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Gilding EK, Jackson MA, Nguyen LTT, Hamilton BR, Farquharson KA, Ho WL, Yap K, Hogg CJ, Belov K, Craik DJ. Hijacking of N-fixing legume albumin-1 genes enables the cyclization and stabilization of defense peptides. Nat Commun 2024; 15:6565. [PMID: 39095373 PMCID: PMC11297342 DOI: 10.1038/s41467-024-50742-x] [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: 12/13/2023] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
The legume albumin-1 gene family, arising after nodulation, encodes linear a- and b-chain peptides for nutrient storage and defense. Intriguingly, in one prominent legume, Clitoria ternatea, the b-chains are replaced by domains producing ultra-stable cyclic peptides called cyclotides. The mechanism of this gene hijacking is until now unknown. Cyclotides require recruitment of ligase-type asparaginyl endopeptidases (AEPs) for maturation (cyclization), necessitating co-evolution of two gene families. Here we compare a chromosome-level C. ternatea genome with grain legumes to reveal an 8 to 40-fold expansion of the albumin-1 gene family, enabling the additional loci to undergo diversification. Iterative rounds of albumin-1 duplication and diversification create four albumin-1 enriched genomic islands encoding cyclotides, where they are physically grouped by similar pI and net charge values. We identify an ancestral hydrolytic AEP that exhibits neofunctionalization and multiple duplication events to yield two ligase-type AEPs. We propose cyclotides arise by convergence in C. ternatea where their presence enhances defense from biotic attack, thus increasing fitness compared to lineages with linear b-chains and ultimately driving the replacement of b-chains with cyclotides.
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Affiliation(s)
- Edward K Gilding
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark A Jackson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Linh T T Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Katherine A Farquharson
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Wing L Ho
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Carolyn J Hogg
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Katherine Belov
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
- 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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Dang TT, Tran TTT, Tran GH, Pham SH, Nguyen THN. Cyclotides derived from Viola dalatensis Gagnep: A novel approach for enrichment and evaluation of antimicrobial activity. Toxicon 2024; 239:107606. [PMID: 38181837 DOI: 10.1016/j.toxicon.2024.107606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/25/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024]
Abstract
Cyclotides, plant-derived cysteine-rich peptides, exhibit a wide range of beneficial biological activities and possess exceptional structural stability. Cyclotides are commonly distributed throughout the Violaceae family. Viola dalatensis Gagnep, a Vietnamese species, has not been well studied, especially for cyclotides. This pioneering research explores cyclotides from V. dalatensis as antimicrobials. This study used a novel approach to enhance cyclotides after extraction. The approach combined 30% ammonium sulfate salt precipitation and RP-HPLC. A comprehensive analysis was performed to ascertain the overall protein content, flavonoids content, polyphenol content, and free radical scavenging capacity of compounds derived from V. dalatensis. Six known cyclotides were sequenced utilizing MS tandem. Semi-purified cyclotide mixtures (M1, M2, and M3) exhibited antibacterial efficacy against Bacillus subtilis (inhibitory diameters: 19.67-23.50 mm), Pseudomonas aeruginosa (22.17-23.50 mm), and Aspergillus flavus (14.67-21.33 mm). The enriched cyclotide precipitate from the stem extract demonstrated a minimum inhibitory concentration (MIC) of 0.08 mg/mL against P. aeruginosa, showcasing significant antibacterial effectiveness compared to the stem extract (MIC: 12.50 mg/mL). Considerable advancements have been achieved in the realm of cyclotides, specifically in their application as antimicrobial agents.
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Affiliation(s)
- Tien T Dang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam.
| | - Tam T T Tran
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Gia-Hoa Tran
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Son H Pham
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Tuan H N Nguyen
- Biomedical Research Center, Pham Ngoc Thach University of Medicine, Viet Nam; Department of Medical Biochemistry & Molecular Biology, Pham Ngoc Thach University of Medicine, Viet Nam
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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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Ho TNT, Turner A, Pham SH, Nguyen HT, Nguyen LTT, Nguyen LT, Dang TT. Cysteine-rich peptides: From bioactivity to bioinsecticide applications. Toxicon 2023; 230:107173. [PMID: 37211058 DOI: 10.1016/j.toxicon.2023.107173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/23/2023]
Abstract
Greater levels of insect resistance and constraints on the use of current pesticides have recently led to increased crop losses in agricultural production. Further, the health and environmental impacts of pesticides now restrict their application. Biologics based on peptides are gaining popularity as efficient crop protection agents with low environmental toxicity. Cysteine-rich peptides (whether originated from venoms or plant defense substances) are chemically stable and effective as insecticides in agricultural applications. Cysteine-rich peptides fulfill the stability and efficacy requirements for commercial uses and provide an environmentally benign alternative to small-molecule insecticides. In this article, cysteine-rich insecticidal peptide classes identified from plants and venoms will be highlighted, focusing on their structural stability, bioactivity and production.
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Affiliation(s)
- Thao N T Ho
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - A Turner
- Molecular Biology Department, University of Texas, 100 E 24th St. Austin, USA
| | - Son H Pham
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Ha T Nguyen
- National Key Laboratory of Polymer and Composite Materials, Department of Energy Materials, Faculty of Materials Technology, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam; Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Linh T T Nguyen
- Department of Chemistry, Ho Chi Minh City University of Education, 280 an Duong Vuong Street, District 5, Ho Chi Minh City, Viet Nam
| | - Luan T Nguyen
- National Key Laboratory of Polymer and Composite Materials, Department of Energy Materials, Faculty of Materials Technology, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam; Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Tien T Dang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam.
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Arguelles J, Lee J, Cardenas LV, Govind S, Singh S. In Silico Analysis of a Drosophila Parasitoid Venom Peptide Reveals Prevalence of the Cation-Polar-Cation Clip Motif in Knottin Proteins. Pathogens 2023; 12:pathogens12010143. [PMID: 36678491 PMCID: PMC9865768 DOI: 10.3390/pathogens12010143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
As generalist parasitoid wasps, Leptopilina heterotoma are highly successful on many species of fruit flies of the genus Drosophila. The parasitoids produce specialized multi-strategy extracellular vesicle (EV)-like structures in their venom. Proteomic analysis identified several immunity-associated proteins, including the knottin peptide, LhKNOT, containing the structurally conserved inhibitor cysteine knot (ICK) fold, which is present in proteins from diverse taxa. Our structural and docking analysis of LhKNOT's 36-residue core knottin fold revealed that in addition to the knottin motif itself, it also possesses a Cation-Polar-Cation (CPC) clip. The CPC clip motif is thought to facilitate antimicrobial activity in heparin-binding proteins. Surprisingly, a majority of ICKs tested also possess the CPC clip motif, including 75 bona fide plant and arthropod knottin proteins that share high sequence and/or structural similarity with LhKNOT. Like LhKNOT and these other 75 knottin proteins, even the Drosophila Drosomycin antifungal peptide, a canonical target gene of the fly's Toll-NF-kappa B immune pathway, contains this CPC clip motif. Together, our results suggest a possible defensive function for the parasitoid LhKNOT. The prevalence of the CPC clip motif, intrinsic to the cysteine knot within the knottin proteins examined here, suggests that the resultant 3D topology is important for their biochemical functions. The CPC clip is likely a highly conserved structural motif found in many diverse proteins with reported heparin binding capacity, including amyloid proteins. Knottins are targets for therapeutic drug development, and insights into their structure-function relationships will advance novel drug design.
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Affiliation(s)
- Joseph Arguelles
- Department of Biology, Brooklyn College, Brooklyn, NY 11210, USA
| | - Jenny Lee
- Department of Biology, Brooklyn College, Brooklyn, NY 11210, USA
| | - Lady V. Cardenas
- Department of Biology, The City College of New York, New York, NY 10031, USA
| | - Shubha Govind
- Department of Biology, The City College of New York, New York, NY 10031, USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- PhD Program in Biology, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Shaneen Singh
- Department of Biology, Brooklyn College, Brooklyn, NY 11210, USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- PhD Program in Biology, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence:
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Mehta L, Shambhawi, Kumar S, Mohanty A. In silico Analysis of Native Cyclotides with Antibacterial Activity against Gram-negative Bacteria. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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7
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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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Wagemans J, Panda SK, Crauwels S, Lood C, Lievens B, Lavigne R, Luyten W. Identification of Spoilage Bacteria in Non-Food Products and Their Inhibition Using Botanical Extracts. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:13805-13815. [DOI: 10.1021/acssuschemeng.2c04174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Affiliation(s)
| | - Sujogya Kumar Panda
- Center of Environment, Climate Change and Public Health, RUSA 2.0, Utkal University, Bhubaneswar 751004, India
- Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Sam Crauwels
- Department of Microbial and Molecular Systems, KU Leuven, Leuven 3001, Belgium
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Leuven 3001, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven 3001, Belgium
| | - Bart Lievens
- Department of Microbial and Molecular Systems, KU Leuven, Leuven 3001, Belgium
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven 3001, Belgium
| | - Walter Luyten
- Department of Biology, KU Leuven, Leuven 3000, Belgium
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Dang TT, Huang YH, Ott S, Harvey PJ, Gilding EK, Tombling BJ, Chan LY, Kaas Q, Claridge-Chang A, Craik DJ. The acyclotide ribe 31 from Rinorea bengalensis has selective cytotoxicity and potent insecticidal properties in Drosophila. J Biol Chem 2022; 298:102413. [PMID: 36007611 PMCID: PMC9513267 DOI: 10.1016/j.jbc.2022.102413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Cyclotides and acyclic versions of cyclotides (acyclotides) are peptides involved in plant defense. These peptides contain a cystine knot motif formed by three interlocked disulfide bonds, with the main difference between the two classes being the presence or absence of a cyclic backbone, respectively. The insecticidal activity of cyclotides is well documented, but no study to date explores the insecticidal activity of acyclotides. Here, we present the first in vivo evaluation of the insecticidal activity of acyclotides from Rinorea bengalensis on the vinegar fly Drosophila melanogaster. Of a group of structurally comparable acyclotides, ribe 31 showed the most potent toxicity when fed to D. melanogaster. We screened a range of acyclotides and cyclotides and found their toxicity toward human red blood cells was substantially lower than toward insect cells, highlighting their selectivity and potential for use as bioinsecticides. Our confocal microscopy experiments indicated their cytotoxicity is likely mediated via membrane disruption. Furthermore, our surface plasmon resonance studies suggested ribe 31 preferentially binds to membranes containing phospholipids with phosphatidyl-ethanolamine headgroups. Despite having an acyclic backbone, we determined the three-dimensional NMR solution structure of ribe 31 is similar to that of cyclotides. In summary, our results suggest that, with further optimization, ribe 31 could have applications as an insecticide due to its potent in vivo activity against D. melanogaster. More broadly, this work advances the field by demonstrating that acyclotides are more common than previously thought, have potent insecticidal activity, and have the advantage of potentially being more easily manufactured than cyclotides.
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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, Queensland, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Stanislav Ott
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - 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, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, 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, Queensland, 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, Queensland, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Adam Claridge-Chang
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore; Institute for Molecular and Cell Biology, A∗STAR, Singapore; Department of Physiology, National University of Singapore, Singapore, Singapore
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
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Aslam L, Kaur R, Hussain S, Kapoor N, Mahajan R. LC-MS/MS identification and structural characterization of isolated cyclotides from precursor sequences of Viola odorata L. petiole tissue using computational approach. J Biosci 2022. [DOI: 10.1007/s12038-022-00283-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Dayani L, Dinani MS, Aliomrani M, Hashempour H, Varshosaz J, Taheri A. Immunomodulatory effects of cyclotides isolated from Viola odorata in an experimental autoimmune encephalomyelitis animal model of multiple sclerosis. Mult Scler Relat Disord 2022; 64:103958. [PMID: 35716476 DOI: 10.1016/j.msard.2022.103958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/19/2022] [Accepted: 06/09/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) is a demyelinating disease of the central nervous system that causes chronic inflammation. Cyclotides are small plant proteins with a wide range of biological activity, making them a target for researchers to investigate. This study was conducted to investigate the possible effects of cyclotide-rich fractions from Viola odorata as an immunomodulatory agent in an experimental autoimmune encephalomyelitis (EAE) model of MS. METHODS At room temperature, the plant materials were subjected to maceration in methanol: dichloromethane (1:1; v/v) for 3 days. The extraction was repeated 3 times, and the final concentrated extract was partitioned 3 times by 1/2 volume of double-distilled water. The aqueous phases were separated and freeze-dried. Finally, the crude extract was fractionated by C18 silicagel using vacuum liquid chromatography, with mobile phases of 30%, 50% and 80% of ethanol: water, respectively. The 50%, and 80% fractions were analyzed by HPLC and MALDI-TOF analysis and administrated intraperitoneally to forty-five female C57BL/6 EAE-induced mice, at 5, 25, and 50 mg/kg doses. After 28 days, the animals were evaluated using EAE clinical scoring which was done every 3 days, cytokine levels, and myelination level. RESULTS The results confirmed the presence of cyclotides in V. odorata based on their retention time and the composition of mobile phase in HPLC and the molecular weight of the peaks in MALDI-TOF analysis. It was observed that cyclotides, especially in the 80% fraction group at the dose of 50 mg/kg significantly reduced the clinical scores, inflammation, and demyelination in EAE mice compared with the normal saline group (P<0.05), and the results of this group were comparable with fingolimod (P>0.05). CONCLUSION It could be concluded that V. odorata is a rich source of cyclotides which they could be extracted by an easily available process and also, they could be used as immunomodulatory agents in MS, with similar effects to fingolimod.
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Affiliation(s)
- Ladan Dayani
- Novel Drug Delivery Systems Research Centre, Department of Pharmaceutics, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Pharmaceutics, Faculty of Pharmacy and Novel Drug Delivery Systems Research Centre, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Masoud Sadeghi Dinani
- Department of Pharmacognosy, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehdi Aliomrani
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Hashempour
- Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Jaleh Varshosaz
- Novel Drug Delivery Systems Research Centre, Department of Pharmaceutics, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Pharmaceutics, Faculty of Pharmacy and Novel Drug Delivery Systems Research Centre, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azade Taheri
- Novel Drug Delivery Systems Research Centre, Department of Pharmaceutics, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Pharmaceutics, Faculty of Pharmacy and Novel Drug Delivery Systems Research Centre, Isfahan University of Medical Sciences, Isfahan, Iran.
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12
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Rezende SB, Oshiro KGN, Júnior NGO, Franco OL, Cardoso MH. Advances on chemically modified antimicrobial peptides for generating peptide antibiotics. Chem Commun (Camb) 2021; 57:11578-11590. [PMID: 34652348 DOI: 10.1039/d1cc03793e] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antimicrobial peptides (AMPs) are pinpointed as promising molecules against antibiotic-resistant bacterial infections. Nevertheless, there is a discrepancy between the AMP sequences generated and the tangible outcomes in clinical trials. AMPs' limitations include enzymatic degradation, chemical/physical instability and toxicity toward healthy human cells. These factors compromise AMPs' bioavailability, resulting in limited therapeutic potential. To overcome such obstacles, peptidomimetic approaches, including glycosylation, PEGylation, lipidation, cyclization, grafting, D-amino acid insertion, stapling and dendrimers are promising strategies to fine-tune AMPs. Here we focused on chemical modifications applied for AMP optimization and how they have helped these peptide-based antibiotic candidates' design and translational potential.
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Affiliation(s)
- Samilla B Rezende
- S-Inova Biotech, Universidade Católica Dom Bosco (UCDB), Campo Grande, MS, Brazil
| | - Karen G N Oshiro
- S-Inova Biotech, Universidade Católica Dom Bosco (UCDB), Campo Grande, MS, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília (UnB), Brasília, DF, Brazil
| | - Nelson G O Júnior
- Centro de Análises Proteômicas e Bioquímicas Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília (UCB), Brasília, DF, Brazil.
| | - Octávio L Franco
- S-Inova Biotech, Universidade Católica Dom Bosco (UCDB), Campo Grande, MS, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília (UnB), Brasília, DF, Brazil.,Centro de Análises Proteômicas e Bioquímicas Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília (UCB), Brasília, DF, Brazil.
| | - Marlon H Cardoso
- S-Inova Biotech, Universidade Católica Dom Bosco (UCDB), Campo Grande, MS, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília (UnB), Brasília, DF, Brazil.,Centro de Análises Proteômicas e Bioquímicas Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília (UCB), Brasília, DF, Brazil.
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13
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S S, Muraleedharan UD. Cationic Clitoria ternatea Seed Peptide as a Potential Novel Bioactive Molecule. Protein Pept Lett 2021; 28:1259-1271. [PMID: 34551687 DOI: 10.2174/0929866528666210922124735] [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: 05/19/2021] [Revised: 07/24/2021] [Accepted: 08/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND While several biologics have been reported from different parts of Clitoria ternatea, a herbaceous climber of the family Fabaceae, specific production of cationic peptides other than cyclotides (<3.7 kDa) has barely been investigated or their bioactive potential looked into. OBJECTIVE To uncover potential bioactivities and characteristics of novel cationic peptides from C. ternatea seeds. METHODS C. ternatea seed cationic peptide purified by simple and cost-effective procedures was analyzed by electrophoresis and mass spectrometry. Antimicrobial efficacy was evaluated against bacterial and fungal pathogens. Antioxidant potential was quantified by in vitro antioxidant assays. Physicochemical characterization and Tandem mass spectrometry were performed. RESULTS An 8.5 kDa cationic peptide purified from C. ternatea seeds was active against Candida albicans, Staphylococcus aureus, Aeromonas hydrophila and Escherichia coli at a minimum inhibitory concentration in the range of 8-32 μg/ml. This activity was totally uncompromised at pH 5-8 or after 1 h of heat treatment at 70-80 ºC, but was sensitive to protease treatment. Concentration-dependent free-radical scavenging activity and ferric-reducing capacity demonstrated the antioxidant potential of the peptide. Tandem MS analysis of trypsin-digested peptide based on shotgun proteomics detected matching peptide sequences with one or two cysteine residues but had low sequence coverage (≤17%) to known sequences in the C. ternatea protein database. Taken together, the distinct characteristics of this novel 8.5 kDa peptide clearly distinguishes it from known cyclotides of C. ternatea. CONCLUSIONS Insights have been obtained into the functional characteristics of what appears to be a novel cationic peptide from C. ternatea seeds, exhibiting significant antimicrobial and antioxidant activities.
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Affiliation(s)
- Sreekala S
- Department of Biotechnology, Goa University, Goa - 403 206. India
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14
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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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15
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Kalmankar NV, Balaram P, Venkatesan R. Mass Spectrometric Analysis of Cyclotides from Clitoria ternatea: Xxx-Pro Bond Fragmentation as Convenient Diagnostic of Pro Residue Positioning. Chem Asian J 2021; 16:2920-2931. [PMID: 34288513 DOI: 10.1002/asia.202100585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/14/2021] [Indexed: 11/06/2022]
Abstract
Cyclotides, a class of macrocyclic plant peptides, characterized by a cyclic backbone and three inter-locking disulfide bonds, may be divided into two major structural subfamilies, Möbius and Bracelet, based on the presence or absence of a specific proline residue. The present study describes the suite of cyclotides obtained from Clitoria ternatea, characterized by LC-MS and MS/MS techniques. Notable variations in product ion distributions were observed in cyclotides belonging to different structural subfamilies based on the number and positions of proline residues. For instance, Cter M which is an abundant Möbius cyclotide in this plant containing three proline residues, displayed distinct b- and y- ion characteristics in the MS/MS spectra compared to Cliotide T1, another commonly identified cyclotide but belonging to the Bracelet subfamily having two proline residues. The distinct fragmentation pattern of prototypical cyclotides of each structural subfamily, determined by Xxx-Pro bond fragmentation, was used to rapidly identify and sequence a novel cyclotide ctr pep 30 from this plant.
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Affiliation(s)
- Neha V Kalmankar
- National Centre for Biological Sciences (NCBS), Tata Institute for Fundamental Research (TIFR), GKVK Campus, 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
| | - Padmanabhan Balaram
- National Centre for Biological Sciences (NCBS), Tata Institute for Fundamental Research (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Radhika Venkatesan
- National Centre for Biological Sciences (NCBS), Tata Institute for Fundamental Research (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.,Department of Biological Sciences, Indian Institute of Science, Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
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16
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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: 18] [Impact Index Per Article: 6.0] [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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17
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Roy S, Kim HJ, Rhim JW. Effect of blended colorants of anthocyanin and shikonin on carboxymethyl cellulose/agar-based smart packaging film. Int J Biol Macromol 2021; 183:305-315. [PMID: 33932410 DOI: 10.1016/j.ijbiomac.2021.04.162] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/20/2021] [Accepted: 04/24/2021] [Indexed: 12/20/2022]
Abstract
Natural colorants (anthocyanin and shikonin) were blended in different ratios (3:1 and 1:3) and used for the preparation of carboxymethyl cellulose (CMC)/agar-based functional halochromic films. The colorants were compatible with the polymer matrix and evenly spread over the polymer matrix. The addition of colorants slightly improved the mechanical strength and significantly improved the water vapor barrier properties of CMC/agar-based films without altering the thermal stability. The color indicator film exhibited excellent UV- barrier properties without substantially reducing the transparency. It also showed distinct pH-responsive color-changing properties in the pH range of 2-12, showing excellent acid and base gas sensing properties. The shikonin-added film showed potent antimicrobial activity against food-borne pathogenic bacteria, and the color indicator films exhibited intense antioxidant activities. The CMC/agar-based color indicator films with improved physical and functional properties are likely to be used in active and intelligent food packaging applications.
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Affiliation(s)
- Swarup Roy
- Department of Food and Nutrition, BioNanocomposite Research Center, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Hyun-Ji Kim
- Department of Food and Nutrition, BioNanocomposite Research Center, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Jong-Whan Rhim
- Department of Food and Nutrition, BioNanocomposite Research Center, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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18
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Attah AF, Fagbemi AA, Olubiyi O, Dada-Adegbola H, Oluwadotun A, Elujoba A, Babalola CP. Therapeutic Potentials of Antiviral Plants Used in Traditional African Medicine With COVID-19 in Focus: A Nigerian Perspective. Front Pharmacol 2021; 12:596855. [PMID: 33981214 PMCID: PMC8108136 DOI: 10.3389/fphar.2021.596855] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by an infectious novel strain of coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which was earlier referred to as 2019-nCoV. The respiratory disease is the most consequential global public health crisis of the 21st century whose level of negative impact increasingly experienced globally has not been recorded since World War II. Up till now, there has been no specific globally authorized antiviral drug, vaccines, supplement or herbal remedy available for the treatment of this lethal disease except preventive measures, supportive care and non-specific treatment options adopted in different countries via divergent approaches to halt the pandemic. However, many of these interventions have been documented to show some level of success particularly the Traditional Chinese Medicine while there is paucity of well reported studies on the impact of the widely embraced Traditional African Medicines (TAM) adopted so far for the prevention, management and treatment of COVID-19. We carried out a detailed review of publicly available data, information and claims on the potentials of indigenous plants used in Sub-Saharan Africa as antiviral remedies with potentials for the prevention and management of COVID-19. In this review, we have provided a holistic report on evidence-based antiviral and promising anti-SARS-CoV-2 properties of African medicinal plants based on in silico evidence, in vitro assays and in vivo experiments alongside the available data on their mechanistic pharmacology. In addition, we have unveiled knowledge gaps, provided an update on the effort of African Scientific community toward demystifying the dreadful SARS-CoV-2 micro-enemy of man and have documented popular anti-COVID-19 herbal claims emanating from the continent for the management of COVID-19 while the risk potentials of herb-drug interaction of antiviral phytomedicines when used in combination with orthodox drugs have also been highlighted. This review exercise may lend enough credence to the potential value of African medicinal plants as possible leads in anti-COVID-19 drug discovery through research and development.
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Affiliation(s)
- Alfred Francis Attah
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin, Nigeria
| | - Adeshola Adebayo Fagbemi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Olujide Olubiyi
- Department of Pharmaceutical Chemistry, Obafemi Awolowo University, Ile-Ife, Nigeria
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Hannah Dada-Adegbola
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Anthony Elujoba
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Chinedum Peace Babalola
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
- Centre for Drug Discovery, Development and Production, University of Ibadan, Ibadan, Nigeria
- College of Basic Medical Sciences, Chrisland University, Abeokuta, Nigeria
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19
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Majumdar S, Verma R, Saha A, Bhattacharyya P, Maji P, Surjit M, Kundu M, Basu J, Saha S. Perspectives About Modulating Host Immune System in Targeting SARS-CoV-2 in India. Front Genet 2021; 12:637362. [PMID: 33664772 PMCID: PMC7921795 DOI: 10.3389/fgene.2021.637362] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/19/2021] [Indexed: 12/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of coronavirus induced disease-2019 (COVID-19), is a type of common cold virus responsible for a global pandemic which requires immediate measures for its containment. India has the world's largest population aged between 10 and 40 years. At the same time, India has a large number of individuals with diabetes, hypertension and kidney diseases, who are at a high risk of developing COVID-19. A vaccine against the SARS-CoV-2, may offer immediate protection from the causative agent of COVID-19, however, the protective memory may be short-lived. Even if vaccination is broadly successful in the world, India has a large and diverse population with over one-third being below the poverty line. Therefore, the success of a vaccine, even when one becomes available, is uncertain, making it necessary to focus on alternate approaches of tackling the disease. In this review, we discuss the differences in COVID-19 death/infection ratio between urban and rural India; and the probable role of the immune system, co-morbidities and associated nutritional status in dictating the death rate of COVID-19 patients in rural and urban India. Also, we focus on strategies for developing masks, vaccines, diagnostics and the role of drugs targeting host-virus protein-protein interactions in enhancing host immunity. We also discuss India's strengths including the resources of medicinal plants, good food habits and the role of information technology in combating COVID-19. We focus on the Government of India's measures and strategies for creating awareness in the containment of COVID-19 infection across the country.
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Affiliation(s)
| | - Rohit Verma
- Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Avishek Saha
- Ubiquitous Analytical Techniques, CSIR-Central Scientific Instruments Organisation, Chandigarh, India
| | | | - Pradipta Maji
- Biomedical Imaging and Bioinformatics Lab, Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
| | - Milan Surjit
- Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | | | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata, India
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20
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Active and intelligent gellan gum-based packaging films for controlling anthocyanins release and monitoring food freshness. Carbohydr Polym 2021; 254:117410. [DOI: 10.1016/j.carbpol.2020.117410] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/08/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022]
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21
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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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22
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Kalmankar NV, Venkatesan R, Balaram P, Sowdhamini R. Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis. Sci Rep 2020; 10:12658. [PMID: 32728092 PMCID: PMC7391643 DOI: 10.1038/s41598-020-69452-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/10/2020] [Indexed: 01/20/2023] Open
Abstract
Clitoria ternatea a perennial climber of the Fabaceae family, is well known for its agricultural and medical applications. It is also currently the only known member of the Fabaceae family that produces abundant amounts of the ultra-stable macrocyclic peptides, cyclotides, across all tissues. Cyclotides are a class of gene-encoded, disulphide-rich, macrocyclic peptides (26–37 residues) acting as defensive metabolites in several plant species. Previous transcriptomic studies have demonstrated the genetic origin of cyclotides from the Fabaceae plant family to be embedded in the albumin-1 genes, unlike its counterparts in other plant families. However, the complete mechanism of its biosynthesis and the repertoire of enzymes involved in cyclotide folding and processing remains to be understood. In this study, using RNA-Seq data and de novo transcriptome assembly of Clitoria ternatea, we have identified 71 precursor genes of cyclotides. Out of 71 unique cyclotide precursor genes obtained, 51 sequences display unique cyclotide domains, of which 26 are novel cyclotide sequences, arising from four individual tissues. MALDI-TOF mass spectrometry analysis of fractions from different tissue extracts, coupled with precursor protein sequences obtained from transcriptomic data, established the cyclotide diversity in this plant species. Special focus in this study has also been on identifying possible enzymes responsible for proper folding and processing of cyclotides in the cell. Transcriptomic mining for oxidative folding enzymes such as protein-disulphide isomerases (PDI), ER oxidoreductin-1 (ERO1) and peptidylprolyl cis-trans isomerases (PPIases)/cyclophilins, and their levels of expression are also reported. In particular, it was observed that the CtPDI genes formed plant-specific clusters among PDI genes as compared to those from other plant species. Collectively, this work provides insights into the biogenesis of the medicinally important cyclotides and establishes the expression of certain key enzymes participating in peptide biosynthesis. Also, several novel cyclotide sequences are reported and precursor sequences are analysed in detail. In the absence of a published reference genome, a comprehensive transcriptomics approach was adopted to provide an overview of diverse properties and constituents of C. ternatea.
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Affiliation(s)
- Neha V Kalmankar
- National Centre for Biological Sciences (TIFR), GKVK Campus, 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
| | - Radhika Venkatesan
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.,Department of Biological Sciences, Indian Institute of Science, Education and Research, Kolkata, Mohanpur, West Bengal, 741246, India
| | - Padmanabhan Balaram
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.
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23
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Zhao N, Cheng M, Lv W, Wu Y, Liu D, Zhang X. Peptides as Potential Biomarkers for Authentication of Mountain-Cultivated Ginseng and Cultivated Ginseng of Different Ages Using UPLC-HRMS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2263-2275. [PMID: 31986019 DOI: 10.1021/acs.jafc.9b05568] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The growth conditions and age of Panax ginseng are vital for determining the quality of the ginseng plant. However, the considerable difference in price according to the cultivation method and period of P. ginseng leads to its adulteration in the trade market. We herein focused on ginseng peptides and the possibility of these peptides to be used as biomarker(s) for discrimination of P. ginseng. We applied an ultraperformance liquid chromatography-high resolution mass spectrometry-based peptidomics approach to characterize ginseng peptides and discover novel peptide biomarkers for authentication of mountain-cultivated ginseng (MCG). We identified 52 high-confidence peptides and screened 20 characteristic peptides differentially expressed between MCG and cultivated ginseng (CG). Intriguingly, 6 differential peptides were expressed significantly in MCG and originated from dehydrins that accumulated during cold or drought conditions. In addition, 14 other differential peptides that were significantly expressed in CG derived from ginseng major protein, an essential protein for nitrogen storage. These biological associations confirmed the reliability and credibility of the differential peptides. Additionally, we determined several robust peptide biomarkers for discrimination of MCG through a precise selection process. These findings demonstrate the potential of peptide biomarkers for identification and quality control of P. ginseng in addition to ginsenoside analysis.
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Affiliation(s)
- Nan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
- University of Chinese Academy of Sciences , Yuquan Road 19 , Beijing 100049 , China
| | - Mengchun Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
| | - Wei Lv
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
- School of Chemistry and Chemical Engineering , North Minzu University , Yinchuan 750021 , China
| | - Yulin Wu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
- Henan University of Chinese Medicine , Jinshui East Road 156 , Zhengzhou 450046 , China
| | - Dan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
| | - Xiaozhe Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China
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Tammineni R, Gulati P, Kumar S, Mohanty A. An overview of acyclotides: Past, present and future. PHYTOCHEMISTRY 2020; 170:112215. [PMID: 31812106 DOI: 10.1016/j.phytochem.2019.112215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
Acyclotides are plant-based, acyclic miniproteins with cystine knot motif formed by three conserved disulfide linkages and lack head to tail ligation. Acyclotides may not necessarily be less stable, even though they lack cyclic backbone, as the conserved cystine knot feature provides the required stability. Violacin A was the first acyclotide, isolated from Viola odorata in 2006. Until now, acyclotides have been reported from five dicot families (Violaceae, Rubiaceae, Cucurbitaceae, Solanaceae, Fabaceae) and one monocot family (Poaceae). In Poaceae, only acyclotides have been found whereas in dicot families both cyclotides and acyclotides have been isolated. In last 15 years, several acyclotides with antimicrobial, cytotoxic and hemolytic bioactivities have been discovered. Thus, although many naturally expressed acyclotides do exhibit bioactivities, the linearization of the cyclic peptides may result in loss of bioactivities. Although, bioactivities of acyclotides are comparable to their cyclic counterparts, the numbers of isolated acyclotides are still few. Further, those discovered, have the scope to be screened for agriculturally important activities (insecticidal, anti-helminthic, molluscicidal) and pharmaceutical properties (anticancer, anti-HIV, immuno-stimulant). The feasibility of application of acyclotides is because of their relatively less complex biological synthesis compared to cyclotides, as the cyclization step is not needed. This attribute facilitates the production of transgenic crops and/or its expression in heterologous organisms, lacking cyclization machinery. Keeping in view the bioactivities and the wide array of emerging potential applications of acyclotides, the present review discusses their distribution in plants, gene and protein structure, biosynthesis, bioactivities and mechanism of action. Further, their potential applications and future perspectives to exploit them in agriculture and pharmaceutical industries have been highlighted.
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Affiliation(s)
- Ramya Tammineni
- Bioinformatics Infrastructure Facility, Gargi College, University of Delhi, India
| | - Pooja Gulati
- Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Sanjay Kumar
- Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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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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26
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Zainab R, Akram M, Daniyal M, Riaz M. Awareness and Current Therapeutics of Asthma. Dose Response 2019; 17:1559325819870900. [PMID: 31523203 PMCID: PMC6728691 DOI: 10.1177/1559325819870900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/11/2019] [Accepted: 06/18/2019] [Indexed: 01/21/2023] Open
Abstract
Introduction: Asthma is a serious allergic disorder of the respiratory system. It affects
about 300 million people worldwide. This has a great burden on medical
treatment. Several medicines are available, but they have many serious side
effects. Therefore, there is a need to search for a new therapeutic agent
with no or minimal side effects while most economical for patients. In folk
medicine, antiasthmatics herbal medicine has been used and showed potential
therapeutic antiasthmatic efficacy due to the presence of potential
bioactive compounds. Methods: Different databases were searched (ie, Embase, PubMed, CBM, AMED, and
CINAHL). We have reviewed the published data of the last 20 years. We used
MeSH terms “asthma” herbal treatment of asthma, allopathic treatment of
asthma, and treatment strategies for asthma. The traditional medicine was
compared with modern medicine and the same pharmacotherapies alone or with
placebo. The methodology was evaluated by using the GRADE summary of Finding
tables and Cochrane Risk of Bias Tool. Results: There have been some clear-cut indications toward the recognition of further
molecular and cellular mechanisms of asthma. Most of them recommend a
further target for treatment. The novel procedures, biologics, and
pharmaceuticals are evaluated. Both allopathic and herbal treatments of
asthma are effective. Due to none or lesser side effects, herbal medicines
are safer than conventional medicine. Conclusion: The preliminary documentation of the plants discussed in the review show the
presence of several secondary metabolites that are responsible for the
management of asthma and its relevant complications. Further research
studies are needed to identify the bioactive compounds from these plants
that have potential efficacy to cure asthma, and clinically based studies
are needed to search for a complete cure for this disease.
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Affiliation(s)
- Rida Zainab
- Department of Eastern Medicine, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Akram
- Department of Eastern Medicine, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Daniyal
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Muhammad Riaz
- Department of Allied Health Sciences, University of Sargodha, Sargodha, Pakistan
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27
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Oguis GK, Gilding EK, Jackson MA, Craik DJ. Butterfly Pea ( Clitoria ternatea), a Cyclotide-Bearing Plant With Applications in Agriculture and Medicine. FRONTIERS IN PLANT SCIENCE 2019; 10:645. [PMID: 31191573 PMCID: PMC6546959 DOI: 10.3389/fpls.2019.00645] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/29/2019] [Indexed: 05/16/2023]
Abstract
The perennial leguminous herb Clitoria ternatea (butterfly pea) has attracted significant interest based on its agricultural and medical applications, which range from use as a fodder and nitrogen fixing crop, to applications in food coloring and cosmetics, traditional medicine and as a source of an eco-friendly insecticide. In this article we provide a broad multidisciplinary review that includes descriptions of the physical appearance, distribution, taxonomy, habitat, growth and propagation, phytochemical composition and applications of this plant. Notable amongst its repertoire of chemical components are anthocyanins which give C. ternatea flowers their characteristic blue color, and cyclotides, ultra-stable macrocyclic peptides that are present in all tissues of this plant. The latter are potent insecticidal molecules and are implicated as the bioactive agents in a plant extract used commercially as an insecticide. We include a description of the genetic origin of these peptides, which interestingly involve the co-option of an ancestral albumin gene to produce the cyclotide precursor protein. The biosynthesis step in which the cyclic peptide backbone is formed involves an asparaginyl endopeptidase, of which in C. ternatea is known as butelase-1. This enzyme is highly efficient in peptide ligation and has been the focus of many recent studies on peptide ligation and cyclization for biotechnological applications. The article concludes with some suggestions for future studies on this plant, including the need to explore possible synergies between the various peptidic and non-peptidic phytochemicals.
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Affiliation(s)
| | | | | | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
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28
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Kam A, Loo S, Dutta B, Sze SK, Tam JP. Plant-derived mitochondria-targeting cysteine-rich peptide modulates cellular bioenergetics. J Biol Chem 2019; 294:4000-4011. [PMID: 30674551 PMCID: PMC6422099 DOI: 10.1074/jbc.ra118.006693] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/07/2019] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are attractive therapeutic targets for developing agents to delay age-related frailty and diseases. However, few promising leads have been identified from natural products. Previously, we identified roseltide rT1, a hyperstable 27-residue cysteine-rich peptide from Hibiscus sabdariffa, as a knottin-type neutrophil elastase inhibitor. Here, we show that roseltide rT1 is also a cell-penetrating, mitochondria-targeting peptide that increases ATP production. Results from flow cytometry, live-cell imaging, pulldown assays, and genetically-modified cell lines supported that roseltide rT1 enters cells via glycosaminoglycan-dependent endocytosis, and enters the mitochondria through TOM20, a mitochondrial protein import receptor. We further showed that roseltide rT1 increases cellular ATP production via mitochondrial membrane hyperpolarization. Using biotinylated roseltide rT1 for target identification and proteomic analysis, we showed that human mitochondrial membrane ATP synthase subunit O is an intramitochondrial target. Collectively, these data support our discovery that roseltide rT1 is a first-in-class mitochondria-targeting, cysteine-rich peptide with potentials to be developed into tools to further our understanding of mitochrondria-related diseases.
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Affiliation(s)
- Antony Kam
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Shining Loo
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Bamaprasad Dutta
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Siu Kwan Sze
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - James P Tam
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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29
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Abstract
A biomimetic one-step ligase-catalyzed cyclo-oligomerization mediated by butelase 1, an Asn/Asp-specific ligase, is introduced that is time-, concentration-, length-, and sequence-dependent. This reaction yields cyclic mono-, di-, tri-, and tetramers from peptide precursors containing 3-15 amino acids ended with Asn and a His-Val tail. The cyclomonomers were favored when the peptide lengths were >9 amino acids. A turn-forming Pro residue at the P2 position favored the formation of higher-order cyclo-oligomers.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Xiaohong Zhang
- 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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30
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Trends in herbgenomics. SCIENCE CHINA-LIFE SCIENCES 2018; 62:288-308. [PMID: 30128965 DOI: 10.1007/s11427-018-9352-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
Abstract
From Shen Nong's Herbal Classic (Shennong Bencao Jing) to the Compendium of Materia Medica (Bencao Gangmu) and the first scientific Nobel Prize for the mainland of China, each milestone in the historical process of the development of traditional Chinese medicine (TCM) involves screening, testing and integrating. After thousands of years of inheritance and development, herbgenomics (bencaogenomics) has bridged the gap between TCM and international advanced omics studies, promoting the application of frontier technologies in TCM. It is a discipline that uncovers the genetic information and regulatory networks of herbs to clarify their molecular mechanism in the prevention and treatment of human diseases. The main theoretical system includes genomics, functional genomics, proteomics, transcriptomics, metabolomics, epigenomics, metagenomics, synthetic biology, pharmacogenomics of TCM, and bioinformatics, among other fields. Herbgenomics is mainly applicable to the study of medicinal model plants, genomic-assisted breeding, herbal synthetic biology, protection and utilization of gene resources, TCM quality evaluation and control, and TCM drug development. Such studies will accelerate the application of cutting-edge technologies, revitalize herbal research, and strongly promote the development and modernization of TCM.
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31
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Liu FJ, Zhu ZH, Jiang Y, Li HJ. A pair of cyclopeptide epimers from the seeds of Celosia argentea. Chin J Nat Med 2018; 16:63-69. [PMID: 29425591 DOI: 10.1016/s1875-5364(18)30030-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Indexed: 12/16/2022]
Abstract
Two cyclopeptides, celogentin L (1) and its epimer lyciumin A (2) were firstly isolated from Celosia argentea L.. The planar structures of the two compounds were fully determined by spectroscopic data, including 1D-, 2D-NMR, and HR-ESI/MS. The absolute configurations of amino acid components were assigned via chiral-phase HPLC analyses after acid hydrolysis. Furthermore, the configuration of C-N linkage at the glycine Cα was elucidated by extensive analyses of 2D-NMR and comparison of the experimental and calculated electronic circular dichroism (ECD) spectra. Cytotoxicity of the two compounds against human alveolar epithelial A549, hepatocellular carcinoma HepG2, and cervical cancer Hela cell lines was assayed. Although both of them were inactive in these cells, the present findings add new facets for the chemistry of Celosia argentea.
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Affiliation(s)
- Feng-Jie Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | | | - Yan Jiang
- School of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Hui-Jun Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
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32
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Molecular basis for the production of cyclic peptides by plant asparaginyl endopeptidases. Nat Commun 2018; 9:2411. [PMID: 29925835 PMCID: PMC6010433 DOI: 10.1038/s41467-018-04669-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/09/2018] [Indexed: 11/08/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) are proteases that have crucial roles in plant defense and seed storage protein maturation. Select plant AEPs, however, do not function as proteases but as transpeptidases (ligases) catalyzing the intra-molecular ligation of peptide termini, which leads to peptide cyclization. These ligase-type AEPs have potential biotechnological applications ranging from in vitro peptide engineering to plant molecular farming, but the structural features enabling these enzymes to catalyze peptide ligation/cyclization rather than proteolysis are currently unknown. Here, we compare the sequences, structures, and functions of diverse plant AEPs by combining molecular modeling, sequence space analysis, and functional testing in planta. We find that changes within the substrate-binding pocket and an adjacent loop, here named the “marker of ligase activity”, together play a key role for AEP ligase efficiency. Identification of these structural determinants may facilitate the discovery of more ligase-type AEPs and the engineering of AEPs with tailored catalytic properties. Asparaginyl endopeptidases (AEPs) are plant proteases that can also function as ligases, catalyzing the production of cyclic plant peptides. Here, the authors identify structural features that govern AEP ligase activity, providing insights to aid the discovery and engineering of ligase-type AEPs.
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33
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Loo S, Kam A, Xiao T, Tam JP. Bleogens: Cactus-Derived Anti-Candida Cysteine-Rich Peptides with Three Different Precursor Arrangements. FRONTIERS IN PLANT SCIENCE 2017; 8:2162. [PMID: 29312404 PMCID: PMC5743680 DOI: 10.3389/fpls.2017.02162] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 12/07/2017] [Indexed: 05/23/2023]
Abstract
Cysteine-rich peptides (CRPs) play important host-defense roles in plants. However, information concerning CRPs in the Cactaceae (cactus) family is limited, with only a single cactus-derived CRP described to date. Here, we report the identification of 15 novel CRPs with three different precursor architectures, bleogens pB1-15 from Pereskia bleo of the Cactaceae family. By combining proteomic and transcriptomic methods, we showed that the prototype, bleogen pB1, contained 36 amino acid residues, a six-cysteine motif typical of the six-cysteine-hevein-like peptide (6C-HLP) family, and a type I two-domain precursor consisting of an endoplasmic reticulum (ER) and a mature domain. In contrast, the precursors of the other 14 bleogens contained a type II three-domain architecture with a propeptide domain inserted between the ER and the mature bleogen domain. Four of these 14 bleogens display a third type of architecture with a tandemly repeating bleogen domain. A search of the Onekp database revealed that <1% plant species possess three different precursor architectures for the biosynthesis of 6C-HLPs, including Lophophora williamsii, Pereskia aculeate, Portulaca cryptopetala, Portulaca oleracea, Portulaca suffruticosa, and Talinum sp. NMR analysis confirmed that bleogen pB1 has cystine-knot disulfide connectivity as well as a two-beta-sheet and a four-loop structural fold that is similar to other 6C-HLPs. Sequence analysis, structural studies, and in silico modeling revealed that bleogen pB1 has a cation-polar-cation motif, a signature heparin-binding motif that was confirmed by heparin affinity chromatography. Cell-based assays showed that bleogen pB1 is non-toxic to mammalian cells but functions as an anti-Candida peptide. Taken together, our findings provide insight into the occurrence, functions and precursor architectures of CRPs in the cactus family.
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34
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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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35
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Tan WL, Wong KH, Lei J, Sakai N, Tan HW, Hilgenfeld R, Tam JP. Lybatides from Lycium barbarum Contain An Unusual Cystine-stapled Helical Peptide Scaffold. Sci Rep 2017; 7:5194. [PMID: 28701689 PMCID: PMC5507927 DOI: 10.1038/s41598-017-05037-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/22/2017] [Indexed: 12/27/2022] Open
Abstract
Cysteine-rich peptides (CRPs) of 2–6 kDa are generally thermally and proteolytically stable because of their multiple cross-bracing disulfide bonds. Here, we report the discovery and characterization of two novel cystine-stapled CRPs, designated lybatide 1 and 2 (lyba1 and lyba2), from the cortex of Lycium barbarum root. Lybatides, 32 to 33 amino acids in length, are hyperstable and display a novel disulfide connectivity with a cysteine motif of C-C-C-C-CC-CC which contains two pairs of adjacent cysteines (-CC-CC). X-ray structure analysis revealed the presence of a single cystine-stabilized (α + π)-helix in lyba2, a rare feature of CRPs. Together, our results suggest that lybatides, one of the smallest four-disulfide-constrained plant CRPs, is a new family of CRPs. Additionally, this study provides new insights into the molecular diversity of plant cysteine-rich peptides and the unusual lybatide scaffold could be developed as a useful template for peptide engineering and therapeutic development.
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Affiliation(s)
- Wei Liang Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ka H Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck, Germany
| | - Naoki Sakai
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Hong Wei Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck, Germany
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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36
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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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37
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Nguyen GKT, Qiu Y, Cao Y, Hemu X, Liu CF, Tam JP. Butelase-mediated cyclization and ligation of peptides and proteins. Nat Protoc 2016; 11:1977-1988. [DOI: 10.1038/nprot.2016.118] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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38
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Nguyen GKT, Hemu X, Quek JP, Tam JP. Butelase-Mediated Macrocyclization ofd-Amino-Acid-Containing Peptides. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607188] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Giang K. T. Nguyen
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Xinya Hemu
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Jun-Ping Quek
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - James P. Tam
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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39
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Nguyen GKT, Hemu X, Quek JP, Tam JP. Butelase-Mediated Macrocyclization of d-Amino-Acid-Containing Peptides. Angew Chem Int Ed Engl 2016; 55:12802-6. [PMID: 27624217 DOI: 10.1002/anie.201607188] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Indexed: 01/19/2023]
Abstract
Macrocyclic compounds have received increasing attention in recent years. With their large surface area, they hold promise for inhibiting protein-protein interactions, a chemical space that was thought to be undruggable. Although many chemical methods have been developed for peptide macrocyclization, enzymatic methods have emerged as a promising new economical approach. Thus far, most enzymes have been shown to act on l-peptides; their ability to cyclize d-amino-acid-containing peptides has rarely been documented. Herein we show that macrocycles consisting of d-amino acids, except for the Asn residue at the ligating site, were efficiently synthesized by butelase 1, an Asn/Asp-specific ligase. Furthermore, by using a peptide-library approach, we show that butelase 1 tolerates most of the d-amino acid residues at the P1'' and P2'' positions.
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Affiliation(s)
- Giang K T Nguyen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jun-Ping Quek
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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