MOLECULAR MODELING OF DERMASEPTINE SP2 EXTRACTED FROM Agalychnis spurrelli
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Published:
Jan 17, 2019
Keywords:
Acoplamiento molecular, Agalychnis spurrelli, dermaseptinas, péptidos antimicrobianos Agalychnis spurrelli, antimicrobial peptides, Dermaseptins, molecular docking
Main Article Content
Abstract
In this research, we present a computational study of Dermaseptine SP2 (DRS-SP2) extracted from the skin of the frog Agalychnis spurrelli. Experimental assays allowed extracting, purifying and obtaining the amino acid sequence of this peptide. Furthermore, they have demonstrated its antimicrobial properties against Escherichia coli, Staphylococcus aureus and Candida albicans. With the sequence, a computational study of the structure was carried out, obtaining its physical-chemical properties, its secondary structure and its similarity with other known peptides. Also, a molecular docking study of this peptide was performed against cell membrane and several enzymes known to kill these microorganisms. Results showed that DRS-SP2 is an α-helical cationic peptide with an isoelectric point of 10.68 and a positive charge +3 at physiological pH. It was determined that its structure is different to all dermaseptines found in databases reaching a maximum identity of 80 %. Molecular docking studies suggest the mechanism of action of this peptide is not given by the inhibition of a vital enzymatic pathway, but by destruction of the microorganism by cell lysis.
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References
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Ortega-Andrade, H.M. (2008). Agalychnis spurrelli Boulenger (Anura: Hylidae): variación, distribución y sinonimia, Papéis Avulsos de Zoologia, 48(103), 1117.
Samgina, T., Vorontsov, E., Gorshkov, V., Hakalehto, E., Hanninen, O., Zubarev, R. y Lebedev1, A. (2012). Composition and Antimicrobial Activity of the Skin Peptidome of Russian Brown Frog Rana temporaria, Journal of Proteome Research, 11(12), 6213-22.
Scorciapino, M., Manzo, G., Rinaldi, A., Sanna, R., Casu, M., Pantic, J., Lukic, M. y Conlon, J. (2013). Conformational analysis of the frog skin peptide, plasticin-L1 and its effects on the production of proinflammatory cytokines by macrophages, Biochemistry, 52(41), 7231-41.
Stutz, K., Muller, A., Hiss, J., Schneider, P., Blatter, M., Pfeiffer, B., Posselt, G., Kanfer, G., Kornmann, B., Wrede, P., Altmann, K., Wessler, S. y Schneider, G. (2017). Peptide-membrane interaction between targeting and lysis, ACS Chemical Biology, 12(9), 2254-2259.
The PyMOL Molecular Graphics System (2017), Version 2.0 Schrödinger, LLC.
Trott, O. y Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry, 31(2), 455–461.
Wishart, D.S., Feunang, Y.D., Guo, A.C., Lo, E.J., Marcu, A., Grant, J.R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., Pon, A., Knox, C. y Wilson, M. (2017) DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Research, 46, 1074-1082
Bio-Synthesis. (2018). Peptide Property Calculator, Bio-Synthesis Inc. https://www.biosyn.com/peptidepropertycalculatorlanding.aspx
ChembioDraw (2009). PerkinElmer Informatics
Conlon, J.M. (2012). The Potential of Frog Skin Antimicrobial Peptides for Development into Therapeutically Valuable Anti-Infective Agents. En Rajasekaran, K., Cary, J.W., Jaynes, J.M. y Montesinos, E. (Ed.). Small Wonders: Peptides for Disease Control. Washington, DC: American Chemical Society.
Drozdetskiy, A., Cole, C., Procter, J. y Barton G.J. JPred4: a protein secondary structure prediction server, Nucleic Acids Research, 43, 389-394.
Duellman, W. E. (2001). Hylid Frogs of Middle America. Society for the Study of Amphibians and Reptiles, New York: Ithaca.
Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D. y Bairoch A. (2005). Protein Identification and Analysis Tools on the ExPASy Server. En Walker, J. (Ed.). The Proteomics Protocols Handbook, London, Springer
Gill, S.C. y von Hippel, P.H. (1989). Calculation of protein extinction coefficients from amino acid sequence data, Analytical Biochemistry, 182(2), 319-326.
Gray, A.R. (1997). Observations on the biology of Agalychnis spurrelli from the Caribbean lowlands of Costa Rica. Journal of the International Herpetological Society, 22, 61-70.
Guruprasad, K., Reddy, B.V.B. y Pandit, M.W. (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence, Protein Engineering, 4, 155-161.
Holthausen, D., Lee, S, Kumar, V., Bouvier, N., Krammer, F., Ellebedy, A., Wrammert, J., Lowen, A., George, S., Pillai, M. y Jacob, J. (2017). An Amphibian Host Defense Peptide Is Virucidal for Human H1 Hemagglutinin-Bearing Influenza Viruses, Immunity, 46, 587–595.
Huang L., Chen, D., Wang, L., Lin, C., Ma, C., Xi, X., Chen, T., Shaw, C., y Zhou, M. (2017). Dermaseptin-PH: A Novel Peptide with Antimicrobial and Anticancer Activities from the Skin Secretion of the South American Orange-Legged Leaf Frog, Pithecopus (Phyllomedusa) hypochondrialis, Molecules, 22, 1805.
Innovagen. (2015). Peptide property calculator, Innovagen AB, https://pepcalc.com/
Jones DT. (1999) Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology, 292, 195-202.
Lacombe, C., Piesse, C., Sagan, S., Combadière, C., Rosenstein, Y. y Auvynet, C. (2015). Pachymodulin, a New Functional Formyl Peptide Receptor 2 Peptidic Ligand Isolated from Frog Skin Has Janus-like Immunomodulatory Capacities, Journal of Medicinal Chemistry, 58, 1089−1099.
Manzo, G., Casu, M., Rinaldi, M., Montaldo, N., Luganini, A., Gribaudo, G. y Scorciapino, M. (2014). Folded Structure and Insertion Depth of the Frog-Skin Antimicrobial Peptide Esculentin-1b(1−18) in the Presence of Differently Charged Membrane-Mimicking Micelles, Journal of Natural Products, 77(11), 2410-7.
Marani, M., Dourado, F., Quelemes, P., Rodrigues de Araujo, A., Gomes Perfeito, M., Alves Barbosa, E., Costa Véras, L., Rodrigues Coelho, A., Barroso Andrade, E., Eaton, P., Figueiró Longo, J., Bentes Azevedo, R., Delerue-Matos, C. y Leite, J. (2015). Characterization and Biological Activities of Ocellatin Peptides from the Skin Secretion of the Frog Leptodactylus pustulatus, Journal of Natural Products, 78(7):1495-504.
MECN. (2010). Serie Herpetofauna del Ecuador: El Choco Esmeraldeño. Monografía. Museo Ecuatoriano de Ciencias Naturales. Quito, 5:1-232.
Melchiorri, P. y Negri, L. (2009). Amphibian Peptides, Encyclopedia of Neuroscience, San Diego: Elsevier Academic Press.
Nicolas, P. y El Amri, C. (2009). The dermaseptin superfamily: A gene-based combinatorial library of antimicrobial peptides, Biochimica et Biophysica Acta- Biomembranes, 1788(8), 1537-1550.
Nicolas, P. y Ladram, A. (2013). Dermaseptins. En Kastin, A.J. (Ed.). Handbook of Biologically Active Peptides, Amsterdam: Elsevier.
Ortega-Andrade, H.M. (2008). Agalychnis spurrelli Boulenger (Anura: Hylidae): variación, distribución y sinonimia, Papéis Avulsos de Zoologia, 48(103), 1117.
Samgina, T., Vorontsov, E., Gorshkov, V., Hakalehto, E., Hanninen, O., Zubarev, R. y Lebedev1, A. (2012). Composition and Antimicrobial Activity of the Skin Peptidome of Russian Brown Frog Rana temporaria, Journal of Proteome Research, 11(12), 6213-22.
Scorciapino, M., Manzo, G., Rinaldi, A., Sanna, R., Casu, M., Pantic, J., Lukic, M. y Conlon, J. (2013). Conformational analysis of the frog skin peptide, plasticin-L1 and its effects on the production of proinflammatory cytokines by macrophages, Biochemistry, 52(41), 7231-41.
Stutz, K., Muller, A., Hiss, J., Schneider, P., Blatter, M., Pfeiffer, B., Posselt, G., Kanfer, G., Kornmann, B., Wrede, P., Altmann, K., Wessler, S. y Schneider, G. (2017). Peptide-membrane interaction between targeting and lysis, ACS Chemical Biology, 12(9), 2254-2259.
The PyMOL Molecular Graphics System (2017), Version 2.0 Schrödinger, LLC.
Trott, O. y Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry, 31(2), 455–461.
Wishart, D.S., Feunang, Y.D., Guo, A.C., Lo, E.J., Marcu, A., Grant, J.R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., Pon, A., Knox, C. y Wilson, M. (2017) DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Research, 46, 1074-1082