1
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Xuan GR, Chen XK, Liu MC, Zhou YB, Wu HY. Deselenylative Acylation and Nitration of Monoselenides. Org Lett 2024. [PMID: 38814147 DOI: 10.1021/acs.orglett.4c01537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
A deselenylative protocol that enables the construction of the C-C and C-N bonds has been disclosed. By using acyl chloride/AgOTf as an efficient acylation reagent, diarylselenides smoothly undergo deselenylative acylation to produce a series of aroyl compounds. In addition, deselenylative nitration can be enabled by a mild nitration reagent consisting of TsCl and AgNO3, furnishing a diverse array of nitroaromatic compounds.
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Affiliation(s)
- Guo-Rong Xuan
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Xin-Kai Chen
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Miao-Chang Liu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Yun-Bing Zhou
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, Wenzhou 325035, China
| | - Hua-Yue Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
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2
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Liao P, He C. Azole reagents enabled ligation of peptide acyl pyrazoles for chemical protein synthesis. Chem Sci 2024; 15:7965-7974. [PMID: 38817582 PMCID: PMC11134319 DOI: 10.1039/d3sc06697e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Native chemical ligation (NCL) has been playing an increasingly important role in chemical protein synthesis (CPS). More efficient ligation methods that circumvent the requirement of a peptidyl thioester and thiol additive-which allow the following desulfurization or refolding in one pot-are urgently needed for the synthesis of more complex protein targets and in large quantities. Herein, we discover that the weak acyl donor peptidyl N-acyl pyrazole can be activated by azole reagents like 3-methylpyrazole or imidazole to facilitate its ligation directly with an N-terminal cysteine peptide. As it requires no thioester or thiol additive, this ligation strategy can be conveniently combined with metal-free desulfurization (MFD) or oxidative protein folding to allow various one-pot protocols. The utility and generality of the strategy are showcased by the total synthesis of ubiquitin via an N-to-C sequential ligation-MFD strategy, the semi-synthesis of the copper protein azurin, and the efficient assembly of a sulfated hirudin variant and the cyclotide kalata B1, all in a one-pot fashion.
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Affiliation(s)
- Peisi Liao
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
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3
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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4
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Wu H, Sun Z, Li X. Selective Peptide Cysteine Manipulation on Demand and Difficult Protein Chemical Synthesis Enabled by Controllable Acidolysis of N,S-Benzylidene Thioacetals. Angew Chem Int Ed Engl 2024; 63:e202403396. [PMID: 38490953 DOI: 10.1002/anie.202403396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/17/2024]
Abstract
Although solid-phase peptide synthesis combining with chemical ligation provides a way to build up customized polypeptides in general, many targets are still presenting challenges for the conventional synthetic process, such as hydrophobic proteins. New methods and strategies are still required to overcome these obstacles. In this study, kinetic studies of Cys/Pen ligation and its acidolysis were performed, from which the fast acidolysis of substituted N,S-benzylidene thioacetals (NBTs) was discovered. The study demonstrates the potential of NBTs as a promising Cys switchable protection, facilitating the chemical synthesis of peptides and proteins by efficiently disrupting peptide aggregation. The compatibility of NBTs with other commonly adopted Cys protecting groups and their applications in sequential disulfide bond formation were also investigated. The first chemical synthesis of the native human programmed death ligand 1 immunoglobulin V-like (PD-L1 IgV) domain was achieved using the NBT strategy, showcasing its potential in difficult protein synthesis.
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Affiliation(s)
- Hongxiang Wu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of, China
| | - Zhenquan Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of, China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Ocean University China, Qingdao, 266237, People's Republic of China
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5
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Karmakar S, Sukumar G, Prasanthkumar S, Jha BK, Mainkar PS, Nayani K, Chandrasekhar S. Metal-free functionalization of tyrosine residues in short peptides and study of the morphological alterations. Chem Commun (Camb) 2024; 60:3802-3805. [PMID: 38487891 DOI: 10.1039/d3cc06115a] [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: 04/04/2024]
Abstract
An efficient functionalization of tyrosine residues in phenolic regions is achieved under metal-free conditions. The strategy involves the conversion of a tyrosine residue to 4-amino phenylalanine or 4-amino-3-methoxy phenylalanine in short peptides through a controlled oxidative dearomatization. This transformation is achieved in one pot with good yields and excellent regioselectivity. Consequently, the self-assembly of the peptide compounds has been studied at the nanoscopic level before and after functionalization. The results suggest that the peptide derivatives comprising amide groups promote intermolecular H-bonding interactions and the difference in -OH and -NH2 functional groups is found to be responsible for the morphological changes. Morphological transitions from 1D nanowires to 2D nanosheets were observed during functional group modification.
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Affiliation(s)
- Santanu Karmakar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Genji Sukumar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.
- Department of Chemistry, Adikavi Nannaya University, Rajamahendravaram, Andhra Pradesh 533296, India
| | - Seelam Prasanthkumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Polymers and Functional Materials, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Babli K Jha
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prathama S Mainkar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Srivari Chandrasekhar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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6
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Zheng Y, Zhang B, Shi WW, Deng X, Wang TY, Han D, Ren Y, Yang Z, Zhou YK, Kuang J, Wang ZW, Tang S, Zheng JS. An Enzyme-Cleavable Solubilizing-Tag Facilitates the Chemical Synthesis of Mirror-Image Proteins. Angew Chem Int Ed Engl 2024; 63:e202318897. [PMID: 38326236 DOI: 10.1002/anie.202318897] [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: 12/08/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/09/2024]
Abstract
Mirror-image proteins (D-proteins) are useful in biomedical research for purposes such as mirror-image screening for D-peptide drug discovery, but the chemical synthesis of many D-proteins is often low yielding due to the poor solubility or aggregation of their constituent peptide segments. Here, we report a Lys-C protease-cleavable solubilizing tag and its use to synthesize difficult-to-obtain D-proteins. Our tag is easily installed onto multiple amino acids such as DLys, DSer, DThr, and/or the N-terminal amino acid of hydrophobic D-peptides, is impervious to various reaction conditions, such as peptide synthesis, ligation, desulfurization, and transition metal-mediated deprotection, and yet can be completely removed by Lys-C protease under denaturing conditions to give the desired D-protein. The efficacy and practicality of the new method were exemplified in the synthesis of two challenging D-proteins: D-enantiomers of programmed cell death protein 1 IgV domain and SARS-CoV-2 envelope protein, in high yield. This work demonstrates that the enzymatic cleavage of solubilizing tags under denaturing conditions is feasible, thus paving the way for the production of more D-proteins.
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Affiliation(s)
- Yupeng Zheng
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, and Division of Life Sciences and Medicine, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Baochang Zhang
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, and Division of Life Sciences and Medicine, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Wei-Wei Shi
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xiangyu Deng
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Tong-Yue Wang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Dongyang Han
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yuxiang Ren
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Ziyi Yang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yong-Kang Zhou
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Jian Kuang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Zhi-Wen Wang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Shan Tang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Ji-Shen Zheng
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, and Division of Life Sciences and Medicine, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230001, China
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7
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Aoki K, Tsuda S, Ogata N, Kataoka M, Sasaki J, Inuki S, Ohno H, Watashi K, Yoshiya T, Oishi S. Synthesis of the full-length hepatitis B virus core protein and its capsid formation. Org Biomol Chem 2024; 22:2218-2225. [PMID: 38358380 DOI: 10.1039/d3ob02099a] [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: 02/16/2024]
Abstract
Chronic infection with hepatitis B virus (HBV) is a major cause of cirrhosis and liver cancer. Capsid assembly modulators can induce error-prone assembly of HBV core proteins to prevent the formation of infectious virions, representing promising candidates for treating chronic HBV infections. To explore novel capsid assembly modulators from unexplored mirror-image libraries of natural products, we have investigated the synthetic process of the HBV core protein for preparing the mirror-image target protein. In this report, the chemical synthesis of full-length HBV core protein (Cp183) containing an arginine-rich nucleic acid-binding domain at the C-terminus is presented. Sequential ligations using four peptide segments enabled the synthesis of Cp183 via convergent and C-to-N direction approaches. After refolding under appropriate conditions, followed by the addition of nucleic acid, the synthetic Cp183 assembled into capsid-like particles.
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Affiliation(s)
- 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.
| | - Shugo Tsuda
- Peptide Institute, Inc. Ibaraki, Osaka 567-0085, Japan
| | - Naoko Ogata
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Michiyo Kataoka
- Department of Pathology, National Institute of Infectious Disease, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Jumpei Sasaki
- 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
| | - Koichi Watashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Taku Yoshiya
- Peptide Institute, Inc. Ibaraki, Osaka 567-0085, Japan
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, 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 Z, Laps S, Gichtin JS, Metanis N. Selenium chemistry for spatio-selective peptide and protein functionalization. Nat Rev Chem 2024; 8:211-229. [PMID: 38388838 DOI: 10.1038/s41570-024-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
The ability to construct a peptide or protein in a spatio-specific manner is of great interest for therapeutic and biochemical research. However, the various functional groups present in peptide sequences and the need to perform chemistry under mild and aqueous conditions make selective protein functionalization one of the greatest synthetic challenges. The fascinating paradox of selenium (Se) - being found in both toxic compounds and also harnessed by nature for essential biochemical processes - has inspired the recent exploration of selenium chemistry for site-selective functionalization of peptides and proteins. In this Review, we discuss such approaches, including metal-free and metal-catalysed transformations, as well as traceless chemical modifications. We report their advantages, limitations and applications, as well as future research avenues.
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Affiliation(s)
- Zhenguang Zhao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shay Laps
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jacob S Gichtin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Casali Center for Applied Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel.
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9
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Lander A, Kong Y, Jin Y, Wu C, Luk LYP. Deciphering the Synthetic and Refolding Strategy of a Cysteine-Rich Domain in the Tumor Necrosis Factor Receptor (TNF-R) for Racemic Crystallography Analysis and d-Peptide Ligand Discovery. ACS BIO & MED CHEM AU 2024; 4:68-76. [PMID: 38404743 PMCID: PMC10885103 DOI: 10.1021/acsbiomedchemau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 02/27/2024]
Abstract
Many cell-surface receptors are promising targets for chemical synthesis because of their critical roles in disease development. This synthetic approach enables investigations by racemic protein crystallography and ligand discovery by mirror-image methodologies. However, due to their complex nature, the chemical synthesis of a receptor can be a significant challenge. Here, we describe the chemical synthesis and folding of a central, cysteine-rich domain of the cell-surface receptor tumor necrosis factor 1 which is integral to binding of the cytokine TNF-α, namely, TNFR-1 CRD2. Racemic protein crystallography at 1.4 Å confirmed that the native binding conformation was preserved, and TNFR-1 CRD2 maintained its capacity to bind to TNF-α (KD ≈ 7 nM). Encouraged by this discovery, we carried out mirror-image phage display using the enantiomeric receptor mimic and identified a d-peptide ligand for TNFR-1 CRD2 (KD = 1 μM). This work demonstrated that cysteine-rich domains, including the central domains, can be chemically synthesized and used as mimics for investigations.
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Affiliation(s)
- Alexander
J. Lander
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
| | - Yifu Kong
- Department
of Chemistry, College of Chemistry and Chemical Engineering, The MOE
Key Laboratory of Spectrochemical Analysis and Instrumentation, State
Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Fujian Province 361005, China
| | - Yi Jin
- Manchester
Institute of Biotechnology, University of
Manchester, Manchester M1 7DN, U.K.
| | - Chuanliu Wu
- Department
of Chemistry, College of Chemistry and Chemical Engineering, The MOE
Key Laboratory of Spectrochemical Analysis and Instrumentation, State
Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Fujian Province 361005, China
| | - Louis Y. P. Luk
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
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10
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Ye F, Li C, Liu FL, Liu X, Xu P, Luo RH, Song W, Zheng YT, Ying T, Yu B, Wang P. Semisynthesis of homogeneous spike RBD glycoforms from SARS-CoV-2 for profiling the correlations between glycan composition and function. Natl Sci Rev 2024; 11:nwae030. [PMID: 38333067 PMCID: PMC10852988 DOI: 10.1093/nsr/nwae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/28/2023] [Accepted: 10/15/2023] [Indexed: 02/10/2024] Open
Abstract
Vaccines have been the primary remedy in the global fight against coronavirus disease 2019 (COVID-19). The receptor-binding domain (RBD) of the spike protein, a critical viral immunogen, is affected by the heterogeneity of its glycan structures and relatively low immunogenicity. Here, we describe a scalable synthetic platform that enables the precise synthesis of homogeneously glycosylated RBD, facilitating the elucidation of carbohydrate structure-function relationships. Five homogeneously glycosylated RBDs bearing biantennary glycans were prepared, three of which were conjugated to T-helper epitope (Tpep) from tetanus toxoid to improve their weak immune response. Relative to natural HEK293-derived RBD, synthetic RBDs with biantennary N-glycan elicited a higher level of neutralising antibodies against SARS-CoV-2 in mice. Furthermore, RBDs containing Tpep elicited significant immune responses in transgenic mice expressing human angiotensin-converting enzyme 2. Our collective data suggest that trimming the N-glycans and Tpep conjugation of RBD could potentially serve as an effective strategy for developing subunit vaccines providing efficient protection.
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Affiliation(s)
- Farong Ye
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng Li
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Engineering Research Center for Synthetic Immunology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Feng-Liang Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xinliang Liu
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wenping Song
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Engineering Research Center for Synthetic Immunology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Engineering Research Center for Synthetic Immunology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Biao Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ping Wang
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Shenzhen Research Institute of Shanghai Jiao Tong University, Shenzhen 518057, China
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11
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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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12
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Gao YP, Sun PF, Guo WC, Zhou YK, Zheng JS, Tang S. Chemical synthesis of a 28 kDa full-length PET degrading enzyme ICCG by the removable backbone modification strategy. Bioorg Chem 2024; 143:107047. [PMID: 38154387 DOI: 10.1016/j.bioorg.2023.107047] [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: 10/25/2023] [Revised: 12/04/2023] [Accepted: 12/17/2023] [Indexed: 12/30/2023]
Abstract
Chemical protein synthesis offers a powerful way to access otherwise-difficult-to-obtain proteins such as mirror-image proteins. Although a large number of proteins have been chemically synthesized to date, the acquisition to proteins containing hydrophobic peptide fragments has proven challenging. Here, we describe an approach that combines the removable backbone modification strategy and the peptide hydrazide-based native chemical ligation for the chemical synthesis of a 28 kDa full-length PET degrading enzyme IGGC (a higher depolymerization efficiency of variant leaf-branch compost cutinase (LCC)) containing hydrophobic peptide segments. The synthetic ICCG exhibits the enzymatic activity and will be useful in establishing the corresponding mirror-image version of ICCG.
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Affiliation(s)
- Yun-Pu Gao
- The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Peng-Fei Sun
- The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Wu-Chen Guo
- The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Yong-Kang Zhou
- The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Ji-Shen Zheng
- The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.
| | - Shan Tang
- The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.
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13
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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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14
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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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15
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Peng J, Hughes GR, Müller MM, Seebeck FP. Enzymatic Fluoromethylation as a Tool for ATP-Independent Ligation. Angew Chem Int Ed Engl 2024; 63:e202312104. [PMID: 37955592 PMCID: PMC10952888 DOI: 10.1002/anie.202312104] [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: 08/18/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
S-adenosylmethionine-dependent methyltransferases are involved in countless biological processes, including signal transduction, epigenetics, natural product biosynthesis, and detoxification. Only a handful of carboxylate methyltransferases have evolved to participate in amide bond formation. In this report we show that enzyme-catalyzed F-methylation of carboxylate substrates produces F-methyl esters that readily react with N- or S-nucleophiles under physiological conditions. We demonstrate the applicability of this approach to the synthesis of small amides, hydroxamates, and thioesters, as well as to site-specific protein modification and native chemical ligation.
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Affiliation(s)
- Jiaming Peng
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
| | - Gregory R. Hughes
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Manuel M. Müller
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Florian P. Seebeck
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
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16
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Peng J, Hughes GR, Müller MM, Seebeck FP. Enzymatic Fluoromethylation as a Tool for ATP-Independent Ligation. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 136:e202312104. [PMID: 38516647 PMCID: PMC10952241 DOI: 10.1002/ange.202312104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Indexed: 03/23/2024]
Abstract
S-adenosylmethionine-dependent methyltransferases are involved in countless biological processes, including signal transduction, epigenetics, natural product biosynthesis, and detoxification. Only a handful of carboxylate methyltransferases have evolved to participate in amide bond formation. In this report we show that enzyme-catalyzed F-methylation of carboxylate substrates produces F-methyl esters that readily react with N- or S-nucleophiles under physiological conditions. We demonstrate the applicability of this approach to the synthesis of small amides, hydroxamates, and thioesters, as well as to site-specific protein modification and native chemical ligation.
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Affiliation(s)
- Jiaming Peng
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
| | - Gregory R. Hughes
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Manuel M. Müller
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Florian P. Seebeck
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
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17
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Zhao J, Ye F, Huang P, Wang P. Recent advances in chemical synthesis of O-linked glycopeptides and glycoproteins: An advanced synthetic tool for exploring the biological realm. Curr Opin Chem Biol 2023; 77:102405. [PMID: 37897925 DOI: 10.1016/j.cbpa.2023.102405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]
Abstract
Glycoproteins play crucial roles in various biological processes. To investigate the relationship between glycan structure and function, researchers have employed various chemical methods to precisely synthesize homogeneous O-glycoproteins. This review summarizes the recent progress of their synthetic strategies, highlighting the significant advancements in this area.
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Affiliation(s)
- Jie Zhao
- Center for Chemical Glycobiology, 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
| | - Farong Ye
- Center for Chemical Glycobiology, 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 Huang
- Center for Chemical Glycobiology, 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, 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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18
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Nithun RV, Yao YM, Lin X, Habiballah S, Afek A, Jbara M. Deciphering the Role of the Ser-Phosphorylation Pattern on the DNA-Binding Activity of Max Transcription Factor Using Chemical Protein Synthesis. Angew Chem Int Ed Engl 2023; 62:e202310913. [PMID: 37642402 DOI: 10.1002/anie.202310913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 08/31/2023]
Abstract
The chemical synthesis of site-specifically modified transcription factors (TFs) is a powerful method to investigate how post-translational modifications (PTMs) influence TF-DNA interactions and impact gene expression. Among these TFs, Max plays a pivotal role in controlling the expression of 15 % of the genome. The activity of Max is regulated by PTMs; Ser-phosphorylation at the N-terminus is considered one of the key regulatory mechanisms. In this study, we developed a practical synthetic strategy to prepare homogeneous full-length Max for the first time, to explore the impact of Max phosphorylation. We prepared a focused library of eight Max variants, with distinct modification patterns, including mono-phosphorylated, and doubly phosphorylated analogues at Ser2/Ser11 as well as fluorescently labeled variants through native chemical ligation. Through comprehensive DNA binding analyses, we discovered that the phosphorylation position plays a crucial role in the DNA-binding activity of Max. Furthermore, in vitro high-throughput analysis using DNA microarrays revealed that the N-terminus phosphorylation pattern does not interfere with the DNA sequence specificity of Max. Our work provides insights into the regulatory role of Max's phosphorylation on the DNA interactions and sequence specificity, shedding light on how PTMs influence TF function.
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Affiliation(s)
- Raj V Nithun
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Yumi Minyi Yao
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Xiaoxi Lin
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Shaimaa Habiballah
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ariel Afek
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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19
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Okamoto R, Shibata H, Yatsuzuka T, Hanao T, Maki Y, Kabayama K, Miura A, Fukase K, Kajihara Y. Convergent synthesis of proteins using peptide-aminothiazoline. Chem Commun (Camb) 2023; 59:13510-13513. [PMID: 37885305 DOI: 10.1039/d3cc04387h] [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: 10/28/2023]
Abstract
Sequential peptide coupling plays a central role in chemical protein synthesis. This paper describes a new peptide derivative, peptide-aminothiazoline (At), whereof the C-terminus is functionalized with 2-aminothiazoline. Peptide-At streamlined the sequential peptide ligation in a one-pot manner and demonstrated the convergent synthesis of a circular protein and homogeneous glycoproteins.
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Affiliation(s)
- Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Forefront Research Center, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroyuki Shibata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takahiro Yatsuzuka
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takuya Hanao
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuta Maki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Forefront Research Center, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kazuya Kabayama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Forefront Research Center, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ayane Miura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Forefront Research Center, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Center for Advanced Modalities and DDS, Osaka University, 1-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Forefront Research Center, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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20
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Wu H, Sun Z, Li X. N,O-Benzylidene Acetal Dipeptides (NBDs) Enable the Synthesis of Difficult Peptides via a Kinked Backbone Strategy. Angew Chem Int Ed Engl 2023; 62:e202310624. [PMID: 37694822 DOI: 10.1002/anie.202310624] [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: 07/24/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/12/2023]
Abstract
Proteins with highly hydrophobic regions or aggregation-prone sequences are typically difficult targets for chemical synthesis at the current stage, as obtaining such type of peptides via solid-phase peptide synthesis requires sophisticated operations. Herein, we report N,O-benzylidene acetal dipeptides (NBDs) as robust and effective building blocks to allow the direct synthesis of difficult peptides and proteins via a kinked backbone strategy. The effectiveness and easy accessibility of NBDs have been well demonstrated in our chemical syntheses of various challenging peptides and proteins, including chemokine, therapeutic hormones, histone, and glycosylated erythropoietin.
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Affiliation(s)
- Hongxiang Wu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Zhenquan Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, P. R. China
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21
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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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22
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Zhang B, Zheng Y, Chu G, Deng X, Wang T, Shi W, Zhou Y, Tang S, Zheng JS, Liu L. Backbone-Installed Split Intein-Assisted Ligation for the Chemical Synthesis of Mirror-Image Proteins. Angew Chem Int Ed Engl 2023; 62:e202306270. [PMID: 37357888 DOI: 10.1002/anie.202306270] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 06/27/2023]
Abstract
Membrane-associated D-proteins are an important class of synthetic molecules needed for D-peptide drug discovery, but their chemical synthesis using canonical ligation methods such as native chemical ligation is often hampered by the poor solubility of their constituent peptide segments. Here, we describe a Backbone-Installed Split Intein-Assisted Ligation (BISIAL) method for the synthesis of these proteins, wherein the native L-forms of the N- and C-intein fragments of the unique consensus-fast (Cfa) (i.e. L-CfaN and L-CfaC ) are separately installed onto the two D-peptide segments to be ligated via a removable backbone modification. The ligation proceeds smoothly at micromolar (μM) concentrations under strongly chaotropic conditions (8.0 M urea), and the subsequent removal of the backbone modification groups affords the desired D-proteins without leaving any "ligation scar" on the products. The effectiveness and practicality of the BISIAL method are exemplified by the synthesis of the D-enantiomers of the extracellular domains of T cell immunoglobulin and ITIM domain (TIGIT) and tropomyosin receptor kinase C (TrkC). The BISIAL method further expands the chemical protein synthesis ligation toolkit and provides practical access to challenging D-protein targets.
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Affiliation(s)
- Baochang Zhang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yupeng Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Guochao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xiangyu Deng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Tongyue Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Weiwei Shi
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yongkang Zhou
- The First Affiliated Hospital of USTC, MOE Key Laboratory of Cellular Dynamics, and Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Shan Tang
- The First Affiliated Hospital of USTC, MOE Key Laboratory of Cellular Dynamics, and Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Ji-Shen Zheng
- The First Affiliated Hospital of USTC, MOE Key Laboratory of Cellular Dynamics, and Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
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23
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Lin S, Mo Z, Wang P, He C. Oxidation and Phenolysis of Peptide/Protein C-Terminal Hydrazides Afford Salicylaldehyde Ester Surrogates for Chemical Protein Synthesis. J Am Chem Soc 2023. [PMID: 37470345 DOI: 10.1021/jacs.3c05190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
With the growing popularity of serine/threonine ligation (STL) and cysteine/penicillamine ligation (CPL) in chemical protein synthesis, facile and general approaches for the preparation of peptide salicylaldehyde (SAL) esters are urgently needed, especially those viable for obtaining expressed protein SAL esters. Herein, we report the access of SAL ester surrogates from peptide hydrazides (obtained either synthetically or recombinantly) via nitrite oxidation and phenolysis by 3-(1,3-dithian-2-yl)-4-hydroxybenzoic acid (SAL(-COOH)PDT). The resulting peptide SAL(-COOH)PDT esters can be activated to afford the reactive peptide SAL(-COOH) esters for subsequent STL/CPL. While being operationally simple for both synthetic peptides and expressed proteins, the current strategy facilitates convergent protein synthesis and combined application of STL with NCL. The generality of the strategy is showcased by the N-terminal ubiquitination of the growth arrest and DNA damage-inducible protein (Gadd45a), the efficient synthesis of ubiquitin-like protein 5 (UBL-5) via a combined N-to-C NCL-STL strategy, and the C-to-N semisynthesis of a myoglobin (Mb) variant.
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Affiliation(s)
- Shaomin Lin
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Zeyuan Mo
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Peng Wang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
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24
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Liu Z, Chen X, Yang S, Tian R, Wang F. Integrated mass spectrometry strategy for functional protein complex discovery and structural characterization. Curr Opin Chem Biol 2023; 74:102305. [PMID: 37071953 DOI: 10.1016/j.cbpa.2023.102305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 04/20/2023]
Abstract
The discovery of functional protein complex and the interrogation of the complex structure-function relationship (SFR) play crucial roles in the understanding and intervention of biological processes. Affinity purification-mass spectrometry (AP-MS) has been proved as a powerful tool in the discovery of protein complexes. However, validation of these novel protein complexes as well as elucidation of their molecular interaction mechanisms are still challenging. Recently, native top-down MS (nTDMS) is rapidly developed for the structural analysis of protein complexes. In this review, we discuss the integration of AP-MS and nTDMS in the discovery and structural characterization of functional protein complexes. Further, we think the emerging artificial intelligence (AI)-based protein structure prediction is highly complementary to nTDMS and can promote each other. We expect the hybridization of integrated structural MS with AI prediction to be a powerful workflow in the discovery and SFR investigation of functional protein complexes.
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Affiliation(s)
- Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shirui Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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25
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Peng T, Das T, Ding K, Hang HC. Functional analysis of protein post-translational modifications using genetic codon expansion. Protein Sci 2023; 32:e4618. [PMID: 36883310 PMCID: PMC10031814 DOI: 10.1002/pro.4618] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Post-translational modifications (PTMs) of proteins not only exponentially increase the diversity of proteoforms, but also contribute to dynamically modulating the localization, stability, activity, and interaction of proteins. Understanding the biological consequences and functions of specific PTMs has been challenging for many reasons, including the dynamic nature of many PTMs and the technical limitations to access homogenously modified proteins. The genetic code expansion technology has emerged to provide unique approaches for studying PTMs. Through site-specific incorporation of unnatural amino acids (UAAs) bearing PTMs or their mimics into proteins, genetic code expansion allows the generation of homogenous proteins with site-specific modifications and atomic resolution both in vitro and in vivo. With this technology, various PTMs and mimics have been precisely introduced into proteins. In this review, we summarize the UAAs and approaches that have been recently developed to site-specifically install PTMs and their mimics into proteins for functional studies of PTMs.
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Affiliation(s)
- Tao Peng
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
- Institute of Chemical Biology, Shenzhen Bay LaboratoryShenzhenChina
| | - Tandrila Das
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
| | - Ke Ding
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
| | - Howard C. Hang
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
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26
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Harel O, Jbara M. Chemical Synthesis of Bioactive Proteins. Angew Chem Int Ed Engl 2023; 62:e202217716. [PMID: 36661212 DOI: 10.1002/anie.202217716] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/21/2023]
Abstract
Nature has developed a plethora of protein machinery to operate and maintain nearly every task of cellular life. These processes are tightly regulated via post-expression modifications-transformations that modulate intracellular protein synthesis, folding, and activation. Methods to prepare homogeneously and precisely modified proteins are essential to probe their function and design new bioactive modalities. Synthetic chemistry has contributed remarkably to protein science by allowing the preparation of novel biomacromolecules that are often challenging or impractical to prepare via common biological means. The ability to chemically build and precisely modify proteins has enabled the production of new molecules with novel physicochemical properties and programmed activity for biomedical research, diagnostic, and therapeutic applications. This minireview summarizes recent developments in chemical protein synthesis to produce bioactive proteins, with emphasis on novel analogs with promising in vitro and in vivo activity.
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Affiliation(s)
- Omer Harel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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27
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Saebi A, Brown JS, Marando VM, Hartrampf N, Chumbler NM, Hanna S, Poskus M, Loas A, Kiessling LL, Hung DT, Pentelute BL. Rapid Single-Shot Synthesis of the 214 Amino Acid-Long N-Terminal Domain of Pyocin S2. ACS Chem Biol 2023; 18:518-527. [PMID: 36821521 PMCID: PMC10460144 DOI: 10.1021/acschembio.2c00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The impermeable outer membrane of Pseudomonas aeruginosa is bypassed by antibacterial proteins known as S-type pyocins. Because of their properties, pyocins are investigated as a potential new class of antimicrobials against Pseudomonas infections. Their production and modification, however, remain challenging. To address this limitation, we employed automated fast-flow peptide synthesis for the rapid production of a pyocin S2 import domain. The N-terminal domain sequence (PyS2NTD) was synthesized in under 10 h and purified to yield milligram quantities of the desired product. To our knowledge, the 214 amino acid sequence of PyS2NTD is among the longest peptides produced from a "single-shot" synthesis, i.e., made in a single stepwise route without the use of ligation techniques. Biophysical characterization of the PyS2NTD with circular dichroism was consistent with the literature reports. Fluorescently labeled PyS2NTD binds to P. aeruginosa expressing the cognate ferripyoverdine receptor and is taken up into the periplasm. This selective uptake was validated with confocal and super resolution microscopy, flow cytometry, and fluorescence recovery after photobleaching. These modified, synthetic S-type pyocin domains can be used to probe import mechanisms of P. aeruginosa and leveraged to develop selective antimicrobial agents that bypass the outer membrane.
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Affiliation(s)
- Azin Saebi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Joseph S Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Victoria M Marando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicole M Chumbler
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mackenzie Poskus
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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28
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Sun Z, Wei T, Cao Y, Li X. Protocol for semisynthesis of serotonylated histone H3 by rapid protein desulfurization in tandem with native chemical ligation. STAR Protoc 2023; 4:102042. [PMID: 36825812 PMCID: PMC9867976 DOI: 10.1016/j.xpro.2022.102042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/30/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Here, we present a protocol of rapid protein desulfurization in tandem with native chemical ligation for facile syntheses of proteins with site-specific modifications. We describe using sodium tetraethylborate (NaBEt4) to carry out this desulfurization in an add-and-done manner under ambient conditions without requirement of inert atmosphere protection, UV irradiation, heating, or exogenous thiol additives. Specifically, we detail the semisynthesis of serotonylated histone H3(H3Q5ser) via one-pot ligation desulfurization. This protocol can be applied to synthesize proteins of interest with homogenous post-translational modifications. For complete information on the generation and use of this protocol, please refer to Sun et al. (2022).1.
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Affiliation(s)
- Zhenquan Sun
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
| | - Tongyao Wei
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Yihui Cao
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Xuechen Li
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China.
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29
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Wu H, Tan Y, Ngai WL, Li X. Total synthesis of interleukin-2 via a tunable backbone modification strategy. Chem Sci 2023; 14:1582-1589. [PMID: 36794182 PMCID: PMC9906654 DOI: 10.1039/d2sc05660g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/06/2023] [Indexed: 01/08/2023] Open
Abstract
Chemical synthesis of hydrophobic proteins presents a formidable task as they are often difficultly achieved via peptide synthesis, purification, and peptide ligation. Thus, peptide solubilizing strategies are needed to integrate with peptide ligation to achieve protein total synthesis. Herein, we report a tunable backbone modification strategy, taking advantage of the tunable stability of the Cys/Pen ligation intermediate, which allows for readily introducing a solubilizing tag for both peptide purification and ligation processes. The effectiveness of this strategy was demonstrated by the chemical synthesis of interleukin-2.
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Affiliation(s)
- Hongxiang Wu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Yi Tan
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Wai Lok Ngai
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology Qingdao 266237 P. R. China
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30
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Huppelschoten Y, Buchardt J, Nielsen TE, van der Heden van Noort GJ. Total Linear Chemical Synthesis of LC3A and LC3B. Methods Mol Biol 2023; 2602:51-61. [PMID: 36446966 DOI: 10.1007/978-1-0716-2859-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Solid-phase peptide synthesis (SPPS) enables the synthesis of chemically modified peptides and proteins. Chemically synthesized ubiquitin(-like) proteins containing a fluorescent tag or reactive warhead have proven to be important tools in elucidating biological processes. Here, we describe the first fully synthetic method for the linear synthesis of two LC3 ubiquitin-like proteins using disaggregating building blocks and heated synthesis. Both LC3A and LC3B were synthesized and equipped with a fluorescent rhodamine tag, followed by folding of the proteins and liquid chromatography-mass spectrometry and SDS-PAGE analysis to prove that the quality of the synthetic material is comparable to expressed material.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
- Global Research Technologies, Novo Nordisk, Novo Nordisk Park, Måløv, Denmark
| | - Jens Buchardt
- Global Research Technologies, Novo Nordisk, Novo Nordisk Park, Måløv, Denmark
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31
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Kloet MS, van der Heden van Noort GJ. Synthetic Diubiquitin Fluorogenic Substrates to Study DUBs. Methods Mol Biol 2023; 2591:17-24. [PMID: 36350540 DOI: 10.1007/978-1-0716-2803-4_2] [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: 06/16/2023]
Abstract
Development of (semi-)synthetic methods to prepare ubiquitin (Ub)-based reagents has proven to be helpful in the classification of deubiquitinating proteases (DUBs). To study DUB selectivity for one or more of the eight possible poly-Ub chains, fluorogenic assay reagents have been reported relying on the appearance of a fluorescent signal upon DUB-mediated cleavage of the reagent. In this protocol, we describe the use of such an assay to profile the selectivity of TRABID, a member of the OTU family of DUBs.
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Affiliation(s)
- Max S Kloet
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
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32
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Huppelschoten Y, van der Heden van Noort GJ. State of the art in (semi-)synthesis of Ubiquitin- and Ubiquitin-like tools. Semin Cell Dev Biol 2022; 132:74-85. [PMID: 34961664 DOI: 10.1016/j.semcdb.2021.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022]
Abstract
Protein ubiquitination is a key post-translational modification in regulating many fundamental cellular processes and dysregulation of these processes can give rise to a vast array of diseases. Unravelling the molecular mechanisms of ubiquitination hence is an important area in current ubiquitin research with as aim to understand this enigmatic process. The complexity of ubiquitin (Ub) signaling arises from the large variety of Ub conjugates, where Ub is attached to other Ub proteins, Ub-like proteins, and protein substrates. The chemical preparation of such Ub conjugates in high homogeneity and in adequate amounts contributes greatly to the deciphering of Ub signaling. The strength of these chemically synthesized conjugates lies in the chemo-selectivity in which they can be created that are sometimes difficult to obtain using biochemical methodology. In this review, we will discuss the progress in the chemical protein synthesis of state-of-the-art Ub and Ub-like chemical probes, their unique concepts and related discoveries in the ubiquitin field.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Dept. Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands; Global Research Technologies, Novo Nordisk Research Park, Måløv, Denmark
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33
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Rezvani Ghomi E, Niazi M, Ramakrishna S. The evolution of wound dressings: From traditional to smart dressings. POLYM ADVAN TECHNOL 2022. [DOI: 10.1002/pat.5929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Erfan Rezvani Ghomi
- Center for Nanotechnology and Sustainability, Department of Mechanical Engineering College of Design and Engineering Singapore Singapore
| | - Mina Niazi
- Department of Biomedical Engineering National University of Singapore Singapore Singapore
| | - Seeram Ramakrishna
- Center for Nanotechnology and Sustainability, Department of Mechanical Engineering College of Design and Engineering Singapore Singapore
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34
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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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35
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Proteins through the eyes of an organic chemist. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Nakatsu K, Okamoto A, Hayashi G, Murakami H. Repetitive Thiazolidine Deprotection Using a Thioester‐Compatible Aldehyde Scavenger for One‐Pot Multiple Peptide Ligation**. Angew Chem Int Ed Engl 2022; 61:e202206240. [DOI: 10.1002/anie.202206240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Koki Nakatsu
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology Graduate School of Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Research Center for Advanced Science and Technology The University of Tokyo 4-6-1 Komaba Meguro-ku Tokyo 153-8904 Japan
| | - 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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37
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Wu H, Wei T, Ngai WL, Zhou H, Li X. Ligation Embedding Aggregation Disruptor Strategy Enables the Chemical Synthesis of PD-1 Immunoglobulin and Extracellular Domains. J Am Chem Soc 2022; 144:14748-14757. [PMID: 35918891 DOI: 10.1021/jacs.2c05350] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Chemical synthesis of proteins with aggregable or colloidal peptide segments presents a formidable task, as such peptides prove to be difficult for both solid-phase peptide synthesis and peptide ligation. To address this issue, we have developed ligation embedding aggregation disruptor (LEAD) as an effective strategy for the chemical synthesis of difficult-to-obtain proteins. The N,O/S-benzylidene acetals generated from Ser/Thr ligation and Cys/Pen ligation are found to effectively disrupt peptide aggregation, and they can be carried for sequential ligations toward protein synthesis. The effectiveness and generality of this strategy have been demonstrated with total syntheses of programmed cell death protein 1 immunoglobulin like V-type domain and extracellular domain.
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Affiliation(s)
- Hongxiang Wu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Tongyao Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Wai Lok Ngai
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Haiyan Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
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38
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Hayashi G, Nakatsu K, Okamoto A, Murakami H. Repetitive Thiazolidine Deprotection Using a Thioester‐Compatible Aldehyde Scavenger for One‐Pot Multiple Peptide Ligation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gosuke Hayashi
- Nagoya University Graduate School of Engineering School of Engineering: Nagoya Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Biomolecular Engineering Furo-choChikusa-ku 464-8603 Nagoya JAPAN
| | - Koki Nakatsu
- Nagoya University Graduate School of Engineering School of Engineering: Nagoya Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Biomolecular Engineering JAPAN
| | - Akimitsu Okamoto
- The University of Tokyo Graduate School of Engineering Faculty of Engineering: Tokyo Daigaku Daigakuin Kogakukei Kenkyuka Kogakubu Chemistry and Biotechnology JAPAN
| | - Hiroshi Murakami
- Nagoya University Graduate School of Engineering School of Engineering: Nagoya Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Biomolecular Engineering JAPAN
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39
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Cai J, Zhao L, Li Y, He C, Wang C, Duan C. Binding of Dual-Function Hybridized Metal -Organic Capsules to Enzymes for Cascade Catalysis. JACS AU 2022; 2:1736-1746. [PMID: 35911460 PMCID: PMC9327082 DOI: 10.1021/jacsau.2c00322] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The combination of chemo- and biocatalysis for multistep syntheses provides attractive advantages in terms of evolvability, promiscuity, and sustainability striving for desirable catalytic performance. Through the encapsulation of flavin analogues by both NADH and heme mimics codecorated heteroleptic metal-organic capsules, herein, we report a progressive host-guest strategy to imitate cytochrome P450s catalysis for cascade oxidative coupling catalysis. Besides the construction of stable dual-function metal-organic capsules and the modification of cofactor-decorated capsules at the domain of enzymes, this supramolecular strategy involves multistage directional electron flow, affording reactive ferric peroxide species for inducing oxygenation. Under light irradiation, the metal-organic capsule selectively converts stilbene to oxidative coupling products (including 2-oxo-1,2-diphenylethyl formate, 2-alkoxy-1,2-diphenylethanone) in tandem with enzymatic reactions respectively, at the domain of natural enzymes. The ingenious combination of capsules and enzymes with the in situ-regenerated capsule-loaded NADH cofactor promises non-native coupling reactions by forming regional cooperation and division. This abiotic-biotic conjugated host-guest strategy is conducive to the de novo creation of multifunctional components approaching active enzymatic sites for reinforced matter and energy transporting, demonstrating a key role of multicomponent supramolecular catalysts for one-pot integrated catalytic conversions.
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Affiliation(s)
- Junkai Cai
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
- State
Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210023, People’s Republic
of China
| | - Liang Zhao
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Yanan Li
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Cheng He
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Chong Wang
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Chunying Duan
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
- State
Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210023, People’s Republic
of China
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40
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Posttranslational Chemical Mutagenesis Methods to Insert Posttranslational Modifications into Recombinant Proteins. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144389. [PMID: 35889261 PMCID: PMC9316245 DOI: 10.3390/molecules27144389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Posttranslational modifications (PTMs) dramatically expand the functional diversity of the proteome. The precise addition and removal of PTMs appears to modulate protein structure and function and control key regulatory processes in living systems. Deciphering how particular PTMs affect protein activity is a current frontier in biology and medicine. The large number of PTMs which can appear in several distinct positions, states, and combinations makes preparing such complex analogs using conventional biological and chemical tools challenging. Strategies to access homogeneous and precisely modified proteins with desired PTMs at selected sites and in feasible quantities are critical to interpreting their molecular code. Here, we summarize recent advances in posttranslational chemical mutagenesis and late-stage functionalization chemistry to transfer novel PTM mimicry into recombinant proteins with emphasis on novel transformations.
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41
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Zhao J, Liu J, Liu X, Ye F, Wang S, Wang P. Semi-synthesis of interleukin-1α via expressed threonine ligation and native chemical ligation-desulfurization. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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Liao P, Liu H, He C. Chemical synthesis of human selenoprotein F and elucidation of its thiol-disulfide oxidoreductase activity. Chem Sci 2022; 13:6322-6327. [PMID: 35733894 PMCID: PMC9159075 DOI: 10.1039/d2sc00492e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/06/2022] [Indexed: 01/16/2023] Open
Abstract
Selenoprotein F (SelF) is an endoplasmic reticulum-residing eukaryotic protein that contains a selenocysteine (Sec) residue. It has been suggested to be involved in a number of physiological processes by acting as a thiol-disulfide oxidoreductase, but the exact role has remained unclear due to the lack of a reliable production method. We document herein a robust synthesis of the human SelF through a three-segment two-ligation semisynthesis strategy. Highlighted in this synthetic route are the use of a mild desulfurization process to protect the side-chain of the Sec residue from being affected and the simultaneous removal of acetamidomethyl and p-methoxybenzyl protection groups by PdCl2, thus facilitating the synthesis of multi-milligrams of homogenous SelF. The reduction potential of SelF was determined and the thiol-disulfide oxidoreductase activity was further supported by its ability to catalyze the reduction and isomerization of disulfide bonds.
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Affiliation(s)
- Peisi Liao
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
| | - Hongmei Liu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology Wuhan 430074 China
- Shenzhen Huazhong University of Science and Technology Research Institute Shenzhen 518057 China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
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43
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Wan C, Yang D, Qin X, Xue Z, Guo X, Hou Z, Jiang C, Yin F, Wang R, Li Z. Flavin catalyzed desulfurization of peptides and proteins in aqueous media. Org Biomol Chem 2022; 20:4105-4109. [PMID: 35546316 DOI: 10.1039/d2ob00641c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A biomimetic method has been established for the chemo-selective desulfurization of cysteinyl peptides and proteins in aqueous media. The derivatives of biocatalytic cofactors, flavins, were found to be efficient photosensitizers in a thiyl-radical-mediated desulfurization of Cys. The reaction was conducted in an ultrafast manner with both polypeptides and proteins.
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Affiliation(s)
- Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China.
| | - Dongyan Yang
- College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xuan Qin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China.
| | - Ziyi Xue
- College of chemistry & chemical engineering, Lanzhou University, Lanzhou, 730000, China
| | - Xiaochun Guo
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China.
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China.
| | - Chenran Jiang
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, China.
| | - Feng Yin
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, China.
| | - Rui Wang
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, China.
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China. .,Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, China.
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44
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Li T, Zhang Y, Li T, Zhuang H, Wang F, Wang N, Schmidt RR, Peng P. Divergent Synthesis of Core m1, Core m2 and Core m3
O
‐Mannosyl
Glycopeptides via a Chemoenzymatic Approach. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tianlu Li
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate Based Medicine, Shandong University Qingdao Shandong 266237 China
| | - Youqin Zhang
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate Based Medicine, Shandong University Qingdao Shandong 266237 China
| | - Tong Li
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate Based Medicine, Shandong University Qingdao Shandong 266237 China
| | - Haoru Zhuang
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate Based Medicine, Shandong University Qingdao Shandong 266237 China
| | - Fengshan Wang
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate Based Medicine, Shandong University Qingdao Shandong 266237 China
| | - Ning Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
| | | | - Peng Peng
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate Based Medicine, Shandong University Qingdao Shandong 266237 China
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45
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Asahina Y, Ando T, Hojo H. Toward the chemical syntheses of fucosylated peptides: A combination of protecting groups for the hydroxy groups of fucose. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuya Asahina
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871
| | - Tatsuya Ando
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871
| | - Hironobu Hojo
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871
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46
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Chen Q, Yuan G, Yuan T, Zeng H, Zou ZR, Tu ZC, Gao J, Zou Y. Set of Cytochrome P450s Cooperatively Catalyzes the Synthesis of a Highly Oxidized and Rearranged Diterpene-Class Sordarinane Architecture. J Am Chem Soc 2022; 144:3580-3589. [PMID: 35170947 DOI: 10.1021/jacs.1c12427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cytochrome P450s are one of the most versatile oxidases that catalyze significant and unique chemical transformations for the construction of complex structural frameworks during natural product biosynthesis. Here, we discovered a set of P450s, including SdnB, SdnH, SdnF, and SdnE, that cooperatively catalyzes the reshaping of the inert cycloaraneosene framework to form a highly oxidized and rearranged sordarinane architecture. Among them, SdnB is confirmed to be the first P450 (or oxidase) that cleaves the C-C bond of the epoxy residue to yield formyl groups in pairs. SdnF selectively oxidizes one generated formyl group to a carboxyl group and accelerates the final Diels-Alder cyclization to furnish the sordarinane architecture. Our work greatly enriches the enzyme functions of the P450 superfamily, supplies the missing skills of the P450 synthetic toolbox, and supports them as biocatalysts in further applications toward the synthesis of new chemical entities.
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Affiliation(s)
- Qibin Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Guanyin Yuan
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Tao Yuan
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Huiting Zeng
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Zheng-Rong Zou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Zong-Cai Tu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Jie Gao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
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47
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Bedding MJ, Kulkarni SS, Payne RJ. Diselenide-selenoester ligation in the chemical synthesis of proteins. Methods Enzymol 2022; 662:363-399. [PMID: 35101218 DOI: 10.1016/bs.mie.2021.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Peptides and proteins represent an important class of biomolecules responsible for a plethora of structural and functional roles in vivo. Following their translation on the ribosome, the majority of eukaryotic proteins are post-translationally modified, leading to a proteome that is much larger than the number of genes present in a given organism. In order to understand the functional role of a given protein modification, it is necessary to access peptides and proteins bearing homogeneous and site-specific modifications. Accordingly, there has been significant research effort centered on the development of peptide ligation methodologies for the chemical synthesis of modified proteins. In this chapter we outline the discovery and development of a contemporary methodology called the diselenide-selenoester ligation (DSL) that enables the rapid and efficient fusion of peptide fragments to generate synthetic proteins. The practical aspects of using DSL for the preparation of chemically modified peptides and proteins in the laboratory is described. In addition, recent advances in the application of the methodology are outlined, exemplified by the synthesis and biological evaluation of a number of complex protein targets.
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Affiliation(s)
- Max J Bedding
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW, Australia
| | - Sameer S Kulkarni
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW, Australia.
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48
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Liu J, Wei T, Tan Y, Liu H, Li X. Enabling chemical protein (semi)synthesis via reducible solubilizing tags (RSTs). Chem Sci 2022; 13:1367-1374. [PMID: 35222920 PMCID: PMC8809390 DOI: 10.1039/d1sc06387a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 01/11/2023] Open
Abstract
The reducible solubilizing tag strategy served as a simple and powerful method for the chemical synthesis and semi-synthesis via Ser/Thr ligation and Cys/Pen ligation of extensive self-assembly peptides, membrane proteins with poor solubility.
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Affiliation(s)
- Jiamei Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Tongyao Wei
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Yi Tan
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Heng Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
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49
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Jiang H, Chen W, Wang J, Zhang R. Selective N-terminal modification of peptides and proteins: Recent progresses and applications. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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50
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Huang DL, Li Y, Zheng JS. Removable Backbone Modification (RBM) Strategy for the Chemical Synthesis of Hydrophobic Peptides/Proteins. Methods Mol Biol 2022; 2530:241-256. [PMID: 35761053 DOI: 10.1007/978-1-0716-2489-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chemical synthesis can provide hydrophobic proteins with natural or man-made modifications (e.g. S-palmitoylation, site-specific isotope labeling and mirror-image proteins) that are difficult to obtain through the recombinant expression technology. The difficulty of chemical synthesis of hydrophobic proteins stems from the hydrophobic nature. Removable backbone modificaiton (RBM) strategy has been developed for solubilizing the hydrophobic peptides/proteins. Here we take the chemical synthesis of a S-palmitoylated peptide as an example to describe the detailed procedure of RBM strategy. Three critical steps of this protocol are: (1) installation of Lys6-tagged RBM groups into the peptides by Fmoc (9-fluorenylmethyloxycarbonyl) solid-phase peptide synthesis, (2) chemical ligation of the peptides, and (3) removal of the RBM tags by TFA (trifluoroacetic acid) cocktails to give the target peptide.
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Affiliation(s)
- Dong-Liang Huang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Ying Li
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Ji-Shen Zheng
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China.
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