1
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Tran GH, Tran TH, Pham SH, Xuan HL, Dang TT. Cyclotides: The next generation in biopesticide development for eco-friendly agriculture. J Pept Sci 2024; 30:e3570. [PMID: 38317283 DOI: 10.1002/psc.3570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 02/07/2024]
Abstract
Chemical pesticides remain the predominant method for pest management in numerous countries. Given the current landscape of agriculture, the development of biopesticides has become increasingly crucial. The strategy empowers farmers to efficiently manage pests and diseases, while prioritizing minimal adverse effects on the environment and human health, hence fostering sustainable management. In recent years, there has been a growing interest and optimism surrounding the utilization of peptide biopesticides for crop protection. These sustainable and environmentally friendly substances have been recognized as viable alternatives to synthetic pesticides due to their outstanding environmental compatibility and efficacy. Numerous studies have been conducted to synthesize and identify peptides that exhibit activity against significant plant pathogens. One of the peptide classes is cyclotides, which are cyclic cysteine-rich peptides renowned for their wide range of sequences and functions. In this review, we conducted a comprehensive analysis of cyclotides, focusing on their structural attributes, developmental history, significant biological functions in crop protection, techniques for identification and investigation, and the application of biotechnology to enhance cyclotide synthesis. The objective is to emphasize the considerable potential of cyclotides as the next generation of plant protection agents on the global scale.
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Affiliation(s)
- Gia-Hoa Tran
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City, Viet Nam
- Institute of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thi-Huyen Tran
- Institute of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Son H Pham
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City, Viet Nam
| | - Huy Luong Xuan
- Faculty of Pharmacy, PHENIKAA University, Hanoi, Vietnam
| | - Tien T Dang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City, Viet Nam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
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2
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Tian S, de Veer SJ, Durek T, Wang CK, Craik DJ. Nucleation of a key beta-turn promotes cyclotide oxidative folding. J Biol Chem 2024; 300:107125. [PMID: 38432638 PMCID: PMC10999817 DOI: 10.1016/j.jbc.2024.107125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Cyclotides are plant-derived peptides characterized by a head-to-tail cyclic backbone and a cystine knot motif comprised of three disulfide bonds. Formation of this motif via in vitro oxidative folding can be challenging and can result in misfolded isomers with nonnative disulfide connectivities. Here, we investigated the effect of β-turn nucleation on cyclotide oxidative folding. Two types of β-turn mimics were grafted into kalata B1, individually replacing each of the four β-turns in the folded cyclotide. Insertion of d-Pro-Gly into loop 5 was beneficial to the folding of both cyclic kB1 and a linear form of the peptide. The linear grafted analog folded four-times faster in aqueous conditions than cyclic kB1 in optimized conditions. Additionally, the cyclic analogue folded without the need for redox agents by transitioning through a native-like intermediate that was on-pathway to product formation. Kalata B1 is from the Möbius subfamily of cyclotides. Grafting d-Pro-Gly into loop 5 of cyclotides from two other subfamilies also had a beneficial effect on folding. Our findings demonstrate the importance of a β-turn nucleation site for cyclotide oxidative folding, which could be adopted as a chemical strategy to improve the in vitro folding of diverse cystine-rich peptides.
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Affiliation(s)
- Sixin Tian
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
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3
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Tian S, Durek T, Wang CK, Zdenek CN, Fry BG, Craik DJ, de Veer SJ. Engineering the Cyclization Loop of MCoTI-II Generates Targeted Cyclotides that Potently Inhibit Factor XIIa. J Med Chem 2022; 65:15698-15709. [PMID: 36383928 DOI: 10.1021/acs.jmedchem.2c01080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Factor XIIa (FXIIa) is a promising target for developing new drugs that prevent thrombosis without causing bleeding complications. A native cyclotide (MCoTI-II) is gaining interest for engineering FXIIa-targeted anticoagulants as this peptide inhibits FXIIa but not other coagulation proteases. Here, we engineered the native biosynthetic cyclization loop of MCoTI-II (loop 6) to generate improved FXIIa inhibitors. Decreasing the loop length led to gains in potency up to 7.7-fold, with the most potent variant having five residues in loop 6 (Ki = 25 nM). We subsequently examined sequence changes within loop 6 and an adjacent loop, with substitutions at P4 and P2' producing a potent FXIIa inhibitor (Ki = 2 nM) that displayed more than 700-fold selectivity, was stable in human serum, and blocked the intrinsic coagulation pathway in human plasma. These findings demonstrate that engineering the biosynthetic cyclization loop can generate improved cyclotide variants, expanding their potential for drug discovery.
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Affiliation(s)
- Sixin Tian
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Christina N Zdenek
- Venom Evolution Lab, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bryan G Fry
- Venom Evolution Lab, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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4
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Liu W, de Veer SJ, Huang YH, Sengoku T, Okada C, Ogata K, Zdenek CN, Fry BG, Swedberg JE, Passioura T, Craik DJ, Suga H. An Ultrapotent and Selective Cyclic Peptide Inhibitor of Human β-Factor XIIa in a Cyclotide Scaffold. J Am Chem Soc 2021; 143:18481-18489. [PMID: 34723512 DOI: 10.1021/jacs.1c07574] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclotides are plant-derived peptides with complex structures shaped by their head-to-tail cyclic backbone and cystine knot core. These structural features underpin the native bioactivities of cyclotides, as well as their beneficial properties as pharmaceutical leads, including high proteolytic stability and cell permeability. However, their inherent structural complexity presents a challenge for cyclotide engineering, particularly for accessing libraries of sufficient chemical diversity to design potent and selective cyclotide variants. Here, we report a strategy using mRNA display enabling us to select potent cyclotide-based FXIIa inhibitors from a library comprising more than 1012 members based on the cyclotide scaffold of Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II). The most potent and selective inhibitor, cMCoFx1, has a pM inhibitory constant toward FXIIa with greater than three orders of magnitude selectivity over related serine proteases, realizing specific inhibition of the intrinsic coagulation pathway. The cocrystal structure of cMCoFx1 and FXIIa revealed interactions at several positions across the contact interface that conveyed high affinity binding, highlighting that such cyclotides are attractive cystine knot scaffolds for therapeutic development.
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Affiliation(s)
- Wenyu Liu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Simon J de Veer
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yen-Hua Huang
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Toru Sengoku
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Chikako Okada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Christina N Zdenek
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,School of Life and Environmental Sciences, School of Chemistry and Sydney Analytical, The University of Sydney, Sydney, NSW 2006, Australia
| | - David J Craik
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Brisbane, QLD 4072, Australia
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5
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Xia Y, To J, Chan N, Hu S, Liew HT, Balamkundu S, Zhang X, Lescar J, Bhattacharjya S, Tam JP, Liu C. N
γ
‐Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yiyin Xia
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Janet To
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Ning‐Yu Chan
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Side Hu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Heng Tai Liew
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Seetharamsing Balamkundu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
- Singapore-MIT Alliance for Research and Technology Singapore 138602 Singapore
| | - Xiaohong Zhang
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Julien Lescar
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - James P. Tam
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Chuan‐Fa Liu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
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6
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Xia Y, To J, Chan NY, Hu S, Liew HT, Balamkundu S, Zhang X, Lescar J, Bhattacharjya S, Tam JP, Liu CF. N γ -Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases. Angew Chem Int Ed Engl 2021; 60:22207-22211. [PMID: 34396662 DOI: 10.1002/anie.202108125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 11/10/2022]
Abstract
Peptidyl asparaginyl ligases (PALs) are powerful tools for peptide macrocyclization. Herein, we report that a derivative of Asn, namely Nγ -hydroxyasparagine or Asn(OH), is an unnatural P1 substrate of PALs. By Asn(OH)-mediated cyclization, we prepared cyclic peptides as new matrix metalloproteinase 2 (MMP2) inhibitors displaying the hydroxamic acid moiety of Asn(OH) as the key pharmacophore. The most potent cyclic peptide (Ki =2.8±0.5 nM) was built on the hyperstable tetracyclic scaffold of rhesus theta defensin-1. The Asn(OH) residue in the cyclized peptides can also be readily oxidized to Asp. By this approach, we synthesized several bioactive Asp-containing cyclic peptides (MCoTI-II, kB2, SFTI, and integrin-targeting RGD peptides) that are otherwise difficult targets for PAL-catalyzed cyclization owing to unfavorable kinetics of the P1-Asp substrates. This study demonstrates that substrate engineering is a useful strategy to expand the application of PAL ligation in the synthesis of therapeutic cyclic peptides.
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Affiliation(s)
- Yiyin Xia
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Heng Tai Liew
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Seetharamsing Balamkundu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.,Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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7
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Gattringer J, Ndogo OE, Retzl B, Ebermann C, Gruber CW, Hellinger R. Cyclotides Isolated From Violet Plants of Cameroon Are Inhibitors of Human Prolyl Oligopeptidase. Front Pharmacol 2021; 12:707596. [PMID: 34322026 PMCID: PMC8311463 DOI: 10.3389/fphar.2021.707596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
Traditional medicine and the use of herbal remedies are well established in the African health care system. For instance, Violaceae plants are used for antimicrobial or anti-inflammatory applications in folk medicine. This study describes the phytochemical analysis and bioactivity screening of four species of the violet tribe Allexis found in Cameroon. Allexis cauliflora, Allexis obanensis, Allexis batangae and Allexis zygomorpha were evaluated for the expression of circular peptides (cyclotides) by mass spectrometry. The unique cyclic cystine-rich motif was identified in several peptides of all four species. Knowing that members of this peptide family are protease inhibitors, the plant extracts were evaluated for the inhibition of human prolyl oligopeptidase (POP). Since all four species inhibited POP activity, a bioactivity-guided fractionation approach was performed to isolate peptide inhibitors. These novel cyclotides, alca 1 and alca 2 exhibited IC50 values of 8.5 and 4.4 µM, respectively. To obtain their amino acid sequence information, combinatorial enzymatic proteolysis was performed. The proteolytic fragments were evaluated in MS/MS fragmentation experiments and the full-length amino acid sequences were obtained by de novo annotation of fragment ions. In summary, this study identified inhibitors of the human protease POP, which is a drug target for inflammatory or neurodegenerative disorders.
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Affiliation(s)
- Jasmin Gattringer
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Olivier Eteme Ndogo
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Bernhard Retzl
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Carina Ebermann
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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8
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Handley TNG, Wang CK, Harvey PJ, Lawrence N, Craik DJ. Cyclotide Structures Revealed by NMR, with a Little Help from X‐ray Crystallography. Chembiochem 2020; 21:3463-3475. [DOI: 10.1002/cbic.202000315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/08/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Thomas N. G. Handley
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
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9
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Mourão CBF, Brand GD, Fernandes JPC, Prates MV, Bloch C, Barbosa JARG, Freitas SM, Restano-Cassulini R, Possani LD, Schwartz EF. Head-to-Tail Cyclization after Interaction with Trypsin: A Scorpion Venom Peptide that Resembles Plant Cyclotides. J Med Chem 2020; 63:9500-9511. [PMID: 32787139 DOI: 10.1021/acs.jmedchem.0c00686] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidase inhibitors (PIs) have been broadly studied due to their wide therapeutic potential for human diseases. A potent trypsin inhibitor from Tityus obscurus scorpion venom was characterized and named ToPI1, with 33 amino acid residues and three disulfide bonds. The X-ray structure of the ToPI1:trypsin complex, in association with the mass spectrometry data, indicate a sequential set of events: the complex formation with the inhibitor Lys32 in the trypsin S1 pocket, the inhibitor C-terminal residue Ser33 cleavage, and the cyclization of ToPI1 via a peptide bond between residues Ile1 and Lys32. Kinetic and thermodynamic characterization of the complex was obtained. ToPI1 shares no sequence similarity with other PIs characterized to date and is the first PI with CS-α/β motif described from animal venoms. In its cyclic form, it shares structural similarities with plant cyclotides that also inhibit trypsin. These results bring new insights for studies with venom compounds, PIs, and drug design.
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Affiliation(s)
- Caroline B F Mourão
- Neuropharma Lab, Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brası́lia, Brasília-DF 70910-900, Brazil.,Instituto Federal de Brası́lia, Campus Ceilándia, Brası́lia-DF 72220-260, Brazil
| | - Guilherme D Brand
- Laboratório de Sı́ntese e Análise de Biomoléculas, LSAB, Instituto de Quı́mica, Universidade de Brası́lia, Brası́lia-DF 70910-900, Brazil
| | - João Paulo C Fernandes
- Laboratório de Biofı́sica Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brası́lia, Brası́lia-DF 70910-900, Brazil
| | - Maura V Prates
- Laboratório de Espectrometria de Massa, EMBRAPA Recursos Genéticos e Biotecnologia, Brası́lia-DF 70770-917, Brazil
| | - Carlos Bloch
- Laboratório de Espectrometria de Massa, EMBRAPA Recursos Genéticos e Biotecnologia, Brası́lia-DF 70770-917, Brazil
| | - João Alexandre R G Barbosa
- Laboratório de Biofı́sica Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brası́lia, Brası́lia-DF 70910-900, Brazil
| | - Sônia M Freitas
- Laboratório de Biofı́sica Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brası́lia, Brası́lia-DF 70910-900, Brazil
| | - Rita Restano-Cassulini
- Instituto de Biotecnologı́a, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Lourival D Possani
- Instituto de Biotecnologı́a, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Elisabeth F Schwartz
- Neuropharma Lab, Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brası́lia, Brasília-DF 70910-900, Brazil
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10
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Abstract
Cyclotides are naturally occurring microproteins (≈30 residues long) present in several families of plants. All cyclotides share a unique head-to-tail circular knotted topology containing three disulfide bridges forming a cystine knot topology. Cyclotides possess high stability to chemical, physical, and biological degradation and have been reported to cross cellular membranes. In addition, naturally occurring and engineered cyclotides have shown to possess various pharmacologically relevant activities. These unique features make the cyclotide scaffold an excellent tool for the design of novel peptide-based therapeutics by using molecular evolution and/or peptide epitope grafting techniques. In this chapter, we provide protocols to recombinantly produce a natively folded cyclotide making use of a standard bacterial expression system in combination with an intein-mediated backbone cyclization with concomitant oxidative folding.
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Affiliation(s)
- Maria Jose Campbell
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jingtan Su
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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11
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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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12
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Jones PM, Mazzio E, Soliman K, George AM. In Silico Investigation of the Binding of MCoTI-II Plant Defense Knottin to the γ-NGF Serine Protease of the 7S Nerve Growth Factor Complex and Biological Activity of Its NGF Mimetic Properties. J Phys Chem B 2019; 123:9104-9110. [PMID: 31580077 DOI: 10.1021/acs.jpcb.9b07547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nerve growth factor (NGF) is an endogenously produced polypeptide that promotes the differentiation, survival, and repair of neurons in the central and peripheral nervous systems. While trophic proteins hold promise for the treatment of neuronal injury and disease, use of NGF is limited by its large molecular weight, lack of permeability through the blood-brain barrier, and peripheral side effects. Previously, we found that an extract of the Momordica cochinchinensis seed stimulated PC-12 neurite outgrowth. Bioactivity-guided fractioning of the seed extract suggested that the NGF mimetic agent was one of few defined proteins from this plant: one group being the defense Knottins and the other group of the lowest mass is the potent trypsin inhibitor MCoTI-II. Here, the NGF mimetic potential of this latter protein was investigated using two concurrent but different approaches. A biological study used recombinant purified MCoTI-II, which when tested in rat PC-12 cells grown on collagen, failed to initiate outgrowth relative to the positive control 7S NGF. In a separate computational study, the possibility was investigated such that MCoTI-II could exert an effect through binding to the serine protease γ-NGF subunit of the 7S NGF complex, analogous to its binding to its native receptor trypsin. Molecular dynamics simulations showed that MCoTI-II can bind stably to γ-NGF for >350 ns. Modeling indicated that this interaction could sterically inhibit 7S NGF complex formation, potentially altering the equilibrium between inactive complexed and free active NFG protein. In conclusion, the biological study now excludes the MCoTI-II protein as the NGF mimetic factor in the Momordica extract, an important and required step to identify the active component in this seed. On the other hand, the theoretical study has revealed a novel observation that may be of use in the development of strategies to affect NGF activity.
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Affiliation(s)
- Peter M Jones
- School of Life Sciences , University of Technology Sydney , P.O. Box 123, Broadway , New South Wales 2007 , Australia
| | - Elizabeth Mazzio
- College of Pharmacy and Pharmaceutical Sciences , Florida Agricultural and Mechanical University , 241 Fred Humphries Science Research Facility , Tallahassee , Florida 32307 , United States
| | - Karam Soliman
- College of Pharmacy and Pharmaceutical Sciences , Florida Agricultural and Mechanical University , 241 Fred Humphries Science Research Facility , Tallahassee , Florida 32307 , United States
| | - Anthony M George
- School of Life Sciences , University of Technology Sydney , P.O. Box 123, Broadway , New South Wales 2007 , Australia
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13
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Silva ON, Pinto MF, Viana JF, Freitas CG, Fensterseifer IC, Craik DJ, Franco OL. Evaluation of the in vitro Antitumor Activity of Nanostructured Cyclotides in Polymers of Eudragit® L 100-55 and RS 30 D. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180801115526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background:
Cancer is a major cause of mortality and morbidity and given the limitations
of many current cancer drugs, there is great need to discover and develop novel treatments. An
alternative to the conventional drug discovery path is to exploit new classes of natural compounds
such as cyclotides. This peptide family is characterized by linked C- and N-termini and a structural
fold called the cyclic cystine knot (CCK). The CCK fold is responsible for the exceptional enzymatic,
chemical and thermal stability of cyclotides.
Methods:
In the present study, an alternative to traditional cancer treatments, involving new nanomaterials
and nanocarriers allowing efficient cyclotide delivery, is proposed. Using the polymers
Eudragit® L 100-55 and RS 30 D, the cyclotides kalata B2 and parigidin-br1 (PBR1) were nanocapsulated,
and nanoparticles 91 nm and 188 nm in diameter, respectively, were produced.
Results:
An encapsulation rate of up to 95% was observed. In vitro bioassays showed that the
nanostructured cyclotides were partially able to control the development of the colorectal adenocarcinoma
cell line CACO2 and the breast cancer cell line MCF-7.
Conclusion:
Data reported herein indicate that nanoformulated cyclotides exhibit antitumor activity
and sustained drug release. Thus, the system using Eudragit® nanocapsules seems to be efficient for
cyclotide encapsulation and probably could be used to target specific tumors in future studies.
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Affiliation(s)
- Osmar N. Silva
- S-Inova Biotech, Universidade Catolica Dom Bosco, Programa de Pós-graduacao em Biotecnologia, Campo Grande, Mato Grosso do Sul, Brazil
| | - Michelle F.S. Pinto
- Faculdade Anhanguera de Ciencias e Tecnologia de Brasilia, Brasilia, Distrito Federal, Brazil
| | | | - Camila G. Freitas
- Centro de Analises Proteomicas e Bioquimicas. Programa de Pos-Graduacao em Ciencias Genomicas e Biotecnologia, Universidade Catolica de Brasilia, Brasilia, Distrito Federal, Brazil
| | - Isabel C.M. Fensterseifer
- Centro de Analises Proteomicas e Bioquimicas. Programa de Pos-Graduacao em Ciencias Genomicas e Biotecnologia, Universidade Catolica de Brasilia, Brasilia, Distrito Federal, Brazil
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Octavio L. Franco
- Centro de Analises Proteomicas e Bioquimicas. Programa de Pos-Graduacao em Ciencias Genomicas e Biotecnologia, Universidade Catolica de Brasilia, Brasilia, Distrito Federal, Brazil
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14
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Swedberg JE, Ghani HA, Harris JM, de Veer SJ, Craik DJ. Potent, Selective, and Cell-Penetrating Inhibitors of Kallikrein-Related Peptidase 4 Based on the Cyclic Peptide MCoTI-II. ACS Med Chem Lett 2018; 9:1258-1262. [PMID: 30613336 DOI: 10.1021/acsmedchemlett.8b00422] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022] Open
Abstract
Kallikrein-related peptidase 4 (KLK4) is a serine protease that has putative intracellular and extracellular functions in prostate cancer progression. Here we show that MCoTI-II, a 34-amino acid cyclic peptide found in the seeds of red gac (Momordica cochinchinensis), is an inhibitor of KLK4. By grafting a preferred KLK4 cleavage sequence into MCoTI-II, we produced a highly potent KLK4 inhibitor (K i = 0.1 nM) that displayed 100,000-fold selectivity over related KLKs and the ability to penetrate cells. Additionally, by substituting positively charged noncontact residues in this compound, we produced a potent and selective KLK4 inhibitor that does not penetrate cells. The inhibitors were shown to be nontoxic to human cells and stable in human serum. These KLK4 inhibitors provide useful chemical tools to further define the role(s) of both intracellular and extracellular KLK4 in prostate cancer cell lines and disease models.
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Affiliation(s)
- Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hafiza Abdul Ghani
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jonathan M. Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Simon J. de Veer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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15
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Kwon S, Duarte JN, Li Z, Ling JJ, Cheneval O, Durek T, Schroeder CI, Craik DJ, Ploegh HL. Targeted Delivery of Cyclotides via Conjugation to a Nanobody. ACS Chem Biol 2018; 13:2973-2980. [PMID: 30248263 DOI: 10.1021/acschembio.8b00653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many naturally occurring peptides have poor proteolytic stability, which limits their therapeutic applications. Cyclotides are plant-derived cyclic peptides that resist proteolysis due to their highly constrained structure, comprising a head-to-tail cyclic backbone and three disulfide bonds that form a cystine-knotted core. This structure makes them useful as scaffolds onto which peptide sequences (epitopes) can be grafted. In this study, VHH7, an alpaca-derived nanobody that targets murine class II MHC molecules, was used for the targeted delivery of cyclotides to antigen-presenting cells (APCs). The cyclotides MCoTI-I, and MCoTI-I with a HA-tag (YPYDVPDYA) grafted into loop 6 (MCoTI-HA), were tested for immunogenic properties. To produce the requisite VHH7-peptide conjugates, a site-specific sortase A-catalyzed reaction in combination with a copper-free strain-promoted cycloaddition reaction was used. MCoTI-I alone did not display any obvious antibody response, thus showing the capacity of cyclotides as immunologically silent scaffolds. By contrast, MCoTI-I conjugated to VHH7 elicited antibodies against cyclic or linear MCoTI-I, thus suggesting a simple and robust approach for targeting cyclotides to APCs, and potentially to other cell types. A similar antibody response was observed when MCoTI-HA was conjugated to VHH7, but there was no reactivity toward a linear HA-tag itself, suggesting differences in conformational constraint between cyclotide-presented and linear epitopes. Studies of commercially available HA antibodies applied to MCoTI-HA confirmed that the conformation of peptide immunogens affects their reactivity. Thus, the production of antibodies that recognize constrained epitopes may benefit from engraftment onto scaffolds such as cyclotides. More broadly, this study validates that a prototypic cyclotide, a member of a peptide family that has proven to be useful as drug design scaffolds in many other studies, can efficiently reach a specific target in vivo.
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Affiliation(s)
- Soohyun Kwon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Joao N. Duarte
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Zeyang Li
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Jingjing J. Ling
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Olivier Cheneval
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Christina I. Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Hidde L. Ploegh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
- Program in Cellular and Molecular Medicine, Division of Molecular Biology, Department of Medicine, Boston Children’s Hospital, 3 Blackfan Circle, Third Floor, Boston, Massachusetts 02115, United States
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16
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Wadhwani P, Heidenreich N, Podeyn B, Bürck J, Ulrich AS. Antibiotic gold: tethering of antimicrobial peptides to gold nanoparticles maintains conformational flexibility of peptides and improves trypsin susceptibility. Biomater Sci 2018; 5:817-827. [PMID: 28275774 DOI: 10.1039/c7bm00069c] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptide-coated nanoparticles are valuable tools for diverse biological applications, such as drug delivery, molecular recognition, and antimicrobial action. The functionalization of pre-fabricated nanoparticles with free peptides in solution is inefficient either due to aggregation of the particles or due to the poor ligand exchange reaction. Here, we present a one-pot synthesis for preparing gold nanoparticles with a homogeneous distribution that are covered in situ with cationic peptides in a site-selective manner via Cys-residue at the N-terminus. Five representative peptides were selected, which are known to perturb cellular membranes and exert their antimicrobial and/or cell penetrating activity by folding into amphiphilic α-helical structures. When tethered to the nanoparticles at a single site, all peptides were found to switch their conformation from unordered state (in aqueous buffers) to their functionally relevant α-helical conformation in the presence of model membranes, as shown by circular dichroism spectroscopy. The conjugated peptides also maintained the same antibacterial activity as in the free form. Most importantly, when tethered to the gold nanoparticles the peptides showed an enormous increase in stability against trypsin digestion compared to the free forms, leading to a dramatic improvement of their lifetimes and activities. These findings suggest that site-selective surface tethering of peptides to gold nanoparticles has several advantages: (i) it does not prevent the peptides from folding into their biologically active conformation, (ii) such conjugation protects the peptides against protease digestion, and (iii) this way it is possible to prepare stable, water soluble antimicrobial nanoparticles as promising antibacterial agents.
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Affiliation(s)
- Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), 1Institute of Biological Interfaces (IBG-2) P.O.B. 3640, D 76021 Karlsruhe, Germany.
| | - Nico Heidenreich
- KIT, 2Institute of Organic Chemistry & CFN, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Benjamin Podeyn
- KIT, 2Institute of Organic Chemistry & CFN, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), 1Institute of Biological Interfaces (IBG-2) P.O.B. 3640, D 76021 Karlsruhe, Germany.
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), 1Institute of Biological Interfaces (IBG-2) P.O.B. 3640, D 76021 Karlsruhe, Germany. and KIT, 2Institute of Organic Chemistry & CFN, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
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17
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Zhang Y, Schulten K, Gruebele M, Bansal PS, Wilson D, Daly NL. Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide. Biophys J 2017; 110:1744-1752. [PMID: 27119635 DOI: 10.1016/j.bpj.2016.03.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/08/2016] [Accepted: 03/21/2016] [Indexed: 10/21/2022] Open
Abstract
Disulfide bridges are commonly found covalent bonds that are usually believed to maintain structural stability of proteins. Here, we investigate the influence of disulfide bridges on protein dynamics through molecular dynamics simulations on the cysteine-rich trypsin inhibitor MCoTI-II with three disulfide bridges. Correlation analysis of the reduced cyclic peptide shows that two of the three disulfide distances (Cys(11)-Cys(23) and Cys(17)-Cys(29)) are anticorrelated within ∼1 μs of bridge formation or dissolution: when the peptide is in nativelike structures and one of the distances shortens to allow bond formation, the other tends to lengthen. Simulations over longer timescales, when the denatured state is less structured, do not show the anticorrelation. We propose that the native state contains structural elements that frustrate one another's folding, and that the two bridges are critical for snapping the frustrated native structure into place. In contrast, the Cys(4)-Cys(21) bridge is predicted to form together with either of the other two bridges. Indeed, experimental chromatography and nuclear magnetic resonance data show that an engineered peptide with the Cys(4)-Cys(21) bridge deleted can still fold into its near-native structure even in its noncyclic form, confirming the lesser role of the Cys(4)-Cys(21) bridge. The results highlight the importance of disulfide bridges in a small bioactive peptide to bring together frustrated structure in addition to maintaining protein structural stability.
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Affiliation(s)
- Yi Zhang
- Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois; Department of Physics and Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois
| | - Martin Gruebele
- Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois; Department of Physics and Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois.
| | - Paramjit S Bansal
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - David Wilson
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Norelle L Daly
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia.
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18
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Schmidt M, Toplak A, Quaedflieg PJLM, Ippel H, Richelle GJJ, Hackeng TM, van Maarseveen JH, Nuijens T. Omniligase-1: A Powerful Tool for Peptide Head-to-Tail Cyclization. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700314] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Marcel Schmidt
- EnzyPep B.V.; Brightlands Campus; Urmonderbaan 22 6167 RD Geleen The Netherlands
- Van 't Hoff Institute of Molecular Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Ana Toplak
- EnzyPep B.V.; Brightlands Campus; Urmonderbaan 22 6167 RD Geleen The Netherlands
| | | | - Hans Ippel
- Department of Biochemistry; CARIM; University of Maastricht; Universiteitsingel 50 6229 ER Maastricht The Netherlands
| | - Gaston J. J. Richelle
- Van 't Hoff Institute of Molecular Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Tilman M. Hackeng
- Department of Biochemistry; CARIM; University of Maastricht; Universiteitsingel 50 6229 ER Maastricht The Netherlands
| | - Jan H. van Maarseveen
- Van 't Hoff Institute of Molecular Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Timo Nuijens
- EnzyPep B.V.; Brightlands Campus; Urmonderbaan 22 6167 RD Geleen The Netherlands
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19
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Cunha NBD, Barbosa AEADD, de Almeida RG, Porto WF, Maximiano MR, Álvares LCS, Munhoz CBR, Eugênio CUO, Viana AAB, Franco OL, Dias SC. Cloning and characterization of novel cyclotides genes from South American plants. Biopolymers 2017; 106:784-795. [PMID: 27554590 DOI: 10.1002/bip.22938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 08/10/2016] [Accepted: 08/21/2016] [Indexed: 01/06/2023]
Abstract
Cyclotides are multifunctional plant cyclic peptides containing 28-37 amino acid residues and a pattern of three disulfide bridges, forming a motif known as the cyclic cystine knot. Due to their high biotechnological potential, the sequencing and characterization of cyclotide genes are crucial not only for cloning and establishing heterologous expression strategies, but also to understand local plant evolution in the context of host-pathogen relationships. Here, two species from the Brazilian Cerrado, Palicourea rigida (Rubiaceae) and Pombalia lanata (A.St.-Hil.) Paula-Souza (Violaceae), were used for cloning and characterizing novel cyclotide genes. Using 3' and 5' RACE PCR and sequencing, two full cDNAs, named parigidin-br2 (P. rigida) and hyla-br1 (P. lanata), were isolated and shown to have similar genetic structures to other cyclotides. Both contained the conserved ER-signal domain, N-terminal prodomain, mature cyclotide domain and a C-terminal region. Genomic sequencing of parigidin-br2 revealed two different gene copies: one intronless allele and one presenting a rare 131-bp intron. In contrast, genomic sequencing of hyla-br1 revealed an intronless gene-a common characteristic of members of the Violaceae family. Parigidin-br2 5' and 3' UTRs showed the presence of 12 putative candidate sites for binding of regulatory proteins, suggesting that the flanking and intronic regions of the parigidin-br2 gene must play important roles in transcriptional rates and in the regulation of temporal and spatial gene expression. The high degree of genetic similarity and structural organization among the cyclotide genes isolated in the present study from the Brazilian Cerrado and other well-characterized plant cyclotides may contribute to a better understanding of cyclotide evolution.
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Affiliation(s)
- Nicolau Brito da Cunha
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | | | - Renato Goulart de Almeida
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - William Farias Porto
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Mariana Rocha Maximiano
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Luana Cristina Silva Álvares
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Cassia Beatriz Rodrigues Munhoz
- Departamento de Botânica, Instituto de Ciências Biológicas. Bloco D. Universidade de Brasília. Campus Darcy Ribeiro 70904-970, Asa Norte. Brasília, DF, Brazil
| | - Chesterton Ulysses Orlando Eugênio
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Antônio Américo Barbosa Viana
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Octavio Luiz Franco
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil.,S-Inova Biotech, Pós Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Simoni Campos Dias
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
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20
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Abdul Ghani H, Henriques ST, Huang YH, Swedberg JE, Schroeder CI, Craik DJ. Structural and functional characterization of chimeric cyclotides from the Möbius and trypsin inhibitor subfamilies. Biopolymers 2017; 108. [DOI: 10.1002/bip.22927] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Hafiza Abdul Ghani
- Institute for Molecular Bioscience, The University of Queensland; Brisbane Queensland 4072 Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland; Brisbane Queensland 4072 Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland; Brisbane Queensland 4072 Australia
| | - Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland; Brisbane Queensland 4072 Australia
| | - Christina I. Schroeder
- Institute for Molecular Bioscience, The University of Queensland; Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland; Brisbane Queensland 4072 Australia
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21
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Abstract
Cyclotides are fascinating microproteins (≈30 residues long) present in several families of plants that share a unique head-to-tail circular knotted topology of three disulfide bridges, with one disulfide penetrating through a macrocycle formed by the two other disulfides and inter-connecting peptide backbones, forming what is called a cystine knot topology. Naturally occurring cyclotides have shown to posses various pharmacologically relevant activities and have been reported to cross cell membranes. Altogether, these features make the cyclotide scaffold an excellent molecular framework for the design of novel peptide-based therapeutics, making them ideal substrates for molecular grafting of biological peptide epitopes. In this chapter we describe how to express a native folded cyclotide using intein-mediated protein trans-splicing in live Escherichia coli cells.
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Affiliation(s)
- Krishnappa Jagadish
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089-9121, USA.
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22
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Wang CK, Craik DJ. Cyclic peptide oral bioavailability: Lessons from the past. Biopolymers 2016; 106:901-909. [DOI: 10.1002/bip.22878] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/19/2016] [Accepted: 05/04/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Conan K Wang
- 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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23
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Jones PM, George AM. Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding. Sci Rep 2016; 6:23174. [PMID: 26975976 PMCID: PMC4791599 DOI: 10.1038/srep23174] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/25/2016] [Indexed: 11/09/2022] Open
Abstract
MCoTI-I and II are plant defence proteins, potent trypsin inhibitors from the bitter gourd Momordica cochinchinensis. They are members of the Knottin Family, which display exceptional stability due to unique topology comprising three interlocked disulfide bridges. Knottins show promise as scaffolds for new drug development. A crystal structure of trypsin-bound MCoTI-II suggested that loop 1, which engages the trypsin active site, would show decreased dynamics in the bound state, an inference at odds with an NMR analysis of MCoTI-I, which revealed increased dynamics of loop 1 in the presence of trypsin. To investigate this question, we performed unrestrained MD simulations of trypsin-bound and free MCoTI-II. This analysis found that loop 1 of MCoTI-II is not more dynamic in the trypsin-bound state than in the free state. However, it revealed an intermediate conformation, transitional between the free and bound MCoTI-II states. The data suggest that MCoTI-II binding involves a process in which initial interaction with trypsin induces transitions between the free and intermediate conformations, and fluctuations between these states account for the increase in dynamics of loop 1 observed for trypsin-bound MCoTI-I. The MD analysis thus revealed new aspects of the inhibitors’ dynamics that may be of utility in drug design.
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Affiliation(s)
- Peter M Jones
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007 Australia
| | - Anthony M George
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007 Australia
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24
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Cyclic thrombospondin-1 mimetics: grafting of a thrombospondin sequence into circular disulfide-rich frameworks to inhibit endothelial cell migration. Biosci Rep 2015; 35:BSR20150210. [PMID: 26464514 PMCID: PMC4660582 DOI: 10.1042/bsr20150210] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/12/2015] [Indexed: 12/22/2022] Open
Abstract
The findings suggest re-engineered cyclic TSP-1 mimetics are non-toxic, highly stable, and possess potent anti-angiogenesis activity without altering the native fold of the cyclic frameworks. This provides an alternative approach for cancer drug development particularly in the thrombospondin field. Tumour formation is dependent on nutrient and oxygen supply from adjacent blood vessels. Angiogenesis inhibitors can play a vital role in controlling blood vessel formation and consequently tumour progression by inhibiting endothelial cell proliferation, sprouting and migration. The primary aim of the present study was to design cyclic thrombospondin-1 (TSP-1) mimetics using disulfide-rich frameworks for anti-angiogenesis therapies and to determine whether these peptides have better potency than the linear parent peptide. A short anti-angiogenic heptapeptide fragment from TSP-1 (GVITRIR) was incorporated into two cyclic disulfide-rich frameworks, namely MCoTI-II (Momordica cochinchinensis trypsin inhibitor-II) and SFTI-1 (sunflower trypsin inhibitor-1). The cyclic peptides were chemically synthesized and folded in oxidation buffers, before being tested in a series of in vitro evaluations. Incorporation of the bioactive heptapeptide fragment into the cyclic frameworks resulted in peptides that inhibited microvascular endothelial cell migration, and had no toxicity against normal primary human endothelial cells or cancer cells. Importantly, all of the designed cyclic TSP-1 mimetics were far more stable than the linear heptapeptide in human serum. The present study has demonstrated a novel approach to stabilize the active region of TSP-1. The anti-angiogenic activity of the native TSP-1 active fragment was maintained in the new TSP-1 mimetics and the results provide a new chemical approach for the design of TSP-1 mimetics.
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25
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Hellinger R, Koehbach J, Puigpinós A, Clark RJ, Tarragó T, Giralt E, Gruber CW. Inhibition of Human Prolyl Oligopeptidase Activity by the Cyclotide Psysol 2 Isolated from Psychotria solitudinum. JOURNAL OF NATURAL PRODUCTS 2015; 78:1073-82. [PMID: 25894999 PMCID: PMC4444998 DOI: 10.1021/np501061t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 05/21/2023]
Abstract
Cyclotides are head-to-tail cyclized peptides comprising a stabilizing cystine-knot motif. To date, they are well known for their diverse bioactivities such as anti-HIV and immunosuppressive properties. Yet little is known about specific molecular mechanisms, in particular the interaction of cyclotides with cellular protein targets. Native and synthetic cyclotide-like peptides from Momordica plants are potent and selective inhibitors of different serine-type proteinases such as trypsin, chymotrypsin, matriptase, and tryptase-beta. This study describes the bioactivity-guided isolation of a cyclotide from Psychotria solitudinum as an inhibitor of another serine-type protease, namely, the human prolyl oligopeptidase (POP). Analysis of the inhibitory potency of Psychotria extracts and subsequent fractionation by liquid chromatography yielded the isolated peptide psysol 2 (1), which exhibited an IC50 of 25 μM. In addition the prototypical cyclotide kalata B1 inhibited POP activity with an IC50 of 5.6 μM. The inhibitory activity appeared to be selective for POP, since neither psysol 2 nor kalata B1 were able to inhibit the proteolytic activity of trypsin or chymotrypsin. The enzyme POP is well known for its role in memory and learning processes, and it is currently being considered as a promising therapeutic target for the cognitive deficits associated with several psychiatric and neurodegenerative diseases, such as schizophrenia and Parkinson's disease. In the context of discovery and development of POP inhibitors with beneficial ADME properties, cyclotides may be suitable starting points considering their stability in biological fluids and possible oral bioavailability.
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Affiliation(s)
- Roland Hellinger
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Koehbach
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Albert Puigpinós
- Institute
for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | - Richard J. Clark
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Teresa Tarragó
- Institute
for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | - Ernest Giralt
- Institute
for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
- Department
of Organic Chemistry, University of Barcelona
(UB), 08028 Barcelona, Spain
| | - Christian W. Gruber
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
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26
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Aboye T, Kuang Y, Neamati N, Camarero JA. Rapid parallel synthesis of bioactive folded cyclotides by using a tea-bag approach. Chembiochem 2015; 16:827-33. [PMID: 25663016 DOI: 10.1002/cbic.201402691] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 11/07/2022]
Abstract
We report here the first rapid parallel production of bioactive folded cyclotides by using Fmoc-based solid-phase peptide synthesis in combination with a "tea-bag" approach. Using this approach, we efficiently synthesized 15 analogues of the CXCR4 antagonist cyclotide MCo-CVX-5c. Cyclotides were synthesized in a single-pot, cyclization/folding reaction in the presence of reduced glutathione. Natively folded cyclotides were quickly purified from the cyclization/folding crude mixture by activated thiol Sepharose-based chromatography. The different folded cyclotide analogues were then tested for their ability to inhibit the CXCR4 receptor in a cell-based assay. The results indicated that this approach can be used for the efficient chemical synthesis of libraries of cyclotides with improved biological properties that can be easily interfaced with solution or cell-based assays for rapid screening.
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Affiliation(s)
- Teshome Aboye
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121 (USA)
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27
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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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28
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Conibear AC, Wang CK, Bi T, Rosengren KJ, Camarero JA, Craik DJ. Insights into the molecular flexibility of θ-defensins by NMR relaxation analysis. J Phys Chem B 2014; 118:14257-66. [PMID: 25375365 PMCID: PMC5811197 DOI: 10.1021/jp507754c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
θ-Defensins are mammalian cyclic peptides that have antimicrobial activity and show potential as stable scaffolds for peptide-based drug design. The cyclic cystine ladder structural motif of θ-defensins has been characterized using NMR spectroscopy and is important for their structure and stability. However, the effect of the pronounced elongated topology of θ-defensins on their molecular motion is not yet understood. Studies of molecular motion by NMR relaxation measurements have been facilitated by the recent development of a semirecombinant method for producing cyclic peptides that allows for isotopic labeling. Here we have undertaken a multifield (15)N NMR relaxation analysis of the anti-HIV θ-defensin, HTD-2, and interpreted the experimental data using various models of overall and internal molecular motion. We found that it was necessary to apply a model that includes internal motion to account for the variations in the experimental T1 and NOE data at different backbone amide sites in the peptide. Although an isotropic model with internal motion was the simplest model that provided a satisfactory fit with the experimental data, we cannot exclude the possibility that overall motion is anisotropic, especially considering the strikingly elongated topology of θ-defensins. The presence of flexible side chains, self-association, interactions with solvent, and internal motions are all potential contributors to the observed relaxation data. Internal motion consistent with the constraints imposed by the cyclic cystine ladder was observed in that the order parameters, S(2), show that residues in the turns are more flexible than those in the β-sheet. This study provides insights into the dynamics of θ-defensins and information that might be useful in their application as scaffolds in drug design.
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Affiliation(s)
- Anne C. Conibear
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tao Bi
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, PSC 616, Los Angeles, CA 90033, USA
| | - K. Johan Rosengren
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, PSC 616, Los Angeles, CA 90033, USA
- Department of Chemistry, College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA9033, USA
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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29
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Mahatmanto T, Mylne JS, Poth AG, Swedberg JE, Kaas Q, Schaefer H, Craik DJ. The evolution of Momordica cyclic peptides. Mol Biol Evol 2014; 32:392-405. [PMID: 25376175 DOI: 10.1093/molbev/msu307] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cyclic proteins have evolved for millions of years across all kingdoms of life to confer structural stability over their acyclic counterparts while maintaining intrinsic functional properties. Here, we show that cyclic miniproteins (or peptides) from Momordica (Cucurbitaceae) seeds evolved in species that diverged from an African ancestor around 19 Ma. The ability to achieve head-to-tail cyclization of Momordica cyclic peptides appears to have been acquired through a series of mutations in their acyclic precursor coding sequences following recent and independent gene expansion event(s). Evolutionary analysis of Momordica cyclic peptides reveals sites that are under selection, highlighting residues that are presumably constrained for maintaining their function as potent trypsin inhibitors. Molecular dynamics of Momordica cyclic peptides in complex with trypsin reveals site-specific residues involved in target binding. In a broader context, this study provides a basis for selecting Momordica species to further investigate the biosynthesis of the cyclic peptides and for constructing libraries that may be screened against evolutionarily related serine proteases implicated in human diseases.
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Affiliation(s)
- Tunjung Mahatmanto
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Chemistry and Biochemistry & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Perth, WA, Australia
| | - Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Hanno Schaefer
- Plant Biodiversity Research, Technische Universität München, Freising, Germany
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
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30
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Stanger K, Maurer T, Kaluarachchi H, Coons M, Franke Y, Hannoush RN. Backbone cyclization of a recombinant cystine-knot peptide by engineered Sortase A. FEBS Lett 2014; 588:4487-96. [DOI: 10.1016/j.febslet.2014.10.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/18/2014] [Accepted: 10/20/2014] [Indexed: 11/15/2022]
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