Abstract
The increase of antibiotic resistance in bacterial species has raised the need to search for novel antimicrobial molecules. Antimicrobial peptides are molecules that commonly display an amphipathic character. In this work, we developed a computational strategy to search for new peptide sequences within the proteome of any organism that includes in-house developed software and the use of artificial intelligence tools available online. Eleven peptides were selected after analyzing 63,343 proteins from the proteomes of bacteria, algae and invertebrates. Then, we validated the results by means of several assays which were carried out against five (5) pathogenic bacterial species and two (2) cancer cell lines. As a result, we found that ten of the peptides were antimicrobial, with minimum inhibitory concentration values between 4 and \(64\,\upmu \hbox {M}\). Furthermore, two of the more active peptides were also cytotoxic to human red blood cells and cancer cells. In general, the antimicrobial peptides we discovered produced damage on the bacterial cell membrane that included membrane wrinkling, cell blebbing, and leakage of cytoplasmic material. Based on these results, we concluded that the computational approach proposed for finding sequences encrypted in proteins is appropriate for the discovery of selective and non-selective antimicrobial and anticancer peptides.
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References
Bacalum M, Radu M (2015) Cationic antimicrobial peptides cytotoxicity on mammalian cells: an analysis using therapeutic index integrative concept. Int J Pep Res Therap 21(1):47–55. https://doi.org/10.1007/s10989-014-9430-z
Boman HG (2003) Antibacterial peptides: basic facts and emerging concepts. J Intern Med 254(3):197–215. https://doi.org/10.1046/j.1365-2796.2003.01228.x
Bulet P, Stöcklin R, Menin L (2004) Anti-microbial peptides: from invertebrates to vertebrates. Immunol Rev 198:169–184. https://doi.org/10.1111/j.0105-2896.2004.0124.x
Deslouches B, Di YP (2017) Antimicrobial peptides with selective antitumor mechanisms: prospect for anticancer applications. Oncotarget 8(28):46635–46651 https://doi.org/10.18632/oncotarget.16743
Evans B, Nelson C, Yu S, Beavers K, Kim A, Li H, Duvall C (2013) Ex vivo red blood cell hemolysis assay for the evaluation of ph-responsive endosomolytic agents for cytosolic delivery of biomacromolecular drugs. J. Visualized Exp. https://doi.org/10.3791/50166
Fair R, Tor Y (2014) Antibiotics and bacterial resistance in the 21st century. Perspect Med Chem 6:25–64. https://doi.org/10.4137/PMC.S14459
Felício MR, Silva ON, Gonçalves S, Santos NC, Franco OL (2017) Peptides with dual antimicrobial and anticancer activities. Front Chem 5(February):1–9. https://doi.org/10.3389/fchem.2017.00005
Fox JL (2013) Antimicrobial peptides stage a comeback. Nat Biotechnol 31(5):379–382. https://doi.org/10.1038/nbt.2572
Fry DE (2018) Antimicrobial peptides. Surg Infect 19(8):804–811. https://doi.org/10.1089/sur.2018.194
Gomez E, Orduz S (2017). PepMultiFinder 1.0. Un algoritmo para buscar péptidos bioactivos en proteomas o listas de secuencias de proteínas. dirección nacional de derechos de autor. ministerio del interior. registro 13-59-134, marzo 17, 2017
Hincapié O, Giraldo P, Orduz S (2018) In silico design of polycationic antimicrobial peptides active against Pseudomonas aeruginosa and Staphylococcus aureus. Antonie van Leeuwenhoek, Int. J. Gen. Mol. Microbiol. 111(10), 1871–1882. https://doi.org/10.1007/s10482-018-1080-2
Houyvet B, Zanuttini B, Corre E, Le Corguillé G, Henry J, Zatylny-Gaudin C (2018) Design of antimicrobial peptides from a cuttlefish database. Amino Acids 50(11):1573–1582. https://doi.org/10.1007/s00726-018-2633-4
Li J, Nation RL, Milne RW, Turnidge JD, Coulthard K (2005) Evaluation of colistin as an agent against multi-resistant Gram-negative bacteria. Int J Antimicrob Agents 25(1):11–25. https://doi.org/10.1016/j.ijantimicag.2004.10.001
Marcellini L, Giammatteo M, Aimola P, Mangoni ML (2010) Fluorescence and electron microscopy methods for exploring antimicrobial peptides mode(s) of action. Methods Mol Biol 618:249–266. https://doi.org/10.1007/978-1-60761-594-1_16
Marqus S, Pirogova E, Piva TJ (2017) Evaluation of the use of therapeutic peptides for cancer treatment. J Biomed Sci 24(1):21. https://doi.org/10.1186/s12929-017-0328-x
Moore RA, Hancock RE (1986) Involvement of outer membrane of Pseudomonas cepacia in aminoglycoside and polymyxin resistance. Antimicrob Agents Chemother 30(6):923–926. https://doi.org/10.1128/AAC.30.6.923
Neundorf I (2019) Antimicrobial and cell-penetrating peptides: how to understand two distinct functions despite similar physicochemical properties. Adv Exp Med Biol 1117:93–109. https://doi.org/10.1007/978-981-13-3588-4_7
O’Driscoll NH, Labovitiadi O, Cushnie TP, Matthews KH, Mercer DK, Lamb AJ (2013) Production and evaluation of an antimicrobial peptide-containing wafer formulation for topical application. Curr Microbiol 66(3):271–278. https://doi.org/10.1007/s00284-012-0268-3
Strandberg E, Tiltak D, Ieronimo M, Kanithasen N, Wadhwani P, Ulrich AS (2007) Influence of C-terminal amidation on the antimicrobial and hemolytic activities of cationic \(\alpha \)-helical peptides. Pure Appl Chem 79(4):717–728. https://doi.org/10.1351/pac200779040717
Tacconelli E, Magrini N (2017) Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics (Tech Rep). World Health Organization. https://doi.org/10.1590/S0100-15742013000100018
Torrent M, Di Tommaso P, Pulido D, Nogués MV, Notredame C, Boix E, Andreu D (2012) AMPA: an automated web server for prediction of protein antimicrobial regions. Bioinformatics 28(1):130–131. https://doi.org/10.1093/bioinformatics/btr604
Waghu FH, Barai RS, Gurung P, Idicula-Thomas S (2016) CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. Nucleic Acids Res 44(D1):D1094–D1097. https://doi.org/10.1093/nar/gkv1051
Wang G (2017) Antimicrobial peptides: discovery, design and novel therapeutic strategies, 2nd edition. CABI
Wang G, Li X, Wang Z (2016) APD3: the antimicrobial peptide database as a tool for research and education. Nucleic Acids Res 44(D1):D1087–D1093. https://doi.org/10.1093/nar/gkv1278
Wiegand I, Hilpert K, Hancock REW (2008) Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat Protoc 3(2):163–175. https://doi.org/10.1038/nprot.2007.521
World Health Organization (2017) Antimicrobial resistance. Retrieved 2019–02-20, fromhttp://www.who.int/mediacentre/factsheets/fs194/en/. Accessed 20 Feb 2019
World Health Organization (2018) The top 10 causes of death. Retrieved 2019–01-15, fromwww.who.int/news-room/fact-sheets/detail/the-top-10-causes-of-death. Accessed 15 Jan 2019
Zhang B, Shi W, Li J, Liao C, Li M, Huang W, Qian H (2017) Synthesis and biological evaluation of novel peptides as potential agents with antitumor and multidrug resistance-reversing activities. Chem Biol Drug Des 90(5):972–980. https://doi.org/10.1111/cbdd.13023
Acknowledgements
This study was supported by Universidad Nacional de Colombia - Sede Medellin, HERMES research Grants Numbers 39323 and 35058.
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Duque-Salazar, G., Mendez-Otalvaro, E., Ceballos-Arroyo, A.M. et al. Design of antimicrobial and cytolytic peptides by computational analysis of bacterial, algal, and invertebrate proteomes. Amino Acids 52, 1403–1412 (2020). https://doi.org/10.1007/s00726-020-02900-w
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DOI: https://doi.org/10.1007/s00726-020-02900-w