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Gui W, Davidson GA, Zhuang Z. Chemical methods for protein site-specific ubiquitination. RSC Chem Biol 2021; 2:450-467. [PMID: 34381999 PMCID: PMC8323803 DOI: 10.1039/d0cb00215a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
Ubiquitination is an important protein post-translational modification regulating many cellular processes in eukaryotes. Ubiquitination is catalyzed by a three-enzyme cascade resulting in the conjugation of the C-terminal carboxylate of ubiquitin (Ub) to the ε-amino group of a lysine residue in the acceptor protein via an isopeptide bond. In vitro enzymatic ubiquitination utilizing Ub ligases has been successfully employed to generate Ub dimers and polymers. However, limitations of the enzymatic approach exist, particularly due to the requirement of specific Ub ligase for any given target protein and the low catalytic efficiency of the Ub ligase. To achieve an in-depth understanding of the molecular mechanism of Ub signaling, new methods are needed to generate mono- and poly-ubiquitinated proteins at a specific site with defined polyubiquitin chain linkage and length. Chemical methods offer an attractive solution to the above-described challenges. In this review, we summarize the recently developed chemical methods for generating ubiquitinated proteins using synthetic and semisynthetic approaches. These new tools and approaches, as an important part of the Ub toolbox, are crucial to our understanding and exploitation of the Ub system for novel therapeutics.
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Affiliation(s)
- Weijun Gui
- Department of Chemistry and Biochemistry, University of Delaware 214A Drake Hall Newark DE 19716 USA
| | - Gregory A Davidson
- Department of Chemistry and Biochemistry, University of Delaware 214A Drake Hall Newark DE 19716 USA
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware 214A Drake Hall Newark DE 19716 USA
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2
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Boto A, González CC, Hernández D, Romero-Estudillo I, Saavedra CJ. Site-selective modification of peptide backbones. Org Chem Front 2021. [DOI: 10.1039/d1qo00892g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Exciting developments in the site-selective modification of peptide backbones are allowing an outstanding fine-tuning of peptide conformation, folding ability, and physico-chemical and biological properties.
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Affiliation(s)
- Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Iván Romero-Estudillo
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos. Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
- Catedrático CONACYT-CIQ-UAEM, Mexico
| | - Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
- Programa Agustín de Betancourt, Universidad de la Laguna, 38200 Tenerife, Spain
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3
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Chambers KA, Abularrage NS, Hill CJ, Khan IH, Scheck RA. A Chemical Probe for Dehydrobutyrine. Angew Chem Int Ed Engl 2020; 59:7350-7355. [DOI: 10.1002/anie.202003631] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Kaitlin A. Chambers
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Nile S. Abularrage
- Department of Chemistry Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Caitlin J. Hill
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Imran H. Khan
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Rebecca A. Scheck
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
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4
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Chambers KA, Abularrage NS, Hill CJ, Khan IH, Scheck RA. A Chemical Probe for Dehydrobutyrine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kaitlin A. Chambers
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Nile S. Abularrage
- Department of Chemistry Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Caitlin J. Hill
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Imran H. Khan
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Rebecca A. Scheck
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
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5
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Dadová J, Galan SR, Davis BG. Synthesis of modified proteins via functionalization of dehydroalanine. Curr Opin Chem Biol 2018; 46:71-81. [PMID: 29913421 DOI: 10.1016/j.cbpa.2018.05.022] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/02/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Dehydroalanine has emerged in recent years as a non-proteinogenic residue with strong chemical utility in proteins for the study of biology. In this review we cover the several methods now available for its flexible and site-selective incorporation via a variety of complementary chemical and biological techniques and examine its reactivity, allowing both creation of modified protein side-chains through a variety of bond-forming methods (C-S, C-N, C-Se, C-C) and as an activity-based probe in its own right. We illustrate its utility with selected examples of biological and technological discovery and application.
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Affiliation(s)
- Jitka Dadová
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sébastien Rg Galan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom.
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6
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Navo CD, Asín A, Gómez-Orte E, Gutiérrez-Jiménez MI, Compañón I, Ezcurra B, Avenoza A, Busto JH, Corzana F, Zurbano MM, Jiménez-Osés G, Cabello J, Peregrina JM. Cell-Penetrating Peptides Containing Fluorescent d
-Cysteines. Chemistry 2018; 24:7991-8000. [DOI: 10.1002/chem.201800603] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Claudio D. Navo
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Alicia Asín
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Eva Gómez-Orte
- Center for Biomedical Research of La Rioja (CIBIR); C/ Piqueras, 98 26006 Logroño La Rioja Spain
| | - Marta I. Gutiérrez-Jiménez
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Ismael Compañón
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Begoña Ezcurra
- Center for Biomedical Research of La Rioja (CIBIR); C/ Piqueras, 98 26006 Logroño La Rioja Spain
| | - Alberto Avenoza
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Jesús H. Busto
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Francisco Corzana
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - María M. Zurbano
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Gonzalo Jiménez-Osés
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Juan Cabello
- Center for Biomedical Research of La Rioja (CIBIR); C/ Piqueras, 98 26006 Logroño La Rioja Spain
| | - Jesús M. Peregrina
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
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7
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Jongkees SAK, Umemoto S, Suga H. Linker-free incorporation of carbohydrates into in vitro displayed macrocyclic peptides. Chem Sci 2016; 8:1474-1481. [PMID: 28572907 PMCID: PMC5452274 DOI: 10.1039/c6sc04381j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022] Open
Abstract
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates.
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates. These reactions are selective for cysteine, and do not interfere with amplification of the nucleic acid component of an mRNA-displayed peptide. Furthermore, these reactions are shown to be compatible with two different macrocyclisation chemistries, and when applied to a peptide containing an N-terminal cysteine give a ketone that can be functionalised in an orthogonal manner. This new strategy can overcome a limitation of ribosomal translation, providing a means to incorporate untranslatable groups such as carbohydrates in amino acid side chains, and will allow for the ribosomal generation of glycopeptides, requiring only the introduction of a free thiol in the molecule to be incorporated. In combination with in vitro selection techniques, this strategy is envisaged to allow the discovery of biologically-active glycopeptides with a near-natural, but hydrolytically stable, thioglycosidic bond.
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Affiliation(s)
- S A K Jongkees
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - S Umemoto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan . .,JST CREST , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan
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8
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Gutiérrez-Jiménez MI, Aydillo C, Navo CD, Avenoza A, Corzana F, Jiménez-Osés G, Zurbano MM, Busto JH, Peregrina JM. Bifunctional Chiral Dehydroalanines for Peptide Coupling and Stereoselective S-Michael Addition. Org Lett 2016; 18:2796-9. [DOI: 10.1021/acs.orglett.6b00840] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marta I. Gutiérrez-Jiménez
- Departamento
de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Carlos Aydillo
- CECB,
Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Claudio D. Navo
- Departamento
de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Alberto Avenoza
- Departamento
de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Francisco Corzana
- Departamento
de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Gonzalo Jiménez-Osés
- Departamento
de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
- Institute
of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC), 50018 Zaragoza, Spain
| | - María M. Zurbano
- Departamento
de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Jesús H. Busto
- Departamento
de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
| | - Jesús M. Peregrina
- Departamento
de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006 Logroño, Spain
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9
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Meledin R, Mali SM, Singh SK, Brik A. Protein ubiquitination via dehydroalanine: development and insights into the diastereoselective 1,4-addition step. Org Biomol Chem 2016; 14:4817-23. [PMID: 27143624 DOI: 10.1039/c6ob00882h] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a strategy for site-specific protein ubiquitination using dehydroalanine (Dha) chemistry for the preparation of ubiquitin conjugates bearing a very close mimic of the native isopeptide bond. Our approach relies on the selective formation of Dha followed by conjugation with hexapeptide bearing a thiol handle derived from the C-terminal of ubiquitin. Subsequently, the resulting synthetic intermediate undergoes native chemical ligation with the complementary part of the ubiquitin polypeptide. It has been proposed that the Michael addition step could result in the formation of a diastereomeric mixture as a result of unselective protonation of the enolate intermediate. It has also been proposed that the chiral protein environment may influence such an addition step. In the protein context these questions remain open and no experimental evidence was provided as to how such a protein environment affects the diastereoselectivity of the addition step. As was previously proposed for the conjugation step on protein bearing Dha, the isopeptide bond formation step in our study resulted in the construction of two protein diastereomers. To assign the ratio of these diastereomers, trypsinization coupled with high-pressure liquid chromatography analysis were performed. Moreover, the obtained peptide diastereomers were compared with identical synthetic peptides having defined stereogenic centers, which enabled the determination of the configuration of the isopeptide mimic in each diastereomer. Our study, which offers a new method for isopeptide bond formation and protein ubiquitination, gives insights into the parameters that affect the stereoselectivity of the addition step to Dha for chemical protein modifications.
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Affiliation(s)
- Roman Meledin
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008 Israel.
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