1
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Liao P, He C. Azole reagents enabled ligation of peptide acyl pyrazoles for chemical protein synthesis. Chem Sci 2024; 15:7965-7974. [PMID: 38817582 PMCID: PMC11134319 DOI: 10.1039/d3sc06697e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Native chemical ligation (NCL) has been playing an increasingly important role in chemical protein synthesis (CPS). More efficient ligation methods that circumvent the requirement of a peptidyl thioester and thiol additive-which allow the following desulfurization or refolding in one pot-are urgently needed for the synthesis of more complex protein targets and in large quantities. Herein, we discover that the weak acyl donor peptidyl N-acyl pyrazole can be activated by azole reagents like 3-methylpyrazole or imidazole to facilitate its ligation directly with an N-terminal cysteine peptide. As it requires no thioester or thiol additive, this ligation strategy can be conveniently combined with metal-free desulfurization (MFD) or oxidative protein folding to allow various one-pot protocols. The utility and generality of the strategy are showcased by the total synthesis of ubiquitin via an N-to-C sequential ligation-MFD strategy, the semi-synthesis of the copper protein azurin, and the efficient assembly of a sulfated hirudin variant and the cyclotide kalata B1, all in a one-pot fashion.
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Affiliation(s)
- Peisi Liao
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
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2
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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:e202400148. [PMID: 38629812 DOI: 10.1002/cbic.202400148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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3
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Wu X, Du Y, Liang LJ, Ding R, Zhang T, Cai H, Tian X, Pan M, Liu L. Structure-guided engineering enables E3 ligase-free and versatile protein ubiquitination via UBE2E1. Nat Commun 2024; 15:1266. [PMID: 38341401 PMCID: PMC10858943 DOI: 10.1038/s41467-024-45635-y] [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] [Received: 08/28/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Ubiquitination, catalyzed usually by a three-enzyme cascade (E1, E2, E3), regulates various eukaryotic cellular processes. E3 ligases are the most critical components of this catalytic cascade, determining both substrate specificity and polyubiquitination linkage specificity. Here, we reveal the mechanism of a naturally occurring E3-independent ubiquitination reaction of a unique human E2 enzyme UBE2E1 by solving the structure of UBE2E1 in complex with substrate SETDB1-derived peptide. Guided by this peptide sequence-dependent ubiquitination mechanism, we developed an E3-free enzymatic strategy SUE1 (sequence-dependent ubiquitination using UBE2E1) to efficiently generate ubiquitinated proteins with customized ubiquitinated sites, ubiquitin chain linkages and lengths. Notably, this strategy can also be used to generate site-specific branched ubiquitin chains or even NEDD8-modified proteins. Our work not only deepens the understanding of how an E3-free substrate ubiquitination reaction occurs in human cells, but also provides a practical approach for obtaining ubiquitinated proteins to dissect the biochemical functions of ubiquitination.
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Affiliation(s)
- Xiangwei Wu
- 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 Chemistry and Chemical Engineering, School of Pharmacy, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yunxiang Du
- 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
| | - Lu-Jun Liang
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China.
| | - Ruichao Ding
- 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
| | - Tianyi Zhang
- 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
| | - Hongyi Cai
- 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
| | - Xiaolin Tian
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Man Pan
- Institute of Translational Medicine, School of Chemistry and Chemical Engineering, School of Pharmacy, 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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4
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Chien MC, Lin YK, Liao Y, Chen SH, Chen YW, Liang CY, Molakaseema V, Hsu SCN, Lin CC, Chen HT, Kao CL. One-Step Synthesis of 3-(Fmoc-amino acid)-3,4-diaminobenzoic Acids. ACS OMEGA 2023; 8:41855-41864. [PMID: 37970022 PMCID: PMC10634083 DOI: 10.1021/acsomega.3c06640] [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: 09/06/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 11/17/2023]
Abstract
A one-step method for synthesizing 3-(Fmoc-amino acid)-3,4-diaminobenzoic acids was used to prepare preloaded diaminobenzoate resin. The coupling of free diaminobenzoic acid and Fmoc-amino acids gave pure products in 40-94% yield without any purification step in addition to precipitation except for histidine. For the proline residue, crude products were collected and used for solid-phase peptide synthesis to give a moderate yield of a pentapeptide. In addition, this method was used to prepare unusual amino acid derivatives, namely, (2-naphthyl) alanine and 6-aminohexanoic acid derivatives, in 50 and 65% yield, respectively.
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Affiliation(s)
- Min-Cheng Chien
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
| | - Yi Kai Lin
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
| | - Yong Liao
- Department
of Pharmacy, National Yang Ming Chiao Tung
University, Taipei 112, Taiwan
| | - Szu-Hsuan Chen
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
| | - Yen-Wei Chen
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
| | - Chien-Yu Liang
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
| | - Vijayasimha Molakaseema
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
| | - Sodio C. N. Hsu
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
| | - Chun-Cheng Lin
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hui-Ting Chen
- Department
of Pharmacy, National Yang Ming Chiao Tung
University, Taipei 112, Taiwan
| | - Chai-Lin Kao
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
- Department
of Medical Research, Kaohsiung Medical University
Hospital, Kaohsiung 807, Taiwan
- Drug
Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department
of Chemistry, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- College
of Professional Studies, National Pingtung
University of Science and Technology, Pingtung 912, Taiwan
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5
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Tatsumi T, Sasamoto K, Matsumoto T, Hirano R, Oikawa K, Nakano M, Yoshida M, Oisaki K, Kanai M. Practical N-to-C peptide synthesis with minimal protecting groups. Commun Chem 2023; 6:231. [PMID: 37884638 PMCID: PMC10603086 DOI: 10.1038/s42004-023-01030-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Accessible drug modalities have continued to increase in number in recent years. Peptides play a central role as pharmaceuticals and biomaterials in these new drug modalities. Although traditional peptide synthesis using chain-elongation from C- to N-terminus is reliable, it produces large quantities of chemical waste derived from protecting groups and condensation reagents, which place a heavy burden on the environment. Here we report an alternative N-to-C elongation strategy utilizing catalytic peptide thioacid formation and oxidative peptide bond formation with main chain-unprotected amino acids under aerobic conditions. This method is applicable to both iterative peptide couplings and convergent fragment couplings without requiring elaborate condensation reagents and protecting group manipulations. A recyclable N-hydroxy pyridone additive effectively suppresses epimerization at the elongating chain. We demonstrate the practicality of this method by showcasing a straightforward synthesis of the nonapeptide DSIP. This method further opens the door to clean and atom-efficient peptide synthesis.
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Affiliation(s)
- Toshifumi Tatsumi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koki Sasamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takuya Matsumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ryo Hirano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kazuki Oikawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masato Nakano
- Interdisciplinary Research Center for Catalytic Chemistry (IRC3), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Masaru Yoshida
- Interdisciplinary Research Center for Catalytic Chemistry (IRC3), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Kounosuke Oisaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Interdisciplinary Research Center for Catalytic Chemistry (IRC3), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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6
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Wei T, Liu J, Li C, Tan Y, Wei R, Wang J, Wu H, Li Q, Liu H, Tang Y, Li X. Revealing the extracellular function of HMGB1 N-terminal region acetylation assisted by a protein semi-synthesis approach. Chem Sci 2023; 14:10297-10307. [PMID: 37772093 PMCID: PMC10530822 DOI: 10.1039/d3sc01109g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023] Open
Abstract
HMGB1 (high-mobility group box 1) is a non-histone chromatin-associated protein that has been widely reported as a representative damage-associated molecular pattern (DAMP) and to play a pivotal role in the proinflammatory process once it is in an extracellular location. Accumulating evidence has shown that HMGB1 undergoes extensive post-translational modifications (PTMs) that actively regulate its conformation, localization, and intermolecular interactions. However, fully characterizing the functional implications of these PTMs has been challenging due to the difficulty in accessing homogeneous HMGB1 with site-specific PTMs of interest. In this study, we developed a streamlined protein semi-synthesis strategy via salicylaldehyde ester-mediated chemical ligations (Ser/Thr ligation and Cys/Pen ligation, STL/CPL). This methodology enabled us to generate a series of N-terminal region acetylated HMGB1 proteins. Further studies revealed that acetylation regulates HMGB1-heparin interaction and modulates HMGB1's stability against thrombin, representing a regulatory switch to control HMGB1's extracellular activity.
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Affiliation(s)
- Tongyao Wei
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Jiamei Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Can Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Yi Tan
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Ruohan Wei
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Jinzheng Wang
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Hongxiang Wu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Qingrong Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Heng Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Yubo Tang
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
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7
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Kriegesmann J, Brik A. Synthesis of ubiquitinated proteins for biochemical and functional analysis. Chem Sci 2023; 14:10025-10040. [PMID: 37772107 PMCID: PMC10529715 DOI: 10.1039/d3sc03664b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/27/2023] [Indexed: 09/30/2023] Open
Abstract
Ubiquitination plays a crucial role in controlling various biological processes such as translation, DNA repair and immune response. Protein degradation for example, is one of the main processes which is controlled by the ubiquitin system and has significant implications on human health. In order to investigate these processes and the roles played by different ubiquitination patterns on biological systems, homogeneously ubiquitinated proteins are needed. Notably, these conjugates that are made enzymatically in cells cannot be easily obtained in large amounts and high homogeneity by employing such strategies. Therefore, chemical and semisynthetic approaches have emerged to prepare different ubiquitinated proteins. In this review, we will present the key synthetic strategies and their applications for the preparation of various ubiquitinated proteins. Furthermore, the use of these precious conjugates in different biochemical and functional studies will be highlighted.
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Affiliation(s)
- Julia Kriegesmann
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology Haifa Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology Haifa Israel
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8
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Harel O, Jbara M. Chemical Synthesis of Bioactive Proteins. Angew Chem Int Ed Engl 2023; 62:e202217716. [PMID: 36661212 DOI: 10.1002/anie.202217716] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/21/2023]
Abstract
Nature has developed a plethora of protein machinery to operate and maintain nearly every task of cellular life. These processes are tightly regulated via post-expression modifications-transformations that modulate intracellular protein synthesis, folding, and activation. Methods to prepare homogeneously and precisely modified proteins are essential to probe their function and design new bioactive modalities. Synthetic chemistry has contributed remarkably to protein science by allowing the preparation of novel biomacromolecules that are often challenging or impractical to prepare via common biological means. The ability to chemically build and precisely modify proteins has enabled the production of new molecules with novel physicochemical properties and programmed activity for biomedical research, diagnostic, and therapeutic applications. This minireview summarizes recent developments in chemical protein synthesis to produce bioactive proteins, with emphasis on novel analogs with promising in vitro and in vivo activity.
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Affiliation(s)
- Omer Harel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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9
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Saebi A, Brown JS, Marando VM, Hartrampf N, Chumbler NM, Hanna S, Poskus M, Loas A, Kiessling LL, Hung DT, Pentelute BL. Rapid Single-Shot Synthesis of the 214 Amino Acid-Long N-Terminal Domain of Pyocin S2. ACS Chem Biol 2023; 18:518-527. [PMID: 36821521 PMCID: PMC10460144 DOI: 10.1021/acschembio.2c00862] [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: 02/24/2023]
Abstract
The impermeable outer membrane of Pseudomonas aeruginosa is bypassed by antibacterial proteins known as S-type pyocins. Because of their properties, pyocins are investigated as a potential new class of antimicrobials against Pseudomonas infections. Their production and modification, however, remain challenging. To address this limitation, we employed automated fast-flow peptide synthesis for the rapid production of a pyocin S2 import domain. The N-terminal domain sequence (PyS2NTD) was synthesized in under 10 h and purified to yield milligram quantities of the desired product. To our knowledge, the 214 amino acid sequence of PyS2NTD is among the longest peptides produced from a "single-shot" synthesis, i.e., made in a single stepwise route without the use of ligation techniques. Biophysical characterization of the PyS2NTD with circular dichroism was consistent with the literature reports. Fluorescently labeled PyS2NTD binds to P. aeruginosa expressing the cognate ferripyoverdine receptor and is taken up into the periplasm. This selective uptake was validated with confocal and super resolution microscopy, flow cytometry, and fluorescence recovery after photobleaching. These modified, synthetic S-type pyocin domains can be used to probe import mechanisms of P. aeruginosa and leveraged to develop selective antimicrobial agents that bypass the outer membrane.
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Affiliation(s)
- Azin Saebi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Joseph S Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Victoria M Marando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicole M Chumbler
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mackenzie Poskus
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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10
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Chemical synthesis of oligosaccharides and their application in new drug research. Eur J Med Chem 2023; 249:115164. [PMID: 36758451 DOI: 10.1016/j.ejmech.2023.115164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
Oligosaccharides are the ubiquitous molecules of life. In order to translate human bioglycosylation into clinical applications, homogeneous samples of oligosaccharides and glycoconjugates can be obtained by chemical, enzymatic or other biological methods for systematic studies. However, the structural complexity and diversity of glycans and their conjugates present a major challenge for the synthesis of such molecules. This review summarizes the chemical synthesis methods of oligosaccharides, the application of oligosaccharides in the field of medicinal chemistry according to their related biological activities, and shows the great prospect of oligosaccharides in the field of pharmaceutical chemistry.
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11
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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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12
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Proteins through the eyes of an organic chemist. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Taylor RJ, Geeson MB, Journeaux T, Bernardes GJL. Chemical and Enzymatic Methods for Post-Translational Protein-Protein Conjugation. J Am Chem Soc 2022; 144:14404-14419. [PMID: 35912579 PMCID: PMC9389620 DOI: 10.1021/jacs.2c00129] [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: 11/28/2022]
Abstract
Fusion proteins play an essential role in the biosciences but suffer from several key limitations, including the requirement for N-to-C terminal ligation, incompatibility of constituent domains, incorrect folding, and loss of biological activity. This perspective focuses on chemical and enzymatic approaches for the post-translational generation of well-defined protein-protein conjugates, which overcome some of the limitations faced by traditional fusion techniques. Methods discussed range from chemical modification of nucleophilic canonical amino acid residues to incorporation of unnatural amino acid residues and a range of enzymatic methods, including sortase-mediated ligation. Through summarizing the progress in this rapidly growing field, the key successes and challenges associated with using chemical and enzymatic approaches are highlighted and areas requiring further development are discussed.
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Affiliation(s)
- Ross J Taylor
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Michael B Geeson
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Toby Journeaux
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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14
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Mann G, Sulkshane P, Sadhu P, Ziv T, Glickman MH, Brik A. Antibody for Serine 65 Phosphorylated Ubiquitin Identifies PLK1-Mediated Phosphorylation of Mitotic Proteins and APC1. Molecules 2022; 27:molecules27154867. [PMID: 35956818 PMCID: PMC9369648 DOI: 10.3390/molecules27154867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022] Open
Abstract
Deciphering the protein posttranslational modification (PTM) code is one of the greatest biochemical challenges of our time. Phosphorylation and ubiquitylation are key PTMs that dictate protein function, recognition, sub-cellular localization, stability, turnover and fate. Hence, failures in their regulation leads to various disease. Chemical protein synthesis allows preparation of ubiquitinated and phosphorylated proteins to study their biochemical properties in great detail. However, monitoring these modifications in intact cells or in cell extracts mostly depends on antibodies, which often have off-target binding. Here, we report that the most widely used antibody for ubiquitin (Ub) phosphorylated at serine 65 (pUb) has significant off-targets that appear during mitosis. These off-targets are connected to polo-like kinase 1 (PLK1) mediated phosphorylation of cell cycle-related proteins and the anaphase promoting complex subunit 1 (APC1).
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Affiliation(s)
- Guy Mann
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000, Israel; (G.M.); (P.S.)
| | - Prasad Sulkshane
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel;
| | - Pradeep Sadhu
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000, Israel; (G.M.); (P.S.)
| | - Tamar Ziv
- The Smoler Protein Research Center, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion Israel Institute of Technology, Haifa 32000, Israel;
| | - Michael H. Glickman
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel;
- Correspondence: (M.H.G.); (A.B.)
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000, Israel; (G.M.); (P.S.)
- Correspondence: (M.H.G.); (A.B.)
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15
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Bremer J, Richter C, Schwalbe H, Richert C. Synthesis of a Peptidoyl RNA Hairpin via a Combination of Solid-Phase and Template-Directed Chain Assembly. Chembiochem 2022; 23:e202200352. [PMID: 35867587 PMCID: PMC9542650 DOI: 10.1002/cbic.202200352] [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: 06/19/2022] [Revised: 07/21/2022] [Indexed: 12/02/2022]
Abstract
Peptidoyl RNAs are the products of ribosome‐free, single‐nucleotide translation. They contain a peptide in the backbone of the oligoribonucleotide and are interesting from a synthetic and a bioorganic point of view. A synthesis of a stabilized version of peptidoyl RNA, with an amide bond between the C‐terminus of a peptide and a 3′‐amino‐2′,3′‐dideoxynucleoside in the RNA chain was developed. The preferred synthetic route used an N‐Teoc‐protected aminonucleoside support and involved a solution‐phase coupling of the amino‐terminal oligonucleotide to a dipeptido dinucleotide. Exploratory UV‐melting and NMR analysis of the hairpin 5′‐UUGGCGAAAGCdC‐LeuLeu‐AA‐3′ indicated that the peptide‐linked RNA segments do not fold in a cooperative fashion. The synthetic access to doubly RNA‐linked peptides on a scale sufficient for structural biology opens the door to the exploration of their structural and biochemical properties.
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Affiliation(s)
- Jennifer Bremer
- University of Stuttgart: Universitat Stuttgart, Chemistry, GERMANY
| | - Christian Richter
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Harald Schwalbe
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Clemens Richert
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, GERMANY
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16
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Carroll EC, Marqusee S. Site-specific ubiquitination: Deconstructing the degradation tag. Curr Opin Struct Biol 2022; 73:102345. [PMID: 35247748 DOI: 10.1016/j.sbi.2022.102345] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/28/2021] [Accepted: 01/17/2022] [Indexed: 02/04/2023]
Abstract
Ubiquitin is a small eukaryotic protein so named for its cellular abundance and originally recognized for its role as the posttranslational modification (PTM) "tag" condemning substrates to degradation by the 26S proteasome. Since its discovery in the 1970s, protein ubiquitination has also been identified as a key regulatory feature in dozens of non-degradative cellular processes. This myriad of roles illustrates the versatility of ubiquitin as a PTM; however, understanding the cellular and molecular factors that enable discrimination between degradative versus non-degradative ubiquitination events has been a persistent challenge. Here, we discuss recent advances in uncovering how site-specificity - the exact residue that gets modified - modulates distinct protein fates and cellular outcomes with an emphasis on how ubiquitination site specificity regulates proteasomal degradation. We explore recent advances in structural biology, biophysics, and cell biology that have enabled a broader understanding of the role of ubiquitination in altering the dynamics of the target protein, including implications for the design of targeted protein degradation therapeutics.
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Affiliation(s)
- Emma C Carroll
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, 94038, USA.
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA; QB3 Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, 94720, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA.
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17
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Akimoto G, Fernandes AP, Bode JW. Site-Specific Protein Ubiquitylation Using an Engineered, Chimeric E1 Activating Enzyme and E2 SUMO Conjugating Enzyme Ubc9. ACS CENTRAL SCIENCE 2022; 8:275-281. [PMID: 35237717 PMCID: PMC8883482 DOI: 10.1021/acscentsci.1c01490] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Indexed: 05/10/2023]
Abstract
Ubiquitylation-the attachment of ubiquitin (Ub) to proteins in eukaryotic cells-involves a vast number of enzymes from three different classes, resulting in heterogeneous attachment sites and ubiquitin chains. Recently, we introduced lysine acylation using conjugating enzymes (LACE) in which ubiquitin or peptide thioester is site-specifically transferred to a short peptide tag by the SUMO E2 conjugating enzyme Ubc9. This process, however, suffers from slow kinetics-due to a rate-limiting thioester loading step-and the requirement for thioesters restricts its use to in vitro reactions. To overcome these challenges, we devised a chimeric E1 containing the Ub fold domain of the SUMO E1 and the remaining domains of the Ub E1, which activates and loads native Ub onto Ubc9 and obviates the need for Ub thioester in LACE. The chimeric E1 was subjected to directed evolution to improve its apparent second-order rate constant (k cat/K M) 400-fold. We demonstrate the utility of the chimeric E1 by site-specific transfer of mono- and oligo-Ub to various target proteins in vitro. Additionally, the chimeric E1, Ubc9, Ub, and the target protein can be coexpressed in Escherichia coli for the facile preparation of monoubiquitylated proteins.
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18
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Chen K, Yu FQ, Zhang YN, Fang GM. Total Chemical Synthesis of a SARS-CoV-2 Miniprotein Inhibitor LCB1. Methods Mol Biol 2022; 2530:19-31. [PMID: 35761039 DOI: 10.1007/978-1-0716-2489-0_2] [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: 06/15/2023]
Abstract
Native chemical ligation is a widely used technique for peptide fragment condensation in aqueous solutions, which has broken through the length limitation of traditional solid-phase peptide synthesis. It can achieve high-efficient chemical synthesis of proteins containing more than 300 amino acid residues. Peptide hydrazide, as a valuable reagent equivalent to a thioester peptide, can be easily and efficiently prepared by the Fmoc-based SPPS method and has been widely used in native chemical ligation. Here we take the chemical synthesis of a SARS-CoV-2 miniprotein inhibitor LCB1 as an example to describe the detailed procedure of hydrazide-based native chemical ligation.
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Affiliation(s)
- Kai Chen
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Fei-Qiang Yu
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Yan-Ni Zhang
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Ge-Min Fang
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, China.
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19
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Fan C, Deng Q, Zhu TF. Bioorthogonal information storage in L-DNA with a high-fidelity mirror-image Pfu DNA polymerase. Nat Biotechnol 2021; 39:1548-1555. [PMID: 34326549 DOI: 10.1038/s41587-021-00969-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
Natural DNA is exquisitely evolved to store genetic information. The chirally inverted L-DNA, possessing the same informational capacity but resistant to biodegradation, may serve as a robust, bioorthogonal information repository. Here we chemically synthesize a 90-kDa high-fidelity mirror-image Pfu DNA polymerase that enables accurate assembly of a kilobase-sized mirror-image gene. We use the polymerase to encode in L-DNA an 1860 paragraph by Louis Pasteur that first proposed a mirror-image world of biology. We realize chiral steganography by embedding a chimeric D-DNA/L-DNA key molecule in a D-DNA storage library, which conveys a false or secret message depending on the chirality of reading. Furthermore, we show that a trace amount of an L-DNA barcode preserved in water from a local pond remains amplifiable and sequenceable for 1 year, whereas a D-DNA barcode under the same conditions could not be amplified after 1 day. These next-generation mirror-image molecular tools may transform the development of advanced mirror-image biology systems and pave the way for the realization of the mirror-image central dogma and exploration of their applications.
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Affiliation(s)
- Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Qiang Deng
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
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20
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Laps S, Atamleh F, Kamnesky G, Uzi S, Meijler MM, Brik A. Insight on the Order of Regioselective Ultrafast Formation of Disulfide Bonds in (Antimicrobial) Peptides and Miniproteins. Angew Chem Int Ed Engl 2021; 60:24137-24143. [PMID: 34524726 DOI: 10.1002/anie.202107861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Indexed: 01/08/2023]
Abstract
Disulfide-rich peptides and proteins are among the most fascinating bioactive molecules. The difficulties associated with the preparation of these targets have prompted the development of various chemical strategies. Nevertheless, the production of these targets remains very challenging or elusive. Recently, we introduced a strategy for one-pot disulfide bond formation, tackling most of the previous limitations. However, the effect of the order of oxidation remained an underexplored issue. Herein we report on the complete synthetic flexibility of the approach with respect to the order of oxidation of three disulfide bonds in targets that lack the knot motif. In contrast, our study reveals an essential order of disulfide bond formation in the EETI-II knotted miniprotein. This synthetic strategy was applied for the synthesis of novel analogues of the plectasin antimicrobial peptide with enhanced activities against methicillin-resistant Staphylococcus aureus (MRSA), a notorious human pathogen.
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Affiliation(s)
- Shay Laps
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Fatima Atamleh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Guy Kamnesky
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Shaked Uzi
- Department of Chemistry and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, 8410501, Israel
| | - Michael M Meijler
- Department of Chemistry and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, 8410501, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
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21
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Laps S, Atamleh F, Kamnesky G, Uzi S, Meijler MM, Brik A. Insight on the Order of Regioselective Ultrafast Formation of Disulfide Bonds in (Antimicrobial) Peptides and Miniproteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107861] [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)
- Shay Laps
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Fatima Atamleh
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Guy Kamnesky
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Shaked Uzi
- Department of Chemistry and National Institute for Biotechnology in the Negev Ben-Gurion University of the Negev Be'er Sheva 8410501 Israel
| | - Michael M. Meijler
- Department of Chemistry and National Institute for Biotechnology in the Negev Ben-Gurion University of the Negev Be'er Sheva 8410501 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
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22
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Li Y, Heng J, Sun D, Zhang B, Zhang X, Zheng Y, Shi WW, Wang TY, Li JY, Sun X, Liu X, Zheng JS, Kobilka BK, Liu L. Chemical Synthesis of a Full-Length G-Protein-Coupled Receptor β 2-Adrenergic Receptor with Defined Modification Patterns at the C-Terminus. J Am Chem Soc 2021; 143:17566-17576. [PMID: 34663067 DOI: 10.1021/jacs.1c07369] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The β2-adrenergic receptor (β2AR) is a G-protein-coupled receptor (GPCR) that responds to the hormone adrenaline and is an important drug target in the context of respiratory diseases, including asthma. β2AR function can be regulated by post-translational modifications such as phosphorylation and ubiquitination at the C-terminus, but access to the full-length β2AR with well-defined and homogeneous modification patterns critical for biochemical and biophysical studies remains challenging. Here, we report a practical synthesis of differentially modified, full-length β2AR based on a combined native chemical ligation (NCL) and sortase ligation strategy. An array of homogeneous samples of full-length β2ARs with distinct modification patterns, including a full-length β2AR bearing both monoubiquitination and octaphosphorylation modifications, were successfully prepared for the first time. Using these homogeneously modified full-length β2AR receptors, we found that different phosphorylation patterns mediate different interactions with β-arrestin1 as reflected in different agonist binding affinities. Our experiments also indicated that ubiquitination can further modulate interactions between β2AR and β-arrestin1. Access to full-length β2AR with well-defined and homogeneous modification patterns at the C-terminus opens a door to further in-depth mechanistic studies into the structure and dynamics of β2AR complexes with downstream transducer proteins, including G proteins, arrestins, and GPCR kinases.
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Affiliation(s)
- Yulei Li
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jie Heng
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Demeng Sun
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Baochang Zhang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xin Zhang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yupeng Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Wei-Wei Shi
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Tong-Yue Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiu-Yi Li
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Xiaoou Sun
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangyu Liu
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Ji-Shen Zheng
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education 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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23
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Erickson PW, Fulcher JM, Spaltenstein P, Kay MS. Traceless Click-Assisted Native Chemical Ligation Enabled by Protecting Dibenzocyclooctyne from Acid-Mediated Rearrangement with Copper(I). Bioconjug Chem 2021; 32:2233-2244. [PMID: 34619957 DOI: 10.1021/acs.bioconjchem.1c00403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The scope of proteins accessible to total chemical synthesis via native chemical ligation (NCL) is often limited by slow ligation kinetics. Here we describe Click-Assisted NCL (CAN), in which peptides are incorporated with traceless "helping hand" lysine linkers that enable addition of dibenzocyclooctyne (DBCO) and azide handles. The resulting strain-promoted alkyne-azide cycloaddition (SPAAC) increases their effective concentration to greatly accelerate ligations. We demonstrate that copper(I) protects DBCO from acid-mediated rearrangement during acidic peptide cleavage, enabling direct production of DBCO synthetic peptides. Excitingly, triazole-linked model peptides ligated rapidly and accumulated little side product due to the fast reaction time. Using the E. coli ribosomal subunit L32 as a model protein, we further demonstrate that SPAAC, ligation, desulfurization, and linker cleavage steps can be performed in one pot. CAN is a useful method for overcoming challenging ligations involving sterically hindered junctions. Additionally, CAN is anticipated to be an important stepping stone toward a multisegment, one-pot, templated ligation system.
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Affiliation(s)
- Patrick W Erickson
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States.,Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - James M Fulcher
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States.,Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Paul Spaltenstein
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States
| | - Michael S Kay
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States
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24
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Mann G, Satish G, Sulkshane P, Mandal S, Glickman MH, Brik A. Synthesis and delivery of a stable phosphorylated ubiquitin probe to study ubiquitin conjugation in mitophagy. Chem Commun (Camb) 2021; 57:9438-9441. [PMID: 34528945 PMCID: PMC8445162 DOI: 10.1039/d1cc04045f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022]
Abstract
Protein post-translational modifications are involved in essentially all aspects of cellular signaling. Their dynamic nature and the difficulties in installing them using enzymatic approaches limits their direct study in human cells. Reported herein is the first synthesis, delivery and cellular study of a stable phosphoubiquitin probe. Our results compare Parkin's substrate preference during mitophagy via direct visualization of a phosphorylated ubiquitin probe in the cellular environment.
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Affiliation(s)
- Guy Mann
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Gandhesiri Satish
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Prasad Sulkshane
- Faculty of Biology, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Shaswati Mandal
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Michael H Glickman
- Faculty of Biology, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
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25
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Zhou Y, Xie Q, Wang H, Sun H. Chemical approaches for the preparation of ubiquitinated proteins via natural linkages. J Pept Sci 2021; 28:e3367. [PMID: 34514672 DOI: 10.1002/psc.3367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022]
Abstract
Ubiquitination is an important posttranslation modification (PTM) that regulates a variety of cellular processes, including protein degradation, DNA repair, and viral infections. In this process, the C-terminal carboxyl group of ubiquitin (Ub) or poly-Ub is attached to the ε-amine of lysine (Lys) side chain of an acceptor protein through an isopeptide bond. Studying a molecular mechanism of ubiquitination and deubiquitination is fundamental for unraveling its precise role in health and disease and hence crucial for drug development. Enzymatic approaches for protein ubiquitination possess limited ability to selectivity install Ub or Ub chain on the desired position of an acceptor protein and often lead to heterogeneous mixtures. In the past decades, chemical protein (semi)synthesis has been proved to be an efficient tool to facilitate site-specific protein ubiquitination, which significantly contributes to decode the Ub signal at molecular and structural levels. In this review, we summarize the synthetic strategies developed for protein ubiquitination, and the achievements to generate monoubiquitinated, di-ubiquitinated, and tetraubiquitinated proteins with native isopeptide and ester bonds.
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Affiliation(s)
- Yuhui Zhou
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qingsong Xie
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Huagui Wang
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hao Sun
- College of Sciences, Nanjing Agricultural University, Nanjing, China
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26
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Liang L, Chu G, Qu Q, Zuo C, Mao J, Zheng Q, Chen J, Meng X, Jing Y, Deng H, Li Y, Liu L. Chemical Synthesis of Activity‐Based E2‐Ubiquitin Probes for the Structural Analysis of E3 Ligase‐Catalyzed Transthiolation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lu‐Jun Liang
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Guo‐Chao Chu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Qian Qu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Junxiong Mao
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Yangwode Jing
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education 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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27
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Liang LJ, Chu GC, Qu Q, Zuo C, Mao J, Zheng Q, Chen J, Meng X, Jing Y, Deng H, Li YM, Liu L. Chemical Synthesis of Activity-Based E2-Ubiquitin Probes for the Structural Analysis of E3 Ligase-Catalyzed Transthiolation. Angew Chem Int Ed Engl 2021; 60:17171-17177. [PMID: 34021957 DOI: 10.1002/anie.202105870] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 12/17/2022]
Abstract
Activity-based E2 conjugating enzyme (E2)-ubiquitin (Ub) probes have recently emerged as effective tools for studying the molecular mechanism of E3 ligase (E3)-catalyzed ubiquitination. However, the preparation of existing activity-based E2-Ub probes depends on recombination technology and bioconjugation chemistry, limiting their structural diversity. Herein we describe an expedient total chemical synthesis of an E2 enzyme variant through a hydrazide-based native chemical ligation, which enabled the construction of a structurally new activity-based E2-Ub probe to covalently capture the catalytic site of Cys-dependent E3s. Chemical cross-linking coupled with mass spectrometry (CXMS) demonstrated the utility of this new probe in structural analysis of the intermediates formed during Nedd4 and Parkin-mediated transthiolation. This study exemplifies the utility of chemical protein synthesis for the development of protein probes for biological studies.
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Affiliation(s)
- Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.,School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Qian Qu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Junxiong Mao
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Jingnan Chen
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yangwode Jing
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education 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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28
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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] [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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29
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Sato K, Tanaka S, Wang J, Ishikawa K, Tsuda S, Narumi T, Yoshiya T, Mase N. Late-Stage Solubilization of Poorly Soluble Peptides Using Hydrazide Chemistry. Org Lett 2021; 23:1653-1658. [PMID: 33570416 DOI: 10.1021/acs.orglett.1c00074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel late-stage solubilization of peptides using hydrazides is described. A solubilizing tag was attached through a selective N-alkylation at a hydrazide moiety with the aid of a 2-picoline-borane complex in 50% acetic acid-hexafluoro-2-propanol. The tag, which tolerates ligation and desulfurization conditions, can be detached by a Cu-mediated selective oxidative hydrolysis of the N-alkyl hydrazide. This new method was validated through the synthesis of HIV-1 protease.
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Affiliation(s)
- Kohei Sato
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Shoko Tanaka
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Junzhen Wang
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Kenya Ishikawa
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Shugo Tsuda
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Tetsuo Narumi
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Research Institute of Green Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Taku Yoshiya
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Nobuyuki Mase
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Research Institute of Green Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
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30
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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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31
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Laps S, Satish G, Brik A. Harnessing the power of transition metals in solid-phase peptide synthesis and key steps in the (semi)synthesis of proteins. Chem Soc Rev 2021; 50:2367-2387. [PMID: 33432943 DOI: 10.1039/d0cs01156h] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Peptides and proteins can be either synthesized using solid-phase peptide synthesis (SPPS) or by applying a combination of SPPS and ligation approaches to address fundamental questions related to human health and disease, among others. The demand for their production either by chemical or biological methods continues to raise significant interests from the synthetic community. In this context, transition metals such as Pd, Ag, Hg, Tl, Au, Zn, Ni, and Cu have also contributed to the field of peptide and protein synthesis such as in peptide conjugation, extending native chemical ligation (NCL), and for regioselective disulfide bonds formation. In this review, we highlight, summarize, and evaluate the use of various transition metals in the chemical synthesis of peptides and proteins with emphasis on recent developments in this exciting research area.
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Affiliation(s)
- Shay Laps
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
| | - Gandhesiri Satish
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
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32
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Abboud SA, Cisse EH, Doudeau M, Bénédetti H, Aucagne V. A straightforward methodology to overcome solubility challenges for N-terminal cysteinyl peptide segments used in native chemical ligation. Chem Sci 2021; 12:3194-3201. [PMID: 34164087 PMCID: PMC8179351 DOI: 10.1039/d0sc06001a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023] Open
Abstract
One of the main limitations encountered during the chemical synthesis of proteins through native chemical ligation (NCL) is the limited solubility of some of the peptide segments. The most commonly used solution to overcome this problem is to derivatize the segment with a temporary solubilizing tag. Conveniently, the tag can be introduced on the thioester segment in such a way that it is removed concomitantly with the NCL reaction. We herein describe a generalization of this approach to N-terminal cysteinyl segment counterparts, using a straightforward synthetic approach that can be easily automated from commercially available building blocks, and applied it to a well-known problematic target, SUMO-2.
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Affiliation(s)
- Skander A Abboud
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - El Hadji Cisse
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Michel Doudeau
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Hélène Bénédetti
- 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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33
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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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34
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Conibear AC. Deciphering protein post-translational modifications using chemical biology tools. Nat Rev Chem 2020; 4:674-695. [PMID: 37127974 DOI: 10.1038/s41570-020-00223-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2020] [Indexed: 02/06/2023]
Abstract
Proteins carry out a wide variety of catalytic, regulatory, signalling and structural functions in living systems. Following their assembly on ribosomes and throughout their lifetimes, most eukaryotic proteins are modified by post-translational modifications; small functional groups and complex biomolecules are conjugated to amino acid side chains or termini, and the protein backbone is cleaved, spliced or cyclized, to name just a few examples. These modifications modulate protein activity, structure, location and interactions, and, thereby, control many core biological processes. Aberrant post-translational modifications are markers of cellular stress or malfunction and are implicated in several diseases. Therefore, gaining an understanding of which proteins are modified, at which sites and the resulting biological consequences is an important but complex challenge requiring interdisciplinary approaches. One of the key challenges is accessing precisely modified proteins to assign functional consequences to specific modifications. Chemical biologists have developed a versatile set of tools for accessing specifically modified proteins by applying robust chemistries to biological molecules and developing strategies for synthesizing and ligating proteins. This Review provides an overview of these tools, with selected recent examples of how they have been applied to decipher the roles of a variety of protein post-translational modifications. Relative advantages and disadvantages of each of the techniques are discussed, highlighting examples where they are used in combination and have the potential to address new frontiers in understanding complex biological processes.
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35
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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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36
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Enhancing native chemical ligation for challenging chemical protein syntheses. Curr Opin Chem Biol 2020; 58:37-44. [PMID: 32745915 DOI: 10.1016/j.cbpa.2020.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 02/01/2023]
Abstract
Native chemical ligation has enabled the chemical synthesis of proteins for a wide variety of applications (e.g., mirror-image proteins). However, inefficiencies of this chemoselective ligation in the context of large or otherwise challenging protein targets can limit the practical scope of chemical protein synthesis. In this review, we focus on recent developments aimed at enhancing and expanding native chemical ligation for challenging protein syntheses. Chemical auxiliaries, use of selenium chemistry, and templating all enable ligations at otherwise suboptimal junctions. The continuing development of these tools is making the chemical synthesis of large proteins increasingly accessible.
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37
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38
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Acosta GA, Murray L, Royo M, de la Torre BG, Albericio F. Solid-Phase Synthesis of Head to Side-Chain Tyr-Cyclodepsipeptides Through a Cyclative Cleavage From Fmoc-MeDbz/MeNbz-resins. Front Chem 2020; 8:298. [PMID: 32391324 PMCID: PMC7189019 DOI: 10.3389/fchem.2020.00298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclic depsipeptides constitute a fascinating class of natural products. Most of them are characterized by an ester formed between the β-hydroxy function of Ser/Thr -and related amino acids- and the carboxylic group of the C-terminal amino acid. Less frequent are those where the thiol of Cys is involved rendering a thioester (cyclo thiodepsipeptides) and even less common are the cyclo depsipeptides with a phenyl ester coming from the side-chain of Tyr. Herein, the preparation of the later through a cyclative cleavage using the Fmoc-MeDbz/MeNbz-resin is described. This resin has previously reported for the synthesis of cyclo thiodepsipeptides and homodetic peptides. The use of that resin for the preparation of all these peptides is also summarized.
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Affiliation(s)
- Gerardo A Acosta
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona (UB), Barcelona, Spain.,Department of Organic Chemistry, University of Barcelona, Barcelona, Spain.,Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Spanish National Research Council (CSIC), Barcelona, Spain.,Associated Unit, Spanish National Research Council-University of Barcelona (CSIC-UB), Barcelona, Spain
| | - Laura Murray
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona (UB), Barcelona, Spain.,Department of Organic Chemistry, University of Barcelona, Barcelona, Spain
| | - Miriam Royo
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Spanish National Research Council (CSIC), Barcelona, Spain.,Associated Unit, Spanish National Research Council-University of Barcelona (CSIC-UB), Barcelona, Spain
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Fernando Albericio
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona (UB), Barcelona, Spain.,Department of Organic Chemistry, University of Barcelona, Barcelona, Spain.,Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Spanish National Research Council (CSIC), Barcelona, Spain.,Associated Unit, Spanish National Research Council-University of Barcelona (CSIC-UB), Barcelona, Spain.,Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
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39
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Jbara M, Eid E, Brik A. Gold(I)-Mediated Decaging or Cleavage of Propargylated Peptide Bond in Aqueous Conditions for Protein Synthesis and Manipulation. J Am Chem Soc 2020; 142:8203-8210. [PMID: 32290655 DOI: 10.1021/jacs.9b13216] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chemists have been interested in the N-alkylation of a peptide bond because such a modification alters the conformation of the amide bond, interferes with hydrogen bond formation, and changes other properties of the peptide (e.g., solubility). This modification also opens the door for attaching functional groups for various applications. Nonetheless, the irreversibility of some of these modifications and the harsh conditions required for their removal currently limits the wide utility of this approach. Herein, we report applying a propargyl group for peptide bond modification at diverse junctions, which can be removed under mild and aqueous conditions via treatment with gold(I). Considering the straightforward conditions for both the installation and removal of this group, the propargyl group provides access to the benefits of backbone N-alkylation, while preserving the ability for on-demand depropargylation and full recovery of the native amide bond. This reversible modification was found to improve solid-phase peptide synthesis as demonstrated in the chemical synthesis of NEDD8 protein, without the use of special dipeptide analogues. Also, the reported approach was found to be useful in decaging a broad range of propargyl-based protecting groups used in chemical protein synthesis. Remarkably, reversing the order of the two residues in the propargylation site resulted in rapid amide bond cleavage, which extends the applicability of this approach beyond a removable backbone modification to a cleavable linker. The easy attach/detach of this functionality was also examined in loading and releasing of biotinylated peptides from streptavidin beads.
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Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Emad Eid
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
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40
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Huang DL, Li Y, Liang J, Yu L, Xue M, Cao XX, Xiao B, Tian CL, Liu L, Zheng JS. The New Salicylaldehyde S,S-Propanedithioacetal Ester Enables N-to-C Sequential Native Chemical Ligation and Ser/Thr Ligation for Chemical Protein Synthesis. J Am Chem Soc 2020; 142:8790-8799. [DOI: 10.1021/jacs.0c01561] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Dong-Liang Huang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Ying Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Jun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Min Xue
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Xiu-Xiu Cao
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Bin Xiao
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Chang-Lin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Lei Liu
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ji-Shen Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
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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] [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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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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