1
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Zhan Q, Shi C, Jiang Y, Gao X, Lin Y. Efficient splicing of the CPE intein derived from directed evolution of the Cryptococcus neoformans PRP8 intein. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1310-1318. [PMID: 37489009 PMCID: PMC10448054 DOI: 10.3724/abbs.2023135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/19/2023] [Indexed: 07/26/2023] Open
Abstract
Intein-mediated protein splicing has been widely used in protein engineering; however, the splicing efficiency and extein specificity usually limit its further application. Thus, there is a demand for more general inteins that can overcome these limitations. Here, we study the trans-splicing of CPE intein obtained from the directed evolution of Cne PRP8, which shows that its splicing rate is ~29- fold higher than that of the wild-type. When the +1 residue of C-extein is changed to cysteine, CPE also shows high splicing activity. Faster association and higher affinity may contribute to the high splicing rate compared with wild-type intein. These findings have important implications for the future engineering of inteins and provide clues for fundamental studies of protein structure and folding.
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Affiliation(s)
- Qin Zhan
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
| | - Changhua Shi
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
| | - Yu Jiang
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
| | - Xianling Gao
- Shandong Guoli Biotechnology Co.Ltd.Jinan250101China
| | - Ying Lin
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
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2
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Boral S, Sen S, Kushwaha T, Inampudi KK, De S. Extein residues regulate the catalytic function of Spl DnaX intein enzyme by restricting the near-attack conformations of the active-site residues. Protein Sci 2023; 32:e4699. [PMID: 37313648 PMCID: PMC10288555 DOI: 10.1002/pro.4699] [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: 03/23/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Intein enzymes catalyze the splicing of their flanking polypeptide chains and have found tremendous biotechnological applications. Their terminal residues form the catalytic core and participate in the splicing reaction. Hence, the neighboring N- and C-terminal extein residues influence the catalytic rate. As these extein residues vary depending on the substrate identity, we tested the influence of 20 amino acids at these sites in the Spl DnaX intein and observed significant variation of spliced product as well as N- and C-terminus cleavage product formation. We investigated the dependence of these reactions on the extein residues by molecular dynamics (MD) simulations on eight extein variants, and found that the conformational sampling of the active-site residues of the intein enzyme differed among these extein variants. We found that the extein variants that sample higher population of near-attack conformers (NACs) of the active-site residues undergo higher product formation in our activity assays. Ground state conformers that closely resemble the transition state are referred to as NACs. Very good correlation was observed between the NAC populations from the MD simulations of eight extein variants and the corresponding product formation from our activity assays. Furthermore, this molecular detail enabled us to elucidate the mechanistic roles of several conserved active-site residues in the splicing reaction. Overall, this study shows that the catalytic power of Spl DnaX intein enzyme, and most likely other inteins, depends on the efficiency of formation of NACs in the ground state, which is further modulated by the extein residues.
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Affiliation(s)
- Soumendu Boral
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
| | - Srijon Sen
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
| | - Tushar Kushwaha
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Krishna K. Inampudi
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Soumya De
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
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3
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Ho TNT, Pham SH, Nguyen LTT, Nguyen HT, Nguyen LT, Dang TT. Insights into the synthesis strategies of plant-derived cyclotides. Amino Acids 2023:10.1007/s00726-023-03271-8. [PMID: 37142771 DOI: 10.1007/s00726-023-03271-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Cyclotides are plant peptides characterized with a head-to-tail cyclized backbone and three interlocking disulfide bonds, known as a cyclic cysteine knot. Despite the variations in cyclotides peptide sequences, this core structure is conserved, underlying their most useful feature: stability against thermal and chemical breakdown. Cyclotides are the only natural peptides known to date that are orally bioavailable and able to cross cell membranes. Cyclotides also display bioactivities that have been exploited and expanded to develop as potential therapeutic reagents for a wide range of conditions (e.g., HIV, inflammatory conditions, multiple sclerosis, etc.). As such, in vitro production of cyclotides is of the utmost importance since it could assist further research on this peptide class, specifically the structure-activity relationship and its mechanism of action. The information obtained could be utilized to assist drug development and optimization. Here, we discuss several strategies for the synthesis of cyclotides using both chemical and biological routes.
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Affiliation(s)
- Thao N T Ho
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Son H Pham
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Linh T T Nguyen
- Department of Chemistry, Ho Chi Minh City University of Education, 280 An Duong Vuong Street, District 5, Ho Chi Minh City, Viet Nam
| | - Ha T Nguyen
- National Key Laboratory of Polymer and Composite Materials, Department of Energy Materials, Faculty of Materials Technology, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Luan T Nguyen
- National Key Laboratory of Polymer and Composite Materials, Department of Energy Materials, Faculty of Materials Technology, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Tien T Dang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam.
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4
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Jacob B, Vogelaar A, Cadenas E, Camarero JA. Using the Cyclotide Scaffold for Targeting Biomolecular Interactions in Drug Development. Molecules 2022; 27:molecules27196430. [PMID: 36234971 PMCID: PMC9570680 DOI: 10.3390/molecules27196430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/28/2022] Open
Abstract
This review provides an overview of the properties of cyclotides and their potential for developing novel peptide-based therapeutics. The selective disruption of protein–protein interactions remains challenging, as the interacting surfaces are relatively large and flat. However, highly constrained polypeptide-based molecular frameworks with cell-permeability properties, such as the cyclotide scaffold, have shown great promise for targeting those biomolecular interactions. The use of molecular techniques, such as epitope grafting and molecular evolution employing the cyclotide scaffold, has shown to be highly effective for selecting bioactive cyclotides.
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Affiliation(s)
- Binu Jacob
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Alicia Vogelaar
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Enrique Cadenas
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 9033, USA
- Correspondence:
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5
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Wu WH, Guo J, Zhang L, Zhang WB, Gao W. Peptide/protein-based macrocycles: from biological synthesis to biomedical applications. RSC Chem Biol 2022; 3:815-829. [PMID: 35866174 PMCID: PMC9257627 DOI: 10.1039/d1cb00246e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Living organisms have evolved cyclic or multicyclic peptides and proteins with enhanced stability and high bioactivity superior to their linear counterparts for diverse purposes. Herein, we review recent progress in applying this concept to artificial peptides and proteins to exploit the functional benefits of these macrocycles. Not only have simple cyclic forms been prepared, numerous macrocycle variants, such as knots and links, have also been developed. The chemical tools and synthetic strategies are summarized for the biological synthesis of these macrocycles, demonstrating it as a powerful alternative to chemical synthesis. Its further application to therapeutic peptides/proteins has led to biomedicines with profoundly improved pharmaceutical performances. Finally, we present our perspectives on the field and its future developments.
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Affiliation(s)
- Wen-Hao 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 100871 P. R. China
| | - Jianwen Guo
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| | - Longshuai Zhang
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 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 100871 P. R. China
| | - Weiping Gao
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
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6
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Beyer HM, Mikula KM, Li M, Wlodawer A, Iwaï H. The crystal structure of the naturally split gp41-1 intein guides the engineering of orthogonal split inteins from cis-splicing inteins. FEBS J 2020; 287:1886-1898. [PMID: 31665813 PMCID: PMC7190452 DOI: 10.1111/febs.15113] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/01/2019] [Accepted: 10/29/2019] [Indexed: 01/09/2023]
Abstract
Protein trans-splicing catalyzed by split inteins has increasingly become useful as a protein engineering tool. We solved the 1.0 Å-resolution crystal structure of a fused variant from the naturally split gp41-1 intein, previously identified from environmental metagenomic sequence data. The structure of the 125-residue gp41-1 intein revealed a compact pseudo-C2-symmetry commonly found in the Hedgehog/Intein superfamily with extensive charge-charge interactions between the split N- and C-terminal intein fragments that are common among naturally occurring split inteins. We successfully created orthogonal split inteins by engineering a similar charge network into the same region of a cis-splicing intein. This strategy could be applicable for creating novel natural-like split inteins from other, more prevalent cis-splicing inteins. DATABASE: Structural data are available in the RCSB Protein Data Bank under the accession number 6QAZ.
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Affiliation(s)
- Hannes Michael Beyer
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Kornelia Malgorzata Mikula
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Mi Li
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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7
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Abstract
Cyclotides are naturally occurring microproteins (≈30 residues long) present in several families of plants. All cyclotides share a unique head-to-tail circular knotted topology containing three disulfide bridges forming a cystine knot topology. Cyclotides possess high stability to chemical, physical, and biological degradation and have been reported to cross cellular membranes. In addition, naturally occurring and engineered cyclotides have shown to possess various pharmacologically relevant activities. These unique features make the cyclotide scaffold an excellent tool for the design of novel peptide-based therapeutics by using molecular evolution and/or peptide epitope grafting techniques. In this chapter, we provide protocols to recombinantly produce a natively folded cyclotide making use of a standard bacterial expression system in combination with an intein-mediated backbone cyclization with concomitant oxidative folding.
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Affiliation(s)
- Maria Jose Campbell
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jingtan Su
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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8
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Abstract
This Review explores the class of plant-derived macrocyclic peptides called cyclotides. We include an account of their discovery, characterization, and distribution in the plant kingdom as well as a detailed analysis of their sequences and structures, biosynthesis and chemical synthesis, biological functions, and applications. These macrocyclic peptides are around 30 amino acids in size and are characterized by their head-to-tail cyclic backbone and cystine knot motif, which render them to be exceptionally stable, with resistance to thermal or enzymatic degradation. Routes to their chemical synthesis have been developed over the past two decades, and this capability has facilitated a wide range of mutagenesis and structure-activity relationship studies. In turn, these studies have both led to an increased understanding of their mechanisms of action as well as facilitated a range of applications in agriculture and medicine, as ecofriendly crop protection agents, and as drug leads or scaffolds for pharmaceutical design. Our overall objective in this Review is to provide readers with a comprehensive overview of cyclotides that we hope will stimulate further work on this fascinating family of peptides.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Meng-Wei Kan
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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9
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Ojeda PG, Cardoso MH, Franco OL. Pharmaceutical applications of cyclotides. Drug Discov Today 2019; 24:2152-2161. [PMID: 31541712 DOI: 10.1016/j.drudis.2019.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023]
Abstract
Cyclotides are cyclic peptides, present in several plant families, that show diverse biological properties. Structurally, cyclotides share a distinctive head-to-tail circular knotted topology of three disulfide bonds. This framework provides cyclotides with extraordinary resistance to thermal and chemical denaturation. There is increasing interest in the therapeutic potential of cyclotides, which combine several promising pharmaceutical properties, including binding affinity, target selectivity, and low toxicity towards healthy mammalian cells. Recently, cyclotides have been reported to be orally bioavailable and have proved to be amenable to modifications. Here, we provide an overview of the structure, properties, and pharmaceutical applications of cyclotides.
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Affiliation(s)
- Paola G Ojeda
- Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Av. San Miguel 3605, Talca 3480112, Chile
| | - Marlon H Cardoso
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil; 3S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil; 3S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.
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10
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Gao DY, Sun XB, Liu MQ, Liu YN, Zhang HE, Shi XL, Li YN, Wang JK, Yin SJ, Wang Q. Characterization of Thermostable and Chimeric Enzymes via Isopeptide Bond-Mediated Molecular Cyclization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6837-6846. [PMID: 31180217 DOI: 10.1021/acs.jafc.9b01459] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mannooligosaccharides are released by mannan-degrading endo-β-1,4-mannanase and are known as functional additives in human and animal diets. To satisfy demands for biocatalysis and bioprocessing in crowed environments, in this study, we employed a recently developed enzyme-engineering system, isopeptide bond-mediated molecular cyclization, to modify a mesophilic mannanase from Bacillus subtilis. The results revealed that the cyclized enzymes showed enhanced thermostability and ion stability and resilience to aggregation and freeze-thaw treatment by maintaining their conformational structures. Additionally, by using the SpyTag/SpyCatcher system, we generated a mannanase-xylanase bifunctional enzyme that exhibited a synergistic activity in substrate deconstruction without compromising substrate affinity. Interestingly, the dual-enzyme ring conformation was observed to be more robust than the linear enzyme but inferior to the single-enzyme ring conformation. Taken together, these findings provided new insights into the mechanisms of molecular cyclization on stability improvement and will be useful in the production of new functional oligosaccharides and feed additives.
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Affiliation(s)
- De-Ying Gao
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Xiao-Bao Sun
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Ming-Qi Liu
- National and Local United Engineering Lab of Quality Controlling Technology and Instrumentation for Marine Food, College of Life Science , China Jiliang University , Hangzhou 310018 , Zhejiang , China
| | - Yan-Ni Liu
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Hui-En Zhang
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Xin-Lei Shi
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Yang-Nan Li
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Jia-Kun Wang
- College of Animal Science , Zhejiang University , Hangzhou 310058 , Zhejiang , China
| | - Shang-Jun Yin
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Qian Wang
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
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11
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Schmidt M, Huang YH, Texeira de Oliveira EF, Toplak A, Wijma HJ, Janssen DB, van Maarseveen JH, Craik DJ, Nuijens T. Efficient Enzymatic Cyclization of Disulfide-Rich Peptides by Using Peptide Ligases. Chembiochem 2019; 20:1524-1529. [PMID: 30735312 DOI: 10.1002/cbic.201900033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Indexed: 12/18/2022]
Abstract
Disulfide-rich macrocyclic peptides-cyclotides, for example-represent a promising class of molecules with potential therapeutic use. Despite their potential their efficient synthesis at large scale still represents a major challenge. Here we report new chemoenzymatic strategies using peptide ligase variants-inter alia, omniligase-1-for the efficient and scalable one-pot cyclization and folding of the native cyclotides MCoTI-II, kalata B1 and variants thereof, as well as of the θ-defensin RTD-1. The synthesis of the kB1 variant T20K was successfully demonstrated at multi-gram scale. The existence of several ligation sites for each macrocycle makes this approach highly flexible and facilitates both the larger-scale manufacture and the engineering of bioactive, grafted cyclotide variants, therefore clearly offering a valuable and powerful extension of the existing toolbox of enzymes for peptide head-to-tail cyclization.
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Affiliation(s)
- Marcel Schmidt
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands.,Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Eduardo F Texeira de Oliveira
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Ana Toplak
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
| | - Hein J Wijma
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dick B Janssen
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jan H van Maarseveen
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Timo Nuijens
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
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12
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Camarero JA, Campbell MJ. The Potential of the Cyclotide Scaffold for Drug Development. Biomedicines 2019; 7:biomedicines7020031. [PMID: 31010257 PMCID: PMC6631875 DOI: 10.3390/biomedicines7020031] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Cyclotides are a novel class of micro-proteins (≈30-40 residues long) with a unique topology containing a head-to-tail cyclized backbone structure further stabilized by three disulfide bonds that form a cystine knot. This unique molecular framework makes them exceptionally stable to physical, chemical, and biological degradation compared to linear peptides of similar size. The cyclotides are also highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot, and are orally bioavailable and able to cross cellular membranes to modulate intracellular protein-protein interactions (PPIs), both in vitro and in vivo. These unique properties make them ideal scaffolds for many biotechnological applications, including drug discovery. This review provides an overview of the properties of cyclotides and their potential for the development of novel peptide-based therapeutics. The selective disruption of PPIs still remains a very challenging task, as the interacting surfaces are relatively large and flat. The use of the cell-permeable highly constrained polypeptide molecular frameworks, such as the cyclotide scaffold, has shown great promise, as it provides unique pharmacological properties. The use of molecular techniques, such as epitope grafting, and molecular evolution have shown to be highly effective for the selection of bioactive cyclotides. However, despite successes in employing cyclotides to target PPIs, some of the challenges to move them into the clinic still remain.
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Affiliation(s)
- Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Los Angeles, CA 9033, USA.
| | - Maria Jose Campbell
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA.
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13
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Sarmiento C, Camarero JA. Biotechnological Applications of Protein Splicing. Curr Protein Pept Sci 2019; 20:408-424. [PMID: 30734675 PMCID: PMC7135711 DOI: 10.2174/1389203720666190208110416] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/12/2022]
Abstract
Protein splicing domains, also called inteins, have become a powerful biotechnological tool for applications involving molecular biology and protein engineering. Early applications of inteins focused on self-cleaving affinity tags, generation of recombinant polypeptide α-thioesters for the production of semisynthetic proteins and backbone cyclized polypeptides. The discovery of naturallyoccurring split-inteins has allowed the development of novel approaches for the selective modification of proteins both in vitro and in vivo. This review gives a general introduction to protein splicing with a focus on their role in expanding the applications of intein-based technologies in protein engineering and chemical biology.
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Affiliation(s)
- Corina Sarmiento
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA9033 USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA9033 USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA9033 USA
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-9121, USA
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14
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Zhang Y, Chen M, Bruner SD, Ding Y. Heterologous Production of Microbial Ribosomally Synthesized and Post-translationally Modified Peptides. Front Microbiol 2018; 9:1801. [PMID: 30135682 PMCID: PMC6092494 DOI: 10.3389/fmicb.2018.01801] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides, or RiPPs, which have mainly isolated from microbes as well as plants and animals, are an ever-expanding group of peptidic natural products with diverse chemical structures and biological activities. They have emerged as a major category of secondary metabolites partly due to a myriad of microbial genome sequencing endeavors and the availability of genome mining software in the past two decades. Heterologous expression of RiPP gene clusters mined from microbial genomes, which are often silent in native producers, in surrogate hosts such as Escherichia coli and Streptomyces strains can be an effective way to elucidate encoded peptides and produce novel derivatives. Emerging strategies have been developed to facilitate the success of the heterologous expression by targeting multiple synthetic biology levels, including individual proteins, pathways, metabolic flux and hosts. This review describes recent advances in heterologous production of RiPPs, mainly from microbes, with a focus on E. coli and Streptomyces strains as the surrogate hosts.
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Affiliation(s)
- Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
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15
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Richardson MB, Brown DB, Vasquez CA, Ziller JW, Johnston KM, Weiss GA. Synthesis and Explosion Hazards of 4-Azido-l-phenylalanine. J Org Chem 2018; 83:4525-4536. [PMID: 29577718 PMCID: PMC6008159 DOI: 10.1021/acs.joc.8b00270] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A reliable, scalable, cost-effective, and chromatography-free synthesis of 4-azido-l-phenylalanine beginning from l-phenylalanine is described. Investigations into the safety of the synthesis reveal that the Ullman-like Cu(I)-catalyzed azidation step does not represent a significant risk. The isolated 4-azido-l-phenylalanine product, however, exhibits previously undocumented explosive characteristics.
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Affiliation(s)
- Mark B. Richardson
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
| | - Derek B. Brown
- Amgen Inc. One Amgen Center Drive, Thousand Oaks CA 91320 USA
| | - Carlos A. Vasquez
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
| | - Joseph W. Ziller
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
| | - Kevin M. Johnston
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
| | - Gregory A. Weiss
- Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, Irvine CA 92697-2025 USA
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16
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Poon S, Harris KS, Jackson MA, McCorkelle OC, Gilding EK, Durek T, van der Weerden NL, Craik DJ, Anderson MA. Co-expression of a cyclizing asparaginyl endopeptidase enables efficient production of cyclic peptides in planta. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:633-641. [PMID: 29309615 PMCID: PMC5853369 DOI: 10.1093/jxb/erx422] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/04/2017] [Indexed: 05/18/2023]
Abstract
Cyclotides are ultra-stable, backbone-cyclized plant defence peptides that have attracted considerable interest in the pharmaceutical industry. This is due to their range of native bioactivities as well as their ability to stabilize other bioactive peptides within their framework. However, a hindrance to their widespread application is the lack of scalable, cost-effective production strategies. Plant-based production is an attractive, benign option since all biosynthetic steps are performed in planta. Nonetheless, cyclization in non-cyclotide-producing plants is poor. Here, we show that cyclic peptides can be produced efficiently in Nicotiana benthamiana, one of the leading plant-based protein production platforms, by co-expressing cyclotide precursors with asparaginyl endopeptidases that catalyse peptide backbone cyclization. This approach was successful in a range of other plants (tobacco, bush bean, lettuce, and canola), either transiently or stably expressed, and was applicable to both native and engineered cyclic peptides. We also describe the use of the transgenic system to rapidly identify new asparaginyl endopeptidase cyclases and interrogate their substrate sequence requirements. Our results pave the way for exploiting cyclotides for pest protection in transgenic crops as well as large-scale production of cyclic peptide pharmaceuticals in plants.
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Affiliation(s)
- Simon Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Karen S Harris
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Mark A Jackson
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Owen C McCorkelle
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Edward K Gilding
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Durek
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole L van der Weerden
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - David J Craik
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Marilyn A Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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17
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Camarero JA. Cyclotides, a versatile ultrastable micro-protein scaffold for biotechnological applications. Bioorg Med Chem Lett 2017; 27:5089-5099. [PMID: 29110985 PMCID: PMC5812341 DOI: 10.1016/j.bmcl.2017.10.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/13/2017] [Accepted: 10/21/2017] [Indexed: 01/26/2023]
Abstract
Cyclotides are fascinating microproteins (≈30-40 residues long) with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique topology makes them exceptionally stable to chemical, thermal and biological degradation compared to other peptides of similar size. Cyclotides have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot, able to cross cellular membranes and modulate intracellular protein-protein interactions both in vitro and in vivo. These properties make them ideal scaffolds for many biotechnological applications. This article provides and overview of the properties of cyclotides and their applications as molecular imaging agents and peptide-based therapeutics.
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Affiliation(s)
- Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089-9121, USA.
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18
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Kick LM, Harteis S, Koch MF, Schneider S. Mechanistic Insights into Cyclic Peptide Generation by DnaE Split-Inteins through Quantitative and Structural Investigation. Chembiochem 2017; 18:2242-2246. [DOI: 10.1002/cbic.201700503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Leonhard M. Kick
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Sabrina Harteis
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Maximilian F. Koch
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Sabine Schneider
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
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19
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Lesniak WG, Aboye T, Chatterjee S, Camarero JA, Nimmagadda S. In vivo Evaluation of an Engineered Cyclotide as Specific CXCR4 Imaging Reagent. Chemistry 2017; 23:14469-14475. [PMID: 28771849 PMCID: PMC5812345 DOI: 10.1002/chem.201702540] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 12/14/2022]
Abstract
The CXCR4 chemokine receptor plays a key regulatory role in many biological functions, including embryonic development and controlling leukocyte functions during inflammation and immunity. CXCR4 has been also associated with multiple types of cancers where its overexpression/activation promotes metastasis, angiogenesis, and tumor growth and/or survival. Furthermore, CXCR4 is involved in HIV replication, as it is a co-receptor for viral entry into host cells. Altogether, these features make CXCR4 a very attractive target for the development of imaging and therapeutic agents. Here, the in vivo evaluation of the MCoTI-based cyclotide, MCo-CVX-5c, for the development of imaging agents that target CXCR4 is reported. Cyclotide MCo-CVX-5c is a potent CXCR4 antagonist with a remarkable in vivo resistance to biological degradation in serum. A [64 Cu]-DOTA-labeled version of this cyclotide demonstrated high and significant uptake in U87-stb-CXCR4 tumors compared to the control U87 tumors. Furthermore, protracted imaging studies demonstrated radiotracer retention in the U87-stb-CXCR4 tumor at 24 h post injection. Uptake in U87-stb-CXCR4 tumors could be blocked by unlabeled MCo-CVX-5c, showing high in vivo specificity. These results demonstrate the in vivo specificity and retention of a bioactive molecularly targeted cyclotide and highlight the potential of bioactive cyclotides for the development of new imaging agents that target CXCR4.
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Affiliation(s)
- Wojciech G. Lesniak
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Teshome Aboye
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, USA
| | - Samit Chatterjee
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, USA
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-9121, USA
| | - Sridhar Nimmagadda
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, Baltimore, Maryland 21287, USA
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20
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In-cell production of a genetically-encoded library based on the θ-defensin RTD-1 using a bacterial expression system. Bioorg Med Chem 2017; 26:1212-1219. [PMID: 28927803 DOI: 10.1016/j.bmc.2017.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 02/08/2023]
Abstract
We report the high-yield heterologous expression of bioactive θ-defensin RTD-1 inside Escherichia coli cells by making use of intracellular protein trans-splicing in combination with a high efficient split-intein. RTD-1 is a small backbone-cyclized polypeptide with three disulfide bridges and a natural inhibitor of anthrax lethal factor protease. Recombinant RTD-1 was natively folded and able to inhibit anthrax lethal factor protease. In-cell expression of RTD-1 was very efficient and yielded ≈0.7mg of folded RTD-1 per gram of wet E. coli cells. This approach was used to generate of a genetically-encoded RTD-1-based peptide library in live E. coli cells. These results clearly demonstrate the possibility of using genetically-encoded RTD-1-based peptide libraries in live E. coli cells, which is a critical first step for developing in-cell screening and directed evolution technologies using the cyclic peptide RTD-1asa molecular scaffold.
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21
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Abstract
Cyclotides are globular microproteins with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to chemical, thermal, and biological degradation compared to other peptides of similar size. In addition, cyclotides have been shown to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot. Cyclotides can also cross cellular membranes and are able to modulate intracellular protein-protein interactions, both in vitro and in vivo. All of these features make cyclotides highly promising as leads or frameworks for the design of peptide-based diagnostic and therapeutic tools. This article provides an overview on cyclotides and their applications as molecular imaging agents and peptide-based therapeutics.
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Affiliation(s)
- Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-9121, USA
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22
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Cyclotides as drug design scaffolds. Curr Opin Chem Biol 2017; 38:8-16. [DOI: 10.1016/j.cbpa.2017.01.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/27/2017] [Indexed: 11/21/2022]
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23
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Li Y, Aboye T, Breindel L, Shekhtman A, Camarero JA. Efficient recombinant expression of SFTI-1 in bacterial cells using intein-mediated protein trans-splicing. Biopolymers 2017; 106:818-824. [PMID: 27178003 DOI: 10.1002/bip.22875] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/07/2016] [Accepted: 05/04/2016] [Indexed: 01/22/2023]
Abstract
We report for the first time the recombinant expression of bioactive wild-type sunflower trypsin inhibitor 1 (SFTI-1) inside E. coli cells by making use of intracellular protein trans-splicing in combination with a high efficient split-intein. SFTI-1 is a small backbone-cyclized polypeptide with a single disulfide bridge and potent trypsin inhibitory activity. Recombinantly produced SFTI-1 was fully characterized by NMR and was observed to actively inhibit trypsin. The in-cell expression of SFTI-1 was very efficient reaching intracellular concentration ≈ 40 µM. This study clearly demonstrates the possibility of generating genetically encoded SFTI-based peptide libraries in live E. coli cells, and is a critical first step for developing in-cell screening and directed evolution technologies using the cyclic peptide SFTI-1 as a molecular scaffold. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 818-824, 2016.
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Affiliation(s)
- Yilong Li
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121
| | - Teshome Aboye
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121
| | - Leonard Breindel
- Department of Chemistry, State University of New York, Albany, NY, 12222
| | | | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121.,Department of Chemistry, University of Southern California, Los Angeles, CA, 90089-9121
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24
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Abstract
Cyclotides are fascinating microproteins (≈30 residues long) present in several families of plants that share a unique head-to-tail circular knotted topology of three disulfide bridges, with one disulfide penetrating through a macrocycle formed by the two other disulfides and inter-connecting peptide backbones, forming what is called a cystine knot topology. Naturally occurring cyclotides have shown to posses various pharmacologically relevant activities and have been reported to cross cell membranes. Altogether, these features make the cyclotide scaffold an excellent molecular framework for the design of novel peptide-based therapeutics, making them ideal substrates for molecular grafting of biological peptide epitopes. In this chapter we describe how to express a native folded cyclotide using intein-mediated protein trans-splicing in live Escherichia coli cells.
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Affiliation(s)
- Krishnappa Jagadish
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089-9121, USA.
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25
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Borra R, Camarero JA. Recombinant expression of backbone-cyclized polypeptides. Biopolymers 2016; 100:502-9. [PMID: 23893781 DOI: 10.1002/bip.22306] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/13/2013] [Accepted: 05/28/2013] [Indexed: 01/08/2023]
Abstract
Here we review the different biochemical approaches available for the expression of backbone-cyclized polypeptides, including peptides and proteins. These methods allow for the production of circular polypeptides either in vitro or in vivo using standard recombinant DNA expression techniques. Polypeptide circularization provides a valuable tool to study the effects of topology on protein stability and folding kinetics. Furthermore, having biosynthetic access to backbone-cyclized polypeptides makes the production of genetically encoded libraries of cyclic polypeptides possible. The production of such libraries, which was previously restricted to the domain of synthetic chemistry, now offers biologists access to highly diverse and stable molecular libraries that can be screened using high-throughput methods for the rapid selection of novel cyclic polypeptide sequences with new biological activities.
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Affiliation(s)
- Radhika Borra
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90033
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26
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Design of a MCoTI-Based Cyclotide with Angiotensin (1-7)-Like Activity. Molecules 2016; 21:152. [PMID: 26821010 PMCID: PMC4795166 DOI: 10.3390/molecules21020152] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 11/17/2022] Open
Abstract
We report for the first time the design and synthesis of a novel cyclotide able to activate the unique receptor of angiotensin (1-7) (AT1-7), the MAS1 receptor. This was accomplished by grafting an AT1-7 peptide analog onto loop 6 of cyclotide MCoTI-I using isopeptide bonds to preserve the α-amino and C-terminal carboxylate groups of AT1-7, which are required for activity. The resulting cyclotide construct was able to adopt a cyclotide-like conformation and showed similar activity to that of AT1-7. This cyclotide also showed high stability in human serum thereby providing a promising lead compound for the design of a novel type of peptide-based in the treatment of cancer and myocardial infarction.
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27
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Braner M, Kollmannsperger A, Wieneke R, Tampé R. 'Traceless' tracing of proteins - high-affinity trans-splicing directed by a minimal interaction pair. Chem Sci 2015; 7:2646-2652. [PMID: 28660037 PMCID: PMC5477019 DOI: 10.1039/c5sc02936h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 12/18/2015] [Indexed: 12/26/2022] Open
Abstract
Using a minimal lock-and-key element the affinity between the intein fragments for N-terminal protein trans-splicing was significantly increased, allowing for site-specific, ‘traceless’ covalent protein labeling in living mammalian cells at nanomolar probe concentrations.
Protein trans-splicing mediated by split inteins is a powerful technique for site-specific protein modification. Despite recent developments there is still an urgent need for ultra-small high-affinity intein tags for in vitro and in vivo approaches. To date, only very few in-cell applications of protein trans-splicing have been reported, all limited to C-terminal protein modifications. Here, we developed a strategy for covalent N-terminal intein-mediated protein labeling at (sub) nanomolar probe concentrations. Combined with a minimal synthetic lock-and-key element, the affinity between the intein fragments was increased more than 50-fold to 10 nM. Site-specific and efficient ‘traceless’ protein modification by high-affinity trans-splicing is demonstrated at nanomolar concentrations in living mammalian cells.
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Affiliation(s)
- M Braner
- Institute of Biochemistry, Biocenter, and Cluster of Excellence - Macromolecular Complexes , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany .
| | - A Kollmannsperger
- Institute of Biochemistry, Biocenter, and Cluster of Excellence - Macromolecular Complexes , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany .
| | - R Wieneke
- Institute of Biochemistry, Biocenter, and Cluster of Excellence - Macromolecular Complexes , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany .
| | - R Tampé
- Institute of Biochemistry, Biocenter, and Cluster of Excellence - Macromolecular Complexes , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany .
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28
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Nguyen GKT, Kam A, Loo S, Jansson AE, Pan LX, Tam JP. Butelase 1: A Versatile Ligase for Peptide and Protein Macrocyclization. J Am Chem Soc 2015; 137:15398-401. [PMID: 26633100 DOI: 10.1021/jacs.5b11014] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Macrocyclization is a valuable tool for drug design and protein engineering. Although various methods have been developed to prepare macrocycles, a general and efficient strategy is needed. Here we report a highly efficient method using butelase 1 to macrocyclize peptides and proteins ranging in sizes from 26 to >200 residues. We achieved cyclizations that are 20,000 times faster than sortase A, the most widely used ligase for protein cyclization. The reactions completed within minutes with up to 95% yields.
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Affiliation(s)
- Giang K T Nguyen
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Antony Kam
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Shining Loo
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Anna E Jansson
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Lucy X Pan
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
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29
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Sankaran S, de Ruiter M, Cornelissen JJLM, Jonkheijm P. Supramolecular Surface Immobilization of Knottin Derivatives for Dynamic Display of High Affinity Binders. Bioconjug Chem 2015; 26:1972-80. [PMID: 26270829 DOI: 10.1021/acs.bioconjchem.5b00419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Knottins are known as a robust and versatile class of miniprotein scaffolds for the presentation of high-affinity binding peptides; however, to date their application in biomaterials, biological coatings, and surface applications have not been explored. We have developed a strategy to recombinantly synthesize a β-trypsin inhibitory knottin with supramolecular guest tags that enable it to adhere to self-assembled monolayers of the supramolecular host cucurbit[8]uril (CB[8]). We have described a strategy to easily express knottins in E. coli by conjugating them to a fluorescent protein after which they are cleaved and purified. Knottin constructs that varied in the number and position of the supramolecular tag at either the N- or C-termini or at both ends have been verified for their trypsin inhibitory function and CB[8]-binding properties in solution and on surfaces. All of the knottin constructs showed strong inhibition of trypsin with inhibition constants between 10 and 30 nM. Using microscale thermophoresis, we determined that the supramolecular guest tags on the knottins bind CB[8] with a Kd of ∼6 μM in solution. At the surface, strong divalent binding has been determined with a Kd of 0.75 μM in the case of the knottin with two supramolecular guest tags, whereas only weak monovalent binding occurred when only one guest tag was present. We also show successful supramolecular surface immobilization of the knottin using CB[8] and prove that they can be used to immobilize β-trypsin at the surface.
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Affiliation(s)
- Shrikrishnan Sankaran
- Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , 7500 AE Enschede, The Netherlands
| | | | | | - Pascal Jonkheijm
- Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , 7500 AE Enschede, The Netherlands
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30
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Jagadish K, Gould A, Borra R, Majumder S, Mushtaq Z, Shekhtman A, Camarero JA. Recombinant Expression and Phenotypic Screening of a Bioactive Cyclotide Against α-Synuclein-Induced Cytotoxicity in Baker's Yeast. Angew Chem Int Ed Engl 2015; 54:8390-4. [PMID: 26096948 PMCID: PMC4545262 DOI: 10.1002/anie.201501186] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/03/2015] [Indexed: 11/08/2022]
Abstract
We report for the first time the recombinant expression of fully folded bioactive cyclotides inside live yeast cells by using intracellular protein trans-splicing in combination with a highly efficient split-intein. This approach was successfully used to produce the naturally occurring cyclotide MCoTI-I and the engineered bioactive cyclotide MCoCP4. Cyclotide MCoCP4 was shown to reduce the toxicity of human α-synuclein in live yeast cells. Cyclotide MCoCP4 was selected by phenotypic screening from cells transformed with a mixture of plasmids encoding MCoCP4 and inactive cyclotide MCoTI-I in a ratio of 1:5×10(4). This demonstrates the potential for using yeast to perform phenotypic screening of genetically encoded cyclotide-based libraries in eukaryotic cells.
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Affiliation(s)
- Krishnappa Jagadish
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033 (USA)
| | - Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033 (USA)
| | - Radhika Borra
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033 (USA)
| | - Subhabrata Majumder
- Department of Chemistry, State University of New York, Albany, NY 12222 (USA)
| | - Zahid Mushtaq
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033 (USA)
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York, Albany, NY 12222 (USA)
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033 (USA).
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033 (USA).
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31
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Recombinant Expression and Phenotypic Screening of a Bioactive Cyclotide Against α-Synuclein-Induced Cytotoxicity in Baker′s Yeast. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Heguri H, Yamamoto T, Tezuka Y. Folding Construction of a Pentacyclic QuadruplyfusedPolymer Topology with Tailoredkyklo-Telechelic Precursors. Angew Chem Int Ed Engl 2015; 54:8688-92. [DOI: 10.1002/anie.201501800] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 12/23/2022]
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33
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Heguri H, Yamamoto T, Tezuka Y. Folding Construction of a Pentacyclic QuadruplyfusedPolymer Topology with Tailoredkyklo-Telechelic Precursors. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Zhang J, Yamaguchi S, Nagamune T. Sortase A-mediated synthesis of ligand-grafted cyclized peptides for modulating a model protein-protein interaction. Biotechnol J 2015; 10:1499-505. [DOI: 10.1002/biot.201500013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/21/2015] [Accepted: 04/21/2015] [Indexed: 12/15/2022]
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35
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Schumann FH, Varadan R, Tayakuniyil PP, Grossman JH, Camarero JA, Fushman D. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain. Front Chem 2015; 3:26. [PMID: 25905098 PMCID: PMC4389572 DOI: 10.3389/fchem.2015.00026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/23/2015] [Indexed: 12/02/2022] Open
Abstract
Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale) were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding.
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Affiliation(s)
- Frank H Schumann
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Ranjani Varadan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Praveen P Tayakuniyil
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Jennifer H Grossman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles, CA, USA ; Department of Chemistry, University of Southern California Los Angeles, CA, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
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36
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Aboye T, Kuang Y, Neamati N, Camarero JA. Rapid parallel synthesis of bioactive folded cyclotides by using a tea-bag approach. Chembiochem 2015; 16:827-33. [PMID: 25663016 DOI: 10.1002/cbic.201402691] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 11/07/2022]
Abstract
We report here the first rapid parallel production of bioactive folded cyclotides by using Fmoc-based solid-phase peptide synthesis in combination with a "tea-bag" approach. Using this approach, we efficiently synthesized 15 analogues of the CXCR4 antagonist cyclotide MCo-CVX-5c. Cyclotides were synthesized in a single-pot, cyclization/folding reaction in the presence of reduced glutathione. Natively folded cyclotides were quickly purified from the cyclization/folding crude mixture by activated thiol Sepharose-based chromatography. The different folded cyclotide analogues were then tested for their ability to inhibit the CXCR4 receptor in a cell-based assay. The results indicated that this approach can be used for the efficient chemical synthesis of libraries of cyclotides with improved biological properties that can be easily interfaced with solution or cell-based assays for rapid screening.
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Affiliation(s)
- Teshome Aboye
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121 (USA)
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37
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Li Y, Bi T, Camarero JA. Chemical and biological production of cyclotides. ADVANCES IN BOTANICAL RESEARCH 2015; 76:271-303. [PMID: 27064329 PMCID: PMC4822716 DOI: 10.1016/bs.abr.2015.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cyclotides are fascinating naturally occurring micro-proteins (≈30 residues long) present in several plant families, and display various biological properties such as protease inhibitory, anti-microbial, insecticidal, cytotoxic, anti-HIV and hormone-like activities. Cyclotides share a unique head-to-tail circular knotted topology of three disulfide bridges, with one disulfide penetrating through a macrocycle formed by the two other disulfides and interconnecting peptide backbones, forming what is called a cystine knot topology. This cyclic cystine knot (CCK) framework gives the cyclotides exceptional rigidity, resistance to thermal and chemical denaturation, and enzymatic stability against degradation. Interestingly, cyclotides have been shown to be orally bioavailable, and other cyclotides have been shown to cross the cell membranes. Moreover, recent reports have also shown that engineered cyclotides can be efficiently used to target extracellular and intracellular protein-protein interactions, therefore making cyclotides ideal tools for drug development to selectively target protein-protein interactions. In this work we will review all the available methods for production of these interesting proteins using chemical or biological methods.
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Affiliation(s)
- Yilong Li
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Tao Bi
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033, USA
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38
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Waldhauer MC, Schmitz SN, Ahlmann-Eltze C, Gleixner JG, Schmelas CC, Huhn AG, Bunne C, Büscher M, Horn M, Klughammer N, Kreft J, Schäfer E, Bayer PA, Krämer SG, Neugebauer J, Wehler P, Mayer MP, Eils R, Di Ventura B. Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation. MOLECULAR BIOSYSTEMS 2015; 11:3231-43. [DOI: 10.1039/c5mb00341e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While using a serine (S) as linker for circularization increases the thermostability, a longer linker (RGKCWE) leads to reduced aggregation after heat shock at elevated temperatures.
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39
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Böcker JK, Friedel K, Matern JCJ, Bachmann AL, Mootz HD. Generation of a Genetically Encoded, Photoactivatable Intein for the Controlled Production of Cyclic Peptides. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409848] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Böcker JK, Friedel K, Matern JCJ, Bachmann AL, Mootz HD. Generation of a Genetically Encoded, Photoactivatable Intein for the Controlled Production of Cyclic Peptides. Angew Chem Int Ed Engl 2014; 54:2116-20. [DOI: 10.1002/anie.201409848] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/04/2014] [Indexed: 01/19/2023]
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41
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Stanger K, Maurer T, Kaluarachchi H, Coons M, Franke Y, Hannoush RN. Backbone cyclization of a recombinant cystine-knot peptide by engineered Sortase A. FEBS Lett 2014; 588:4487-96. [DOI: 10.1016/j.febslet.2014.10.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/18/2014] [Accepted: 10/20/2014] [Indexed: 11/15/2022]
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42
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Suzuki T, Yamamoto T, Tezuka Y. Constructing a Macromolecular K3,3 Graph through Electrostatic Self-Assembly and Covalent Fixation with a Dendritic Polymer Precursor. J Am Chem Soc 2014; 136:10148-55. [DOI: 10.1021/ja504891x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Takuya Suzuki
- Department
of Organic and
Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takuya Yamamoto
- Department
of Organic and
Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Yasuyuki Tezuka
- Department
of Organic and
Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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43
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Wood DW, Camarero JA. Intein applications: from protein purification and labeling to metabolic control methods. J Biol Chem 2014; 289:14512-9. [PMID: 24700459 DOI: 10.1074/jbc.r114.552653] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The discovery of inteins in the early 1990s opened the door to a wide variety of new technologies. Early engineered inteins from various sources allowed the development of self-cleaving affinity tags and new methods for joining protein segments through expressed protein ligation. Some applications were developed around native and engineered split inteins, which allow protein segments expressed separately to be spliced together in vitro. More recently, these early applications have been expanded and optimized through the discovery of highly efficient trans-splicing and trans-cleaving inteins. These new inteins have enabled a wide variety of applications in metabolic engineering, protein labeling, biomaterials construction, protein cyclization, and protein purification.
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Affiliation(s)
- David W Wood
- From the Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210 and
| | - Julio A Camarero
- the Departments of Pharmacology and Pharmaceutical Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90033
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44
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Shah NH, Eryilmaz E, Cowburn D, Muir TW. Naturally split inteins assemble through a "capture and collapse" mechanism. J Am Chem Soc 2013; 135:18673-81. [PMID: 24236406 PMCID: PMC3865799 DOI: 10.1021/ja4104364] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Split
inteins are a class of naturally occurring proteins that
carry out protein splicing in trans. The chemical
mechanism of protein trans-splicing is well-understood
and has been exploited to develop several powerful protein engineering
technologies. Split intein chemistry is preceded by efficient molecular
recognition between two protomers that become intertwined in their
bound state. It is currently unclear how this unique topology is achieved
upon fragment association. Using biophysical techniques in conjunction
with protein engineering methods, including segmental isotopic labeling,
we show that one split intein fragment is partly folded, while the
other is completely disordered. These polypeptides capture each other
through their disordered regions and form an ordered intermediate
with native-like structure at their interface. This intermediate then
collapses into the canonical intein fold. This mechanism provides
insight into the evolutionary constraints on split intein assembly
and should enhance the development of split intein-based technologies.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
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45
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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46
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Gründemann C, Thell K, Lengen K, Garcia-Käufer M, Huang YH, Huber R, Craik DJ, Schabbauer G, Gruber CW. Cyclotides Suppress Human T-Lymphocyte Proliferation by an Interleukin 2-Dependent Mechanism. PLoS One 2013; 8:e68016. [PMID: 23840803 PMCID: PMC3694003 DOI: 10.1371/journal.pone.0068016] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/24/2013] [Indexed: 02/07/2023] Open
Abstract
Cyclotides are a diverse and abundant group of ribosomally synthesized plant peptides containing a unique cyclic cystine-knotted topology that confers them with remarkable stability. Kalata B1, a representative member of this family of mini-proteins, has been found to inhibit the proliferation of human peripheral blood mononuclear cells. Analysis of T-cell proliferation upon treatment with chemically synthesized kalata B1 mutants revealed a region comprising inter-cysteine loops 1 and 2 of the cyclotide framework to be important for biological activity. Cytokine signaling analysis using an 'active' kalata B1 mutant [T20K], and the reference drug cyclosporin A (CsA) demonstrated that treatment of activated T-lymphocytes with these compounds decreased the expression of the interleukin-2 (IL-2) surface receptor as well as IL-2 cytokine secretion and IL-2 gene expression, whereas the 'inactive' kalata B1 mutant [V10K] did not cause any effects. The anti-proliferative activity of [T20K] kalata B1 was antagonized by addition of exogenous IL-2. Furthermore, treatment with [T20K] kalata B1 led to an initial reduction of the effector function, as indicated by the reduced IFN-γ and TNF-α production, but the levels of both cytokines stabilized over time and returned to their normal levels. On the other hand, the degranulation activity remained reduced. This indicated that cyclotides interfere with T-cell polyfunctionality and arrest the proliferation of immune-competent cells through inhibiting IL-2 biology at more than one site. The results open new avenues to utilize native and synthetically-optimized cyclotides for applications in immune-related disorders and as immunosuppressant peptides.
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Affiliation(s)
- Carsten Gründemann
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
- Center for Complementary Medicine, Department of Environmental Health Sciences, University Medical Center Freiburg, Freiburg, Germany
| | - Kathrin Thell
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Karin Lengen
- Center for Complementary Medicine, Department of Environmental Health Sciences, University Medical Center Freiburg, Freiburg, Germany
| | - Manuel Garcia-Käufer
- Center for Complementary Medicine, Department of Environmental Health Sciences, University Medical Center Freiburg, Freiburg, Germany
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland, Australia
| | - Roman Huber
- Center for Complementary Medicine, Department of Environmental Health Sciences, University Medical Center Freiburg, Freiburg, Germany
| | - David J. Craik
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland, Australia
| | - Gernot Schabbauer
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Christian W. Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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47
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Craik DJ. Joseph Rudinger memorial lecture: discovery and applications of cyclotides. J Pept Sci 2013; 19:393-407. [PMID: 23737440 DOI: 10.1002/psc.2523] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 12/31/2022]
Abstract
Cyclotides are plant-derived peptides of approximately 30 amino acids that have the characteristic structural features of a head-to-tail cyclized backbone and a cystine knot arrangement of their three conserved disulfide bonds. This article gives a personal account of the discovery of cyclotides, their characterization and their applications, based on work carried out in my laboratory over the last 20 years. It describes some of the background to their discovery and focuses on how their unique structural features lead to exceptional stability. This stability and their amenability to chemical synthesis have made it possible to use cyclotides as templates in protein engineering and drug design applications. These applications complement the interest in cyclotides deriving from their unique structures and natural function as host defense molecules.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, 4072, Australia.
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48
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Cowper B, Craik DJ, Macmillan D. Making ends meet: chemically mediated circularization of recombinant proteins. Chembiochem 2013; 14:809-12. [PMID: 23559418 PMCID: PMC4016753 DOI: 10.1002/cbic.201300105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 01/16/2023]
Abstract
A selective N→S acyl transfer reaction facilitates semi-synthesis of the plant cyclotide kalata B1 from a linear precursor peptide of bacterial origin, through simple appendage of N-terminal cysteine and a thiol-labile C-terminal Gly-Cys motif. This constitutes the first synthesis of a ribosomally derived circular miniprotein, without recourse to protein splicing elements.
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Affiliation(s)
- Ben Cowper
- Department of Chemistry, University College London, Christopher Ingold Building20 Gordon Street, London, WC1H 0AJ (UK) E-mail:
| | - David J Craik
- Institute for Molecular Bioscience, University of QueenslandBrisbane, Queensland, 4072 (Australia)
| | - Derek Macmillan
- Department of Chemistry, University College London, Christopher Ingold Building20 Gordon Street, London, WC1H 0AJ (UK) E-mail:
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49
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Shah NH, Eryilmaz E, Cowburn D, Muir TW. Extein residues play an intimate role in the rate-limiting step of protein trans-splicing. J Am Chem Soc 2013; 135:5839-47. [PMID: 23506399 PMCID: PMC3630739 DOI: 10.1021/ja401015p] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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Split
inteins play an important role in modern protein semisynthesis
techniques. These naturally occurring protein splicing domains can
be used for in vitro and in vivo protein modification, peptide and
protein cyclization, segmental isotopic labeling, and the construction
of biosensors. The most well-characterized family of split inteins,
the cyanobacterial DnaE inteins, show particular promise, as many
of these can splice proteins in less than 1 min. Despite this fact,
the activity of these inteins is context-dependent: certain peptide
sequences surrounding their ligation junction (called local N- and
C-exteins) are strongly preferred, while other sequences cause a dramatic
reduction in the splicing kinetics and yield. These sequence constraints
limit the utility of inteins, and thus, a more detailed understanding
of their participation in protein splicing is needed. Here we present
a thorough kinetic analysis of the relationship between C-extein composition
and split intein activity. The results of these experiments were used
to guide structural and molecular dynamics studies, which revealed
that the motions of catalytic residues are constrained by the second
C-extein residue, likely forcing them into an active conformation
that promotes rapid protein splicing. Together, our structural and
functional studies also highlight a key region of the intein structure
that can be re-engineered to increase intein promiscuity.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
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