1
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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2
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Immler F, Schneider T, Kovermann M. Targeted Preparation and NMR Spectroscopic Characterization of Lys11-Linked Ubiquitin Trimers. Chembiochem 2024; 25:e202300670. [PMID: 37983597 DOI: 10.1002/cbic.202300670] [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: 09/29/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
Abstract
Ubiquitylation refers to the attachment of mono- or poly-ubiquitin molecules to a substrate protein. To shield ubiquitin chains against potential hydrolysis, a facile, click-chemistry based approach was recently established for the generation of site-specifically conjugated ubiquitin dimers relying on triazole-linkage. Here, the preparation of such ubiquitin chains was advanced by the generation of homotypic Lys11-linked ubiquitin trimers considering an isotopic labeling scheme in a moiety-wise manner. The structural and dynamical impact on the ubiquitin unit at proximal, central, or distal position that is potentially invoked by the respective other two moieties was systematically probed by heteronuclear high-resolution NMR spectroscopic approaches. As a result, conjugating a third ubiquitin moiety to the proximal or distal site of a ubiquitin dimer does not alter structural and dynamical characteristics as it has been seen for ubiquitin dimers. This observation suggests that recognition of a homotypically assembled ubiquitin chain by a potential substrate is primarily done by screening the length of a ubiquitin chain rather than relying on subtle changes in structure or dynamic properties of single ubiquitin moieties composing the chain.
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Affiliation(s)
- Fabian Immler
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
| | - Tobias Schneider
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
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3
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Galan SRG, Raj R, Mamalis D, Jones LH, Mohammed S, Davis BG. The Minimum Protein Staple? - Towards 'bio'-Baldwin's rules via inter-phosphosite linking in the MEK1 activation loop. Chem Sci 2024; 15:1306-1317. [PMID: 38274071 PMCID: PMC10806838 DOI: 10.1039/d3sc04631a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/25/2023] [Indexed: 01/27/2024] Open
Abstract
In small molecule organic chemistry, the heuristic insight into ring-forming processes that was enabled by Baldwin's rules some 50 years ago proved a step-change in the role of mechanistically guided synthesis. It created a lens upon and marker of fundamental stereoelectronic and conformation-guided chemical processes. However, despite the widespread role of stereoelectronics and conformational control in Biology, no equivalent coherent exploitation of trapped, ring-forming processes yet exists in biomolecules. In the development of a minimal ring-closing process in intact proteins that might prove suitable in a coherent rule-set, we have tested endo-trig ring-closing conjugate thioether lanthionine (Lan) -CH2-S-CH2- formation as a limiting cyclization. Spontaneous Lan formation in proteins is rare if not non-existent and when found in natural product cyclic peptides it requires the mediation of corresponding biosynthetic enzymes as well as productive reactive conformations to guide it. Here, we show that within a conformationally flexible and functionally important protein loop - the MAPK kinase phosphorylation-targeted activation loop - Lan ring-closing is possible. Ring-closing proves to be critically dependent on the location of a trig electrophilic site in just one of two regioisomeric potential precursors to allow phosphosite-to-phosphosite 'stapling'. This first example of spontaneous protein thioether ring-closing/'stapling' and its accessibility from just one precursor (despite the potential for both to form an identical 'staple') now reveals the potential for Lan formation not only as an accessible form of minimal stapling in proteins but also as an exquisitely sensitive probe of associated protein geometries. We suggest that the use of this (as well as the development of other such, intramolecular protein traps that are dependent on inherent protein-controlled reactivity rather than forced crosslinking) may allow the broader trapping and mapping of relevant, even minor, protein states. In this way, protein ring formation may enable a form of extended 'bio-Baldwin's rules' that help to delineate relevant protein conformational space.
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Affiliation(s)
- Sébastien R G Galan
- Department of Chemistry, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Ritu Raj
- Department of Chemistry, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Dimitrios Mamalis
- Department of Chemistry, University of Oxford Mansfield Road Oxford OX1 3TA UK
- The Rosalind Franklin Institute Oxfordshire OX11 0FA UK
| | - Lyn H Jones
- Dana-Farber Cancer Institute Boston Massachusetts USA
| | - Shabaz Mohammed
- Department of Chemistry, University of Oxford Mansfield Road Oxford OX1 3TA UK
- The Rosalind Franklin Institute Oxfordshire OX11 0FA UK
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford Mansfield Road Oxford OX1 3TA UK
- The Rosalind Franklin Institute Oxfordshire OX11 0FA UK
- Department of Pharmacology, University of Oxford Mansfield Road Oxford OX1 3QT UK
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4
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Pelgrom LR, Davis GM, O'Shaughnessy S, Wezenberg EJM, Van Kasteren SI, Finlay DK, Sinclair LV. QUAS-R: An SLC1A5-mediated glutamine uptake assay with single-cell resolution reveals metabolic heterogeneity with immune populations. Cell Rep 2023; 42:112828. [PMID: 37478011 DOI: 10.1016/j.celrep.2023.112828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/26/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023] Open
Abstract
System-level analysis of single-cell data is rapidly transforming the field of immunometabolism. Given the competitive demand for nutrients in immune microenvironments, there is a need to understand how and when immune cells access these nutrients. Here, we describe a new approach for single-cell analysis of nutrient uptake where we use in-cell biorthogonal labeling of a functionalized amino acid after transport into the cell. In this manner, the bona fide active uptake of glutamine via SLC1A5/ASCT2 could be quantified. We used this assay to interrogate the transport capacity of complex immune subpopulations, both in vitro and in vivo. Taken together, our findings provide an easy sensitive single-cell assay to assess which cells support their function via SLC1A5-mediated uptake. This is a significant addition to the single-cell metabolic toolbox required to decode the metabolic landscape of complex immune microenvironments.
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Affiliation(s)
- Leonard R Pelgrom
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Gavin M Davis
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland
| | - Simon O'Shaughnessy
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland
| | - Emilie J M Wezenberg
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Sander I Van Kasteren
- Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
| | - David K Finlay
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland; School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02R590 Dublin, Ireland.
| | - Linda V Sinclair
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.
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5
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Chen X, Josephson B, Davis BG. Carbon-Centered Radicals in Protein Manipulation. ACS CENTRAL SCIENCE 2023; 9:614-638. [PMID: 37122447 PMCID: PMC10141601 DOI: 10.1021/acscentsci.3c00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 05/03/2023]
Abstract
Methods to directly post-translationally modify proteins are perhaps the most straightforward and operationally simple ways to create and study protein post-translational modifications (PTMs). However, precisely altering or constructing the C-C scaffolds pervasive throughout biology is difficult with common two-electron chemical approaches. Recently, there has been a surge of new methods that have utilized single electron/radical chemistry applied to site-specifically "edit" proteins that have started to create this potential-one that in principle could be near free-ranging. This review provides an overview of current methods that install such "edits", including those that generate function and/or PTMs, through radical C-C bond formation (as well as C-X bond formation via C• where illustrative). These exploit selectivity for either native residues, or preinstalled noncanonical protein side-chains with superior radical generating or accepting abilities. Particular focus will be on the radical generation approach (on-protein or off-protein, use of light and photocatalysts), judging the compatibility of conditions with proteins and cells, and novel chemical biology applications afforded by these methods. While there are still many technical hurdles, radical C-C bond formation on proteins is a promising and rapidly growing area in chemical biology with long-term potential for biological editing.
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Affiliation(s)
- Xuanxiao Chen
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
| | - Brian Josephson
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
| | - Benjamin G. Davis
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford, OX1 3QT, U.K.
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6
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Carballares D, Fernandez-Lafuente R, Rocha-Martin J. Immobilization-stabilization of the dimeric D-amino acid oxidase from porcine kidney. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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McBerney R, Dolan JP, Cawood EE, Webb ME, Turnbull WB. Bioorthogonal, Bifunctional Linker for Engineering Synthetic Glycoproteins. JACS AU 2022; 2:2038-2047. [PMID: 36186556 PMCID: PMC9516712 DOI: 10.1021/jacsau.2c00312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Post-translational glycosylation of proteins results in complex mixtures of heterogeneous protein glycoforms. Glycoproteins have many potential applications from fundamental studies of glycobiology to potential therapeutics, but generating homogeneous recombinant glycoproteins using chemical or chemoenzymatic reactions to mimic natural glycoproteins or creating homogeneous synthetic neoglycoproteins is a challenging synthetic task. In this work, we use a site-specific bioorthogonal approach to produce synthetic homogeneous glycoproteins. We develop a bifunctional, bioorthogonal linker that combines oxime ligation and strain-promoted azide-alkyne cycloaddition chemistry to functionalize reducing sugars and glycan derivatives for attachment to proteins. We demonstrate the utility of this minimal length linker by producing neoglycoprotein inhibitors of cholera toxin in which derivatives of the disaccharide lactose and GM1os pentasaccharide are attached to a nonbinding variant of the cholera toxin B-subunit that acts as a size- and valency-matched multivalent scaffold. The resulting neoglycoproteins decorated with GM1 ligands inhibit cholera toxin B-subunit adhesion with a picomolar IC50.
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8
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Sustainable functionalization and modification of materials via multicomponent reactions in water. Front Chem Sci Eng 2022. [DOI: 10.1007/s11705-022-2150-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Doelman W, van Kasteren SI. Synthesis of glycopeptides and glycopeptide conjugates. Org Biomol Chem 2022; 20:6487-6507. [PMID: 35903971 PMCID: PMC9400947 DOI: 10.1039/d2ob00829g] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein glycosylation is a key post-translational modification important to many facets of biology. Glycosylation can have critical effects on protein conformation, uptake and intracellular routing. In immunology, glycosylation of antigens has been shown to play a role in self/non-self distinction and the effective uptake of antigens. Improperly glycosylated proteins and peptide fragments, for instance those produced by cancerous cells, are also prime candidates for vaccine design. To study these processes, access to peptides bearing well-defined glycans is of critical importance. In this review, the key approaches towards synthetic, well-defined glycopeptides, are described, with a focus on peptides useful for and used in immunological studies. Special attention is given to the glycoconjugation approaches that have been developed in recent years, as these enable rapid synthesis of various (unnatural) glycopeptides, enabling powerful carbohydrate structure/activity studies. These techniques, combined with more traditional total synthesis and chemoenzymatic methods for the production of glycopeptides, should help unravel some of the complexities of glycobiology in the near future.
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Affiliation(s)
- Ward Doelman
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
| | - Sander I van Kasteren
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
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10
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Morellon-Sterling R, Tavano O, Bolivar JM, Berenguer-Murcia Á, Vela-Gutiérrez G, Sabir JSM, Tacias-Pascacio VG, Fernandez-Lafuente R. A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values. Int J Biol Macromol 2022; 210:682-702. [PMID: 35508226 DOI: 10.1016/j.ijbiomac.2022.04.224] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/05/2022]
Abstract
Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.
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Affiliation(s)
- Roberto Morellon-Sterling
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Olga Tavano
- Faculty of Nutrition, Alfenas Federal Univ., 700 Gabriel Monteiro da Silva St, Alfenas, MG 37130-000, Brazil
| | - Juan M Bolivar
- Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., Madrid 28040, Spain
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, Alicante, Spain
| | - Gilber Vela-Gutiérrez
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Veymar G Tacias-Pascacio
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico; Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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11
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Design of Artificial Enzymes Bearing Several Active Centers: New Trends, Opportunities and Problems. Int J Mol Sci 2022; 23:ijms23105304. [PMID: 35628115 PMCID: PMC9141793 DOI: 10.3390/ijms23105304] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/28/2022] [Accepted: 05/08/2022] [Indexed: 12/11/2022] Open
Abstract
Harnessing enzymes which possess several catalytic activities is a topic where intense research has been carried out, mainly coupled with the development of cascade reactions. This review tries to cover the different possibilities to reach this goal: enzymes with promiscuous activities, fusion enzymes, enzymes + metal catalysts (including metal nanoparticles or site-directed attached organometallic catalyst), enzymes bearing non-canonical amino acids + metal catalysts, design of enzymes bearing a second biological but artificial active center (plurizymes) by coupling enzyme modelling and directed mutagenesis and plurizymes that have been site directed modified in both or in just one active center with an irreversible inhibitor attached to an organometallic catalyst. Some examples of cascade reactions catalyzed by the enzymes bearing several catalytic activities are also described. Finally, some foreseen problems of the use of these multi-activity enzymes are described (mainly related to the balance of the catalytic activities, necessary in many instances, or the different operational stabilities of the different catalytic activities). The design of new multi-activity enzymes (e.g., plurizymes or modified plurizymes) seems to be a topic with unarguable interest, as this may link biological and non-biological activities to establish new combo-catalysis routes.
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12
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Genetic and Molecular Characterization Revealed the Prognosis Efficiency of Histone Acetylation in Pan-Digestive Cancers. JOURNAL OF ONCOLOGY 2022; 2022:3938652. [PMID: 35422864 PMCID: PMC9005301 DOI: 10.1155/2022/3938652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 11/18/2022]
Abstract
The imbalance between acetylation and deacetylation of histone proteins, important for epigenetic modifications, is closely associated with various diseases, including cancer. However, knowledge regarding the modification of histones across the different types of digestive cancers is still lacking. The purpose of this research was to analyze the role of histone acetylation and deacetylation in pan-digestive cancers. We systematically characterized the molecular alterations and clinical relevance of 13 histone acetyltransferase (HAT) and 18 histone deacetylase (HDAC) genes in five types of digestive cancers, including esophageal carcinoma, gastric cancer, hepatocellular carcinoma, pancreatic cancer, and colorectal cancer. Recurrent mutations and copy number variation (CNV) were extensively found in acetylation-associated genes across pan-digestive cancers. HDAC9 and KAT6A showed widespread copy number amplification across five pan-digestive cancers, while ESCO2, EP300, and HDAC10 had prevalent copy number deletions. Accordingly, we found that HAT and HDAC genes correlated with multiple cancer hallmark-related pathways, especially the histone modification-related pathway, PRC2 complex pathway. Furthermore, the expression pattern of HAT and HDAC genes stratified patients with clinical benefit in hepatocellular carcinoma and pancreatic cancer. These results indicated that acetylation acts as a key molecular regulation of pan-digestive tumor progression.
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13
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Cobo I, Matheu MI, Castillón S, Davis BG, Boutureira O. Probing Site-Selective Conjugation Chemistries for the Construction of Homogeneous Synthetic Glycodendriproteins. Chembiochem 2022; 23:e202200020. [PMID: 35322922 PMCID: PMC9322419 DOI: 10.1002/cbic.202200020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/14/2022] [Indexed: 11/22/2022]
Abstract
Methods that site‐selectively attach multivalent carbohydrate moieties to proteins can be used to generate homogeneous glycodendriproteins as synthetic functional mimics of glycoproteins. Here, we study aspects of the scope and limitations of some common bioconjugation techniques that can give access to well‐defined glycodendriproteins. A diverse reactive platform was designed via use of thiol‐Michael‐type additions, thiol‐ene reactions, and Cu(I)‐mediated azide‐alkyne cycloadditions from recombinant proteins containing the non‐canonical amino acids dehydroalanine, homoallylglycine, homopropargylglycine, and azidohomoalanine.
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Affiliation(s)
- Isidro Cobo
- Universitat Rovira i Virgili, departament de quimica analitica i quimica organica, SPAIN
| | - M Isabel Matheu
- Universitat Rovira i Virgili, departament de quimica analitica i quimica organica, SPAIN
| | - Sergio Castillón
- Universitat Rovira i Virgili, departament de quimica analitica i quimica organica, SPAIN
| | | | - Omar Boutureira
- Universitat Rovira i Virgili, Departament de Quimica Analitica i Qu�mica Org�nica, Departament de Qu�mica Anal, C/ Marcel.li Domingo 1, 43007, Tarragona, SPAIN
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14
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Polyak D, Krauss IJ. An Optimized Synthesis of Fmoc-l-Homopropargylglycine-OH. J Org Chem 2022; 87:3841-3844. [PMID: 35133817 DOI: 10.1021/acs.joc.1c03027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient multigram synthesis of alkynyl amino acid Fmoc-l-homopropargylglycine-OH is described. A double Boc protection is optimized for high material throughput, and the key Seyferth-Gilbert homologation is optimized to avoid racemization. Eighteen grams of the enantiopure (>98% ee) noncanonical amino acid was readily generated for use in solid phase synthesis to make peptides that can be functionalized by copper-assisted alkyne-azide cycloaddition.
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Affiliation(s)
- Daniel Polyak
- Department of Chemistry, Brandeis University, MS 015, Waltham, Massachusetts 02454-9110, United States
| | - Isaac J Krauss
- Department of Chemistry, Brandeis University, MS 015, Waltham, Massachusetts 02454-9110, United States
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15
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Abdullayev S, Roy R. Practical non-enzymatic synthesis of propargyl sialyl-α-(2-3’)-lactosamine trisaccharide using minimal protecting groups manipulation. Carbohydr Res 2022; 514:108543. [DOI: 10.1016/j.carres.2022.108543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/02/2022]
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16
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Moon S, Javed A, Hard ER, Pratt MR. Methods for Studying Site-Specific O-GlcNAc Modifications: Successes, Limitations, and Important Future Goals. JACS AU 2022; 2:74-83. [PMID: 35098223 PMCID: PMC8791055 DOI: 10.1021/jacsau.1c00455] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Indexed: 06/14/2023]
Abstract
O-GlcNAcylation is a dynamic post-translational modification which affects myriad proteins, cellular functions, and disease states. Its presence or absence modulates protein function via differential protein- and site-specific mechanisms, necessitating innovative techniques to probe the modification in highly selective manners. To this end, a variety of biological and chemical methods have been developed to study specific O-GlcNAc modification events both in vitro and in vivo, each with their own respective strengths and shortcomings. Together, they comprise a potent chemical biology toolbox for the analysis of O-GlcNAcylation (and, in theory, other post-translational modifications) while highlighting the need and space for more facile, generalizable, and biologically authentic techniques.
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Affiliation(s)
- Stuart
P. Moon
- Departments
of Chemistry and Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Afraah Javed
- Departments
of Chemistry and Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Eldon R. Hard
- Departments
of Chemistry and Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Matthew R. Pratt
- Departments
of Chemistry and Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
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17
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Wang S, Zhou Q, Li Y, Wei B, Liu X, Zhao J, Ye F, Zhou Z, Ding B, Wang P. Quinoline-Based Photolabile Protection Strategy Facilitates Efficient Protein Assembly. J Am Chem Soc 2022; 144:1232-1242. [PMID: 35034454 DOI: 10.1021/jacs.1c10324] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Native chemical ligation (NCL) provides a powerful solution to assemble proteins with precise chemical features, which enables a detailed investigation of the protein structure-function relationship. As an extension to NCL, the discovery of desulfurization and expressed protein ligation (EPL) techniques has greatly expanded the efficient access to large or challenging protein sequences via chemical ligations. Despite its superior reliability, the NCL-desulfurization protocol requires orthogonal protection strategies to allow selective desulfurization in the presence of native Cys, which is crucial to its synthetic application. In contrast to traditional thiol protecting groups, photolabile protecting groups (PPGs), which are removed upon irradiation, simplify protein assembly and therefore provide minimal perturbation to the peptide scaffold. However, current PPG strategies are mainly limited to nitro-benzyl derivatives, which are incompatible with NCL-desulfurization. Herein, we present for the first time that quinoline-based PPG for cysteine can facilitate various ligation strategies, including iterative NCL and EPL-desulfurization methods. 7-(Piperazin-1-yl)-2-(methyl)quinolinyl (PPZQ) caging of multiple cysteine residues within the protein sequence can be readily introduced via late-stage modification, while the traceless removal of PPZQ is highly efficient via photolysis in an aqueous buffer. In addition, the PPZQ group is compatible with radical desulfurization. The efficiency of this strategy has been highlighted by the synthesis of γ-synuclein and phosphorylated cystatin-S via one-pot iterative ligation and EPL-desulfurization methods. Besides, successful sextuple protection and deprotection of the expressed Interleukin-34 fragment demonstrate the great potential of this strategy in protein caging/uncaging investigations.
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Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qingqing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yunxue Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Bingcheng Wei
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xinliang Liu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jie Zhao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Farong Ye
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhongneng Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Bei Ding
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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18
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Shen MH, Wang YJ, Wang Y, Zhou Y, Gu J, Liu XQ, Guo J, Ouyang M, Deng L, Xu HD. α-Vinyl azide–cysteine click coupling reaction enabled bioorthogonal peptide/protein modification. Org Chem Front 2022. [DOI: 10.1039/d2qo00736c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Alkyl and α-aryl vinyl azides were found to be able to couple with cysteine-derived alkyl thiols chemoselectively under mild conditions, providing the corresponding β-ketosulfides with simultaneous extrusion of N2 and ammonia.
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Affiliation(s)
- Mei-Hua Shen
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yu-Jiao Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yong Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Ying Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jie Gu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Xiao-Qian Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jia Guo
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Mingxing Ouyang
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Linhong Deng
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Hua-Dong Xu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
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19
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Robichon M, Branquet D, Uziel J, Lubin‐Germain N, Ferry A. Directed Nickel‐Catalyzed
pseudo
‐Anomeric C−H Alkynylation of Glycals as an Approach towards
C
‐Glycoconjugate Synthesis. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Morgane Robichon
- CY Cergy Paris University BioCIS, CNRS 5 mail Gay-Lussac 95000 Cergy-Pontoise cedex France
- Paris-Saclay University BioCIS, CNRS 5 rue J.-B. Clément 92296 Châtenay-Malabry cedex France
| | - David Branquet
- CY Cergy Paris University BioCIS, CNRS 5 mail Gay-Lussac 95000 Cergy-Pontoise cedex France
- Paris-Saclay University BioCIS, CNRS 5 rue J.-B. Clément 92296 Châtenay-Malabry cedex France
| | - Jacques Uziel
- CY Cergy Paris University BioCIS, CNRS 5 mail Gay-Lussac 95000 Cergy-Pontoise cedex France
- Paris-Saclay University BioCIS, CNRS 5 rue J.-B. Clément 92296 Châtenay-Malabry cedex France
| | - Nadège Lubin‐Germain
- CY Cergy Paris University BioCIS, CNRS 5 mail Gay-Lussac 95000 Cergy-Pontoise cedex France
- Paris-Saclay University BioCIS, CNRS 5 rue J.-B. Clément 92296 Châtenay-Malabry cedex France
| | - Angélique Ferry
- CY Cergy Paris University BioCIS, CNRS 5 mail Gay-Lussac 95000 Cergy-Pontoise cedex France
- Paris-Saclay University BioCIS, CNRS 5 rue J.-B. Clément 92296 Châtenay-Malabry cedex France
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20
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Keenan T, Spears RJ, Akkad S, Mahon CS, Hatton NE, Walton J, Noble A, Yates ND, Baumann CG, Parkin A, Signoret N, Fascione MA. A Tale of Two Bioconjugations: pH Controlled Divergent Reactivity of Protein α-oxo-Aldehydes in Competing α-oxo-Mannich and Catalyst-Free Aldol Ligations. ACS Chem Biol 2021; 16:2387-2400. [PMID: 34751550 DOI: 10.1021/acschembio.1c00531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Site-selective chemical methods for protein bioconjugation have revolutionized the fields of cell and chemical biology through the development of novel protein/enzyme probes bearing fluorescent, spectroscopic, or even toxic cargos. Herein, we report two new methods for the bioconjugation of α-oxo aldehyde handles within proteins using small molecule aniline and/or phenol probes. The "α-oxo-Mannich" and "catalyst-free aldol" ligations both compete for the electrophilic α-oxo aldehyde, which displays pH divergent reactivity proceeding through the "Mannich" pathway at acidic pH to afford bifunctionalized bioconjugates, and the "catalyst-free aldol" pathway at neutral pH to afford monofunctionalized bioconjugates. We explore the substrate scope and utility of both of these bioconjugations in the construction of neoglycoproteins, in the process formulating a mechanistic rationale for how both pathways intersect with each other at different reaction pH's.
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Affiliation(s)
- Tessa Keenan
- Department of Chemistry, University of York, York, United Kingdom YO10 5DD
| | - Richard J. Spears
- Department of Chemistry, University of York, York, United Kingdom YO10 5DD
| | - Saeed Akkad
- Department of Chemistry, University of York, York, United Kingdom YO10 5DD
| | - Clare S. Mahon
- Department of Chemistry, Durham University, Durham, United Kingdom DH1 3LE
| | - Natasha E. Hatton
- Department of Chemistry, University of York, York, United Kingdom YO10 5DD
| | - Julia Walton
- Department of Chemistry, University of York, York, United Kingdom YO10 5DD
| | - Amanda Noble
- Department of Chemistry, University of York, York, United Kingdom YO10 5DD
| | - Nicholas D. Yates
- Department of Chemistry, University of York, York, United Kingdom YO10 5DD
| | | | - Alison Parkin
- Department of Chemistry, University of York, York, United Kingdom YO10 5DD
| | - Nathalie Signoret
- Hull York Medical School, University of York, York, United Kingdom YO10 5DD
| | - Martin A. Fascione
- Department of Chemistry, University of York, York, United Kingdom YO10 5DD
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21
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Giri P, Pagar AD, Patil MD, Yun H. Chemical modification of enzymes to improve biocatalytic performance. Biotechnol Adv 2021; 53:107868. [PMID: 34774927 DOI: 10.1016/j.biotechadv.2021.107868] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022]
Abstract
Improvement in intrinsic enzymatic features is in many instances a prerequisite for the scalable applicability of many industrially important biocatalysts. To this end, various strategies of chemical modification of enzymes are maturing and now considered as a distinct way to improve biocatalytic properties. Traditional chemical modification methods utilize reactivities of amine, carboxylic, thiol and other side chains originating from canonical amino acids. On the other hand, noncanonical amino acid- mediated 'click' (bioorthogoal) chemistry and dehydroalanine (Dha)-mediated modifications have emerged as an alternate and promising ways to modify enzymes for functional enhancement. This review discusses the applications of various chemical modification tools that have been directed towards the improvement of functional properties and/or stability of diverse array of biocatalysts.
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Affiliation(s)
- Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mahesh D Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali 140306, Punjab, India
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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22
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Hyun JY, Kim S, Lee CH, Lee HS, Shin I. Efficient Preparation and Bioactivity Evaluation of Glycan-Defined Glycoproteins. ACS Chem Biol 2021; 16:1930-1940. [PMID: 33232137 DOI: 10.1021/acschembio.0c00629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Owing to the generation of heterogeneous glycoproteins in cells, it is highly difficult to study glycoprotein-mediated biological events and to develop biomedical agents. Thus, general and efficient methods to prepare homogeneous glycoproteins are in high demand. Herein, we report a general method for the efficient preparation of homogeneous glycoproteins that utilizes a combination of genetic code expansion and chemoselective ligation techniques. In the protocol to produce glycan-defined glycoproteins, an alkyne tag-containing protein, generated by genetic encoding of an alkynylated unnatural amino acid, was quantitatively coupled via click chemistry to versatile azide-appended glycans. The glycoproteins produced by the present strategy were found to recognize mammalian cell-surface lectins and enter the cells through lectin-mediated internalization. Also, cell studies exhibited that the glycoprotein containing multiple mannose-6-phosphate residues enters diseased cells lacking specific lysosomal glycosidases by binding to the cell-surface M6P receptor, and subsequently migrates to lysosomes for efficient degradation of stored glycosphingolipids.
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Affiliation(s)
- Ji Young Hyun
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Sanggil Kim
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Chang-Hee Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Injae Shin
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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23
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Park HJ, Jung HM, Lee A, Jo SH, Lee HJ, Kim HS, Jung CK, Min SR, Cho HS. SUMO Modification of OsFKBP20-1b Is Integral to Proper Pre-mRNA Splicing upon Heat Stress in Rice. Int J Mol Sci 2021; 22:ijms22169049. [PMID: 34445755 PMCID: PMC8396655 DOI: 10.3390/ijms22169049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 11/18/2022] Open
Abstract
OsFKBP20-1b, a plant-specific cyclophilin protein, has been implicated to regulate pre-mRNA splicing under stress conditions in rice. Here, we demonstrated that OsFKBP20-1b is SUMOylated in a reconstituted SUMOylation system in E.coli and in planta, and that the SUMOylation-coupled regulation was associated with enhanced protein stability using a less SUMOylated OsFKBP20-1b mutant (5KR_OsFKBP20-1b). Furthermore, OsFKBP20-1b directly interacted with OsSUMO1 and OsSUMO2 in the nucleus and cytoplasm, whereas the less SUMOylated 5KR_OsFKBP20-1b mutant had an impaired interaction with OsSUMO1 and 2 in the cytoplasm but not in the nucleus. Under heat stress, the abundance of an OsFKBP20-1b-GFP fusion protein was substantially increased in the nuclear speckles and cytoplasmic foci, whereas the heat-responsiveness was remarkably diminished in the presence of the less SUMOylated 5KR_OsFKBP20-1b-GFP mutant. The accumulation of endogenous SUMOylated OsFKBP20-1b was enhanced by heat stress in planta. Moreover, 5KR_OsFKBP20-1b was not sufficiently associated with the U snRNAs in the nucleus as a spliceosome component. A protoplast transfection assay indicated that the low SUMOylation level of 5KR_OsFKBP20-1b led to inaccurate alternative splicing and transcription under heat stress. Thus, our results suggest that OsFKBP20-1b is post-translationally regulated by SUMOylation, and the modification is crucial for proper RNA processing in response to heat stress in rice.
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Affiliation(s)
- Hyun-Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
| | - Hae-Myeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Seung-Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Functional Genomics, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
| | - Choon-Kyun Jung
- Department of International Agricultural Technology and Crop Biotechnology Institute/Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea;
- Department of Agriculture, Forestry, and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sung-Ran Min
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Correspondence: (S.-R.M.); (H.-S.C.); Tel.: +82-42-860-4463 (S.-R.M.); +82-42-860-4469 (H.-S.C.)
| | - Hye-Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
- Correspondence: (S.-R.M.); (H.-S.C.); Tel.: +82-42-860-4463 (S.-R.M.); +82-42-860-4469 (H.-S.C.)
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24
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Xu L, Kuan SL, Weil T. Contemporary Approaches for Site-Selective Dual Functionalization of Proteins. Angew Chem Int Ed Engl 2021; 60:13757-13777. [PMID: 33258535 PMCID: PMC8248073 DOI: 10.1002/anie.202012034] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Indexed: 12/16/2022]
Abstract
Site-selective protein functionalization serves as an invaluable tool for investigating protein structures and functions in complicated cellular environments and accomplishing semi-synthetic protein conjugates such as traceable therapeutics with improved features. Dual functionalization of proteins allows the incorporation of two different types of functionalities at distinct location(s), which greatly expands the features of native proteins. The attachment and crosstalk of a fluorescence donor and an acceptor dye provides fundamental insights into the folding and structural changes of proteins upon ligand binding in their native cellular environments. Moreover, the combination of drug molecules with different modes of action, imaging agents or stabilizing polymers provides new avenues to design precision protein therapeutics in a reproducible and well-characterizable fashion. This review aims to give a timely overview of the recent advancements and a future perspective of this relatively new research area. First, the chemical toolbox for dual functionalization of proteins is discussed and compared. The strengths and limitations of each strategy are summarized in order to enable readers to select the most appropriate method for their envisaged applications. Thereafter, representative applications of these dual-modified protein bioconjugates benefiting from the synergistic/additive properties of the two synthetic moieties are highlighted.
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Affiliation(s)
- Lujuan Xu
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Tanja Weil
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
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25
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Lai KY, Galan SRG, Zeng Y, Zhou TH, He C, Raj R, Riedl J, Liu S, Chooi KP, Garg N, Zeng M, Jones LH, Hutchings GJ, Mohammed S, Nair SK, Chen J, Davis BG, van der Donk WA. LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome. Cell 2021; 184:2680-2695.e26. [PMID: 33932340 DOI: 10.1016/j.cell.2021.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 01/22/2021] [Accepted: 03/31/2021] [Indexed: 12/13/2022]
Abstract
Enzyme-mediated damage repair or mitigation, while common for nucleic acids, is rare for proteins. Examples of protein damage are elimination of phosphorylated Ser/Thr to dehydroalanine/dehydrobutyrine (Dha/Dhb) in pathogenesis and aging. Bacterial LanC enzymes use Dha/Dhb to form carbon-sulfur linkages in antimicrobial peptides, but the functions of eukaryotic LanC-like (LanCL) counterparts are unknown. We show that LanCLs catalyze the addition of glutathione to Dha/Dhb in proteins, driving irreversible C-glutathionylation. Chemo-enzymatic methods were developed to site-selectively incorporate Dha/Dhb at phospho-regulated sites in kinases. In human MAPK-MEK1, such "elimination damage" generated aberrantly activated kinases, which were deactivated by LanCL-mediated C-glutathionylation. Surveys of endogenous proteins bearing damage from elimination (the eliminylome) also suggest it is a source of electrophilic reactivity. LanCLs thus remove these reactive electrophiles and their potentially dysregulatory effects from the proteome. As knockout of LanCL in mice can result in premature death, repair of this kind of protein damage appears important physiologically.
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Affiliation(s)
- Kuan-Yu Lai
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sébastien R G Galan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK
| | - Yibo Zeng
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK; UK Catalysis Hub, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxford OX11 0FA, UK; The Rosalind Franklin Institute, Oxfordshire OX11 0FA, UK
| | - Tianhui Hina Zhou
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang He
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ritu Raj
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK
| | - Jitka Riedl
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK
| | - Shi Liu
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - K Phin Chooi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK
| | - Neha Garg
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Min Zeng
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lyn H Jones
- Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, MA 02115, USA
| | - Graham J Hutchings
- UK Catalysis Hub, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxford OX11 0FA, UK; Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Shabaz Mohammed
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK; The Rosalind Franklin Institute, Oxfordshire OX11 0FA, UK
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jie Chen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Benjamin G Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK; The Rosalind Franklin Institute, Oxfordshire OX11 0FA, UK.
| | - Wilfred A van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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26
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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27
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Groenevelt JM, Corey DJ, Fehl C. Chemical Synthesis and Biological Applications of O-GlcNAcylated Peptides and Proteins. Chembiochem 2021; 22:1854-1870. [PMID: 33450137 DOI: 10.1002/cbic.202000843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/15/2021] [Indexed: 12/25/2022]
Abstract
All human cells use O-GlcNAc protein modifications (O-linked N-acetylglucosamine) to rapidly adapt to changing nutrient and stress conditions through signaling, epigenetic, and proteostasis mechanisms. A key challenge for biologists in defining precise roles for specific O-GlcNAc sites is synthetic access to homogenous isoforms of O-GlcNAc proteins, a result of the non-genetically templated, transient, and heterogeneous nature of O-GlcNAc modifications. Toward a solution, this review details the state of the art of two strategies for O-GlcNAc protein modification: advances in "bottom-up" O-GlcNAc peptide synthesis and direct "top-down" installation of O-GlcNAc on full proteins. We also describe key applications of synthetic O-GlcNAc peptide and protein tools as therapeutics, biophysical structure-function studies, biomarkers, and as disease mechanistic probes to advance translational O-GlcNAc biology.
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Affiliation(s)
- Jessica M Groenevelt
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, 48202, USA
| | - Daniel J Corey
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, 48202, USA
| | - Charlie Fehl
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, 48202, USA
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28
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Xu L, Kuan SL, Weil T. Contemporary Approaches for Site‐Selective Dual Functionalization of Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Lujuan Xu
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Institute of Inorganic Chemistry I Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Institute of Inorganic Chemistry I Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Institute of Inorganic Chemistry I Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
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29
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van Leeuwen T, Araman C, Pieper Pournara L, Kampstra ASB, Bakkum T, Marqvorsen MHS, Nascimento CR, Groenewold GJM, van der Wulp W, Camps MGM, Janssen GMC, van Veelen PA, van Westen GJP, Janssen APA, Florea BI, Overkleeft HS, Ossendorp FA, Toes REM, van Kasteren SI. Bioorthogonal protein labelling enables the study of antigen processing of citrullinated and carbamylated auto-antigens. RSC Chem Biol 2021; 2:855-862. [PMID: 34212151 PMCID: PMC8190914 DOI: 10.1039/d1cb00009h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/22/2021] [Indexed: 11/21/2022] Open
Abstract
Proteolysis is fundamental to many biological processes. In the immune system, it underpins the activation of the adaptive immune response: degradation of antigenic material into short peptides and presentation thereof on major histocompatibility complexes, leads to activation of T-cells. This initiates the adaptive immune response against many pathogens. Studying proteolysis is difficult, as the oft-used polypeptide reporters are susceptible to proteolytic sequestration themselves. Here we present a new approach that allows the imaging of antigen proteolysis throughout the processing pathway in an unbiased manner. By incorporating bioorthogonal functionalities into the protein in place of methionines, antigens can be followed during degradation, whilst leaving reactive sidechains open to templated and non-templated post-translational modifications, such as citrullination and carbamylation. Using this approach, we followed and imaged the post-uptake fate of the commonly used antigen ovalbumin, as well as the post-translationally citrullinated and/or carbamylated auto-antigen vinculin in rheumatoid arthritis, revealing differences in antigen processing and presentation.
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Affiliation(s)
- Tyrza van Leeuwen
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Can Araman
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Linda Pieper Pournara
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Arieke S B Kampstra
- Department of Rheumatology, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - Thomas Bakkum
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Mikkel H S Marqvorsen
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Clarissa R Nascimento
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - G J Mirjam Groenewold
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Willemijn van der Wulp
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Marcel G M Camps
- Department of Immunology, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - Gerard J P van Westen
- Computational Drug Discovery, Drug Discovery and Safety, LACDR, Leiden University Leiden The Netherlands
| | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry and the Oncode Institute, Leiden University Leiden The Netherlands
| | - Bogdan I Florea
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Herman S Overkleeft
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
| | - Ferry A Ossendorp
- Department of Immunology, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center P.O. Box 9600 2300 RC Leiden The Netherlands
| | - Sander I van Kasteren
- Division of Bio-organic Synthesis, Leiden Institute of Chemistry and the Institute of Chemical Immunology, Leiden University Leiden The Netherlands
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30
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Doelman W, Marqvorsen MHS, Chiodo F, Bruijns SCM, van der Marel GA, van Kooyk Y, van Kasteren SI, Araman C. Synthesis of Asparagine Derivatives Harboring a Lewis X Type DC-SIGN Ligand and Evaluation of their Impact on Immunomodulation in Multiple Sclerosis. Chemistry 2020; 27:2742-2752. [PMID: 33090600 PMCID: PMC7898482 DOI: 10.1002/chem.202004076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Indexed: 01/13/2023]
Abstract
The protein myelin oligodendrocyte glycoprotein (MOG) is a key component of myelin and an autoantigen in the disease multiple sclerosis (MS). Post‐translational N‐glycosylation of Asn31 of MOG seems to play a key role in modulating the immune response towards myelin. This is mediated by the interaction of Lewis‐type glycan structures in the N‐glycan of MOG with the DC‐SIGN receptor on dendritic cells (DCs). Here, we report the synthesis of an unnatural Lewis X (LeX)‐containing Fmoc‐SPPS‐compatible asparagine building block (SPPS=solid‐phase peptide synthesis), as well as asparagine building blocks containing two LeX‐derived oligosaccharides: LacNAc and Fucα1‐3GlcNAc. These building blocks were used for the glycosylation of the immunodominant portion of MOG (MOG31‐55) and analyzed with respect to their ability to bind to DC‐SIGN in different biological setups, as well as their ability to inhibit the citrullination‐induced aggregation of MOG31‐55. Finally, a cytokine secretion assay was carried out on human monocyte‐derived DCs, which showed the ability of the neoglycopeptide decorated with a single LeX to alter the balance of pro‐ and anti‐inflammatory cytokines, inducing a tolerogenic response.
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Affiliation(s)
- Ward Doelman
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mikkel H S Marqvorsen
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Fabrizio Chiodo
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC-Location Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Sven C M Bruijns
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC-Location Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Yvette van Kooyk
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC-Location Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Sander I van Kasteren
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Can Araman
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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31
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Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
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Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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32
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Holloran N, Collins D, Rathnayake U, Zhang B, Koh M, Kang C, Garner P. Site-Specific Synthesis of Cysteine-Bridged Glycoproteins via Expressed Protein Glycoligation. Bioconjug Chem 2020; 31:2362-2366. [PMID: 32931248 DOI: 10.1021/acs.bioconjchem.0c00437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Site-specific glycosylation of a functional recombinant protein thioester is reported. The thioester functionalized protein sfGFP-Y151ThioD, prepared by genetic code expansion, underwent native chemical ligation with the cysteine-conjugated glycans H-Cys-NH-GlcNAc and H-Cys-NH-(GlcNAc)2(Man)3 to give the corresponding cysteine-bridged glycoproteins. The intact glycoproteins, which retained their fluorescence, were characterized by top-down mass spectrometry and gel electrophoresis. The bridging cysteine provided a convenient handle for affinity chromatography purification of the glycoproteins via a removable biotin tag. Given the influence that specific glycoforms can have on a protein's function, the ability to attach a homogeneous glycan to an intact protein in a functional group controlled yet sequon-independent manner could find widespread application. These preliminary results set the stage for development of the expressed protein glycoligation (EPG) concept.
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Affiliation(s)
- Nicholas Holloran
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Daniel Collins
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Upendra Rathnayake
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Minseob Koh
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Philip Garner
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
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33
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The tip of the iceberg for diagnostic dilemmas: Performance of current diagnostics and future complementary screening approaches. Eur J Med Genet 2020; 63:104089. [PMID: 33069933 DOI: 10.1016/j.ejmg.2020.104089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/15/2020] [Accepted: 10/12/2020] [Indexed: 11/24/2022]
Abstract
Genetic testing is currently the leading edge of clinical care when it comes to diagnostics. However, many questions remain unanswered even when employing next-generation sequencing techniques due to our inability to decode genetic variations and our limited repertoire of available diagnoses. Accordingly, diagnostic yields for current genomic screenings are <50% and fail to provide the whole picture, leaving the remaining patients without a definitive diagnosis. Human phenotypic/disease expression is explained by alterations not only at the genome, but also at the transcriptome, proteome and metabolome levels. These "higher" complexity levels represent at wealth of information, and diagnostic screenings tests at these levels have been shown to significantly improve diagnostic yields in specific populations compared to conventional diagnostic workup or gold standards in use (7-30% increase in diagnostic yields, depending on the population, approach and gold standard being compared against). However, these are not yet routinely available to clinicians. Due to their dynamic and modifiable nature, tapping into data from different omics will improve our understanding of the pathophysiological bases underlying (many yet to characterize) human disorders. We herein review how alterations at these levels (e.g. post-transcriptional and post-translational) may be pathogenic, how such tests may be implemented and in which situations they are of significant utility.
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34
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Matos MJ, Brown L, Bernardim B, Guerreiro A, Jiménez-Osés G, Bernardes GJL. Sequential dual site-selective protein labelling enabled by lysine modification. Bioorg Med Chem 2020; 28:115783. [PMID: 33007561 DOI: 10.1016/j.bmc.2020.115783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 02/07/2023]
Abstract
Methods that allow for chemical site-selective dual protein modification are scarce. Here, we provide proof-of-concept for the orthogonality and compatibility of a method for regioselective lysine modification with strategies for protein modification at cysteine and genetically encoded ketone-tagged amino acids. This sequential, orthogonal approach was applied to albumin and a therapeutic antibody to create functional dual site-selectively labelled proteins.
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Affiliation(s)
- Maria J Matos
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Libby Brown
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Barbara Bernardim
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Ana Guerreiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.
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35
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Rodríguez J, Martínez-Calvo M. Transition-Metal-Mediated Modification of Biomolecules. Chemistry 2020; 26:9792-9813. [PMID: 32602145 DOI: 10.1002/chem.202001287] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/25/2020] [Indexed: 01/15/2023]
Abstract
The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.
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Affiliation(s)
- Jessica Rodríguez
- Laboratoire Hétérochimie Fondamentale et Appliquée, Université Paul Sabatier/CNRS UMR 5069, 118 Route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Miguel Martínez-Calvo
- Centro de Investigaciones Científicas Avanzadas (CICA), AE CICA-INIBIC, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Campus de Elviña, 15071 A, Coruña, Galicia, Spain
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36
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Tomás RMF, Gibson MI. 100th Anniversary of Macromolecular Science Viewpoint: Re-Engineering Cellular Interfaces with Synthetic Macromolecules Using Metabolic Glycan Labeling. ACS Macro Lett 2020; 9:991-1003. [PMID: 32714634 PMCID: PMC7377358 DOI: 10.1021/acsmacrolett.0c00317] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/15/2020] [Indexed: 01/08/2023]
Abstract
Cell-surface functionality is largely programmed by genetically encoded information through modulation of protein expression levels, including glycosylation enzymes. Genetic tools enable control over protein-based functionality, but are not easily adapted to recruit non-native functionality such as synthetic polymers and nanomaterials to tune biological responses and attach therapeutic or imaging payloads. Similar to how polymer-protein conjugation evolved from nonspecific PEGylation to site-selective bioconjugates, the same evolution is now occurring for polymer-cell conjugation. This Viewpoint discusses the potential of using metabolic glycan labeling to install bio-orthogonal reactive cell-surface anchors for the recruitment of synthetic polymers and nanomaterials to cell surfaces, exploring the expanding therapeutic and diagnostic potential. Comparisons to conventional approaches that target endogenous membrane components, such as hydrophobic, protein coupling and electrostatic conjugation, as well as enzymatic and genetic tools, have been made to highlight the huge potential of this approach in the emerging cellular engineering field.
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Affiliation(s)
- Ruben M. F. Tomás
- Department of Chemistry and Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Matthew I. Gibson
- Department of Chemistry and Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
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37
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Huang KY, Lee TY, Kao HJ, Ma CT, Lee CC, Lin TH, Chang WC, Huang HD. dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications. Nucleic Acids Res 2020; 47:D298-D308. [PMID: 30418626 PMCID: PMC6323979 DOI: 10.1093/nar/gky1074] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/19/2018] [Indexed: 12/25/2022] Open
Abstract
The dbPTM (http://dbPTM.mbc.nctu.edu.tw/) has been maintained for over 10 years with the aim to provide functional and structural analyses for post-translational modifications (PTMs). In this update, dbPTM not only integrates more experimentally validated PTMs from available databases and through manual curation of literature but also provides PTM-disease associations based on non-synonymous single nucleotide polymorphisms (nsSNPs). The high-throughput deep sequencing technology has led to a surge in the data generated through analysis of association between SNPs and diseases, both in terms of growth amount and scope. This update thus integrated disease-associated nsSNPs from dbSNP based on genome-wide association studies. The PTM substrate sites located at a specified distance in terms of the amino acids encoded from nsSNPs were deemed to have an association with the involved diseases. In recent years, increasing evidence for crosstalk between PTMs has been reported. Although mass spectrometry-based proteomics has substantially improved our knowledge about substrate site specificity of single PTMs, the fact that the crosstalk of combinatorial PTMs may act in concert with the regulation of protein function and activity is neglected. Because of the relatively limited information about concurrent frequency and functional relevance of PTM crosstalk, in this update, the PTM sites neighboring other PTM sites in a specified window length were subjected to motif discovery and functional enrichment analysis. This update highlights the current challenges in PTM crosstalk investigation and breaks the bottleneck of how proteomics may contribute to understanding PTM codes, revealing the next level of data complexity and proteomic limitation in prospective PTM research.
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Affiliation(s)
- Kai-Yao Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Life and Health Science, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Tzong-Yi Lee
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Life and Health Science, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Hui-Ju Kao
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 32003, Taiwan
| | - Chen-Tse Ma
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 32003, Taiwan
| | - Chao-Chun Lee
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 32003, Taiwan
| | - Tsai-Hsuan Lin
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 32003, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Hsien-Da Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Life and Health Science, The Chinese University of Hong Kong, Shenzhen 518172, China
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38
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Yang K, Wu H, Zhang Z, Leisten ED, Nie X, Liu B, Wen Z, Zhang J, Cunningham MD, Tang W. Development of Selective Histone Deacetylase 6 (HDAC6) Degraders Recruiting Von Hippel-Lindau (VHL) E3 Ubiquitin Ligase. ACS Med Chem Lett 2020; 11:575-581. [PMID: 32292566 DOI: 10.1021/acsmedchemlett.0c00046] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Histone deacetylase 6 (HDAC6) is involved in multiple cellular processes such as aggresome formation, protein stability, and cell motility. Numerous HDAC6-selective inhibitors have been developed as cellular chemical tools to elucidate the function of HDAC6. Since HDAC6 has multiple domains that cannot be studied by HDAC6-selective inhibitors, CRISPR-CAS9 and siRNA/shRNA have been employed to elucidate the nonenzymatic functions of HDAC6. However, these genetic methods have many limitations. Proteolysis targeting chimera (PROTAC) is an emerging technology for the development of small molecules that can quickly remove the entire protein in cells. We previously developed multifunctional HDAC6 degraders that can recruit cereblon (CRBN) E3 ubiquitin ligase. These HDAC6 degraders can degrade not only HDAC6 but also neo-substrates of CRBN. They are excellent candidates for the development of anticancer therapeutics, but the multifunctional nature of the CRBN-based HDAC6 degraders has limited their utility as specific chemical probes for the study of HDAC6-related cellular pathways. Herein we report the development of the first cell-permeable HDAC6-selective degraders employing Von Hippel-Lindau (VHL) E3 ubiquitin ligase, which does not have any known neo-substrates. The DC50's of the most potent compound 3j are 7.1 nM and 4.3 nM in human MM1S and mouse 4935 cell lines, respectively. The D max's of 3j in these two cell lines are 90% and 57%, respectively.
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Affiliation(s)
- Ka Yang
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Hao Wu
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Zhongrui Zhang
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Eric D. Leisten
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Xueqing Nie
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Binkai Liu
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Zhi Wen
- McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Jing Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Michael D. Cunningham
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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39
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Scheibel DM, Hossain MS, Smith AL, Lynch CJ, Mozhdehi D. Post-Translational Modification Mimicry for Programmable Assembly of Elastin-Based Protein Polymers. ACS Macro Lett 2020; 9:371-376. [PMID: 35648543 DOI: 10.1021/acsmacrolett.0c00041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Post-translational modification (PTM) of protein polymers is emerging as a powerful bioinspired strategy to create protein-based hybrid materials with molecularly encoded assembly and function for applications in nanobiotechnology and medicine. While these modifications can be accomplished by harnessing native biological machinery (i.e., enzymes), the evolutionarily programmed specificity of these enzymes (recognition of select substrates and the limited repertoire of ligation chemistries catalyzed by these enzymes) can limit the type and linkage of PTMs appended to proteins. One approach to overcome this limitation is to leverage advances in site-selective biomolecular modification to prepare synthetic mimics of naturally occurring PTMs that are absent in nature. As a proof of concept, we used scalable bio-orthogonal reactions to prepare synthetic mimics of lipidated proteins with tunable assembly and disassembly. Additionally, we demonstrated that our PTM mimicry regulates the stimuli-responsive phase behavior of intrinsically disordered biopolymers, modulates their self-assembly at the nanoscale, and can be used for programmable disassembly of these materials in acidic environments. Synthetic PTM mimicry opens a path to encode new assembly and disassembly capabilities into hybrid materials that cannot be produced via biosynthesis.
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Affiliation(s)
- Dieter M. Scheibel
- Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, New York 13244, United States
| | - Md. Shahadat Hossain
- Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, New York 13244, United States
| | - Amy L. Smith
- Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, New York 13244, United States
| | - Christopher J. Lynch
- Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, New York 13244, United States
| | - Davoud Mozhdehi
- Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, New York 13244, United States
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40
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Lin L, Kightlinger W, Prabhu SK, Hockenberry AJ, Li C, Wang LX, Jewett MC, Mrksich M. Sequential Glycosylation of Proteins with Substrate-Specific N-Glycosyltransferases. ACS CENTRAL SCIENCE 2020; 6:144-154. [PMID: 32123732 PMCID: PMC7047269 DOI: 10.1021/acscentsci.9b00021] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Indexed: 05/28/2023]
Abstract
Protein glycosylation is a common post-translational modification that influences the functions and properties of proteins. Despite advances in methods to produce defined glycoproteins by chemoenzymatic elaboration of monosaccharides, the understanding and engineering of glycoproteins remain challenging, in part, due to the difficulty of site-specifically controlling glycosylation at each of several positions within a protein. Here, we address this limitation by discovering and exploiting the unique, conditionally orthogonal peptide acceptor specificities of N-glycosyltransferases (NGTs). We used cell-free protein synthesis and mass spectrometry of self-assembled monolayers to rapidly screen 41 putative NGTs and rigorously characterize the unique acceptor sequence preferences of four NGT variants using 1254 acceptor peptides and 8306 reaction conditions. We then used the optimized NGT-acceptor sequence pairs to sequentially install monosaccharides at four sites within one target protein. This strategy to site-specifically control the installation of N-linked monosaccharides for elaboration to a variety of functional N-glycans overcomes a major limitation in synthesizing defined glycoproteins for research and therapeutic applications.
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Affiliation(s)
- Liang Lin
- Department
of Biomedical Engineering, Center for Synthetic Biology, Department of Chemical
and Biological Engineering, Interdisciplinary Biological Sciences Program, and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Weston Kightlinger
- Department
of Biomedical Engineering, Center for Synthetic Biology, Department of Chemical
and Biological Engineering, Interdisciplinary Biological Sciences Program, and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Sunaina Kiran Prabhu
- Department
of Chemistry and Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Adam J. Hockenberry
- Department
of Biomedical Engineering, Center for Synthetic Biology, Department of Chemical
and Biological Engineering, Interdisciplinary Biological Sciences Program, and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chao Li
- Department
of Chemistry and Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Lai-Xi Wang
- Department
of Chemistry and Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Michael C. Jewett
- Department
of Biomedical Engineering, Center for Synthetic Biology, Department of Chemical
and Biological Engineering, Interdisciplinary Biological Sciences Program, and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department
of Biomedical Engineering, Center for Synthetic Biology, Department of Chemical
and Biological Engineering, Interdisciplinary Biological Sciences Program, and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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41
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Seifried BM, Qi W, Yang YJ, Mai DJ, Puryear WB, Runstadler JA, Chen G, Olsen BD. Glycoprotein Mimics with Tunable Functionalization through Global Amino Acid Substitution and Copper Click Chemistry. Bioconjug Chem 2020; 31:554-566. [PMID: 32078297 DOI: 10.1021/acs.bioconjchem.9b00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glycoproteins and their mimics are challenging to produce because of their large number of polysaccharide side chains that form a densely grafted protein-polysaccharide brush architecture. Herein a new approach to protein bioconjugate synthesis is demonstrated that can approach the functionalization densities of natural glycoproteins through oligosaccharide grafting. Global amino acid substitution is used to replace the methionine residues in a methionine-enriched elastin-like polypeptide with homopropargylglycine (HPG); the substitution was found to replace 93% of the 41 methionines in the protein sequence as well as broaden and increase the thermoresponsive transition. A series of saccharides were conjugated to the recombinant protein backbones through copper(I)-catalyzed alkyne-azide cycloaddition to determine reactivity trends, with 83-100% glycosylation of HPGs. Only an acetyl-protected sialyllactose moiety showed a lower level of 42% HPG glycosylation that is attributed to steric hindrance. The recombinant glycoproteins reproduced the key biofunctional properties of their natural counterparts such as viral inhibition and lectin binding.
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Affiliation(s)
- Brian M Seifried
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wenjing Qi
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Yun Jung Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Danielle J Mai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Macromolecular Science, Fudan University, Shanghai 200000, China
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42
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Mahesh S, Adebomi V, Muneeswaran ZP, Raj M. Bioinspired Nitroalkylation for Selective Protein Modification and Peptide Stapling. Angew Chem Int Ed Engl 2020; 59:2793-2801. [DOI: 10.1002/anie.201908593] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Sriram Mahesh
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
| | - Victor Adebomi
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
| | - Zilma P. Muneeswaran
- Department of Chemistry and Biochemistry Seton Hall University South Orange NJ USA
| | - Monika Raj
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
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43
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Mahesh S, Adebomi V, Muneeswaran ZP, Raj M. Bioinspired Nitroalkylation for Selective Protein Modification and Peptide Stapling. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201908593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sriram Mahesh
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
| | - Victor Adebomi
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
| | - Zilma P. Muneeswaran
- Department of Chemistry and Biochemistry Seton Hall University South Orange NJ USA
| | - Monika Raj
- Department of Chemistry and Biochemistry Auburn University Auburn AL 36830 USA
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44
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Rosselin M, Xiao Y, Belhomme L, Lecommandoux S, Garanger E. Expanding the Toolbox of Chemoselective Modifications of Protein-Like Polymers at Methionine Residues. ACS Macro Lett 2019; 8:1648-1653. [PMID: 35619386 DOI: 10.1021/acsmacrolett.9b00862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Selective modifications at methionyl residues in proteins have attracted particular attention in recent years. Previously described methods to chemoselectively modify the methionine side chain in elastin-like polypeptides (ELPs) involved nucleophilic addition using alkyl halides or epoxides yielding a sulfonium group with a positive charge strongly affecting ELPs' physicochemical properties, in particular their thermal responsiveness. We herein explored the recently reported ReACT method (Redox-Activated Chemical Tagging) based on the use of oxaziridine derivatives, yielding an uncharged sulfimide as an alternative route for chemoselective modifications of methionine-containing ELPs in aqueous medium. The different synthetic strategies are herein compared in order to provide a furnished toolbox for further biorthogonal postmodifications of any protein polymers.
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Affiliation(s)
- Marie Rosselin
- Universite Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Ye Xiao
- Universite Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Ludovic Belhomme
- Universite Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | | | - Elisabeth Garanger
- Universite Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
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45
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Brinkø A, Risinger C, Lambert A, Blixt O, Grandjean C, Jensen HH. Combining Click Reactions for the One-Pot Synthesis of Modular Biomolecule Mimetics. Org Lett 2019; 21:7544-7548. [PMID: 31502847 DOI: 10.1021/acs.orglett.9b02811] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report on the first combined one-pot use of the two so-called "click reactions": the thiol-ene coupling and the copper-catalyzed alkyne-azide cycloaddition. These reactions were employed in an alternating and one-pot fashion to combine appropriately functionalized monomeric carbohydrate building blocks to create mimics of trisaccharides and tetrasaccharides as single anomers, with only minimal purification necessary. The deprotected oligosaccharide mimics were found to bind both plant lectins and human galectin-3.
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Affiliation(s)
- Anne Brinkø
- Department of Chemistry , Aarhus University , Langelandsgade 140 , 8000 Aarhus C, Denmark
| | - Christian Risinger
- Department of Chemistry, Chemical Biology , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg C, Denmark
| | - Annie Lambert
- Faculté des Sciences et des Techniques, Unité Fonctionnalité et Ingénierie des Protéines (UFIP) , Université de Nantes , UMR CNRS 6286, 2, rue de la Houssinière , BP92208, 44322 Nantes Cedex 3, France
| | - Ola Blixt
- Department of Chemistry, Chemical Biology , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg C, Denmark
| | - Cyrille Grandjean
- Faculté des Sciences et des Techniques, Unité Fonctionnalité et Ingénierie des Protéines (UFIP) , Université de Nantes , UMR CNRS 6286, 2, rue de la Houssinière , BP92208, 44322 Nantes Cedex 3, France
| | - Henrik H Jensen
- Department of Chemistry , Aarhus University , Langelandsgade 140 , 8000 Aarhus C, Denmark
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46
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Tomás RMF, Gibson MI. Optimization and Stability of Cell-Polymer Hybrids Obtained by "Clicking" Synthetic Polymers to Metabolically Labeled Cell Surface Glycans. Biomacromolecules 2019; 20:2726-2736. [PMID: 31141666 PMCID: PMC6831485 DOI: 10.1021/acs.biomac.9b00478] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Re-engineering of mammalian cell surfaces with polymers enables the introduction of functionality including imaging agents, drug cargoes or antibodies for cell-based therapies, without resorting to genetic techniques. Glycan metabolic labeling has been reported as a tool for engineering cell surface glycans with synthetic polymers through the installation of biorthogonal handles, such as azides. Quantitative assessment of this approach and the robustness of the engineered coatings has yet to be explored. Here, we graft poly(hydroxyethyl acrylamide) onto azido-labeled cell surface glycans using strain-promoted azide-alkyne "click" cycloaddition and, using a combination of flow cytometry and confocal microscopy, evaluate the various parameters controlling the outcome of this "grafting to" process. In all cases, homogeneous cell coatings were formed with >95% of the treated cells being covalently modified, superior to nonspecific "grafting to" approaches. Controllable grafting densities could be achieved through modulation of polymer chain length and/or concentration, with longer polymers having lower densities. Cell surface bound polymers were retained for at least 72 h, persisting through several mitotic divisions during this period. Furthermore, we postulate that glycan/membrane recycling is slowed by the steric bulk of the polymers, demonstrating robustness and stability even during normal biological processes. This cytocompatible, versatile and simple approach shows potential for re-engineering of cell surfaces with new functionality for future use in cell tracking or cell-based therapies.
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Affiliation(s)
- Ruben M. F. Tomás
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Matthew I. Gibson
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
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47
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Wu H, Yang K, Zhang Z, Leisten ED, Li Z, Xie H, Liu J, Smith KA, Novakova Z, Barinka C, Tang W. Development of Multifunctional Histone Deacetylase 6 Degraders with Potent Antimyeloma Activity. J Med Chem 2019; 62:7042-7057. [DOI: 10.1021/acs.jmedchem.9b00516] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Zora Novakova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
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48
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Siar EH, Morellon-Sterling R, Zidoune MN, Fernandez-Lafuente R. Amination of ficin extract to improve its immobilization on glyoxyl-agarose: Improved stability and activity versus casein. Int J Biol Macromol 2019; 133:412-419. [DOI: 10.1016/j.ijbiomac.2019.04.123] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 01/24/2023]
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49
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Abstract
![]()
The manipulation
and modulation of biomolecules has the potential
to herald new modes of Biology and Medicine through chemical “editing”.
Key to the success of such processes will be the selectivities, reactivities
and efficiencies that may be brought to bear in bond-formation and
bond-cleavage in a benign manner. In this Perspective, we use select
examples, primarily from our own research, to examine the current
opportunities, limitations and the particular potential of metal-mediated
processes as exemplars of possible alternative catalytic modes and
manifolds to those already found in nature.
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Affiliation(s)
- Patrick G Isenegger
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Benjamin G Davis
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
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50
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Gil de Montes E, Jiménez-Moreno E, Oliveira BL, Navo CD, Cal PMSD, Jiménez-Osés G, Robina I, Moreno-Vargas AJ, Bernardes GJL. Azabicyclic vinyl sulfones for residue-specific dual protein labelling. Chem Sci 2019; 10:4515-4522. [PMID: 31057781 PMCID: PMC6482879 DOI: 10.1039/c9sc00125e] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/18/2019] [Indexed: 12/31/2022] Open
Abstract
We have developed [2.2.1]azabicyclic vinyl sulfone reagents that simultaneously enable cysteine-selective protein modification and introduce a handle for further bioorthogonal ligation.
We have developed [2.2.1]azabicyclic vinyl sulfone reagents that simultaneously enable cysteine-selective protein modification and introduce a handle for further bioorthogonal ligation. The reaction is fast and selective for cysteine relative to other amino acids that have nucleophilic side-chains, and the formed products are stable in human plasma and are moderately resistant to retro Diels–Alder degradation reactions. A model biotinylated [2.2.1]azabicyclic vinyl sulfone reagent was shown to efficiently label two cysteine-tagged proteins, ubiquitin and C2Am, under mild conditions (1–5 equiv. of reagent in NaPi pH 7.0, room temperature, 30 min). The resulting thioether-linked conjugates were stable and retained the native activity of the proteins. Finally, the dienophile present in the azabicyclic moiety on a functionalised C2Am protein could be fluorescently labelled through an inverse electron demand Diels–Alder reaction in cells to allow selective apoptosis imaging. The combined advantages of directness, site-specificity and easy preparation mean [2.2.1]azabicyclic vinyl sulfones can be used for residue-specific dual protein labelling/construction strategies with minimal perturbation of native function based simply on the attachment of an [2.2.1]azabicyclic moiety to cysteine.
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Affiliation(s)
- Enrique Gil de Montes
- Departamento de Química Orgánica , Facultad de Química , Universidad de Sevilla , C/Prof. García González, 1 , 41012-Sevilla , Spain .
| | - Ester Jiménez-Moreno
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW Cambridge , UK .
| | - Bruno L Oliveira
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW Cambridge , UK . .,Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av. Prof. Egas Moniz , 1649-028 Lisboa , Portugal
| | - Claudio D Navo
- Departamento de Química , Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain.,CIC bioGUNE , Bizkaia Technology Park, Building 801A , 48170 Derio , Spain
| | - Pedro M S D Cal
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av. Prof. Egas Moniz , 1649-028 Lisboa , Portugal
| | - Gonzalo Jiménez-Osés
- Departamento de Química , Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain.,CIC bioGUNE , Bizkaia Technology Park, Building 801A , 48170 Derio , Spain
| | - Inmaculada Robina
- Departamento de Química Orgánica , Facultad de Química , Universidad de Sevilla , C/Prof. García González, 1 , 41012-Sevilla , Spain .
| | - Antonio J Moreno-Vargas
- Departamento de Química Orgánica , Facultad de Química , Universidad de Sevilla , C/Prof. García González, 1 , 41012-Sevilla , Spain .
| | - Gonçalo J L Bernardes
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW Cambridge , UK . .,Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av. Prof. Egas Moniz , 1649-028 Lisboa , Portugal
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