identity regulate cholera toxin subunit B (CTB) internalization. Interface Focus 2019; 9:20180076. [PMID: 30842875 PMCID: PMC6388018 DOI: 10.1098/rsfs.2018.0076] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2019] [Indexed: 12/21/2022] Open
Abstract
Cholera toxin (CT) is a secreted bacterial toxin that binds to glycoconjugate receptors on the surface of mammalian cells, enters mammalian cells through endocytic mechanisms and intoxicates mammalian cells by activating cytosolic adenylate cyclase. CT recognizes cell surface receptors through its B subunit (CTB). While the ganglioside GM1 has been historically described as the sole receptor, CTB is also capable of binding to fucosylated glycoconjugates, and fucosylated molecules have been shown to play a functional role in host cell intoxication by CT. Here, we use colonic epithelial and respiratory epithelial cell lines to examine how two types of CT receptors-gangliosides and fucosylated glycoconjugates-contribute to CTB internalization. We show that fucosylated glycoconjugates contribute to CTB binding to and internalization into host cells, even when the ganglioside GM1 is present. The contributions of the two classes of receptors to CTB internalization depend on cell type. Additionally, in a cell line that harbours both classes of receptors, gangliosides dictate the efficiency of CTB internalization. Together, the results lend support to the idea that fucosylated glycoconjugates play a functional role in CTB internalization, and suggest that CT internalization depends on both receptor identity and cell type.
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Affiliation(s)
- Anirudh Sethi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Amberlyn M Wands
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marcel Mettlen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Soumya Krishnamurthy
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Han Wu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer J Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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20
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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21
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Arguello AE, Srikumar T, Kleiner RE. A Photocrosslinking-Based RNA Chemical Proteomics Approach to Profile m6A-Regulated Protein-RNA Interactions. ACTA ACUST UNITED AC 2018; 75:e69. [DOI: 10.1002/cpnc.69] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Tharan Srikumar
- Proteomics and Mass Spectrometry Core, Princeton University; Princeton New Jersey
| | - Ralph E. Kleiner
- Department of Chemistry, Princeton University; Princeton New Jersey
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22
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Gilormini PA, Batt AR, Pratt MR, Biot C. Asking more from metabolic oligosaccharide engineering. Chem Sci 2018; 9:7585-7595. [PMID: 30393518 PMCID: PMC6187459 DOI: 10.1039/c8sc02241k] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/17/2018] [Indexed: 01/20/2023] Open
Abstract
Glycans form one of the four classes of biomolecules, are found in every living system and present a huge structural and functional diversity. As an illustration of this diversity, it has been reported that more than 50% of the human proteome is glycosylated and that 2% of the human genome is dedicated to glycosylation processes. Glycans are involved in many biological processes such as signalization, cell-cell or host pathogen interactions, immunity, etc. However, fundamental processes associated with glycans are not yet fully understood and the development of glycobiology is relatively recent compared to the study of genes or proteins. Approximately 25 years ago, the studies of Bertozzi's and Reutter's groups paved the way for metabolic oligosaccharide engineering (MOE), a strategy which consists in the use of modified sugar analogs which are taken up into the cells, metabolized, incorporated into glycoconjugates, and finally detected in a specific manner. This groundbreaking strategy has been widely used during the last few decades and the concomitant development of new bioorthogonal ligation reactions has allowed many advances in the field. Typically, MOE has been used to either visualize glycans or identify different classes of glycoproteins. The present review aims to highlight recent studies that lie somewhat outside of these more traditional approaches and that are pushing the boundaries of MOE applications.
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Affiliation(s)
- Pierre-André Gilormini
- University of Lille , CNRS UMR 8576 , UGSF - Unité de Glycobiologie Structurale et Fonctionnelle , F-59000 Lille , France .
| | - Anna R Batt
- Department of Chemistry , University of Southern California , 840 Downey Way , LJS 250 Los Angeles , CA 90089 , USA
| | - Matthew R Pratt
- Department of Chemistry , University of Southern California , 840 Downey Way , LJS 250 Los Angeles , CA 90089 , USA
- Department of Biological Sciences , University of Southern California , 840 Downey Way , LJS 250 Los Angeles , CA 90089 , USA
| | - Christophe Biot
- University of Lille , CNRS UMR 8576 , UGSF - Unité de Glycobiologie Structurale et Fonctionnelle , F-59000 Lille , France .
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23
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Ge SS, Chen B, Wu YY, Long QS, Zhao YL, Wang PY, Yang S. Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry. RSC Adv 2018; 8:29428-29454. [PMID: 35547988 PMCID: PMC9084484 DOI: 10.1039/c8ra03538e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/07/2018] [Indexed: 12/21/2022] Open
Abstract
Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule-protein and macromolecule-protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades.
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Affiliation(s)
- Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yuan-Yuan Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Qing-Su Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yong-Liang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Pei-Yi Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
- College of Pharmacy, East China University of Science & Technology Shanghai 200237 China
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24
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Park DD, Xu G, Wong M, Phoomak C, Liu M, Haigh NE, Wongkham S, Yang P, Maverakis E, Lebrilla CB. Membrane glycomics reveal heterogeneity and quantitative distribution of cell surface sialylation. Chem Sci 2018; 9:6271-6285. [PMID: 30123482 PMCID: PMC6063140 DOI: 10.1039/c8sc01875h] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/26/2018] [Indexed: 12/13/2022] Open
Abstract
Sialic acid distribution was quantified by LC-MS/MS. The number of sialylated glycoforms increases at sites nearest to the transmembrane domain.
Given that unnatural sugar expression is metabolically achieved, the kinetics and disposition of incorporation can lend insight into the temporal and localization preferences of sialylation across the cell surface. However, common detection schemes lack the ability to detail the molecular diversity and distribution of target moieties. Here we employed a mass spectrometric approach to trace the placement of azido sialic acids on membrane glycoconjugates, which revealed substantial variations in incorporation efficiencies between N-/O-glycans, glycosites, and glycosphingolipids. To further explore the propensity for sialylation, we subsequently mapped the native glycome of model epithelial cell surfaces and illustrate that while glycosylation sites span broadly across the extracellular region, a higher number of heterogeneous glycoforms occur on sialylated sites closest to the transmembrane domain. Beyond imaging techniques, this integrative approach provides unprecedented details about the frequency and structure-specific distribution of cell surface sialylation, a critical feature that regulates cellular interactions and homeostatic pathways.
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Affiliation(s)
- Diane Dayoung Park
- Department of Chemistry , University of California , Davis , CA 95616 , USA.,Department of Surgery , Beth Israel Deaconess Medical Center , Harvard Medical School , Boston , MA 02115 , USA .
| | - Gege Xu
- Department of Chemistry , University of California , Davis , CA 95616 , USA
| | - Maurice Wong
- Department of Chemistry , University of California , Davis , CA 95616 , USA
| | - Chatchai Phoomak
- Department of Biochemistry , Faculty of Medicine , Khon Kaen University , Khon Kaen 40002 , Thailand
| | - Mingqi Liu
- Department of Chemistry , Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , China
| | - Nathan E Haigh
- Department of Dermatology , University of California , Davis School of Medicine , Sacramento , CA 95817 , USA
| | - Sopit Wongkham
- Department of Biochemistry , Faculty of Medicine , Khon Kaen University , Khon Kaen 40002 , Thailand
| | - Pengyuan Yang
- Department of Chemistry , Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , China
| | - Emanual Maverakis
- Department of Dermatology , University of California , Davis School of Medicine , Sacramento , CA 95817 , USA
| | - Carlito B Lebrilla
- Department of Chemistry , University of California , Davis , CA 95616 , USA
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25
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Mathew MP, Tan E, Labonte JW, Shah S, Saeui CT, Liu L, Bhattacharya R, Bovonratwet P, Gray JJ, Yarema KJ. Glycoengineering of Esterase Activity through Metabolic Flux-Based Modulation of Sialic Acid. Chembiochem 2017; 18:1204-1215. [PMID: 28218815 PMCID: PMC5757160 DOI: 10.1002/cbic.201600698] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Indexed: 01/09/2023]
Abstract
This report describes the metabolic glycoengineering (MGE) of intracellular esterase activity in human colon cancer (LS174T) and Chinese hamster ovary (CHO) cells. In silico analysis of carboxylesterases CES1 and CES2 suggested that these enzymes are modified with sialylated N-glycans, which are proposed to stabilize the active multimeric forms of these enzymes. This premise was supported by treating cells with butanolylated ManNAc to increase sialylation, which in turn increased esterase activity. By contrast, hexosamine analogues not targeted to sialic acid biosynthesis (e.g., butanoylated GlcNAc or GalNAc) had minimal impact. Measurement of mRNA and protein confirmed that esterase activity was controlled through glycosylation and not through transcription or translation. Azide-modified ManNAc analogues widely used in MGE also enhanced esterase activity and provided a way to enrich targeted glycoengineered proteins (such as CES2), thereby providing unambiguous evidence that the compounds were converted to sialosides and installed into the glycan structures of esterases as intended. Overall, this study provides a pioneering example of the modulation of intracellular enzyme activity through MGE, which expands the value of this technology from its current status as a labeling strategy and modulator of cell surface biological events.
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Affiliation(s)
- Mohit P. Mathew
- Department of Biomedical Engineering and the Translational Tissue Engineering Center
| | - Elaine Tan
- Department of Biomedical Engineering and the Translational Tissue Engineering Center
| | - Jason W. Labonte
- Department of Chemical and Biochemical Engineering The Johns Hopkins University, Baltimore, Maryland, USA
| | - Shivam Shah
- Department of Biomedical Engineering and the Translational Tissue Engineering Center
| | - Christopher T. Saeui
- Department of Biomedical Engineering and the Translational Tissue Engineering Center
| | - Lingshu Liu
- Department of Biomedical Engineering and the Translational Tissue Engineering Center
| | - Rahul Bhattacharya
- Department of Biomedical Engineering and the Translational Tissue Engineering Center
| | - Patawut Bovonratwet
- Department of Biomedical Engineering and the Translational Tissue Engineering Center
| | - Jeffrey J. Gray
- Department of Chemical and Biochemical Engineering The Johns Hopkins University, Baltimore, Maryland, USA
| | - Kevin J. Yarema
- Department of Biomedical Engineering and the Translational Tissue Engineering Center
- Department of Chemical and Biochemical Engineering The Johns Hopkins University, Baltimore, Maryland, USA
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26
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Pham ND, Pang PC, Krishnamurthy S, Wands AM, Grassi P, Dell A, Haslam SM, Kohler JJ. Effects of altered sialic acid biosynthesis on N-linked glycan branching and cell surface interactions. J Biol Chem 2017; 292:9637-9651. [PMID: 28424265 PMCID: PMC5465488 DOI: 10.1074/jbc.m116.764597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 04/17/2017] [Indexed: 12/22/2022] Open
Abstract
GNE (UDP-GlcNAc 2-epimerase/ManNAc kinase) myopathy is a rare muscle disorder associated with aging and is related to sporadic inclusion body myositis, the most common acquired muscle disease of aging. Although the cause of sporadic inclusion body myositis is unknown, GNE myopathy is associated with mutations in GNE. GNE harbors two enzymatic activities required for biosynthesis of sialic acid in mammalian cells. Mutations to both GNE domains are linked to GNE myopathy. However, correlation between mutation-associated reductions in sialic acid production and disease severity is imperfect. To investigate other potential effects of GNE mutations, we compared sialic acid production in cell lines expressing wild type or mutant forms of GNE. Although we did not detect any differences attributable to disease-associated mutations, lectin binding and mass spectrometry analysis revealed that GNE deficiency is associated with unanticipated effects on the structure of cell-surface glycans. In addition to exhibiting low levels of sialylation, GNE-deficient cells produced distinct N-linked glycan structures with increased branching and extended poly-N-acetyllactosamine. GNE deficiency may affect levels of UDP-GlcNAc, a key metabolite in the nutrient-sensing hexosamine biosynthetic pathway, but this modest effect did not fully account for the change in N-linked glycan structure. Furthermore, GNE deficiency and glucose supplementation acted independently and additively to increase N-linked glycan branching. Notably, N-linked glycans produced by GNE-deficient cells displayed enhanced binding to galectin-1, indicating that changes in GNE activity can alter affinity of cell-surface glycoproteins for the galectin lattice. These findings suggest an unanticipated mechanism by which GNE activity might affect signaling through cell-surface receptors.
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Affiliation(s)
- Nam D Pham
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038 and
| | - Poh-Choo Pang
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Soumya Krishnamurthy
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038 and
| | - Amberlyn M Wands
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038 and
| | - Paola Grassi
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Anne Dell
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Stuart M Haslam
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Jennifer J Kohler
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038 and
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27
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Badr HA, AlSadek DMM, El-Houseini ME, Saeui CT, Mathew MP, Yarema KJ, Ahmed H. Harnessing cancer cell metabolism for theranostic applications using metabolic glycoengineering of sialic acid in breast cancer as a pioneering example. Biomaterials 2017; 116:158-173. [PMID: 27926828 PMCID: PMC5193387 DOI: 10.1016/j.biomaterials.2016.11.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 12/18/2022]
Abstract
Abnormal cell surface display of sialic acids - a family of unusual 9-carbon sugars - is widely recognized as distinguishing feature of many types of cancer. Sialoglycans, however, typically cannot be identified with sufficiently high reproducibility and sensitivity to serve as clinically accepted biomarkers and similarly, almost all efforts to exploit cancer-specific differences in sialylation signatures for therapy remain in early stage development. In this report we provide an overview of important facets of glycosylation that contribute to cancer in general with a focus on breast cancer as an example of malignant disease characterized by aberrant sialylation. We then describe how cancer cells experience nutrient deprivation during oncogenesis and discuss how the resulting metabolic reprogramming, which endows breast cancer cells with the ability to obtain nutrients during scarcity, constitutes an "Achilles' heel" that we believe can be exploited by metabolic glycoengineering (MGE) strategies to develop new diagnostic methods and therapeutic approaches. In particular, we hypothesize that adaptations made by breast cancer cells that allow them to efficiently scavenge sialic acid during times of nutrient deprivation renders them vulnerable to MGE, which refers to the use of exogenously-supplied, non-natural monosaccharide analogues to modulate targeted aspects of glycosylation in living cells and animals. In specific, once non-natural sialosides are incorporated into the cancer "sialome" they can be exploited as epitopes for immunotherapy or as chemical tags for targeted delivery of imaging or therapeutic agents selectively to tumors.
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Affiliation(s)
- Haitham A Badr
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Dina M M AlSadek
- Department of Histology and Cytology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Motawa E El-Houseini
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Christopher T Saeui
- Department of Biomedical Engineering and Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD 21231, USA
| | - Mohit P Mathew
- Department of Biomedical Engineering and Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD 21231, USA
| | - Kevin J Yarema
- Department of Biomedical Engineering and Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD 21231, USA.
| | - Hafiz Ahmed
- GlycoMantra, Inc., Baltimore, MD 21227, USA.
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28
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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29
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Protasova I, Bulat B, Jung N, Bräse S. Synthesis of Diaziridines and Diazirines via Resin-Bound Sulfonyl Oximes. Org Lett 2016; 19:34-37. [PMID: 27959555 DOI: 10.1021/acs.orglett.6b03252] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Diazirines are one of the most prominent functionalities in labeling experiments in vivo and in vitro because they allow photochemical generation of carbenes. The strategy presented herein describes the formation of diaziridines, being essential precursors in diazirine syntheses, using solid-supported procedures with immobilized sulfonyl oximes. The solid-supported building blocks have been shown to be valuable intermediates for CuAAC and amidation reactions, offering the possibility to build complex compounds with diverse functionalities.
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Affiliation(s)
- Irina Protasova
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Bekir Bulat
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Stefan Bräse
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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30
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Horning BD, Suciu RM, Ghadiri DA, Ulanovskaya OA, Matthews ML, Lum KM, Backus KM, Brown SJ, Rosen H, Cravatt BF. Chemical Proteomic Profiling of Human Methyltransferases. J Am Chem Soc 2016; 138:13335-13343. [PMID: 27689866 DOI: 10.1021/jacs.6b07830] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methylation is a fundamental mechanism used in Nature to modify the structure and function of biomolecules, including proteins, DNA, RNA, and metabolites. Methyl groups are predominantly installed into biomolecules by a large and diverse class of S-adenosyl methionine (SAM)-dependent methyltransferases (MTs), of which there are ∼200 known or putative members in the human proteome. Deregulated MT activity contributes to numerous diseases, including cancer, and several MT inhibitors are in clinical development. Nonetheless, a large fraction of the human MT family remains poorly characterized, underscoring the need for new technologies to characterize MTs and their inhibitors in native biological systems. Here, we describe a suite of S-adenosyl homocysteine (SAH) photoreactive probes and their application in chemical proteomic experiments to profile and enrich a large number of MTs (>50) from human cancer cell lysates with remarkable specificity over other classes of proteins. We further demonstrate that the SAH probes can enrich MT-associated proteins and be used to screen for and assess the selectivity of MT inhibitors, leading to the discovery of a covalent inhibitor of nicotinamide N-methyltransferase (NNMT), an enzyme implicated in cancer and metabolic disorders. The chemical proteomics probes and methods for their utilization reported herein should prove of value for the functional characterization of MTs, MT complexes, and MT inhibitors in mammalian biology and disease.
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Affiliation(s)
- Benjamin D Horning
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Radu M Suciu
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Darian A Ghadiri
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Olesya A Ulanovskaya
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Megan L Matthews
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Kenneth M Lum
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Keriann M Backus
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Steven J Brown
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Hugh Rosen
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Benjamin F Cravatt
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
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31
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Wratil PR, Horstkorte R, Reutter W. Metabolic Glycoengineering with N-Acyl Side Chain Modified Mannosamines. Angew Chem Int Ed Engl 2016; 55:9482-512. [PMID: 27435524 DOI: 10.1002/anie.201601123] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 12/14/2022]
Abstract
In metabolic glycoengineering (MGE), cells or animals are treated with unnatural derivatives of monosaccharides. After entering the cytosol, these sugar analogues are metabolized and subsequently expressed on newly synthesized glycoconjugates. The feasibility of MGE was first discovered for sialylated glycans, by using N-acyl-modified mannosamines as precursor molecules for unnatural sialic acids. Prerequisite is the promiscuity of the enzymes of the Roseman-Warren biosynthetic pathway. These enzymes were shown to tolerate specific modifications of the N-acyl side chain of mannosamine analogues, for example, elongation by one or more methylene groups (aliphatic modifications) or by insertion of reactive groups (bioorthogonal modifications). Unnatural sialic acids are incorporated into glycoconjugates of cells and organs. MGE has intriguing biological consequences for treated cells (aliphatic MGE) and offers the opportunity to visualize the topography and dynamics of sialylated glycans in vitro, ex vivo, and in vivo (bioorthogonal MGE).
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Affiliation(s)
- Paul R Wratil
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité-Universitätsmedizin Berlin, Arnimallee 22, 14195, Berlin, Germany.
| | - Rüdiger Horstkorte
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystrasse 1, 06114, Halle, Germany.
| | - Werner Reutter
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité-Universitätsmedizin Berlin, Arnimallee 22, 14195, Berlin, Germany
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32
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Wratil PR, Horstkorte R, Reutter W. Metabolisches Glykoengineering mitN-Acyl-Seiten- ketten-modifizierten Mannosaminen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601123] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Paul R. Wratil
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie; Charité - Universitätsmedizin Berlin; Arnimallee 22 14195 Berlin Deutschland
| | - Rüdiger Horstkorte
- Institut für Physiologische Chemie; Martin-Luther-Universität Halle-Wittenberg; Hollystraße 1 06114 Halle Deutschland
| | - Werner Reutter
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie; Charité - Universitätsmedizin Berlin; Arnimallee 22 14195 Berlin Deutschland
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33
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Fahie K, Zachara NE. Molecular Functions of Glycoconjugates in Autophagy. J Mol Biol 2016; 428:3305-3324. [PMID: 27345664 DOI: 10.1016/j.jmb.2016.06.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/27/2016] [Accepted: 06/16/2016] [Indexed: 02/07/2023]
Abstract
Glycoconjugates, glycans, carbohydrates, and sugars: these terms encompass a class of biomolecules that are diverse in both form and function ranging from free oligosaccharides, glycoproteins, and proteoglycans, to glycolipids that make up a complex glycan code that impacts normal physiology and disease. Recent data suggest that one mechanism by which glycoconjugates impact physiology is through the regulation of the process of autophagy. Autophagy is a degradative pathway necessary for differentiation, organism development, and the maintenance of cell and tissue homeostasis. In this review, we will highlight what is known about the regulation of autophagy by glycoconjugates focusing on signaling mechanisms from the extracellular surface and the regulatory roles of intracellular glycans. Glycan signaling from the extracellular matrix converges on "master" regulators of autophagy including AMPK and mTORC1, thus impacting their localization, activity, and/or expression. Within the intracellular milieu, gangliosides are constituents of the autophagosome membrane, a subset of proteins composing the autophagic machinery are regulated by glycosylation, and oligosaccharide exposure in the cytosol triggers an autophagic response. The examples discussed provide some mechanistic insights into glycan regulation of autophagy and reveal areas for future investigation.
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Affiliation(s)
- Kamau Fahie
- Department of Biological Chemistry, The Johns Hopkins University, School of Medicine, 725 N. Wolfe St, Baltimore, MD 21205-2185, USA
| | - Natasha E Zachara
- Department of Biological Chemistry, The Johns Hopkins University, School of Medicine, 725 N. Wolfe St, Baltimore, MD 21205-2185, USA.
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34
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McCombs JE, Diaz JP, Luebke KJ, Kohler JJ. Glycan specificity of neuraminidases determined in microarray format. Carbohydr Res 2016; 428:31-40. [PMID: 27131125 PMCID: PMC4885666 DOI: 10.1016/j.carres.2016.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/31/2016] [Accepted: 04/05/2016] [Indexed: 11/27/2022]
Abstract
Neuraminidases hydrolytically remove sialic acids from glycoconjugates. Neuraminidases are produced by both humans and their pathogens, and function in normal physiology and in pathological events. Identification of neuraminidase substrates is needed to reveal their mechanism of action, but high-throughput methods to determine glycan specificity of neuraminidases are limited. Here we use two glycan labeling reactions to monitor neuraminidase activity toward glycan substrates. While both periodate oxidation and aniline-catalyzed oxime ligation (PAL) and galactose oxidase and aniline-catalyzed oxime ligation (GAL) can be used to monitor neuraminidase activity toward glycans in microtiter plates, only GAL accurately measured neuraminidase activity toward glycans displayed on a commercial glass slide microarray. Using GAL, we confirm known linkage specificities of three pneumococcal neuraminidases and obtain new information about underlying glycan specificity.
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Affiliation(s)
- Janet E McCombs
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jason P Diaz
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin J Luebke
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer J Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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35
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Admas TH, Bernat V, Heinrich MR, Tschammer N. Development of Photoactivatable Allosteric Modulators for the Chemokine Receptor CXCR3. ChemMedChem 2016; 11:575-84. [PMID: 26880380 DOI: 10.1002/cmdc.201500573] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Indexed: 11/05/2022]
Abstract
The CXCR3 receptor, a class A G protein-coupled receptor (GPCR), is involved in the regulation and trafficking of various immune cells. CXCR3 antagonists have been proposed to be beneficial for the treatment of a wide range of disorders including but not limited to inflammatory and autoimmune diseases. The structure-based design of CXCR3 ligands remains, however, hampered by a lack of structural information describing in detail the interactions between an allosteric ligand and the receptor. We designed and synthesized photoactivatable probes for the structural and functional characterization, using photoaffinity labeling followed by mass spectrometry, of the CXCR3 allosteric binding pocket of AMG 487 and RAMX3, two potent and selective CXCR3 negative allosteric modulators. Photoaffinity labeling is a common approach to elucidate binding modes of small-molecule ligands of GPCRs through the aid of photoactivatable probes that convert to extremely reactive intermediates upon photolysis. The photolabile probe N-[({1-[3-(4-ethoxyphenyl)-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl]ethyl}-2-[4-fluoro-3-(trifluoromethyl)phenyl]-N-{1-[4-(3-(trifluoromethyl)-3H-diazirin-3-yl]benzyl}piperidin-4-yl)methyl]acetamide (10) showed significant labeling of the CXCR3 receptor (80%) in a [(3) H]RAMX3 radioligand displacement assay. Compound 10 will serve as an important tool compound for the detailed investigation of the binding pocket of CXCR3 by mass spectrometry.
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Affiliation(s)
- Tizita Haimanot Admas
- Department of Chemistry & Pharmacy, Emil Fischer Center, Friedrich Alexander University Erlangen-Nürnberg, Schuhstr. 19, 91052, Erlangen, Germany
| | - Viachaslau Bernat
- Department of Chemistry & Pharmacy, Emil Fischer Center, Friedrich Alexander University Erlangen-Nürnberg, Schuhstr. 19, 91052, Erlangen, Germany.,Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, 3A1, 33458, Jupiter, FL, USA
| | - Markus R Heinrich
- Department of Chemistry & Pharmacy, Emil Fischer Center, Friedrich Alexander University Erlangen-Nürnberg, Schuhstr. 19, 91052, Erlangen, Germany
| | - Nuska Tschammer
- Department of Chemistry & Pharmacy, Emil Fischer Center, Friedrich Alexander University Erlangen-Nürnberg, Schuhstr. 19, 91052, Erlangen, Germany. .,NanoTemper Technologies GmbH, Flößergasse 4, 81369, München, Germany.
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36
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McCombs JE, Zou C, Parker RB, Cairo CW, Kohler JJ. Enhanced Cross-Linking of Diazirine-Modified Sialylated Glycoproteins Enabled through Profiling of Sialidase Specificities. ACS Chem Biol 2016; 11:185-92. [PMID: 26541974 DOI: 10.1021/acschembio.5b00775] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sialic-acid-mediated interactions play critical roles on the cell surface, providing an impetus for the development of methods to study this important monosaccharide. In particular, photo-cross-linking sialic acids incorporated onto cell surfaces have allowed covalent capture of transient interactions between sialic acids and sialic-acid-recognizing proteins via cross-linking. However, natural sialic acids also present on the cell surface compete with photo-cross-linking sialic acids in binding events, limiting cross-linking yields. In order to improve the utility of one such photo-cross-linking sialic acid, SiaDAz, we examined a number of sialidases, enzymes that remove sialic acids from glycoconjugates, to find one that would cleave natural sialic acids but remain inactive toward SiaDAz. Using this sialidase, we improved SiaDAz-mediated cross-linking of an antisialyl Lewis X antibody and of endoglin. This protocol can be applied generally to sialic-acid-mediated interactions and will facilitate identification of sialic acid binding partners.
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Affiliation(s)
- Janet E. McCombs
- Department
of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, United States
| | - Chunxia Zou
- Alberta
Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Randy B. Parker
- Department
of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, United States
| | - Christopher W. Cairo
- Alberta
Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Jennifer J. Kohler
- Department
of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, United States
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37
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Xiong DC, Zhu J, Han MJ, Luo HX, Wang C, Yu Y, Ye Y, Tai G, Ye XS. Rapid probing of sialylated glycoproteins in vitro and in vivo via metabolic oligosaccharide engineering of a minimal cyclopropene reporter. Org Biomol Chem 2015; 13:3911-7. [PMID: 25735895 DOI: 10.1039/c5ob00069f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
ManNAc analogues are important chemical tools for probing sialylation dynamically via metabolic oligosaccharide engineering (MOE). The size of N-acyl and the nature of the chemical handle are two determinants of metabolic incorporation efficiency. We demonstrated a minimal, stable, bioorthogonal, and reactive N-Cp (N-(cycloprop-2-ene-1-ylcarbonyl)) group and the imaging of sialylated glycans using Ac4ManNCp in vitro and in vivo. The results revealed that the Cp group can efficiently be incorporated into the cellular sialic acid and detected rapidly by the reaction with FITC-Tz in different cells. The metabolic incorporation efficiency of non-cytotoxic Ac4ManNCp is not only superior to Ac4ManNMCp, but also superior to the widely-used Ac4ManNAz in some cell lines. Moreover, when Ac4ManNCp was administered to mice, a rapid and intense labelling of splenocytes as well as glycoproteins of sera and organs was observed. This is the first reported metabolic labelling of cyclopropene-modified sugars in vivo. Therefore, Ac4ManNCp is a powerful probe for efficient and rapid MOE and it may find wide applications in the labelling of glycans.
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Affiliation(s)
- De-Cai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, and Center for Molecular and Translational Medicine, Peking University, Xue Yuan Road No. 38, Beijing 100191, China.
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38
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Wands AM, Fujita A, McCombs JE, Cervin J, Dedic B, Rodriguez AC, Nischan N, Bond MR, Mettlen M, Trudgian DC, Lemoff A, Quiding-Järbrink M, Gustavsson B, Steentoft C, Clausen H, Mirzaei H, Teneberg S, Yrlid U, Kohler JJ. Fucosylation and protein glycosylation create functional receptors for cholera toxin. eLife 2015; 4:e09545. [PMID: 26512888 PMCID: PMC4686427 DOI: 10.7554/elife.09545] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/26/2015] [Indexed: 12/14/2022] Open
Abstract
Cholera toxin (CT) enters and intoxicates host cells after binding cell surface receptors using its B subunit (CTB). The ganglioside (glycolipid) GM1 is thought to be the sole CT receptor; however, the mechanism by which CTB binding to GM1 mediates internalization of CT remains enigmatic. Here we report that CTB binds cell surface glycoproteins. Relative contributions of gangliosides and glycoproteins to CTB binding depend on cell type, and CTB binds primarily to glycoproteins in colonic epithelial cell lines. Using a metabolically incorporated photocrosslinking sugar, we identified one CTB-binding glycoprotein and demonstrated that the glycan portion of the molecule, not the protein, provides the CTB interaction motif. We further show that fucosylated structures promote CTB entry into a colonic epithelial cell line and subsequent host cell intoxication. CTB-binding fucosylated glycoproteins are present in normal human intestinal epithelia and could play a role in cholera. DOI:http://dx.doi.org/10.7554/eLife.09545.001 Cholera is a serious diarrheal disease that can be deadly if left untreated. It is caused by eating food, or drinking water, contaminated by the bacterium Vibrio cholerae. This bacterium can survive passage through the acidic conditions of the stomach. Inside the small intestine, V. cholerae attaches to the intestinal wall and starts producing cholera toxin. The toxin enters intestinal cells, causing them to release water and ions, including sodium and chloride ions. The salt-water environment created inside the intestine can, by osmosis, draw up to a further six liters of water into the intestine each day. This results in the copious production of watery diarrhea and severe dehydration. Cholera toxin is composed of six protein subunits, including five copies of cholera toxin subunit B (CTB). CTB subunits help the uptake of the toxin by intestinal cells, and it has long been reported that CTB subunits attach to intestinal cells by binding to a cell surface molecule called GM1. CTB subunits have a high affinity for GM1, yet recent work suggests CTB may not bind exclusively to GM1; one or more additional cell surface molecules may be directly involved in cholera toxin uptake. Wands et al. now reveal that numerous cell surface molecules are recognized by CTB, and that these molecules can assist cholera toxin uptake by host cells. Glycoproteins, proteins that are marked with sugar molecules, were shown to be the primary CTB binding sites on human colon cells, and it was the glycoprotein’s sugar component, not the protein itself, that interacted with CTB. Wands et al. discovered that in particular glycoproteins containing a sugar called fucose were largely responsible for CTB binding and toxin uptake. Together these findings reveal a previously unrecognized mechanism for cholera toxin entry into host cells, and suggest that fucose-containing or fucose-mimicking molecules could be developed as new treatments for cholera. DOI:http://dx.doi.org/10.7554/eLife.09545.002
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Affiliation(s)
- Amberlyn M Wands
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Akiko Fujita
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Janet E McCombs
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jakob Cervin
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Mucosal Immunobiology and Vaccine Center, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Benjamin Dedic
- Department of Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Andrea C Rodriguez
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nicole Nischan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michelle R Bond
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Marcel Mettlen
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - David C Trudgian
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Marianne Quiding-Järbrink
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Mucosal Immunobiology and Vaccine Center, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Gustavsson
- Department of Surgery, University of Gothenburg, Gothenburg, Sweden
| | - Catharina Steentoft
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Susann Teneberg
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ulf Yrlid
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Mucosal Immunobiology and Vaccine Center, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Jennifer J Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
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39
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Yamamoto K, Chikaoka Y, Hayashi G, Sakamoto R, Yamamoto R, Sugiyama A, Kodama T, Okamoto A, Kawamura T. Middle-Down and Chemical Proteomic Approaches to Reveal Histone H4 Modification Dynamics in Cell Cycle: Label-Free Semi-Quantification of Histone Tail Peptide Modifications Including Phosphorylation and Highly Sensitive Capture of Histone PTM Binding Proteins Using Photo-Reactive Crosslinkers. ACTA ACUST UNITED AC 2015; 4:A0039. [PMID: 26819910 DOI: 10.5702/massspectrometry.a0039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/04/2015] [Indexed: 12/13/2022]
Abstract
Mass spectrometric proteomics is an effective approach for identifying and quantifying histone post-translational modifications (PTMs) and their binding proteins, especially in the cases of methylation and acetylation. However, another vital PTM, phosphorylation, tends to be poorly quantified because it is easily lost and inefficiently ionized. In addition, PTM binding proteins for phosphorylation are sometimes resistant to identification because of their variable binding affinities. Here, we present our efforts to improve the sensitivity of detection of histone H4 tail peptide phosphorylated at serine 1 (H4S1ph) and our successful identification of an H4S1ph binder candidate by means of a chemical proteomics approach. Our nanoLC-MS/MS system permitted semi-quantitative label-free analysis of histone H4 PTM dynamics of cell cycle-synchronized HeLa S3 cells, including phosphorylation, methylation, and acetylation. We show that H4S1ph abundance on nascent histone H4 unmethylated at lysine 20 (H4K20me0) peaks from late S-phase to M-phase. We also attempted to characterize effects of phosphorylation at H4S1 on protein-protein interactions. Specially synthesized photoaffinity bait peptides specifically captured 14-3-3 proteins as novel H4S1ph binding partners, whose interaction was otherwise undetectable by conventional peptide pull-down experiments. This is the first report that analyzes dynamics of PTM pattern on the whole histone H4 tail during cell cycle and enables the identification of PTM binders with low affinities using high-resolution mass spectrometry and photo-affinity bait peptides.
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Affiliation(s)
- Kazuki Yamamoto
- Department of Systems Biology and Medicine, Research Center for Advanced Science and Technology,
The University of Tokyo; The Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine,
Faculty of Medicine, University of Tokyo
| | - Yoko Chikaoka
- Department of Systems Biology and Medicine, Research Center for Advanced Science and Technology,
The University of Tokyo; The Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine,
Faculty of Medicine, University of Tokyo
| | - Gosuke Hayashi
- Department of Chemistry and Biotechnology, The University of Tokyo
| | - Ryosuke Sakamoto
- Department of Chemistry and Biotechnology, The University of Tokyo
| | - Ryuji Yamamoto
- Department of Systems Biology and Medicine, Research Center for Advanced Science and Technology,
The University of Tokyo
| | | | - Tatsuhiko Kodama
- Department of Systems Biology and Medicine, Research Center for Advanced Science and Technology,
The University of Tokyo
| | - Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo
| | - Takeshi Kawamura
- Department of Systems Biology and Medicine, Research Center for Advanced Science and Technology,
The University of Tokyo; The Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine,
Faculty of Medicine, University of Tokyo
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40
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Bartuschat AL, Schellhorn T, Hübner H, Gmeiner P, Heinrich MR. Fluoro-substituted phenylazocarboxamides: Dopaminergic behavior and N-arylating properties for irreversible binding. Bioorg Med Chem 2015; 23:3938-47. [DOI: 10.1016/j.bmc.2014.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 10/24/2022]
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41
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Pham ND, Fermaintt CS, Rodriguez AC, McCombs JE, Nischan N, Kohler JJ. Cellular metabolism of unnatural sialic acid precursors. Glycoconj J 2015; 32:515-29. [PMID: 25957566 DOI: 10.1007/s10719-015-9593-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/10/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022]
Abstract
Carbohydrates, in addition to their metabolic functions, serve important roles as receptors, ligands, and structural molecules for diverse biological processes. Insight into carbohydrate biology and mechanisms has been aided by metabolic oligosaccharide engineering (MOE). In MOE, unnatural carbohydrate analogs with novel functional groups are incorporated into cellular glycoconjugates and used to probe biological systems. While MOE has expanded knowledge of carbohydrate biology, limited metabolism of unnatural carbohydrate analogs restricts its use. Here we assess metabolism of SiaDAz, a diazirine-modified analog of sialic acid, and its cell-permeable precursor, Ac4ManNDAz. We show that the efficiency of Ac4ManNDAz and SiaDAz metabolism depends on cell type. Our results indicate that different cell lines can have different metabolic roadblocks in the synthesis of cell surface SiaDAz. These findings point to roles for promiscuous intracellular esterases, kinases, and phosphatases during unnatural sugar metabolism and provide guidance for ways to improve MOE.
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Affiliation(s)
- Nam D Pham
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Charles S Fermaintt
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Andrea C Rodriguez
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Janet E McCombs
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nicole Nischan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jennifer J Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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42
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43
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Fujita A, Kohler JJ. Photocrosslinking Sugars for Capturing Glycan-dependent Interactions (Jpn. Ed.). TRENDS GLYCOSCI GLYC 2015. [DOI: 10.4052/tigg.1439.1j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Akiko Fujita
- Department of Biochemistry, University of Texas Southwestern Medical Center
| | - Jennifer J. Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center
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44
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Fujita A, Kohler JJ. Photocrosslinking Sugars for Capturing Glycan-dependent Interactions. TRENDS GLYCOSCI GLYC 2015. [DOI: 10.4052/tigg.1439.1e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Akiko Fujita
- Department of Biochemistry, University of Texas Southwestern Medical Center
| | - Jennifer J. Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center
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45
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Stewart JA, Piligian BF, Rundell SR, Swarts BM. A trifunctional cyclooctyne for modifying azide-labeled biomolecules with photocrosslinking and affinity tags. Chem Commun (Camb) 2015; 51:17600-3. [DOI: 10.1039/c5cc07536j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A trifunctional cyclooctyne-based reagent that harnesses bioorthogonal chemistry to facilitate the probing of biomolecular interactions is described.
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Affiliation(s)
- Jessica A. Stewart
- Department of Chemistry and Biochemistry
- Central Michigan University
- Mount Pleasant
- USA
| | - Brent F. Piligian
- Department of Chemistry and Biochemistry
- Central Michigan University
- Mount Pleasant
- USA
| | - Sarah R. Rundell
- Department of Chemistry and Biochemistry
- Central Michigan University
- Mount Pleasant
- USA
| | - Benjamin M. Swarts
- Department of Chemistry and Biochemistry
- Central Michigan University
- Mount Pleasant
- USA
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46
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Kennedy EJ. EMBO conference series: Chemical Biology 2014. Chembiochem 2014; 15:2783-7. [PMID: 25318996 DOI: 10.1002/cbic.201402527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 11/07/2022]
Abstract
Around 300 people from 18 countries took part in the fourth biennial Chemical Biology conference at The European Molecular Biology Laboratory (EMBL) in Heidelberg, from August 20 to 23, 2014. Many advances in the field of chemical biology were presented in talks and poster sessions. Picture: Petra Riedinger (EMBL).
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Affiliation(s)
- Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 240 W. Green Street, Athens, GA 30602 (USA).
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47
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Vervacke J, Funk AL, Wang YC, Strom M, Hrycyna CA, Distefano MD. Diazirine-containing photoactivatable isoprenoid: synthesis and application in studies with isoprenylcysteine carboxyl methyltransferase. J Org Chem 2014; 79:1971-8. [PMID: 24502619 PMCID: PMC3985442 DOI: 10.1021/jo402600b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 12/19/2022]
Abstract
Photoaffinity labeling is a useful technique employed to identify protein-ligand and protein-protein noncovalent interactions. Photolabeling experiments have been particularly informative for probing membrane-bound proteins where structural information is difficult to obtain. The most widely used classes of photoactive functionalities include aryl azides, diazocarbonyls, diazirines, and benzophenones. Diazirines are intrinsically smaller than benzophenones and generate carbenes upon photolysis that react with a broader range of amino acid side chains compared with the benzophenone-derived diradical; this makes diazirines potentially more general photoaffinity-labeling agents. In this article, we describe the development and application of a new isoprenoid analogue containing a diazirine moiety that was prepared in six steps and incorporated into an a-factor-derived peptide produced via solid-phase synthesis. In addition to the diazirine moiety, fluorescein and biotin groups were also incorporated into the peptide to aid in the detection and enrichment of photo-cross-linked products. This multifuctional diazirine-containing peptide was a substrate for Ste14p, the yeast homologue of the potential anticancer target Icmt, with K(m) (6.6 μM) and V(max) (947 pmol min(-1) mg(-1)) values comparable or better than a-factor peptides functionalized with benzophenone-based isoprenoids. Photo-cross-linking experiments demonstrated that the diazirine probe photo-cross-linked to Ste14p with observably higher efficiency than benzophenone-containing a-factor peptides.
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Affiliation(s)
- Jeffrey
S. Vervacke
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Amy L. Funk
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907−2084, United States
| | - Yen-Chih Wang
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark Strom
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christine A. Hrycyna
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907−2084, United States
| | - Mark D. Distefano
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
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48
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Yestrepsky BD, Kretz CA, Xu Y, Holmes A, Sun H, Ginsburg D, Larsen SD. Development of tag-free photoprobes for studies aimed at identifying the target of novel Group A Streptococcus antivirulence agents. Bioorg Med Chem Lett 2014; 24:1538-44. [PMID: 24559768 DOI: 10.1016/j.bmcl.2014.01.079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 01/27/2014] [Indexed: 02/07/2023]
Abstract
We previously reported the identification and development of novel inhibitors of streptokinase (SK) expression by Group A Streptococcus (GAS), originating from a high throughput cell-based phenotypic screen. Although phenotypic screening is well-suited to identifying compounds that exert desired biological effects in potentially novel ways, it requires follow-up experiments to determine the macromolecular target(s) of active compounds. We therefore designed and synthesized several classes of chemical probes for target identification studies, guided by previously established structure-activity relationships. The probes were designed to first irreversibly photolabel target proteins in the intact bacteria, followed by cell lysis and click ligation with fluorescent tags to allow for visualization on SDS-PAGE gels. This stepwise, 'tag-free' approach allows for a significant reduction in molecular weight and polar surface area compared to full-length fluorescent or biotinylated probes, potentially enhancing membrane permeability and the maintenance of activity. Of the seven probes produced, the three most biologically active were employed in preliminary target identification trials. Despite the potent activity of these probes, specific labeling events were not conclusively observed due to a considerable degree of nonspecific protein binding. Nevertheless, the successful synthesis of potent biologically active probe molecules will serve as a starting point for initiating more sensitive methods of probe-based target identification.
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Affiliation(s)
- Bryan D Yestrepsky
- Vahlteich Medicinal Chemistry Core, Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI 48109, United States
| | - Colin A Kretz
- Department of Human Genetics, Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, United States
| | - Yuanxi Xu
- Department of Internal Medicine, School of Medicine, University of Missouri-Columbia, 1 Hospital Dr., DC043.00, Columbia, MO 65212, United States
| | - Autumn Holmes
- Department of Human Genetics, Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, United States
| | - Hongmin Sun
- Department of Internal Medicine, School of Medicine, University of Missouri-Columbia, 1 Hospital Dr., DC043.00, Columbia, MO 65212, United States
| | - David Ginsburg
- Department of Human Genetics, Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, United States
| | - Scott D Larsen
- Vahlteich Medicinal Chemistry Core, Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI 48109, United States.
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49
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Haberkant P, Holthuis JCM. Fat & fabulous: bifunctional lipids in the spotlight. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1022-30. [PMID: 24440797 DOI: 10.1016/j.bbalip.2014.01.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/02/2014] [Accepted: 01/05/2014] [Indexed: 01/25/2023]
Abstract
Understanding biological processes at the mechanistic level requires a systematic charting of the physical and functional links between all cellular components. While protein-protein and protein-nucleic acid networks have been subject to many global surveys, other critical cellular components such as membrane lipids have rarely been studied in large-scale interaction screens. Here, we review the development of photoactivatable and clickable lipid analogues-so-called bifunctional lipids-as novel chemical tools that enable a global profiling of lipid-protein interactions in biological membranes. Recent studies indicate that bifunctional lipids hold great promise in systematic efforts to dissect the elaborate crosstalk between proteins and lipids in live cells and organisms. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Per Haberkant
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Joost C M Holthuis
- Molecular Cell Biology, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany.
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50
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Smith CC, Hollenstein M, Leumann CJ. The synthesis and application of a diazirine-modified uridine analogue for investigating RNA–protein interactions. RSC Adv 2014. [DOI: 10.1039/c4ra08682a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A uridine analogue equipped with a photoactive diazirine unit was generated and incorporated into RNA either syntheticallyviaphosphoramidite chemistry or by enzymatic polymerization. The new analogue was developed to identify and investigate RNA–protein interactions.
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Affiliation(s)
- Christine C. Smith
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern, Switzerland
| | - Marcel Hollenstein
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern, Switzerland
| | - Christian J. Leumann
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern, Switzerland
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