1
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Fan X, Wen Y, Chen H, Tian B, Zhang Q. Polypeptide Preparation by β-Lactone-Mediated Chemical Ligation. Org Lett 2024; 26:5436-5440. [PMID: 38900935 PMCID: PMC11232016 DOI: 10.1021/acs.orglett.4c01587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
Native chemical ligation (NCL) represents a cornerstone strategy in accessing synthetic peptides and proteins, remaining one of the most efficacious methodologies in this domain. The fundamental requisites for achieving a proficient NCL reaction involve chemoselective coupling between a C-terminal thioester peptide and a thiol-bearing N-terminal peptide. However, achieving coupling at sterically congested residues remains challenging. In addition, while most NCLs proceed without epimerization, β-branched (e.g., Ile, Thr, Val) and Pro-derived C-terminal thioesters react slowly and can be susceptible to significant epimerization and hydrolysis. Herein, we report an epimerization-free NCL reaction via β-lactone-mediated native chemical ligation which constructs sterically congested Thr residues. The constrained ring from the β-lactone allows rapid peptide ligation without detectable epimerization. The method has a broad side-chain tolerance and was applied to the preparation of cyclic peptides and polypeptidyl thioester, which could be difficult to obtained otherwise.
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Affiliation(s)
- Xinhao Fan
- Department
of Chemistry, School of Pharmacy, North
Sichuan Medical College, Nanchong, Sichuan 637000, China
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Yuming Wen
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Huan Chen
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Baotong Tian
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Qiang Zhang
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
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2
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Iwamoto N, Kai T, Inuki S, Ohno H, Maeda H, Watanabe H, Maruyama T, Oishi S. Mirror-Image Human Serum Albumin Domain III as a Tool for Analyzing Site II-Dependent Molecular Recognition. Bioconjug Chem 2024; 35:816-825. [PMID: 38781049 DOI: 10.1021/acs.bioconjchem.4c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Human serum albumin (HSA) as a drug carrier can significantly improve the pharmacokinetic profiles of short-lived therapeutics. Conjugation of albumin-binding moieties (ABMs) to therapeutic agents may prolong their serum half-life by promoting their association with endogenous HSA. To discover a new molecular class of ABMs from mirror-image chemical space, a preparation protocol for bioactive HSA domain III and its d-enantiomer (d-HSA domain III) was established. Structural and functional analyses suggested that the synthetic protein enantiomers exhibited mirror-image structures and stereoselective neonatal fragement crystallizable receptor (FcRn) recognition. Additionally, the ligand-binding properties of synthetic l-HSA domain III were comparable with those of site II in native HSA, as confirmed using site II-selective fluorescent probes and an esterase substrate. Synthetic d-HSA domain III is an attractive tool for analyzing the site II-dependent molecular recognition properties of HSA.
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Affiliation(s)
- Naoya Iwamoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo ku, Kyoto 606-8501, Japan
| | - Takuma Kai
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo ku, Kyoto 606-8501, Japan
| | - Hitoshi Maeda
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Hiroshi Watanabe
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Toru Maruyama
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo ku, Kyoto 606-8501, Japan
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina ku, Kyoto 607-8412, Japan
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3
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Schmid A, Bello C, Becker CFW. Synthesis of N-Glycosylated Soluble Fas Ligand. Chemistry 2024; 30:e202400120. [PMID: 38363216 DOI: 10.1002/chem.202400120] [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: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/17/2024]
Abstract
Controlled cell death is essential for the regulation of the immune system and plays a role in pathogen defense. It is often altered in pathogenic conditions such as cancer, viral infections and autoimmune diseases. The Fas receptor and its corresponding membrane-bound ligand (FasL) are part of the extrinsic apoptosis pathway activated in these cases. A soluble form of FasL (sFasL), produced by ectodomain shedding, displays a diverse but still elusive set of non-apoptotic functions and sometimes even serves as a pro-survival factor. To gather more knowledge about the characteristics of this protein and the impact N-glycosylations may have, access to homogeneous posttranslationally modified variants of sFasL is needed. Therefore, we developed a flexible strategy to obtain such homogeneously N-glycosylated variants of sFasL by applying chemical protein synthesis. This strategy can be flexibly combined with enzymatic methods to introduce more complex, site selective glycosylations.
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Affiliation(s)
- Alanca Schmid
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria
| | - Claudia Bello
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino FI, Italy
| | - Christian F W Becker
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria
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4
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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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5
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Bosbach C, Gatzemeier LM, Bloch von Blottnitz KI, König A, Diederichsen U, Steinem C, Outeiro TF. Chemical synthesis of site-selective advanced glycation end products in α-synuclein and its fragments. Org Biomol Chem 2024; 22:2670-2676. [PMID: 38483440 DOI: 10.1039/d4ob00225c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Advanced glycation end products (AGEs) arise from the Maillard reaction between dicarbonyls and proteins, nucleic acids, or specific lipids. Notably, AGEs are linked to aging and implicated in various disorders, spanning from cancer to neurodegenerative diseases. While dicarbonyls like methylglyoxal preferentially target arginine residues, lysine-derived AGEs, such as N(6)-(1-carboxymethyl)lysine (CML) and N(6)-(1-carboxyethyl)lysine (CEL), are also abundant. Predicting protein glycation in vivo proves challenging due to the intricate nature of glycation reactions. In vitro, glycation is difficult to control, especially in proteins that harbor multiple glycation-prone amino acids. α-Synuclein (aSyn), pivotal in Parkinson's disease and synucleinopathies, has 15 lysine residues and is known to become glycated at multiple lysine sites. To understand the influence of glycation in specific regions of aSyn on its behavior, a strategy for site-specific glycated protein production is imperative. To fulfill this demand, we devised a synthetic route integrating solid-phase peptide synthesis, orthogonal protection of amino acid side-chain functionalities, and reductive amination strategies. This methodology yielded two disease-related N-terminal peptide fragments, each featuring five and six CML and CEL modifications, alongside a full-length aSyn protein containing a site-selective E46CEL modification. Our synthetic approach facilitates the broad introduction of glycation motifs at specific sites, providing a foundation for generating glycated forms of synucleinopathy-related and other disease-relevant proteins.
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Affiliation(s)
- Clara Bosbach
- Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Waldweg 33, 37073 Göttingen, Germany.
| | - Luisa Maria Gatzemeier
- Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Waldweg 33, 37073 Göttingen, Germany.
| | - Katja Ilme Bloch von Blottnitz
- Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Annekatrin König
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Waldweg 33, 37073 Göttingen, Germany.
| | - Ulf Diederichsen
- Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Waldweg 33, 37073 Göttingen, Germany.
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
- Max Planck Institute for Multidisciplinary Sciences, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
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6
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Li W, Jacobsen MT, Park C, Jung JU, Lin NP, Huang PS, Lal RA, Chou DHC. A cysteine-specific solubilizing tag strategy enables efficient chemical protein synthesis of difficult targets. Chem Sci 2024; 15:3214-3222. [PMID: 38425513 PMCID: PMC10901488 DOI: 10.1039/d3sc06032b] [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: 11/09/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
We developed a new cysteine-specific solubilizing tag strategy via a cysteine-conjugated succinimide. This solubilizing tag remains stable under common native chemical ligation conditions and can be efficiently removed with palladium-based catalysts. Utilizing this approach, we synthesized two proteins containing notably difficult peptide segments: interleukin-2 (IL-2) and insulin. This IL-2 chemical synthesis represents the simplest and most efficient approach to date, which is enabled by the cysteine-specific solubilizing tag to synthesize and ligate long peptide segments. Additionally, we synthesized a T8P insulin variant, previously identified in an infant with neonatal diabetes. We show that T8P insulin exhibits reduced bioactivity (a 30-fold decrease compared to standard insulin), potentially contributing to the onset of diabetes in these patients. In summary, our work provides an efficient tool to synthesize challenging proteins and opens new avenues for exploring research directions in understanding their biological functions.
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Affiliation(s)
- Wenchao Li
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Michael T Jacobsen
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Claire Park
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Jae Un Jung
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Nai-Pin Lin
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University Palo Alto CA 94305 USA
| | - Rayhan A Lal
- Division of Endocrinology, Department of Medicine, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Danny Hung-Chieh Chou
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
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7
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Iwamoto N, Sasaki J, Ohno S, Aoki K, Usui Y, Inuki S, Ohno H, Oishi S. Synthetic studies on the extracellular domain of the T cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) using Trt-K 10 solubilizing tags. Bioorg Med Chem 2024; 99:117585. [PMID: 38219557 DOI: 10.1016/j.bmc.2023.117585] [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: 11/23/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/16/2024]
Abstract
The T cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) is an inhibitory immunoreceptor expressed on lymphocytes that serves as a promising target for cancer immunotherapy. In this study, facile synthetic protocols to produce the extracellular domain of TIGIT were investigated for applications of TIGIT in mirror-image screening. During the synthesis via sequential native chemical ligations, we encountered problems with significantly poor solubility of the ligated products. Introducing trityl-type solubilizing auxiliaries, which also functioned as temporary protecting groups for cysteine residues, facilitated a flexible order of ligations and efficient purification protocols. After refolding under appropriate conditions, the synthetic TIGIT showed a sufficient affinity toward its target ligand CD155.
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Affiliation(s)
- Naoya Iwamoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jumpei Sasaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Saya Ohno
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Keisuke Aoki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Yusuke Usui
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.
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8
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Zhao J, Liu X, Liu J, Ye F, Wei B, Deng M, Li T, Huang P, Wang P. Chemical Synthesis Creates Single Glycoforms of the Ectodomain of Herpes Simplex Virus-1 Glycoprotein D. J Am Chem Soc 2024; 146:2615-2623. [PMID: 38117537 DOI: 10.1021/jacs.3c11543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Herpes simplex virus-1 (HSV-1) utilizes multiple viral surface glycoproteins to trigger virus entry and fusion. Among these glycoproteins, glycoprotein D (gD) functions as a receptor-binding protein, which makes it an attractive target for the development of vaccines against HSV-1 infection. Several recombinant gD subunit vaccines have been investigated in both preclinical and clinical phases with varying degrees of success. It is fundamentally critical to explore the functions of gD glycans. In light of this, we report an efficient synthetic platform to construct glycosylated gDs bearing homogeneous glycans at N94 and N121. The oligosaccharides were prepared by enzymatic synthesis and conjugated to peptidyl sectors. The glycoproteins were constructed via a combination of 7-(piperazin-1-yl)-2-(methyl)quinolinyl (PPZQ)-assisted expressed protein ligation and β-mercapto amino acid-assisted-desulfurization strategies. Biological studies showed that synthetic gDs exhibited potent in vivo activity in mice.
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Affiliation(s)
- Jie Zhao
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinliang Liu
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jialin Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Farong Ye
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bingcheng Wei
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Minggang Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tiehai Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ping Huang
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Wang
- Center for Chemical Glycobiology, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- Shenzhen Research Institute of Shanghai Jiao Tong University, Shenzhen 518057, China
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9
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Kar A, Jana M, Malik V, Sarkar A, Mandal K. Total Chemical Synthesis of the SARS-CoV-2 Spike Receptor-Binding Domain. Chemistry 2024; 30:e202302969. [PMID: 37815536 DOI: 10.1002/chem.202302969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
SARS-CoV-2 and its global spread have created an unprecedented public health crisis. The spike protein of SARS-CoV-2 has gained significant attention due to its crucial role in viral entry into host cells and its potential as both a prophylactic and a target for therapeutic interventions. Herein, we report the first successful total synthesis of the SARS-CoV-2 spike protein receptor binding domain (RBD), highlighting the key challenges and the strategies employed to overcome them. Appropriate utilization of advanced solid phase peptide synthesis and cutting-edge native chemical ligation methods have facilitated the synthesis of this moderately large protein molecule. We discuss the problems encountered during the chemical synthesis and approaches taken to optimize the yield and the purity of the synthetic protein molecule. Furthermore, we demonstrate that the chemically synthesized homogeneous spike RBD efficiently binds to the known mini-protein binder LCB1. The successful chemical synthesis of the spike RBD presented here can be utilized to gain valuable insights into SARS-CoV-2 spike RBD biology, advancing our understanding and aiding the development of intervention strategies to combat future coronavirus outbreaks. The modular synthetic approach described in this study can be effectively implemented in the synthesis of other mutated variants or enantiomer of the spike RBD for mirror-image drug discovery.
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Affiliation(s)
- Abhisek Kar
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Mrinmoy Jana
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Vishal Malik
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Arighna Sarkar
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Kalyaneswar Mandal
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
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10
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Duengo S, Muhajir MI, Hidayat AT, Musa WJA, Maharani R. Epimerisation in Peptide Synthesis. Molecules 2023; 28:8017. [PMID: 38138507 PMCID: PMC10745333 DOI: 10.3390/molecules28248017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/11/2023] [Accepted: 10/23/2023] [Indexed: 12/24/2023] Open
Abstract
Epimerisation is basically a chemical conversion that includes the transformation of an epimer into another epimer or its chiral partner. Epimerisation of amino acid is a side reaction that sometimes happens during peptide synthesis. It became the most avoided reaction because the process affects the overall conformation of the molecule, eventually even altering the bioactivity of the peptide. Epimerised products have a high similarity of physical characteristics, thus making it difficult for them to be purified. In regards to amino acids, epimerisation is very important in keeping the chirality of the assembled amino acids unchanged during the peptide synthesis and obtaining the desirable product without any problematic purification. In this review, we report several factors that induce epimerisation during peptide synthesis, including how to characterise and affect the bioactivities. To avoid undesirable epimerisation, we also describe several methods of suppressing the process.
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Affiliation(s)
- Suleman Duengo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia; (S.D.); (M.I.M.); (A.T.H.)
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Negeri Gorontalo, Gorontalo 96128, North Sulawesi, Indonesia;
| | - Muhamad Imam Muhajir
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia; (S.D.); (M.I.M.); (A.T.H.)
| | - Ace Tatang Hidayat
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia; (S.D.); (M.I.M.); (A.T.H.)
- Central Laboratory, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia
| | - Weny J. A. Musa
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Negeri Gorontalo, Gorontalo 96128, North Sulawesi, Indonesia;
| | - Rani Maharani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia; (S.D.); (M.I.M.); (A.T.H.)
- Central Laboratory, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia
- Research Collaboration Centre for Theranostic Radiopharmaceutical, National Research and Innovation Agency (BRIN), Sumedang 45363, West Java, Indonesia
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11
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Iwamoto N, Sato Y, Manabe A, Inuki S, Ohno H, Nonaka M, Oishi S. Design and Synthesis of Monobody Variants with Low Immunogenicity. ACS Med Chem Lett 2023; 14:1596-1601. [PMID: 37974939 PMCID: PMC10641909 DOI: 10.1021/acsmedchemlett.3c00342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 11/19/2023] Open
Abstract
Mirror-image proteins (d-proteins) are promising scaffolds for drug discovery because of their high proteolytic stability and low immunogenic properties. Facile and reproducible processes for the preparation of functional d-proteins are required for their application in therapeutic biologics. In this study, we designed and synthesized a novel monobody variant with two cysteine substitutions that facilitate the synthetic process via sequential native chemical ligations and improve protein stability by disulfide bond formation. The synthetic anti-GFP monobody in this model study exhibited good binding affinity to the target enhanced green fluorescent protein. In vivo administration of the synthetic anti-GFP monobody (l-monobody) to mice induced antidrug antibody (ADA) production, whereas no ADA production was observed following immunization with the mirror-image anti-GFP monobody (d-monobody). These results suggest that the synthetic d-monobody is a non-antibody protein scaffold with low immunogenic properties.
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Affiliation(s)
- Naoya Iwamoto
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukino Sato
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Asako Manabe
- Graduate
School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinsuke Inuki
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Motohiro Nonaka
- Graduate
School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinya Oishi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
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12
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Abstract
Deposits of the microtubule-associated protein Tau (MAPT) serve as a hallmark of neurodegenerative diseases known as tauopathies. Numerous studies have demonstrated that in diseases such as Alzheimer's disease (AD), Tau undergoes extensive remodeling. The attachment of post-translational modifications distributed throughout the entire sequence of the protein correlates with clinical presentation. A systematic examination of these protein alterations can shed light on their roles in both healthy and diseased states. However, the ability to access these modifications in the entire protein chain is limited as Tau can only be produced recombinantly or through semisynthesis. In this article, we describe the first chemical synthesis of the longest 2N4R isoform of Tau, consisting of 441 amino acids. The 2N4R Tau was divided into 3 major segments and a total of 11 fragments, all of which were prepared via solid-phase peptide synthesis. The successful chemical strategy has relied on the strategic use of two cysteine sites (C291 and C322) for the native chemical ligations (NCLs). This was combined with modern preparative protein chemistries, such as mercaptothreonine ligation (T205), diselenide-selenoester ligation (D358), and mutations of mercaptoamino acids into native residues via homogeneous radical desulfurization (A40, A77, A119, A157, A246, and A390). The successful completion of the synthesis has established a robust and scalable route to the native protein in multimilligram quantities and high purity. In broader terms, the presented strategy can be applied to the preparation of other shorter isoforms of Tau as well as to introduce all post-translational modifications that are characteristic of tauopathies such as AD.
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Affiliation(s)
- Wyatt C Powell
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Ruiheng Jing
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Maciej A Walczak
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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13
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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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14
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Ho TNT, Pham SH, Nguyen LTT, Nguyen HT, Nguyen LT, Dang TT. Insights into the synthesis strategies of plant-derived cyclotides. Amino Acids 2023:10.1007/s00726-023-03271-8. [PMID: 37142771 DOI: 10.1007/s00726-023-03271-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Cyclotides are plant peptides characterized with a head-to-tail cyclized backbone and three interlocking disulfide bonds, known as a cyclic cysteine knot. Despite the variations in cyclotides peptide sequences, this core structure is conserved, underlying their most useful feature: stability against thermal and chemical breakdown. Cyclotides are the only natural peptides known to date that are orally bioavailable and able to cross cell membranes. Cyclotides also display bioactivities that have been exploited and expanded to develop as potential therapeutic reagents for a wide range of conditions (e.g., HIV, inflammatory conditions, multiple sclerosis, etc.). As such, in vitro production of cyclotides is of the utmost importance since it could assist further research on this peptide class, specifically the structure-activity relationship and its mechanism of action. The information obtained could be utilized to assist drug development and optimization. Here, we discuss several strategies for the synthesis of cyclotides using both chemical and biological routes.
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Affiliation(s)
- Thao N T Ho
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Son H Pham
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Linh T T Nguyen
- Department of Chemistry, Ho Chi Minh City University of Education, 280 An Duong Vuong Street, District 5, Ho Chi Minh City, Viet Nam
| | - Ha T Nguyen
- National Key Laboratory of Polymer and Composite Materials, Department of Energy Materials, Faculty of Materials Technology, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Luan T Nguyen
- National Key Laboratory of Polymer and Composite Materials, Department of Energy Materials, Faculty of Materials Technology, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Tien T Dang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam.
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15
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Suzuki S, Nakajima Y, Kamo N, Osakabe A, Okamoto A, Hayashi G, Murakami H. Thiocholine-Mediated One-Pot Peptide Ligation and Desulfurization. Molecules 2023; 28:molecules28093655. [PMID: 37175065 PMCID: PMC10179797 DOI: 10.3390/molecules28093655] [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: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Thiol catalysts are essential in native chemical ligation (NCL) to increase the reaction efficiency. In this paper, we report the use of thiocholine in chemical protein synthesis, including NCL-based peptide ligation and metal-free desulfurization. Evaluation of thiocholine peptide thioester in terms of NCL and hydrolysis kinetics revealed its practical utility, which was comparable to that of other alkyl thioesters. Importantly, thiocholine showed better reactivity as a thiol additive in desulfurization, which is often used in chemical protein synthesis to convert Cys residues to more abundant Ala residues. Finally, we achieved chemical synthesis of two differently methylated histone H3 proteins via one-pot NCL and desulfurization with thiocholine.
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Affiliation(s)
- Sae Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yuya Nakajima
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Naoki Kamo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akihisa Osakabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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16
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Pehlivan Ö, Waliczek M, Kijewska M, Stefanowicz P. Selenium in Peptide Chemistry. Molecules 2023; 28:molecules28073198. [PMID: 37049961 PMCID: PMC10096412 DOI: 10.3390/molecules28073198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/29/2023] [Accepted: 04/02/2023] [Indexed: 04/07/2023] Open
Abstract
In recent years, researchers have been exploring the potential of incorporating selenium into peptides, as this element possesses unique properties that can enhance the reactivity of these compounds. Selenium is a non-metallic element that has a similar electronic configuration to sulfur. However, due to its larger atomic size and lower electronegativity, it is more nucleophilic than sulfur. This property makes selenium more reactive toward electrophiles. One of the most significant differences between selenium and sulfur is the dissociation of the Se-H bond. The Se-H bond is more easily dissociated than the S-H bond, leading to higher acidity of selenocysteine (Sec) compared to cysteine (Cys). This difference in acidity can be exploited to selectively modify the reactivity of peptides containing Sec. Furthermore, Se-H bonds in selenium-containing peptides are more susceptible to oxidation than their sulfur analogs. This property can be used to selectively modify the peptides by introducing new functional groups, such as disulfide bonds, which are important for protein folding and stability. These unique properties of selenium-containing peptides have found numerous applications in the field of chemical biology. For instance, selenium-containing peptides have been used in native chemical ligation (NCL). In addition, the reactivity of Sec can be harnessed to create cyclic and stapled peptides. Other chemical modifications, such as oxidation, reduction, and photochemical reactions, have also been applied to selenium-containing peptides to create novel molecules with unique biological properties.
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Affiliation(s)
- Özge Pehlivan
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Monika Kijewska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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17
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Digal LD, Kirkeby EK, Austin MJ, Roberts AG. Design and Evaluation of Ambiphilic Aryl Thiol-Iminium-Based Molecules for Organocatalyzed Thioacyl Aminolysis. ACS OMEGA 2023; 8:9319-9325. [PMID: 36936301 PMCID: PMC10018527 DOI: 10.1021/acsomega.2c07586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Progress toward the design and synthesis of ambiphilic aryl thiol-iminium-based small molecules for organocatalyzed thioacyl aminolysis is reported. Here we describe the synthesis of a novel tetrahydroisoquinoline-derived scaffold, bearing both thiol and iminium functionalities, capable of promoting the transthioesterification and subsequent amine capture reactions necessary to achieve organocatalyzed thioacyl aminolysis. Model studies demonstrate the ability of this designed organocatalyst to deliver critical intermediates capable of undergoing these individual reactions necessary for the proposed process. Future design improvements and directions toward cysteine-independent organocatalyzed native chemical ligation are discussed.
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18
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Brazeau-Henrie JT, Paquette AR, Boddy CN. In Vitro Biochemical Characterization of Excised Macrocyclizing Thioesterase Domains from Non-ribosomal Peptide Synthetases. Methods Mol Biol 2023; 2670:101-125. [PMID: 37184701 DOI: 10.1007/978-1-0716-3214-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Characterization of thioesterases (TEs) is an important step in understanding natural product biosynthesis. Studying non-ribosomal peptide synthetase (NRPS) TEs presents a unique set of challenges with specific cloning and expression issues as well as the challenging synthesis of the thioester peptides substrate required for characterization of the TE. In this method, we describe the cloning and expression of NRPS TEs, the synthesis of thioester peptides, and the in vitro biochemical characterization of the enzyme.
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Affiliation(s)
| | - André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada.
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19
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Huppelschoten Y, Elhebieshy AF, Hameed DS, Sapmaz A, Buchardt J, Nielsen TE, Ovaa H, van der Heden van Noort GJ. Total Chemical Synthesis of a Functionalized GFP Nanobody. Chembiochem 2022; 23:e202200304. [PMID: 35920208 PMCID: PMC9804225 DOI: 10.1002/cbic.202200304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 01/05/2023]
Abstract
Chemical protein synthesis has proven to be a powerful tool to access homogenously modified proteins. The chemical synthesis of nanobodies (Nb) would create possibilities to design tailored Nbs with a range of chemical modifications such as tags, linkers, reporter groups, and subsequently, Nb-drug conjugates. Herein, we describe the total chemical synthesis of a 123 amino-acid Nb against GFP. A native chemical ligation- desulfurization strategy was successfully applied for the synthesis of this GFP Nb, modified with a propargyl (PA) moiety for on-demand functionalization. Biophysical characterization indicated that the synthetic GFP Nb-PA was correctly folded after internal disulfide bond formation. The synthetic Nb-PA was functionalized with a biotin or a sulfo-cyanine5 dye by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), resulting in two distinct probes used for functional in vitro validation in pull-down and confocal microscopy settings.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands,Global Research Technologies, Novo NordiskNovo Nordisk Park2760MåløvDenmark
| | - Angela F. Elhebieshy
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
| | - Dharjath S. Hameed
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
| | - Aysegul Sapmaz
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
| | - Jens Buchardt
- Global Research Technologies, Novo NordiskNovo Nordisk Park2760MåløvDenmark
| | - Thomas E. Nielsen
- Global Research Technologies, Novo NordiskNovo Nordisk Park2760MåløvDenmark
| | - Huib Ovaa
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
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20
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Kerul L, Schrems M, Schmid A, Meli R, Becker CFW, Bello C. Semisynthesis of Homogeneous, Active Granulocyte Colony-Stimulating Factor Glycoforms. Angew Chem Int Ed Engl 2022; 61:e202206116. [PMID: 35853828 PMCID: PMC9804750 DOI: 10.1002/anie.202206116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 01/09/2023]
Abstract
Granulocyte colony stimulating factor (G-CSF) is a cytokine used to treat neutropenia. Different glycosylated and non-glycosylated variants of G-CSF for therapeutic application are currently generated by recombinant expression. Here, we describe our approaches to establish a first semisynthesis strategy to access the aglycone and O-glycoforms of G-CSF, thereby enabling the preparation of selectively and homogeneously post-translationally modified variants of this important cytokine. Eventually, we succeeded by combining selenocysteine ligation of a recombinantly produced N-terminal segment with a synthetic C-terminal part, transiently equipped with a side-chain-linked, photocleavable PEG moiety, at low concentration. The transient PEGylation enabled quantitative enzymatic elongation of the carbohydrate at Thr133. Overall, we were able to significantly reduce the problems related to the low solubility and the tendency to aggregate of the two protein segments, which allowed the preparation of four G-CSF variants that were successfully folded and demonstrated biological activity in cell proliferation assays.
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Affiliation(s)
- Lukas Kerul
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
| | - Maximilian Schrems
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
| | - Alanca Schmid
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
| | - Rajeshwari Meli
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
| | - Christian F. W. Becker
- Institute of Biological Chemistry, Faculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
| | - Claudia Bello
- Interdepartmental Research Unit of Peptide and Protein Chemistry and BiologyDepartment of Chemistry “Ugo Schiff”University of Florencevia della Lastruccia 1350019Sesto Fiorentino (Florence)Italy
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21
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Roles of Focal Adhesion Kinase PTK2 and Integrin αIIbβ3 Signaling in Collagen- and GPVI-Dependent Thrombus Formation under Shear. Int J Mol Sci 2022; 23:ijms23158688. [PMID: 35955827 PMCID: PMC9369275 DOI: 10.3390/ijms23158688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
Glycoprotein (GP)VI and integrin αIIbβ3 are key signaling receptors in collagen-dependent platelet aggregation and in arterial thrombus formation under shear. The multiple downstream signaling pathways are still poorly understood. Here, we focused on disclosing the integrin-dependent roles of focal adhesion kinase (protein tyrosine kinase 2, PTK2), the shear-dependent collagen receptor GPR56 (ADGRG1 gene), and calcium and integrin-binding protein 1 (CIB1). We designed and synthetized peptides that interfered with integrin αIIb binding (pCIB and pCIBm) or mimicked the activation of GPR56 (pGRP). The results show that the combination of pGRP with PTK2 inhibition or of pGRP with pCIB > pCIBm in additive ways suppressed collagen- and GPVI-dependent platelet activation, thrombus buildup, and contraction. Microscopic thrombus formation was assessed by eight parameters (with script descriptions enclosed). The suppressive rather than activating effects of pGRP were confined to blood flow at a high shear rate. Blockage of PTK2 or interference of CIB1 no more than slightly affected thrombus formation at a low shear rate. Peptides did not influence GPVI-induced aggregation and Ca2+ signaling in the absence of shear. Together, these data reveal a shear-dependent signaling axis of PTK2, integrin αIIbβ3, and CIB1 in collagen- and GPVI-dependent thrombus formation, which is modulated by GPR56 and exclusively at high shear. This work thereby supports the role of PTK2 in integrin αIIbβ3 activation and signaling.
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22
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Kerul L, Schrems M, Schmid A, Meli R, Becker CF, Bello C. Semisynthesis of Homogeneous, Active Granulocyte Colony‐Stimulating Factor Glycoforms. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lukas Kerul
- University of Vienna: Universitat Wien Chemistry AUSTRIA
| | | | - Alanca Schmid
- University of Vienna: Universitat Wien Chemistry AUSTRIA
| | | | - Christian F.W. Becker
- Universitat Wien Institute of Biological Chemistry Währinger Str. 38 1090 Vienna AUSTRIA
| | - Claudia Bello
- University of Florence: Universita degli Studi di Firenze Chemistry ITALY
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23
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Lomont JP, Smith JP. In situ Raman spectroscopy for real time detection of cysteine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 274:121068. [PMID: 35276471 DOI: 10.1016/j.saa.2022.121068] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Cysteine serves a wide range of important biological and chemical functions and may have an association to neurodegenerative disease and cancer. Rapid, accurate analytical methods for cysteine detection are thus highly desirable. In this work, we report an investigation into the utility of in situ Raman spectroscopy as a Process Analytical Technology (PAT) for real time monitoring of cysteine. Cysteine concentrations are tracked in real time using Raman spectroscopy across a range of pharmaceutically-relevant concentrations, demonstrating the capability of Raman spectroscopy detection for in situ cysteine monitoring. The concentration range over which this analytical methodology can be applied is successfully established. As such, the results herein serve as a proof-of-principle investigation to demonstrate and evaluate the capabilities of a real time Raman spectroscopic approach for in situ cysteine detection, thus informing the range of important chemical and biological processes to which this approach can be applied. To the best of our knowledge, this is the first report of in situ Raman spectroscopy for real time monitoring of dynamically changing cysteine process concentrations.
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Affiliation(s)
- Justin P Lomont
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA
| | - Joseph P Smith
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA.
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24
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Clark ET, Sievers EE, Debelouchina GT. A Chemical Biology Primer for NMR Spectroscopists. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100044. [PMID: 35494416 PMCID: PMC9053072 DOI: 10.1016/j.jmro.2022.100044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Among structural biology techniques, NMR spectroscopy offers unique capabilities that enable the atomic resolution studies of dynamic and heterogeneous biological systems under physiological and native conditions. Complex biological systems, however, often challenge NMR spectroscopists with their low sensitivity, crowded spectra or large linewidths that reflect their intricate interaction patterns and dynamics. While some of these challenges can be overcome with the development of new spectroscopic approaches, chemical biology can also offer elegant and efficient solutions at the sample preparation stage. In this tutorial, we aim to present several chemical biology tools that enable the preparation of selectively and segmentally labeled protein samples, as well as the introduction of site-specific spectroscopic probes and post-translational modifications. The four tools covered here, namely cysteine chemistry, inteins, native chemical ligation, and unnatural amino acid incorporation, have been developed and optimized in recent years to be more efficient and applicable to a wider range of proteins than ever before. We briefly introduce each tool, describe its advantages and disadvantages in the context of NMR experiments, and offer practical advice for sample preparation and analysis. We hope that this tutorial will introduce beginning researchers in the field to the possibilities chemical biology can offer to NMR spectroscopists, and that it will inspire new and exciting applications in the quest to understand protein function in health and disease.
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Affiliation(s)
- Evan T. Clark
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Elanor E. Sievers
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Corresponding author: Galia Debelouchina, University of California, San Diego, Natural Sciences Building 4322, 9500 Gilman Dr., La Jolla, CA 92093, 858-534-3038,
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25
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Guan I, Williams K, Liu JST, Liu X. Synthetic Thiol and Selenol Derived Amino Acids for Expanding the Scope of Chemical Protein Synthesis. Front Chem 2022; 9:826764. [PMID: 35237567 PMCID: PMC8883728 DOI: 10.3389/fchem.2021.826764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/29/2021] [Indexed: 01/18/2023] Open
Abstract
Cells employ post-translational modifications (PTMs) as key mechanisms to expand proteome diversity beyond the inherent limitations of a concise genome. The ability to incorporate post-translationally modified amino acids into protein targets via chemical ligation of peptide fragments has enabled the access to homogeneous proteins bearing discrete PTM patterns and empowered functional elucidation of individual modification sites. Native chemical ligation (NCL) represents a powerful and robust means for convergent assembly of two homogeneous, unprotected peptides bearing an N-terminal cysteine residue and a C-terminal thioester, respectively. The subsequent discovery that protein cysteine residues can be chemoselectively desulfurized to alanine has ignited tremendous interest in preparing unnatural thiol-derived variants of proteogenic amino acids for chemical protein synthesis following the ligation-desulfurization logic. Recently, the 21st amino acid selenocysteine, together with other selenyl derivatives of amino acids, have been shown to facilitate ultrafast ligation with peptidyl selenoesters, while the advancement in deselenization chemistry has provided reliable bio-orthogonality to PTMs and other amino acids. The combination of these ligation techniques and desulfurization/deselenization chemistries has led to streamlined synthesis of multiple structurally-complex, post-translationally modified proteins. In this review, we aim to summarize the latest chemical synthesis of thiolated and selenylated amino-acid building blocks and exemplify their important roles in conquering challenging protein targets with distinct PTM patterns.
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Affiliation(s)
- Ivy Guan
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
- The Heart Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Kayla Williams
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
- The Heart Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Joanna Shu Ting Liu
- The Heart Research Institute, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Xuyu Liu
- School of Chemistry, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
- The Heart Research Institute, The University of Sydney, Sydney, NSW, Australia
- *Correspondence: Xuyu Liu,
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26
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Chemical Synthesis of a Functional Fluorescent-Tagged α-Bungarotoxin. Toxins (Basel) 2022; 14:toxins14020079. [PMID: 35202107 PMCID: PMC8879871 DOI: 10.3390/toxins14020079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 11/30/2022] Open
Abstract
α-bungarotoxin is a large, 74 amino acid toxin containing five disulphide bridges, initially identified in the venom of Bungarus multicinctus snake. Like most large toxins, chemical synthesis of α-bungarotoxin is challenging, explaining why all previous reports use purified or recombinant α-bungarotoxin. However, only chemical synthesis allows easy insertion of non-natural amino acids or new chemical functionalities. Herein, we describe a procedure for the chemical synthesis of a fluorescent-tagged α-bungarotoxin. The full-length peptide was designed to include an alkyne function at the amino-terminus through the addition of a pentynoic acid linker. Chemical synthesis of α-bungarotoxin requires hydrazide-based coupling of three peptide fragments in successive steps. After completion of the oxidative folding, an azide-modified Cy5 fluorophore was coupled by click chemistry onto the toxin. Next, we determined the efficacy of the fluorescent-tagged α-bungarotoxin to block acetylcholine (ACh)-mediated currents in response to muscle nicotinic receptor activation in TE671 cells. Using automated patch-clamp recordings, we demonstrate that fluorescent synthetic α-bungarotoxin has the expected nanomolar affinity for the nicotinic receptor. The blocking effect of fluorescent α-bungarotoxin could be displaced by incubation with a 20-mer peptide mimicking the α-bungarotoxin binding site. In addition, TE671 cells could be labelled with fluorescent toxin, as witnessed by confocal microscopy, and this labelling was partially displaced by the 20-mer competitive peptide. We thus demonstrate that synthetic fluorescent-tagged α-bungarotoxin preserves excellent properties for binding onto muscle nicotinic receptors.
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27
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Zhang D, Wang Z, Hu S, Chan NY, Liew HT, Lescar J, Tam JP, Liu CF. Asparaginyl Endopeptidase-Mediated Protein C-Terminal Hydrazinolysis for the Synthesis of Bioconjugates. Bioconjug Chem 2022; 33:238-247. [PMID: 34985285 DOI: 10.1021/acs.bioconjchem.1c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asparaginyl endopeptidases (AEPs) are cysteinyl enzymes naturally catalyzing the hydrolysis and transpeptidation reactions at Asx-Xaa bonds. These reactions go by a common acyl-enzyme thioester intermediate, which is either attacked by water (for a protease-AEP) or by a peptidic amine nucleophile (for a ligase-AEP) to form the respective hydrolysis or aminolysis product. Herein, we show that hydrazine and hydroxylamine, two α-effect nucleophiles, are capable of resolving the thioester intermediate to yield peptide and protein products containing a C-terminal hydrazide and hydroxamic acid functionality, respectively. The hydrazinolysis reaction exhibits very high efficiency and can be completed in minutes at a low enzyme-to-substrate ratio. We further show the utility of the so-formed asparaginyl hydrazide in native chemical ligation and hydrazone conjugation. Using an EGFR-targeting affibody as a model protein, we have showcased our methodology in the preparation of a number of protein ligation or conjugation products, which are decorated with various functional moieties. The ZEGFR affibody-doxorubicin conjugate shows high selective binding and cytotoxicity toward the EGFR-positive A431 cells. Our results demonstrate the advantages of AEP-mediated protein hydrazinolysis as a simple and straightforward strategy for the precision manufacturing of protein bioconjugates.
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Affiliation(s)
- Dingpeng Zhang
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Zhen Wang
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Side Hu
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Ning-Yu Chan
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Heng Tai Liew
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Julien Lescar
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - James P Tam
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Chuan-Fa Liu
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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28
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Jacobsen MT, Spaltenstein P, Giesler RJ, Chou DHC, Kay MS. Improved Handling of Peptide Segments Using Side Chain-Based "Helping Hand" Solubilizing Tools. Methods Mol Biol 2022; 2530:81-107. [PMID: 35761044 DOI: 10.1007/978-1-0716-2489-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Maintaining high, or even sufficient, solubility of every peptide segment in chemical protein synthesis (CPS) remains a critical challenge; insolubility of just a single peptide segment can thwart a total synthesis venture. Multiple approaches have been used to address this challenge, most commonly by employing a chemical tool to temporarily improve peptide solubility. In this chapter, we discuss chemical tools for introducing semipermanent solubilizing sequences (termed helping hands) at the side chains of Lys and Glu residues. We describe the synthesis, incorporation by Fmoc-SPPS, and cleavage conditions for utilizing these two tools. For Lys sites, we discuss the Fmoc-Ddap-OH dimedone-based linker, which is achiral, synthesized in one step, can be introduced directly at primary amines, and is removed using hydroxylamine (or hydrazine). For Glu sites, we detail the new Fmoc-SPPS building block, Fmoc-Glu(AlHx)-OH, which can be prepared in an efficient process over two purifications. Solubilizing sequences are introduced directly on-resin and later cleaved with palladium-catalyzed transfer under aqueous conditions to restore a native Glu side chain. These two chemical tools are straightforward to prepare and implement, and we anticipate continued usage in "difficult" peptide segments following the protocols described herein.
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Affiliation(s)
- Michael T Jacobsen
- Division of Diabetes and Endocrinology, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Paul Spaltenstein
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Riley J Giesler
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Danny Hung-Chieh Chou
- Division of Diabetes and Endocrinology, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Michael S Kay
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
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29
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Chong YK, Chandrashekar C, Zhao D, Maki Y, Okamoto R, Kajihara Y. Optimization of Semisynthetic Approach for Glycosyl Interferon-β-polypeptide by Utilizing Bacterial Protein Expression and Chemical Modification. Org Biomol Chem 2022; 20:1907-1915. [DOI: 10.1039/d1ob02391h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of a sufficient amount of homogenous glycoprotein is of great interest because the natural glycoproteins show a considerable heterogeneity in oligosaccharide structures making the studies of glycan structure-function relationship...
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30
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Tvardovskiy A, Nguyen N, Bartke T. Identifying Specific Protein Interactors of Nucleosomes Carrying Methylated Histones Using Quantitative Mass Spectrometry. Methods Mol Biol 2022; 2529:327-403. [PMID: 35733023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chemical modification of histone proteins by methylation plays a central role in chromatin regulation by recruiting epigenetic "readers" via specialized binding domains. Depending on the degree of methylation, the exact modified amino acid, and the associated reader proteins histone methylations are involved in the regulation of all DNA-based processes, such as transcription, DNA replication, and DNA repair. Here we present methods to identify histone methylation readers using a mass spectrometry-linked nucleosome affinity purification approach. We provide detailed protocols for the generation of semisynthetic methylated histones, their assembly into biotinylated nucleosomes, and the identification of methylation-specific nucleosome-interacting proteins from nuclear extracts via nucleosome pull-downs and label-free quantitative proteomics. Due to their versatility, these protocols allow the identification of readers of various histone methylations, and can also be adapted to different cell types and tissues, and other types of modifications.
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Affiliation(s)
- Andrey Tvardovskiy
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nhuong Nguyen
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
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31
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Butts M, Nam Chu. Utilizing a Baculovirus/Insect Cell Expression System and Expressed Protein Ligation (EPL) for Protein Semisynthesis. Curr Protoc 2022; 2:e348. [PMID: 35044726 PMCID: PMC8855479 DOI: 10.1002/cpz1.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein semisynthesis has been used for the chemoselective linking of synthetic peptides and recombinant protein fragments to generate complete native proteins in good yield. The ability to site-selectively incorporate multiple post-translational chemical modifications (PTMs) into proteins via this approach shows great potential for enhancing understanding of the molecular basis of protein function and regulation. Protein semisynthesis, however, often requires high expression efficiency of the recombinant protein fragments (i.e., high expression yield and ability to preserve protein biological functions), which can be hard to achieve for some human enzymes when using bacterial expression systems. Here, we describe how to use a baculovirus/insect cell expression system and a protein semisynthesis strategy known as expressed protein ligation (EPL) to produce workable levels of proteins of interest containing site-specific chemical modifications. The protocol provides detailed guidance for generating protein C-terminal thioesters for use with the EPL reaction, performing the EPL reaction, and purifying the protein ligation product. We exemplify the protocols by generating protein kinase Akt1 with site-specific phosphorylations installed into its C-terminal tail, for kinetic kinase assays. We hope these methods will help increase the use of protein semisynthesis for elucidating the post-translational regulation of human enzymes involved in cell signaling. © 2022 Wiley Periodicals LLC Basic Protocol 1: Generation of the N-terminal protein of interest (POI) fragment containing a C-terminal thioester moiety Basic Protocol 2: Expressed protein ligation (EPL) of the protein thioester with a synthetic peptide and purification of the protein ligation product Basic Protocol 3: Semisynthesis and biochemical analysis of site-specifically phosphorylated Akt1.
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Affiliation(s)
- Marie Butts
- Department of Cancer Biology and Genetics, the Comprehensive Cancer Center, College of Medicine, The Ohio State University; Columbus, OH 43210, USA
| | - Nam Chu
- Department of Cancer Biology and Genetics, the Comprehensive Cancer Center, College of Medicine, The Ohio State University; Columbus, OH 43210, USA,Corresponding author:
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32
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Chaudhuri D, Ganesan R, Vogelaar A, Dughbaj MA, Beringer PM, Camarero JA. Chemical Synthesis of a Potent Antimicrobial Peptide Murepavadin Using a Tandem Native Chemical Ligation/Desulfurization Reaction. J Org Chem 2021; 86:15242-15246. [PMID: 34641669 DOI: 10.1021/acs.joc.1c01858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Classical approaches for the backbone cyclization of polypeptides require conditions that may compromise the chirality of the C-terminal residue during the activation step of the cyclization reaction. Here, we describe an efficient epimerization-free approach for the Fmoc-based synthesis of murepavadin using intramolecular native chemical ligation in combination with a concomitant desulfurization reaction. Using this approach, bioactive murepavadin was produced in a good yield in two steps. The synthetic peptide antibiotic showed potent activity against different clinical isolates of P. aeruginosa. This approach can be easily adapted for the production of murepavadin analogues and other backbone-cyclized peptides.
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Affiliation(s)
- Dipankar Chaudhuri
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
| | - Rajasekaran Ganesan
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
| | - Alicia Vogelaar
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
| | - Mansour A Dughbaj
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
| | - Paul M Beringer
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States.,Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
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33
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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 PMCID: PMC9769386 DOI: 10.1021/acs.bioconjchem.1c00403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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34
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Ackermann BE, Debelouchina GT. Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology. Front Mol Biosci 2021; 8:741581. [PMID: 34708075 PMCID: PMC8544521 DOI: 10.3389/fmolb.2021.741581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic genome is packaged into chromatin, a polymer of DNA and histone proteins that regulates gene expression and the spatial organization of nuclear content. The repetitive character of chromatin is diversified into rich layers of complexity that encompass DNA sequence, histone variants and post-translational modifications. Subtle molecular changes in these variables can often lead to global chromatin rearrangements that dictate entire gene programs with far reaching implications for development and disease. Decades of structural biology advances have revealed the complex relationship between chromatin structure, dynamics, interactions, and gene expression. Here, we focus on the emerging contributions of magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS NMR), a relative newcomer on the chromatin structural biology stage. Unique among structural biology techniques, MAS NMR is ideally suited to provide atomic level information regarding both the rigid and dynamic components of this complex and heterogenous biological polymer. In this review, we highlight the advantages MAS NMR can offer to chromatin structural biologists, discuss sample preparation strategies for structural analysis, summarize recent MAS NMR studies of chromatin structure and dynamics, and close by discussing how MAS NMR can be combined with state-of-the-art chemical biology tools to reconstitute and dissect complex chromatin environments.
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Affiliation(s)
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
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35
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Spiller S, Wippold T, Bellmann-Sickert K, Franz S, Saalbach A, Anderegg U, Beck-Sickinger AG. Protease-Triggered Release of Stabilized CXCL12 from Coated Scaffolds in an Ex Vivo Wound Model. Pharmaceutics 2021; 13:pharmaceutics13101597. [PMID: 34683890 PMCID: PMC8539926 DOI: 10.3390/pharmaceutics13101597] [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: 08/27/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
Biomaterials are designed to improve impaired healing of injured tissue. To accomplish better cell integration, we suggest to coat biomaterial surfaces with bio-functional proteins. Here, a mussel-derived surface-binding peptide is used and coupled to CXCL12 (stromal cell-derived factor 1α), a chemokine that activates CXCR4 and consequently recruits tissue-specific stem and progenitor cells. CXCL12 variants with either non-releasable or protease-mediated-release properties were designed and compared. Whereas CXCL12 was stabilized at the N-terminus for protease resistance, a C-terminal linker was designed that allowed for specific cleavage-mediated release by matrix metalloproteinase 9 and 2, since both enzymes are frequently found in wound fluid. These surface adhesive CXCL12 derivatives were produced by expressed protein ligation. Functionality of the modified chemokines was assessed by inositol phosphate accumulation and cell migration assays. Increased migration of keratinocytes and primary mesenchymal stem cells was demonstrated. Immobilization and release were studied for bioresorbable PCL-co-LC scaffolds, and accelerated wound closure was demonstrated in an ex vivo wound healing assay on porcine skin grafts. After 24 h, a significantly improved CXCL12-specific growth stimulation of the epithelial tips was already observed. The presented data display a successful application of protein-coated biomaterials for skin regeneration.
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Affiliation(s)
- Sabrina Spiller
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; (S.S.); (K.B.-S.)
| | - Tom Wippold
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
| | - Kathrin Bellmann-Sickert
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; (S.S.); (K.B.-S.)
| | - Sandra Franz
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
| | - Anja Saalbach
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
| | - Ulf Anderegg
- Department of Dermatology, Venerology and Allergology, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany; (T.W.); (S.F.); (A.S.)
- Correspondence: (U.A.); (A.G.B.-S.); Tel.: +49-341-972-5881 (U.A.); +49-341-973-6900 (A.G.B.-S.); Fax: +49-341-972-5878 (U.A.); +49-341-973-6909 (A.G.B.-S.)
| | - Annette G. Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; (S.S.); (K.B.-S.)
- Correspondence: (U.A.); (A.G.B.-S.); Tel.: +49-341-972-5881 (U.A.); +49-341-973-6900 (A.G.B.-S.); Fax: +49-341-972-5878 (U.A.); +49-341-973-6909 (A.G.B.-S.)
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36
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Miao X, Paikar A, Lerner B, Diskin‐Posner Y, Shmul G, Semenov SN. Kinetic Selection in the Out‐of‐Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105790] [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)
- Xiaoming Miao
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Arpita Paikar
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Benjamin Lerner
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Yael Diskin‐Posner
- Department of Chemical Research Support Weizmann Institute of Science Rehovot 7610001 Israel
| | - Guy Shmul
- Department of Chemical Research Support Weizmann Institute of Science Rehovot 7610001 Israel
| | - Sergey N. Semenov
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
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37
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Dao Y, Wang B, Dong W, Zhang J, Zhong C, Zhang Z, Dong S. Facile Generation of Strained Peptidyl Thiolactones from Hydrazides and Its Application in Assembling
MUC
‐1
VNTR
Oligomers
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yuankun Dao
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
- Institute of Systems Biomedicine, School of Basic Medical Sciences Peking University Health Science Center Beijing 100191 China
| | - Biao Wang
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Weidong Dong
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Jun Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Chao Zhong
- Institute of Systems Biomedicine, School of Basic Medical Sciences Peking University Health Science Center Beijing 100191 China
| | - Zhili Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, and Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
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38
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Miao X, Paikar A, Lerner B, Diskin-Posner Y, Shmul G, Semenov SN. Kinetic Selection in the Out-of-Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides. Angew Chem Int Ed Engl 2021; 60:20366-20375. [PMID: 34144635 DOI: 10.1002/anie.202105790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/03/2021] [Indexed: 02/05/2023]
Abstract
Autocatalytic reaction networks are instrumental for validating scenarios for the emergence of life on Earth and for synthesizing life de novo. Here, we demonstrate that dimeric thioesters of tripeptides with the general structure (Cys-Xxx-Gly-SEt)2 form strongly interconnected autocatalytic reaction networks that predominantly generate macrocyclic peptides up to 69 amino acids long. Some macrocycles of 6-12 amino acids were isolated from the product pool and were characterized by NMR spectroscopy and single-crystal X-ray analysis. We studied the autocatalytic formation of macrocycles in a flow reactor in the presence of acrylamide, whose conjugate addition to thiols served as a model "removal" reaction. These results indicate that even not template-assisted autocatalytic production combined with competing removal of molecular species in an open compartment could be a feasible route for selecting functional molecules during the pre-Darwinian stages of molecular evolution.
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Affiliation(s)
- Xiaoming Miao
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Arpita Paikar
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Benjamin Lerner
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yael Diskin-Posner
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Guy Shmul
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sergey N Semenov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
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39
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Reif A, Lam K, Weidler S, Lott M, Boos I, Lokau J, Bretscher C, Mönnich M, Perkams L, Schmälzlein M, Graf C, Fischer J, Lechner C, Hallstein K, Becker S, Weyand M, Steegborn C, Schultheiss G, Rose‐John S, Garbers C, Unverzagt C. Natural Glycoforms of Human Interleukin 6 Show Atypical Plasma Clearance. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Andreas Reif
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Kevin Lam
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Sascha Weidler
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Marie Lott
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Irene Boos
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Juliane Lokau
- Department of Pathology Medical Faculty Otto von Guericke University Magdeburg 39120 Magdeburg Germany
| | | | - Manuel Mönnich
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Lukas Perkams
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Marina Schmälzlein
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Christopher Graf
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Jan‐Patrick Fischer
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Carolin Lechner
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Kerstin Hallstein
- Protein Engineering & Antibody Technologies Merck Healthcare KGaA Frankfurter Str. 250 64293 Darmstadt Germany
| | - Stefan Becker
- Protein Engineering & Antibody Technologies Merck Healthcare KGaA Frankfurter Str. 250 64293 Darmstadt Germany
| | - Michael Weyand
- Department of Biochemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Clemens Steegborn
- Department of Biochemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | | | | | - Christoph Garbers
- Department of Pathology Medical Faculty Otto von Guericke University Magdeburg 39120 Magdeburg Germany
| | - Carlo Unverzagt
- Bioorganic Chemistry University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
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40
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Margiola S, Gerecht K, Müller MM. Semisynthetic 'designer' p53 sheds light on a phosphorylation-acetylation relay. Chem Sci 2021; 12:8563-8570. [PMID: 34221338 PMCID: PMC8221199 DOI: 10.1039/d1sc00396h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022] Open
Abstract
The tumor suppressor protein p53 is a master regulator of cell fate. The activity of p53 is controlled by a plethora of posttranslational modifications (PTMs). However, despite extensive research, the mechanisms of this regulation are still poorly understood due to a paucity of biochemical studies with p53 carrying defined PTMs. Here, we report a protein semi-synthesis approach to access site-specifically modified p53. We synthesized a set of chemically homogeneous full-length p53 carrying one (Ser20ph and Ser15ph) or two (Ser15,20ph) naturally occurring, damage-associated phosphoryl marks. Refolding and biochemical characterization of semisynthetic p53 variants confirmed their structural and functional integrity. Furthermore, we show that phosphorylation within the N-terminal domain directly enhances p300-dependent acetylation approximately twofold, consistent with the role of these marks in p53 activation. Given that the p53 N-terminus is a hotspot for PTMs, we believe that our approach will contribute greatly to a mechanistic understanding of how p53 is controlled by PTMs.
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Affiliation(s)
- Sofia Margiola
- Department of Chemistry, King's College London 7 Trinity Street London SE1 1DB UK
| | - Karola Gerecht
- Department of Chemistry, King's College London 7 Trinity Street London SE1 1DB UK
| | - Manuel M Müller
- Department of Chemistry, King's College London 7 Trinity Street London SE1 1DB UK
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41
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Fiore KE, Phan HAT, Robkis DM, Walters CR, Petersson EJ. Incorporating thioamides into proteins by native chemical ligation. Methods Enzymol 2021; 656:295-339. [PMID: 34325791 PMCID: PMC8617429 DOI: 10.1016/bs.mie.2021.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thioamide is a versatile replacement of the peptide backbone with altered hydrogen bonding and conformational preferences, as well the ability participate in energy and electron transfer processes. Semi-synthetic incorporation of a thioamide into a protein can be used to study protein folding or protein/protein interactions using these properties. Semi-synthesis also provides the opportunity to study the role of thioamides in natural proteins. Here we outline the semi-synthesis of a model protein, the B1 domain of protein G (GB1) with a thioamide at the N-terminus or the C-terminus. The thioamide is synthetically incorporated into a fragment by solid-phase peptide synthesis, whereas the remainder of the protein is recombinantly expressed. Then, the two fragments are joined by native chemical ligation. The explicit protocol for GB1 synthesis is accompanied by examples of applications with GB1 and other proteins in structural biology and protein misfolding studies.
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Affiliation(s)
- Kristen E Fiore
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Hoang Anh T Phan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - D Miklos Robkis
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Christopher R Walters
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States.
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42
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Reif A, Lam K, Weidler S, Lott M, Boos I, Lokau J, Bretscher C, Mönnich M, Perkams L, Schmälzlein M, Graf C, Fischer JP, Lechner C, Hallstein K, Becker S, Weyand M, Steegborn C, Schultheiss G, Rose-John S, Garbers C, Unverzagt C. Natural Glycoforms of Human Interleukin 6 Show Atypical Plasma Clearance. Angew Chem Int Ed Engl 2021; 60:13380-13387. [PMID: 33756033 PMCID: PMC8251587 DOI: 10.1002/anie.202101496] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/18/2022]
Abstract
A library of glycoforms of human interleukin 6 (IL‐6) comprising complex and mannosidic N‐glycans was generated by semisynthesis. The three segments were connected by sequential native chemical ligation followed by two‐step refolding. The central glycopeptide segments were assembled by pseudoproline‐assisted Lansbury aspartylation and subsequent enzymatic elongation of complex N‐glycans. Nine IL‐6 glycoforms were synthesized, seven of which were evaluated for in vivo plasma clearance in rats and compared to non‐glycosylated recombinant IL‐6 from E. coli. Each IL‐6 glycoform was tested in three animals and reproducibly showed individual serum clearances depending on the structure of the N‐glycan. The clearance rates were atypical, since the 2,6‐sialylated glycoforms of IL‐6 cleared faster than the corresponding asialo IL‐6 with terminal galactoses. Compared to non‐glycosylated IL‐6 the plasma clearance of IL‐6 glycoforms was delayed in the presence of larger and multibranched N‐glycans in most cases
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Affiliation(s)
- Andreas Reif
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Kevin Lam
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Sascha Weidler
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Marie Lott
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Irene Boos
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Juliane Lokau
- Department of Pathology, Medical Faculty, Otto von Guericke University Magdeburg, 39120, Magdeburg, Germany
| | | | - Manuel Mönnich
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Lukas Perkams
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Marina Schmälzlein
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Christopher Graf
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Jan-Patrick Fischer
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Carolin Lechner
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Kerstin Hallstein
- Protein Engineering & Antibody Technologies, Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Stefan Becker
- Protein Engineering & Antibody Technologies, Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Michael Weyand
- Department of Biochemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | | | - Stefan Rose-John
- Department of Biochemistry, Kiel University, 24098, Kiel, Germany
| | - Christoph Garbers
- Department of Pathology, Medical Faculty, Otto von Guericke University Magdeburg, 39120, Magdeburg, Germany
| | - Carlo Unverzagt
- Bioorganic Chemistry, University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
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43
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Folikumah MY, Behl M, Lendlein A. Thiol-Thioester Exchange Reactions in Precursors Enable pH-Triggered Hydrogel Formation. Biomacromolecules 2021; 22:1875-1884. [PMID: 33724816 DOI: 10.1021/acs.biomac.0c01690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bio-interactive hydrogel formation in situ requires sensory capabilities toward physiologically relevant stimuli. Here, we report on pH-controlled in situ hydrogel formation relying on latent cross-linkers, which transform from pH sensors to reactive molecules. In particular, thiopeptolide/thio-depsipeptides were capable of pH-sensitive thiol-thioester exchange reactions to yield α,ω-dithiols, which react with maleimide-functionalized multi-arm polyethylene glycol to polymer networks. Their water solubility and diffusibility qualify thiol/thioester-containing peptide mimetics as sensory precursors to drive in situ localized hydrogel formation with potential applications in tissue regeneration such as treatment of inflamed tissues of the urinary tract.
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Affiliation(s)
- Makafui Y Folikumah
- Institute of Active Polymers and Berlin-Brandenburg Centre for Regenerative Therapies, Helmholtz-Zentrum Geesthacht, 14513 Teltow, Germany.,Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Marc Behl
- Institute of Active Polymers and Berlin-Brandenburg Centre for Regenerative Therapies, Helmholtz-Zentrum Geesthacht, 14513 Teltow, Germany
| | - Andreas Lendlein
- Institute of Active Polymers and Berlin-Brandenburg Centre for Regenerative Therapies, Helmholtz-Zentrum Geesthacht, 14513 Teltow, Germany.,Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
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44
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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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45
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Zhang J, Yuan J, Li Z, Fu C, Xu M, Yang J, Jiang X, Zhou B, Ye X, Xu C. Exploring and exploiting plant cyclic peptides for drug discovery and development. Med Res Rev 2021; 41:3096-3117. [PMID: 33599316 DOI: 10.1002/med.21792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/10/2021] [Accepted: 01/31/2021] [Indexed: 01/07/2023]
Abstract
Ever since the discovery of insulin, natural peptides have become an important resource for therapeutic development. Decades of research has led to the discovery of a long list of peptide drugs with broad applications in clinics, from antibiotics to hypertension treatment to pain management. Many of these US FDA-approved peptide drugs are derived from microorganisms and animals. By contrast, the great potential of plant cyclic peptides as therapeutics remains largely unexplored. These macrocyclic peptides typically have rigid structures, good bioavailability and membrane permeability, making them appealing candidates for drug development and engineering. In this review, we introduce the three major classes of plant cyclic peptides and summarize their potential medical applications. We discuss how we can leverage the genome information of many different plants to quickly search for new cyclic peptides and how we can take advantage of the insights gained from their biosynthetic pathways to transform the process of production and drug development. These recent developments have provided a new angle for exploring and exploiting plant cyclic peptides, and we believe that many more peptide drugs derived from plants are about to come.
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Affiliation(s)
- Jingjing Zhang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Jimin Yuan
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Zhijie Li
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chunjin Fu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Menglong Xu
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jing Yang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xin Jiang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Boping Zhou
- Department of Infectious Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xiufeng Ye
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chengchao Xu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
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46
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Design and synthesis of a multivalent catch-and-release assay to measure circulating FXIa. Thromb Res 2021; 200:16-22. [PMID: 33513452 DOI: 10.1016/j.thromres.2021.01.002] [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: 09/15/2020] [Revised: 12/11/2020] [Accepted: 01/04/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Decreased blood coagulation factor (F)XIa levels have been shown to protect from thrombosis without bleeding side effects, but less is known on effects of increased FXIa levels. Studies are hampered by lack of a reliable and robust method for FXIa quantification in blood. We aim to develop a new assay employing a unique multivalent catch-and-release system. The system selectively isolates and protects homodimeric FXIa from plasma and releases free FXIa allowing subsequent quantification. METHODS A dynamic multivalent construct was synthesized by complexing four identical FXIa inhibitors from the snake Bungarus Fasxiatus to avidin through desthiobiotin-PEG-linkers, allowing dissociation of FXIa by excess biotin. PEG-linker lengths were optimised for FXIa inhibitory activity and analysed by Michaelis-Menten kinetics. Finally, the catch-and-release assay was validated in buffer and plasma model systems. RESULTS Monovalent and multivalent inhibitor constructs were successfully obtained by total chemical synthesis. Multimerisation of Fasxiator resulted in a 30-fold increase in affinity for FXIa from 1.6 nM to 0.05 nM. With use of this system, FXIa could be quantified down to a concentration of 7 pM in buffer and 20 pM in plasma. CONCLUSION In this proof-of-concept study, we have shown that the catch-and-release approach is a promising technique to quantify FXIa in plasma or buffer. By binding FXIa to the multivalent construct directly after blood drawing, FXIa is hypothesized to be inaccessible for serpin inhibition or auto inactivation. This results in a close reflection of actual circulating FXIa levels at the moment of blood drawing.
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47
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van den Kerkhof DL, Nagy M, Wichapong K, Brouns SL, Heemskerk JWM, Hackeng TM, Dijkgraaf I. Inhibition of platelet adhesion, thrombus formation, and fibrin formation by a potent αIIbβ3 integrin inhibitor from ticks. Res Pract Thromb Haemost 2021; 5:231-242. [PMID: 33537548 PMCID: PMC7845065 DOI: 10.1002/rth2.12466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/15/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Ticks puncture the skin of their hosts and secrete saliva, containing antiplatelet proteins, into the blood. Here, we studied disagregin, a potent platelet-inhibiting protein derived from the salivary glands of Ornithodoros moubata, an African soft tick. Whereas conventional αIIbβ3 antagonists contain an Arg-Gly-Asp (RGD) sequence for platelet integrin binding, disagregin contains an Arg-Glu-Asp (RED) sequence, hypothesizing a different mode of inhibitory action. OBJECTIVES We aimed to compare the inhibitory effects of disagregin and its RGD variant (RGD-disagregin) on platelet activation and to unravel the molecular basis of disagregin-αIIbβ3 integrin interactions. METHODS Disagregin and RGD-disagregin were synthesized by tert-butyloxycarbonyl -based solid-phase peptide synthesis. Effects of both disagregins on platelet aggregation were assessed by light transmission aggregometry in human platelet-rich plasma. Whole-blood thrombus formation was investigated by perfusing blood over collagen I with and without tissue factor at a high wall-shear rate (1000 s-1) in the presence of disagregin, RGD-disagregin, or eptifibatide. RESULTS Disagregin showed inhibition of collagen- and ADP-induced platelet aggregation with half maximal inhibitory concentration values of 64 and 99 nM, respectively. This resembled the complete antiaggregatory effect of eptifibatide. Multiparameter assessment of thrombus formation showed highly suppressed platelet adhesion and aggregate formation with both disagregins, in contrast to eptifibatide treatment, which incompletely blocked aggregation under flow. Fibrin formation under flow was delayed by both disagregin and RGD-disagregin (P < .01) and eptifibatide (P < .05). CONCLUSIONS Both αIIbβ3-blocking disagregins have a strong potential to suppress collagen-tissue factor-mediated platelet adhesion, thrombus formation, and fibrin formation. Both disagregins can be seen as potential new αIIbβ3 inhibitors.
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Affiliation(s)
- Danique L. van den Kerkhof
- Department of BiochemistryCardiovascular Research Institute Maastricht (CARIM)Maastricht UniversityMaastrichtThe Netherlands
| | - Magdolna Nagy
- Department of BiochemistryCardiovascular Research Institute Maastricht (CARIM)Maastricht UniversityMaastrichtThe Netherlands
| | - Kanin Wichapong
- Department of BiochemistryCardiovascular Research Institute Maastricht (CARIM)Maastricht UniversityMaastrichtThe Netherlands
| | - Sanne L.N. Brouns
- Department of BiochemistryCardiovascular Research Institute Maastricht (CARIM)Maastricht UniversityMaastrichtThe Netherlands
| | - Johan W. M. Heemskerk
- Department of BiochemistryCardiovascular Research Institute Maastricht (CARIM)Maastricht UniversityMaastrichtThe Netherlands
| | - Tilman M. Hackeng
- Department of BiochemistryCardiovascular Research Institute Maastricht (CARIM)Maastricht UniversityMaastrichtThe Netherlands
| | - Ingrid Dijkgraaf
- Department of BiochemistryCardiovascular Research Institute Maastricht (CARIM)Maastricht UniversityMaastrichtThe Netherlands
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48
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Rowe SM, Spring DR. The role of chemical synthesis in developing RiPP antibiotics. Chem Soc Rev 2021; 50:4245-4258. [DOI: 10.1039/d0cs01386b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This tutorial review discusses the potential of ribosomally synthesised and post-translationally modified peptides (RiPPs) as antimicrobials and looks at the chemical synthesis of three classes of RiPP: lasso peptides, cyclotides, and lanthipeptides.
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Affiliation(s)
- Sam M. Rowe
- Department of Chemistry
- University of Cambridge
- Cambridge
- UK
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49
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Lee J, Schwarz KJ, Yu H, Krüger A, Anslyn EV, Ellington AD, Moore JS, Jewett MC. Ribosome-mediated incorporation of fluorescent amino acids into peptides in vitro. Chem Commun (Camb) 2021; 57:2661-2664. [DOI: 10.1039/d0cc07740b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We expand the substrate scope of ribosome-mediated incorporation to α-amino acids with a variety of fluorescent groups on the sidechain.
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Affiliation(s)
- Joongoo Lee
- Department of Chemical and Biological Engineering and Center for Synthetic Biology
- Northwestern University
- Evanston
- USA
| | - Kevin J. Schwarz
- Department of Chemistry
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Hao Yu
- Departments of Chemical and Biomolecular Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering and Center for Synthetic Biology
- Northwestern University
- Evanston
- USA
| | - Eric V. Anslyn
- Department of Chemistry and Biochemistry
- University of Texas at Austin
- Austin
- USA
| | - Andrew D. Ellington
- Department of Chemistry and Biochemistry
- Institute for Cellular and Molecular Biology
- University of Texas at Austin
- Austin
- USA
| | - Jeffrey S. Moore
- Department of Chemistry
- University of Illinois at Urbana-Champaign
- Urbana
- USA
- Beckman Institute for Advanced Science and Technology
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology
- Northwestern University
- Evanston
- USA
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50
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Ueda M, Komiya C, Arii S, Kusumoto K, Denda M, Okuhira K, Shigenaga A, Otaka A. Sequence-Independent Traceless Method for Preparation of Peptide/Protein Thioesters Using CPaseY-Mediated Hydrazinolysis. Chem Pharm Bull (Tokyo) 2020; 68:1226-1232. [PMID: 33028801 DOI: 10.1248/cpb.c20-00674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteins incorporating artificial moieties such as fluorophores and drugs have enjoyed increasing use in chemical biology and drug development research. Preparation of such artificial protein derivatives has relied mainly on native chemical ligation in which peptide/protein thioesters chemoselectively react with N-terminal cysteine (Cys) peptides to afford protein molecules. The protein thioesters derived from expressed proteins represent thioesters that are very useful for the preparation of artificial proteins by native chemical ligation with synthetic peptides with N-terminal Cys. We recently have developed a traceless thioester-producing protocol using carboxypeptidase Y (CPaseY) which is compatible with an expressed protein. The traceless character is ensured by CPaseY-mediated hydrazinolysis of C-terminal Xaa (X)-Cys-proline (Pro)-leucine (Leu)-OH sequence followed by an auto-processing of the Cys-Pro (CP) dipeptide unit, affording the corresponding X-thioester (X-SR). However, hydrazinolysis of the amide bond in the prolyl leucine junction depends significantly on the nature of X. In the case of hydrophobic X residues, the hydrazinolysis overreacts to give several hydrazides while the reaction of hydrophilic X residues proceeds slowly. In this research, we attempted to develop an X-independent CPaseY-mediated protocol and found that the incorporation of a triple CP sequence into the C-terminal end (X-(CP)3-Leu-OH) allows for efficient X-SR formation in a manner that is independent of X.
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Affiliation(s)
- Masahiro Ueda
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Chiaki Komiya
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Sayuki Arii
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Kohshi Kusumoto
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Masaya Denda
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Keiichiro Okuhira
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University.,Osaka University of Pharmaceutical Sciences
| | - Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University.,Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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