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Machine learning-guided discovery and design of non-hemolytic peptides. Sci Rep 2020; 10:16581. [PMID: 33024236 PMCID: PMC7538962 DOI: 10.1038/s41598-020-73644-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 09/18/2020] [Indexed: 12/13/2022] Open
Abstract
Reducing hurdles to clinical trials without compromising the therapeutic promises of peptide candidates becomes an essential step in peptide-based drug design. Machine-learning models are cost-effective and time-saving strategies used to predict biological activities from primary sequences. Their limitations lie in the diversity of peptide sequences and biological information within these models. Additional outlier detection methods are needed to set the boundaries for reliable predictions; the applicability domain. Antimicrobial peptides (AMPs) constitute an extensive library of peptides offering promising avenues against antibiotic-resistant infections. Most AMPs present in clinical trials are administrated topically due to their hemolytic toxicity. Here we developed machine learning models and outlier detection methods that ensure robust predictions for the discovery of AMPs and the design of novel peptides with reduced hemolytic activity. Our best models, gradient boosting classifiers, predicted the hemolytic nature from any peptide sequence with 95–97% accuracy. Nearly 70% of AMPs were predicted as hemolytic peptides. Applying multivariate outlier detection models, we found that 273 AMPs (~ 9%) could not be predicted reliably. Our combined approach led to the discovery of 34 high-confidence non-hemolytic natural AMPs, the de novo design of 507 non-hemolytic peptides, and the guidelines for non-hemolytic peptide design.
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Romero SM, Cardillo AB, Martínez Ceron MC, Camperi SA, Giudicessi SL. Temporins: An Approach of Potential Pharmaceutic Candidates. Surg Infect (Larchmt) 2019; 21:309-322. [PMID: 31804896 DOI: 10.1089/sur.2019.266] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial peptides (AMPs), also known as host defense peptides, are small and mostly polycationic molecules that form part of the innate immune response. There are currently more than 3000 experimentally reported AMPs. Particularly in frogs, the temporin family has been discovered as potential AMPs. The aim of this work is to review the latest publications about this class of peptides, discuss their properties, and present an update of the last studies and new discoveries in the field. More than 130 temporins have been identified in this family. The most studied temporins are temporin A (TA), temporin B (TB), and temporin L (TL). These peptides showed antimicrobial activity against gram-negative, gram-positive bacteria and fungi. Since the discovery of temporins in 1996, several groups of researchers isolated different peptides from various species of frogs that were included as members of this family. Although antimicrobial activity of many temporins has not been analyzed yet, most of them showed antimicrobial and antifungal activities. A combination of nanotechnology and AMPs for temporins in different antimicrobial treatments could be a promising alternative for resistant pathogens. These studies demonstrate that, even with the advancement in scientific research on the composition and antimicrobial activity of temporins, further studies are necessary to wholly understand their components and mechanisms of action.
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Affiliation(s)
- Stella Maris Romero
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Alejandra Beatriz Cardillo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina
| | - María Camila Martínez Ceron
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina
| | - Silvia Andrea Camperi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina
| | - Silvana Laura Giudicessi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina
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3
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Juretić D, Sonavane Y, Ilić N, Gajski G, Goić-Barišić I, Tonkić M, Kozic M, Maravić A, Pellay FX, Zoranić L. Designed peptide with a flexible central motif from ranatuerins adapts its conformation to bacterial membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2655-2668. [DOI: 10.1016/j.bbamem.2018.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/28/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022]
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Ockleford C, Adriaanse P, Berny P, Brock T, Duquesne S, Grilli S, Hernandez-Jerez AF, Bennekou SH, Klein M, Kuhl T, Laskowski R, Machera K, Pelkonen O, Pieper S, Stemmer M, Sundh I, Teodorovic I, Tiktak A, Topping CJ, Wolterink G, Aldrich A, Berg C, Ortiz-Santaliestra M, Weir S, Streissl F, Smith RH. Scientific Opinion on the state of the science on pesticide risk assessment for amphibians and reptiles. EFSA J 2018; 16:e05125. [PMID: 32625798 PMCID: PMC7009658 DOI: 10.2903/j.efsa.2018.5125] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Following a request from EFSA, the Panel on Plant Protection Products and their Residues developed an opinion on the science to support the potential development of a risk assessment scheme of plant protection products for amphibians and reptiles. The coverage of the risk to amphibians and reptiles by current risk assessments for other vertebrate groups was investigated. Available test methods and exposure models were reviewed with regard to their applicability to amphibians and reptiles. Proposals were made for specific protection goals aiming to protect important ecosystem services and taking into consideration the regulatory framework and existing protection goals for other vertebrates. Uncertainties, knowledge gaps and research needs were highlighted.
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5
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Ockleford C, Adriaanse P, Berny P, Brock T, Duquesne S, Grilli S, Hernandez-Jerez AF, Bennekou SH, Klein M, Kuhl T, Laskowski R, Machera K, Pelkonen O, Pieper S, Stemmer M, Sundh I, Teodorovic I, Tiktak A, Topping CJ, Wolterink G, Aldrich A, Berg C, Ortiz-Santaliestra M, Weir S, Streissl F, Smith RH. Scientific Opinion on the state of the science on pesticide risk assessment for amphibians and reptiles. EFSA J 2018. [PMID: 32625798 DOI: 10.2903/j.efsa.2018.5125issn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
Following a request from EFSA, the Panel on Plant Protection Products and their Residues developed an opinion on the science to support the potential development of a risk assessment scheme of plant protection products for amphibians and reptiles. The coverage of the risk to amphibians and reptiles by current risk assessments for other vertebrate groups was investigated. Available test methods and exposure models were reviewed with regard to their applicability to amphibians and reptiles. Proposals were made for specific protection goals aiming to protect important ecosystem services and taking into consideration the regulatory framework and existing protection goals for other vertebrates. Uncertainties, knowledge gaps and research needs were highlighted.
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6
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Walke JB, Becker MH, Loftus SC, House LL, Teotonio TL, Minbiole KPC, Belden LK. Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus. PLoS One 2015; 10:e0139848. [PMID: 26445500 PMCID: PMC4596541 DOI: 10.1371/journal.pone.0139848] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/16/2015] [Indexed: 01/21/2023] Open
Abstract
The vertebrate microbiome contributes to disease resistance, but few experiments have examined the link between microbiome community structure and disease resistance functions. Chytridiomycosis, a major cause of amphibian population declines, is a skin disease caused by the fungus, Batrachochytrium dendrobatidis (Bd). In a factorial experiment, bullfrog skin microbiota was reduced with antibiotics, augmented with an anti-Bd bacterial isolate (Janthinobacterium lividum), or unmanipulated, and individuals were then either exposed or not exposed to Bd. We found that the microbial community structure of individual frogs prior to Bd exposure influenced Bd infection intensity one week following exposure, which, in turn, was negatively correlated with proportional growth during the experiment. Microbial community structure and function differed among unmanipulated, antibiotic-treated, and augmented frogs only when frogs were exposed to Bd. Bd is a selective force on microbial community structure and function, and beneficial states of microbial community structure may serve to limit the impacts of infection.
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Affiliation(s)
- Jenifer B. Walke
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
- * E-mail:
| | - Matthew H. Becker
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
| | - Stephen C. Loftus
- Department of Statistics, Virginia Tech, Blacksburg, VA, United States of America
| | - Leanna L. House
- Department of Statistics, Virginia Tech, Blacksburg, VA, United States of America
| | - Thais L. Teotonio
- Department of Chemistry, James Madison University, Harrisonburg, VA, United States of America
| | - Kevin P. C. Minbiole
- Department of Chemistry, Villanova University, Philadelphia, PA, United States of America
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
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Kozić M, Vukičević D, Simunić J, Rončević T, Antcheva N, Tossi A, Juretić D. Predicting the Minimal Inhibitory Concentration for Antimicrobial Peptides with Rana-Box Domain. J Chem Inf Model 2015; 55:2275-87. [PMID: 26332863 DOI: 10.1021/acs.jcim.5b00161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The global spreading of multidrug resistance has motivated the search for new antibiotic classes including different types of antimicrobial peptides (AMPs). Computational methods for predicting activity in terms of the minimal inhibitory concentration (MIC) of AMPs can facilitate "in silico" design and reduce the cost of synthesis and testing. We have used an original method for separating training and test data sets, both of which contain the sequences and measured MIC values of non-homologous anuran peptides having the Rana-box disulfide motif at their C-terminus. Using a more flexible profiling methodology (sideways asymmetry moment, SAM) than the standard hydrophobic moment, we have developed a two-descriptor model to predict the bacteriostatic activity of Rana-box peptides against Gram-negative bacteria--the first multilinear quantitative structure-activity relationship model capable of predicting MIC values for AMPs of widely different lengths and low identity using such a small number of descriptors. Maximal values for SAMs, as defined and calculated in our method, furthermore offer new structural insight into how different segments of a peptide contribute to its bacteriostatic activity, and this work lays the foundations for the design of active artificial AMPs with this type of disulfide bridge.
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Affiliation(s)
- Mara Kozić
- Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB, U.K
| | - Damir Vukičević
- Faculty of Science, University of Split , 21000 Split, Croatia
| | - Juraj Simunić
- Mediterranean Institute for Life Sciences , 21000 Split, Croatia
| | | | - Nikolinka Antcheva
- Department of Life Sciences, University of Trieste , 34127 Trieste, Italy
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste , 34127 Trieste, Italy
| | - Davor Juretić
- Faculty of Science, University of Split , 21000 Split, Croatia
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Wang G, Mishra B, Lau K, Lushnikova T, Golla R, Wang X. Antimicrobial peptides in 2014. Pharmaceuticals (Basel) 2015; 8:123-50. [PMID: 25806720 PMCID: PMC4381204 DOI: 10.3390/ph8010123] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 12/13/2022] Open
Abstract
This article highlights new members, novel mechanisms of action, new functions, and interesting applications of antimicrobial peptides reported in 2014. As of December 2014, over 100 new peptides were registered into the Antimicrobial Peptide Database, increasing the total number of entries to 2493. Unique antimicrobial peptides have been identified from marine bacteria, fungi, and plants. Environmental conditions clearly influence peptide activity or function. Human α-defensin HD-6 is only antimicrobial under reduced conditions. The pH-dependent oligomerization of human cathelicidin LL-37 is linked to double-stranded RNA delivery to endosomes, where the acidic pH triggers the dissociation of the peptide aggregate to release its cargo. Proline-rich peptides, previously known to bind to heat shock proteins, are shown to inhibit protein synthesis. A model antimicrobial peptide is demonstrated to have multiple hits on bacteria, including surface protein delocalization. While cell surface modification to decrease cationic peptide binding is a recognized resistance mechanism for pathogenic bacteria, it is also used as a survival strategy for commensal bacteria. The year 2014 also witnessed continued efforts in exploiting potential applications of antimicrobial peptides. We highlight 3D structure-based design of peptide antimicrobials and vaccines, surface coating, delivery systems, and microbial detection devices involving antimicrobial peptides. The 2014 results also support that combination therapy is preferred over monotherapy in treating biofilms.
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Affiliation(s)
- Guangshun Wang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA.
| | - Biswajit Mishra
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - Kyle Lau
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - Tamara Lushnikova
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - Radha Golla
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - Xiuqing Wang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
- Institute of Clinical Laboratory, Ningxia Medical University, Yinchuan 750004, China
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9
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Antwis RE, Purcell R, Walker SL, Fidgett AL, Preziosi RF. Effects of visible implanted elastomer marking on physiological traits of frogs. CONSERVATION PHYSIOLOGY 2014; 2:cou042. [PMID: 27293663 PMCID: PMC4732488 DOI: 10.1093/conphys/cou042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/15/2014] [Accepted: 08/19/2014] [Indexed: 06/06/2023]
Abstract
Amphibians possess innate immune defences, including antimicrobial peptides and symbiotic bacterial communities, that can protect them from infectious diseases, including chytridiomycosis. On-going research is attempting to use amphibian symbiotic bacteria to develop probiotic treatments that can protect hosts from the causative agent of chytridiomycosis, the fungal pathogen Batrachochytrium dendrobatidis. Events that cause disruption of symbiotic bacterial communities or deplete peptide stores could increase the susceptibility of individuals to disease and may have implications for amphibians involved in probiotic trials or time course studies that investigate symbiotic bacterial communities. It has previously been shown that passive integrated transponder tagging of frogs causes a rapid (within 24 h) and major proliferation of micro-organisms on the skin. Here, we show that marking of red-eyed tree frogs (Agalychnis callidryas) with visible elastomer has no effect on adrenal response (represented by faecal glucocorticoid metabolite concentrations) or peptide production, although there was evidence of a slightly greater microbial abundance associated with the skin of marked frogs 2 weeks after tagging. The results indicate that visible elastomer may be a preferable marking technique to passive integrated transponder tagging, particularly in the context of probiotic trials or time course studies that investigate symbiotic bacterial communities. More work is required to determine the effects of different marking techniques on physiological responses of amphibians, whether these physiological responses are consistent across host species and whether such 'non-invasive' marking methods affect the susceptibility of amphibians to infectious pathogens, such as B. dendrobatidis.
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Affiliation(s)
- Rachael E. Antwis
- Faculty of Life Sciences, University of Manchester, Carys Bannister Building, Dover Street, Manchester M13 9PL, UK
| | | | | | | | - Richard F. Preziosi
- Faculty of Life Sciences, University of Manchester, Carys Bannister Building, Dover Street, Manchester M13 9PL, UK
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Siano A, Húmpola MV, de Oliveira E, Albericio F, Simonetta AC, Lajmanovich R, Tonarelli GG. Antimicrobial peptides from skin secretions of Hypsiboas pulchellus (Anura: Hylidae). JOURNAL OF NATURAL PRODUCTS 2014; 77:831-841. [PMID: 24717080 DOI: 10.1021/np4009317] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The skin of many amphibians produces a large repertoire of antimicrobial peptides that are crucial in the first line of defense against microbial invasion. Despite the immense richness of wild amphibians in Argentina, knowledge about peptides with antimicrobial properties is limited to a few species. Here we used LC-MS-MS to analyze samples of Hypsiboas pulchellus skin with the aim to identify antimicrobial peptides in the mass range of 1000 to 2000 Da. Twenty-three novel sequences were identified by MS, three of which were selected for chemical synthesis and further studies. The three synthetic peptides, named P1-Hp-1971, P2-Hp-1935, and P3-Hp-1891, inhibited the growth of two ATCC strains: Escherichia coli (MIC: 16, 33, and 17 μM, respectively) and Staphylococcus aureus (MIC: 8, 66, and 17 μM, respectively). P1-Hp-1971 and P3-Hp-1891 were the most active peptides. P1-Hp-1971, which showed the highest therapeutic indices (40 for E. coli and 80 for S. aureus), is a proline-glycine-rich peptide with a highly unordered structure, while P3-Hp-1891 adopts an amphipathic α-helical structure in the presence of 2,2,2-trifluoroethanol and anionic liposomes. This is the first peptidomic study of Hypsiboas pulchellus skin secretions to allow the identification of antimicrobial peptides.
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Affiliation(s)
- Alvaro Siano
- Departamento de Química Orgánica, Facultad de Bioquímica y Cs. Biológicas (FBCB), Universidad Nacional del Litoral (UNL) , Ciudad Universitaria, 3000, Santa Fe, Argentina
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Parallel peptidome and transcriptome analyses of amphibian skin secretions using archived frozen acid-solvated samples. Mol Biotechnol 2013; 54:187-97. [PMID: 22573142 DOI: 10.1007/s12033-012-9551-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Amphibian skin secretions are unique sources of bioactive peptides and their donor species are currently rapidly disappearing from the biosphere. Here, we report that both peptides and polyadenylated mRNAs from skin granular glands remain amenable to study in samples of stimulated skin secretions following their storage in 0.1 % aqueous trifluoroacetic acid at -20 °C for many years. Frozen acidified solutions of toad (Bombina variegata) skin secretions, stored for 12 years, were thawed and samples removed for direct reverse phase HPLC fractionation. Additional samples were removed, snap frozen and lyophilised for construction of cDNA libraries following polyadenylated mRNA capture using magnetic oligo-dT beads and reverse transcription. Using the bombesin and bradykinin peptides found in bombinid toad skin as models, individual variant peptides of each type were located in reverse phase HPLC fractions and their corresponding biosynthetic precursor-encoding mRNA transcripts were cloned from the cDNA library using a RACE PCR strategy. This study illustrates unequivocally that both amphibian skin secretion peptides and their biosynthetic precursor-encoding polyadenylated mRNAs are stable in frozen acid-solvated skin secretion samples for considerable periods of time-a finding that may have fundamental implications in the study of archived materials but also in the wider field of molecular biology.
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12
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Skin Gland Morphology and Secretory Peptides in NaturalizedLitoriaSpecies in New Zealand. J HERPETOL 2013. [DOI: 10.1670/12-246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Cologna CT, Cardoso JDS, Jourdan E, Degueldre M, Upert G, Gilles N, Uetanabaro APT, Costa Neto EM, Thonart P, de Pauw E, Quinton L. Peptidomic comparison and characterization of the major components of the venom of the giant ant Dinoponera quadriceps collected in four different areas of Brazil. J Proteomics 2013; 94:413-22. [DOI: 10.1016/j.jprot.2013.10.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/04/2013] [Accepted: 10/02/2013] [Indexed: 10/26/2022]
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Evaluation of the skin peptide defenses of the Oregon spotted frog Rana pretiosa against infection by the chytrid fungus Batrachochytrium dendrobatidis. J Chem Ecol 2013; 39:797-805. [PMID: 23653106 DOI: 10.1007/s10886-013-0294-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 04/08/2013] [Accepted: 04/23/2013] [Indexed: 12/30/2022]
Abstract
Population declines due to amphibian chytridiomycosis among selected species of ranid frogs from western North America have been severe, but there is evidence that the Oregon spotted frog, Rana pretiosa Baird and Girard, 1853, displays resistance to the disease. Norepinephrine-stimulated skin secretions were collected from a non-declining population of R. pretiosa that had been exposed to the causative agent Batrachochytrium dendrobatidis. Peptidomic analysis led to identification and isolation, in pure form, of a total of 18 host-defense peptides that were characterized structurally. Brevinin-1PRa, -1PRb, -1PRc, and -1PRd, esculentin-2PRa and -PRb, ranatuerin-2PRa, -2PRb, -2PRc, and -2PRe, temporin-PRb and -PRc were identified in an earlier study of skin secretions of frogs from a different population of R. pretiosa known to be declining. Ranatuerin-2PRf, -2PRg, -2PRh, temporin-PRd, -PRe, and -PRf were not identified in skin secretions from frogs from the declining population, whereas temporin-PRa and ranatuerin-2PRd, present in skin secretions from the declining population, were not detected in the current study. All purified peptides inhibited the growth of B. dendrobatidis zoospores. Peptides of the brevinin-1 and esculentin-2 families displayed the highest potency (minimum inhibitory concentration = 6.25-12.5 μM). The study provides support for the hypothesis that the multiplicity and diversity of the antimicrobial peptide repertoire in R. pretiosa and the high growth-inhibitory potency of certain peptides against B. dendrobatidis are important in conferring a measure of resistance to fatal chytridiomycosis.
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Purification, molecular cloning, and antimicrobial activity of peptides from the skin secretion of the black-spotted frog, Rana nigromaculata. World J Microbiol Biotechnol 2013; 29:1941-9. [DOI: 10.1007/s11274-013-1360-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/22/2013] [Indexed: 02/07/2023]
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16
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Attoub S, Mechkarska M, Sonnevend A, Radosavljevic G, Jovanovic I, Lukic ML, Conlon JM. Esculentin-2CHa: a host-defense peptide with differential cytotoxicity against bacteria, erythrocytes and tumor cells. Peptides 2013; 39:95-102. [PMID: 23159562 DOI: 10.1016/j.peptides.2012.11.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 11/06/2012] [Accepted: 11/06/2012] [Indexed: 02/02/2023]
Abstract
The host-defense peptide, esculentin-2CHa (GFSSIFRGVA(10)KFASKGLGK D(20)LAKLGVDLVA(30) CKISKQC) shows potent (MIC≤6 μM) growth inhibitory activity against clinical isolates of multidrug-resistant strains of Staphylococcus aureus, Acinetobacter baumannii, and Stenotrophomonas maltophilia and differential cytotoxic activity against human erythrocytes (LC(50)=150 μM) and human non-small cell lung adenocarcinoma A549 cells (LC(50)=10 μM). Esculentin-2CHa significantly (P<0.01) stimulates the release of the anti-inflammatory cytokine IL-10 by mouse lymphoid cells and elevates its production after stimulation with concanavalin A and significantly (P<0.05) stimulates TNF-α production by peritoneal macrophages. Effects on IL-6 and IL-1β production were not significant. Removal of the hydrophobic N-terminal hexapeptide (GFSSIF) from esculentin-2CHa results in abolition of growth inhibitory activity against S. aureus and cytotoxic activity against erythrocytes and A549 cells as well as a marked (≥16-fold) reduction in potency against A. baumannii and S. maltophilia. The primary structure of esculentin-2 has been poorly conserved between frog species but evolutionary pressure has acted to maintain the hydrophobic character of this N-terminal hexapeptide sequence. Removal of the cyclic C-terminal domain (CKISKQC) and replacement of the Cys(31) and Cys(37) residues by serine resulted in appreciable decreases in cytotoxicity against all microorganisms and against mammalian cells. The more cationic [D20K, D27K] analog showed a modest increase in potency against all microorganisms (up to 4-fold) but a marked increase in cytotoxicity against erythrocytes (LC(50)=11 μM) and A549 cells (LC(50)=3 μM).
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Affiliation(s)
- Samir Attoub
- Department of Pharmacology, College of Medicine and Health Sciences, United Arab Emirates University, 17666 Al-Ain, United Arab Emirates
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Yang X, Xia J, Yu Z, Hu Y, Li F, Meng H, Yang S, Liu J, Wang H. Characterization of diverse antimicrobial peptides in skin secretions of Chungan torrent frog Amolops chunganensis. Peptides 2012; 38:41-53. [PMID: 22951323 DOI: 10.1016/j.peptides.2012.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/10/2012] [Accepted: 08/10/2012] [Indexed: 12/27/2022]
Abstract
We have cloned, synthesized, and characterized 11 novel antimicrobial peptides from a skin derived cDNA library of the Chungan torrent frog, Amolops chunganensis. Seven of the 11 antimicrobial peptides were present in authentic A. chunganensis skin secretions. Sequence analysis indicated that the 11 peptides belonged to the temporin, esculentin-2, palustrin-2, brevinin-1, and brevinin-2 families. The peptides displayed potent antimicrobial activities against several strains of microorganisms. One peptide, brevinin-1CG5, demonstrated antimicrobial activity against all tested Gram-positive and Gram-negative bacteria and fungi, and showed high antimicrobial potency (MIC=0.6 μM) against Gram-positive bacterium Rhodococcus rhodochrous. Some peptides also demonstrated weak hemolytic activity against human erythrocytes in vitro. Phylogenetic analysis based on the amino acid sequences of brevinin-1, brevinin-2, and esculentin-2 peptides from family Ranidae confirmed that the current taxonomic status of A. chunganensis is correct.
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Affiliation(s)
- Xiaohong Yang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China
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Wang H, Yu Z, Hu Y, Yu H, Ran R, Xia J, Wang D, Yang S, Yang X, Liu J. Molecular cloning and characterization of antimicrobial peptides from skin of the broad-folded frog, Hylarana latouchii. Biochimie 2012; 94:1317-26. [DOI: 10.1016/j.biochi.2012.02.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 02/26/2012] [Indexed: 11/30/2022]
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Wang H, Yu Z, Hu Y, Li F, Liu L, Zheng H, Meng H, Yang S, Yang X, Liu J. Novel antimicrobial peptides isolated from the skin secretions of Hainan odorous frog, Odorrana hainanensis. Peptides 2012; 35:285-90. [PMID: 22450466 DOI: 10.1016/j.peptides.2012.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/08/2012] [Accepted: 03/08/2012] [Indexed: 12/27/2022]
Abstract
Long time geographical isolation of Hainan Island from the China continent has resulted in appearance of many novel frog species. As one of them, Hainan odorous frog, Odorrana hainanensis possesses some special antimicrobial peptides distinct from those found in other Odorrana. In this study, three antimicrobial peptides have been purified and characterized from the skin secretion of O. hainanensis. With the similarity to the temporin family, two peptides are characterized by amidated C-terminals, so they are named as temporin-HN1 (AILTTLANWARKFL-NH(2)) and temporin-HN2 (NILNTIINLAKKIL-NH(2)). The third antimicrobial peptide belongs to the brevinin-1 family which is widely distributed in Eurasian ranids, and thus, it is named as brevinin-1HN1 (FLPLIASLAANFVPKIFCKITKKC). Furthermore, after sequencing 68 clones, eight cDNAs encoding antimicrobial peptide precursors were cloned from the skin-derived cDNA library of O. hainanensis. These eight cDNAs can encode seven mature antimicrobial peptides including the above three, as well as brevinin-1V, brevinin-2HS2, odorranain-A6, and odorranain-B1. Twelve different species of microorganisms were chosen, including Gram-positive, Gram-negative and fungi, to test the antimicrobial activities of temporin-HN1, temporin-HN2, brevinin-1HN1, brevinin-1V, and brevinin-2HS2. The result shows that, in addition to their activities against Gram-positive bacteria, temporin-HN1 and temporin-HN2 also possess activities against some Gram-negative bacteria and fungi. However, the two antimicrobial peptides, brevinin-1HN1 and brevinin-1V of the brevinin-1 family have stronger antimicrobial activities than temporin-HN1 and temporin-HN2 of the temporin family. Brevinin-1HN1 possesses activity against Staphylococcus aureus (ATCC25923), Rhodococcus rhodochrous X15, and Slime mould 090223 at the concentration of 1.2 μM.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
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Characterization of selective antibacterial peptides by polarity index. INTERNATIONAL JOURNAL OF PEPTIDES 2012; 2012:585027. [PMID: 22611416 PMCID: PMC3348531 DOI: 10.1155/2012/585027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/18/2012] [Accepted: 01/19/2012] [Indexed: 01/08/2023]
Abstract
In the recent decades, antibacterial peptides have occupied a strategic position for pharmaceutical drug applications and became subject of intense research activities since they are used to strengthen the immune system of all living organisms by protecting them from pathogenic bacteria. This work proposes a simple and easy statistical/computational method through a peptide polarity index measure by which an antibacterial peptide subgroup can be efficiently identified, that is, characterized by a high toxicity to bacterial membranes but presents a low toxicity to mammal cells. These peptides also have the feature not to adopt to an alpha-helicoidal structure in aqueous solution. The double-blind test carried out to the whole Antimicrobial Peptide Database (November 2011) showed an accuracy of 90% applying the polarity index method for the identification of such antibacterial peptide groups.
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Wang H, Ran R, Yu H, Yu Z, Hu Y, Zheng H, Wang D, Yang F, Liu R, Liu J. Identification and characterization of antimicrobial peptides from skin of Amolops ricketti (Anura: Ranidae). Peptides 2012; 33:27-34. [PMID: 22100518 DOI: 10.1016/j.peptides.2011.10.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 10/28/2011] [Accepted: 10/28/2011] [Indexed: 01/23/2023]
Abstract
As one of large amphibian group, there are a total of 45 species of Amolops in the world. However, the antimicrobial peptides (AMPs) existing in this genus has not been extensively studied. In this study, cDNAs encoding five novel AMP precursors were cloned by screening the skin-derived cDNA library of Amolops ricketti, a frog species that exists in southern and western parts of China. Protein sequence analysis led to the identification of five deduced peptides, three belonging to the brevinin-1 family and two belonging to the brevinin-2 family of amphibian AMPs. Thus, they were named as brevinin-1RTa (FLPLLAGVVANFLPQIICKIARKC), brevinin-1RTb (FLGSLLGLVGKVVPTLFCKISKKC), brevinin-1RTc (FLGSLLGLVGKIVPTLICKISKKC), brevinin-2RTa (GLMSTLKDFGKTAAKEIAQSLLSTASCKLAKTC), and brevinin-2RTb (GILDTLKEFGKTAAKGIAQSLLSTASCKLAKTC), respectively. The purification of brevinin-1RTa, brevinin-1RTb, and brevinin-2RTb was carried out by RP-HPLC, and confirmed by the LC-MS/MS-based proteomics approach. All of the peptides displayed different antimicrobial potency against a variety of microorganisms. In addition, brevinin-2RTa and brevinin-2RTb were found to have relatively low hemolytic activity (>400μg/ml) against mammalian red blood cells in vitro, which could potentially be as candidates for developing novel anti-infection agents.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050016, China
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