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Kalmankar NV, Gehi BR, Sowdhamini R. Effects of a plant cyclotide on conformational dynamics and destabilization of β-amyloid fibrils through molecular dynamics simulations. Front Mol Biosci 2022; 9:986704. [PMID: 36250019 PMCID: PMC9561823 DOI: 10.3389/fmolb.2022.986704] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/14/2022] [Indexed: 11/28/2022] Open
Abstract
Aggregation of β-amyloid (Aβ) peptide is one of the hallmarks of Alzheimer’s disease (AD) which results in chronic and progressive neurodegeneration of the brain. A recent study by our group have shown the ability of cyclic disulfide-rich peptides (“cyclotides”) isolated from a medicinal plant, Clitoria ternatea, to inhibit the aggregation of Aβ peptides and reduce oxidative stress caused by reactive oxygen species using in vivo models of transgenic Caenorhabditis elegans. In the present study, through extensive computational docking and multi-ns molecular dynamics (MD) simulation, we evaluated if cyclotides can stably bind to Aβ molecules and/or destabilize the Aβ fibril by preventing conformational changes from α-helical to β-sheet rich structures. We demonstrate that cyclotides bind effectively and stably to different forms of Aβ structures via hydrogen bonding and hydrophobic interactions. One of the conserved hydrophobic interface residues, Tyr10 was mutated to Ala and the impact of this virtual mutation was estimated by additional MD simulations for the wild-type (WT) and mutant protein-peptide complexes. A detailed MD simulation analyses revealed that cyclotides form hydrogen bonds with the toxic amyloid assemblies thereby weakening the inter-strand hydrogen bonds between the Aβ peptide. The φ-ѱ distribution map of residues in the cyclotide binding pocket that ideally adopt β-sheet conformation show deviation towards right-handed ɑ-helical (ɑR) conformation. This effect was similar to that observed for the Tyr10Ala mutant and doubly so, for the cyclotide bound form. It is therefore possible to hypothesise that the opening up of amyloid β-sheet is due to an unfolding process occurring in the Aβ caused by cyclotide binding and inhibition. Our current findings provide novel structural insights on the mode of interaction between cyclotides and Aβ fibrils and describe their anti-amyloid aggregation potential. This sheds light on the future of cyclotide-based drug design against protein aggregation, a hallmark event in many neurodegenerative diseases.
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Affiliation(s)
- Neha V. Kalmankar
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bengaluru, Karnataka, India
| | | | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bengaluru, Karnataka, India
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
- *Correspondence: Ramanathan Sowdhamini,
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Fernández-Bobey A, Pinto MEF, de Almeida LC, de Souza BM, Dias NB, de Paula-Souza J, Cilli EM, Lopes NP, Costa-Lotufo LV, Palma MS, da Silva Bolzani V. Cytotoxic Cyclotides from Anchietea pyrifolia, a South American Plant Species. JOURNAL OF NATURAL PRODUCTS 2022; 85:2127-2134. [PMID: 36044031 DOI: 10.1021/acs.jnatprod.1c01129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cyclotides are mini-proteins with potent bioactivities and outstanding potential for agricultural and pharmaceutical applications. More than 450 different plant cyclotides have been isolated from six angiosperm families. In Brazil, studies involving this class of natural products are still scarce, despite its rich floristic diversity. Herein were investigated the cyclotides from Anchietea pyrifolia roots, a South American medicinal plant from the family Violaceae. Fourteen putative cyclotides were annotated by LC-MS. Among these, three new bracelet cyclotides, anpy A-C, and the known cycloviolacins O4 (cyO4) and O17 (cyO17) were sequenced through a combination of chemical and enzymatic reactions followed by MALDI-MS/MS analysis. Their cytotoxic activity was evaluated by a cytotoxicity assay against three human cancer cell lines (colorectal carcinoma cells: HCT 116 and HCT 116 TP53-/- and breast adenocarcinoma, MCF 7). For all assays, the IC50 values of isolated compounds ranged between 0.8 and 7.3 μM. CyO17 was the most potent cyclotide for the colorectal cancer cell lines (IC50, 0.8 and 1.2 μM). Furthermore, the hemolytic activity of anpy A and B, cyO4, and cyO17 was assessed, and the cycloviolacins were the least hemolytic (HD50 > 156 μM). This work sheds light on the cytotoxic effects of the anpy cyclotides against cancer cells. Moreover, this study expands the number of cyclotides obtained to date from Brazilian plant biodiversity and adds one more genus containing these molecules to the list of the Violaceae family.
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Affiliation(s)
- Antonio Fernández-Bobey
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, Sao Paulo State University (UNESP), 14800-060, Araraquara, Sao Paulo, Brazil
- Department of Basic and Applied Biology, Laboratory of Structural Biology and Zoochemistry, Institute of Biosciences, Sao Paulo State University (UNESP), 13506-900, Rio Claro, Sao Paulo, Brazil
| | - Meri Emili Ferreira Pinto
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, Sao Paulo State University (UNESP), 14800-060, Araraquara, Sao Paulo, Brazil
| | - Larissa Costa de Almeida
- Department of Pharmacology, Institute of Biomedical Science, University of Sao Paulo (USP), 05508-900, Sao Paulo, Brazil
| | - Bibiana Monson de Souza
- Department of Basic and Applied Biology, Laboratory of Structural Biology and Zoochemistry, Institute of Biosciences, Sao Paulo State University (UNESP), 13506-900, Rio Claro, Sao Paulo, Brazil
| | - Nathalia Baptista Dias
- Scientific and Technological Bioresource Nucleus (BIOREN), University of The Frontier (UFRO), 4881-176, Temuco, Chile
| | - Juliana de Paula-Souza
- Department of Botany, Federal University of Santa Catarina (UFSC), 88040-535, Florianopolis, Santa Catarina, Brazil
| | - Eduardo Maffud Cilli
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, Sao Paulo State University (UNESP), 14800-060, Araraquara, Sao Paulo, Brazil
| | - Norberto Peporine Lopes
- Nucleus Research in Natural and Synthetic Products (NPPNS), Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo (USP), 14040-903, Ribeirao Preto, Sao Paulo, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Science, University of Sao Paulo (USP), 05508-900, Sao Paulo, Brazil
| | - Mario Sergio Palma
- Department of Basic and Applied Biology, Laboratory of Structural Biology and Zoochemistry, Institute of Biosciences, Sao Paulo State University (UNESP), 13506-900, Rio Claro, Sao Paulo, Brazil
| | - Vanderlan da Silva Bolzani
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, Sao Paulo State University (UNESP), 14800-060, Araraquara, Sao Paulo, Brazil
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3
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Taghizadeh MS, Retzl B, Muratspahić E, Trenk C, Casanova E, Moghadam A, Afsharifar A, Niazi A, Gruber CW. Discovery of the cyclotide caripe 11 as a ligand of the cholecystokinin-2 receptor. Sci Rep 2022; 12:9215. [PMID: 35654807 PMCID: PMC9163038 DOI: 10.1038/s41598-022-13142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/20/2022] [Indexed: 11/08/2022] Open
Abstract
The cholecystokinin-2 receptor (CCK2R) is a G protein-coupled receptor (GPCR) that is expressed in peripheral tissues and the central nervous system and constitutes a promising target for drug development in several diseases, such as gastrointestinal cancer. The search for ligands of this receptor over the past years mainly resulted in the discovery of a set of distinct synthetic small molecule chemicals. Here, we carried out a pharmacological screening of cyclotide-containing plant extracts using HEK293 cells transiently-expressing mouse CCK2R, and inositol phosphate (IP1) production as a readout. Our data demonstrated that cyclotide-enriched plant extracts from Oldenlandia affinis, Viola tricolor and Carapichea ipecacuanha activate the CCK2R as measured by the production of IP1. These findings prompted the isolation of a representative cyclotide, namely caripe 11 from C. ipecacuanha for detailed pharmacological analysis. Caripe 11 is a partial agonist of the CCK2R (Emax = 71%) with a moderate potency of 8.5 µM, in comparison to the endogenous full agonist cholecystokinin-8 (CCK-8; EC50 = 11.5 nM). The partial agonism of caripe 11 is further characterized by an increase on basal activity (at low concentrations) and a dextral-shift of the potency of CCK-8 (at higher concentrations) following its co-incubation with the cyclotide. Therefore, cyclotides such as caripe 11 may be explored in the future for the design and development of cyclotide-based ligands or imaging probes targeting the CCK2R and related peptide GPCRs.
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Affiliation(s)
- Mohammad Sadegh Taghizadeh
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Bernhard Retzl
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Edin Muratspahić
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Christoph Trenk
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Emilio Casanova
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | | | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria.
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Khan A, Waqas M, Khan M, Halim SA, Rehman NU, Al-Harrasi A. Identification of novel prolyl oligopeptidase inhibitors from resin of Boswella papyrifera (Del.) Hochst. and their mechanism: Virtual and biochemical studies. Int J Biol Macromol 2022; 213:751-767. [DOI: 10.1016/j.ijbiomac.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/22/2022] [Accepted: 06/01/2022] [Indexed: 11/05/2022]
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Dang TT, Harvey PJ, Chan LY, Huang Y, Kaas Q, Craik DJ. Mutagenesis of cyclotide Cter 27 exemplifies a robust folding strategy for bracelet cyclotides. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tien T. Dang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
- Institute of Applied Materials Science Vietnam Academy of Science and Technology Ho Chi Minh City Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Lai Yue Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Yen‐Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
| | - David J. Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland
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Pandey A, Yadav R, Sanyal I. Evaluating the pesticidal impact of plant protease inhibitors: lethal weaponry in the co-evolutionary battle. PEST MANAGEMENT SCIENCE 2022; 78:855-868. [PMID: 34570437 DOI: 10.1002/ps.6659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
In the arsenal of plant defense, protease inhibitors (PIs) are well-designed defensive products to counter field pests. PIs are produced in plant tissues by means of 'stable defense metabolite' and triggered on demand as the perception of the signal and well established as a part of plant active defense. PIs have been utilized for approximately four decades, initially as a gene-alone approach that was later replaced by multiple gene pyramiding/gene stacking due to insect adaptability towards the PI alone. By considering the adaptive responses of the pest to the single insecticidal gene, the concept of gene pyramiding gained continuous appreciation for the development of transgenic crops to deal with co-evolving pests. Gene pyramiding approaches are executed to bypass the insect's adaptive responses against PIs. Stacking PIs with additional insecticidal proteins, plastid engineering, recombinant proteinase inhibitors, RNAi-based methods and CRISPR/Cas9-mediated genome editing are the advanced tools and methods for next-generation pest management. Undoubtedly, the domain associated with the mechanism of PIs in the course of plant-pest interactions will occupy a central role for the advancement of more efficient and sustainable pest control strategies. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Ankesh Pandey
- CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Reena Yadav
- CSIR-National Botanical Research Institute, Lucknow, India
- Department of Biotechnology, Kumaun University, Nainital, India
| | - Indraneel Sanyal
- CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Gupta R, Kumari J, Pati S, Singh S, Mishra M, Ghosh SK. Interaction of cyclotide Kalata B1 protein with model cellular membranes of varied electrostatics. Int J Biol Macromol 2021; 191:852-860. [PMID: 34592223 DOI: 10.1016/j.ijbiomac.2021.09.147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/27/2022]
Abstract
A uni-molecular layer of lipids at air-water interface mimicking one of the leaflets of the cellular membrane provides a simple model to understand the interaction of any foreign molecules with the membrane. Here, the interactions of protein Kalata B1 (KB1) of cyclotide family with the phospholipids 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol) sodium salt (DPPG), and 1,2-distearoyl-sn-glycero-3-ethylphosphocholine chloride salt (DSEPC) have been investigated. The addition of KB1 induces a change in pressure of the lipid monolayers. The characteristic time of the change in pressure is found to be dependent on the electrostatic nature of the lipid. Even though the protein is weakly surface active, it is capable of modifying the phase behavior and elastic properties of lipid monolayers with differences in their strength and nature making the layers more floppy. The KB1-lipid interaction has been quantified by calculating the excess Gibb's free energy of interaction and the 1-anilino-8-naphthalenesulfonate (ANS) binding studies. The interaction with zwitterionic DPPC and negatively charged DPPG lipids are found to be thermodynamically favorable whereas the protein shows a weaker response to positively charged DSEPC lipid. Therefore, the long ranged electrostatic is the initial driving force for the KB1 to recognize and subsequently attach to a cellular membrane. Thereafter, the hydrophobic region of the protein may penetrate into the hydrophobic core of the membrane via specific amino acid residues.
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Affiliation(s)
- Ritika Gupta
- Department of Physics, School of Natural Sciences, Shiv Nadar University, NH-91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh 201314, India
| | - Jyoti Kumari
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, NH-91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh 201314, India
| | - Soumya Pati
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, NH-91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh 201314, India
| | - Shailja Singh
- Special Center for Molecular Medicine, Jawaharlal Nehru university, New Delhi 110067, India
| | - Manasi Mishra
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, NH-91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh 201314, India.
| | - Sajal K Ghosh
- Department of Physics, School of Natural Sciences, Shiv Nadar University, NH-91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh 201314, India.
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Ogbole OO, Akinleye TE, Nkumah AO, Awogun AO, Attah AF, Adewumi MO, Adeniji AJ. In vitro antiviral activity of peptide-rich extracts from seven Nigerian plants against three non-polio enterovirus species C serotypes. Virol J 2021; 18:161. [PMID: 34348755 PMCID: PMC8335448 DOI: 10.1186/s12985-021-01628-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/22/2021] [Indexed: 08/30/2023] Open
Abstract
Background As frequent viral outbreaks continue to pose threat to public health, the unavailability of antiviral drugs and challenges associated with vaccine development underscore the need for antiviral drugs discovery in emergent moments (endemic or pandemic). Plants in response to microbial and pest attacks are able to produce defence molecules such as antimicrobial peptides as components of their innate immunity, which can be explored for viral therapeutics. Methods In this study, partially purified peptide-rich fraction (P-PPf) were obtained from aqueous extracts of seven plants by reverse-phase solid-phase extraction and cysteine-rich peptides detected by a modified TLC method. The peptide-enriched fractions and the aqueous (crude polar) were screened for antiviral effect against three non-polio enterovirus species C members using cytopathic effect reduction assay. Results In this study, peptide fraction obtained from Euphorbia hirta leaf showed most potent antiviral effect against Coxsackievirus A13, Coxsackievirus A20, and Enterovirus C99 (EV-C99) with IC50 < 2.0 µg/mL and selective index ≥ 81. EV-C99 was susceptible to all partially purified peptide fractions except Allamanda blanchetii leaf. Conclusion These findings establish the antiviral potentials of plants antimicrobial peptides and provides evidence for the anti-infective use of E. hirta in ethnomedicine. This study provides basis for further scientific investigation geared towards the isolation, characterization and mechanistic pharmacological study of the detected cysteine-rich peptides.
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Affiliation(s)
- Omonike O Ogbole
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.
| | - Toluwanimi E Akinleye
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Abraham O Nkumah
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Aminat O Awogun
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Alfred F Attah
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Moses O Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Adekunle J Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria.,WHO Polio National Laboratory, Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
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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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Kalmankar NV, Hari H, Sowdhamini R, Venkatesan R. Disulfide-Rich Cyclic Peptides from Clitoria ternatea Protect against β-Amyloid Toxicity and Oxidative Stress in Transgenic Caenorhabditis elegans. J Med Chem 2021; 64:7422-7433. [PMID: 34048659 DOI: 10.1021/acs.jmedchem.1c00033] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Neurotoxic aggregation of β-amyloid (Aβ) peptides is a hallmark of Alzheimer's disease and increased reactive oxygen species (ROS) is an associated process. In the present study, we report the neuroprotective effects of disulfide-rich, circular peptides from Clitoria ternatea (C. ternatea) (butterfly pea) on Aβ-induced toxicity in transgenic Caenorhabditis elegans. Cyclotides (∼30 amino acids long) are a special class of cyclic cysteine knot peptides. We show that cyclotide-rich fractions from different plant tissues delay Aβ-induced paralysis in the transgenic CL4176 strain expressing the human muscle-specific Aβ1-42 gene. They also improved Aβ-induced chemotaxis defects in CL2355 strain expressing Aβ1-42 in the neuronal cells. ROS assay suggests that this protection is likely mediated by the inhibition of Aβ oligomerization. Furthermore, Aβ deposits were reduced in the CL2006 strain treated with the fractions. The study shows that cyclotides from C. ternatea could be a source of a novel pharmacophore scaffold against neurodegenerative diseases.
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Affiliation(s)
- Neha V Kalmankar
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), #74/2, Jarakabande Kaval, Post Attur, via Yelahanka, Bangalore, Karnataka 560064, India
| | - Hrudya Hari
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India
| | - Radhika Venkatesan
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India.,Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal 741246, India
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Computer-Aided Drug Discovery Identifies Alkaloid Inhibitors of Parkinson's Disease Associated Protein, Prolyl Oligopeptidase. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:6687572. [PMID: 33897801 PMCID: PMC8052153 DOI: 10.1155/2021/6687572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/25/2020] [Accepted: 02/19/2021] [Indexed: 01/18/2023]
Abstract
Parkinson's disease is a common neurodegenerative disorder marked by the accumulation of the protein alpha synuclein. Studies have indicated the role of prolyl oligopeptidase (POP), a serine protease, in alpha synuclein accumulation. Therefore, POP emerges as an attractive medicinal target. Traditionally, most of the early medicines have been plant-based owing to their ready availability and negligible side effects. Alkaloids owing to their neurotransmitter modulatory, anti-amyloid, anti-oxidant, and anti-inflammatory activities have shown potential in neurodegenerative disease. In this work, we computationally evaluated alkaloid class of phytochemicals for their therapeutic efficacy against POP. Alkaloids were retrieved from the publically available database, Chemical Entities of Biological Interest (ChEBI), and screened for their drug likeness (Lipinski's rule of 5) and absorption, distribution, metabolism, and excretion, and toxicity (ADMET) in Discovery Studio by ensuring parameters suitable for a central nervous system disease such as blood-brain barrier (BBB) level set to ≤2, absorption level set to 0 and solubility level permitted set to 2, 3, or 4. Next, molecular docking was performed to learn about the affinity of the filtered alkaloids with the POP. Subsequently, molecular dynamic simulations were conducted to assess the reliability and stability of the alkaloid-protein complex. Our study identified metergoline, pipercallosine, celacinnine, lobeline, cystodytin G, lycoperine A, hookerianamide J, and martefragin A as putative lead compounds against POP. Among these, metergoline, pipercallosine, hookerianamide J, and lobeline showed the most promising results. These compounds demonstrated better or equivalent molecular docking scores in comparison to three POP inhibitors that had reached clinical trials, i.e., Z-321, S-17092, and JTP-4819. MD simulations indicated that these compounds remained intact at the active site while adhering to the binding mode and interaction patterns as that of the reported inhibitors. The research conducted here, therefore, provides evidence for conducting in vitro POP inhibitory studies of these newly identified plant-based POP inhibitors.
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Dang TT, Chan LY, Tombling BJ, Harvey PJ, Gilding EK, Craik DJ. In Planta Discovery and Chemical Synthesis of Bracelet Cystine Knot Peptides from Rinorea bengalensis. JOURNAL OF NATURAL PRODUCTS 2021; 84:395-407. [PMID: 33570395 DOI: 10.1021/acs.jnatprod.0c01065] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cyclotides are plant-derived peptides that have attracted interest as biocides and scaffolds for the development of stable peptide therapeutics. Cyclotides are characterized by their cyclic backbone and cystine knot framework, which engenders them with remarkably high stability. This study reports the cystine knot-related peptidome of Rinorea bengalensis, a small rainforest tree in the Violaceae family that is distributed from Australia westward to India. Surprisingly, many more acyclic knotted peptides (acyclotides) were discovered than cyclic counterparts (cyclotides), with 32 acyclotides and 1 cyclotide sequenced using combined transcriptome and proteomic analyses. Nine acyclotides were isolated and screened against a panel of mammalian cell lines, showing they had the cytotoxic properties normally associated with cyclotide-like peptides. NMR analysis of the acyclotide ribes 21 and 22 and the cyclotide ribe 33 confirmed that these peptides contained the cystine knot structural motif. The bracelet-subfamily cyclotide ribe 33 was amenable to chemical synthesis in reasonable yield, an achievement that has long eluded previous attempts to synthetically produce bracelet cyclotides. Accordingly, ribe 33 represents an exciting new bracelet cyclotide scaffold that can be subject to chemical modification for future molecular engineering applications.
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Affiliation(s)
- Tien T Dang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lai Y Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin J Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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13
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Pinto MEF, Chan LY, Koehbach J, Devi S, Gründemann C, Gruber CW, Gomes M, Bolzani VS, Cilli EM, Craik DJ. Cyclotides from Brazilian Palicourea sessilis and Their Effects on Human Lymphocytes. JOURNAL OF NATURAL PRODUCTS 2021; 84:81-90. [PMID: 33397096 PMCID: PMC7836058 DOI: 10.1021/acs.jnatprod.0c01069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cyclotides are plant-derived peptides found within five families of flowering plants (Violaceae, Rubiaceae, Fabaceae, Solanaceae, and Poaceae) that have a cyclic backbone and six conserved cysteine residues linked by disulfide bonds. Their presence within the Violaceae species seems ubiquitous, yet not all members of other families produce these macrocyclic peptides. The genus Palicourea Aubl. (Rubiaceae) contains hundreds of neotropical species of shrubs and small trees; however, only a few cyclotides have been discovered hitherto. Herein, five previously uncharacterized Möbius cyclotides within Palicourea sessilis and their pharmacological activities are described. Cyclotides were isolated from leaves and stems of this plant and identified as pase A-E, as well as the known peptide kalata S. Cyclotides were de novo sequenced by MALDI-TOF/TOF mass spectrometry, and their structures were solved by NMR spectroscopy. Because some cyclotides have been reported to modulate immune cells, pase A-D were assayed for cell proliferation of human primary activated T lymphocytes, and the results showed a dose-dependent antiproliferative function. The toxicity on other nonimmune cells was also assessed. This study reveals that pase cyclotides have potential for applications as immunosuppressants and in immune-related disorders.
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Affiliation(s)
- Meri Emili F. Pinto
- Institute
of Chemistry, São Paulo State University−UNESP, Araraquara, 14800-060 SP, Brazil
- Institute
for Molecular Bioscience, Australian Research Council Centre of Excellence
for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, 4072 Queensland, Australia
- Phone: 55-16-33019510.
| | - Lai Yue Chan
- Institute
for Molecular Bioscience, Australian Research Council Centre of Excellence
for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Johannes Koehbach
- Institute
for Molecular Bioscience, Australian Research Council Centre of Excellence
for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Seema Devi
- Institute
for Infection Prevention and Hospital Epidemiology, Center for Complementary
Medicine, University of Freiburg, 79111 Freiburg, Germany
| | - Carsten Gründemann
- Translational
Complementary Medicine, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Christian W. Gruber
- Center
for Physiology and Pharmacology, Medical
University of Vienna, 1090 Vienna, Austria
| | - Mario Gomes
- Rio
de Janeiro
Botanic Garden Research Institute−JBRJ, Rio de Janeiro, 22470-180 RJ, Brazil
| | - Vanderlan S. Bolzani
- Institute
of Chemistry, São Paulo State University−UNESP, Araraquara, 14800-060 SP, Brazil
| | - Eduardo Maffud Cilli
- Institute
of Chemistry, São Paulo State University−UNESP, Araraquara, 14800-060 SP, Brazil
| | - 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, 4072 Queensland, Australia
- Phone: 61-7-3346-2019.
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14
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Retzl B, Hellinger R, Muratspahić E, Pinto MEF, Bolzani VS, Gruber CW. Discovery of a Beetroot Protease Inhibitor to Identify and Classify Plant-Derived Cystine Knot Peptides. JOURNAL OF NATURAL PRODUCTS 2020; 83:3305-3314. [PMID: 33118348 PMCID: PMC7705960 DOI: 10.1021/acs.jnatprod.0c00648] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Indexed: 05/04/2023]
Abstract
Plant peptide protease inhibitors are important molecules in seed storage metabolism and to fight insect pests. Commonly they contain multiple disulfide bonds and are exceptionally stable molecules. In this study, a novel peptide protease inhibitor from beetroot (Beta vulgaris) termed bevuTI-I was isolated, and its primary structure was determined via mass spectrometry-based amino acid sequencing. By sequence homology analysis a few peptides with high similarity to bevuTI-I, also known as the Mirabilis jalapa trypsin inhibitor subfamily of knottin-type protease inhibitors, were discovered. Hence, we assessed bevuTI-I for inhibitory activity toward trypsin (IC50 = 471 nM) and human prolyl oligopeptidase (IC50 = 11 μM), which is an emerging drug target for neurodegenerative and inflammatory disorders. Interestingly, using a customized bioinformatics approach, bevuTI-I was found to be the missing link to annotate 243 novel sequences of M. jalapa trypsin inhibitor-like peptides. According to their phylogenetic distribution they appear to be common in several plant families. Therefore, the presented approach and our results may help to discover and classify other plant-derived cystine knot peptides, a class of plant molecules that play important functions in plant physiology and are currently being explored as lead molecules and scaffolds in drug development.
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Affiliation(s)
- Bernhard Retzl
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Roland Hellinger
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Edin Muratspahić
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Meri E. F. Pinto
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
- Institute
of Chemistry, São Paulo State University-UNESP, 14800-060, Araraquara, SP, Brazil
| | - Vanderlan S. Bolzani
- Institute
of Chemistry, São Paulo State University-UNESP, 14800-060, Araraquara, SP, Brazil
| | - Christian W. Gruber
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
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15
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Shahin-Kaleybar B, Niazi A, Afsharifar A, Nematzadeh G, Yousefi R, Retzl B, Hellinger R, Muratspahić E, Gruber CW. Isolation of Cysteine-Rich Peptides from Citrullus colocynthis. Biomolecules 2020; 10:E1326. [PMID: 32948080 PMCID: PMC7565491 DOI: 10.3390/biom10091326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022] Open
Abstract
The plant Citrullus colocynthis, a member of the squash (Cucurbitaceae) family, has a long history in traditional medicine. Based on the ancient knowledge about the healing properties of herbal preparations, plant-derived small molecules, e.g., salicylic acid, or quinine, have been integral to modern drug discovery. Additionally, many plant families, such as Cucurbitaceae, are known as a rich source for cysteine-rich peptides, which are gaining importance as valuable pharmaceuticals. In this study, we characterized the C. colocynthis peptidome using chemical modification of cysteine residues, and mass shift analysis via matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. We identified the presence of at least 23 cysteine-rich peptides in this plant, and eight novel peptides, named citcol-1 to -8, with a molecular weight between ~3650 and 4160 Da, were purified using reversed-phase high performance liquid chromatography (HPLC), and their amino acid sequences were determined by de novo assignment of b- and y-ion series of proteolytic peptide fragments. In silico analysis of citcol peptides revealed a high sequence similarity to trypsin inhibitor peptides from Cucumis sativus, Momordica cochinchinensis, Momordica macrophylla and Momordica sphaeroidea. Using genome/transcriptome mining it was possible to identify precursor sequences of this peptide family in related Cucurbitaceae species that cluster into trypsin inhibitor and antimicrobial peptides. Based on our analysis, the presence or absence of a crucial Arg/Lys residue at the putative P1 position may be used to classify these common cysteine-rich peptides by functional properties. Despite sequence homology and the common classification into the inhibitor cysteine knot family, these peptides appear to have diverse and additional bioactivities yet to be revealed.
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Affiliation(s)
- Behzad Shahin-Kaleybar
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria; (B.S.-K.); (B.R.); (R.H.); (E.M.)
- Department of Plant Biotechnology, Shiraz University, Shiraz 7144165186, Iran;
| | - Ali Niazi
- Department of Plant Biotechnology, Shiraz University, Shiraz 7144165186, Iran;
| | - Alireza Afsharifar
- Department of Plant Protection, Shiraz University, Shiraz 7144165186, Iran;
| | | | - Reza Yousefi
- Department of Biology, Shiraz University, Shiraz 7194684795, Iran;
| | - Bernhard Retzl
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria; (B.S.-K.); (B.R.); (R.H.); (E.M.)
| | - Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria; (B.S.-K.); (B.R.); (R.H.); (E.M.)
| | - Edin Muratspahić
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria; (B.S.-K.); (B.R.); (R.H.); (E.M.)
| | - Christian W. Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria; (B.S.-K.); (B.R.); (R.H.); (E.M.)
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16
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Dang TT, Chan LY, Huang YH, Nguyen LTT, Kaas Q, Huynh T, Craik DJ. Exploring the Sequence Diversity of Cyclotides from Vietnamese Viola Species. JOURNAL OF NATURAL PRODUCTS 2020; 83:1817-1828. [PMID: 32437150 DOI: 10.1021/acs.jnatprod.9b01218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Viola is the largest genus in the Violaceae plant family and is known for its ubiquitous natural production of cyclotides. Many Viola species are used as medicinal herbs across Asia and are often consumed by humans in teas for the treatment of diseases, including ulcers and asthma. Previous studies reported the isolation of cyclotides from Viola species in many countries in the hope of discovering novel compounds with anti-cancer activities; however, Viola species from Vietnam have not been investigated to date. Here, the discovery of cyclotides from three Viola species (V. arcuata, V. tonkinensis, and V. austrosinensis) collected in the northern mountainous region of Vietnam is reported. Ten cyclotides were isolated from these three Viola species: four are novel and six were previously reported to be expressed in other plants. The structures of three of the new bracelet cyclotides are similar to that of cycloviolacin O2. Because cycloviolacin O2 has previously been shown to have potent activity against a wide range of cancer cell lines including HeLa (human cervical cancer cells) and PC-3 (human prostate cancer cells), the cancer cytotoxicity of the cyclotides isolated from V. arcuata was assessed. All tested cyclotides were cytotoxic against cancer cells, albeit to varying degrees. The sequences discovered in this study significantly expand the understanding of cyclotide diversity, especially in comparison with other cyclotides found in plants from the Asian region.
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Affiliation(s)
- Tien T Dang
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lai Y Chan
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Linh T T Nguyen
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Tien Huynh
- Department of Biosciences and Food Technology, RMIT University, Victoria 3001, Australia
| | - David J Craik
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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17
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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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18
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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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19
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Hellinger R, Gruber CW. Peptide-based protease inhibitors from plants. Drug Discov Today 2019; 24:1877-1889. [PMID: 31170506 PMCID: PMC6753016 DOI: 10.1016/j.drudis.2019.05.026] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/03/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023]
Abstract
Proteases have an important role in homeostasis, and dysregulation of protease function can lead to pathogenesis. Therefore, proteases are promising drug targets in cancer, inflammation, and neurodegenerative disease research. Although there are well-established pharmaceuticals on the market, drug development for proteases is challenging. This is often caused by the limited selectivity of currently available lead compounds. Proteinaceous plant protease inhibitors are a diverse family of (poly)peptides that are important to maintain physiological homeostasis and to serve the innate defense machinery of the plant. In this review, we provide an overview of the diversity of plant peptide- and protein-based protease inhibitors (PIs), provide examples of such compounds that target human proteases, and discuss opportunities for these molecules in protease drug discovery and development.
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Affiliation(s)
- Roland Hellinger
- Center for Pharmacology and Physiology, Medical University of Vienna, Schwarzspanierstr. 17, 1090 Vienna, Austria
| | - Christian W Gruber
- Center for Pharmacology and Physiology, Medical University of Vienna, Schwarzspanierstr. 17, 1090 Vienna, Austria.
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20
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Camarero JA, Campbell MJ. The Potential of the Cyclotide Scaffold for Drug Development. Biomedicines 2019; 7:biomedicines7020031. [PMID: 31010257 PMCID: PMC6631875 DOI: 10.3390/biomedicines7020031] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Cyclotides are a novel class of micro-proteins (≈30-40 residues long) with a unique topology containing a head-to-tail cyclized backbone structure further stabilized by three disulfide bonds that form a cystine knot. This unique molecular framework makes them exceptionally stable to physical, chemical, and biological degradation compared to linear peptides of similar size. The cyclotides are also highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot, and are orally bioavailable and able to cross cellular membranes to modulate intracellular protein-protein interactions (PPIs), both in vitro and in vivo. These unique properties make them ideal scaffolds for many biotechnological applications, including drug discovery. This review provides an overview of the properties of cyclotides and their potential for the development of novel peptide-based therapeutics. The selective disruption of PPIs still remains a very challenging task, as the interacting surfaces are relatively large and flat. The use of the cell-permeable highly constrained polypeptide molecular frameworks, such as the cyclotide scaffold, has shown great promise, as it provides unique pharmacological properties. The use of molecular techniques, such as epitope grafting, and molecular evolution have shown to be highly effective for the selection of bioactive cyclotides. However, despite successes in employing cyclotides to target PPIs, some of the challenges to move them into the clinic still remain.
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Affiliation(s)
- Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Los Angeles, CA 9033, USA.
| | - Maria Jose Campbell
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA.
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21
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Huang J, Wong KH, Tay SV, Serra A, Sze SK, Tam JP. Astratides: Insulin-Modulating, Insecticidal, and Antifungal Cysteine-Rich Peptides from Astragalus membranaceus. JOURNAL OF NATURAL PRODUCTS 2019; 82:194-204. [PMID: 30758201 DOI: 10.1021/acs.jnatprod.8b00521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Astragalus membranaceus root, Huang Qi in Chinese, is a popular medicinal herb traditionally used to regulate blood glucose. Herein, the identification and characterization of two families of cysteine-rich peptides (CRPs), designated α- and β-astratides, from A. membranaceus roots are reported. Proteomic analysis showed that α-astratide aM1 and β-astratide bM1 belong to two distinct CRP families. The six-cysteine-containing and proline-rich α-astratide aM1 displayed high sequence identity to Pea Albumin 1 Subunit b (PA1b), while the eight-cysteine-containing β-astratide bM1 showed sequence similarity to plant defensins. An antifungal assay revealed that bM1 possessed potent antifungal activity. In contrast, aM1 showed a cytotoxic effect against insect Sf9 cells. More importantly, aM1 decreased insulin secretion in mouse pancreatic β cells, suggesting it could interfere in glucose homeostasis, which accounts for the adaptogenic property of A. membranaceus. Phylogenetic clustering analysis suggested that the proline-rich aM1 is a putative prolyl oligopeptidase inhibitor and belongs to a novel subfamily of PA1b-like peptides, while bM1 belongs to a new subfamily of plant defensins. Together, the study reveals that astratides are multifunctional CRPs in plants, which expand the existing library of PA1b-like peptides and plant defensins and further our understanding of their roles in host-defense system and leads as peptidyl therapeutics.
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Affiliation(s)
- Jiayi Huang
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Ka H Wong
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Stephanie V Tay
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Aida Serra
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Siu Kuan Sze
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - James P Tam
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
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22
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Ramalho SD, Wang CK, King GJ, Byriel KA, Huang YH, Bolzani VS, Craik DJ. Synthesis, Racemic X-ray Crystallographic, and Permeability Studies of Bioactive Orbitides from Jatropha Species. JOURNAL OF NATURAL PRODUCTS 2018; 81:2436-2445. [PMID: 30345754 DOI: 10.1021/acs.jnatprod.8b00447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Orbitides are small cyclic peptides with a diverse range of therapeutic bioactivities. They are produced by many plant species, including those of the Jatropha genus. Here, the objective was to provide new structural information on orbitides to complement the growing knowledge base on orbitide sequences and activities by focusing on three Jatropha orbitides: ribifolin (1), pohlianin C (7), and jatrophidin (12). To determine three-dimensional structures, racemic crystallography, an emerging structural technique that enables rapid crystallization of biomolecules by combining equal amounts of the two enantiomers, was used. The high-resolution structure of ribifolin (0.99 Å) was elucidated from its racemate and showed it was identical to the structure crystallized from its l-enantiomer only (1.35 Å). Racemic crystallography was also used to elucidate high-resolution structures of pohlianin C (1.20 Å) and jatrophidin (1.03 Å), for which there was difficulty forming crystals without using racemic mixtures. The structures were used to interpret membrane permeability data in PAMPA and a Caco-2 cell assay, showing they had poor permeability. Overall, the results show racemic crystallography can be used to obtain high-resolution structures of orbitides and is useful when enantiopure samples are difficult to crystallize or solution structures from NMR are of low resolution.
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Affiliation(s)
- Suelem D Ramalho
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Gordon J King
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Karl A Byriel
- 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
| | - Vanderlan S Bolzani
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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23
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Synthesis of polyozellin, a prolyl oligopeptidase inhibitor, and its structural revision. Bioorg Med Chem Lett 2018; 28:930-933. [PMID: 29429833 DOI: 10.1016/j.bmcl.2018.01.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/24/2018] [Accepted: 01/26/2018] [Indexed: 11/23/2022]
Abstract
Polyozellin is a p-terphenyl compound which was isolated from Polyozellus multiplex, and exhibits an inhibitory activity against prolyl oligopeptidase (POP). Its structure was assigned as 1 having a p-terphenyl skeleton including a p-substituted dibenzofuran moiety by spectroscopic analyses and chemical means. This paper describes the total syntheses of the proposed structure 1 for polyozellin and its o-isomer 2, revising the structure of polyozellin to the latter. These syntheses involved a double Suzuki-Miyaura coupling using chlorophenylboronic acid as a common key building block, and Cu mediated Ullmann cyclization as key steps. The inhibitory activities of synthetic compounds against POP and cancer cells were also evaluated.
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24
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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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25
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Fahradpour M, Keov P, Tognola C, Perez-Santamarina E, McCormick PJ, Ghassempour A, Gruber CW. Cyclotides Isolated from an Ipecac Root Extract Antagonize the Corticotropin Releasing Factor Type 1 Receptor. Front Pharmacol 2017; 8:616. [PMID: 29033832 PMCID: PMC5627009 DOI: 10.3389/fphar.2017.00616] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/23/2017] [Indexed: 12/22/2022] Open
Abstract
Cyclotides are plant derived, cystine-knot stabilized peptides characterized by their natural abundance, sequence variability and structural plasticity. They are abundantly expressed in Rubiaceae, Psychotrieae in particular. Previously the cyclotide kalata B7 was identified to modulate the human oxytocin and vasopressin G protein-coupled receptors (GPCRs), providing molecular validation of the plants' uterotonic properties and further establishing cyclotides as valuable source for GPCR ligand design. In this study we screened a cyclotide extract derived from the root powder of the South American medicinal plant ipecac (Carapichea ipecacuanha) for its GPCR modulating activity of the corticotropin-releasing factor type 1 receptor (CRF1R). We identified and characterized seven novel cyclotides. One cyclotide, caripe 8, isolated from the most active fraction, was further analyzed and found to antagonize the CRF1R. A nanomolar concentration of this cyclotide (260 nM) reduced CRF potency by ∼4.5-fold. In contrast, caripe 8 did not inhibit forskolin-, or vasopressin-stimulated cAMP responses at the vasopressin V2 receptor, suggesting a CRF1R-specific mode-of-action. These results in conjunction with our previous findings establish cyclotides as modulators of both classes A and B GPCRs. Given the diversity of cyclotides, our data point to other cyclotide-GPCR interactions as potentially important sources of drug-like molecules.
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Affiliation(s)
- Mohsen Fahradpour
- Center for Physiology and Pharmacology, Medical University of ViennaVienna, Austria.,Medicinal Plants and Drugs Research Institute, Shahid Beheshti UniversityTehran, Iran
| | - Peter Keov
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, BrisbaneQLD, Australia
| | - Carlotta Tognola
- Center for Physiology and Pharmacology, Medical University of ViennaVienna, Austria
| | | | - Peter J McCormick
- School of Veterinary Medicine, University of SurreyGuildford, United Kingdom
| | - Alireza Ghassempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti UniversityTehran, Iran
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of ViennaVienna, Austria.,Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, BrisbaneQLD, Australia
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26
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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: 31] [Impact Index Per Article: 4.4] [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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27
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Molesini B, Treggiari D, Dalbeni A, Minuz P, Pandolfini T. Plant cystine-knot peptides: pharmacological perspectives. Br J Clin Pharmacol 2017; 83:63-70. [PMID: 26987851 PMCID: PMC5338163 DOI: 10.1111/bcp.12932] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/07/2016] [Accepted: 03/09/2016] [Indexed: 12/29/2022] Open
Abstract
Cystine-knot miniproteins are a class of 30-50 amino acid long peptides widespread in eukaryotic organisms. Due to their very peculiar three-dimensional structure, they exhibit high resistance to heat and peptidase attack. The cystine-knot peptides are well represented in several plant species including medicinal herbs and crops. The pharmacological interest in plant cystine-knot peptides derives from their broad biological activities, mainly cytotoxic, antimicrobial and peptidase inhibitory and in the possibility to engineer them to incorporate pharmacophoric information for oral delivery or disease biomonitoring. The mechanisms of action of plant cystine-knot peptides are still largely unknown, although the capacity to interfere with plasma membranes seems a feature common to several cystine-knot peptides. In some cases, such as potato carboxypetidase inhibitor (PCI) and tomato cystine-knot miniproteins (TCMPs), the cystine-knot peptides target human growth factor receptors either by acting as growth factor antagonist or by altering their signal transduction pathway. The possibility to identify specific molecular targets of plant cystine-knot peptides in human cells opens novel possibilities for the pharmacological use of these peptides besides their use as scaffold to develop stable disease molecular markers and therapeutic agents.
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Affiliation(s)
| | - Davide Treggiari
- Department of Medicine, Section of Internal MedicineUniversity of VeronaVeronaItaly
| | - Andrea Dalbeni
- Department of Medicine, Section of Internal MedicineUniversity of VeronaVeronaItaly
| | - Pietro Minuz
- Department of Medicine, Section of Internal MedicineUniversity of VeronaVeronaItaly
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28
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Matsuura HN, Poth AG, Yendo ACA, Fett-Neto AG, Craik DJ. Isolation and Characterization of Cyclotides from Brazilian Psychotria: Significance in Plant Defense and Co-occurrence with Antioxidant Alkaloids. JOURNAL OF NATURAL PRODUCTS 2016; 79:3006-3013. [PMID: 28006906 DOI: 10.1021/acs.jnatprod.6b00492] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plants from the genus Psychotria include species bearing cyclotides and/or alkaloids. The elucidation of factors affecting the metabolism of these molecules as well as their activities may help to understand their ecological function. In the present study, high concentrations of antioxidant indole alkaloids were found to co-occur with cyclotides in Psychotria leiocarpa and P. brachyceras. The concentrations of the major cyclotides and alkaloids in P. leiocarpa and P. brachyceras were monitored following herbivore- and pathogen-associated challenges, revealing a constitutive, phytoanticipin-like accumulation pattern. Psyleio A, the most abundant cyclotide found in the leaves of P. leiocarpa, and also found in P. brachyceras leaves, exhibited insecticidal activity against Helicoverpa armigera larvae. Addition of ethanol in the vehicle for peptide solubilization in larval feeding trials proved deleterious to insecticidal activity and resulted in increased rates of larval survival in treatments containing indole alkaloids. This suggests that plant alkaloids ingested by larvae might contribute to herbivore oxidative stress detoxification, corroborating, in a heterologous system with artificial oxidative stress stimulation, the antioxidant efficiency of Psychotria alkaloids previously observed in planta. Overall, the present study reports data for eight novel cyclotides, the identification of P. leiocarpa as a cyclotide-bearing species, and the absence of these peptides in P. umbellata.
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Affiliation(s)
- Hélio N Matsuura
- Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul , Porto Alegre, RS, Brazil
| | - Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD, Australia
| | - Anna C A Yendo
- Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul , Porto Alegre, RS, Brazil
| | - Arthur G Fett-Neto
- Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul , Porto Alegre, RS, Brazil
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD, Australia
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29
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Niyomploy P, Chan LY, Poth AG, Colgrave ML, Sangvanich P, Craik DJ. Discovery, isolation, and structural characterization of cyclotides from
Viola sumatrana
Miq. Pept Sci (Hoboken) 2016; 106:796-805. [DOI: 10.1002/bip.22914] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/21/2016] [Accepted: 06/29/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Ploypat Niyomploy
- Institute for Molecular Bioscience, The University of QueenslandBrisbane QLD4072 Australia
- Department of Chemistry, Faculty of ScienceChulalongkorn UniversityBangkok10330 Thailand
| | - Lai Yue Chan
- Institute for Molecular Bioscience, The University of QueenslandBrisbane QLD4072 Australia
| | - Aaron G. Poth
- Institute for Molecular Bioscience, The University of QueenslandBrisbane QLD4072 Australia
| | | | - Polkit Sangvanich
- Department of Chemistry, Faculty of ScienceChulalongkorn UniversityBangkok10330 Thailand
| | - David J. Craik
- Institute for Molecular Bioscience, The University of QueenslandBrisbane QLD4072 Australia
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30
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Cabrera-Muñoz A, Rojas L, Gil DF, González-González Y, Mansur M, Camejo A, Pires JR, Alonso-Del-Rivero Antigua M. Heterologous expression of Cenchritis muricatus protease inhibitor II (CmPI-II) in Pichia pastoris system: Purification, isotopic labeling and preliminary characterization. Protein Expr Purif 2016; 126:127-136. [PMID: 27353494 DOI: 10.1016/j.pep.2016.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 10/21/2022]
Abstract
Cenchritis muricatus protease inhibitor II (CmPI-II) is a tight-binding serine protease inhibitor of the Kazal family with an atypical broad specificity, being active against several proteases such as bovine pancreatic trypsin, human neutrophil elastase and subtilisin A. CmPI-II 3D structures are necessary for understanding the molecular basis of its activity. In the present work, we describe an efficient and straightforward recombinant expression strategy, as well as a cost-effective procedure for isotope labeling for NMR structure determination purposes. The vector pCM101 containing the CmPI-II gene, under the control of Pichia pastoris AOX1 promoter was constructed. Methylotrophic Pichia pastoris strain KM71H was then transformed with the plasmid and the recombinant protein (rCmPI-II) was expressed in benchtop fermenter in unlabeled or (15)N-labeled forms using ammonium chloride ((15)N, 99%) as the sole nitrogen source. Protein purification was accomplished by sequential cation exchange chromatography in STREAMLINE DirectHST, anion exchange chromatography on Hitrap Q-Sepharose FF and gel filtration on Superdex 75 10/30, yielding high quantities of pure rCmPI-II and (15)N rCmPI-II. Recombinant proteins displayed similar functional features as compared to the natural inhibitor and NMR spectra indicated folded and homogeneously labeled samples, suitable for further studies of structure and protease-inhibitor interactions.
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Affiliation(s)
- Aymara Cabrera-Muñoz
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - Laritza Rojas
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - Dayrom F Gil
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - Yamile González-González
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - Manuel Mansur
- Institut de Biotecnología i de Biomedicina, Universitat Autònoma de Barcelona, Campus Universitari, 08193, Bellaterra, Cerdanyola del Vallès, Barcelona, Spain.
| | - Ayamey Camejo
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - José R Pires
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Bloco E, Sala 10, 21941-902, Rio de Janeiro, RJ, Brazil.
| | - Maday Alonso-Del-Rivero Antigua
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
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31
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Hellinger R, Koehbach J, Soltis DE, Carpenter EJ, Wong GKS, Gruber CW. Peptidomics of Circular Cysteine-Rich Plant Peptides: Analysis of the Diversity of Cyclotides from Viola tricolor by Transcriptome and Proteome Mining. J Proteome Res 2015; 14:4851-62. [PMID: 26399495 PMCID: PMC4642221 DOI: 10.1021/acs.jproteome.5b00681] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Cyclotides are plant-derived mini proteins. They are genetically
encoded as precursor proteins that become post-translationally modified
to yield circular cystine-knotted molecules. Because of this structural
topology cyclotides resist enzymatic degradation in biological fluids,
and hence they are considered as promising lead molecules for pharmaceutical
applications. Despite ongoing efforts to discover novel cyclotides
and analyze their biodiversity, it is not clear how many individual
peptides a single plant specimen can express. Therefore, we investigated
the transcriptome and cyclotide peptidome of Viola tricolor. Transcriptome mining enabled the characterization of cyclotide
precursor architecture and processing sites important for biosynthesis
of mature peptides. The cyclotide peptidome was explored by mass spectrometry
and bottom-up proteomics using the extracted peptide sequences as
queries for database searching. In total 164 cyclotides were discovered
by nucleic acid and peptide analysis in V. tricolor. Therefore, violaceous plants at a global scale may be the source
to as many as 150 000 individual cyclotides. Encompassing the
diversity of V. tricolor as a combinatorial library
of bioactive peptides, this commercially available medicinal herb
may be a suitable starting point for future bioactivity-guided screening
studies.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Koehbach
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria.,School of Biomedical Sciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida , Gainesville, Florida 32611, United States
| | - Eric J Carpenter
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta T6G 2E9, Canada
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta T6G 2E9, Canada.,Department of Medicine, University of Alberta , Edmonton, Alberta T6G 2E1, Canada.,BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria.,School of Biomedical Sciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
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