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Chekan JR, Mydy LS, Pasquale MA, Kersten RD. Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides. Nat Prod Rep 2024; 41:1020-1059. [PMID: 38411572 PMCID: PMC11253845 DOI: 10.1039/d3np00042g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Indexed: 02/28/2024]
Abstract
Covering 1965 to February 2024Plants are prolific peptide chemists and are known to make thousands of different peptidic molecules. These peptides vary dramatically in their size, chemistry, and bioactivity. Despite their differences, all plant peptides to date are biosynthesized as ribosomally synthesized and post-translationally modified peptides (RiPPs). Decades of research in plant RiPP biosynthesis have extended the definition and scope of RiPPs from microbial sources, establishing paradigms and discovering new families of biosynthetic enzymes. The discovery and elucidation of plant peptide pathways is challenging due to repurposing and evolution of housekeeping genes as both precursor peptides and biosynthetic enzymes and due to the low rates of gene clustering in plants. In this review, we highlight the chemistry, biosynthesis, and function of the known RiPP classes from plants and recommend a nomenclature for the recent addition of BURP-domain-derived RiPPs termed burpitides. Burpitides are an emerging family of cyclic plant RiPPs characterized by macrocyclic crosslinks between tyrosine or tryptophan side chains and other amino acid side chains or their peptide backbone that are formed by copper-dependent BURP-domain-containing proteins termed burpitide cyclases. Finally, we review the discovery of plant RiPPs through bioactivity-guided, structure-guided, and gene-guided approaches.
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Affiliation(s)
- Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Michael A Pasquale
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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2
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Sharma A, Butool B, Sahu P, Mishra R, Mohanty A. In Silico Analysis of Natural Plant-Derived Cyclotides with Antifungal Activity against Pathogenic Fungi. Protein Pept Lett 2024; 31:247-260. [PMID: 38445693 DOI: 10.2174/0109298665295545240223114346] [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: 12/02/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Fungal infections in plants, animals, and humans are widespread across the world. Limited classes of antifungal drugs to treat fungal infections and loss of drug efficacy due to rapidly evolving fungal strains pose a challenge in the agriculture and health sectors. Hence, the search for a new class of antifungal agents is imperative. Cyclotides are cyclic plant peptides with multiple bioactivities, including antifungal activity. They have six conserved cysteine residues forming three disulfide linkages (CI-CIV, CII-CV, CIII-CVI) that establish a Cyclic Cystine Knot (CCK) structure, making them extremely resistant to chemical, enzymatic, and thermal attacks. AIM This in silico analysis of natural, plant-derived cyclotides aimed to assess the parameters that can assist and hasten the process of selecting the cyclotides with potent antifungal activity and prioritize them for in vivo/ in vitro experiments. OBJECTIVE The objective of this study was to conduct in silico studies to compare the physicochemical parameters, sequence diversity, surface structures, and membrane-cyclotide interactions of experimentally screened (from literature survey) potent (MIC ≤ 20 μM) and non-potent (MIC > 20 μM) cyclotides for antifungal activity. METHODOLOGY Cyclotide sequences assessed for antifungal activity were retrieved from the database (Cybase). Various online and offline tools were used for sequence-based studies, such as physicochemical parameters, sequence diversity, and neighbor-joining trees. Structure-based studies involving surface structure analysis and membrane-cyclotide interaction were also carried out. All investigations were conducted in silico. RESULTS Physicochemical parameter values, viz. isoelectric point, net charge, and the number of basic amino acids, were significantly higher in potent cyclotides compared to non-potent cyclotides. The surface structure of potent cyclotides showed a larger hydrophobic patch with a higher number of hydrophobic amino acids. Furthermore, the membrane-cyclotide interaction studies of potent cyclotides revealed lower transfer free energy (ΔG transfer) and higher penetration depth into fungal membranes, indicating higher binding stability and membrane-disruption ability. CONCLUSION These in silico studies can be applied for rapidly identifying putatively potent antifungal cyclotides for in vivo and in vitro experiments, which will ultimately be relevant in the agriculture and pharmaceutical sectors.
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Affiliation(s)
- Akshita Sharma
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Bisma Butool
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Pallavi Sahu
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Reema Mishra
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Aparajita Mohanty
- Department of Botany, Gargi College, University of Delhi, Delhi, India
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Salah A, El-Khateeb EA, Gaafar RM, Mohamed Atia MA. Genome-wide in silico and in vitro mining to develop a novel cyclotide-based marker system in plants. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2023.2176175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Affiliation(s)
- Arwa Salah
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | | | | | - Mohamed Atia Mohamed Atia
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
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Attah FA, Lawal BA, Yusuf AB, Adedeji OJ, Folahan JT, Akhigbe KO, Roy T, Lawal AA, Ogah NB, Olorundare OE, Chamcheu JC. Nutritional and Pharmaceutical Applications of Under-Explored Knottin Peptide-Rich Phytomedicines. PLANTS (BASEL, SWITZERLAND) 2022; 11:3271. [PMID: 36501311 PMCID: PMC9737898 DOI: 10.3390/plants11233271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/02/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Phytomedicines reportedly rich in cystine knot peptides (Knottins) are found in several global diets, food/herbal supplements and functional foods. However, their knottin peptide content has largely been unexplored, notably for their emerging dual potentials at both the food and medicine space. The nutritional roles, biological targets and mechanism(s) of activity of these knotted peptides are largely unknown. Meanwhile, knottins have recently been unveiled as emerging peptide therapeutics and nutraceuticals of primary choice due to their broad spectrum of bioactivity, hyper stability, selective toxicity, impressive selectivity for biomolecular targets, and their bioengineering applications. In addition to their potential dietary benefits, some knottins have displayed desirable limited toxicity to human erythrocytes. In an effort to appraise what has been accomplished, unveil knowledge gaps and explore the future prospects of knottins, an elaborate review of the nutritional and pharmaceutical application of phytomedicines rich in knottins was carried out. Herein, we provide comprehensive data on common dietary and therapeutic knottins, the majority of which are poorly investigated in many food-grade phytomedicines used in different cultures and localities. Findings from this review should stimulate scientific interest to unveil novel dietary knottins and knottin-rich nutraceutical peptide drug candidates/leads with potential for future clinical application.
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Affiliation(s)
- Francis Alfred Attah
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Bilqis Abiola Lawal
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Abdulmalik Babatunde Yusuf
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Oluwakorede Joshua Adedeji
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Joy Temiloluwa Folahan
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana-Monroe, Monroe, LA 71209, USA
| | - Kelvin Oluwafemi Akhigbe
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Tithi Roy
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana-Monroe, Monroe, LA 71209, USA
| | - Azeemat Adeola Lawal
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Ngozi Blessing Ogah
- Department of Biotechnology, Ebonyi State University, Abakaliki 480101, Nigeria
| | | | - Jean Christopher Chamcheu
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana-Monroe, Monroe, LA 71209, USA
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5
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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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Rajendran S, Slazak B, Mohotti S, Strömstedt AA, Göransson U, Hettiarachchi CM, Gunasekera S. Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis. PHYTOCHEMISTRY 2021; 187:112749. [PMID: 33932786 DOI: 10.1016/j.phytochem.2021.112749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Cyclotides are an extremely stable class of peptides, ubiquitously distributed in Violaceae. The aim of the present study was to investigate the presence of cyclotides in Sri Lankan Violaceae plants, using combined tools of transcriptomics and mass spectrometry. New cyclotides were discovered for the first time in the wild flora of Sri Lanka, within Viola betonicifolia, a plant used in traditional medicine as an antimicrobial. Plant extracts prepared in small scale from Viola betonicifolia were first subjected to LC-MS analysis. Subsequent transcriptome de novo sequencing of Viola betonicifolia uncovered 25 new (vibe 1-25) and three known (varv A/kalata S, viba 17, viba 11) peptide sequences from Möbius and bracelet cyclotide subfamilies as well as hybrid cyclotides. Among the transcripts, putative linear acyclotide sequences (vibe 4, vibe 10, vibe 11 and vibe 22) that lack a conserved asparagine or aspartic acid vital for cyclisation were also present. Four asparagine endopeptidases (AEPs), VbAEP1-4 were found within the Viola betonicifolia transcriptome, including a peptide asparaginyl ligase (PAL), potentially involved in cyclotide backbone cyclisation, showing >93% sequence homology to Viola yedoensis peptide asparaginyl ligases, VyPALs. In addition, we identified two protein disulfide isomerases (PDIs), VbPDI1-2, likely involved in cyclotide oxidative folding, having high sequence homology (>74%) with previously reported Rubiaceae and Violaceae PDIs. The current study highlights the ubiquity of cyclotides in Violaceae as well as the utility of transcriptomic analysis for cyclotides and their putative processing enzyme discovery. The high variability of cyclotide sequences in terms of loop sizes and residues in V. betonicifolia showcase the cyclotide structure as an adaptable scaffold as well as their importance as a combinatorial library, implicated in plant defense.
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Affiliation(s)
- Sanjeevan Rajendran
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden; Department of Chemistry, Faculty of Science, University of Colombo, Thurston Rd, Colombo 03, Sri Lanka
| | - Blazej Slazak
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden; W. Szafer Institute of Botany, Polish Academy of Science, 46 Lubicz St., 31-512, Cracow, Poland
| | - Supun Mohotti
- Department of Chemistry, Faculty of Science, University of Colombo, Thurston Rd, Colombo 03, Sri Lanka
| | - Adam A Strömstedt
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden
| | - Ulf Göransson
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden
| | - Chamari M Hettiarachchi
- Department of Chemistry, Faculty of Science, University of Colombo, Thurston Rd, Colombo 03, Sri Lanka
| | - Sunithi Gunasekera
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden.
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7
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Comparison of a Short Linear Antimicrobial Peptide with Its Disulfide-Cyclized and Cyclotide-Grafted Variants against Clinically Relevant Pathogens. Microorganisms 2021; 9:microorganisms9061249. [PMID: 34201398 PMCID: PMC8228819 DOI: 10.3390/microorganisms9061249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
According to the World Health Organization (WHO) the development of resistance against antibiotics by microbes is one of the most pressing health concerns. The situation will intensify since only a few pharmacological companies are currently developing novel antimicrobial compounds. Discovery and development of novel antimicrobial compounds with new modes of action are urgently needed. Antimicrobial peptides (AMPs) are known to be able to kill multidrug-resistant bacteria and, therefore, of interest to be developed into antimicrobial drugs. Proteolytic stability and toxicities of these peptides are challenges to overcome, and one strategy frequently used to address stability is cyclization. Here we introduced a disulfide-bond to cyclize a potent and nontoxic 9mer peptide and, in addition, as a proof-of-concept study, grafted this peptide into loop 6 of the cyclotide MCoTI-II. This is the first time an antimicrobial peptide has been successfully grafted onto the cyclotide scaffold. The disulfide-cyclized and grafted cyclotide showed moderate activity in broth and strong activity in 1/5 broth against clinically relevant resistant pathogens. The linear peptide showed superior activity in both conditions. The half-life time in 100% human serum was determined, for the linear peptide, to be 13 min, for the simple disulfide-cyclized peptide, 9 min, and, for the grafted cyclotide 7 h 15 min. The addition of 10% human serum led to a loss of antimicrobial activity for the different organisms, ranging from 1 to >8-fold for the cyclotide. For the disulfide-cyclized version and the linear version, activity also dropped to different degrees, 2 to 18-fold, and 1 to 30-fold respectively. Despite the massive difference in stability, the linear peptide still showed superior antimicrobial activity. The cyclotide and the disulfide-cyclized version demonstrated a slower bactericidal effect than the linear version. All three peptides were stable at high and low pH, and had very low hemolytic and cytotoxic activity.
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8
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Grover T, Mishra R, Gulati P, Mohanty A. An insight into biological activities of native cyclotides for potential applications in agriculture and pharmaceutics. Peptides 2021; 135:170430. [PMID: 33096195 DOI: 10.1016/j.peptides.2020.170430] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023]
Abstract
Cyclotides are plant-derived mini-proteins of 28 - 37 amino acids. They have a characteristic head-to-tail cyclic backbone and three disulfide cross-linkages formed by six highly conserved cysteine residues, creating a unique knotted ring structure, known as a cyclic cystine knot (CCK) motif. The CCK topology confers immense stability to cyclotides with resistance to thermal and enzymatic degradation. Native cyclotides are of interest due to their multiple biological activities with several potential applications in agricultural (e.g. biopesticides, antifungal) and pharmaceutical (e.g. anti-HIV, cytotoxic to tumor cells) sectors. The most recent application of insecticidal activity of cyclotides is the commercially available biopesticidal spray known as 'Sero X' for cotton crops. Cyclotides have a general mode of action and their potency of bioactivity is determined through their binding ability, pore formation and disruption of the target biological membranes. Keeping in view the important potential applications of biological activities of cyclotides and the lack of an extensive and analytical compilation of bioactive cyclotides, the present review systematically describes eight major biological activities of the native cyclotides from four angiosperm families viz. Fabaceae, Poaceae, Rubiaceae, Violaceae. The bioactivities of 94 cytotoxic, 57 antibacterial, 44 hemolytic, 25 antifungal, 21 anti-HIV, 20 nematocidal, 10 insecticidal and 5 molluscicidal cyclotides have been comprehensively elaborated. Further, their distribution in angiosperm families, mode of action and future prospects have also been discussed.
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Affiliation(s)
- Tripti Grover
- Bioinformatics Infrastructure Facility, Gargi College, University of Delhi, India
| | - Reema Mishra
- Department of Botany, Gargi College, University of Delhi, India
| | - Pooja Gulati
- Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Aparajita Mohanty
- Bioinformatics Infrastructure Facility, Gargi College, University of Delhi, India.
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9
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Matiadis D, Karagiaouri M, Mavroidi B, Nowak KE, Katsipis G, Pelecanou M, Pantazaki A, Sagnou M. Synthesis and antimicrobial evaluation of a pyrazoline-pyridine silver(I) complex: DNA-interaction and anti-biofilm activity. Biometals 2020; 34:67-85. [PMID: 33156436 DOI: 10.1007/s10534-020-00263-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022]
Abstract
The emergence of resistant bacterial strains mainly due to misuse of antibiotics has seriously affected our ability to treat bacterial illness, and the development of new classes of potent antimicrobial agents is desperately needed. In this study, we report the efficient synthesis of a new pyrazoline-pyridine containing ligand L1 which acts as an NN-donor for the formation of a novel silver (I) complex 2. The free ligand did not show antibacterial activity. High potency was exhibited by the complex against three Gram-negative bacteria, namely Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumanii with the minimum inhibitory concentration (MIC) ranging between 4 and 16 μg/mL (4.2-16.7 μM), and excellent activity against the fungi Candida albicans and Cryptococcus neoformans (MIC ≤ 0.25 μg/mL = 0.26 μM). Moreover, no hemolytic activity within the tested concentration range was observed. In addition to the planktonic growth inhibition, the biofilm formation of both Methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa was significantly reduced by the complex at MIC concentrations in a dose-dependent manner for Pseudomonas aeruginosa, whereas a biphasic response was obtained for MRSA showing that the sub-MIC doses enhanced biofilm formation before its reduction at higher concentration. Finally, complex 2 exhibited strong DNA binding with a large drop in DNA viscosity indicating the absence of classical intercalation and suggesting the participation of the silver ion in DNA binding which may be related to its antibacterial activity. Taken together, the current results reveal that the pyrazoline-pyridine silver complexes are of high interest as novel antibacterial agents, justifying further in vitro and in vivo investigation.
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Affiliation(s)
- Dimitris Matiadis
- National Centre for Scientific Research "Demokritos", Institute of Biosciences and Applications, Athens, Greece
| | - Maria Karagiaouri
- Department of Chemistry, Laboratory of Biochemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Barbara Mavroidi
- National Centre for Scientific Research "Demokritos", Institute of Biosciences and Applications, Athens, Greece
| | - Katarzyna E Nowak
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St. 141/143, 90-236, Lodz, Poland
| | - Georgios Katsipis
- Department of Chemistry, Laboratory of Biochemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Maria Pelecanou
- National Centre for Scientific Research "Demokritos", Institute of Biosciences and Applications, Athens, Greece
| | - Anastasia Pantazaki
- Department of Chemistry, Laboratory of Biochemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Marina Sagnou
- National Centre for Scientific Research "Demokritos", Institute of Biosciences and Applications, Athens, Greece.
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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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11
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Du Q, Chan LY, Gilding EK, Henriques ST, Condon ND, Ravipati AS, Kaas Q, Huang YH, Craik DJ. Discovery and mechanistic studies of cytotoxic cyclotides from the medicinal herb Hybanthus enneaspermus. J Biol Chem 2020; 295:10911-10925. [PMID: 32414842 DOI: 10.1074/jbc.ra120.012627] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/08/2020] [Indexed: 12/12/2022] Open
Abstract
Cyclotides are plant-derived peptides characterized by an ∼30-amino acid-long cyclic backbone and a cystine knot motif. Cyclotides have diverse bioactivities, and their cytotoxicity has attracted significant attention for its potential anticancer applications. Hybanthus enneaspermus (Linn) F. Muell is a medicinal herb widely used in India as a libido enhancer, and a previous study has reported that it may contain cyclotides. In the current study, we isolated 11 novel cyclotides and 1 known cyclotide (cycloviolacin O2) from H. enneaspermus and used tandem MS to determine their amino acid sequences. We found that among these cyclotides, hyen C comprises a unique sequence in loops 1, 2, 3, 4, and 6 compared with known cyclotides. The most abundant cyclotide in this plant, hyen D, had anticancer activity comparable to that of cycloviolacin O2, one of the most cytotoxic known cyclotides. We also provide mechanistic insights into how these novel cyclotides interact with and permeabilize cell membranes. Results from surface plasmon resonance experiments revealed that hyen D, E, L, and M and cycloviolacin O2 preferentially interact with model lipid membranes that contain phospholipids with phosphatidyl-ethanolamine headgroups. The results of a lactate dehydrogenase assay indicated that exposure to these cyclotides compromises cell membrane integrity. Using live-cell imaging, we show that hyen D induces rapid membrane blebbing and cell necrosis. Cyclotide-membrane interactions correlated with the observed cytotoxicity, suggesting that membrane permeabilization and disintegration underpin cyclotide cytotoxicity. These findings broaden our knowledge on the indigenous Indian herb H. enneaspermus and have uncovered cyclotides with potential anticancer activity.
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Affiliation(s)
- Qingdan Du
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Lai Y Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.,School of Biomedical Sciences, Institute of Health & Biomedical Innovation and Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Nicholas D Condon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Anjaneya S Ravipati
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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12
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Mehta L, Dhankhar R, Gulati P, Kapoor RK, Mohanty A, Kumar S. Natural and grafted cyclotides in cancer therapy: An insight. J Pept Sci 2020; 26:e3246. [DOI: 10.1002/psc.3246] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Lovekesh Mehta
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
| | - Rakhi Dhankhar
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
| | - Rajeev Kumar Kapoor
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
| | - Aparajita Mohanty
- Department of Botany, Gargi CollegeUniversity of Delhi New Delhi India
| | - Sanjay Kumar
- Medical Microbiology and Bioprocess Laboratory, Department of MicrobiologyMaharshi Dayanand University Rohtak India
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13
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Shelenkov A, Slavokhotova A, Odintsova T. Predicting Antimicrobial and Other Cysteine-Rich Peptides in 1267 Plant Transcriptomes. Antibiotics (Basel) 2020; 9:antibiotics9020060. [PMID: 32032999 PMCID: PMC7168108 DOI: 10.3390/antibiotics9020060] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 02/02/2023] Open
Abstract
Antimicrobial peptides (AMPs) are a key component of innate immunity in various organisms including bacteria, insects, mammals, and plants. Their mode of action decreases the probability of developing resistance in pathogenic organisms, which makes them a promising object of study. However, molecular biology methods for searching for AMPs are laborious and expensive, especially for plants. Earlier, we developed a computational pipeline for identifying potential AMPs based on the cysteine motifs they usually possess. Since most motifs are too species-specific, a wide-scale screening of novel data is required to maintain the accuracy of searching algorithms. We have performed a search for potential AMPs in 1267 plant transcriptomes using our pipeline. On average, 50–150 peptides were revealed in each transcriptome. The data was verified by a BLASTp search in nr database to confirm peptide functions and by using random nucleotide sequences to estimate the fraction of erroneous predictions. The datasets obtained will be useful both for molecular biologists investigating AMPs in various organisms and for bioinformaticians developing novel algorithms of motif searching in transcriptomic and genomic sequences. The results obtained will represent a good reference point for future investigations in the fields mentioned above.
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Affiliation(s)
- Andrey Shelenkov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, Moscow 119991, Russia
- Central Research Institute of Epidemiology, Rospotrebnadzor, Novogireevskaya str. 3a, Moscow 111123, Russia
- Correspondence:
| | - Anna Slavokhotova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, Moscow 119991, Russia
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia
| | - Tatyana Odintsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, Moscow 119991, Russia
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14
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Kan MW, Craik DJ. Discovery of Cyclotides from Australasian Plants. Aust J Chem 2020. [DOI: 10.1071/ch19658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This article is part of a special issue celebrating the contributions of Professor Paul Alewood to peptide science. We begin by providing a summary of collaborative projects between the Alewood and Craik groups at The University of Queensland and highlighting the impacts of some of these studies. In particular, studies on the discovery, synthesis, structures, and bioactivities of disulfide-rich toxins from animal venoms have led to a greater understanding of the biology of ion channels and to applications of these bioactive peptides in drug design. The second part of the article focuses on plant-derived disulfide-rich cyclic peptides, known as cyclotides, and includes an analysis of the geographical distribution of Australasian plant species that contain cyclotides as well as an analysis of the diversity of cyclotide sequences found in Australasian plants. This should provide a useful resource for researchers to access native cyclotides and explore their chemistry and biology.
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15
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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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16
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Synthesis, characterization and antimicrobial activity of N-acetyl-3-acetyl-5-benzylidene tetramic acid-metal complexes. X-ray analysis and identification of the Cd(II) complex as a potent antifungal agent. J Inorg Biochem 2019; 194:65-73. [DOI: 10.1016/j.jinorgbio.2019.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/10/2019] [Accepted: 02/18/2019] [Indexed: 12/23/2022]
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17
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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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18
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Al Saiqali M, Tangutur AD, Banoth C, Bhukya B. Antimicrobial and anticancer potential of low molecular weight polypeptides extracted and characterized from leaves of Azadirachta indica. Int J Biol Macromol 2018; 114:906-921. [DOI: 10.1016/j.ijbiomac.2018.03.169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/25/2018] [Accepted: 03/27/2018] [Indexed: 12/11/2022]
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19
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Abstract
Over the past two decades, developing medical applications for peptides has, and continues to be a highly active area of research. At present there are over 60 peptide-based drugs on the market and more than 140 in various stages of clinical trials. The interest in peptide-based therapeutics arises from their biocompatibility and their ability to form defined secondary and tertiary structures, resulting in a high selectivity for complex targets. However, there are significant challenges associated with the development of peptide-based therapeutics, namely peptides are readily metabolised in vivo. Peptoids are an emerging class of peptidomimetic and they offer an alternative to peptides. Peptoids are comprised of N-substituted glycines where side-chains are located on the nitrogen atom of the amide backbone rather than the α-carbon as is the case in peptides. This change in structure confers a high degree of resistance to proteolytic degradation but the absence of any backbone hydrogen bonding means that peptoids exhibit a high degree of conformational flexibility. Cyclisation has been explored as one possible route to rigidify peptoid structures, making them more selective, and, therefore more desirable as potential therapeutics. This review outlines the various strategies that have been developed over the last decade to access new types of macrocyclic peptoids.
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Affiliation(s)
| | - Steven L. Cobb
- Department of ChemistryDurham UniversitySouth RoadDurhamDH1 3LEUK
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20
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Uddin SJ, Muhammad T, Shafiullah M, Slazak B, Rouf R, Göransson U. Single-step purification of cyclotides using affinity chromatography. Biopolymers 2018; 108. [PMID: 28009046 DOI: 10.1002/bip.23010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 10/07/2016] [Accepted: 12/06/2016] [Indexed: 11/08/2022]
Abstract
Cyclotides are considered promising scaffolds for drug development owing to their inherent host defence activities and highly stable structure, defined by the cyclic cystine knot. These proteins are expressed as complex mixtures in plants. Although several methods have been developed for their isolation and analysis, purification of cyclotides is still a lengthy process. Here, we describe the use of affinity chromatography for the purification of cyclotides using polyclonal IgG antibodies raised in rabbits against cycloviolacin O2 and immobilized on NHS-activated Sepharose columns. Cycloviolacin O2 was used as a model substance to evaluate the chromatographic principle, first as a pure compound and then in combination with other cyclotides, that is, bracelet cyclotide cycloviolacin O19 and Möbius cyclotide kalata B1, and in a plant extract. We demonstrate that single-step purification of cyclotides by affinity chromatography is possible but cross reactivity may occur between homologue cyclotides of the bracelet subfamily.
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Affiliation(s)
- Shaikh Jamal Uddin
- Division of Pharmacognosy, Uppsala University, Biomedical Center, Uppsala, SE, 75123, Sweden.,Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, Uppsala, SE, 75123, Sweden.,Pharmacy Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Taj Muhammad
- Division of Pharmacognosy, Uppsala University, Biomedical Center, Uppsala, SE, 75123, Sweden.,Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, Uppsala, SE, 75123, Sweden
| | - Md Shafiullah
- Division of Pharmacognosy, Uppsala University, Biomedical Center, Uppsala, SE, 75123, Sweden.,Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, Uppsala, SE, 75123, Sweden
| | - Blazej Slazak
- W. Szafer Institute of Botany, Polish Academy of Science, Cracow, 31-512, Poland
| | - Razina Rouf
- Pharmacy Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Ulf Göransson
- Division of Pharmacognosy, Uppsala University, Biomedical Center, Uppsala, SE, 75123, Sweden.,Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, Uppsala, SE, 75123, Sweden
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21
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Zheng Y, Meng X, Wu Y, Zhao Y, Wu C. De novo design of constrained and sequence-independent peptide scaffolds with topologically-formidable disulfide connectivities. Chem Sci 2018; 9:569-575. [PMID: 29629120 PMCID: PMC5869988 DOI: 10.1039/c7sc03956e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 11/17/2017] [Indexed: 12/22/2022] Open
Abstract
Disulfide-rich peptides are interesting scaffolds for drug design and discovery. However, peptide scaffolds constrained by disulfide bonds, either naturally occurring or computationally designed, have been suffering from the elusive (oxidative) folding behavior complying with Anfinsen's dogma, which strongly restricts their applicability in bioactive peptide design and discovery; because when primary peptide sequences are extensively manipulated, their disulfide connectivities might become scrambled. Here we present the design of cysteine/penicillamine (C/Pen)-mixed peptide frameworks that are capable of folding into specific regioisomers without dependence on primary amino acid sequences. Even certain folds that are considered to be topologically formidable can be generated in high yields. Currently, almost all disulfide-rich peptide scaffolds are vitally correlated to primary amino acid sequences, but ours are exceptional. These scaffolds should be of particular interest for further designing constrained peptides with new structures and functions, and more importantly, the ultimately designed peptides would not suffer from general oxidative folding problems.
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Affiliation(s)
- Yiwu Zheng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , State Key Laboratory of Physical Chemistry of Solid Surfaces , Department of Chemistry , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , P. R. China .
| | - Xiaoting Meng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , State Key Laboratory of Physical Chemistry of Solid Surfaces , Department of Chemistry , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , P. R. China .
| | - Yaqi Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , State Key Laboratory of Physical Chemistry of Solid Surfaces , Department of Chemistry , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , P. R. China .
| | - Yibing Zhao
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , State Key Laboratory of Physical Chemistry of Solid Surfaces , Department of Chemistry , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , P. R. China .
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , State Key Laboratory of Physical Chemistry of Solid Surfaces , Department of Chemistry , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , P. R. China .
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22
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Edwards IA, Elliott AG, Kavanagh AM, Blaskovich MAT, Cooper MA. Structure-Activity and -Toxicity Relationships of the Antimicrobial Peptide Tachyplesin-1. ACS Infect Dis 2017; 3:917-926. [PMID: 28960954 DOI: 10.1021/acsinfecdis.7b00123] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tachyplesin-1 (TP1; 1) is a cationic β-hairpin antimicrobial peptide with a membranolytic mechanism of action. While it possesses broad-spectrum, potent antimicrobial activity, 1 is highly hemolytic against mammalian erythrocytes, which precludes it from further development. In this study, we report a template-based approach to investigate the structure-function and structure-toxicity relationships of each amino acid of 1. We modulated charge and hydrophobicity by residue modification and truncation of the peptide. Antimicrobial activity was then assessed against six key bacterial pathogens and two fungi, with toxicity profiled against mammalian cells. The internal disulfide bridge Cys7-Cys12 of 1 was shown to play an important role in broad-spectrum antimicrobial activity against all pathogenic strains tested. Novel peptides based on the progenitor were then designed, including 5 (TP1[F4A]), 12 (TP1[I11A]), and 19 (TP1[C3A,C16A]). These had 26- to 64-fold improved activity/toxicity indices and show promise for further development. Structural studies of 5 (TP1[F4A]) and 12 (TP1[I11A]) identified a conserved β-hairpin secondary structure motif correlating with their very high stablility in mouse and human plasma. Membrane binding affinity determined by surface plasmon resonance confirmed their selectivity toward bacterial membranes, but the degree of membrane binding did not correlate with the degree of hemolysis, suggesting that other factors may drive toxicity.
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Affiliation(s)
- Ingrid A. Edwards
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road (Building 80), Brisbane, Queensland 4072 Australia
| | - Alysha G. Elliott
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road (Building 80), Brisbane, Queensland 4072 Australia
| | - Angela M. Kavanagh
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road (Building 80), Brisbane, Queensland 4072 Australia
| | - Mark A. T. Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road (Building 80), Brisbane, Queensland 4072 Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road (Building 80), Brisbane, Queensland 4072 Australia
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23
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Camarero JA. Cyclotides, a versatile ultrastable micro-protein scaffold for biotechnological applications. Bioorg Med Chem Lett 2017; 27:5089-5099. [PMID: 29110985 PMCID: PMC5812341 DOI: 10.1016/j.bmcl.2017.10.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/13/2017] [Accepted: 10/21/2017] [Indexed: 01/26/2023]
Abstract
Cyclotides are fascinating microproteins (≈30-40 residues long) with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique topology makes them exceptionally stable to chemical, thermal and biological degradation compared to other peptides of similar size. Cyclotides have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot, able to cross cellular membranes and modulate intracellular protein-protein interactions both in vitro and in vivo. These properties make them ideal scaffolds for many biotechnological applications. This article provides and overview of the properties of cyclotides and their applications as molecular imaging agents and peptide-based therapeutics.
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Affiliation(s)
- Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089-9121, USA.
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24
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Bactericidal activity of cyclotides where phosphatidylethanolamine-lipid selectivity determines antimicrobial spectra. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1986-2000. [DOI: 10.1016/j.bbamem.2017.06.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 12/17/2022]
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25
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Abstract
Cyclotides are globular microproteins with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to chemical, thermal, and biological degradation compared to other peptides of similar size. In addition, cyclotides have been shown to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot. Cyclotides can also cross cellular membranes and are able to modulate intracellular protein-protein interactions, both in vitro and in vivo. All of these features make cyclotides highly promising as leads or frameworks for the design of peptide-based diagnostic and therapeutic tools. This article provides an overview on cyclotides and their applications as molecular imaging agents and peptide-based therapeutics.
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Affiliation(s)
- Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-9121, USA
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26
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Ravipati AS, Poth AG, Troeira Henriques S, Bhandari M, Huang YH, Nino J, Colgrave ML, Craik DJ. Understanding the Diversity and Distribution of Cyclotides from Plants of Varied Genetic Origin. JOURNAL OF NATURAL PRODUCTS 2017; 80:1522-1530. [PMID: 28471681 DOI: 10.1021/acs.jnatprod.7b00061] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cyclotides are a large family of naturally occurring plant-derived macrocyclic cystine-knot peptides, with more than 400 having been identified in species from the Violaceae, Rubiaceae, Cucurbitaceae, Fabaceae, and Solanaceae families. Nevertheless, their specialized distribution within the plant kingdom remains poorly understood. In this study, the diversity of cyclotides was explored through the screening of 197 plants belonging to 43 different families. In total, 28 cyclotides were sequenced from 15 plant species, one of which belonged to the Rubiaceae and 14 to the Violaceae. Every Violaceae species screened contained cyclotides, but they were only sparsely represented in Rubiaceae and nonexistent in other families. The study thus supports the hypothesis that cyclotides are ubiquitous in the Violaceae, and it adds to the list of plants found to express kalata S and cycloviolacin O12. Finally, previous studies suggested the existence of cyclotide isoforms with either an Asn or an Asp at the C-terminal processing site of the cyclotide domain within the precursor proteins. Here we found that despite the discovery of a few cyclotides genuinely containing an Asp in loop 6 as evidenced by gene sequencing, deamidation of Asn during enzymatic digestion resulted in the artifactual presence of Asp isoforms. This result is consistent with studies suggesting that peptides can undergo deamidation after being subjected to external factors, including pH, temperature, and enzymatic digestion.
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Affiliation(s)
- Anjaneya S Ravipati
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Murari Bhandari
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Jaime Nino
- Universidad Tecnológica de Pereira , Cra 27 No 10-02-Los Álamos, Pereira, Risaralda, Colombia
| | - Michelle L Colgrave
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, St Lucia 4067, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
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27
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Hazam PK, Jerath G, Kumar A, Chaudhary N, Ramakrishnan V. Effect of tacticity-derived topological constraints in bactericidal peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1388-1395. [PMID: 28479275 DOI: 10.1016/j.bbamem.2017.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 04/16/2017] [Accepted: 05/03/2017] [Indexed: 12/25/2022]
Abstract
Topology is a key element in structure-activity relationship estimation while designing physiologically-active molecular constructs. Peptides may be a preferred choice for therapeutics, principally due to their biocompatibility, low toxicity and predictable metabolism. Peptide design only guarantees functional group constitution by opting specific amino acid sequence, and not their spatial orientation to bind and incite physiological response on chosen targets. This is principally because peptide conformation is subject to external flux, due to the isotactic stereochemistry of the peptide chain. Stereochemical engineering of the peptide main chain offers the possibility of multiplying the structural space of a typical sequence to many orders of magnitude, and limiting the otherwise fluxional non-specific functional group dispensation in space by offering greater conformational rigidity. We put to test, this conceptual possibility already established in theoretical models, by designing amphipathic peptide systems and experimenting with them on Gram-positive, Gram-negative and antibiotic-resistant bacteria. The unusual conformational rigidity and stability of syndiotactic peptides enable them to retain the designed electrostatic environment, while they encounter the membrane surface. All the six designed systems exhibited bactericidal activity, pointing to the utility and specificity of stereo-engineered peptide systems for therapeutic applications. Overall, we hope that this work provides important insights and useful directives in designing novel peptide systems with antimicrobial activity, by expanding the design space, incorporating D-amino acid as an additional design variable.
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Affiliation(s)
- Prakash Kishore Hazam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Gaurav Jerath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Anil Kumar
- Biological and Organic Chemistry, University of Toronto, Ontario M5S 3H6, Canada
| | - Nitin Chaudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India.
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28
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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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Troeira Henriques S, Craik DJ. Cyclotide Structure and Function: The Role of Membrane Binding and Permeation. Biochemistry 2017; 56:669-682. [DOI: 10.1021/acs.biochem.6b01212] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
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30
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Park S, Yoo KO, Marcussen T, Backlund A, Jacobsson E, Rosengren KJ, Doo I, Göransson U. Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets ( Viola). FRONTIERS IN PLANT SCIENCE 2017; 8:2058. [PMID: 29326730 PMCID: PMC5741643 DOI: 10.3389/fpls.2017.02058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/17/2017] [Indexed: 05/20/2023]
Abstract
Cyclotides are a family of plant proteins that are characterized by a cyclic backbone and a knotted disulfide topology. Their cyclic cystine knot (CCK) motif makes them exceptionally resistant to thermal, chemical, and enzymatic degradation. By disrupting cell membranes, the cyclotides function as host defense peptides by exhibiting insecticidal, anthelmintic, antifouling, and molluscicidal activities. In this work, we provide the first insight into the evolution of this family of plant proteins by studying the Violaceae, in particular species of the genus Viola. We discovered 157 novel precursor sequences by the transcriptomic analysis of six Viola species: V. albida var. takahashii, V. mandshurica, V. orientalis, V. verecunda, V. acuminata, and V. canadensis. By combining these precursor sequences with the phylogenetic classification of Viola, we infer the distribution of cyclotides across 63% of the species in the genus (i.e., ~380 species). Using full precursor sequences from transcriptomes, we show an evolutionary link to the structural diversity of the cyclotides, and further classify the cyclotides by sequence signatures from the non-cyclotide domain. Also, transcriptomes were compared to cyclotide expression on a peptide level determined using liquid chromatography-mass spectrometry. Furthermore, the novel cyclotides discovered were associated with the emergence of new biological functions.
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Affiliation(s)
- Sungkyu Park
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ki-Oug Yoo
- Department of Biological Sciences, Kangwon National University, Chuncheon, South Korea
| | - Thomas Marcussen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Anders Backlund
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Erik Jacobsson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - K. Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Inseok Doo
- Biotech Research Team, Biotech Research Center of Dong-A Pharm Co Ltd., Seoul, South Korea
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
- *Correspondence: Ulf Göransson
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