1
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Bachelart T, Kumar S, Jouin A, Yousef M, Kieffer B, Torbeev V. Design, Synthesis and Catalytic Activity of Protein Containing Thiotyrosine as an Active Site Residue. Chembiochem 2024; 25:e202400148. [PMID: 38629812 DOI: 10.1002/cbic.202400148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/16/2024] [Indexed: 06/05/2024]
Abstract
Native chemical ligation is a key reaction in the toolbox of chemical methods for the synthesis of native and modified proteins. The catalysis of ligation is commonly performed by using small aryl-thiol molecules added at high concentrations. In this work, we incorporated thiotyrosine, a non-canonical amino acid containing an aryl-thiol moiety, into a designed cyclic protein « sans queue ni tête ». Importantly, the protein environment reduced the pKa of the thiol group to 5.8-5.9, which is significantly lower than the previously reported value for thiotyrosine in a short peptide (pKa 6.4). Furthermore, we demonstrated the catalytic activity of this protein both as hydrolase and in native chemical ligation of peptides. These results will be useful for the development of efficient protein catalysts (enzymes) for protein synthesis and modification.
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Affiliation(s)
- Thomas Bachelart
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Shailesh Kumar
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Alexis Jouin
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Mo'ath Yousef
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Bruno Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 1258, University of Strasbourg, 67400, Illkirch, France
| | - Vladimir Torbeev
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
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2
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Ai H, Pan M, Liu L. Chemical Synthesis of Human Proteoforms and Application in Biomedicine. ACS CENTRAL SCIENCE 2024; 10:1442-1459. [PMID: 39220697 PMCID: PMC11363345 DOI: 10.1021/acscentsci.4c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Limited understanding of human proteoforms with complex posttranslational modifications and the underlying mechanisms poses a major obstacle to research on human health and disease. This Outlook discusses opportunities and challenges of de novo chemical protein synthesis in human proteoform studies. Our analysis suggests that to develop a comprehensive, robust, and cost-effective methodology for chemical synthesis of various human proteoforms, new chemistries of the following types need to be developed: (1) easy-to-use peptide ligation chemistries allowing more efficient de novo synthesis of protein structural domains, (2) robust temporary structural support strategies for ligation and folding of challenging targets, and (3) efficient transpeptidative protein domain-domain ligation methods for multidomain proteins. Our analysis also indicates that accurate chemical synthesis of human proteoforms can be applied to the following aspects of biomedical research: (1) dissection and reconstitution of the proteoform interaction networks, (2) structural mechanism elucidation and functional analysis of human proteoform complexes, and (3) development and evaluation of drugs targeting human proteoforms. Overall, we suggest that through integrating chemical protein synthesis with in vivo functional analysis, mechanistic biochemistry, and drug development, synthetic chemistry would play a pivotal role in human proteoform research and facilitate the development of precision diagnostics and therapeutics.
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Affiliation(s)
- Huasong Ai
- New
Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life
Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and
Chemical Biology, Center for Synthetic and Systems Biology, Department
of Chemistry, Tsinghua University, Beijing 100084, China
- Institute
of Translational Medicine, School of Pharmacy, School of Chemistry
and Chemical Engineering, National Center for Translational Medicine
(Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Man Pan
- Institute
of Translational Medicine, School of Pharmacy, School of Chemistry
and Chemical Engineering, National Center for Translational Medicine
(Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Liu
- New
Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life
Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and
Chemical Biology, Center for Synthetic and Systems Biology, Department
of Chemistry, Tsinghua University, Beijing 100084, China
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3
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Diemer V, Roy E, Agouridas V, Melnyk O. Protein desulfurization and deselenization. Chem Soc Rev 2024; 53:8521-8545. [PMID: 39010733 DOI: 10.1039/d4cs00135d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Methods enabling the dechalcogenation of thiols or selenols have been investigated and developed for a long time in fields of research as diverse as the study of prebiotic chemistry, the engineering of fuel processing techniques, the study of biomolecule structures and function or the chemical synthesis of biomolecules. The dechalcogenation of thiol or selenol amino acids is nowadays a particularly flourishing area of research for being a pillar of modern chemical protein synthesis, when used in combination with thiol or selenol-based chemoselective peptide ligation chemistries. This review offers a comprehensive and scholarly overview of the field, emphasizing emerging trends and providing a detailed and critical mechanistic discussion of the dechalcogenation methods developed so far. Taking advantage of recently published reports, it also clarifies some unexpected desulfurization reactions that were observed in the past and for which no explanation was provided at the time. Additionally, the review includes a discussion on principal desulfurization methods within the framework of newly introduced green chemistry metrics and toolkits, providing a well-rounded exploration of the subject.
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Affiliation(s)
- Vincent Diemer
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Eliott Roy
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
| | - Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
- Centrale Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017, Center for Infection and Immunity of Lille, F-59000 Lille, France.
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4
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Fan X, Wen Y, Chen H, Tian B, Zhang Q. Polypeptide Preparation by β-Lactone-Mediated Chemical Ligation. Org Lett 2024; 26:5436-5440. [PMID: 38900935 PMCID: PMC11232016 DOI: 10.1021/acs.orglett.4c01587] [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] [Received: 04/29/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
Native chemical ligation (NCL) represents a cornerstone strategy in accessing synthetic peptides and proteins, remaining one of the most efficacious methodologies in this domain. The fundamental requisites for achieving a proficient NCL reaction involve chemoselective coupling between a C-terminal thioester peptide and a thiol-bearing N-terminal peptide. However, achieving coupling at sterically congested residues remains challenging. In addition, while most NCLs proceed without epimerization, β-branched (e.g., Ile, Thr, Val) and Pro-derived C-terminal thioesters react slowly and can be susceptible to significant epimerization and hydrolysis. Herein, we report an epimerization-free NCL reaction via β-lactone-mediated native chemical ligation which constructs sterically congested Thr residues. The constrained ring from the β-lactone allows rapid peptide ligation without detectable epimerization. The method has a broad side-chain tolerance and was applied to the preparation of cyclic peptides and polypeptidyl thioester, which could be difficult to obtained otherwise.
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Affiliation(s)
- Xinhao Fan
- Department
of Chemistry, School of Pharmacy, North
Sichuan Medical College, Nanchong, Sichuan 637000, China
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Yuming Wen
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Huan Chen
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Baotong Tian
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Qiang Zhang
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
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5
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Nakamura G, Nakatsu K, Hayashi G. One-pot ligation of multiple peptide segments via N-terminal thiazolidine deprotection chemistry. Methods Enzymol 2024; 698:169-194. [PMID: 38886031 DOI: 10.1016/bs.mie.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Peptide ligation chemistries have revolutionized the synthesis of proteins with site-specific modifications or proteomimetics through assembly of multiple peptide segments. In order to prepare polypeptide chains consisting of 100-150 amino acid residues or larger generally assembled from three or more peptide segments, iterative purification process that decreases the product yield is usually demanded. Accordingly, methodologies for one-pot peptide ligation that omit the purification steps of intermediate peptide segments have been vigorously developed so far to improve the efficiency of chemical protein synthesis. In this chapter, we first outline the concept and recent advances of one-pot peptide ligation strategies. Then, the practical guideline for the preparation of peptide segments for one-pot peptide ligation is described with an emphasis on diketopiperazine thioester synthesis. Finally, we disclose the explicit protocols for one-pot four segment ligation via repetitive deprotection of N-terminal thiazolidine by a 2-aminobenzamide type aldehyde scavenger.
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Affiliation(s)
- Genki Nakamura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Koki Nakatsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan.
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6
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Ludwig BA, Forbes CR, Zondlo NJ. N-Terminal Proline Editing for the Synthesis of Peptides with Mercaptoproline and Selenoproline: Mechanistic Insights Lead to Greater Efficiency in Proline Native Chemical Ligation. ACS Chem Biol 2024; 19:536-550. [PMID: 38324914 DOI: 10.1021/acschembio.3c00705] [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: 02/09/2024]
Abstract
Native chemical ligation (NCL) at proline has been limited by cost and synthetic access. In addition, prior examples of NCL using mercaptoproline have exhibited stalling of the reaction after thioester exchange, due to inefficient S → N acyl transfer. Herein, we develop methods, using inexpensive Boc-4R-hydroxyproline, for the solid-phase synthesis of peptides containing N-terminal 4R-mercaptoproline and 4R-selenoproline. The synthesis proceeds via proline editing on the N-terminus of fully synthesized peptides on the solid phase, converting an N-terminal Boc-4R-hydroxyproline to the 4S-bromoproline, followed by an SN2 reaction with potassium thioacetate or selenobenzoic acid. After cleavage from the resin and deprotection, peptides with functionalized N-terminal proline amino acids were obtained. NCL reactions with mercaptoproline proceeded slowly under standard NCL conditions, with the S-acyl transthioesterification intermediate observed as a major species. Computational investigations indicated that the bicyclic intermediates and transition states for S → N acyl transfer are sufficiently low in energy (10-15 kcal mol-1 above starting material) that ring strain cannot explain the slow S → N acyl transfer. Instead, the bicyclic zwitterionic tetrahedral intermediate has a low barrier for reversion to the S-acyl intermediate, causing reversion to the thioester (reverse reaction) to occur preferentially over elimination to generate the amide (forward reaction). We hypothesized that a buffer capable of general acid and/or general base catalysis could promote S → N acyl transfer and thus achieve greater efficiency in proline NCL. In the presence of 2 M imidazole at pH 6.8, NCL with mercaptoproline proceeded efficiently to generate the peptide with a native amide bond. NCL with selenoproline also proceeded efficiently to generate the desired products when a thiophenol thioester was employed as a ligation partner. After desulfurization or deselenization, the products obtained were identical to those synthesized directly, confirming that the solid-phase proline editing reactions proceeded stereospecifically and without epimerization.
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Affiliation(s)
- Brice A Ludwig
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Christina R Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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7
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Zhao J, Liu X, Liu J, Ye F, Wei B, Deng M, Li T, Huang P, Wang P. Chemical Synthesis Creates Single Glycoforms of the Ectodomain of Herpes Simplex Virus-1 Glycoprotein D. J Am Chem Soc 2024; 146:2615-2623. [PMID: 38117537 DOI: 10.1021/jacs.3c11543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Herpes simplex virus-1 (HSV-1) utilizes multiple viral surface glycoproteins to trigger virus entry and fusion. Among these glycoproteins, glycoprotein D (gD) functions as a receptor-binding protein, which makes it an attractive target for the development of vaccines against HSV-1 infection. Several recombinant gD subunit vaccines have been investigated in both preclinical and clinical phases with varying degrees of success. It is fundamentally critical to explore the functions of gD glycans. In light of this, we report an efficient synthetic platform to construct glycosylated gDs bearing homogeneous glycans at N94 and N121. The oligosaccharides were prepared by enzymatic synthesis and conjugated to peptidyl sectors. The glycoproteins were constructed via a combination of 7-(piperazin-1-yl)-2-(methyl)quinolinyl (PPZQ)-assisted expressed protein ligation and β-mercapto amino acid-assisted-desulfurization strategies. Biological studies showed that synthetic gDs exhibited potent in vivo activity in mice.
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Affiliation(s)
- Jie Zhao
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinliang Liu
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jialin Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Farong Ye
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bingcheng Wei
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Minggang Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tiehai Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ping Huang
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Wang
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- Shenzhen Research Institute of Shanghai Jiao Tong University, Shenzhen 518057, China
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8
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Grain B, Desmet R, Snella B, Melnyk O, Agouridas V. Incorporation of a Highly Reactive Oxalyl Thioester-Based Interacting Handle into Proteins. Org Lett 2023; 25:5117-5122. [PMID: 37384828 PMCID: PMC10353032 DOI: 10.1021/acs.orglett.3c01846] [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] [Received: 06/06/2023] [Indexed: 07/01/2023]
Abstract
Providing biomolecules with extended physicochemical, biochemical, or biological properties is a contemporary challenge motivated by impactful benefits in life or materials sciences. In this study, we show that a latent and highly reactive oxalyl thioester precursor can be efficiently introduced as a pending functionality into a fully synthetic protein domain following a protection/late-stage deprotection strategy and can serve as an on-demand reactive handle. The approach is illustrated with the production of a 10 kDa ubiquitin Lys48 conjugate.
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Affiliation(s)
- Benjamin Grain
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Rémi Desmet
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoît Snella
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Vangelis Agouridas
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
- Centrale
Lille, F-59000 Lille, France
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9
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Digal LD, Kirkeby EK, Austin MJ, Roberts AG. Design and Evaluation of Ambiphilic Aryl Thiol-Iminium-Based Molecules for Organocatalyzed Thioacyl Aminolysis. ACS OMEGA 2023; 8:9319-9325. [PMID: 36936301 PMCID: PMC10018527 DOI: 10.1021/acsomega.2c07586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Progress toward the design and synthesis of ambiphilic aryl thiol-iminium-based small molecules for organocatalyzed thioacyl aminolysis is reported. Here we describe the synthesis of a novel tetrahydroisoquinoline-derived scaffold, bearing both thiol and iminium functionalities, capable of promoting the transthioesterification and subsequent amine capture reactions necessary to achieve organocatalyzed thioacyl aminolysis. Model studies demonstrate the ability of this designed organocatalyst to deliver critical intermediates capable of undergoing these individual reactions necessary for the proposed process. Future design improvements and directions toward cysteine-independent organocatalyzed native chemical ligation are discussed.
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10
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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11
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Ollivier N, Sénéchal M, Desmet R, Snella B, Agouridas V, Melnyk O. A biomimetic electrostatic assistance for guiding and promoting N-terminal protein chemical modification. Nat Commun 2022; 13:6667. [PMID: 36335111 PMCID: PMC9637170 DOI: 10.1038/s41467-022-34392-5] [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: 04/26/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
The modification of protein electrostatics by phosphorylation is a mechanism used by cells to promote the association of proteins with other biomolecules. In this work, we show that introducing negatively charged phosphoserines in a reactant is a powerful means for directing and accelerating the chemical modification of proteins equipped with oppositely charged arginines. While the extra charged amino acid residues induce no detectable affinity between the reactants, they bring site-selectivity to a reaction that is otherwise devoid of such a property. They also enable rate accelerations of four orders of magnitude in some cases, thereby permitting chemical processes to proceed at the protein level in the low micromolar range, using reactions that are normally too slow to be useful in such dilute conditions.
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Affiliation(s)
- Nathalie Ollivier
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Magalie Sénéchal
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Rémi Desmet
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoît Snella
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Vangelis Agouridas
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France ,Centrale Lille, F-59000 Lille, France
| | - Oleg Melnyk
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
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12
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Agouridas V, Ollivier N, Vicogne J, Diemer V, Melnyk O. Redox-Controlled Chemical Protein Synthesis: Sundry Shades of Latency. Acc Chem Res 2022; 55:2685-2697. [PMID: 36083810 PMCID: PMC9494750 DOI: 10.1021/acs.accounts.2c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The last two decades have witnessed the rise in power of chemical protein synthesis to the point where it now constitutes an established corpus of synthetic methods efficiently complementing biological approaches. One factor explaining this spectacular evolution is the emergence of a new class of chemoselective reactions enabling the formation of native peptide bonds between two unprotected peptidic segments, also known as native ligation reactions. In recent years, their application has fueled the production of homogeneous batches of large and highly decorated protein targets with a control of their composition at the atomic level. In doing so, native ligation reactions have provided the means for successful applications in chemical biology, medicinal chemistry, materials science, and nanotechnology research.The native chemical ligation (NCL) reaction has had a major impact on the field by enabling the chemoselective formation of a native peptide bond between a C-terminal peptidyl thioester and an N-terminal cysteinyl peptide. Since its introduction in 1994, the NCL reaction has been made the object of significant improvements and its scope and limitations have been thoroughly investigated. Furthermore, the diversification of peptide segment assembly strategies has been essential to access proteins of increasing complexity and has had to overcome the challenge of controlling the reactivity of ligation partners.One hallmark of NCL is its dependency on thiol reactivity, including for its catalysis. While Nature constantly plays with the redox properties of biological thiols for the regulation of numerous biochemical pathways, such a control of reactivity is challenging to achieve in synthetic organic chemistry and, in particular, for those methods used for assembling peptide segments by chemical ligation. This Account covers the studies conducted by our group in this area. A leading theme of our research has been the conception of controllable acyl donors and cysteine surrogates that place the chemoselective formation of amide bonds by NCL-like reactions under the control of dichalcogenide-based redox systems. The dependency of the redox potential of dichalcogenide bonds on the nature of the chalcogenides involved (S, Se) has appeared as a powerful means for diversifying the systems, while allowing their sequential activation for protein synthesis. Such a control of reactivity mediated by the addition of harmless redox additives has greatly facilitated the modular and efficient preparation of multiple targets of biological relevance. Taken together, these endeavors provide a practical and robust set of methods to address synthetic challenges in chemical protein synthesis.
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Affiliation(s)
- Vangelis Agouridas
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France,Centrale
Lille, F-59000 Lille, France
| | - Nathalie Ollivier
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Jérôme Vicogne
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Vincent Diemer
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France,
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13
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Snella B, Grain B, Vicogne J, Capet F, Wiltschi B, Melnyk O, Agouridas V. Fast Protein Modification in the Nanomolar Concentration Range Using an Oxalyl Amide as Latent Thioester. Angew Chem Int Ed Engl 2022; 61:e202204992. [PMID: 35557487 DOI: 10.1002/anie.202204992] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Indexed: 11/08/2022]
Abstract
We show that latent oxalyl thioester surrogates are a powerful means to modify peptides and proteins in highly dilute conditions in purified aqueous media or in mixtures as complex as cell lysates. Designed to be shelf-stable reagents, they can be activated on demand to enable ligation reactions with peptide concentrations as low as a few hundred nM at rates approaching 30 M-1 s-1 .
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Affiliation(s)
- Benoît Snella
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Benjamin Grain
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Jérôme Vicogne
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Frédéric Capet
- Univ. Lille, CNRS, Centrale Lille, Univ. Artois, UMR 8181, UCCS, Unité de Catalyse et Chimie du Solide, 59000, Lille, France
| | - Birgit Wiltschi
- Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France.,Centrale Lille, 59000, Lille, France
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14
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Snella B, Grain B, Vicogne J, Capet F, Wiltschi B, Melnyk O, Agouridas V. Fast Protein Modification in the Nanomolar Concentration Range Using an Oxalyl Amide as Latent Thioester. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Benjamin Grain
- University of Lille: Universite de Lille Chemistry FRANCE
| | - Jérôme Vicogne
- Centre National de la Recherche Scientifique Biology FRANCE
| | | | | | - Oleg Melnyk
- CNRS: Centre National de la Recherche Scientifique UMR 9017 FRANCE
| | - Vangelis Agouridas
- Ecole Centrale de Lille ENSCL Av. Mendeleiev 59652 Villeneuve d'Ascq FRANCE
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15
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Diemer V, Firstova O, Agouridas V, Melnyk O. Pedal to the Metal: The Homogeneous Catalysis of the Native Chemical Ligation Reaction. Chemistry 2022; 28:e202104229. [PMID: 35048443 DOI: 10.1002/chem.202104229] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 11/08/2022]
Abstract
The native chemical ligation reaction of peptide thioesters with cysteinyl peptides is a pivotal chemical process in the production of native or modified peptides and proteins, and well beyond in the preparation of various biomolecule analogs and materials. To benefit from this reaction at its fullest and to access all the possible applications, the experimentalist needs to know the factors affecting its rate and how to control it. This concept article presents the fundamental principles underlying the rate of the native chemical ligation and its homogeneous catalysis by nucleophiles. It has been prepared to serve as a quick guide in the search for an appropriate catalyst.
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Affiliation(s)
- Vincent Diemer
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -, UMR 9017 -, CIIL -, Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Olga Firstova
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -, UMR 9017 -, CIIL -, Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -, UMR 9017 -, CIIL -, Center for Infection and Immunity of Lille, 59000, Lille, France.,Centrale Lille, 59000, Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -, UMR 9017 -, CIIL -, Center for Infection and Immunity of Lille, 59000, Lille, France
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16
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Chemical Synthesis of a Functional Fluorescent-Tagged α-Bungarotoxin. Toxins (Basel) 2022; 14:toxins14020079. [PMID: 35202107 PMCID: PMC8879871 DOI: 10.3390/toxins14020079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 11/30/2022] Open
Abstract
α-bungarotoxin is a large, 74 amino acid toxin containing five disulphide bridges, initially identified in the venom of Bungarus multicinctus snake. Like most large toxins, chemical synthesis of α-bungarotoxin is challenging, explaining why all previous reports use purified or recombinant α-bungarotoxin. However, only chemical synthesis allows easy insertion of non-natural amino acids or new chemical functionalities. Herein, we describe a procedure for the chemical synthesis of a fluorescent-tagged α-bungarotoxin. The full-length peptide was designed to include an alkyne function at the amino-terminus through the addition of a pentynoic acid linker. Chemical synthesis of α-bungarotoxin requires hydrazide-based coupling of three peptide fragments in successive steps. After completion of the oxidative folding, an azide-modified Cy5 fluorophore was coupled by click chemistry onto the toxin. Next, we determined the efficacy of the fluorescent-tagged α-bungarotoxin to block acetylcholine (ACh)-mediated currents in response to muscle nicotinic receptor activation in TE671 cells. Using automated patch-clamp recordings, we demonstrate that fluorescent synthetic α-bungarotoxin has the expected nanomolar affinity for the nicotinic receptor. The blocking effect of fluorescent α-bungarotoxin could be displaced by incubation with a 20-mer peptide mimicking the α-bungarotoxin binding site. In addition, TE671 cells could be labelled with fluorescent toxin, as witnessed by confocal microscopy, and this labelling was partially displaced by the 20-mer competitive peptide. We thus demonstrate that synthetic fluorescent-tagged α-bungarotoxin preserves excellent properties for binding onto muscle nicotinic receptors.
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17
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Lee J, Oh ET, Lee E, Park HJ, Kim C. Induced cytotoxicity of peptides by intracellular native chemical ligation. NEW J CHEM 2022. [DOI: 10.1039/d2nj02053j] [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
The intracellular NCL reaction of peptide with both N-terminal cysteine and C-terminal crypto-thioester with protecting groups occurs naturally in cancer cells, which endows peptide with induced cytotoxicity.
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Affiliation(s)
- Jeonghun Lee
- Department of Polymer Science and Engineering, Program in Environmental and Polymer Engineering, Inha University, Incheon, 22212, Korea
| | - Eun-Taex Oh
- Department of Biomedical Sciences, School of Medicine, Inha University, Incheon, 22212, Korea
| | - Eunkyung Lee
- Department of Polymer Science and Engineering, Program in Environmental and Polymer Engineering, Inha University, Incheon, 22212, Korea
| | - Heon Joo Park
- Department of Microbiology, Hypoxia-related Disease Research Center, College of Medicine, Inha University, Incheon, 22212, Korea
| | - Chulhee Kim
- Department of Polymer Science and Engineering, Program in Environmental and Polymer Engineering, Inha University, Incheon, 22212, Korea
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18
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Firstova O, Agouridas V, Diemer V, Melnyk O. A Selenium-based Cysteine Surrogate for Protein Chemical Synthesis. Methods Mol Biol 2022; 2530:213-239. [PMID: 35761052 DOI: 10.1007/978-1-0716-2489-0_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
N-selenoethyl cysteine (SetCys) in the form of its cyclic selenosulfide is a cysteine surrogate, whose reactivity depends on the reducing power of the medium. SetCys does not interfere with the native chemical ligation reaction under mild reducing conditions, that is in the absence of tris(2-carboxyethyl)phosphine (TCEP). In contrast, subjecting SetCys to TCEP results in the spontaneous loss of its N-selenoethyl appendage and thus to its conversion into a Cys residue. Therefore, SetCys can be used for the redox-controlled assembly of peptide segments using NCL. We provide in this protocol detailed procedures for the synthesis of Fmoc-protected SetCys residue and for its incorporation into peptides using standard solid-phase peptide synthesis protocols. We also describe its use for the chemical synthesis of proteins through the redox-controlled assembly of three peptide segments in one-pot.
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Affiliation(s)
- Olga Firstova
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
- Centrale Lille; F-59000, Lille, France
| | - Vincent Diemer
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France.
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France.
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19
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Spears RJ, McMahon C, Chudasama V. Cysteine protecting groups: applications in peptide and protein science. Chem Soc Rev 2021; 50:11098-11155. [PMID: 34605832 DOI: 10.1039/d1cs00271f] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protecting group chemistry for the cysteine thiol group has enabled a vast array of peptide and protein chemistry over the last several decades. Increasingly sophisticated strategies for the protection, and subsequent deprotection, of cysteine have been developed, facilitating synthesis of complex disulfide-rich peptides, semisynthesis of proteins, and peptide/protein labelling in vitro and in vivo. In this review, we analyse and discuss the 60+ individual protecting groups reported for cysteine, highlighting their applications in peptide synthesis and protein science.
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Affiliation(s)
| | - Clíona McMahon
- Department of Chemistry, University College London, London, UK.
| | - Vijay Chudasama
- Department of Chemistry, University College London, London, UK.
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20
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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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21
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Premdjee B, Andersen AS, Larance M, Conde-Frieboes KW, Payne RJ. Chemical Synthesis of Phosphorylated Insulin-like Growth Factor Binding Protein 2. J Am Chem Soc 2021; 143:5336-5342. [PMID: 33797881 DOI: 10.1021/jacs.1c02280] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chemical protein synthesis is a powerful avenue for accessing homogeneously modified proteins. While a significant number of small modified proteins bearing native post-translational modifications and non-natural modifications have been generated to date, access to larger targets has proved challenging. Herein, we describe the use of two ligation manifolds, namely, diselenide-selenoester ligation and native chemical ligation, to assemble a 31.5 kDa phosphorylated insulin-like growth factor binding protein (IGFBP-2) that comprises 290 amino acid residues, a phosphoserine post-translational modification, and nine disulfide bonds.
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Affiliation(s)
- Bhavesh Premdjee
- Department of Research Chemistry. Novo Nordisk A/S, Måløv 2760, Denmark
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Asser S Andersen
- Department of Recombinant Technologies, Novo Nordisk A/S, Måløv 2760, Denmark
| | - Mark Larance
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
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22
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Kerdraon F, Bogard G, Snella B, Drobecq H, Pichavant M, Agouridas V, Melnyk O. Insights into the Mechanism and Catalysis of Peptide Thioester Synthesis by Alkylselenols Provide a New Tool for Chemical Protein Synthesis. Molecules 2021; 26:1386. [PMID: 33806630 PMCID: PMC7961367 DOI: 10.3390/molecules26051386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 11/17/2022] Open
Abstract
While thiol-based catalysts are widely employed for chemical protein synthesis relying on peptide thioester chemistry, this is less true for selenol-based catalysts whose development is in its infancy. In this study, we compared different selenols derived from the selenocysteamine scaffold for their capacity to promote thiol-thioester exchanges in water at mildly acidic pH and the production of peptide thioesters from bis(2-sulfanylethyl)amido (SEA) peptides. The usefulness of a selected selenol compound is illustrated by the total synthesis of a biologically active human chemotactic protein, which plays an important role in innate and adaptive immunity.
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Affiliation(s)
- Florent Kerdraon
- U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille, Institut Pasteur de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (F.K.); (G.B.); (B.S.); (H.D.); (M.P.)
| | - Gemma Bogard
- U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille, Institut Pasteur de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (F.K.); (G.B.); (B.S.); (H.D.); (M.P.)
| | - Benoît Snella
- U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille, Institut Pasteur de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (F.K.); (G.B.); (B.S.); (H.D.); (M.P.)
| | - Hervé Drobecq
- U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille, Institut Pasteur de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (F.K.); (G.B.); (B.S.); (H.D.); (M.P.)
| | - Muriel Pichavant
- U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille, Institut Pasteur de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (F.K.); (G.B.); (B.S.); (H.D.); (M.P.)
| | - Vangelis Agouridas
- U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille, Institut Pasteur de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (F.K.); (G.B.); (B.S.); (H.D.); (M.P.)
- Centrale Lille, F-59000 Lille, France
| | - Oleg Melnyk
- U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille, Institut Pasteur de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (F.K.); (G.B.); (B.S.); (H.D.); (M.P.)
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23
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Abstract
Historically, ligase activity by proteases was theoretically derived due to their catalyst nature, and it was experimentally observed as early as around 1900. Initially, the digestive proteases, such as pepsin, chymotrypsin, and trypsin were employed to perform in vitro syntheses of small peptides. Protease-catalyzed ligation is more efficient than peptide bond hydrolysis in organic solvents, representing control of the thermodynamic equilibrium. Peptide esters readily form acyl intermediates with serine and cysteine proteases, followed by peptide bond synthesis at the N-terminus of another residue. This type of reaction is under kinetic control, favoring aminolysis over hydrolysis. Although only a few natural peptide ligases are known, such as ubiquitin ligases, sortases, and legumains, the principle of proteases as general catalysts could be adapted to engineer some proteases accordingly. In particular, the serine proteases subtilisin and trypsin were converted to efficient ligases, which are known as subtiligase and trypsiligase. Together with sortases and legumains, they turned out to be very useful in linking peptides and proteins with a great variety of molecules, including biomarkers, sugars or building blocks with non-natural amino acids. Thus, these engineered enzymes are a promising branch for academic research and for pharmaceutical progress.
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24
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Abstract
Although the majority of proteins used for biomedical research are produced using living systems such as bacteria, biological means for producing proteins can be advantageously complemented by protein semisynthesis or total chemical synthesis. The latter approach is particularly useful when the proteins to be produced are toxic for the expression system or show unusual features that cannot be easily programmed in living organisms. The aim of this review is to provide a wide overview of the use of chemical protein synthesis in medicinal chemistry with a special focus on the production of post-translationally modified proteins and backbone cyclized proteins.
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Affiliation(s)
- Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 9017, CIIL, Center for Infection and Immunity of Lille, F-59000 Lille, France.,Centrale Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza gare, Morocco
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 9017, CIIL, Center for Infection and Immunity of Lille, F-59000 Lille, France
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25
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Nolan MD, Scanlan EM. Applications of Thiol-Ene Chemistry for Peptide Science. Front Chem 2020; 8:583272. [PMID: 33282831 PMCID: PMC7689097 DOI: 10.3389/fchem.2020.583272] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Radical thiol-ene chemistry has been demonstrated for a range of applications in peptide science, including macrocyclization, glycosylation and lipidation amongst a myriad of others. The thiol-ene reaction offers a number of advantages in this area, primarily those characteristic of "click" reactions. This provides a chemical approach to peptide modification that is compatible with aqueous conditions with high orthogonality and functional group tolerance. Additionally, the use of a chemical approach for peptide modification affords homogeneous peptides, compared to heterogeneous mixtures often obtained through biological methods. In addition to peptide modification, thiol-ene chemistry has been applied in novel approaches to biological studies through synthesis of mimetics and use in development of probes. This review will cover the range of applications of the radical-mediated thiol-ene reaction in peptide and protein science.
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Affiliation(s)
- Mark D Nolan
- School of Chemistry, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Eoin M Scanlan
- School of Chemistry, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
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26
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Abboud SA, Aucagne V. An optimized protocol for the synthesis of N-2-hydroxybenzyl-cysteine peptide crypto-thioesters. Org Biomol Chem 2020; 18:8199-8208. [PMID: 33034311 DOI: 10.1039/d0ob01737j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We herein report a robust upgraded synthetic protocol for the synthesis of N-Hnb-Cys crypto-thioester peptides, useful building blocks for segment-based chemical protein synthesis through native chemical ligation. We recently observed the formation of an isomeric co-product when using a different solid support than the originally-reported one, thus hampering the general applicability of the methodology. We undertook a systematic study to characterize this compound and identify the parameters favouring its formation. We show here that epimerization from l- to d-cysteine occurred during the key solid-supported reductive amination step. We also observed the formation of imidazolidinones by-products arising from incomplete reduction of the imine. Structural characterization combined with the deciphering of underlying reaction mechanisms allowed us to optimize conditions that abolished the formation of all these side-products.
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Affiliation(s)
- Skander A Abboud
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France.
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France.
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27
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Yim VV, Kavianinia I, Cameron AJ, Harris PWR, Brimble MA. Direct synthesis of cyclic lipopeptides using intramolecular native chemical ligation and thiol-ene CLipPA chemistry. Org Biomol Chem 2020; 18:2838-2844. [PMID: 32048704 DOI: 10.1039/d0ob00203h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Naturally occurring cyclic lipopeptides exhibit a diverse range of biological activities and possess several favourable properties. Chemically synthesising and modifying these natural compounds can alter their biological and physical properties. Cyclic lipopeptides are often difficult to synthesise, especially when the lipid moiety is directly attached to the cyclic scaffold. The construction of a series of cyclic lipopeptide analogues of the antifungal peptide iturin A is reported herein. The synthesis of the parent peptide macrocycle was achieved using native chemical ligation (NCL), whereupon the regenerated free thiol was used to attach a lipid moiety using Cysteine Lipidation on a Peptide or Amino acid (CLipPA) technology.
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Affiliation(s)
- Victor V Yim
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
| | - Iman Kavianinia
- School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
| | - Alan J Cameron
- School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
| | - Paul W R Harris
- School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
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28
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Strategies and open questions in solid-phase protein chemical synthesis. Curr Opin Chem Biol 2020; 58:1-9. [DOI: 10.1016/j.cbpa.2020.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 12/21/2022]
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29
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Diemer V, Ollivier N, Leclercq B, Drobecq H, Vicogne J, Agouridas V, Melnyk O. A cysteine selenosulfide redox switch for protein chemical synthesis. Nat Commun 2020; 11:2558. [PMID: 32444769 PMCID: PMC7244499 DOI: 10.1038/s41467-020-16359-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/23/2020] [Indexed: 01/08/2023] Open
Abstract
The control of cysteine reactivity is of paramount importance for the synthesis of proteins using the native chemical ligation (NCL) reaction. We report that this goal can be achieved in a traceless manner during ligation by appending a simple N-selenoethyl group to cysteine. While in synthetic organic chemistry the cleavage of carbon-nitrogen bonds is notoriously difficult, we describe that N-selenoethyl cysteine (SetCys) loses its selenoethyl arm in water under mild conditions upon reduction of its selenosulfide bond. Detailed mechanistic investigations show that the cleavage of the selenoethyl arm proceeds through an anionic mechanism with assistance of the cysteine thiol group. The implementation of the SetCys unit in a process enabling the modular and straightforward assembly of linear or backbone cyclized polypeptides is illustrated by the synthesis of biologically active cyclic hepatocyte growth factor variants.
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Affiliation(s)
- Vincent Diemer
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Nathalie Ollivier
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Bérénice Leclercq
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Hervé Drobecq
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Jérôme Vicogne
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France.
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France.
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Kirkeby EK, Roberts AG. Design, synthesis and characterization of structurally dynamic cyclic N,S-acetals. Chem Commun (Camb) 2020; 56:9118-9121. [DOI: 10.1039/d0cc03503c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis, characterization and comparison of a series of electronically perturbed, cyclic N,S-acetals.
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31
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Chisholm TS, Kulkarni SS, Hossain KR, Cornelius F, Clarke RJ, Payne RJ. Peptide Ligation at High Dilution via Reductive Diselenide-Selenoester Ligation. J Am Chem Soc 2019; 142:1090-1100. [DOI: 10.1021/jacs.9b12558] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Sameer S. Kulkarni
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Flemming Cornelius
- Department of Biomedicine, University of Aarhus, DK-8000 Aarhus C, Denmark
| | - Ronald J. Clarke
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- The University of Sydney Nano Institute, Sydney, NSW 2006, Australia
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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32
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Bouchenna J, Sénéchal M, Drobecq H, Vicogne J, Melnyk O. Total Chemical Synthesis of All SUMO-2/3 Dimer Combinations. Bioconjug Chem 2019; 30:2967-2973. [PMID: 31702897 DOI: 10.1021/acs.bioconjchem.9b00661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
One hallmark of protein chemical synthesis is its capacity to access proteins that living systems can hardly produce. This is typically the case for proteins harboring post-translational modifications such as ubiquitin or ubiquitin-like modifiers. Various methods have been developed for accessing polyubiquitin conjugates by semi- or total synthesis. Comparatively, the preparation of small-ubiquitin-like modifier (SUMO) conjugates, and more particularly of polySUMO scaffolds, is much less developed. We describe hereinafter a synthetic strategy for accessing all SUMO-2/3 dimer combinations.
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Affiliation(s)
- Jennifer Bouchenna
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
| | - Magalie Sénéchal
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
| | - Hervé Drobecq
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
| | - Jérôme Vicogne
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
| | - Oleg Melnyk
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
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33
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Bouchenna J, Sénéchal M, Drobecq H, Stankovic-Valentin N, Vicogne J, Melnyk O. The Role of the Conserved SUMO-2/3 Cysteine Residue on Domain Structure Investigated Using Protein Chemical Synthesis. Bioconjug Chem 2019; 30:2684-2696. [PMID: 31532181 DOI: 10.1021/acs.bioconjchem.9b00598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
While the semi or total synthesis of ubiquitin or polyubiquitin conjugates has attracted a lot of attention the past decade, the preparation of small ubiquitin-like modifier (SUMO) conjugates is much less developed. We describe hereinafter some important molecular features to consider when preparing SUMO-2/3 conjugates by chemical synthesis using the native chemical ligation and extended methods. In particular, we clarify the role of the conserved cysteine residue on SUMO-2/3 domain stability and properties. Our data reveal that SUMO-2 and -3 proteins behave differently from the Cys → Ala modification with SUMO-2 being less impacted than SUMO-3, likely due to a stabilizing interaction occurring in SUMO-2 between its tail and the SUMO core domain. While the Cys → Ala modification has no effect on the enzyme-catalyzed conjugation, it shows a deleterious effect on the enzyme-catalyzed deconjugation process, especially with the SUMO-3 conjugate. Whereas it is often stated that SUMO-2 and SUMO-3 are structurally and functionally indistinguishable, here we show that these proteins have specific structural and biochemical properties. This information is important to consider when designing and preparing SUMO-2/3 conjugates, and should help in making progress in the understanding of the specific role of SUMO-2 and/or SUMO-3 modifications on protein structure and function.
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Affiliation(s)
- Jennifer Bouchenna
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Magalie Sénéchal
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Hervé Drobecq
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) , DKFZ - ZMBH Alliance, 69120 , Heidelberg , Germany
| | - Jérôme Vicogne
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Oleg Melnyk
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
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Baldauf S, Schauenburg D, Bode JW. A Threonine‐Forming Oxazetidine Amino Acid for the Chemical Synthesis of Proteins through KAHA Ligation. Angew Chem Int Ed Engl 2019; 58:12599-12603. [DOI: 10.1002/anie.201906486] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Simon Baldauf
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied biosciencesETH Zürich Wolfgang Pauli Strasse 10 8093 Zürich Switzerland
| | - Dominik Schauenburg
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied biosciencesETH Zürich Wolfgang Pauli Strasse 10 8093 Zürich Switzerland
| | - Jeffrey W. Bode
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied biosciencesETH Zürich Wolfgang Pauli Strasse 10 8093 Zürich Switzerland
- Institute of Transformative Bio-Molecules (WPI-ITbM)Nagoya University, Chisuka Nagoya 464-8602 Japan
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35
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Baldauf S, Schauenburg D, Bode JW. Eine Threonin‐bildende Oxazetidinaminosäure für die chemische Synthese von Proteinen mittels KAHA‐Ligation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Simon Baldauf
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied biosciencesETH Zürich Wolfgang-Pauli-Strasse 10 8093 Zürich Schweiz
| | - Dominik Schauenburg
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied biosciencesETH Zürich Wolfgang-Pauli-Strasse 10 8093 Zürich Schweiz
| | - Jeffrey W. Bode
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied biosciencesETH Zürich Wolfgang-Pauli-Strasse 10 8093 Zürich Schweiz
- Institute of Transformative Bio-Molecules (WPI-ITbM)Nagoya University, Chisuka Nagoya 464-8602 Japan
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36
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Yanase M, Nakatsu K, Cardos CJ, Konda Y, Hayashi G, Okamoto A. Cysteinylprolyl imide (CPI) peptide: a highly reactive and easily accessible crypto-thioester for chemical protein synthesis. Chem Sci 2019; 10:5967-5975. [PMID: 31360403 PMCID: PMC6566460 DOI: 10.1039/c9sc00646j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/09/2019] [Indexed: 12/21/2022] Open
Abstract
A new crypto-thioester, cysteinylprolyl imide (CPI) peptide, offers a practical synthetic pathway and reliable reaction rate to be successfully applied to chemical protein synthesis.
Native chemical ligation (NCL) between the C-terminal peptide thioester and the N-terminal cysteinyl-peptide revolutionized the field of chemical protein synthesis. The difficulty of direct synthesis of the peptide thioester in the Fmoc method has prompted the development of crypto-thioesters that can be efficiently converted into thioesters. Cysteinylprolyl ester (CPE), which is an N–S acyl shift-driven crypto-thioester that relies on an intramolecular O–N acyl shift to displace the amide-thioester equilibrium, enabled trans-thioesterification and subsequent NCL in one pot. However, the utility of CPE is limited because of the moderate thioesterification rates and the synthetic complexity introduced by the ester group. Herein, we develop a new crypto-thioester, cysteinylprolyl imide (CPI), which replaces the alcohol leaving group of CPE with other leaving groups such as benzimidazolidinone, oxazolidinone, and pyrrolidinone. CPI peptides were efficiently synthesized by using standard Fmoc solid-phase peptide synthesis (SPPS) and subsequent on-resin imide formation. Screening of the several imide structures indicated that methyloxazolidinone-t-leucine (MeOxd-Tle) showed faster conversion into thioester and higher stability against hydrolysis under NCL conditions. Finally, by using CPMeOxd-Tle peptides, we demonstrated the chemical synthesis of affibody via N-to-C sequential, three-segment ligation and histone H2A.Z via convergent four-segment ligation. This facile and straightforward method is expected to be broadly applicable to chemical protein synthesis.
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Affiliation(s)
- Masafumi Yanase
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Koki Nakatsu
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Charlane Joy Cardos
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Yoshiki Konda
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Gosuke Hayashi
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan . .,Department of Biomolecular Engineering , Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan .
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan . .,Research Center for Advanced Science and Technology , The University of Tokyo , 4-6-1 Komaba, Meguro-ku , Tokyo 153-8904 , Japan
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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38
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Lombardo CM, Kumar M. V. V, Douat C, Rosu F, Mergny JL, Salgado GF, Guichard G. Design and Structure Determination of a Composite Zinc Finger Containing a Nonpeptide Foldamer Helical Domain. J Am Chem Soc 2019; 141:2516-2525. [DOI: 10.1021/jacs.8b12240] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Caterina Maria Lombardo
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Vasantha Kumar M. V.
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33076 Pessac, France
| | - Céline Douat
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie, UMS3033/US001, Univ. Bordeaux, INSERM, CNRS, 2 rue Robert Escarpit, 33076 Pessac, France
| | - Jean-Louis Mergny
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33076 Pessac, France
| | - Gilmar F. Salgado
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33076 Pessac, France
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France
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39
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Zuo C, Zhang B, Yan B, Zheng JS. One-pot multi-segment condensation strategies for chemical protein synthesis. Org Biomol Chem 2019; 17:727-744. [DOI: 10.1039/c8ob02610f] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This paper describes recent advances of one-pot multi-segment condensation strategies based on kinetically controlled strategies and/or protecting group-removal strategies in chemical protein synthesis.
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Affiliation(s)
- Chong Zuo
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230027
- China
- Department of Chemistry
| | - Baochang Zhang
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Bingjia Yan
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Ji-Shen Zheng
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230027
- China
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40
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Snella B, Diemer V, Drobecq H, Agouridas V, Melnyk O. Native Chemical Ligation at Serine Revisited. Org Lett 2018; 20:7616-7619. [DOI: 10.1021/acs.orglett.8b03355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Benoît Snella
- University of Lille, Pasteur Institute of Lille, UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, F-59000 Lille, France
| | - Vincent Diemer
- University of Lille, Pasteur Institute of Lille, UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, F-59000 Lille, France
| | - Hervé Drobecq
- University of Lille, Pasteur Institute of Lille, UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, F-59000 Lille, France
| | - Vangelis Agouridas
- University of Lille, Pasteur Institute of Lille, UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, F-59000 Lille, France
| | - Oleg Melnyk
- University of Lille, Pasteur Institute of Lille, UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, F-59000 Lille, France
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Cargoët M, Diemer V, Snella B, Desmet R, Blanpain A, Drobecq H, Agouridas V, Melnyk O. Catalysis of Thiol-Thioester Exchange by Water-Soluble Alkyldiselenols Applied to the Synthesis of Peptide Thioesters and SEA-Mediated Ligation. J Org Chem 2018; 83:12584-12594. [PMID: 30230829 DOI: 10.1021/acs.joc.8b01903] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N-Alkyl bis(2-selanylethyl)amines catalyze the synthesis of peptide thioesters or peptide ligation from bis(2-sulfanylethyl)amido (SEA) peptides. These catalysts are generated in situ by reduction of the corresponding cyclic diselenides by tris(2-carboxyethyl)phosphine. They are particularly efficient at pH 4.0 by accelerating the thiol-thioester exchange processes, which are otherwise rate-limiting at this pH. By promoting SEA-mediated reactions at mildly acidic pH, they facilitate the synthesis of complex peptides such as cyclic O-acyl isopeptides that are otherwise hardly accessible.
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Affiliation(s)
- Marine Cargoët
- Université de Lille , Institut Pasteur de Lille, UMR CNRS 8204 , 1 rue du Pr Calmette , 59021 Lille , France
| | - Vincent Diemer
- Université de Lille , Institut Pasteur de Lille, UMR CNRS 8204 , 1 rue du Pr Calmette , 59021 Lille , France
| | - Benoît Snella
- Université de Lille , Institut Pasteur de Lille, UMR CNRS 8204 , 1 rue du Pr Calmette , 59021 Lille , France
| | - Rémi Desmet
- Université de Lille , Institut Pasteur de Lille, UMR CNRS 8204 , 1 rue du Pr Calmette , 59021 Lille , France
| | - Annick Blanpain
- Université de Lille , Institut Pasteur de Lille, UMR CNRS 8204 , 1 rue du Pr Calmette , 59021 Lille , France
| | - Hervé Drobecq
- Université de Lille , Institut Pasteur de Lille, UMR CNRS 8204 , 1 rue du Pr Calmette , 59021 Lille , France
| | - Vangelis Agouridas
- Université de Lille , Institut Pasteur de Lille, UMR CNRS 8204 , 1 rue du Pr Calmette , 59021 Lille , France
| | - Oleg Melnyk
- Université de Lille , Institut Pasteur de Lille, UMR CNRS 8204 , 1 rue du Pr Calmette , 59021 Lille , France
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42
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Sato K, Tanaka S, Yamamoto K, Tashiro Y, Narumi T, Mase N. Direct synthesis of N-terminal thiazolidine-containing peptide thioesters from peptide hydrazides. Chem Commun (Camb) 2018; 54:9127-9130. [PMID: 29882948 DOI: 10.1039/c8cc03591a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report a simple and promising synthetic method to oxidize peptide hydrazides containing N-terminal thiazolidine as a protected cysteine. This yields the corresponding thioester via a peptide azide without decomposition of the thiazolidine ring. The newly developed protocol was validated by the synthesis of the bioactive peptide LacZα.
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Affiliation(s)
- Kohei Sato
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.
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Accelerated microfluidic native chemical ligation at difficult amino acids toward cyclic peptides. Nat Commun 2018; 9:2847. [PMID: 30030439 PMCID: PMC6054628 DOI: 10.1038/s41467-018-05264-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/21/2018] [Indexed: 01/09/2023] Open
Abstract
Cyclic peptide-based therapeutics have a promising growth forecast that justifies the development of microfluidic systems dedicated to their production, in phase with the actual transitioning toward continuous flow and microfluidic technologies for pharmaceutical production. The application of the most popular method for peptide cyclization in water, i.e., native chemical ligation, under microfluidic conditions is still unexplored. Herein, we report a general strategy for fast and efficient peptide cyclization using native chemical ligation under homogeneous microfluidic conditions. The strategy relies on a multistep sequence that concatenates the formation of highly reactive S-(2-((2-sulfanylethyl)amino)ethyl) peptidyl thioesters from stable peptide amide precursors with an intramolecular ligation step. With very fast ligation rates (<5 min), even for the most difficult junctions (including threonine, valine, isoleucine, or proline), this technology opens the door toward the scale-independent, expedient preparation of bioactive macrocyclic peptides. Flow-based peptide synthesis is a well-established method, yet difficult to combine with native chemical ligation (NCL), the go-to method for peptide cyclization. Here, the authors developed a microfluidic procedure for peptide cyclization within minutes, using NCL and an SEA alkylthioester peptide.
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44
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Du JJ, Xin LM, Lei Z, Zou SY, Xu WB, Wang CW, Zhang L, Gao XF, Guo J. Glycopeptide ligation via direct aminolysis of selenoester. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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45
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46
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Rapid and efficient protein synthesis through expansion of the native chemical ligation concept. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0122] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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47
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Cheng WM, Lu X, Shi J, Liu L. Selective modification of natural nucleophilic residues in peptides and proteins using arylpalladium complexes. Org Chem Front 2018. [DOI: 10.1039/c8qo00765a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The present review outlines the recent methodologies for selective arylation of natural nucleophilic residues within unprotected peptides and proteins promoted by arylpalladium complexes, which demonstrate the advantages and potential of organometallic palladium complexes in bioconjugation.
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Affiliation(s)
- Wan-Min Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale
- CAS Key Laboratory of Urban Pollutant Conversion
- Anhui Province Key Laboratory of Biomass Clean Energy
- iChEM
- University of Science and Technology of China
| | - Xi Lu
- Hefei National Laboratory for Physical Sciences at the Microscale
- CAS Key Laboratory of Urban Pollutant Conversion
- Anhui Province Key Laboratory of Biomass Clean Energy
- iChEM
- University of Science and Technology of China
| | - Jing Shi
- Hefei National Laboratory for Physical Sciences at the Microscale
- CAS Key Laboratory of Urban Pollutant Conversion
- Anhui Province Key Laboratory of Biomass Clean Energy
- iChEM
- University of Science and Technology of China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Department of Chemistry
- Tsinghua University
- Beijing 100084
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