1
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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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2
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Liew HT, To J, Zhang X, Hemu X, Chan NY, Serra A, Sze SK, Liu CF, Tam JP. The legumain McPAL1 from Momordica cochinchinensis is a highly stable Asx-specific splicing enzyme. J Biol Chem 2021; 297:101325. [PMID: 34710371 PMCID: PMC8600085 DOI: 10.1016/j.jbc.2021.101325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
Legumains, also known as asparaginyl endopeptidases (AEPs), cleave peptide bonds after Asn/Asp (Asx) residues. In plants, certain legumains also have ligase activity that catalyzes biosynthesis of Asx-containing cyclic peptides. An example is the biosynthesis of MCoTI-I/II, a squash family-derived cyclic trypsin inhibitor, which involves splicing to remove the N-terminal prodomain and then N-to-C-terminal cyclization of the mature domain. To identify plant legumains responsible for the maturation of these cyclic peptides, we have isolated and characterized a legumain involved in splicing, McPAL1, from Momordica cochinchinensis (Cucurbitaceae) seeds. Functional studies show that recombinantly expressed McPAL1 displays a pH-dependent, trimodal enzymatic profile. At pH 4 to 6, McPAL1 selectively catalyzed Asp-ligation and Asn-cleavage, but at pH 6.5 to 8, Asn-ligation predominated. With peptide substrates containing N-terminal Asn and C-terminal Asp, such as is found in precursors of MCoTI-I/II, McPAL1 mediates proteolysis at the Asn site and then ligation at the Asp site at pH 5 to 6. Also, McPAL1 is an unusually stable legumain that is tolerant of heat and high pH. Together, our results support that McPAL1 is a splicing legumain at acidic pH that can mediate biosynthesis of MCoTI-I/II. We purport that the high thermal and pH stability of McPAL1 could have applications for protein engineering.
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Affiliation(s)
- Heng Tai Liew
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Aida Serra
- IMDEA Food Research Institute, +Pec Proteomics, Campus of International Excellence UAM+CSIC, Old Cantoblanco Hospital, Cantoblanco, Madrid, Spain; Proteored - Instituto de Salud Carlos III (ISCIII), Campus UAM, Cantoblanco, Madrid, Spain
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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3
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Zhang J, Yuan J, Li Z, Fu C, Xu M, Yang J, Jiang X, Zhou B, Ye X, Xu C. Exploring and exploiting plant cyclic peptides for drug discovery and development. Med Res Rev 2021; 41:3096-3117. [PMID: 33599316 DOI: 10.1002/med.21792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/10/2021] [Accepted: 01/31/2021] [Indexed: 01/07/2023]
Abstract
Ever since the discovery of insulin, natural peptides have become an important resource for therapeutic development. Decades of research has led to the discovery of a long list of peptide drugs with broad applications in clinics, from antibiotics to hypertension treatment to pain management. Many of these US FDA-approved peptide drugs are derived from microorganisms and animals. By contrast, the great potential of plant cyclic peptides as therapeutics remains largely unexplored. These macrocyclic peptides typically have rigid structures, good bioavailability and membrane permeability, making them appealing candidates for drug development and engineering. In this review, we introduce the three major classes of plant cyclic peptides and summarize their potential medical applications. We discuss how we can leverage the genome information of many different plants to quickly search for new cyclic peptides and how we can take advantage of the insights gained from their biosynthetic pathways to transform the process of production and drug development. These recent developments have provided a new angle for exploring and exploiting plant cyclic peptides, and we believe that many more peptide drugs derived from plants are about to come.
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Affiliation(s)
- Jingjing Zhang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Jimin Yuan
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Zhijie Li
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chunjin Fu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Menglong Xu
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jing Yang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xin Jiang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Boping Zhou
- Department of Infectious Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xiufeng Ye
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chengchao Xu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
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4
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Hemu X, Zhang X, Nguyen GKT, To J, Serra A, Loo S, Sze SK, Liu CF, Tam JP. Characterization and application of natural and recombinant butelase-1 to improve industrial enzymes by end-to-end circularization. RSC Adv 2021; 11:23105-23112. [PMID: 35480425 PMCID: PMC9034278 DOI: 10.1039/d1ra03763c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/23/2021] [Indexed: 01/14/2023] Open
Abstract
Butelase-1, an asparaginyl endopeptidase or legumain, is the prototypical and fastest known Asn/Asp-specific peptide ligase that could be used for improving other enzymes by catalyzing simple and efficient end-to-end circularization.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Xiaohong Zhang
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Giang K. T. Nguyen
- WIL@NUS Corporate Lab
- MD6 Centre for Translational Medicine
- Wilmar International Limited
- National University of Singapore
- Singapore
| | - Janet To
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Aida Serra
- IMDEA Food Research Institute
- +Pec Proteomics
- Campus of International Excellence UAM+CSIC
- Old Cantoblanco Hospital
- Madrid 28049
| | - Shining Loo
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Siu Kwan Sze
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - James P. Tam
- School of Biological Sciences
- Nanyang Technological University
- Singapore
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5
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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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6
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Huang YH, Du Q, Craik DJ. Cyclotides: Disulfide-rich peptide toxins in plants. Toxicon 2019; 172:33-44. [DOI: 10.1016/j.toxicon.2019.10.244] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/27/2022]
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7
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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: 135] [Impact Index Per Article: 27.0] [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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8
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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9
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Accelerated microfluidic native chemical ligation at difficult amino acids toward cyclic peptides. Nat Commun 2018; 9:2847. [PMID: 30030439 PMCID: PMC6054628 DOI: 10.1038/s41467-018-05264-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/21/2018] [Indexed: 01/09/2023] Open
Abstract
Cyclic peptide-based therapeutics have a promising growth forecast that justifies the development of microfluidic systems dedicated to their production, in phase with the actual transitioning toward continuous flow and microfluidic technologies for pharmaceutical production. The application of the most popular method for peptide cyclization in water, i.e., native chemical ligation, under microfluidic conditions is still unexplored. Herein, we report a general strategy for fast and efficient peptide cyclization using native chemical ligation under homogeneous microfluidic conditions. The strategy relies on a multistep sequence that concatenates the formation of highly reactive S-(2-((2-sulfanylethyl)amino)ethyl) peptidyl thioesters from stable peptide amide precursors with an intramolecular ligation step. With very fast ligation rates (<5 min), even for the most difficult junctions (including threonine, valine, isoleucine, or proline), this technology opens the door toward the scale-independent, expedient preparation of bioactive macrocyclic peptides. Flow-based peptide synthesis is a well-established method, yet difficult to combine with native chemical ligation (NCL), the go-to method for peptide cyclization. Here, the authors developed a microfluidic procedure for peptide cyclization within minutes, using NCL and an SEA alkylthioester peptide.
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10
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Hemu X, Tam JP. Macrocyclic Antimicrobial Peptides Engineered from ω-Conotoxin. Curr Pharm Des 2018; 23:2131-2138. [PMID: 28245769 PMCID: PMC5470054 DOI: 10.2174/1381612822666161027120518] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/13/2016] [Indexed: 11/22/2022]
Abstract
The potent calcium channel blocker ω-conotoxin MVIIA is a linear cystine-knot peptide with multiple basic amino acids at both termini. This work shows that macrocyclization of MVIIA linking two positive-charge terminal clusters as a contiguous segment converts a conotoxin into an antimicrobial peptide. In addition, conversion of disulfide bonds to amino butyric acids improved the antimicrobial activity of the cyclic analogs. Ten macrocyclic analogs, with or without disulfide bonds, were prepared by both Boc and Fmoc chemistry using native chemical ligation. All cyclic analogs were active against selected Gram-positive and Gram-negative bacteria with minimal inhibitory concentrations in a low μM range. In contrast, MVIIA and its linear analog were inactive at concentrations up to 0.5 mM. The cyclic analogs also showed 2 to 3-fold improved chemotactic activity against human monocytes THP-1 compared with MVIIA. Reduction of molecular stability against thermal and acid treatment due to the reduced number of disulfide crosslinks can be partly restored by backbone cyclization. Together, these results show that macrocyclization and side chain modification of a linear conopeptide lead to a gain-of-function, which brings a new perspective in designing and engineering of peptidyl therapeutics.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 03s-71, Singapore 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 03s-71, Singapore 637551, Singapore
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11
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Hellinger R, Thell K, Vasileva M, Muhammad T, Gunasekera S, Kümmel D, Göransson U, Becker CW, Gruber CW. Chemical Proteomics for Target Discovery of Head-to-Tail Cyclized Mini-Proteins. Front Chem 2017; 5:73. [PMID: 29075625 PMCID: PMC5641551 DOI: 10.3389/fchem.2017.00073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/19/2017] [Indexed: 11/24/2022] Open
Abstract
Target deconvolution is one of the most challenging tasks in drug discovery, but a key step in drug development. In contrast to small molecules, there is a lack of validated and robust methodologies for target elucidation of peptides. In particular, it is difficult to apply these methods to cyclic and cysteine-stabilized peptides since they exhibit reduced amenability to chemical modification and affinity capture; however, such ribosomally synthesized and post-translationally modified peptide natural products are rich sources of promising drug candidates. For example, plant-derived circular peptides called cyclotides have recently attracted much attention due to their immunosuppressive effects and oral activity in the treatment of multiple sclerosis in mice, but their molecular target has hitherto not been reported. In this study, a chemical proteomics approach using photo-affinity crosslinking was developed to determine a target for the circular peptide [T20K]kalata B1. Using this prototypic nature-derived peptide enabled the identification of a possible functional modulation of 14-3-3 proteins. This biochemical interaction was validated via competition pull down assays as well as a cellular reporter assay indicating an effect on 14-3-3-dependent transcriptional activity. As proof of concept, the presented approach may be applicable for target elucidation of various cyclic peptides and mini-proteins, in particular cyclotides, which represent a promising class of molecules in drug discovery and development.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Kathrin Thell
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Mina Vasileva
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Taj Muhammad
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Sunithi Gunasekera
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Daniel Kümmel
- School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Christian W Becker
- Department of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.,School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
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12
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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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13
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Taguchi A, Kobayashi K, Kotani A, Muguruma K, Kobayashi M, Fukumoto K, Takayama K, Hakamata H, Hayashi Y. 3-Nitro-2-pyridinesulfenates as Efficient Solution- and Solid-Phase Disulfide Bond Forming Agents. Chemistry 2017; 23:8262-8267. [DOI: 10.1002/chem.201700952] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Akihiro Taguchi
- Department of Medicinal Chemistry; School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Kiyotaka Kobayashi
- Department of Medicinal Chemistry; School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Akira Kotani
- Department of Analytical Chemistry; School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; Japan
| | - Kyohei Muguruma
- Department of Medicinal Chemistry; School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Misaki Kobayashi
- Department of Medicinal Chemistry; School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Kentarou Fukumoto
- Department of Medicinal Chemistry; School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
- Kokusan Chemical Co., Ltd.; 3-1-3 Nihonbashihoncho, Chuo-ku Tokyo 103-0023 Japan
| | - Kentaro Takayama
- Department of Medicinal Chemistry; School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Hideki Hakamata
- Department of Analytical Chemistry; School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry; School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
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14
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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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15
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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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Tam JP, Wang S, Wong KH, Tan WL. Antimicrobial Peptides from Plants. Pharmaceuticals (Basel) 2015; 8:711-57. [PMID: 26580629 PMCID: PMC4695807 DOI: 10.3390/ph8040711] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 12/25/2022] Open
Abstract
Plant antimicrobial peptides (AMPs) have evolved differently from AMPs from other life forms. They are generally rich in cysteine residues which form multiple disulfides. In turn, the disulfides cross-braced plant AMPs as cystine-rich peptides to confer them with extraordinary high chemical, thermal and proteolytic stability. The cystine-rich or commonly known as cysteine-rich peptides (CRPs) of plant AMPs are classified into families based on their sequence similarity, cysteine motifs that determine their distinctive disulfide bond patterns and tertiary structure fold. Cystine-rich plant AMP families include thionins, defensins, hevein-like peptides, knottin-type peptides (linear and cyclic), lipid transfer proteins, α-hairpinin and snakins family. In addition, there are AMPs which are rich in other amino acids. The ability of plant AMPs to organize into specific families with conserved structural folds that enable sequence variation of non-Cys residues encased in the same scaffold within a particular family to play multiple functions. Furthermore, the ability of plant AMPs to tolerate hypervariable sequences using a conserved scaffold provides diversity to recognize different targets by varying the sequence of the non-cysteine residues. These properties bode well for developing plant AMPs as potential therapeutics and for protection of crops through transgenic methods. This review provides an overview of the major families of plant AMPs, including their structures, functions, and putative mechanisms.
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Affiliation(s)
- James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Shujing Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Ka H Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Wei Liang Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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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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Design of substrate-based BCR-ABL kinase inhibitors using the cyclotide scaffold. Sci Rep 2015; 5:12974. [PMID: 26264857 PMCID: PMC4532999 DOI: 10.1038/srep12974] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/15/2015] [Indexed: 12/20/2022] Open
Abstract
The constitutively active tyrosine kinase BCR-ABL is the underlying cause of chronic myeloid leukemia (CML). Current CML treatments rely on the long-term use of tyrosine kinase inhibitors (TKIs), which target the ATP binding site of BCR-ABL. Over the course of treatment, 20–30% of CML patients develop TKI resistance, which is commonly attributed to point mutations in the drug-binding region. We design a new class of peptide inhibitors that target the substrate-binding site of BCR-ABL by grafting sequences derived from abltide, the optimal substrate of Abl kinase, onto a cell-penetrating cyclotide MCoTI-II. Three grafted cyclotides show significant Abl kinase inhibition in vitro in the low micromolar range using a novel kinase inhibition assay. Our work also demonstrates that a reengineered MCoTI-II with abltide sequences grafted in both loop 1 and 6 inhibits the activity of [T315I]Abl in vitro, a mutant Abl kinase harboring the “gatekeeper” mutation which is notorious for being multidrug resistant. Results from serum stability and cell internalization studies confirm that the MCoTI-II scaffold provides enzymatic stability and cell-penetrating properties to the lead molecules. Taken together, our study highlights that reengineered cyclotides incorporating abltide-derived sequences are promising substrate-competitive inhibitors for Abl kinase and the T315I mutant.
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Henriques S, Huang YH, Chaousis S, Sani MA, Poth A, Separovic F, Craik D. The Prototypic Cyclotide Kalata B1 Has a Unique Mechanism of Entering Cells. ACTA ACUST UNITED AC 2015; 22:1087-97. [DOI: 10.1016/j.chembiol.2015.07.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/20/2015] [Accepted: 07/08/2015] [Indexed: 12/29/2022]
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Schumann FH, Varadan R, Tayakuniyil PP, Grossman JH, Camarero JA, Fushman D. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain. Front Chem 2015; 3:26. [PMID: 25905098 PMCID: PMC4389572 DOI: 10.3389/fchem.2015.00026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/23/2015] [Indexed: 12/02/2022] Open
Abstract
Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale) were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding.
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Affiliation(s)
- Frank H Schumann
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Ranjani Varadan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Praveen P Tayakuniyil
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Jennifer H Grossman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles, CA, USA ; Department of Chemistry, University of Southern California Los Angeles, CA, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
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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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23
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Qiu Y, Hemu X, Liu DX, Tam JP. Selective Bi-directional Amide Bond Cleavage ofN-Methylcysteinyl Peptide. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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24
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Burman R, Gunasekera S, Strömstedt AA, Göransson U. Chemistry and biology of cyclotides: circular plant peptides outside the box. JOURNAL OF NATURAL PRODUCTS 2014; 77:724-36. [PMID: 24527877 DOI: 10.1021/np401055j] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cyclotides stand out as the largest family of circular proteins of plant origin hitherto known, with more than 280 sequences isolated at peptide level and many more predicted from gene sequences. Their unusual stability resulting from the signature cyclic cystine knot (CCK) motif has triggered a broad interest in these molecules for potential therapeutic and agricultural applications. Since the time of the first cyclotide discovery, our laboratory in Uppsala has been engaged in cyclotide discovery as well as the development of protocols to isolate and characterize these seamless peptides. We have also developed methods to chemically synthesize cyclotides by Fmoc-SPPS, which are useful in protein grafting applications. In this review, experience in cyclotide research over two decades and the recent literature related to their structures, synthesis, and folding as well the recent proof-of-concept findings on their use as "epitope" stabilizing scaffolds are summarized.
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Affiliation(s)
- Robert Burman
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University , Biomedical Centre, Box 574, SE-751 23 Uppsala, Sweden
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25
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Biomimetic synthesis of cyclic peptides using novel thioester surrogates. Biopolymers 2013; 100:492-501. [DOI: 10.1002/bip.22308] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/13/2013] [Accepted: 05/28/2013] [Indexed: 11/07/2022]
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26
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Craik DJ. Joseph Rudinger memorial lecture: discovery and applications of cyclotides. J Pept Sci 2013; 19:393-407. [PMID: 23737440 DOI: 10.1002/psc.2523] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 12/31/2022]
Abstract
Cyclotides are plant-derived peptides of approximately 30 amino acids that have the characteristic structural features of a head-to-tail cyclized backbone and a cystine knot arrangement of their three conserved disulfide bonds. This article gives a personal account of the discovery of cyclotides, their characterization and their applications, based on work carried out in my laboratory over the last 20 years. It describes some of the background to their discovery and focuses on how their unique structural features lead to exceptional stability. This stability and their amenability to chemical synthesis have made it possible to use cyclotides as templates in protein engineering and drug design applications. These applications complement the interest in cyclotides deriving from their unique structures and natural function as host defense molecules.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, 4072, Australia.
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Quimbar P, Malik U, Sommerhoff CP, Kaas Q, Chan LY, Huang YH, Grundhuber M, Dunse K, Craik DJ, Anderson MA, Daly NL. High-affinity cyclic peptide matriptase inhibitors. J Biol Chem 2013; 288:13885-96. [PMID: 23548907 DOI: 10.1074/jbc.m113.460030] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sunflower trypsin inhibitor-1 (SFTI-1) and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II) are potent protease inhibitors comprising a cyclic backbone. RESULTS Elucidation of structure-activity relationships for SFTI-1 and MCoTI-II was used to design inhibitors with enhanced inhibitory activity. CONCLUSION An analog of MCoTI-II is one of the most potent inhibitors of matriptase. SIGNIFICANCE These results provide a solid basis for the design of selective peptide inhibitors of matriptase with therapeutic potential. The type II transmembrane serine protease matriptase is a key activator of multiple signaling pathways associated with cell proliferation and modification of the extracellular matrix. Deregulated matriptase activity correlates with a number of diseases, including cancer and hence highly selective matriptase inhibitors may have therapeutic potential. The plant-derived cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), is a promising drug scaffold with potent matriptase inhibitory activity. In the current study we have analyzed the structure-activity relationships of SFTI-1 and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a structurally divergent trypsin inhibitor from Momordica cochinchinensis that also contains a cyclic backbone. We show that MCoTI-II is a significantly more potent matriptase inhibitor than SFTI-1 and that all alanine mutants of both peptides, generated using positional scanning mutagenesis, have decreased trypsin affinity, whereas several mutations either maintain or result in enhanced matriptase inhibitory activity. These intriguing results were used to design one of the most potent matriptase inhibitors known to date with a 290 pm equilibrium dissociation constant, and provide the first indication on how to modulate affinity for matriptase over trypsin in cyclic peptides. This information might be useful for the design of more selective and therapeutically relevant inhibitors of matriptase.
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Affiliation(s)
- Pedro Quimbar
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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Sudheer PDVN, Pack SP, Kang TJ. Cyclization tag for the detection and facile purification of backbone-cyclized proteins. Anal Biochem 2013; 436:137-41. [PMID: 23439382 DOI: 10.1016/j.ab.2013.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/08/2013] [Accepted: 02/11/2013] [Indexed: 11/27/2022]
Abstract
Backbone-cyclized proteins, with their characteristic stability toward denaturants such as heat and chemicals, are becoming increasingly significant in many applications. Intein-mediated protein cyclization is the most efficient and frequently used method of choice and has been successfully applied to various targets, achieving stable proteins. However, the detection and isolation of the cyclic protein from the linear one after cyclization is very difficult because the backbone-cyclized protein and the linear one (a by-product formed during the cyclization reaction), which originated from the same molecule, are almost identical in terms of their size. Thus, we first developed a split c-myc tag system; the active c-myc tag was formed only in the backbone-cyclized protein and not in the linear by-product from the inactive precursor, and this helps both the detection and purification of the backbone-cyclized proteins. This tag system, which we called a cyclization tag, was further engineered in its sequence to develop an engineered c-myc (e-myc) tag with enhanced efficiency in the backbone cyclization reaction while keeping its specificity toward the commercial antibody intact. Using two different proteins as models, we show that the cyclization tag developed here can be used as a specific tag for the backbone-cyclized protein, thereby facilitating detection and purification.
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Affiliation(s)
- Pamidimarri D V N Sudheer
- Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, Seoul 100-715, Republic of Korea
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Chan LY, Zhang VM, Huang YH, Waters NC, Bansal PS, Craik DJ, Daly NL. Cyclization of the Antimicrobial Peptide Gomesin with Native Chemical Ligation: Influences on Stability and Bioactivity. Chembiochem 2013; 14:617-24. [DOI: 10.1002/cbic.201300034] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Indexed: 11/06/2022]
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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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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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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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33
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Eade CR, Wood MP, Cole AM. Mechanisms and modifications of naturally occurring host defense peptides for anti-HIV microbicide development. Curr HIV Res 2012; 10:61-72. [PMID: 22264047 DOI: 10.2174/157016212799304580] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 09/30/2011] [Accepted: 10/27/2011] [Indexed: 11/22/2022]
Abstract
Despite advances in the treatment of HIV infection, heterosexual transmission of HIV remains high, and vaccines to prevent HIV acquisition have been unfruitful. Vaginal microbicides, on the other hand, have demonstrated considerable potential for HIV prevention, and a variety of compounds have been screened for their activity and safety as anti-HIV microbicides. Among these are the naturally occurring host defense peptides, small peptides from diverse lineages with intrinsic antiviral activity. Naturally occurring host defense peptides with anti-HIV activity are promising candidates for vaginal microbicide development. Their structural variance and accompanying mechanistic diversity provide a wide range of inhibitors whose antiviral activity can be exerted at nearly every stage of the HIV lifecycle. Additionally, peptide modification has been explored as a method for improving the anti-HIV activity of host defense peptides. Structure- and sequence-based alterations have achieved varying success in improving the potency and specificity of anti-HIV peptides. Overall, peptides have been discovered or engineered to inhibit HIV with therapeutic indices of > 1000, encouraging their advancement toward clinical trials. Here we review the naturally occurring anti-HIV host defense peptides, demonstrating their breadth of mechanistic diversity, and exploring approaches to enhance and optimize their activity in order to expedite their development as safe and effective anti-HIV vaginal microbicides.
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Affiliation(s)
- Colleen R Eade
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL 32816, USA.
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34
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Clark RJ, Akcan M, Kaas Q, Daly NL, Craik DJ. Cyclization of conotoxins to improve their biopharmaceutical properties. Toxicon 2012; 59:446-55. [DOI: 10.1016/j.toxicon.2010.12.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
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35
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Craik DJ, Swedberg JE, Mylne JS, Cemazar M. Cyclotides as a basis for drug design. Expert Opin Drug Discov 2012; 7:179-94. [PMID: 22468950 DOI: 10.1517/17460441.2012.661554] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Cyclotides are plant-made defence proteins with a head-to-tail cyclic backbone combined with a conserved, six cystine knot. They have a range of biological activities, including uterotonic and anti-HIV activity, which have attracted attention to their potential pharmaceutical applications. Furthermore, their unique structures and high stability make them appealing as peptide-based templates for drug design applications. Methods have been developed for their production, including solid phase peptide synthesis as well as recombinant methods. AREAS COVERED This article reviews the recent literature associated with therapeutic applications of naturally occurring and synthetically modified cyclotides. It includes applications of cyclotides and cyclotide-like molecules as peptide-based drug leads and diagnostic agents. EXPERT OPINION The ultra-stable cyclotides are promising templates for drug development applications and are currently being assessed for the potential breadth of their applications. For synthetic versions of cyclotides to enter human clinical trials further studies to examine their biopharmaceutical properties and toxicities are required. However, several promising proof-of-concept studies have established that pharmaceutically relevant bioactive peptide sequences can be grafted into cyclotide frameworks and thereby stabilised, while maintaining biological activity. These studies include examples directed at cancer, cardiovascular disease and infectious diseases. Solid phase peptide synthesis has been the preferred approach for making pharmaceutically modified cyclotides so far, but promising progress is being made in biological approaches to cyclotide production.
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Affiliation(s)
- David J Craik
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Australia.
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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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37
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Garcia AE, Tai KP, Puttamadappa SS, Shekhtman A, Ouellette AJ, Camarero JA. Biosynthesis and antimicrobial evaluation of backbone-cyclized α-defensins. Biochemistry 2011; 50:10508-19. [PMID: 22040603 DOI: 10.1021/bi201430f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Defensins are antimicrobial peptides that are important in the innate immune defense of mammals. Upon stimulation by bacterial antigens, enteric α-defensins are secreted into the intestinal lumen where they have potent microbicidal activities. Cryptdin-4 (Crp4) is an α-defensin expressed in Paneth cells of the mouse small intestine and the most bactericidal of the known cryptdin isoforms. The structure of Crp4 consists of a triple-stranded antiparallel β-sheet but lacks three amino acids between the fourth and fifth cysteine residues, making them distinct from other α-defensins. The structure also reveals that the α-amino and C-terminal carboxylic groups are in the proximity of each other (d ≈ 3 Å) in the folded structure. We present here the biosynthesis of backbone-cyclized Crp4 using a modified protein splicing unit or intein. Our data show that cyclized Crp4 can be biosynthesized by using this approach both in vitro and in vivo, although the expression yield was significantly lower when the protein was produced inside the cell. The resulting cyclic defensins retained the native α-defensin fold and showed equivalent or better microbicidal activities against several Gram-positive and Gram-negative bacteria when compared to native Crp4. No detectable hemolytic activity against human red blood cells was observed for either native Crp4 or its cyclized variants. Moreover, both forms of Crp4 also showed high stability to degradation when incubated with human serum. Altogether, these results indicate the potential for backbone-cyclized defensins in the development of novel peptide-based antimicrobial compounds.
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Affiliation(s)
- Angie E Garcia
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, Calofornia 90033, USA
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38
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Sando L, Henriques ST, Foley F, Simonsen SM, Daly NL, Hall KN, Gustafson KR, Aguilar MI, Craik DJ. A Synthetic mirror image of kalata B1 reveals that cyclotide activity is independent of a protein receptor. Chembiochem 2011; 12:2456-62. [PMID: 21928440 PMCID: PMC6364095 DOI: 10.1002/cbic.201100450] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Indexed: 11/08/2022]
Abstract
Featuring a circular, knotted structure and diverse bioactivities, cyclotides are a fascinating family of peptides that have inspired applications in drug design. Most likely evolved to protect plants against pests and herbivores, cyclotides also exhibit anti-cancer, anti-HIV, and hemolytic activities. In all of these activities, cell membranes appear to play an important role. However, the question of whether the activity of cyclotides depends on the recognition of chiral receptors or is primarily modulated by the lipid-bilayer environment has remained unknown. To determine the importance of lipid membranes on the activity of the prototypic cyclotide, kalata B1, we synthesized its all-D enantiomer and assessed its bioactivities. After the all-D enantiomer had been confirmed by (1)H NMR to be the structural mirror image of the native kalata B1, it was tested for anti-HIV activity, cytotoxicity, and hemolytic properties. The all-D peptide is active in these assays, albeit with less efficiency; this reveals that kalata B1 does not require chiral recognition to be active. The lower activity than the native peptide correlates with a lower affinity for phospholipid bilayers in model membranes. These results exclude a chiral receptor mechanism and support the idea that interaction with phospholipid membranes plays a role in the activity of kalata B1. In addition, studies with mixtures of L and D enantiomers of kalata B1 suggested that biological activity depends on peptide oligomerization at the membrane surface, which determines affinity for membranes by modulating the association-dissociation equilibrium.
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Affiliation(s)
- Lillian Sando
- Institute for Molecular Bioscience, The University of Queensland Brisbane, QLD, 4072 (Australia),
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland Brisbane, QLD, 4072 (Australia),
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa Av. Egas Moniz, 1649-028 Lisbon (Portugal)
| | - Fiona Foley
- Institute for Molecular Bioscience, The University of Queensland Brisbane, QLD, 4072 (Australia),
| | - Shane M. Simonsen
- Institute for Molecular Bioscience, The University of Queensland Brisbane, QLD, 4072 (Australia),
| | - Norelle L. Daly
- Institute for Molecular Bioscience, The University of Queensland Brisbane, QLD, 4072 (Australia),
| | - Kristopher N. Hall
- Department of Biochemistry and Molecular Biology, Monash University Victoria, 3800 Clayton (Australia)
| | - Kirk R. Gustafson
- Molecular Targets Laboratory, Center for Cancer Research National Cancer Institute at Frederick, Frederick, MD 21702 (USA)
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University Victoria, 3800 Clayton (Australia)
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland Brisbane, QLD, 4072 (Australia),
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39
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Abstract
Fragments from the extracellular matrix proteins laminin and osteopontin and a sequence from VEGF have potent proangiogenic activity despite their small size (< 10 residues). However, these linear peptides have limited potential as drug candidates for therapeutic angiogenesis because of their poor stability. In the present study, we show that the therapeutic potential of these peptides can be significantly improved by "grafting" them into cyclic peptide scaffolds. Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II) and sunflower trypsin inhibitor-1 (SFTI-1), naturally occurring, plant-derived cyclic peptides of 34 and 14 residues, respectively, were used as scaffolds in this study. Using this approach, we have designed a peptide that, in contrast to the small peptide fragments, is stable in human serum and at nanomolar concentration induces angiogenesis in vivo. This is the first report of using these scaffolds to improve the activity and stability of angiogenic peptide sequences and is a promising approach for promoting angiogenesis for therapeutic uses.
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40
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41
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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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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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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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44
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Discovery of an unusual biosynthetic origin for circular proteins in legumes. Proc Natl Acad Sci U S A 2011; 108:10127-32. [PMID: 21593408 DOI: 10.1073/pnas.1103660108] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyclotides are plant-derived proteins that have a unique cyclic cystine knot topology and are remarkably stable. Their natural function is host defense, but they have a diverse range of pharmaceutically important activities, including uterotonic activity and anti-HIV activity, and have also attracted recent interest as templates in drug design. Here we report an unusual biosynthetic origin of a precursor protein of a cyclotide from the butterfly pea, Clitoria ternatea, a representative member of the Fabaceae plant family. Unlike all previously reported cyclotides, the domain corresponding to the mature cyclotide from this Fabaceae plant is embedded within an albumin precursor protein. We confirmed the expression and correct processing of the cyclotide encoded by the Cter M precursor gene transcript following extraction from C. ternatea leaf and sequencing by tandem mass spectrometry. The sequence was verified by direct chemical synthesis and the peptide was found to adopt a classic knotted cyclotide fold as determined by NMR spectroscopy. Seven additional cyclotide sequences were also identified from C. ternatea leaf and flower, five of which were unique. Cter M displayed insecticidal activity against the cotton budworm Helicoverpa armigera and bound to phospholipid membranes, suggesting its activity is modulated by membrane disruption. The Fabaceae is the third largest family of flowering plants and many Fabaceous plants are of huge significance for human nutrition. Knowledge of Fabaceae cyclotide gene transcripts should enable the production of modified cyclotides in crop plants for a variety of agricultural or pharmaceutical applications, including plant-produced designer peptide drugs.
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45
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Ireland DC, Clark RJ, Daly NL, Craik DJ. Isolation, sequencing, and structure-activity relationships of cyclotides. JOURNAL OF NATURAL PRODUCTS 2010; 73:1610-1622. [PMID: 20718473 DOI: 10.1021/np1000413] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Cyclotides are a topologically fascinating family of miniproteins discovered over the past decade that have expanded the diversity of plant-derived natural products. They are approximately 30 amino acids in size and occur in plants of the Violaceae, Rubiaceae, and Cucurbitaceae families. Despite their proteinaceous composition, cyclotides behave in much the same way as many nonpeptidic natural products in that they are resistant to degradation by enzymes or heat and can be extracted from plants using methanol. Their stability arises, in large part, due to their characteristic cyclic cystine knot (CCK) structural motif. Cystine knots are present in a variety of proteins of insect, plant, and animal origin, comprising a ring formed by two disulfide bonds and their connecting backbone segments that is threaded by a third disulfide bond. In cyclotides, the cystine knot is uniquely embedded within a head-to-tail cyclized peptide backbone, leading to the ultrastable CCK structural motif. Apart from the six absolutely conserved cysteine residues, the majority of amino acids in the six backbone loops of cyclotides are tolerant to variation. It has been predicted that the family might include up to 50,000 members; although, so far, sequences for only 140 have been reported. Cyclotides exhibit a variety of biological activities, including insecticidal, nematocidal, molluscicidal, antimicrobial, antibarnacle, anti-HIV, and antitumor activities. Due to their diverse activities and common structural core from which variable loops protrude, cyclotides can be thought of as combinatorial peptide templates capable of displaying a variety of amino acid sequences. They have thus attracted interest in drug design as well as in crop protection applications.
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Affiliation(s)
- David C Ireland
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Clark RJ, Craik DJ. Native chemical ligation applied to the synthesis and bioengineering of circular peptides and proteins. Biopolymers 2010; 94:414-22. [PMID: 20593458 DOI: 10.1002/bip.21372] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native chemical ligation methodology developed in the laboratory of Stephen Kent is a versatile approach to the linkage of peptide fragments using a native peptide bond. It is readily adaptable to the task of joining the N- and C-termini of peptides to produce cyclic molecules and we have used it for the cyclization of a range of disulfide-rich peptides. Specifically, it has been valuable for the synthesis of cyclotides, naturally occurring peptides characterized by a head-to-tail cyclized backbone and a knotted arrangement of three conserved disulfide bonds. Cyclotides have a diverse range of biological activities, including anti-HIV, antimicrobial, and insecticidal activities. They are ultrastable owing to their cyclic cystine knot motif, and native chemical ligation methodology has been invaluable in the synthesis of a range of native and modified cyclotides to explore their structure-activity relationships and applications in drug design. Similar studies have also been applied to a smaller cyclic peptide produced in sunflower seeds, sunflower trypsin inhibitor-1, which also shows promise as a template in drug design applications. We have also found native chemical ligation to be a valuable methodology for the cyclization of conotoxins, small disulfide-rich peptides from the venoms of marine cone snails. Conotoxins target a range of ions channels and receptors and are exciting leads in drug design applications. The synthetic cyclization of conotoxins with peptide linkers stabilizes them and improves their biopharmaceutical properties. In summary, this article illustrates the use of native chemical ligation technology in the cyclization of cyclotides, sunflower trypsin inhibitor-1, and conotoxins in our laboratory.
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Affiliation(s)
- Richard J Clark
- 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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Huang YH, Colgrave ML, Clark RJ, Kotze AC, Craik DJ. Lysine-scanning mutagenesis reveals an amendable face of the cyclotide kalata B1 for the optimization of nematocidal activity. J Biol Chem 2010; 285:10797-805. [PMID: 20103593 DOI: 10.1074/jbc.m109.089854] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclotides are a family of macrocyclic peptides that combine the unique features of a head-to-tail cyclic backbone and a cystine knot motif, the combination of which imparts them with extraordinary stability. The prototypic cyclotide kalata B1 is toxic against two economically important gastrointestinal nematode parasites of sheep, Haemonchus contortus and Trichostrongylus colubriformis. A lysine scan was conducted to examine the effect of the incorporation of positive charges into the kalata B1 cyclotide framework. Each of the non-cysteine residues in this 29-amino acid peptide was successively substituted with lysine, and the nematocidal and hemolytic activities of the suite of mutants were determined. Substitution of 11 residues within kalata B1 decreased the nematocidal activity dramatically. On the other hand, six other residues that are clustered on the surface of kalata B1 were tolerant to Lys substitution, and indeed the introduction of positively charged residues into this region increased nematocidal activity. This activity was increased further in double and triple lysine mutants, with a maximal increase (relative to the native kalata B1) of 13-fold obtained with a triple lysine mutant (mutated at positions Thr-20, Asn-29, and Gly-1). Hemolytic activity correlated with the nematocidal activity of all lysine mutants. Our data clearly highlight the residues crucial for nematocidal and hemolytic activity in cyclotides, and demonstrate that the nematocidal activity of cyclotides can be increased by incorporation of basic amino acids.
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Affiliation(s)
- Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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48
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Gunasekera S, Daly NL, Clark RJ, Craik DJ. Dissecting the oxidative folding of circular cystine knot miniproteins. Antioxid Redox Signal 2009; 11:971-80. [PMID: 19025420 DOI: 10.1089/ars.2008.2295] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Cyclotides are plant proteins with exceptional stability owing to the presence of a cyclic backbone and three disulfide bonds arranged in a cystine knot motif. Accordingly, they have been proposed as templates to stabilize bioactive epitopes in drug-design applications. The two main subfamilies, referred to as the Möbius and bracelet cyclotides, require dramatically different in vitro folding conditions to achieve the native fold. To determine the underlying elements that influence cyclotide folding, we examined the in vitro folding of a suite of hybrid cyclotides based on combination of the Möbius cyclotide kalata B1 and the bracelet cyclotide cycloviolacin O1. The folding pathways of the two cyclotide subfamilies were found to be different and influenced by specific residues within intercysteine loops 2 and 6. Two changes in these loops, a substitution in loop 2 and an addition in loop 6, enabled the folding of a cycloviolacin O1 analogue under conditions in which folding does not occur in vitro for the native peptide. A key intermediate contains a native-like hairpin structure that appears to be a nucleation locus early in the folding process. Overall, these mechanistic findings on the folding of cyclotides are potentially valuable for the design of new drug leads.
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Affiliation(s)
- Sunithi Gunasekera
- The University of Queensland, Institute for Molecular Bioscience and Australian Research Council Special Research Centre for Functional and Applied Genomics, Brisbane, Australia
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49
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Sze SK, Wang W, Meng W, Yuan R, Guo T, Zhu Y, Tam JP. Elucidating the structure of cyclotides by partial acid hydrolysis and LC-MS/MS analysis. Anal Chem 2009; 81:1079-88. [PMID: 19178340 DOI: 10.1021/ac802175r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe here a rapid method to determine the cyclic structure and disulfide linkages of highly stable cyclotides via a combination of flash partial acid hydrolysis, LC-MS/MS, and computational tools. Briefly, a mixture of closely related cyclotides, kalata B1 and varv A purified from Viola yedoensis was partially hydrolyzed in 2 M HCl for 5 min by microwave-assisted hydrolysis or for 30 min in an autoclave oven (121 degrees C and 15 psi). The partially hydrolyzed peptide mixture was then subjected to LC-MS/MS analysis, with the disulfide linked-peptides fragmented by collision activated dissociation (CAD). A computer program written in-house (available for download at http://proteomics.sbs.ntu.edu.sg/cyclotide_SS ) was used for interpreting LC-MS/MS spectra and assigning the disulfide bonds. Time-point analysis of single-disulfide fragments revealed that nonrandom acid catalyzed fragmentation mostly occurred at the turns which are solvent-exposed and often contain side chain functionalized amino acids such as Asx/Glx and Ser/Thr. In particular, the most susceptible bond for acid hydrolysis in kalata B1 and varv A was found to be the highly conserved N25-G26 which is also the head-to-tail ligation site of the linear precursor proteins, indicating that formation of the three disulfide bonds might precede cyclic structure closure by N25-G26 ligation. This observation is consistent with the recent report that the N25-G26 bond formation is the last step in the cyclotide biosynthetic pathway. The process demonstrated here can potentially be a high throughput method that is generally applicable to determine disulfide bonds of other relatively low-abundance cyclotides.
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Affiliation(s)
- Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore.
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50
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Jacob MK, Leena S, Kumar KS. Peptide-polymer biotherapeutic synthesis on novel cross-linked beads with “spatially tunable” and “isolated” functional sites. Biopolymers 2008; 90:512-25. [DOI: 10.1002/bip.20969] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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