1
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Jiang Z, Huang YH, Kaas Q, Craik DJ, Wang CK. Structure and Activity of Reconstructed Pseudo-Ancestral Cyclotides. ChemMedChem 2024; 19:e202400124. [PMID: 38632079 DOI: 10.1002/cmdc.202400124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Cyclotides are cyclic peptides that are promising scaffolds for the design of drug candidates and chemical tools. However, despite there being hundreds of reported cyclotides, drug design studies have commonly focussed on a select few prototypic examples. Here, we explored whether ancestral sequence reconstruction could be used to generate new cyclotides for further optimization. We show that the reconstructed 'pseudo-ancestral' sequences, named Ancy-m (for the ancestral cyclotide of the Möbius sub-family) and Ancy-b (for the bracelet sub-family), have well-defined structures like their extant members, comprising the core structural feature of a cyclic cystine knot. This motif underpins efforts to re-engineer cyclotides for agrochemical and therapeutic applications. We further show that the reconstructed sequences are resistant to temperatures approaching boiling, bind to phosphatidyl-ethanolamine lipid bilayers at micromolar affinity, and inhibit the growth of insect cells at inhibitory concentrations in the micromolar range. Interestingly, the Ancy-b cyclotide had a higher oxidative folding yield than its comparator cyclotide cyO2, which belongs to the bracelet cyclotide subfamily known to be notoriously difficult to fold. Overall, this study provides new cyclotide sequences not yet found naturally that could be valuable starting points for the understanding of cyclotide evolution and for further optimization as drug leads.
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Affiliation(s)
- Zhihao Jiang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
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2
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Le T, Zhang D, Martini RM, Biswas S, van der Donk WA. Use of a head-to-tail peptide cyclase to prepare hybrid RiPPs. Chem Commun (Camb) 2024; 60:6508-6511. [PMID: 38833296 PMCID: PMC11189026 DOI: 10.1039/d3cc04919a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 04/25/2024] [Indexed: 06/06/2024]
Abstract
Cyclotides and lanthipeptides are cyclic peptide natural products with promising bioengineering potential. No peptides have been isolated that contain both structural motifs defining these two families, an N-to-C cyclised backbone and lanthionine linkages. We combined their biosynthetic machineries to produce hybrid structures that possess improved activity or stability, demonstrate how the AEP-1 plant cyclase can be utilised to complete the maturation of the sactipeptide subtilosin A, and present head-to-tail cyclisation of the glycocin sublancin. These studies show the plasticity of AEP-1 and its utilisation alongside other post-translational modifications.
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Affiliation(s)
- Tung Le
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Dongtianyu Zhang
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Rachel M Martini
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Subhanip Biswas
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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3
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Koehbach J, Muratspahić E, Ahmed ZM, White AM, Tomašević N, Durek T, Clark RJ, Gruber CW, Craik DJ. Chemical synthesis of grafted cyclotides using a "plug and play" approach. RSC Chem Biol 2024; 5:567-571. [PMID: 38846076 PMCID: PMC11151825 DOI: 10.1039/d4cb00008k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/23/2024] [Indexed: 06/09/2024] Open
Abstract
Cyclotides are a diverse class of plant-derived cyclic, disulfide-rich peptides with a unique cyclic cystine knot topology. Their remarkable structural stability and resistance to proteolytic degradation can lead to improved pharmacokinetics and oral activity as well as selectivity and high enzymatic stability. Thus, cyclotides have emerged as powerful scaffold molecules for designing peptide-based therapeutics. The chemical engineering of cyclotides has generated novel peptide ligands of G protein-coupled receptors (GPCRs), today's most exploited drug targets. However key challenges potentially limit the widespread use of cyclotides in molecular grafting applications. Folding of cyclotides containing bioactive epitopes remains a major bottleneck in cyclotide synthesis. Here we present a modular 'plug and play' approach that effectively bypasses problems associated with the oxidative folding of cyclotides. By grafting onto a pre-formed acyclic cyclotide-like scaffold we show that difficult-to-graft sequences can be easily obtained and can target GPCRs with nanomolar affinities and potencies. We further show the suitability of this new method to graft other complex epitopes including structures with additional disulfide bonds that are not readily available via currently employed chemical methods, thus fully unlocking cyclotides to be used in drug design applications.
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Affiliation(s)
- Johannes Koehbach
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland Australia
- School of Biomedical Sciences, The University of Queensland Brisbane Queensland Australia
| | - Edin Muratspahić
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Vienna Austria
| | - Zakaria M Ahmed
- School of Biomedical Sciences, The University of Queensland Brisbane Queensland Australia
| | - Andrew M White
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland Australia
- Research School of Chemistry, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University Australia
| | - Nataša Tomašević
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Vienna Austria
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland Australia
| | - Richard J Clark
- School of Biomedical Sciences, The University of Queensland Brisbane Queensland Australia
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Vienna Austria
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland Australia
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4
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Tian S, de Veer SJ, Durek T, Wang CK, Craik DJ. Nucleation of a key beta-turn promotes cyclotide oxidative folding. J Biol Chem 2024; 300:107125. [PMID: 38432638 PMCID: PMC10999817 DOI: 10.1016/j.jbc.2024.107125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Cyclotides are plant-derived peptides characterized by a head-to-tail cyclic backbone and a cystine knot motif comprised of three disulfide bonds. Formation of this motif via in vitro oxidative folding can be challenging and can result in misfolded isomers with nonnative disulfide connectivities. Here, we investigated the effect of β-turn nucleation on cyclotide oxidative folding. Two types of β-turn mimics were grafted into kalata B1, individually replacing each of the four β-turns in the folded cyclotide. Insertion of d-Pro-Gly into loop 5 was beneficial to the folding of both cyclic kB1 and a linear form of the peptide. The linear grafted analog folded four-times faster in aqueous conditions than cyclic kB1 in optimized conditions. Additionally, the cyclic analogue folded without the need for redox agents by transitioning through a native-like intermediate that was on-pathway to product formation. Kalata B1 is from the Möbius subfamily of cyclotides. Grafting d-Pro-Gly into loop 5 of cyclotides from two other subfamilies also had a beneficial effect on folding. Our findings demonstrate the importance of a β-turn nucleation site for cyclotide oxidative folding, which could be adopted as a chemical strategy to improve the in vitro folding of diverse cystine-rich peptides.
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Affiliation(s)
- Sixin Tian
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
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5
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Paquette AR, Brazeau-Henrie JT, Boddy CN. Thioesterases as tools for chemoenzymatic synthesis of macrolactones. Chem Commun (Camb) 2024; 60:3379-3388. [PMID: 38456624 DOI: 10.1039/d4cc00401a] [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: 03/09/2024]
Abstract
Macrocycles are a key functional group that can impart unique properties into molecules. Their synthesis has led to the development of many outstanding chemical methodologies and yet still remains challenging. Thioesterase (TE) domains are frequently responsible for macrocyclization in natural product biosynthesis and provide unique strengths for the enzymatic synthesis of macrocycles. In this feature article, we describe our work to characterize the substrate selectivity of TEs and to use these enzymes as biocatalysts. Our efforts have shown that the linear thioester activated substrates are loaded on TEs with limited substrate selectivity to generate acyl-enzyme intermediates. We show that cyclization of the acyl-enzyme intermediates can be highly selective, with competing hydrolysis of the acyl-enzyme intermediates. The mechanisms controlling TE-mediated macrocyclization versus hydrolysis are a significant unsolved problem in TE biochemistry. The potential of TEs as biocatalysts was demonstrated by using them in the chemoenzymatic total synthesis of macrocyclic depsipeptide natural products. This article highlights the strengths and potential of TEs as biocatalysts as well as their limitations, opening exciting research opportunities including TE engineering to optimize these powerful biocatalysts.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
| | - Jordan T Brazeau-Henrie
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5.
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6
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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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7
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Dang TT, Harvey PJ, Chan LY, Huang Y, Kaas Q, Craik DJ. Mutagenesis of cyclotide Cter 27 exemplifies a robust folding strategy for bracelet cyclotides. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tien T. Dang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
- Institute of Applied Materials Science Vietnam Academy of Science and Technology Ho Chi Minh City Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Lai Yue Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Yen‐Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - David J. Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
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8
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Doffek B, Huang Y, Huang YH, Chan LY, Gilding EK, Jackson MA, Craik DJ. Comparative analysis of cyclotide-producing plant cell suspensions presents opportunities for cyclotide plant molecular farming. PHYTOCHEMISTRY 2022; 195:113053. [PMID: 34923360 DOI: 10.1016/j.phytochem.2021.113053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Cyclotides are a class of ribosomally-synthesized plant peptides that function in plants as a defense against insects and fungal pathogens. Their unique structure comprises a cyclized peptide backbone threaded by three disulfide bonds, that imparts structural stability, a desirable quality for peptide-based therapeutics or insecticides. Producing these peptides synthetically is challenging due to the amount of chemical waste produced and inefficiency of folding certain cyclotides. Thus, it is desirable to develop a means to access cyclotide biosynthesis in their native hosts, cultured in defined conditions, at both laboratory and commercial scale. Here we developed suspension cell cultures from two species previously unexplored for cyclotide production in suspension cells, Clitoria ternatea L., Hybanthus enneaspermus F. Muell., as well as with Oldenlandia affinis (Roem. & Schult.) DC., a species reported previously to accumulate cyclotides in cell suspensions. We assessed the growth rate, cyclotide production and gene expression for the various species. We found that while many cyclotides had reduced expression in Oldenlandia affinis suspension cells when compared to plant organs, those in Clitoria ternatea and Hybanthus enneaspermus maintained or increased expression levels. The cyclotides that continued to be expressed in suspension cultures shared similar sequence and biophysical properties as a group, regardless of phylogenetic origin of the host. Of particular interest was the discovery of inducibility by NaCl of cyclotide expression in O. affinis, cycloviolacin O2 expression in O. affinis, and the scale up of cycloviolacin O2 production in H. enneaspermus. Together the results presented here highlight the utility of plant cell suspensions as modalities to produce macrocyclic peptides.
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Affiliation(s)
- Benjamin Doffek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Yvonne Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Lai Yue Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Mark A Jackson
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 4072, Australia.
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9
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Huang YH, Du Q, Jiang Z, King GJ, Collins BM, Wang CK, Craik DJ. Enabling Efficient Folding and High-Resolution Crystallographic Analysis of Bracelet Cyclotides. Molecules 2021; 26:5554. [PMID: 34577034 PMCID: PMC8467136 DOI: 10.3390/molecules26185554] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 11/23/2022] Open
Abstract
Cyclotides have attracted great interest as drug design scaffolds because of their unique cyclic cystine knotted topology. They are classified into three subfamilies, among which the bracelet subfamily represents the majority and comprises the most bioactive cyclotides, but are the most poorly utilized in drug design applications. A long-standing challenge has been the very low in vitro folding yields of bracelets, hampering efforts to characterize their structures and activities. Herein, we report substantial increases in bracelet folding yields enabled by a single point mutation of residue Ile-11 to Leu or Gly. We applied this discovery to synthesize mirror image enantiomers and used quasi-racemic crystallography to elucidate the first crystal structures of bracelet cyclotides. This study provides a facile strategy to produce bracelet cyclotides, leading to a general method to easily access their atomic resolution structures and providing a basis for development of biotechnological applications.
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Affiliation(s)
- Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Qingdan Du
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zhihao Jiang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gordon J. King
- The Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
| | - Conan K. Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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10
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11
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Dang TT, Chan LY, Tombling BJ, Harvey PJ, Gilding EK, Craik DJ. In Planta Discovery and Chemical Synthesis of Bracelet Cystine Knot Peptides from Rinorea bengalensis. JOURNAL OF NATURAL PRODUCTS 2021; 84:395-407. [PMID: 33570395 DOI: 10.1021/acs.jnatprod.0c01065] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cyclotides are plant-derived peptides that have attracted interest as biocides and scaffolds for the development of stable peptide therapeutics. Cyclotides are characterized by their cyclic backbone and cystine knot framework, which engenders them with remarkably high stability. This study reports the cystine knot-related peptidome of Rinorea bengalensis, a small rainforest tree in the Violaceae family that is distributed from Australia westward to India. Surprisingly, many more acyclic knotted peptides (acyclotides) were discovered than cyclic counterparts (cyclotides), with 32 acyclotides and 1 cyclotide sequenced using combined transcriptome and proteomic analyses. Nine acyclotides were isolated and screened against a panel of mammalian cell lines, showing they had the cytotoxic properties normally associated with cyclotide-like peptides. NMR analysis of the acyclotide ribes 21 and 22 and the cyclotide ribe 33 confirmed that these peptides contained the cystine knot structural motif. The bracelet-subfamily cyclotide ribe 33 was amenable to chemical synthesis in reasonable yield, an achievement that has long eluded previous attempts to synthetically produce bracelet cyclotides. Accordingly, ribe 33 represents an exciting new bracelet cyclotide scaffold that can be subject to chemical modification for future molecular engineering applications.
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Affiliation(s)
- Tien T Dang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lai Y Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin J Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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12
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Handley TNG, Wang CK, Harvey PJ, Lawrence N, Craik DJ. Cyclotide Structures Revealed by NMR, with a Little Help from X‐ray Crystallography. Chembiochem 2020; 21:3463-3475. [DOI: 10.1002/cbic.202000315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/08/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Thomas N. G. Handley
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
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13
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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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14
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Yathursan S, Wiles S, Read H, Sarojini V. A review on anti-tuberculosis peptides: Impact of peptide structure on anti-tuberculosis activity. J Pept Sci 2019; 25:e3213. [PMID: 31515916 DOI: 10.1002/psc.3213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 12/18/2022]
Abstract
Antibiotic resistance is a major public health problem globally. Particularly concerning amongst drug-resistant human pathogens is Mycobacterium tuberculosis that causes the deadly infectious tuberculosis (TB) disease. Significant issues associated with current treatment options for drug-resistant TB and the high rate of mortality from the disease makes the development of novel treatment options against this pathogen an urgent need. Antimicrobial peptides are part of innate immunity in all forms of life and could provide a potential solution against drug-resistant TB. This review is a critical analysis of antimicrobial peptides that are reported to be active against the M tuberculosis complex exclusively. However, activity on non-TB strains such as Mycobacterium avium and Mycobacterium intracellulare, whenever available, have been included at appropriate sections for these anti-TB peptides. Natural and synthetic antimicrobial peptides of diverse sequences, along with their chemical structures, are presented, discussed, and correlated to their observed antimycobacterial activities. Critical analyses of the structure allied to the anti-mycobacterial activity have allowed us to draw important conclusions and ideas for research and development on these promising molecules to realise their full potential. Even though the review is focussed on peptides, we have briefly summarised the structures and potency of the various small molecule drugs that are available and under development, for TB treatment.
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Affiliation(s)
- Sutharsana Yathursan
- School of Chemical Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Hannah Read
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, 6140, New Zealand
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15
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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: 132] [Impact Index Per Article: 26.4] [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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16
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Using backbone-cyclized Cys-rich polypeptides as molecular scaffolds to target protein-protein interactions. Biochem J 2019; 476:67-83. [PMID: 30635453 DOI: 10.1042/bcj20180792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022]
Abstract
The use of disulfide-rich backbone-cyclized polypeptides, as molecular scaffolds to design a new generation of bioimaging tools and drugs that are potent and specific, and thus might have fewer side effects than traditional small-molecule drugs, is gaining increasing interest among the scientific and in the pharmaceutical industries. Highly constrained macrocyclic polypeptides are exceptionally more stable to chemical, thermal and biological degradation and show better biological activity when compared with their linear counterparts. Many of these relatively new scaffolds have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the disulfide bonds, able to cross cellular membranes and modulate intracellular protein-protein interactions both in vitro and in vivo These properties make them ideal tools for many biotechnological applications. The present study provides an overview of the new developments on the use of several disulfide-rich backbone-cyclized polypeptides, including cyclotides, θ-defensins and sunflower trypsin inhibitor peptides, in the development of novel bioimaging reagents and therapeutic leads.
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17
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Craik DJ, Lee MH, Rehm FBH, Tombling B, Doffek B, Peacock H. Ribosomally-synthesised cyclic peptides from plants as drug leads and pharmaceutical scaffolds. Bioorg Med Chem 2017; 26:2727-2737. [PMID: 28818463 DOI: 10.1016/j.bmc.2017.08.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/12/2017] [Accepted: 08/06/2017] [Indexed: 12/28/2022]
Abstract
Owing to their exceptional stability and favourable pharmacokinetic properties, plant-derived cyclic peptides have recently attracted significant attention in the field of peptide-based drug design. This article describes the three major classes of ribosomally-synthesised plant peptides - the cyclotides, the PawS-derived peptides and the orbitides - and reviews their applications as leads or scaffolds in drug design. These ribosomally-produced peptides have a range of biological activities, including anti-HIV, cytotoxic and immunomodulatory activity. In addition, recent interest has focused on their use as scaffolds to stabilise bioactive peptide sequences, thereby enhancing their biopharmaceutical properties. There are now more than 30 published papers on such 'grafting' applications, most of which have been reported only in the last few years, and several such studies have reported in vivo activity of orally delivered cyclic peptides. In this article, we describe approaches to the synthesis of cyclic peptides and their pharmaceutically-grafted derivatives as well as outlining their biosynthetic routes. Finally, we describe possible bioproduction routes for pharmaceutically active cyclic peptides, involving plants and plant suspension cultures.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Meng-Han Lee
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Fabian B H Rehm
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin Tombling
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin Doffek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hayden Peacock
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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18
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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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19
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Qu H, Smithies BJ, Durek T, Craik DJ. Synthesis and Protein Engineering Applications of Cyclotides. Aust J Chem 2017. [DOI: 10.1071/ch16589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclotides are a group of plant-derived peptides with a head-to-tail cyclized backbone that is stabilized by three knotted disulfide bonds. Their exceptional stability and tolerance for residue substitutions have led to interest in their application as drug design scaffolds. To date, chemical synthesis has been the dominant methodology for producing cyclotides and their analogues. Native chemical ligation is the most common strategy to generate the cyclic backbone and has been highly successful at producing a wide range of cyclotides for studies of structure–activity relationships. Both this and other chemical approaches require a specific linker at the C-terminus and typically involve a non-directed folding (disulfide oxidation) regimen, which can sometimes be a limiting factor in final yields. Following the recent discovery of enzymes involved in peptide cyclization in planta, site-specific and highly efficient enzymatic ligations have been used for synthetic cyclotide backbone cyclization. In this review, chemical synthesis strategies and approaches involving cyclization via enzymes for the production of cyclotides are described.
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20
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Terrier VP, Delmas AF, Aucagne V. Efficient synthesis of cysteine-rich cyclic peptides through intramolecular native chemical ligation of N-Hnb-Cys peptide crypto-thioesters. Org Biomol Chem 2017; 15:316-319. [DOI: 10.1039/c6ob02546c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We herein introduce a straightforward synthetic route to cysteine-containing cyclic peptides. It is based on the intramolecular native chemical ligation of thioesters generated in situ from N-Hnb-Cys crypto-thioesters. The strategy is applied to a representative range of natural cyclic disulfide-rich peptide sequences.
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Affiliation(s)
- Victor P. Terrier
- Centre de Biophysique Moléculaire
- CNRS UPR 4301
- 45071 Orléans Cedex 2
- France
| | - Agnès F. Delmas
- Centre de Biophysique Moléculaire
- CNRS UPR 4301
- 45071 Orléans Cedex 2
- France
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire
- CNRS UPR 4301
- 45071 Orléans Cedex 2
- France
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21
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Synthetic Cystine-Knot Miniproteins - Valuable Scaffolds for Polypeptide Engineering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:121-44. [PMID: 27236555 DOI: 10.1007/978-3-319-32805-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Peptides with the cystine-knot architecture, often termed knottins, are promising scaffolds for biomolecular engineering. These unique molecules combine diverse bioactivities with excellent structural, thermal, and proteolytical stability. Being different in the composition and structure of their amino acid backbone, knottins share the same core element, namely cystine knot, which is built by six cysteine residues forming three disulfides upon oxidative folding. This motif ensures a notably rigid framework that highly tolerates both rational and combinatorial changes in the primary structure. Being accessible through recombinant production and total chemical synthesis, cystine-knot miniproteins can be endowed with novel bioactivities by variation of surface-exposed loops and incorporation of non-natural elements within their non-conserved regions towards the generation of tailor-made peptidic compounds. In this chapter the topology of cystine-knot peptides, their synthesis and applications for diagnostics and therapy is discussed.
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22
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Hellinger R, Koehbach J, Soltis DE, Carpenter EJ, Wong GKS, Gruber CW. Peptidomics of Circular Cysteine-Rich Plant Peptides: Analysis of the Diversity of Cyclotides from Viola tricolor by Transcriptome and Proteome Mining. J Proteome Res 2015; 14:4851-62. [PMID: 26399495 PMCID: PMC4642221 DOI: 10.1021/acs.jproteome.5b00681] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Cyclotides are plant-derived mini proteins. They are genetically
encoded as precursor proteins that become post-translationally modified
to yield circular cystine-knotted molecules. Because of this structural
topology cyclotides resist enzymatic degradation in biological fluids,
and hence they are considered as promising lead molecules for pharmaceutical
applications. Despite ongoing efforts to discover novel cyclotides
and analyze their biodiversity, it is not clear how many individual
peptides a single plant specimen can express. Therefore, we investigated
the transcriptome and cyclotide peptidome of Viola tricolor. Transcriptome mining enabled the characterization of cyclotide
precursor architecture and processing sites important for biosynthesis
of mature peptides. The cyclotide peptidome was explored by mass spectrometry
and bottom-up proteomics using the extracted peptide sequences as
queries for database searching. In total 164 cyclotides were discovered
by nucleic acid and peptide analysis in V. tricolor. Therefore, violaceous plants at a global scale may be the source
to as many as 150 000 individual cyclotides. Encompassing the
diversity of V. tricolor as a combinatorial library
of bioactive peptides, this commercially available medicinal herb
may be a suitable starting point for future bioactivity-guided screening
studies.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Koehbach
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria.,School of Biomedical Sciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida , Gainesville, Florida 32611, United States
| | - Eric J Carpenter
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta T6G 2E9, Canada
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta T6G 2E9, Canada.,Department of Medicine, University of Alberta , Edmonton, Alberta T6G 2E1, Canada.,BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria.,School of Biomedical Sciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
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23
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Slazak B, Jacobsson E, Kuta E, Göransson U. Exogenous plant hormones and cyclotide expression in Viola uliginosa (Violaceae). PHYTOCHEMISTRY 2015; 117:527-536. [PMID: 26246035 DOI: 10.1016/j.phytochem.2015.07.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/30/2015] [Accepted: 07/20/2015] [Indexed: 05/18/2023]
Abstract
Plants from Violaceae produce cyclotides, peptides characterized by a circular peptide backbone and a cystine knot. This signature motif gives stability that can harness a wide spectrum of biological activities, with implications in plant defense and with applications in medicine and biotechnology. In the current work, cyclotide expressing in vitro cultures were established from Viola uliginosa. These cultures are useful models for studying biosynthesis of cyclotides and can also be used in their production. The cyclotide expression pattern is shown to be dependent on exogenous plant growth regulators, both on peptide and gene expression levels. The highest yields of cyclotides were obtained on media containing only a cytokinin and were correlated with storage material accumulation. Exposure to auxins decreased cyclotide production and caused shifting of the biosynthesis pattern to root specific cyclotides. The response to stimuli in terms of cyclotide expression pattern appears to be developmental, and related to polar auxin transportation and the auxin/cytokinin ratio regulating tissue differentiation. By the use of whole transcriptome shotgun sequencing (WTSS) and peptidomics, 20 cyclotide sequences from V. uliginosa (including 12 new) and 12 complete precursor proteins could be identified. The most abundant cyclotides were cycloviolacin O3 (CyO3), CyO8 and CyO13. A suspension culture was obtained that grew exponentially with a doubling time of approximately 3 days. After ten days of growth, the culture provided a yield of more than 4 mg CyO13 per gram dry mass.
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Affiliation(s)
- Blazej Slazak
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, 9 Gronostajowa Str., 30-387 Cracow, Poland; Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, 751 23 Uppsala, Sweden; W. Szafer Istitute of Botany, Polish Academy of Sciences, 46 Lubicz St., 31-512 Cracow, Poland.
| | - Erik Jacobsson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, 751 23 Uppsala, Sweden
| | - Elżbieta Kuta
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, 9 Gronostajowa Str., 30-387 Cracow, Poland
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, 751 23 Uppsala, Sweden
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24
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Pardo A, Hogenauer TJ, Cai Z, Vellucci JA, Castillo EM, Dirk CW, Franz AH, Michael K. Efficient Photochemical Synthesis of Peptide-α-Phenylthioesters. Chembiochem 2015; 16:1884-1889. [DOI: 10.1002/cbic.201500266] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Indexed: 01/16/2023]
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25
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Aboye TL, Strömstedt AA, Gunasekera S, Bruhn JG, El-Seedi H, Rosengren KJ, Göransson U. A Cactus-Derived Toxin-Like Cystine Knot Peptide with Selective Antimicrobial Activity. Chembiochem 2015; 16:1068-77. [DOI: 10.1002/cbic.201402704] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Indexed: 11/10/2022]
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26
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Dames SA. One short cysteine-rich sequence pattern - two different disulfide-bonded structures - a molecular dynamics simulation study. J Pept Sci 2015; 21:480-94. [PMID: 25781269 DOI: 10.1002/psc.2765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/28/2015] [Accepted: 01/28/2015] [Indexed: 11/09/2022]
Abstract
The nematocyst walls of Hydra are formed by proteins containing small cysteine-rich domains (CRDs) of ~25 amino acids. The first CRD of nematocyst outer all antigen (NW1) and the C-terminal CRD of minicollagen-1 (Mcol1C) contain six cysteines at identical sequence positions, however adopt different disulfide bonded structures. NW1 shows the disulfide connectivities C2-C14/C6-C19/C10-C18 and Mcol1C C2-C18/C6-C14/C10-C19. To analyze if both show structural preferences in the open, non-disulfide bonded form, which explain the formation of either disulfide connectivity pattern, molecular dynamics (MD) simulations at different temperatures were performed. NW1 maintained in the 100-ns MD simulations at 283 K a rather compact fold that is stabilized by specific hydrogen bonds. The Mcol1C structure fluctuated overall more, however stayed most of the time also rather compact. The analysis of the backbone Φ/ψ angles indicated different turn propensities for NW1 and Mcol1C, which mostly can be explained based on published data about the influence of different amino acid side chains on the local backbone conformation. Whereas a folded precursor mechanism may be considered for NW1, Mcol1C may fold according to the quasi-stochastic folding model involving disulfide bond reshuffling and conformational changes, locking the native disulfide conformations. The study further demonstrates the power of MD simulations to detect local structural preferences in rather dynamic systems such as the open, non-disulfide bonded forms of NW1 and Mcol1C, which complement published information from NMR backbone residual dipolar couplings. Because the backbone structural preferences encoded by the amino acid sequence embedding the cysteines influence which disulfide connectivities are formed, the data are generally interesting for a better understanding of oxidative folding and the design of disulfide stabilized therapeutics.
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Affiliation(s)
- Sonja A Dames
- Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, 85747, Garching, Germany.,Helmholtz Zentrum München, Germany and Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
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27
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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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28
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Burman R, Yeshak MY, Larsson S, Craik DJ, Rosengren KJ, Göransson U. Distribution of circular proteins in plants: large-scale mapping of cyclotides in the Violaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:855. [PMID: 26579135 PMCID: PMC4621522 DOI: 10.3389/fpls.2015.00855] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/28/2015] [Indexed: 05/02/2023]
Abstract
During the last decade there has been increasing interest in small circular proteins found in plants of the violet family (Violaceae). These so-called cyclotides consist of a circular chain of approximately 30 amino acids, including six cysteines forming three disulfide bonds, arranged in a cyclic cystine knot (CCK) motif. In this study we map the occurrence and distribution of cyclotides throughout the Violaceae. Plant material was obtained from herbarium sheets containing samples up to 200 years of age. Even the oldest specimens contained cyclotides in the preserved leaves, with no degradation products observable, confirming their place as one of the most stable proteins in nature. Over 200 samples covering 17 of the 23-31 genera in Violaceae were analyzed, and cyclotides were positively identified in 150 species. Each species contained a unique set of between one and 25 cyclotides, with many exclusive to individual plant species. We estimate the number of different cyclotides in the Violaceae to be 5000-25,000, and propose that cyclotides are ubiquitous among all Violaceae species. Twelve new cyclotides from six phylogenetically dispersed genera were sequenced. Furthermore, the first glycosylated derivatives of cyclotides were identified and characterized, further increasing the diversity and complexity of this unique protein family.
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Affiliation(s)
- Robert Burman
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
| | - Mariamawit Y. Yeshak
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
- Department of Pharmacognosy, School of Pharmacy, Addis Ababa UniversityAddis Ababa, Ethiopia
| | - Sonny Larsson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
| | - David J. Craik
- Craik Lab, Chemistry and Structural Biology Division, Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
| | - K. Johan Rosengren
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
- Laboratory for Peptide Structural Biology, School of Biomedical Sciences, The University of QueenslandBrisbane, QLD, Australia
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
- *Correspondence: Ulf Göransson
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29
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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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30
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Cheneval O, Schroeder CI, Durek T, Walsh P, Huang YH, Liras S, Price DA, Craik DJ. Fmoc-based synthesis of disulfide-rich cyclic peptides. J Org Chem 2014; 79:5538-44. [PMID: 24918986 DOI: 10.1021/jo500699m] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Disulfide-rich cyclic peptides have exciting potential as leads or frameworks in drug discovery; however, their use is faced with some synthetic challenges, mainly associated with construction of the circular backbone and formation of the correct disulfides. Here we describe a simple and efficient Fmoc solid-phase peptide synthesis (SPPS)-based method for synthesizing disulfide-rich cyclic peptides. This approach involves SPPS on 2-chlorotrityl resin, cyclization of the partially protected peptide in solution, cleavage of the side-chain protecting groups, and oxidization of cysteines to yield the desired product. We illustrate this method with the synthesis of peptides from three different classes of cyclic cystine knot motif-containing cyclotides: Möbius (M), trypsin inhibitor (T), and bracelet (B). We show that the method is broadly applicable to peptide engineering, illustrated by the synthesis of two mutants and three grafted analogues of kalata B1. The method reduces the use of highly caustic and toxic reagents and is better suited for high-throughput synthesis than previously reported methods for producing disulfide-rich cyclic peptides, thus offering great potential to facilitate pharmaceutical optimization of these scaffolds.
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Affiliation(s)
- Olivier Cheneval
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, 4072, QLD Australia
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31
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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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32
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Optimal cleavage and oxidative folding of α-conotoxin TxIB as a therapeutic candidate peptide. Mar Drugs 2013; 11:3537-53. [PMID: 24048271 PMCID: PMC3806463 DOI: 10.3390/md11093537] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/19/2022] Open
Abstract
Alpha6beta2 nicotinic acetylcholine receptors (nAChRs) are potential therapeutic targets for the treatment of several neuropsychiatric diseases, including addiction and Parkinson’s disease. Alpha-conotoxin (α-CTx) TxIB is a uniquely selective ligand, which blocks α6/α3β2β3 nAChRs only, but does not block the other subtypes. Therefore, α-CTx TxIB is a valuable therapeutic candidate peptide. Synthesizing enough α-CTx TxIB with high yield production is required for conducting wide-range testing of its potential medicinal applications. The current study optimized the cleavage of synthesized α-CTx TxIB resin-bounded peptide and folding of the cleaved linear peptide. Key parameters influencing cleavage and oxidative folding of α-CTx TxIB were examined, such as buffer, redox agents, pH, salt, co-solvent and temperature. Twelve conditions were used for cleavage optimization. Fifty-four kinds of one-step oxidative solution were used to assess their effects on each α-CTx TxIB isomers’ yield. The result indicated that co-solvent choices were particularly important. Completely oxidative folding of globular isomer was achieved when the NH4HCO3 or Tris-HCl folding buffer at 4 °C contained 40% of co-solvent DMSO, and GSH:GSSG (2:1) or GSH only with pH 8~8.7.
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33
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Chemical synthesis, backbone cyclization and oxidative folding of cystine-knot peptides: promising scaffolds for applications in drug design. Molecules 2012; 17:12533-52. [PMID: 23095896 PMCID: PMC6268209 DOI: 10.3390/molecules171112533] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/19/2012] [Accepted: 10/22/2012] [Indexed: 02/03/2023] Open
Abstract
Cystine-knot peptides display exceptional structural, thermal, and biological stability. Their eponymous motif consists of six cysteine residues that form three disulfide bonds, resulting in a notably rigid structural core. Since they highly tolerate either rational or combinatorial changes in their primary structure, cystine knots are considered to be promising frameworks for the development of peptide-based pharmaceuticals. Despite their relatively small size (two to three dozens amino acid residues), the chemical synthesis route is challenging since it involves critical steps such as head-to-tail cyclization and oxidative folding towards the respective bioactive isomer. Herein we describe the topology of cystine-knot peptides, their synthetic availability and briefly discuss potential applications of engineered variants in diagnostics and therapy.
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Making Ends Meet: Microwave-Accelerated Synthesis of Cyclic and Disulfide Rich Proteins Via In Situ Thioesterification and Native Chemical Ligation. Int J Pept Res Ther 2012; 19:43-54. [PMID: 23504256 PMCID: PMC3597280 DOI: 10.1007/s10989-012-9331-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2012] [Indexed: 12/21/2022]
Abstract
The development of synthetic methodologies for cyclic peptides is driven by the discovery of cyclic peptide drug scaffolds such as the plant-derived cyclotides, sunflower trypsin inhibitor 1 (SFTI-1) and the development of cyclized conotoxins. Currently, the native chemical ligation reaction between an N-terminal cysteine and C-terminal thioester group remains the most robust method to obtain a head-to-tail cyclized peptide. Peptidyl thioesters are effectively generated by Boc SPPS. However, their generation is challenging using Fmoc SPPS because thioester linkers are not stable to repeated piperidine exposure during deprotection. Herein we describe a Fmoc-based protocol for synthesizing cyclic peptides adapted for microwave assisted solid phase peptide synthesis. The protocol relies on the linker Di-Fmoc-3,4-diaminobenzoic acid, and we demonstrate the use of Gly, Ser, Arg and Ile as C-terminal amino acids (using HBTU and HATU as coupling reagents). Following synthesis, an N-acylurea moiety is generated at the C-terminal of the peptide; the resin bound acylurea peptide is then deprotected and cleaved from the resin. The fully deprotected peptide undergoes thiolysis in aqueous buffer, generating the thioester in situ. Ultimately, the head-to-tail cyclized peptide is obtained via native chemical ligation. Two naturally occurring cyclic peptides, the prototypical Möbius cyclotide kalata B1 and SFTI-1 were synthesized efficiently, avoiding potential branching at the diamino linker, using the optimized protocol. In addition, we demonstrate the possibility to use the approach for the synthesis of long and synthetically challenging linear sequences, by the ligation of two truncated fragments of a 50-residue long plant defensin.
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35
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Yeshak MY, Göransson U, Burman R, Hellman B. Genotoxicity and cellular uptake of cyclotides: Evidence for multiple modes of action. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2012; 747:176-81. [DOI: 10.1016/j.mrgentox.2012.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 03/20/2012] [Accepted: 05/02/2012] [Indexed: 10/28/2022]
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36
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Hashempour H, Koehbach J, Daly NL, Ghassempour A, Gruber CW. Characterizing circular peptides in mixtures: sequence fragment assembly of cyclotides from a violet plant by MALDI-TOF/TOF mass spectrometry. Amino Acids 2012; 44:581-95. [PMID: 22890611 PMCID: PMC3549257 DOI: 10.1007/s00726-012-1376-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/20/2012] [Indexed: 11/29/2022]
Abstract
Cyclotides are a very abundant class of plant peptides that display significant sequence variability around a conserved cystine-knot motif and a head-to-tail cyclized backbone conferring them with remarkable stability. Their intrinsic bioactivities combined with tools of peptide engineering make cyclotides an interesting template for the design of novel agrochemicals and pharmaceuticals. However, laborious isolation and purification prior to de novo sequencing limits their discovery and hence their use as scaffolds for peptide-based drug development. Here we extend the knowledge about their sequence diversity by analysing the cyclotide content of a violet species native to Western Asia and the Caucasus region. Using an experimental approach, which was named sequence fragment assembly by MALDI-TOF/TOF, it was possible to characterize 13 cyclotides from Viola ignobilis, whereof ten (vigno 1–10) display previously unknown sequences. Amino acid sequencing of various enzymatic digests of cyclotides allowed the accurate assembly and alignment of smaller fragments to elucidate their primary structure, even when analysing mixtures containing multiple peptides. As a model to further dissect the combinatorial nature of the cyclotide scaffold, we employed in vitro oxidative refolding of representative vigno cyclotides and confirmed the high dependency of folding yield on the inter-cysteine loop sequences. Overall this work highlights the immense structural diversity and plasticity of the unique cyclotide framework. The presented approach for the sequence analysis of peptide mixtures facilitates and accelerates the discovery of novel plant cyclotides.
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Affiliation(s)
- Hossein Hashempour
- Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
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37
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Abstract
Circular proteins, once thought to be rare, are now commonly found in plants. Their chemical synthesis, once thought to be difficult, is now readily achievable. The enabling methodology is largely due to the advances in entropic chemical ligation to overcome the entropy barrier in coupling the N- and C-terminal ends of large peptide segments for either intermolecular ligation or intramolecular ligation in end-to-end cyclization. Key elements of an entropic chemical ligation consist of a chemoselective capture step merging the N and C termini as a covalently linked O/S-ester intermediate to permit the subsequent step of an intramolecular O/S-N acyl shift to form an amide. Many ligation methods exploit the supernucleophilicity of a thiol side chain at the N terminus for the capture reaction, which makes cysteine-rich peptides ideal candidates for the entropy-driven macrocyclization. Advances in desulfurization and modification of the thiol-containing amino acids at the ligation sites to other amino acids add extra dimensions to the entropy-driven ligation methods. This minireview describes recent advances of entropy-driven ligation to prepare circular proteins with or without a cysteinyl side chain.
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Affiliation(s)
- James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551.
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38
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Gould A, Ji Y, Aboye TL, Camarero JA. Cyclotides, a novel ultrastable polypeptide scaffold for drug discovery. Curr Pharm Des 2012; 17:4294-307. [PMID: 22204428 DOI: 10.2174/138161211798999438] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 09/15/2011] [Indexed: 11/22/2022]
Abstract
Cyclotides are a unique and growing family of backbone cyclized peptides that also contain a cystine knot motif built from six conserved cysteine residues. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to thermal, chemical, and enzymatic degradation compared to other peptides of similar size. Aside from the conserved residues forming the cystine knot, cyclotides have been shown to have high variability in their sequences. Consisting of over 160 known members, cyclotides have many biological activities, ranging from anti-HIV, antimicrobial, hemolytic, and uterotonic capabilities; additionally, some cyclotides have been shown to have cell penetrating properties. Originally discovered and isolated from plants, cyclotides can also be produced synthetically and recombinantly. The high sequence variability, stability, and cell penetrating properties of cyclotides make them potential scaffolds to be used to graft known active peptides or engineer peptide-based drug design. The present review reports recent findings in the biological diversity and therapeutic potential of natural and engineered cyclotides.
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Affiliation(s)
- Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
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39
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Zheng JS, Tang S, Guo Y, Chang HN, Liu L. Synthesis of Cyclic Peptides and Cyclic Proteins via Ligation of Peptide Hydrazides. Chembiochem 2012; 13:542-6. [DOI: 10.1002/cbic.201100580] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Indexed: 02/01/2023]
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40
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Craik DJ. Host-defense activities of cyclotides. Toxins (Basel) 2012; 4:139-56. [PMID: 22474571 PMCID: PMC3317112 DOI: 10.3390/toxins4020139] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 01/25/2012] [Accepted: 01/31/2012] [Indexed: 11/27/2022] Open
Abstract
Cyclotides are plant mini-proteins whose natural function is thought to be to protect plants from pest or pathogens, particularly insect pests. They are approximately 30 amino acids in size and are characterized by a cyclic peptide backbone and a cystine knot arrangement of three conserved disulfide bonds. This article provides an overview of the reported pesticidal or toxic activities of cyclotides, discusses a possible common mechanism of action involving disruption of biological membranes in pest species, and describes methods that can be used to produce cyclotides for potential applications as novel pesticidal agents.
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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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41
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Pinto MFS, Almeida RG, Porto WF, Fensterseifer ICM, Lima LA, Dias SC, Franco OL. Cyclotides. J Evid Based Complementary Altern Med 2011. [DOI: 10.1177/2156587211428077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In recent years, a number of peptides containing a cyclic structural fold have been described. Among them, the cyclotides family was widely reported in different plant tissues, being composed of small cyclic peptides containing 6 conserved cysteine residues connected by disulfide bonds and forming a cysteine-binding cyclic structure known as a cyclic cysteine knot. This structural scaffold is responsible for an enhanced structural stability against chemical, thermal, and proteolytic degradation. Because of the observed stability and multifunctionality, including insecticidal, antimicrobial, and anti-HIV (human immunodeficiency virus) action, much effort has gone into trying to elucidate the structural-function relations of cyclotide compounds. This review focuses on the novelties involving gene structure, precursor formation and processing, and protein folding of the cyclotide family, shedding some light on molecular mechanisms of cyclotide production. Because cyclotides are clear targets for drug development and also biotechnology applications, their chemical synthesis, heterologous systems production, and protein grafting are also addressed.
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42
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Zheng JS, Chang HN, Shi J, Liu L. Chemical synthesis of a cyclotide via intramolecular cyclization of peptide O-esters. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4434-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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43
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Conibear AC, Craik DJ. Chemical Synthesis of Naturally-Occurring Cyclic Mini-Proteins from Plants and Animals. Isr J Chem 2011. [DOI: 10.1002/ijch.201100067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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44
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He W, Chan LY, Zeng G, Daly NL, Craik DJ, Tan N. Isolation and characterization of cytotoxic cyclotides from Viola philippica. Peptides 2011; 32:1719-23. [PMID: 21723349 DOI: 10.1016/j.peptides.2011.06.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 06/16/2011] [Accepted: 06/16/2011] [Indexed: 11/24/2022]
Abstract
Cyclotides are a large family of plant peptides characterized by a macrocyclic backbone and knotted arrangement of three disulfide bonds. This unique structure renders cyclotides exceptionally stable to thermal, chemical and enzymatic treatments. They exhibit a variety of bioactivities, including uterotonic, anti-HIV, cytotoxic and hemolytic activity and it is these properties that make cyclotides an interesting peptide scaffold for drug design. In this study, eight new cyclotides (Viphi A-H), along with eight known cyclotides, were isolated from Viola philippica, a plant from the Violaceae family. In addition, Viba 17 and Mram 8 were isolated for the first time as peptides. The sequences of these cyclotides were elucidated primarily by using a strategy involving reduction, enzymatic digestion and tandem mass spectroscopy sequencing. Several of the cyclotides showed cytotoxic activities against the cancer cell lines MM96L, HeLa and BGC-823. The novel cyclotides reported here: (1) enhance the known sequence variation observed for cyclotides; (2) extend the number of species known to contain cyclotides; (3) provide interesting structure-activity relationships that delineate residues important for cytotoxic activity. In addition, this study provides insights into the potential active ingredients of traditional Chinese medicines.
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Affiliation(s)
- Wenjun He
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132# Lanhei Road, Heilongtan, Kunming 650204, Yunnan, PR China
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45
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Wong CTT, Taichi M, Nishio H, Nishiuchi Y, Tam JP. Optimal Oxidative Folding of the Novel Antimicrobial Cyclotide from Hedyotis biflora Requires High Alcohol Concentrations. Biochemistry 2011; 50:7275-83. [DOI: 10.1021/bi2007004] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Clarence T. T. Wong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Misako Taichi
- SAITO
Research Center, Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki-shi,
Osaka 567-0085, Japan
| | - Hideki Nishio
- SAITO
Research Center, Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki-shi,
Osaka 567-0085, Japan
| | - Yuji Nishiuchi
- SAITO
Research Center, Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki-shi,
Osaka 567-0085, Japan
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
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46
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Abstract
Cyclotides are head-to-tail cyclic peptides that contain a cystine knot motif built from six conserved cysteine residues. They occur in plants of the Rubiaceae, Violaceae, Cucurbitaceae, and Fabaceae families and, aside from their natural role in host defense, have a range of interesting pharmaceutical activities, including anti-HIV activity. The variation seen in sequences of their six backbone loops has resulted in cyclotides being described as a natural combinatorial template. Their exceptional stability and resistance to enzymatic degradation has led to their use as scaffolds for peptide-based drug design. To underpin such applications, methods for the chemical synthesis of cyclotides have been developed and are described here. Cyclization using thioester chemistry has been instrumental in the synthesis of cyclotides for structure-activity studies. This approach involves a native chemical ligation reaction between an N-terminal Cys and a C-terminal thioester in the linear cyclotide precursor. Since cyclotides contain six Cys residues their syntheses can be designed around any of six linear precursors, thus providing flexibility in synthesis. The ease with which cyclotides fold, despite their topologically complex knot motif, as well as the ability to introduce combinatorial variation in the loops, makes cyclotides a promising drug-design scaffold.
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Affiliation(s)
- David J Craik
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia.
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47
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Yeshak MY, Burman R, Asres K, Göransson U. Cyclotides from an extreme habitat: characterization of cyclic peptides from Viola abyssinica of the Ethiopian highlands. JOURNAL OF NATURAL PRODUCTS 2011; 74:727-31. [PMID: 21434649 DOI: 10.1021/np100790f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
As part of ongoing explorations of the structural diversity of cyclotides, the cyclotide content of a native violet of the East African highlands, Viola abyssinica (which grows at altitudes up to 3400 m), was studied. Six new cyclotides, vaby A-E (1-5) and varv E (6), were isolated and characterized by employing HPLC and MS techniques and quantitative amino acid analysis. Cyclotides 1-5 were found to have new sequences, and 1-3 have a further novel feature in their sequences, an alanine moiety in loop 2. Two of the cyclotides (1 and 4) also exhibited cytotoxic properties in a flourometric microculture cytotoxicity assay. The findings corroborate the hypothesis that investigating the cyclotide contents of violets growing in diverse environments is a promising approach for extending our knowledge of both the structural and biological diversity of cyclotides.
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Affiliation(s)
- Mariamawit Y Yeshak
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Centre, Box 574, SE-751 23 Uppsala, Sweden
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48
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Daly NL, Rosengren KJ, Troeira Henriques S, Craik DJ. NMR and protein structure in drug design: application to cyclotides and conotoxins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:359-70. [DOI: 10.1007/s00249-011-0672-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 12/28/2010] [Accepted: 01/03/2011] [Indexed: 01/14/2023]
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49
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Aboye TL, Clark RJ, Burman R, Roig MB, Craik DJ, Göransson U. Interlocking disulfides in circular proteins: toward efficient oxidative folding of cyclotides. Antioxid Redox Signal 2011; 14:77-86. [PMID: 20486762 DOI: 10.1089/ars.2010.3112] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Cyclotides are ultrastable plant proteins characterized by the presence of a cyclic amide backbone and three disulfide bonds that form a cystine knot. Because of their extreme stability, there has been significant interest in developing these molecules as a drug design scaffold. For this potential to be realized, efficient methods for the synthesis and oxidative folding of cyclotides need to be developed, yet we currently have only a basic understanding of the folding mechanism and the factors influencing this process. In this study, we determine the major factors influencing oxidative folding of the different subfamilies of cyclotides. The folding of all the cyclotides examined was heavily influenced by the concentration of redox reagents, with the folding rate and final yield of the native isomer greatly enhanced by high concentrations of oxidized glutathione. Addition of hydrophobic solvents to the buffer also enhanced the folding rates and appeared to alter the folding pathway. Significant deamidation and isoaspartate formation were seen when oxidation conditions were conducive to slow folding. The identification of factors that influence the folding and degradation pathways of cyclotides will facilitate the development of folding screens and optimized conditions for producing cyclotides and grafted analogs as stable peptide-based therapeutics.
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Affiliation(s)
- Teshome Leta Aboye
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
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50
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Mende F, Seitz O. 9-Fluorenylmethyloxycarbonyl-basierte Festphasensynthese von α-Peptidthioestern. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005180] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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