1
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Wan XC, Zhu WJ, Chen Y, Cui ZH, Zhang H, Zheng FH, Zhang YN, Fang GM. Thioproline-Based Oxidation Strategy for Direct Preparation of N-Terminal Thiazolidine-Containing Peptide Thioesters from Peptide Hydrazides. Org Lett 2024; 26:5021-5026. [PMID: 38842216 DOI: 10.1021/acs.orglett.4c01687] [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: 06/07/2024]
Abstract
We describe a simple and robust oxidation strategy for preparing N-terminal thiazolidine-containing peptide thioesters from peptide hydrazides. We find for the first time that l-thioproline can be used as a protective agent to prevent the nitrosation of N-terminal thiazolidine during peptide hydrazide oxidation. The thioproline-based oxidation strategy has been successfully applied to the chemical synthesis of CC chemokine ligand-2 (69aa) and omniligase-C (113aa), thereby demonstrating its utility in hydrazide-based native chemical ligation.
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Affiliation(s)
- Xiao-Cui Wan
- School of Life Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P. R. China
| | - Wen-Jing Zhu
- School of Life Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P. R. China
| | - Ying Chen
- School of Life Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P. R. China
| | - Zhi-Hui Cui
- School of Life Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P. R. China
| | - Hua Zhang
- School of Life Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P. R. China
| | - Feng-Hao Zheng
- School of Life Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P. R. China
| | - Yan-Ni Zhang
- School of Life Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P. R. China
| | - Ge-Min Fang
- School of Life Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P. R. China
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2
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Zhang J, Zhao L, Tang W, Li J, Tang T, Sun X, Qiao X, He Z. Characterization of a novel circular bacteriocin from Bacillus velezensis 1-3, and its mode of action against Listeria monocytogenes. Heliyon 2024; 10:e29701. [PMID: 38726204 PMCID: PMC11078769 DOI: 10.1016/j.heliyon.2024.e29701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 05/12/2024] Open
Abstract
In this study, isolate Bacillus velezensis1-3 was selected out for its anti- Listeria potency, from which a novel circular bacteriocin, velezin, was purified out of the fermentate, and then characterized. Facilitated with a broad antibacterial spectrum, velezin has demonstrated decent inhibitive activity against of foodborne pathogen L. monocytogenes ATCC 19115. It exerted the antibacterial activity through damaging the membrane integrity of targeted cell and causing leakage of vital elements, including K+ ion. It was noteworthy that velezin also inhibited the biofilm formation by L. monocytogenes ATCC 19115. At the challenge of velezin, L. monocytogenes ATCC 19115 up-regulated expression of genes associated with membrane, ion transporters, stressing-related proteins as well as the genes responsible for the synthesis of small molecule. Taken together, velezin may have potential to be a candidate as natural additive used in food/feed in the future.
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Affiliation(s)
- Jun Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Bioantai Biotechnology Co., Ltd., Qingdao, 266071, China
| | - Lihong Zhao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Wei Tang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Marine Biomedical Research Institute of Qingdao, Qingdao, 266000, China
| | - Jiaxin Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Tao Tang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Marine Biomedical Research Institute of Qingdao, Qingdao, 266000, China
| | - Xiaowen Sun
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Bioantai Biotechnology Co., Ltd., Qingdao, 266071, China
| | - Xiaoni Qiao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Bioantai Biotechnology Co., Ltd., Qingdao, 266071, China
| | - Zengguo He
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Bioantai Biotechnology Co., Ltd., Qingdao, 266071, China
- Marine Biomedical Research Institute of Qingdao, Qingdao, 266000, China
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3
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Zhu T, Zhang X, Li R, Wu B. Efficient production of peptidylglycine α-hydroxylating monooxygenase in yeast for protein C-terminal functionalization. Int J Biol Macromol 2024; 263:130443. [PMID: 38417749 DOI: 10.1016/j.ijbiomac.2024.130443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Peptidylglycine α-hydroxylating monooxygenase (PHM) is pivotal for C-terminal amidation of bioactive peptides in animals, offering substantial potential for customized protein synthesis. However, efficient PHM production has been hindered by the complexity of animal cell culture and the absence of glycosylation in bacterial hosts. Here, we demonstrate the recombinant expression of Caenorhabditis elegans PHM in the yeast Pichia pastoris, achieving a remarkable space-time yield of 28.8 U/L/day. This breakthrough surpasses prior PHM production rates and eliminates the need for specialized cultivation equipment or complex transfection steps. Mass spectrometry revealed N-glycosylation at residue N182 of recombinant CePHM, which impacts the enzyme's activity as indicated by biochemical experiments. To showcase the utility of CePHM, we performed C-terminal amidation on ubiquitin at a substrate loading of 30 g/L, a concentration meeting the requirements for pharmaceutical peptide production. Overall, this work establishes an efficient PHM production method, promising advancements in scalable manufacturing of C-terminally modified bioactive peptides and probe proteins.
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Affiliation(s)
- Tong Zhu
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuanshuo Zhang
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruifeng Li
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Bian Wu
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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4
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Zhu T, Sun J, Pang H, Wu B. Computational Enzyme Redesign Enhances Tolerance to Denaturants for Peptide C-Terminal Amidation. JACS AU 2024; 4:788-797. [PMID: 38425901 PMCID: PMC10900485 DOI: 10.1021/jacsau.3c00792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical computational redesign protocol for improving enzyme tolerance to denaturants is challenging due to the limitations of relying solely on model-driven approaches to adequately capture denaturant-enzyme interactions. In this study, we introduce an enzyme redesign strategy termed GRAPE_DA, which integrates multiple data-driven and model-driven computational methods to mitigate the sampling biases inherent in a single approach and comprehensively predict beneficial mutations on both the protein surface and backbone. To illustrate the methodology's effectiveness, we applied it to engineer a peptidylamidoglycolate lyase, resulting in a variant exhibiting up to a 24-fold increase in peptide C-terminal amidation activity under 2.5 M guanidine hydrochloride. We anticipate that this integrated engineering strategy will facilitate the development of enzymatic peptide synthesis and functionalization under denaturing conditions and highlight the role of engineering surface residues in governing protein stability.
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Affiliation(s)
- Tong Zhu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinyuan Sun
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Pang
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bian Wu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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5
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He J, Ghosh P, Nitsche C. Biocompatible strategies for peptide macrocyclisation. Chem Sci 2024; 15:2300-2322. [PMID: 38362412 PMCID: PMC10866349 DOI: 10.1039/d3sc05738k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Peptides are increasingly important drug candidates, offering numerous advantages over conventional small molecules. However, they face significant challenges related to stability, cellular uptake and overall bioavailability. While individual modifications may not address all these challenges, macrocyclisation stands out as a single modification capable of enhancing affinity, selectivity, proteolytic stability and membrane permeability. The recent successes of in situ peptide modifications during screening in combination with genetically encoded peptide libraries have increased the demand for peptide macrocyclisation reactions that can occur under biocompatible conditions. In this perspective, we aim to distinguish biocompatible conditions from those well-known examples that are fully bioorthogonal. We introduce key strategies for biocompatible peptide macrocyclisation and contextualise them within contemporary screening methods, providing an overview of available transformations.
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Affiliation(s)
- Junming He
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Pritha Ghosh
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT Australia
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6
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Wang J, Chen L, Qin S, Xie M, Luo SZ, Li W. Advances in biosynthesis of peptide drugs: Technology and industrialization. Biotechnol J 2024; 19:e2300256. [PMID: 37884278 DOI: 10.1002/biot.202300256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/24/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023]
Abstract
Peptide drugs are developed from endogenous or synthetic peptides with specific biological activities. They have advantages of strong target specificity, high efficacy and low toxicity, thus showing great promise in the treatment of many diseases such as cancer, infections, and diabetes. Although an increasing number of peptide drugs have entered market in recent years, the preparation of peptide drug substances is yet a bottleneck problem for their industrial production. Comparing to the chemical synthesis method, peptide biosynthesis has advantages of simple synthesis, low cost, and low contamination. Therefore, the biosynthesis technology of peptide drugs has been widely used for manufacturing. Herein, we reviewed the development of peptide drugs and recent advances in peptide biosynthesis technology, in order to shed a light to the prospect of industrial production of peptide drugs based on biosynthesis technology.
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Affiliation(s)
- Jing Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
- College of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Long Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
| | - Mingyuan Xie
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics, Sun Yat-Sen University, Guangzhou, China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
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7
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Mahmoudzadeh K, Habibi Z, Yousefi M, Mostafavi M, Mohammadi M. Peptiligase, an enzyme for efficient chemo-enzymatic synthesis of aviptadil. Int J Biol Macromol 2023; 253:127089. [PMID: 37774815 DOI: 10.1016/j.ijbiomac.2023.127089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/04/2023] [Accepted: 09/24/2023] [Indexed: 10/01/2023]
Abstract
Increasing attention to peptides as prospective therapeutics has created a renaissance in searching for new alternatives to the current peptide synthetic approaches as well as their modification. In this context, it is necessary to develop different approaches for peptide ligation. Using enzymes as a novel strategy and powerful tool for the peptide and protein ligation has recently received a lot of attention. We here designed a fully convergent chemo-enzymatic peptide synthesis (CEPS) process for the synthesis of aviptadil a 28-mer therapeutic peptide with potential therapeutic effects in various medical contexts specially in the treatment of acute respiratory distress syndrome (ARDS) by coupling two peptide segments with four different peptiligase variants in aqueous environments. Our study reveals that peptiligase variants are capable of ligation reaction in 15 min. The overall time of ligation is shorter than those peptides with similar lengths and hinderance to aviptadil which reported for conventional synthesis by full solid-phase peptide synthesis. Yields ranged from 54 % to 76 %.
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Affiliation(s)
- Kazem Mahmoudzadeh
- Department of Organic Chemistry and Oil, Faculty of Chemistry, Shahid Beheshti University, Tehran, Iran
| | - Zohreh Habibi
- Department of Organic Chemistry and Oil, Faculty of Chemistry, Shahid Beheshti University, Tehran, Iran.
| | - Maryam Yousefi
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
| | - Mostafa Mostafavi
- Department of Organic Chemistry and Oil, Faculty of Chemistry, Shahid Beheshti University, Tehran, Iran
| | - Mehdi Mohammadi
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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8
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Alexander AK, Elshahawi SI. Promiscuous Enzymes for Residue-Specific Peptide and Protein Late-Stage Functionalization. Chembiochem 2023; 24:e202300372. [PMID: 37338668 PMCID: PMC10496146 DOI: 10.1002/cbic.202300372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The late-stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late-stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications.
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Affiliation(s)
- Ashley K Alexander
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
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9
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Debon A, Siirola E, Snajdrova R. Enzymatic Bioconjugation: A Perspective from the Pharmaceutical Industry. JACS AU 2023; 3:1267-1283. [PMID: 37234110 PMCID: PMC10207132 DOI: 10.1021/jacsau.2c00617] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 05/27/2023]
Abstract
Enzymes have firmly established themselves as bespoke catalysts for small molecule transformations in the pharmaceutical industry, from early research and development stages to large-scale production. In principle, their exquisite selectivity and rate acceleration can also be leveraged for modifying macromolecules to form bioconjugates. However, available catalysts face stiff competition from other bioorthogonal chemistries. In this Perspective, we seek to illuminate applications of enzymatic bioconjugation in the face of an expanding palette of new drug modalities. With these applications, we wish to highlight some examples of current successes and pitfalls of using enzymes for bioconjugation along the pipeline and try to illustrate opportunities for further development.
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Affiliation(s)
- Aaron Debon
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Elina Siirola
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Radka Snajdrova
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
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10
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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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11
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Jia X, Chin YKY, Zhang AH, Crawford T, Zhu Y, Fletcher NL, Zhou Z, Hamilton BR, Stroet M, Thurecht KJ, Mobli M. Self-cyclisation as a general and efficient platform for peptide and protein macrocyclisation. Commun Chem 2023; 6:48. [PMID: 36871076 PMCID: PMC9985607 DOI: 10.1038/s42004-023-00841-5] [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: 01/19/2023] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Macrocyclisation of proteins and peptides results in a remarkable increase in structural stability, making cyclic peptides and proteins of great interest in drug discovery-either directly as drug leads or as in the case of cyclised nanodiscs (cNDs), as tools for studies of trans-membrane receptors and membrane-active peptides. Various biological methods have been developed that are capable of yielding head-to-tail macrocyclised products. Recent advances in enzyme-catalysed macrocyclisation include discovery of new enzymes or design of new engineered enzymes. Here, we describe the engineering of a self-cyclising "autocyclase" protein, capable of performing a controllable unimolecular reaction for generation of cyclic biomolecules in high yield. We characterise the self-cyclisation reaction mechanism, and demonstrate how the unimolecular reaction path provides alternative avenues for addressing existing challenges in enzymatic cyclisation. We use the method to produce several notable cyclic peptides and proteins, demonstrating how autocyclases offer a simple, alternative way to access a vast diversity of macrocyclic biomolecules.
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Affiliation(s)
- Xinying Jia
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Yanni K-Y Chin
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Alan H Zhang
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Theo Crawford
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Yifei Zhu
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Nicholas L Fletcher
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Zihan Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Brett R Hamilton
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Martin Stroet
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Kristofer J Thurecht
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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12
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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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13
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Kellmann SJ, Hentrich C, Putyrski M, Hanuschka H, Cavada M, Knappik A, Ylera F. SpyDisplay: A versatile phage display selection system using SpyTag/SpyCatcher technology. MAbs 2023; 15:2177978. [PMID: 36803166 PMCID: PMC9980448 DOI: 10.1080/19420862.2023.2177978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Phage display is an established method for the in vitro selection of recombinant antibodies and other proteins or peptides from gene libraries. Here we describe SpyDisplay, a phage display method in which the display is achieved via SpyTag/SpyCatcher protein ligation instead of genetically fusing the displayed protein to a phage coat protein. In our implementation, SpyTagged antibody antigen-binding fragments (Fabs) are displayed via protein ligation on filamentous phages carrying SpyCatcher fused to the pIII coat protein. A library of genes encoding Fab antibodies was cloned in an expression vector containing an f1 replication origin, and SpyCatcher-pIII was separately expressed from a genomic locus in engineered E. coli. We demonstrate the functional, covalent display of Fab on phage, and rapidly isolate specific high-affinity clones via phage panning, confirming the robustness of this selection system. SpyTagged Fabs, the direct outcome of the panning campaign, are compatible with modular antibody assembly using prefabricated SpyCatcher modules and can be directly tested in diverse assays. Furthermore, SpyDisplay streamlines additional applications that have traditionally been challenging for phage display: we show that it can be applied to N-terminal display of the protein of interest and it enables display of cytoplasmically folding proteins exported to periplasm via the TAT pathway.
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14
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Biologic Evaluation of a Heterodimeric HER2-Albumin Targeted Affibody Molecule Produced by Chemo-Enzymatic Peptide Synthesis. Pharmaceutics 2022; 14:pharmaceutics14112519. [PMID: 36432709 PMCID: PMC9698269 DOI: 10.3390/pharmaceutics14112519] [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: 10/18/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Targeted molecular radiation therapy is a promising emerging treatment modality in oncology, and peptide synthesis may shorten the time to reach the clinical stage. In this study, we have explored Chemo-Enzymatic Peptide Synthesis, or CEPS, as a new means of producing a therapeutic HER2 targeted Affibody® molecule, comprising a C-terminal albumin binding domain (ABD) for half-life extension and a total length of 108 amino acids. In addition, a DOTA moiety could be incorporated at N-terminus directly during the synthesis step and subsequently utilized for site-specific radiolabeling with the therapeutic radionuclide 177Lu. Retained thermodynamic stability as well as retained binding to both HER2 and albumin was verified. Furthermore, HER2 binding specificity of the radiolabeled Affibody molecule was confirmed by an in vitro saturation assay showing a significantly higher cell-bound activity of SKOV-3 (high HER2 expression) compared with BxPC3 (low HER2 expression), both in the presence and absence of HSA. In vivo evaluation in mice bearing HER2 expressing xenografts also showed specific tumor targeting as well as extended time in circulation and reduced kidney uptake compared with a HER2 targeted Affibody molecule without the ABD moiety. To conclude, we have demonstrated that CEPS can be used for production of Affibody-fusion molecules with retained in vitro and in vivo functionality.
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15
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Pei J, Gao X, Pan D, Hua Y, He J, Liu Z, Dang Y. Advances in the stability challenges of bioactive peptides and improvement strategies. Curr Res Food Sci 2022; 5:2162-2170. [PMID: 36387592 PMCID: PMC9664347 DOI: 10.1016/j.crfs.2022.10.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/08/2022] Open
Abstract
Bioactive peptides are widely used in functional foods due to their remarkable efficacy, selectivity, and low toxicity. However, commercially produced bioactive peptides lack quality stability between batches. Furthermore, the efficacies of bioactive peptides cannot be guaranteed in vivo due to gastrointestinal digestion and rapid plasma, liver, and kidney metabolism. The problem of poor stability has restricted the development of peptides. Bioactive peptide stability assessments use different stability assays, so the results of different studies are not always comparable. This review summarizes the quality stability challenges in the enzymatic hydrolysis production of bioactive peptides and the metabolism stability challenges after oral administration. Future directions on the strategies for improving their stability are provided. It was proposed that we use fingerprinting as a quality control measure using qualitative and quantitative characteristic functional peptide sequences. The chemical modification and encapsulation of bioactive peptides in microcapsules and liposomes are widely used to improve the digestive and metabolic stability of bioactive peptides. Additionally, the establishment of a universal stability test and a unified index would greatly improve uniformity and comparability in research into bioactive peptides. In summary, the reliable evaluation of stability is an essential component of peptide characterization, and these ideas may facilitate further development and utilization of bioactive peptides. Stability challenges encountered by bioactive peptides were summarized. Strategies to improve the stability of bioactive peptides were provided. A universal stability test and unified index would improve uniformity and comparability in research into bioactive peptides. It was proposed that we use a method of traditional Chinese medicine fingerprinting as a quality control measure.
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Affiliation(s)
- Jingyan Pei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroProducts, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Xinchang Gao
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
- Corresponding author.
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroProducts, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
- National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China
| | - Ying Hua
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Jun He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroProducts, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Zhu Liu
- Zhejiang Institute for Food and Drug Control, Hangzhou, 310052, Zhejiang, China
- Corresponding author.
| | - Yali Dang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroProducts, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
- Corresponding author. School of Food and Pharmaceutical Science, Ningbo University, Ningbo, Zhejiang, 315211, China.
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16
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Su X, Zhang L, Zhao L, Pan B, Chen B, Chen J, Zhai C, Li B. Efficient Protein–Protein Couplings Mediated by Small Molecules under Mild Conditions. Angew Chem Int Ed Engl 2022; 61:e202205597. [DOI: 10.1002/anie.202205597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Xun‐Cheng Su
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Ling‐Yang Zhang
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Li‐Na Zhao
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Bin‐Bin Pan
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Ben‐Guang Chen
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Jia‐Liang Chen
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Cheng‐Liang Zhai
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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17
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Su XC, Zhang LY, Zhao LN, Pan BB, Chen BG, Chen JL, Zhai CL, Li B. Efficient Protein‐Protein Couplings Mediated by Small Molecules under Mild Conditions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xun-Cheng Su
- Nankai University College of Chemistry Stat Key Laboratory of Elemento-organic Chemistry Weijing Road 94 300071 Tianjin CHINA
| | | | - Li-Na Zhao
- Nankai University college of chemistry CHINA
| | - Bin-Bin Pan
- Nankai University college of chemistry CHINA
| | | | | | | | - Bin Li
- Nankai University college of chemistry CHINA
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18
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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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19
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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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20
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Narayanan KB, Han SS. Peptide ligases: A Novel and potential enzyme toolbox for catalytic cross-linking of protein/peptide-based biomaterial scaffolds for tissue engineering. Enzyme Microb Technol 2022; 155:109990. [PMID: 35030384 DOI: 10.1016/j.enzmictec.2022.109990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022]
Abstract
The fabrication of novel biomaterial scaffolds with improved biological interactions and mechanical properties is an important aspect of tissue engineering. The three-dimensional (3D) protein/peptide-based polymeric scaffolds are promising in vitro biomaterials to replicate the in vivo microenvironment mimicking the extracellular matrix (ECM) for cell differentiation and subsequent tissue formation. Among different strategies in the fabrication of scaffolds, bioorthogonal enzymatic reactions for rapid in situ zero-length cross-linking are advantageous. Peptide ligases as a novel toolbox have the potentiality to enzymatically cross-link natural/synthetic protein/peptide-based polymeric chains for a wide range of biomedical applications. Although natural peptide ligases, such as sortases and butelase 1 are known cysteine proteases with ligase activity, some serine proteases, such as trypsin and subtilisin, are protein engineered to form trypsiligase and subtiligase, respectively, which exhibited efficient ligase activity by linking proteins/peptides with a great variety of molecules. Peptide ligase activity by these engineered proteases is more efficient than the hydrolysis of peptide bonds (peptidase activity). Peptide esters form acyl-enzyme intermediate with serine/cysteine residues of these proteases, with subsequent aminolysis forming covalent peptide bond with N-terminal residue of another polymeric chain. In addition, peptide ligases have the potential to conjugate with cell-adhesive ECM proteins or motifs and growth factors to (bio)polymeric networks to enhance cell attachment, growth, and differentiation. Here, we review the potential and limitations of natural and engineered peptide ligases as an enzyme toolbox with a focus on sortases (classes A-D), butelase 1, trypsiligase, and subtilisin variants, and the mechanisms for their zero-length cross-linking of (bio)polymeric scaffolds for various tissue engineering and regenerative applications.
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Affiliation(s)
- Kannan Badri Narayanan
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Sung Soo Han
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
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21
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Vogl DP, Conibear AC, Becker CFW. Segmental and site-specific isotope labelling strategies for structural analysis of posttranslationally modified proteins. RSC Chem Biol 2021; 2:1441-1461. [PMID: 34704048 PMCID: PMC8496066 DOI: 10.1039/d1cb00045d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Posttranslational modifications can alter protein structures, functions and locations, and are important cellular regulatory and signalling mechanisms. Spectroscopic techniques such as nuclear magnetic resonance, infrared and Raman spectroscopy, as well as small-angle scattering, can provide insights into the structural and dynamic effects of protein posttranslational modifications and their impact on interactions with binding partners. However, heterogeneity of modified proteins from natural sources and spectral complexity often hinder analyses, especially for large proteins and macromolecular assemblies. Selective labelling of proteins with stable isotopes can greatly simplify spectra, as one can focus on labelled residues or segments of interest. Employing chemical biology tools for modifying and isotopically labelling proteins with atomic precision provides access to unique protein samples for structural biology and spectroscopy. Here, we review site-specific and segmental isotope labelling methods that are employed in combination with chemical and enzymatic tools to access posttranslationally modified proteins. We discuss illustrative examples in which these methods have been used to facilitate spectroscopic studies of posttranslationally modified proteins, providing new insights into biology.
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Affiliation(s)
- Dominik P Vogl
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
| | - Anne C Conibear
- The University of Queensland, School of Biomedical Sciences St Lucia Brisbane 4072 QLD Australia
| | - Christian F W Becker
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
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22
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Da XD, Wu XL, Liu Y, Zhang WB. Protein Conjugation via SpyStapler-Mediated SpyTag/BDTag Coupling. Curr Protoc 2021; 1:e99. [PMID: 33826806 DOI: 10.1002/cpz1.99] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genetically encoded peptide-protein coupling reactions, such as the SpyTag/SpyCatcher chemistry, are recent additions to the expanding toolbox of protein bioconjugation. The alternative three-component ligation system, e.g., SpyStapler-mediated SpyTag/BDTag coupling, retains most advantages of the Tag/Catcher chemistry, yet requires only two short peptide tags in the genetic fusion for side-chain ligation. Not only does this facilitate the construction of large protein conjugates directly from as-expressed protein components with minimal disruption to their function, but it also provides an entirely new mode of bioconjugation via mechanical bonding, which could impart additional functional benefits such as improved activity and enhanced stability to the conjugate. Such features are attractive for improving the pharmacokinetic performance of protein therapeutics. Herein we describe protocols for SpyStapler-mediated SpyTag/BDTag coupling for protein bioconjugation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Conjugation via isopeptide bond Support Protocol: Purification by size-exclusion chromatography Basic Protocol 2: Conjugation via mechanical bond.
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Affiliation(s)
- Xiao-Di Da
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Xia-Ling Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
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23
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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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24
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Hayes HC, Luk LYP, Tsai YH. Approaches for peptide and protein cyclisation. Org Biomol Chem 2021; 19:3983-4001. [PMID: 33978044 PMCID: PMC8114279 DOI: 10.1039/d1ob00411e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022]
Abstract
The cyclisation of polypeptides can play a crucial role in exerting biological functions, maintaining stability under harsh conditions and conferring proteolytic resistance, as demonstrated both in nature and in the laboratory. To date, various approaches have been reported for polypeptide cyclisation. These approaches range from the direct linkage of N- and C- termini to the connection of amino acid side chains, which can be applied both in reaction vessels and in living systems. In this review, we categorise the cyclisation approaches into chemical methods (e.g. direct backbone cyclisation, native chemical ligation, aldehyde-based ligations, bioorthogonal reactions, disulphide formation), enzymatic methods (e.g. subtiligase variants, sortases, asparaginyl endopeptidases, transglutaminases, non-ribosomal peptide synthetases) and protein tags (e.g. inteins, engineered protein domains for isopeptide bond formation). The features of each approach and the considerations for selecting an appropriate method of cyclisation are discussed.
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Affiliation(s)
- Heather C Hayes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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25
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Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of α-Helix As Oxyanion-Binding Site. J Am Chem Soc 2021; 143:3330-3339. [PMID: 33635059 PMCID: PMC8012002 DOI: 10.1021/jacs.0c10053] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The design of catalytic proteins with functional sites capable of specific chemistry is gaining momentum and a number of artificial enzymes have recently been reported, including hydrolases, oxidoreductases, retro-aldolases, and others. Our goal is to develop a peptide ligase for robust catalysis of amide bond formation that possesses no stringent restrictions to the amino acid composition at the ligation junction. We report here the successful completion of the first step in this long-term project by building a completely de novo protein with predefined acyl transfer catalytic activity. We applied a minimalist approach to rationally design an oxyanion hole within a small cavity that contains an adjacent thiol nucleophile. The N-terminus of the α-helix with unpaired hydrogen-bond donors was exploited as a structural motif to stabilize negatively charged tetrahedral intermediates in nucleophilic addition-elimination reactions at the acyl group. Cysteine acting as a principal catalytic residue was introduced at the second residue position of the α-helix N-terminus in a designed three-α-helix protein based on structural informatics prediction. We showed that this minimal set of functional elements is sufficient for the emergence of catalytic activity in a de novo protein. Using peptide-αthioesters as acyl-donors, we demonstrated their catalyzed amidation concomitant with hydrolysis and proved that the environment at the catalytic site critically influences the reaction outcome. These results represent a promising starting point for the development of efficient catalysts for protein labeling, conjugation, and peptide ligation.
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Affiliation(s)
- Elise A Naudin
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Alastair G McEwen
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Pierre Poussin-Courmontagne
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Jean-Louis Schmitt
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Catherine Birck
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
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26
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Yeast-based bioproduction of disulfide-rich peptides and their cyclization via asparaginyl endopeptidases. Nat Protoc 2021; 16:1740-1760. [PMID: 33597770 DOI: 10.1038/s41596-020-00483-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/10/2020] [Indexed: 11/09/2022]
Abstract
Cyclic disulfide-rich peptides have attracted significant interest in drug development and biotechnology. Here, we describe a protocol for producing cyclic peptide precursors in Pichia pastoris that undergo in vitro enzymatic maturation into cyclic peptides using recombinant asparaginyl endopeptidases (AEPs). Peptide precursors are expressed with a C-terminal His tag and secreted into the media, enabling facile purification by immobilized metal affinity chromatography. After AEP-mediated cyclization, cyclic peptides are purified by reverse-phase high-performance liquid chromatography and characterized by mass spectrometry, peptide mass fingerprinting, NMR spectroscopy, and activity assays. We demonstrate the broad applicability of this protocol by generating cyclic peptides from three distinct classes that are either naturally occurring or synthetically backbone cyclized, and range in size from 14 amino acids with one disulfide bond, to 34 amino acids with a cystine knot comprising three disulfide bonds. The protocol requires 14 d to identify and optimize a high-expressing Pichia clone in small-scale cultures (24 well plates or 50 mL tubes), after which large-scale production in a bioreactor and peptide purification can be completed in 10 d. We use the cyclotide Momordica cochinchinensis trypsin inhibitor II as an example. We also include a protocol for recombinant AEP production in Escherichia coli as AEPs are emerging tools for orthogonal peptide and protein ligation. We focus on two AEPs that preferentially cyclize different peptide precursors, namely an engineered AEP with improved catalytic efficiency [C247A]OaAEP1b and the plant-derived MCoAEP2. Rudimentary proficiency and equipment in molecular biology, protein biochemistry and analytical chemistry are needed.
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27
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Toplak A, Teixeira de Oliveira EF, Schmidt M, Rozeboom HJ, Wijma HJ, Meekels LKM, de Visser R, Janssen DB, Nuijens T. From thiol-subtilisin to omniligase: Design and structure of a broadly applicable peptide ligase. Comput Struct Biotechnol J 2021; 19:1277-1287. [PMID: 33717424 PMCID: PMC7921005 DOI: 10.1016/j.csbj.2021.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/01/2021] [Accepted: 02/01/2021] [Indexed: 11/05/2022] Open
Abstract
Omniligase-1 is a broadly applicable enzyme for peptide bond formation between an activated acyl donor peptide and a non-protected acyl acceptor peptide. The enzyme is derived from an earlier subtilisin variant called peptiligase by several rounds of protein engineering aimed at increasing synthetic yields and substrate range. To examine the contribution of individual mutations on S/H ratio and substrate scope in peptide synthesis, we selected peptiligase variant M222P/L217H as a starting enzyme and introduced successive mutations. Mutation A225N in the S1′ pocket and F189W of the S2′ pocket increased the synthesis to hydrolysis (S/H) ratio and overall coupling efficiency, whereas the I107V mutation was added to S4 pocket to increase the reaction rate. The final omniligase variants appeared to have a very broad substrate range, coupling more than 250 peptides in a 400-member library of acyl acceptors, as indicated by a high-throughput FRET assay. Crystal structures and computational modelling could rationalize the exceptional properties of omniligase-1 in peptide synthesis
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Affiliation(s)
- Ana Toplak
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Eduardo F Teixeira de Oliveira
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcel Schmidt
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Henriëtte J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Linda K M Meekels
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Rowin de Visser
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Timo Nuijens
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
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Small and Simple, yet Sturdy: Conformationally Constrained Peptides with Remarkable Properties. Int J Mol Sci 2021; 22:ijms22041611. [PMID: 33562633 PMCID: PMC7915549 DOI: 10.3390/ijms22041611] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The sheer size and vast chemical space (i.e., diverse repertoire and spatial distribution of functional groups) underlie peptides’ ability to engage in specific interactions with targets of various structures. However, the inherent flexibility of the peptide chain negatively affects binding affinity and metabolic stability, thereby severely limiting the use of peptides as medicines. Imposing conformational constraints to the peptide chain offers to solve these problems but typically requires laborious structure optimization. Alternatively, libraries of constrained peptides with randomized modules can be screened for specific functions. Here, we present the properties of conformationally constrained peptides and review rigidification chemistries/strategies, as well as synthetic and enzymatic methods of producing macrocyclic peptides. Furthermore, we discuss the in vitro molecular evolution methods for the development of constrained peptides with pre-defined functions. Finally, we briefly present applications of selected constrained peptides to illustrate their exceptional properties as drug candidates, molecular recognition probes, and minimalist catalysts.
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Martin V, Egelund PHG, Johansson H, Thordal Le Quement S, Wojcik F, Sejer Pedersen D. Greening the synthesis of peptide therapeutics: an industrial perspective. RSC Adv 2020; 10:42457-42492. [PMID: 35516773 PMCID: PMC9057961 DOI: 10.1039/d0ra07204d] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Solid-phase peptide synthesis (SPPS) is generally the method of choice for the chemical synthesis of peptides, allowing routine synthesis of virtually any type of peptide sequence, including complex or cyclic peptide products. Importantly, SPPS can be automated and is scalable, which has led to its widespread adoption in the pharmaceutical industry, and a variety of marketed peptide-based drugs are now manufactured using this approach. However, SPPS-based synthetic strategies suffer from a negative environmental footprint mainly due to extensive solvent use. Moreover, most of the solvents used in peptide chemistry are classified as problematic by environmental agencies around the world and will soon need to be replaced, which in recent years has spurred a movement in academia and industry to make peptide synthesis greener. These efforts have been centred around solvent substitution, recycling and reduction, as well as exploring alternative synthetic methods. In this review, we focus on methods pertaining to solvent substitution and reduction with large-scale industrial production in mind, and further outline emerging technologies for peptide synthesis. Specifically, the technical requirements for large-scale manufacturing of peptide therapeutics are addressed.
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Affiliation(s)
- Vincent Martin
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | - Peter H G Egelund
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | - Henrik Johansson
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | | | - Felix Wojcik
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | - Daniel Sejer Pedersen
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
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30
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Wills R, Adebomi V, Raj M. Site-Selective Peptide Macrocyclization. Chembiochem 2020; 22:52-62. [PMID: 32794268 DOI: 10.1002/cbic.202000398] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/11/2020] [Indexed: 12/11/2022]
Abstract
Cyclized peptides have seen a rise in popularity in the pharmaceutical industry as drug molecules. As such, new macrocyclization methodologies have become abundant in the last several decades. However, efficient methods of cyclization without the formation of side products remain a great challenge. Herein, we review cyclization approaches that focus on site-selective chemistry. Site selectivity in macrocyclization decreases the generation of side products, leading to a greater yield of the desired peptide macrocycles. We will also take an in-depth look at the new exclusively intramolecular N-terminal site-selective CyClick strategy for the synthesis of cyclic peptides. The CyClick method uses imine formation between an aldehyde and the N terminus. The imine is then trapped by a nucleophilic attack from the second amidic nitrogen in an irreversible site-selective fashion.
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Affiliation(s)
- Rachel Wills
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - Victor Adebomi
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - Monika Raj
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
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31
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Apostol CR, Hay M, Polt R. Glycopeptide drugs: A pharmacological dimension between "Small Molecules" and "Biologics". Peptides 2020; 131:170369. [PMID: 32673700 PMCID: PMC7448947 DOI: 10.1016/j.peptides.2020.170369] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/12/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Peptides are an important class of molecules with diverse biological activities. Many endogenous peptides, especially neuropeptides and peptide hormones, play critical roles in development and regulating homeostasis. Furthermore, as drug candidates their high receptor selectivity and potent binding leads to reduced off-target interactions and potential negative side effects. However, the therapeutic potential of peptides is severely hampered by their poor stability in vivo and low permeability across biological membranes. Several strategies have been successfully employed over the decades to address these concerns, and one of the most promising strategies is glycosylation. It has been demonstrated in numerous cases that glycosylation is an effective synthetic approach to improve the pharmacokinetic profiles and membrane permeability of peptides. The effects of glycosylation on peptide stability and peptide-membrane interactions in the context of blood-brain barrier penetration will be explored. Numerous examples of glycosylated analogues of endogenous peptides targeting class A and B G-protein coupled receptors (GPCRs) with an emphasis on O-linked glycopeptides will be reviewed. Notable examples of N-, S-, and C-linked glycopeptides will also be discussed. A small section is devoted to synthetic methods for the preparation of glycopeptides and requisite amino acid glycoside building blocks.
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Affiliation(s)
- Christopher R Apostol
- Dept. of Chemistry & Biochemistry, BIO5, The University of Arizona, Tucson, AZ 85721, USA.
| | - Meredith Hay
- Evelyn F. McKnight Brain Institute, Dept. of Physiology, The University of Arizona, Tucson, AZ 85724, USA
| | - Robin Polt
- Dept. of Chemistry & Biochemistry, BIO5, The University of Arizona, Tucson, AZ 85721, USA
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32
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Frazier CL, Weeks AM. Engineered peptide ligases for cell signaling and bioconjugation. Biochem Soc Trans 2020; 48:1153-1165. [PMID: 32539119 PMCID: PMC8350744 DOI: 10.1042/bst20200001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022]
Abstract
Enzymes that catalyze peptide ligation are powerful tools for site-specific protein bioconjugation and the study of cellular signaling. Peptide ligases can be divided into two classes: proteases that have been engineered to favor peptide ligation, and protease-related enzymes with naturally evolved peptide ligation activity. Here, we provide a review of key natural peptide ligases and proteases engineered to favor peptide ligation activity. We cover the protein engineering approaches used to generate and improve these tools, along with recent biological applications, advantages, and limitations associated with each enzyme. Finally, we address future challenges and opportunities for further development of peptide ligases as tools for biological research.
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Affiliation(s)
- Clara L. Frazier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy M. Weeks
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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33
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Shinbara K, Liu W, van Neer RHP, Katoh T, Suga H. Methodologies for Backbone Macrocyclic Peptide Synthesis Compatible With Screening Technologies. Front Chem 2020; 8:447. [PMID: 32626683 PMCID: PMC7314982 DOI: 10.3389/fchem.2020.00447] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 12/23/2022] Open
Abstract
Backbone macrocyclic structures are often found in diverse bioactive peptides and contribute to greater conformational rigidity, peptidase resistance, and potential membrane permeability compared to their linear counterparts. Therefore, such peptide scaffolds are an attractive platform for drug-discovery endeavors. Recent advances in synthetic methods for backbone macrocyclic peptides have enabled the discovery of novel peptide drug candidates against diverse targets. Here, we overview recent technical advancements in the synthetic methods including 1) enzymatic synthesis, 2) chemical synthesis, 3) split-intein circular ligation of peptides and proteins (SICLOPPS), and 4) in vitro translation system combined with genetic code reprogramming. We also discuss screening methodologies compatible with those synthetic methodologies, such as one-beads one-compound (OBOC) screening compatible with the synthetic method 2, cell-based assay compatible with 3, limiting-dilution PCR and mRNA display compatible with 4.
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Affiliation(s)
| | | | | | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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34
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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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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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Matsuda K, Kuranaga T, Wakimoto T. A New Cyclase Family Catalyzing Head-to-Tail Macrolactamization of Non-ribosomal Peptides. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.1106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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38
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Abstract
Subtiligase-catalyzed peptide ligation is a powerful approach for site-specific protein bioconjugation, synthesis and semisynthesis of proteins and peptides, and chemoproteomic analysis of cellular N termini. Here, we provide a comprehensive review of the subtiligase technology, including its development, applications, and impacts on protein science. We highlight key advantages and limitations of the tool and compare it to other peptide ligase enzymes. Finally, we provide a perspective on future applications and challenges and how they may be addressed.
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Affiliation(s)
- Amy M Weeks
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, United States
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39
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Chow HY, Zhang Y, Matheson E, Li X. Ligation Technologies for the Synthesis of Cyclic Peptides. Chem Rev 2019; 119:9971-10001. [PMID: 31318534 DOI: 10.1021/acs.chemrev.8b00657] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cyclic peptides have been attracting a lot of attention in recent decades, especially in the area of drug discovery, as more and more naturally occurring cyclic peptides with diverse biological activities have been discovered. Chemical synthesis of cyclic peptides is essential when studying their structure-activity relationships. Conventional peptide cyclization methods via direct coupling have inherent limitations, like the susceptibility to epimerization at the C-terminus, poor solubility of fully protected peptide precursors, and low yield caused by oligomerization. In this regard, chemoselective ligation-mediated cyclization methods have emerged as effective strategies for cyclic peptide synthesis. The toolbox for cyclic peptide synthesis has been expanded substantially in the past two decades, allowing more efficient synthesis of cyclic peptides with various scaffolds and modifications. This Review will explore different chemoselective ligation technologies used for cyclic peptide synthesis that generate both native and unnatural peptide linkages. The practical issues and limitations of different methods will be discussed. The advance in cyclic peptide synthesis will benefit the biological and medicinal study of cyclic peptides, an important class of macrocycles with potentials in numerous fields, notably in therapeutics.
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Affiliation(s)
- Hoi Yee Chow
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong SAR , P. R. China
| | - Yue Zhang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong SAR , P. R. China
| | - Eilidh Matheson
- School of Chemistry , University of Edinburgh , Edinburgh EH8 9LE , United Kingdom
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong SAR , P. R. China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , P. R. China
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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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Shemsi AM, Khanday FA, Qurashi A, Khalil A, Guerriero G, Siddiqui KS. Site-directed chemically-modified magnetic enzymes: fabrication, improvements, biotechnological applications and future prospects. Biotechnol Adv 2019; 37:357-381. [DOI: 10.1016/j.biotechadv.2019.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/13/2019] [Accepted: 02/08/2019] [Indexed: 02/08/2023]
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42
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Conibear AC, Muttenthaler M. Advancing the Frontiers of Chemical Protein Synthesis-The 7 th CPS Meeting, Haifa, Israel. Cell Chem Biol 2019; 25:247-254. [PMID: 29547714 DOI: 10.1016/j.chembiol.2018.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The 7th Chemical Protein Synthesis Meeting took place in September 2017 in Haifa, Israel, bringing together 100 scientists from 11 countries. The cutting-edge scientific program included new synthetic strategies and ligation auxiliaries, novel insights into protein signaling and post-translational modifications, and a range of promising therapeutic applications.
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Affiliation(s)
- Anne C Conibear
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Markus Muttenthaler
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, 4072 Brisbane, Australia.
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43
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Schmidt M, Toplak A, Rozeboom HJ, Wijma HJ, Quaedflieg PJLM, van Maarseveen JH, Janssen DB, Nuijens T. Design of a substrate-tailored peptiligase variant for the efficient synthesis of thymosin-α 1. Org Biomol Chem 2019; 16:609-618. [PMID: 29300408 DOI: 10.1039/c7ob02812a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The synthesis of thymosin-α1, an acetylated 28 amino acid long therapeutic peptide, via conventional chemical methods is exceptionally challenging. The enzymatic coupling of unprotected peptide segments in water offers great potential for a more efficient synthesis of peptides that are difficult to synthesize. Based on the design of a highly engineered peptide ligase, we developed a fully convergent chemo-enzymatic peptide synthesis (CEPS) process for the production of thymosin-α1via a 14-mer + 14-mer segment condensation strategy. Using structure-inspired enzyme engineering, the thiol-subtilisin variant peptiligase was tailored to recognize the respective 14-mer thymosin-α1 segments in order to create a clearly improved biocatalyst, termed thymoligase. Thymoligase catalyzes peptide bond formation between both segments with a very high efficiency (>94% yield) and is expected to be well applicable to many other ligations in which residues with similar characteristics (e.g. Arg and Glu) are present in the respective positions P1 and P1'. The crystal structure of thymoligase was determined and shown to be in good agreement with the model used for the engineering studies. The combination of the solid phase peptide synthesis (SPPS) of the 14-mer segments and their thymoligase-catalyzed ligation on a gram scale resulted in a significantly increased, two-fold higher overall yield (55%) of thymosin-α1 compared to those typical of existing industrial processes.
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Affiliation(s)
- Marcel Schmidt
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
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44
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Abstract
Omniligase-1-catalyzed ligation represents a powerful tool for the efficient intermolecular and intramolecular (head-to-tail cyclization) ligation of peptides. Reactions are irreversible and proceed with unprotected peptides (μM-mM concentration) in aqueous solution at slightly basic pH. Due to its high catalytic efficiency, only very low molar equivalents of omniligase-1 are required. In this chapter, a chemoenzymatic peptide synthesis (CEPS) approach for the assembly of medium-to-long-sized linear peptides as well as for efficient peptide head-to-tail cyclization is described. In particular, we provide protocols for the chemoenzymatic synthesis of the peptide therapeutic exenatide, a GLP-1 (glucagon-like peptide) analogue, and the macrocyclization and oxidative folding of the cyclotide MCoTI-II in a one-pot procedure.
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45
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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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46
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Aguirre-Díaz IS, Montiel C, Bustos-Jaimes I, Medina-Gonzalez Y, Tecante A, Gimeno M. Chemoenzymatic synthesis of polypeptides in neat 1,1,1,2-tetrafluoroethane solvent. RSC Adv 2018; 8:35936-35945. [PMID: 35558459 PMCID: PMC9088702 DOI: 10.1039/c8ra06657d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/17/2018] [Indexed: 11/21/2022] Open
Abstract
Chemoenzymatic polypeptide synthesis offers several advantages over chemical or other biological routes, however, the use of aqueous-based media suffers from reverse hydrolysis reactions that challenge peptide chain propagation. Herein, the protease from subtilisin Carlsberg biocatalyzed the synthesis of poly-l-PheOEt, poly-l-LeuOEt, and the copolymers poly-l-PheOEt-co-l-LeuOEt from their amino acid ethyl ester substrates in a neat liquid 1,1,1,2-tetrafluoroethane solvent. The products, achieved in acceptable yields (ca. 50%), were fully characterized showing relatively high molar mass (ca. 20 000 Da for poly-l-PheOEt). This non-toxic low-boiling hydrofluorocarbon enhances enzymatic peptide propagation by limiting hydrolysis owing to its hydrophobic and relatively polar characteristics that sustain the protease activity and solubilize substrates and products. Computational molecular dynamic calculations were used to assess the l-PheOEt/l-LeuOEt-solvent and polypeptide-solvent interactions in this system. Additionally, the homopolypeptides displayed higher crystallinity than the copolypeptides with random incorporation of amino acid ethyl esters, notwithstanding the significantly highest specificity for Phe in this system. Interestingly, secondary structure characterization of the products by FTIR and circular dichroism suggests a non-common peptide folding.
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Affiliation(s)
- Isabel S Aguirre-Díaz
- Facultad de Química, Depto. de Alimentos y Biotecnología, Universidad Nacional Autónoma de México (UNAM) CDMX Mexico
| | - Carmina Montiel
- Facultad de Química, Depto. de Alimentos y Biotecnología, Universidad Nacional Autónoma de México (UNAM) CDMX Mexico
| | - Ismael Bustos-Jaimes
- Facultad de Medicina, Depto. de Bioquímica, Universidad Nacional Autónoma de México (UNAM) CDMX Mexico
| | - Yaocihuatl Medina-Gonzalez
- INPT, UPS, Laboratoire de Genie Chimique UMR CNRS 5503, Universite de Toulouse 4, Allee Emile Monso F-31030 Toulouse France
| | - Alberto Tecante
- Facultad de Química, Depto. de Alimentos y Biotecnología, Universidad Nacional Autónoma de México (UNAM) CDMX Mexico
| | - Miquel Gimeno
- Facultad de Química, Depto. de Alimentos y Biotecnología, Universidad Nacional Autónoma de México (UNAM) CDMX Mexico
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Agwa AJ, Blomster LV, Craik DJ, King GF, Schroeder CI. Efficient Enzymatic Ligation of Inhibitor Cystine Knot Spider Venom Peptides: Using Sortase A To Form Double-Knottins That Probe Voltage-Gated Sodium Channel NaV1.7. Bioconjug Chem 2018; 29:3309-3319. [DOI: 10.1021/acs.bioconjchem.8b00505] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Akello J. Agwa
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Linda V. Blomster
- 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
| | - Glenn F. King
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Christina I. Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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Żądło-Dobrowolska A, Schmidt NG, Kroutil W. Promiscuous activity of C-acyltransferase from Pseudomonas protegens: synthesis of acetanilides in aqueous buffer. Chem Commun (Camb) 2018; 54:3387-3390. [PMID: 29553154 PMCID: PMC5885802 DOI: 10.1039/c8cc00290h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A C-acyltransferase was found to show promiscuous activity catalyzing C–N bond formation in aqueous buffer instead of C–C bond formation.
Amide bond formation has considerable significance in synthetic chemistry. Although the C-acyltransferase from Pseudomonas protegens has been found to catalyze C–C bond formation in nature as well as in in vitro experiments with non-natural substrates, it is now shown that the enzyme is also able to catalyze amide formation using aniline derivatives as substrates with promiscuous activity. Importantly, the amide formation was enabled in aqueous buffer. Identifying phenyl acetate as the most suitable acetyl donor, the products were obtained with up to >99% conversion and up to 99% isolated yield.
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Affiliation(s)
- Anna Żądło-Dobrowolska
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Harrachgasse 21/3, Graz, Austria.
| | - Nina G Schmidt
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Harrachgasse 21/3, Graz, Austria. and Austrian Centre of Industrial Biotechnology, acib GmbH, Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Harrachgasse 21/3, Graz, Austria. and Austrian Centre of Industrial Biotechnology, acib GmbH, Graz, Austria
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