1
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Liu Y, Kajihara Y, Okamoto R. Post-translational activation of the C-terminus of polypeptides for the synthesis of peptide thioesters and peptide thioester surrogates. Front Chem 2024; 12:1424953. [PMID: 39076613 PMCID: PMC11284063 DOI: 10.3389/fchem.2024.1424953] [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: 04/29/2024] [Accepted: 05/31/2024] [Indexed: 07/31/2024] Open
Abstract
Semisynthesis using recombinant polypeptides is a powerful approach for the synthesis of proteins having a variety of modifications. Peptide thioesters, of which the peptide C-terminus is activated by a thioester, are utilized for coupling peptide building blocks. Biological methods employing intein have been a center for the C-terminal thioesterification of recombinant polypeptides. Chemical activation has emerged as an alternative methodology for synthesizing peptide thioesters from recombinant polypeptides. Chemical reactions are compatible with various solutions containing organic solvents, chaotropic reagents, or detergents that are generally incompatible with biomolecules such as intein. Despite the potential utility of chemical activation, available methods remain limited. This article introduces the methods for the chemical activation of a peptide C-terminus applied to the chemical synthesis of proteins. By showcasing these methodologies, we aim to accelerate the advancement of new chemical reactions and methodologies and broaden the frontiers for the chemical synthesis of proteins.
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Affiliation(s)
- Yanbo Liu
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- Forefront Research Center, Osaka University, Osaka, Japan
| | - Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- Forefront Research Center, Osaka University, Osaka, Japan
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2
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Tang J, Hao M, Liu J, Chen Y, Wufuer G, Zhu J, Zhang X, Zheng T, Fang M, Zhang S, Li T, Ge S, Zhang J, Xia N. Design of a recombinant asparaginyl ligase for site-specific modification using efficient recognition and nucleophile motifs. Commun Chem 2024; 7:87. [PMID: 38637620 PMCID: PMC11026461 DOI: 10.1038/s42004-024-01173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Asparaginyl ligases have been extensively utilized as valuable tools for site-specific bioconjugation or surface-modification. However, the application is hindered by the laborious and poorly reproducible preparation processes, unstable activity and ambiguous substrate requirements. To address these limitations, this study employed a structure-based rational approach to obtain a high-yield and high-activity protein ligase called OaAEP1-C247A-aa55-351. It was observed that OaAEP1-C247A-aa55-351 exhibits appreciable catalytic activities across a wide pH range, and the addition of the Fe3+ metal ion effectively enhances the catalytic power. Importantly, this study provides insight into the recognition and nucleophile peptide profiles of OaAEP1-C247A-aa55-351. The ligase demonstrates a higher recognition ability for the "Asn-Ala-Leu" motif and an N-terminus "Arg-Leu" as nucleophiles, which significantly increases the reaction yield. Consequently, the catalytic activity of OaAEP1-C247A-aa55-351 with highly efficient recognition and nucleophile motif, "Asn-Ala-Leu" and "Arg-Leu" under the buffer containing Fe3+ is 70-fold and 2-fold higher than previously reported OaAEP1-C247A and the most efficient butelase-1, respectively. Thus, the designed OaAEP1-C247A-aa55-351, with its highly efficient recognition and alternative nucleophile options, holds promising potential for applications in protein engineering, chemo-enzymatic modification, and the development of drugs.
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Affiliation(s)
- Jiabao Tang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mengling Hao
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Junxian Liu
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Yaling Chen
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Gulimire Wufuer
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Jie Zhu
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, 213164, Changzhou, China
| | - Xuejie Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingquan Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mujin Fang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Shiyin Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingdong Li
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Shengxiang Ge
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Jun Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
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3
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Hemu X, Chan NY, Liew HT, Hu S, Zhang X, Serra A, Lescar J, Liu CF, Tam JP. Substrate-binding glycine residues are major determinants for hydrolase and ligase activity of plant legumains. THE NEW PHYTOLOGIST 2023; 238:1534-1545. [PMID: 36843268 DOI: 10.1111/nph.18841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Peptide asparaginyl ligases (PALs) are useful tools for precision modifications of proteins and live-cell surfaces by ligating peptides after Asn/Asp (Asx). They share high sequence and structural similarity to plant legumains that are generally known as asparaginyl endopeptidases (AEPs), thus making it challenging to identify PALs from AEPs. In this study, we investigate 875 plant species from algae to seed plants with available sequence data in public databases to identify new PALs. We conducted evolutionary trace analysis on 1500 plant legumains, including eight known PALs, to identify key residues that could differentiate ligases and proteases, followed by recombinant expression and functional validation of 16 novel legumains. Previously, we showed that the substrate-binding sequences flanking the catalytic site can strongly influence the enzymatic direction of a legumain and which we named as ligase-activity determinants (LADs). Here, we show that two conserved substrate-binding Gly residues of LADs are critical, but negative determinants for ligase activity. Our results suggest that specific glycine residues are molecular determinants to identify PALs and AEPs as two different legumain subfamilies, accounting for c. 1% and 88%, respectively.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Heng Tai Liew
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Side Hu
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Aida Serra
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- Neuroscience Area, +Pec Proteomics Research Group (+PPRG), Faculty of Medicine, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRB Lleida), University of Lleida, Av. Rovira Roure, 80, Lleida, 25198, Spain
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
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4
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Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
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Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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5
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Muhammad T, Houssen WE, Thomas L, Alexandru-Crivac CN, Gunasekera S, Jaspars M, Göransson U. Exploring the Limits of Cyanobactin Macrocyclase PatGmac: Cyclization of PawS-Derived Peptide Sunflower Trypsin Inhibitor-1 and Cyclotide Kalata B1. JOURNAL OF NATURAL PRODUCTS 2023; 86:566-573. [PMID: 36917740 PMCID: PMC10043927 DOI: 10.1021/acs.jnatprod.2c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Indexed: 06/18/2023]
Abstract
The subtilisin-like macrocyclase PatGmac is produced by the marine cyanobacterium Prochloron didemni. This enzyme is involved in the last step of the biosynthesis of patellamides, a cyanobactin type of ribosomally expressed and post-translationally modified cyclic peptides. PatGmac recognizes, cleaves, and cyclizes precursor peptides after a specific recognition motif comprised of a C-terminal tail with the sequence motif -AYDG. The result is the native macrocyclic patellamide, which has eight amino acid residues. Macrocyclase activity can be exploited by incorporating that motif in other short linear peptide precursors, which then are formed into head-to-tail cyclized peptides. Here, we explore the possibility of using PatGmac in the cyclization of peptides larger than the patellamides, namely, the PawS-derived peptide sunflower trypsin inhibitor-1 (SFTI-1) and the cyclotide kalata B1. These peptides fall under two distinct families of disulfide constrained macrocyclic plant peptides. They are both implicated as scaffolds for drug design due to their structures and unusual stability. We show that PatGmac can be used to efficiently cyclize the 14 amino acid residue long SFTI-1, but less so the 29 amino acid residue long kalata B1.
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Affiliation(s)
- Taj Muhammad
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Box 591, SE-75124 Uppsala, Sweden
| | - Wael E Houssen
- Department
of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Aberdeen AB24 3UE, Scotland, U.K.
- Institute
of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K.
| | - Louise Thomas
- Department
of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Aberdeen AB24 3UE, Scotland, U.K.
- Institute
of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K.
| | - Cristina-Nicoleta Alexandru-Crivac
- Department
of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Aberdeen AB24 3UE, Scotland, U.K.
- Institute
of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K.
| | - Sunithi Gunasekera
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Box 591, SE-75124 Uppsala, Sweden
| | - Marcel Jaspars
- Department
of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Aberdeen AB24 3UE, Scotland, U.K.
| | - Ulf Göransson
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Box 591, SE-75124 Uppsala, Sweden
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6
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Xia Y, Li F, Zhang X, Balamkundu S, Tang F, Hu S, Lescar J, Tam JP, Liu CF. A Cascade Enzymatic Reaction Scheme for Irreversible Transpeptidative Protein Ligation. J Am Chem Soc 2023; 145:6838-6844. [PMID: 36924109 DOI: 10.1021/jacs.2c13628] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Enzymatic peptide ligation holds great promise in the study of protein functions and development of protein therapeutics. Owing to their high catalytic efficiency and a minimal tripeptide recognition motif, peptidyl asparaginyl ligases (PALs) are particularly useful tools for bioconjugation. However, as an inherent limitation of transpeptidases, PAL-mediated ligation is reversible, requiring a large excess of one of the ligation partners to shift the reaction equilibrium in the forward direction. Herein, we report a method to make PAL-mediated intermolecular ligation irreversible by coupling it to glutaminyl cyclase (QC)-catalyzed pyroglutamyl formation. In this method, the acyl donor substrate of PALs is designed to have glutamine at the P1' position of the Asn-P1'-P2' tripeptide PAL recognition motif. Upon ligation with an acyl acceptor substrate, the acyl donor substrate releases a leaving group in which the exposed N-terminal glutamine is cyclized by QC, quenching the Gln Nα-amine in a lactam. Using this method, PAL-mediated ligation can achieve near-quantitative yields even at an equal molar ratio between the two ligation partners. We have demonstrated this method for a wide range of applications, including protein-to-protein ligations. We anticipate that this cascade enzymatic reaction scheme will make PAL enzymes well suited for numerous new uses in biotechnology.
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Affiliation(s)
- Yiyin Xia
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Fupeng Li
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | | | - Fan Tang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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7
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Miyata T, Shimamura H, Asano R, Yoshida W. Universal Design of Luciferase Fusion Proteins for Epigenetic Modifications Detection Based on Bioluminescence Resonance Energy Transfer. Anal Chem 2023; 95:3799-3805. [PMID: 36748925 DOI: 10.1021/acs.analchem.2c05066] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Global hypomethylation and promoter hypermethylation of tumor-suppressor genes are the hallmarks of cancer. We previously reported a global DNA methylation level sensing system based on dual-color bioluminescence resonance energy transfer (BRET) using methyl-CpG binding domain (MBD)-fused firefly luciferase (Fluc) and unmethyl-CpG binding domain (CXXC)-fused Oplophorus luciferase (Oluc). Moreover, BRET-based hydroxymethylation and hemi-methylation level sensing systems have been developed using hydroxymethyl-CpG and hemi-methyl-CpG binding domain-fused Fluc. These studies suggest that target epigenetic modifications can be simultaneously quantified using target-modification-binding protein-fused luciferases. In this study, we focused on the SnoopTag (SnT)/SnoopCatcher (SnC) protein ligation system to establish a universal design for fusion protein construction for any combination. SnT spontaneously forms an isopeptide bond with SnC; therefore, any kind of fusion protein would be constructed by the SnT/SnC system. To establish the proof of concept, MBD-SnT, CXXC-SnT, and SnC-Oluc were prepared and ligated MBD-SnT or CXXC-SnT to SnC-Oluc. The ligation products of MBD-SnT-SnC-Oluc and CXXC-SnT-SnC-Oluc showed luciferase activity and specific binding activity to methyl-CpG and unmethyl-CpG, respectively. The BRET signal using MBD-SnT-SnC-Oluc and CXXC-SnT-SnC-Oluc increased the amount of methyl-CpG and unmethyl-CpG in genomic DNA, respectively. There was a significant negative correlation between the BRET signals; therefore, the global DNA methylation level was quantified using the BRET signals (R2 = 0.99, and R.S.D. <3.5%). These results indicate that the SnT/SnC protein ligation system can be utilized to construct target modification-binding protein-fused luciferases in any combination that detects target modifications in genomic DNA based on BRET.
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Affiliation(s)
- Takamichi Miyata
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo192-0982, Japan
| | - Hazuki Shimamura
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo192-0982, Japan
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo184-8588, Japan
| | - Wataru Yoshida
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo192-0982, Japan.,School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo192-0982, Japan
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8
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Hemu X, Zhang X, Chang HY, Poh JE, Tam JP. Consensus design and engineering of an efficient and high-yield peptide asparaginyl ligase for protein cyclization and ligation. J Biol Chem 2023; 299:102997. [PMID: 36764523 PMCID: PMC10017362 DOI: 10.1016/j.jbc.2023.102997] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Plant legumains are Asn/Asp-specific endopeptidases that have diverse functions in plants. Peptide asparaginyl ligases (PALs) are a special legumain subtype that primarily catalyze peptide bond formation rather than hydrolysis. PALs are versatile protein engineering tools but are rarely found in nature. To overcome this limitation, here we describe a two-step method to design and engineer a high-yield and efficient recombinant PAL based on commonly found asparaginyl endopeptidases. We first constructed a consensus sequence derived from 1500 plant legumains to design the evolutionarily stable legumain conLEG that could be produced in E. coli with 20-fold higher yield relative to that for natural legumains. We then applied the ligase-activity determinant hypothesis to exploit conserved residues in PAL substrate-binding pockets and convert conLEG into conPAL1-3. Functional studies showed that conLEG is primarily a hydrolase, whereas conPALs are ligases. Importantly, conPAL3 is a superefficient and broadly active PAL for protein cyclization and ligation.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hong Yi Chang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Jin En Poh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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9
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Hu S, El Sahili A, Kishore S, Wong YH, Hemu X, Goh BC, Zhipei S, Wang Z, Tam JP, Liu CF, Lescar J. Structural basis for proenzyme maturation, substrate recognition, and ligation by a hyperactive peptide asparaginyl ligase. THE PLANT CELL 2022; 34:4936-4949. [PMID: 36099055 PMCID: PMC9709980 DOI: 10.1093/plcell/koac281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Peptide ligases are versatile enzymes that can be utilized for precise protein conjugation for bioengineering applications. Hyperactive peptide asparaginyl ligases (PALs), such as butelase-1, belong to a small class of enzymes from cyclotide-producing plants that can perform site-specific, rapid ligation reactions after a target peptide asparagine/aspartic acid (Asx) residue binds to the active site of the ligase. How PALs specifically recognize their polypeptide substrates has remained elusive, especially at the prime binding side of the enzyme. Here we report crystal structures that capture VyPAL2, a catalytically efficient PAL from Viola yedoensis, in an activated state, with and without a bound substrate. The bound structure shows one ligase with the N-terminal polypeptide tail from another ligase molecule trapped at its active site, revealing how Asx inserts in the enzyme's S1 pocket and why a hydrophobic residue is required at the P2' position. Besides illustrating the anchoring role played by P1 and P2' residues, these results uncover a role for the Gatekeeper residue at the surface of the S2 pocket in shifting the nonprime portion of the substrate and, as a result, the activity toward ligation or hydrolysis. These results suggest a picture for proenzyme maturation in the vacuole and will inform the rational design of peptide ligases with tailored specificities.
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Affiliation(s)
- Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
| | - Srujana Kishore
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
| | - Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - Boon Chong Goh
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore City, 138602, Singapore
| | - Sang Zhipei
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - Zhen Wang
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
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10
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Otaka A. Development of Naturally Inspired Peptide and Protein Chemistry. Chem Pharm Bull (Tokyo) 2022; 70:748-764. [DOI: 10.1248/cpb.c22-00623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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11
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Morgan HE, Turnbull WB, Webb ME. Challenges in the use of sortase and other peptide ligases for site-specific protein modification. Chem Soc Rev 2022; 51:4121-4145. [PMID: 35510539 PMCID: PMC9126251 DOI: 10.1039/d0cs01148g] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Site-specific protein modification is a widely-used biochemical tool. However, there are many challenges associated with the development of protein modification techniques, in particular, achieving site-specificity, reaction efficiency and versatility. The engineering of peptide ligases and their substrates has been used to address these challenges. This review will focus on sortase, peptidyl asparaginyl ligases (PALs) and variants of subtilisin; detailing how their inherent specificity has been utilised for site-specific protein modification. The review will explore how the engineering of these enzymes and substrates has led to increased reaction efficiency mainly due to enhanced catalytic activity and reduction of reversibility. It will also describe how engineering peptide ligases to broaden their substrate scope is opening up new opportunities to expand the biochemical toolkit, particularly through the development of techniques to conjugate multiple substrates site-specifically onto a protein using orthogonal peptide ligases. We highlight chemical and biochemical strategies taken to optimise peptide and protein modification using peptide ligases.![]()
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Affiliation(s)
- Holly E Morgan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - W Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Michael E Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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12
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Denda M, Otaka A. Advances in Preparation of Peptide and Protein Thioesters Aiming to Use in Medicinal Sciences. Chem Pharm Bull (Tokyo) 2022; 70:316-323. [DOI: 10.1248/cpb.c21-01019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Masaya Denda
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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13
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Li R, Schmidt M, Zhu T, Yang X, Feng J, Tian Y, Cui Y, Nuijens T, Wu B. Traceless enzymatic protein synthesis without ligation sites constraint. Natl Sci Rev 2022; 9:nwab158. [PMID: 35663243 PMCID: PMC9155641 DOI: 10.1093/nsr/nwab158] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis and semisynthesis offer immense promise for life sciences and have impacted pharmaceutical innovation. The absence of a generally applicable method for traceless peptide conjugation with a flexible choice of junction sites remains a bottleneck for accessing many important synthetic targets, however. Here we introduce the PALME (protein activation and ligation with multiple enzymes) platform designed for sequence-unconstrained synthesis and modification of biomacromolecules. The upstream activating modules accept and process easily accessible synthetic peptides and recombinant proteins, avoiding the challenges associated with preparation and manipulation of activated peptide substrates. Cooperatively, the downstream coupling module provides comprehensive solutions for sequential peptide condensation, cyclization and protein N/C-terminal or internal functionalization. The practical utility of this methodology is demonstrated by synthesizing a series of bioactive targets ranging from pharmaceutical ingredients to synthetically challenging proteins. The modular PALME platform exhibits unprecedentedly broad accessibility for traceless protein synthesis and functionalization, and holds enormous potential to extend the scope of protein chemistry and synthetic biology.
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Affiliation(s)
- Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Marcel Schmidt
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen 6167 RD, the Netherlands
| | - Tong Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinyu Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Feng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu'e Tian
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Timo Nuijens
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen 6167 RD, the Netherlands
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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14
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Mo Z, Lin S, Chen W, He C. Protein Ligation and Labeling Enabled by a C-Terminal Tetracysteine Tag. Angew Chem Int Ed Engl 2022; 61:e202115377. [PMID: 35060269 DOI: 10.1002/anie.202115377] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Indexed: 01/01/2023]
Abstract
The hydrazinolysis of S-cyanylated peptide provides an alternative way to afford protein α-hydrazide, a key reagent used in native chemical ligation (NCL), without the aid of any inteins or enzymes. The currently used non-selective S-cyanylation, however, allows no other cysteine in the protein besides the one at the cleavage site. Herein, we report a regioselective S-cyanylation and hydrazinolysis strategy achieved via the fusion of a tetracysteine tag to the C-terminal of the protein of interest. We term it tetracysteine enabled protein ligation (TCEPL). While highly selective, the strategy is applicable for proteins expressed as inclusion bodies, and this was showcased by the efficient semi-synthesis of an iron-sulfur protein rubredoxin and the catalytic and hinge domains of matrix metalloprotease-14 (MMP-14) containing 207 amino acid residues. Furthermore, the TCEPL strategy was exploited for protein C-terminal labeling with amino reagents bearing a variety of functional groups, demonstrating its versatility and generality.
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Affiliation(s)
- Zeyuan Mo
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, P. R. China
| | - Shaomin Lin
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, P. R. China
| | - Wentao Chen
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, P. R. China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, P. R. China
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15
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Mo Z, Lin S, Chen W, He C. Protein Ligation and Labeling Enabled by a C‐Terminal Tetracysteine Tag. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zeyuan Mo
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 P. R. China
| | - Shaomin Lin
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 P. R. China
| | - Wentao Chen
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 P. R. China
| | - Chunmao He
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 P. R. China
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16
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Zhang D, Wang Z, Hu S, Chan NY, Liew HT, Lescar J, Tam JP, Liu CF. Asparaginyl Endopeptidase-Mediated Protein C-Terminal Hydrazinolysis for the Synthesis of Bioconjugates. Bioconjug Chem 2022; 33:238-247. [PMID: 34985285 DOI: 10.1021/acs.bioconjchem.1c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asparaginyl endopeptidases (AEPs) are cysteinyl enzymes naturally catalyzing the hydrolysis and transpeptidation reactions at Asx-Xaa bonds. These reactions go by a common acyl-enzyme thioester intermediate, which is either attacked by water (for a protease-AEP) or by a peptidic amine nucleophile (for a ligase-AEP) to form the respective hydrolysis or aminolysis product. Herein, we show that hydrazine and hydroxylamine, two α-effect nucleophiles, are capable of resolving the thioester intermediate to yield peptide and protein products containing a C-terminal hydrazide and hydroxamic acid functionality, respectively. The hydrazinolysis reaction exhibits very high efficiency and can be completed in minutes at a low enzyme-to-substrate ratio. We further show the utility of the so-formed asparaginyl hydrazide in native chemical ligation and hydrazone conjugation. Using an EGFR-targeting affibody as a model protein, we have showcased our methodology in the preparation of a number of protein ligation or conjugation products, which are decorated with various functional moieties. The ZEGFR affibody-doxorubicin conjugate shows high selective binding and cytotoxicity toward the EGFR-positive A431 cells. Our results demonstrate the advantages of AEP-mediated protein hydrazinolysis as a simple and straightforward strategy for the precision manufacturing of protein bioconjugates.
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Affiliation(s)
- Dingpeng Zhang
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Zhen Wang
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Side Hu
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Ning-Yu Chan
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Heng Tai Liew
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Julien Lescar
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - James P Tam
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Chuan-Fa Liu
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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17
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Zhang D, Wang Z, Hu S, Lescar J, Tam JP, Liu CF. Vypal2: A Versatile Peptide Ligase for Precision Tailoring of Proteins. Int J Mol Sci 2021; 23:ijms23010458. [PMID: 35008882 PMCID: PMC8745061 DOI: 10.3390/ijms23010458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/19/2022] Open
Abstract
The last two decades have seen an increasing demand for new protein-modification methods from the biotech industry and biomedical research communities. Owing to their mild aqueous reaction conditions, enzymatic methods based on the use of peptide ligases are particularly desirable. In this regard, the recently discovered peptidyl Asx-specific ligases (PALs) have emerged as powerful biotechnological tools in recent years. However, as a new class of peptide ligases, their scope and application remain underexplored. Herein, we report the use of a new PAL, VyPAL2, for a diverse range of protein modifications. We successfully showed that VyPAL2 was an efficient biocatalyst for protein labelling, inter-protein ligation, and protein cyclization. The labelled or cyclized protein ligands remained functionally active in binding to their target receptors. We also demonstrated on-cell labelling of protein ligands pre-bound to cellular receptors and cell-surface engineering via modifying a covalently anchored peptide substrate pre-installed on cell-surface glycans. Together, these examples firmly establish Asx-specific ligases, such as VyPAL2, as the biocatalysts of the future for site-specific protein modification, with a myriad of applications in basic research and drug discovery.
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18
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Cao Y, Bi X. Butelase-1 as the Prototypical Peptide Asparaginyl Ligase and Its Applications: A Review. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Zhou Y, Liang XW. Recent applications of solid-phase strategy in total synthesis of antibiotics. RSC Adv 2021; 11:37942-37951. [PMID: 35498098 PMCID: PMC9043915 DOI: 10.1039/d1ra07503a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Antibiotics produced by soil microorganisms have been widespread and have cured the most prevalent diseases since 1940s. However, recent bacterial resistance to existing antibacterial drugs is causing a public health crisis. The structure–activity relationship of antibiotics needs to be established to search for existing antibiotics-based next-generation drug candidates that can conquer the challenge of bacterial resistance preparedness, which relies on the development of highly efficient total synthesis strategies. The solid-phase strategy has become important to circumvent tedious intermediate isolation and purification procedures with simple filtrations. This review will give a brief overview of recent applications of solid-phase strategy in the total synthesis of antibiotics. The recent applications of solid-phase strategy in total synthesis of antibiotics were summarized, and the structure–activity relationship could be established to conquer the challenge of bacterial resistance preparedness.![]()
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Affiliation(s)
- Yuxin Zhou
- Jinling High School 169 Zhongshan Road Nanjing Jiangsu 210005 China
| | - Xiao-Wei Liang
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University Changsha 410008 China .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University Changsha 410013 China
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20
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Chen Y, Zhang D, Zhang X, Wang Z, Liu CF, Tam JP. Site-Specific Protein Modifications by an Engineered Asparaginyl Endopeptidase from Viola canadensis. Front Chem 2021; 9:768854. [PMID: 34746098 PMCID: PMC8568951 DOI: 10.3389/fchem.2021.768854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/06/2021] [Indexed: 12/04/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) or legumains are Asn/Asp (Asx)-specific proteases that break peptide bonds, but also function as peptide asparaginyl ligases (PALs) that make peptide bonds. This ligase activity can be used for site-specific protein modifications in biochemical and biotechnological applications. Although AEPs are common, PALs are rare. We previously proposed ligase activity determinants (LADs) of these enzymes that could determine whether they catalyze formation or breakage of peptide bonds. LADs are key residues forming the S2 and S1' substrate-binding pockets flanking the S1 active site. Here, we build on the LAD hypothesis with the engineering of ligases from proteases by mutating the S2 and S1' pockets of VcAEP, an AEP from Viola canadensis. Wild type VcAEP yields <5% cyclic product from a linear substrate at pH 6.5, whereas the single mutants VcAEP-V238A (Vc1a) and VcAEP-Y168A (Vc1b) targeting the S2 and S1' substrate-binding pockets yielded 34 and 61% cyclic products, respectively. The double mutant VcAEP-V238A/Y168A (Vc1c) targeting both the S2 and S1' substrate-binding pockets yielded >90% cyclic products. Vc1c had cyclization efficiency of 917,759 M-1s-1, which is one of the fastest rates for ligases yet reported. Vc1c is useful for protein engineering applications, including labeling of DARPins and cell surface MCF-7, as well as producing cyclic protein sfGFP. Together, our work validates the importance of LADs for AEP ligase activity and provides valuable tools for site-specific modification of proteins and biologics.
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Affiliation(s)
- Yu Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Dingpeng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Zhen Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
- Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
- Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
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21
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Xia Y, To J, Chan N, Hu S, Liew HT, Balamkundu S, Zhang X, Lescar J, Bhattacharjya S, Tam JP, Liu C. N
γ
‐Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yiyin Xia
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Janet To
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Ning‐Yu Chan
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Side Hu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Heng Tai Liew
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Seetharamsing Balamkundu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
- Singapore-MIT Alliance for Research and Technology Singapore 138602 Singapore
| | - Xiaohong Zhang
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Julien Lescar
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - James P. Tam
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Chuan‐Fa Liu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
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22
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Xia Y, To J, Chan NY, Hu S, Liew HT, Balamkundu S, Zhang X, Lescar J, Bhattacharjya S, Tam JP, Liu CF. N γ -Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases. Angew Chem Int Ed Engl 2021; 60:22207-22211. [PMID: 34396662 DOI: 10.1002/anie.202108125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 11/10/2022]
Abstract
Peptidyl asparaginyl ligases (PALs) are powerful tools for peptide macrocyclization. Herein, we report that a derivative of Asn, namely Nγ -hydroxyasparagine or Asn(OH), is an unnatural P1 substrate of PALs. By Asn(OH)-mediated cyclization, we prepared cyclic peptides as new matrix metalloproteinase 2 (MMP2) inhibitors displaying the hydroxamic acid moiety of Asn(OH) as the key pharmacophore. The most potent cyclic peptide (Ki =2.8±0.5 nM) was built on the hyperstable tetracyclic scaffold of rhesus theta defensin-1. The Asn(OH) residue in the cyclized peptides can also be readily oxidized to Asp. By this approach, we synthesized several bioactive Asp-containing cyclic peptides (MCoTI-II, kB2, SFTI, and integrin-targeting RGD peptides) that are otherwise difficult targets for PAL-catalyzed cyclization owing to unfavorable kinetics of the P1-Asp substrates. This study demonstrates that substrate engineering is a useful strategy to expand the application of PAL ligation in the synthesis of therapeutic cyclic peptides.
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Affiliation(s)
- Yiyin Xia
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Heng Tai Liew
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Seetharamsing Balamkundu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.,Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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23
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Miura D, Kimura H, Tsugawa W, Ikebukuro K, Sode K, Asano R. Rapid, convenient, and highly sensitive detection of human hemoglobin in serum using a high-affinity bivalent antibody-enzyme complex. Talanta 2021; 234:122638. [PMID: 34364447 DOI: 10.1016/j.talanta.2021.122638] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022]
Abstract
Human hemoglobin (Hb) is a biomarker of several diseases, and monitoring of Hb levels is required during emergent surgery. However, rapid and sensitive Hb detection methods are yet to be developed. The present study established a rapid, convenient, and highly sensitive detection method for Hb in human serum using a bivalent antibody-enzyme complex (AEC). AECs are promising sensing elements because of their ability to bind specific targets and their catalytic activity that produce signals. We recently reported a convenient and universal method to fabricate bivalent AECs with two antibody fragments, using the SpyCatcher/SpyTag system. The present study applied a bivalent AEC for highly sensitive and quantitative detection of human Hb. The bivalent anti-Hb AEC was successfully prepared by incubating both N- and C-terminus SpyCatcher-fused glucose dehydrogenase and SpyTag-fused anti-Hb single-chain variable fragments at 4 °C. As expected, the bivalent AEC for Hb with a multimeric structure showed higher affinity than the monovalent AEC, by means of avidity effects, unlike that for soluble epidermal growth factor receptor with a monomeric structure; this contributed to a great improvement in sensitivity. Finally, we established a rapid and wash-free homogeneous electrochemical detection system for Hb by integrating magnetic beads. The linear range of the system completely covered the clinically required Hb levels, even in human serum. This technology provides an ideal point-of-care test for Hb and other multimeric biomarkers.
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Affiliation(s)
- Daimei Miura
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan
| | - Hayato Kimura
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan
| | - Wakako Tsugawa
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan.
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24
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Tang TMS, Luk LYP. Asparaginyl endopeptidases: enzymology, applications and limitations. Org Biomol Chem 2021; 19:5048-5062. [PMID: 34037066 PMCID: PMC8209628 DOI: 10.1039/d1ob00608h] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Asparaginyl endopeptidases (AEP) are cysteine proteases found in mammalian and plant cells. Several AEP isoforms from plant species were found to exhibit transpeptidase activity which is integral for the key head-to-tail cyclisation reaction during the biosynthesis of cyclotides. Since many plant AEPs exhibit excellent enzyme kinetics for peptide ligation via a relatively short substrate recognition sequence, they have become appealing tools for peptide and protein modification. In this review, research focused on the enzymology of AEPs and their applications in polypeptide cyclisation and labelling will be presented. Importantly, the limitations of using AEPs and opportunities for future research and innovation will also be discussed.
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Affiliation(s)
- T M Simon Tang
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK.
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK. and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
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25
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Zhang D, Wang Z, Hu S, Balamkundu S, To J, Zhang X, Lescar J, Tam JP, Liu CF. pH-Controlled Protein Orthogonal Ligation Using Asparaginyl Peptide Ligases. J Am Chem Soc 2021; 143:8704-8712. [PMID: 34096285 DOI: 10.1021/jacs.1c02638] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptide asparaginyl ligases (PALs) catalyze transpeptidation at the Asn residue of a short Asn-Xaa1-Xaa2 tripeptide motif. Due to their high catalytic activity toward the P1-Asn substrates at around neutral pH, PALs have been used extensively for peptide ligation at asparaginyl junctions. PALs also bind to aspartyl substrates, but only when the γCOOH of P1-Asp remains in its neutral, protonated form, which usually requires an acidic pH. However, this limits the availability of the amine nucleophile and, consequently, the ligation efficiency at aspartyl junctions. Because of this perceived inefficiency, the use of PALs for Asp-specific ligation remains largely unexplored. We found that PAL enzymes, such as VyPAL2, display appreciable catalytic activities toward P1-Asp substrates at pH 4-5, which are at least 2 orders of magnitude higher than that of sortase A, making them practically useful for both intra- and intermolecular ligations. This also allows sequential ligations, first at Asp and then at Asn junctions, because the newly formed aspartyl peptide bond is resistant to the ligase at the pH used for asparaginyl ligation in the second step. Using this pH-controlled orthogonal ligation method, we dually labeled truncated sfGFP with a cancer-targeting peptide and a doxorubicin derivative at the respective N- and C-terminal ends in the N-to-C direction. In addition, a fluorescein tag and doxorubicin derivative were tagged to an EGFR-targeting affibody in the C-to-N direction. This study shows that the pH-dependent catalytic activity of PAL enzymes can be exploited to prepare multifunction protein biologics for pharmacological applications.
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Affiliation(s)
- Dingpeng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Zhen Wang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | | | - Janet To
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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26
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Nonis SG, Haywood J, Mylne JS. Plant asparaginyl endopeptidases and their structural determinants of function. Biochem Soc Trans 2021; 49:965-976. [PMID: 33666219 PMCID: PMC8106488 DOI: 10.1042/bst20200908] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Asparaginyl endopeptidases (AEPs) are versatile enzymes that in biological systems are involved in producing three different catalytic outcomes for proteins, namely (i) routine cleavage by bond hydrolysis, (ii) peptide maturation, including macrocyclisation by a cleavage-coupled intramolecular transpeptidation and (iii) circular permutation involving separate cleavage and transpeptidation reactions resulting in a major reshuffling of protein sequence. AEPs differ in their preference for cleavage or transpeptidation reactions, catalytic efficiency, and preference for asparagine or aspartate target residues. We look at structural analyses of various AEPs that have laid the groundwork for identifying important determinants of AEP function in recent years, with much of the research impetus arising from the potential biotechnological and pharmaceutical applications.
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Affiliation(s)
- Samuel G. Nonis
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joshua S. Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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27
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Wang Z, Zhang D, Hemu X, Hu S, To J, Zhang X, Lescar J, Tam JP, Liu CF. Engineering protein theranostics using bio-orthogonal asparaginyl peptide ligases. Theranostics 2021; 11:5863-5875. [PMID: 33897886 PMCID: PMC8058723 DOI: 10.7150/thno.53615] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Protein theranostics integrate both diagnostic and treatment functions on a single disease-targeting protein. However, the preparation of these multimodal agents remains a major challenge. Ideally, conventional recombinant proteins should be used as starting materials for modification with the desired detection and therapeutic functionalities, but simple chemical strategies that allow the introduction of two different modifications into a protein in a site-specific manner are not currently available. We recently discovered two highly efficient peptide ligases, namely butelase-1 and VyPAL2. Although both ligate at asparaginyl peptide bonds, these two enzymes are bio-orthogonal with distinguishable substrate specificities, which can be exploited to introduce distinct modifications onto a protein. Methods: We quantified substrate specificity differences between butelase-1 and VyPAL2, which provide orthogonality for a tandem ligation method for protein dual modifications. Recombinant proteins or synthetic peptides engineered with the preferred recognition motifs of butelase-1 and VyPAL2 at their respective C- and N-terminal ends could be modified consecutively by the action of the two ligases. Results: Using this method, we modified an EGFR-targeting affibody with a fluorescein tag and a mitochondrion-lytic peptide at its respective N- and C-terminal ends. The dual-labeled protein was found to be a selective bioimaging and cytotoxic agent for EGFR-positive A431 cancer cells. In addition, the method was used to prepare a cyclic form of the affibody conjugated with doxorubicin. Both modified affibodies showed increased cytotoxicity to A431 cells by 10- and 100-fold compared to unconjugated doxorubicin and the free peptide, respectively. Conclusion: Bio-orthogonal tandem ligation using two asparaginyl peptide ligases with differential substrate specificities is a straightforward approach for the preparation of multifunctional protein biologics as potential theranostics.
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28
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Rapid and homogeneous electrochemical detection by fabricating a high affinity bispecific antibody-enzyme complex using two Catcher/Tag systems. Biosens Bioelectron 2021; 175:112885. [DOI: 10.1016/j.bios.2020.112885] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/27/2020] [Accepted: 12/07/2020] [Indexed: 02/08/2023]
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29
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Jackson MA, Nguyen LT, Gilding EK, Durek T, Craik DJ. Make it or break it: Plant AEPs on stage in biotechnology. Biotechnol Adv 2020; 45:107651. [DOI: 10.1016/j.biotechadv.2020.107651] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/02/2020] [Accepted: 10/20/2020] [Indexed: 12/11/2022]
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30
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Ueda M, Komiya C, Arii S, Kusumoto K, Denda M, Okuhira K, Shigenaga A, Otaka A. Sequence-Independent Traceless Method for Preparation of Peptide/Protein Thioesters Using CPaseY-Mediated Hydrazinolysis. Chem Pharm Bull (Tokyo) 2020; 68:1226-1232. [PMID: 33028801 DOI: 10.1248/cpb.c20-00674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteins incorporating artificial moieties such as fluorophores and drugs have enjoyed increasing use in chemical biology and drug development research. Preparation of such artificial protein derivatives has relied mainly on native chemical ligation in which peptide/protein thioesters chemoselectively react with N-terminal cysteine (Cys) peptides to afford protein molecules. The protein thioesters derived from expressed proteins represent thioesters that are very useful for the preparation of artificial proteins by native chemical ligation with synthetic peptides with N-terminal Cys. We recently have developed a traceless thioester-producing protocol using carboxypeptidase Y (CPaseY) which is compatible with an expressed protein. The traceless character is ensured by CPaseY-mediated hydrazinolysis of C-terminal Xaa (X)-Cys-proline (Pro)-leucine (Leu)-OH sequence followed by an auto-processing of the Cys-Pro (CP) dipeptide unit, affording the corresponding X-thioester (X-SR). However, hydrazinolysis of the amide bond in the prolyl leucine junction depends significantly on the nature of X. In the case of hydrophobic X residues, the hydrazinolysis overreacts to give several hydrazides while the reaction of hydrophilic X residues proceeds slowly. In this research, we attempted to develop an X-independent CPaseY-mediated protocol and found that the incorporation of a triple CP sequence into the C-terminal end (X-(CP)3-Leu-OH) allows for efficient X-SR formation in a manner that is independent of X.
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Affiliation(s)
- Masahiro Ueda
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Chiaki Komiya
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Sayuki Arii
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Kohshi Kusumoto
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Masaya Denda
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Keiichiro Okuhira
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University.,Osaka University of Pharmaceutical Sciences
| | - Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University.,Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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31
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Tang TMS, Cardella D, Lander AJ, Li X, Escudero JS, Tsai YH, Luk LYP. Use of an asparaginyl endopeptidase for chemo-enzymatic peptide and protein labeling. Chem Sci 2020; 11:5881-5888. [PMID: 32874509 PMCID: PMC7441500 DOI: 10.1039/d0sc02023k] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) are ideal for peptide and protein labeling. However, because of the reaction reversibility, a large excess of labels or backbone modified substrates are needed. In turn, simple and cheap reagents can be used to label N-terminal cysteine, but its availability inherently limits the potential applications. Aiming to address these issues, we have created a chemo-enzymatic labeling system that exploits the substrate promiscuity of AEP with the facile chemical reaction between N-terminal cysteine and 2-formyl phenylboronic acid (FPBA). In this approach, AEP is used to ligate polypeptides with a Asn-Cys-Leu recognition sequence with counterparts possessing an N-terminal Gly-Leu. Instead of being a labeling reagent, the commercially available FPBA serves as a scavenger converting the byproduct Cys-Leu into an inert thiazolidine derivative. This consequently drives the AEP labeling reaction forward to product formation with a lower ratio of label to protein substrate. By carefully screening the reaction conditions for optimal compatibility and minimal hydrolysis, conversion to the ligated product in the model reaction resulted in excellent yields. The versatility of this AEP-ligation/FPBA-coupling system was further demonstrated by site-specifically labeling the N- or C-termini of various proteins.
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Affiliation(s)
- T M Simon Tang
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Davide Cardella
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Alexander J Lander
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Xuefei Li
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Jorge S Escudero
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Yu-Hsuan Tsai
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Louis Y P Luk
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
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32
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Du J, Yap K, Chan LY, Rehm FBH, Looi FY, Poth AG, Gilding EK, Kaas Q, Durek T, Craik DJ. A bifunctional asparaginyl endopeptidase efficiently catalyzes both cleavage and cyclization of cyclic trypsin inhibitors. Nat Commun 2020; 11:1575. [PMID: 32221295 PMCID: PMC7101308 DOI: 10.1038/s41467-020-15418-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
Asparaginyl endopeptidases (AEPs) catalyze the key backbone cyclization step during the biosynthesis of plant-derived cyclic peptides. Here, we report the identification of two AEPs from Momordica cochinchinensis and biochemically characterize MCoAEP2 that catalyzes the maturation of trypsin inhibitor cyclotides. Recombinantly produced MCoAEP2 catalyzes the backbone cyclization of a linear cyclotide precursor (MCoTI-II-NAL) with a kcat/Km of 620 mM−1 s−1, making it one of the fastest cyclases reported to date. We show that MCoAEP2 can mediate both the N-terminal excision and C-terminal cyclization of cyclotide precursors in vitro. The rate of cyclization/hydrolysis is primarily influenced by varying pH, which could potentially control the succession of AEP-mediated processing events in vivo. Furthermore, MCoAEP2 efficiently catalyzes the backbone cyclization of an engineered MCoTI-II analog with anti-angiogenic activity. MCoAEP2 provides enhanced synthetic access to structures previously inaccessible by direct chemistry approaches and enables the wider application of trypsin inhibitor cyclotides in biotechnology applications. Asparaginyl endopeptidases (AEPs) catalyze the cyclization step during the biosynthesis of cyclic peptides in plants. Here, the authors report a recombinantly produced AEP that catalyzes the backbone cyclization of a linear cyclotide precursor and an engineered analog with high efficiency and in a pH-dependent manner.
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Affiliation(s)
- Junqiao Du
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Lai Yue Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Fabian B H Rehm
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Fong Yang Looi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia.
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33
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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34
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Hemu X, To J, Zhang X, Tam JP. Immobilized Peptide Asparaginyl Ligases Enhance Stability and Facilitate Macrocyclization and Site-Specific Ligation. J Org Chem 2019; 85:1504-1512. [DOI: 10.1021/acs.joc.9b02524] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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35
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Nuijens T, Toplak A, Schmidt M, Ricci A, Cabri W. Natural Occurring and Engineered Enzymes for Peptide Ligation and Cyclization. Front Chem 2019; 7:829. [PMID: 31850317 PMCID: PMC6895249 DOI: 10.3389/fchem.2019.00829] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
The renaissance of peptides as prospective therapeutics has fostered the development of novel strategies for their synthesis and modification. In this context, besides the development of new chemical peptide ligation approaches, especially the use of enzymes as a versatile tool has gained increased attention. Nowadays, due to their inherent properties such as excellent regio- and chemoselectivity, enzymes represent invaluable instruments in both academic and industrial laboratories. This mini-review focuses on natural- and engineered peptide ligases that can form a new peptide (amide) bond between the C-terminal carboxy and N-terminal amino group of a peptide and/or protein. The pro's and cons of several enzyme classes such as Sortases, Asparaginyl Endoproteases, Trypsin related enzymes and as a central focus subtilisin-derived variants are summarized. Most recent developments with regards to ligation and cyclization are highlighted.
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Affiliation(s)
- Timo Nuijens
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | - Ana Toplak
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | - Marcel Schmidt
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | | | - Walter Cabri
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
- Fresenius Kabi iPSUM Srl, Villadose, Italy
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36
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Jing X, Jin K. A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies. Med Res Rev 2019; 40:753-810. [PMID: 31599007 DOI: 10.1002/med.21639] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022]
Abstract
As a versatile therapeutic modality, peptides attract much attention because of their great binding affinity, low toxicity, and the capability of targeting traditionally "undruggable" protein surfaces. However, the deficiency of cell permeability and metabolic stability always limits the success of in vitro bioactive peptides as drug candidates. Peptide macrocyclization is one of the most established strategies to overcome these limitations. Over the past decades, more than 40 cyclic peptide drugs have been clinically approved, the vast majority of which are derived from natural products. The de novo discovered cyclic peptides on the basis of rational design and in vitro evolution, have also enabled the binding with targets for which nature provides no solutions. The current review summarizes different classes of cyclic peptides with diverse biological activities, and presents an overview of various approaches to develop cyclic peptide-based drug candidates, drawing upon series of examples to illustrate each strategy.
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Affiliation(s)
- Xiaoshu Jing
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kang Jin
- Department of Medicinal Chemistry, School of Pharmacy, Shandong University, Jinan, Shandong, China
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37
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A suite of kinetically superior AEP ligases can cyclise an intrinsically disordered protein. Sci Rep 2019; 9:10820. [PMID: 31346249 PMCID: PMC6658665 DOI: 10.1038/s41598-019-47273-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/11/2019] [Indexed: 11/29/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) are a class of enzymes commonly associated with proteolysis in the maturation of seed storage proteins. However, a subset of AEPs work preferentially as peptide ligases, coupling release of a leaving group to formation of a new peptide bond. These “ligase-type” AEPs require only short recognition motifs to ligate a range of targets, making them useful tools in peptide and protein engineering for cyclisation of peptides or ligation of separate peptides into larger products. Here we report the recombinant expression, ligase activity and cyclisation kinetics of three new AEPs from the cyclotide producing plant Oldenlandia affinis with superior kinetics to the prototypical recombinant AEP ligase OaAEP1b. These AEPs work preferentially as ligases at both acidic and neutral pH and we term them “canonical AEP ligases” to distinguish them from other AEPs where activity preferences shift according to pH. We show that these ligases intrinsically favour ligation over hydrolysis, are highly efficient at cyclising two unrelated peptides and are compatible with organic co-solvents. Finally, we demonstrate the broad scope of recombinant AEPs in biotechnology by the backbone cyclisation of an intrinsically disordered protein, the 25 kDa malarial vaccine candidate Plasmodium falciparum merozoite surface protein 2 (MSP2).
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38
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Pi N, Gao M, Cheng X, Liu H, Kuang Z, Yang Z, Yang J, Zhang B, Chen Y, Liu S, Huang Y, Su Z. Recombinant Butelase-Mediated Cyclization of the p53-Binding Domain of the Oncoprotein MdmX-Stabilized Protein Conformation as a Promising Model for Structural Investigation. Biochemistry 2019; 58:3005-3015. [DOI: 10.1021/acs.biochem.9b00263] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ni Pi
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Meng Gao
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Xiyao Cheng
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
- Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan 430075, China
| | - Huili Liu
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei 430071 China
| | - Zhengkun Kuang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Zixin Yang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Jing Yang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Bailing Zhang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Yao Chen
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Sen Liu
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
- Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan 430075, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
- Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan 430075, China
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Komiya C, Shigenaga A, Tsukimoto J, Ueda M, Morisaki T, Inokuma T, Itoh K, Otaka A. Traceless synthesis of protein thioesters using enzyme-mediated hydrazinolysis and subsequent self-editing of the cysteinyl prolyl sequence. Chem Commun (Camb) 2019; 55:7029-7032. [PMID: 31140482 DOI: 10.1039/c9cc03583d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A traceless thioester-producing protocol featuring carboxypeptidase Y-mediated hydrazinolysis of cysteinyl prolyl leucine-tagged peptides has been developed. The hydrazinolysis followed by thioesterification affords cysteinyl prolyl thioesters. Self-editing of the tag and subsequent trans-thioesterification yields peptide thioesters. The developed protocol was successfully applied to the conversion of recombinant proteins to thioesters.
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Affiliation(s)
- Chiaki Komiya
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan.
| | - Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan.
| | - Jun Tsukimoto
- Institute of Medicinal Resources, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Masahiro Ueda
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan.
| | - Takuya Morisaki
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan.
| | - Tsubasa Inokuma
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan.
| | - Kohji Itoh
- Institute of Medicinal Resources, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan.
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40
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Structural determinants for peptide-bond formation by asparaginyl ligases. Proc Natl Acad Sci U S A 2019; 116:11737-11746. [PMID: 31123145 DOI: 10.1073/pnas.1818568116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Asparaginyl endopeptidases (AEPs) are cysteine proteases which break Asx (Asn/Asp)-Xaa bonds in acidic conditions. Despite sharing a conserved overall structure with AEPs, certain plant enzymes such as butelase 1 act as a peptide asparaginyl ligase (PAL) and catalyze Asx-Xaa bond formation in near-neutral conditions. PALs also serve as macrocyclases in the biosynthesis of cyclic peptides. Here, we address the question of how a PAL can function as a ligase rather than a protease. Based on sequence homology of butelase 1, we identified AEPs and PALs from the cyclic peptide-producing plants Viola yedoensis (Vy) and Viola canadensis (Vc) of the Violaceae family. Using a crystal structure of a PAL obtained at 2.4-Å resolution coupled to mutagenesis studies, we discovered ligase-activity determinants flanking the S1 site, namely LAD1 and LAD2 located around the S2 and S1' sites, respectively, which modulate ligase activity by controlling the accessibility of water or amine nucleophile to the S-ester intermediate. Recombinantly expressed VyPAL1-3, predicted to be PALs, were confirmed to be ligases by functional studies. In addition, mutagenesis studies on VyPAL1-3, VyAEP1, and VcAEP supported our prediction that LAD1 and LAD2 are important for ligase activity. In particular, mutagenesis targeting LAD2 selectively enhanced the ligase activity of VyPAL3 and converted the protease VcAEP into a ligase. The definition of structural determinants required for ligation activity of the asparaginyl ligases presented here will facilitate genomic identification of PALs and engineering of AEPs into PALs.
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41
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Luo S, Dong SH. Recent Advances in the Discovery and Biosynthetic Study of Eukaryotic RiPP Natural Products. Molecules 2019; 24:molecules24081541. [PMID: 31003555 PMCID: PMC6514808 DOI: 10.3390/molecules24081541] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/22/2022] Open
Abstract
Natural products have played indispensable roles in drug development and biomedical research. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of fast-expanding natural products attribute to genome mining efforts in recent years. Most RiPP natural products were discovered from bacteria, yet many eukaryotic cyclic peptides turned out to be of RiPP origin. This review article presents recent advances in the discovery of eukaryotic RiPP natural products, the elucidation of their biosynthetic pathways, and the molecular basis for their biosynthetic enzyme catalysis.
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Affiliation(s)
- Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
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42
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Abstract
A biomimetic one-step ligase-catalyzed cyclo-oligomerization mediated by butelase 1, an Asn/Asp-specific ligase, is introduced that is time-, concentration-, length-, and sequence-dependent. This reaction yields cyclic mono-, di-, tri-, and tetramers from peptide precursors containing 3-15 amino acids ended with Asn and a His-Val tail. The cyclomonomers were favored when the peptide lengths were >9 amino acids. A turn-forming Pro residue at the P2 position favored the formation of higher-order cyclo-oligomers.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Xiaohong Zhang
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - James P Tam
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
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Hemu X, Zhang X, Bi X, Liu CF, Tam JP. Butelase 1-Mediated Ligation of Peptides and Proteins. Methods Mol Biol 2019; 2012:83-109. [PMID: 31161505 DOI: 10.1007/978-1-4939-9546-2_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structurally, butelase 1 is a cysteine protease of the asparaginyl endoprotease (AEP) family, but functionally, it displays intense Asn/Asp-specific (Asx) ligase activity and is virtually devoid of protease activity. Butelase 1 recognizes specifically a C-terminal Asx-containing tripeptide motif, Asx-His-Val, to form an Asx-Xaa peptide bond (Xaa = any amino acid), either intramolecularly or intermolecularly, resulting in cyclic peptides or site-specific modified peptides/proteins, respectively. Our work in the past 4 years has validated that butelase 1 is a potent and versatile tool for peptide and protein modification. Here we describe our protocols using butelase 1 for efficient and site-specific peptide and protein ligation, N-terminal labeling, preparation of thioesters, and bioconjugation of dendrimers. Additionally, we provide an example using butelase 1 for protein cyclization in combination with genetic code expansion in order to incorporate unnatural building blocks.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiaobao Bi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Wang XW, Zhang WB. SpyTag-SpyCatcher Chemistry for Protein Bioconjugation In Vitro and Protein Topology Engineering In Vivo. Methods Mol Biol 2019; 2033:287-300. [PMID: 31332761 DOI: 10.1007/978-1-4939-9654-4_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The emergence of "molecular superglue," such as SpyTag-SpyCatcher chemistry, has tremendously expanded our capability in manipulating protein shape and architecture via conjugation. Telechelic proteins bearing the SpyTag and SpyCatcher reactive sequences can be expressed and purified for bioconjugation in vitro, giving protein conjugates, branched proteins, and circular proteins. By encoding both reactive sequences in the same construct for expression in vivo, the nascent protein undergoes programmed posttranslational modification guided by protein folding and reaction, leading to diverse nonlinear topologies in situ. In this chapter, we present the SpyTag-SpyCatcher chemistry as a versatile platform for protein bioconjugation and topology engineering.
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Affiliation(s)
- Xiao-Wei Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China.
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45
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Kimura H, Asano R, Tsukamoto N, Tsugawa W, Sode K. Convenient and Universal Fabrication Method for Antibody–Enzyme Complexes as Sensing Elements Using the SpyCatcher/SpyTag System. Anal Chem 2018; 90:14500-14506. [DOI: 10.1021/acs.analchem.8b04344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | | | | | | | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina 27599, United States
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48
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Bédard F, Biron E. Recent Progress in the Chemical Synthesis of Class II and S-Glycosylated Bacteriocins. Front Microbiol 2018; 9:1048. [PMID: 29875754 PMCID: PMC5974097 DOI: 10.3389/fmicb.2018.01048] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 05/02/2018] [Indexed: 12/11/2022] Open
Abstract
A wide variety of antimicrobial peptides produced by lactic acid bacteria (LAB) have been identified and studied in the last decades. Known as bacteriocins, these ribosomally synthesized peptides inhibit the growth of a wide range of bacterial species through numerous mechanisms and show a great variety of spectrum of activity. With their great potential as antimicrobial additives and alternatives to traditional antibiotics in food preservation and handling, animal production and in veterinary and medical medicine, the demand for bacteriocins is rapidly increasing. Bacteriocins are most often produced by fermentation but, in several cases, the low isolated yields and difficulties associated with their purification seriously limit their use on a large scale. Chemical synthesis has been proposed for their production and recent advances in peptide synthesis methodologies have allowed the preparation of several bacteriocins. Moreover, the significant cost reduction for peptide synthesis reagents and building blocks has made chemical synthesis of bacteriocins more attractive and competitive. From a protein engineering point of view, the chemical approach offers many advantages such as the possibility to rapidly perform amino acid substitution, use unnatural or modified residues, and make backbone and side chain modifications to improve potency, modify the activity spectrum or increase the stability of the targeted bacteriocin. This review summarized synthetic approaches that have been developed and used in recent years to allow the preparation of class IIa bacteriocins and S-linked glycopeptides from LAB. Synthetic strategies such as the use of pseudoprolines, backbone protecting groups, microwave irradiations, selective disulfide bridge formation and chemical ligations to prepare class II and S-glycosylsated bacteriocins are discussed.
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Affiliation(s)
- François Bédard
- Faculty of Pharmacy and Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
- Laboratory of Medicinal Chemistry, CHU de Québec Research Centre, Québec, QC, Canada
| | - Eric Biron
- Faculty of Pharmacy and Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
- Laboratory of Medicinal Chemistry, CHU de Québec Research Centre, Québec, QC, Canada
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49
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Xu Z, Moyle PM. Bioconjugation Approaches to Producing Subunit Vaccines Composed of Protein or Peptide Antigens and Covalently Attached Toll-Like Receptor Ligands. Bioconjug Chem 2017; 29:572-586. [PMID: 28891637 DOI: 10.1021/acs.bioconjchem.7b00478] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Traditional vaccines derived from attenuated or inactivated pathogens are effective at inducing antibody-based protective immune responses but tend to be highly reactogenic, causing notable adverse effects. Vaccines with superior safety profiles can be produced by subunit approaches, utilizing molecularly defined antigens (e.g., proteins and polysaccharides). These antigens, however, often elicit poor immunological responses, necessitating the use of adjuvants. Immunostimulatory adjuvants have the capacity to activate antigen presenting cells directly through specific receptors (e.g., Toll-like receptors (TLRs)), resulting in enhanced presentation of antigens as well as the secretion of proinflammatory chemokines and cytokines. Consequently, innate immune responses are amplified and adaptive immunity is generated. Recently, site-specific conjugation of such immunostimulatory adjuvants (e.g., TLR ligands) onto defined antigens has shown superior efficacy over unconjugated mixtures, suggesting that the development of chemically characterized immunostimulatory adjuvants and optimized approaches for their conjugation with antigens may provide a better opportunity for the development of potent, novel vaccines. This review briefly summarizes various TLR agonists utilized as immunostimulatory adjuvants and focuses on the development of techniques (e.g., recombinant, synthetic, and semisynthetic) for generating adjuvant-antigen fusion vaccines incorporating peptide or protein antigens.
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Affiliation(s)
- Zhenghui Xu
- School of Pharmacy , The University of Queensland , Woolloongabba 4102 , Queensland , Australia
| | - Peter Michael Moyle
- School of Pharmacy , The University of Queensland , Woolloongabba 4102 , Queensland , Australia
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50
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Bi X, Yin J, Nguyen GKT, Rao C, Halim NBA, Hemu X, Tam JP, Liu CF. Enzymatic Engineering of Live Bacterial Cell Surfaces Using Butelase 1. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703317] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiaobao Bi
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Juan Yin
- Lee Kong Chian School of Medicine; Nanyang Technological University; 59 Nanyang Drive Singapore 636921 Singapore
| | - Giang K. T. Nguyen
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Chang Rao
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Nurashikin Bte Abdul Halim
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Xinya Hemu
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - James P. Tam
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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