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Rational design of syn-safencin, a novel linear antimicrobial peptide derived from the circular bacteriocin safencin AS-48

The Journal of Antibiotics volume 71, pages 592–600 (2018)Cite this article

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Abstract

Bacteriocins hold unprecedented promise as a largely untapped source of antibiotic alternatives in the age of multidrug resistance. Here, we describe the first approach to systematically design variants of a novel AS-48 bacteriocin homologue, which we have termed safencin AS-48, from Bacillus safensis, to gain insights into engineering improved activity of bacteriocins. A library of synthetic peptides in which systematic amino acid substitutions to vary the periodicity and abundance of polar, acidic, aliphatic, and hydrophobic residues were generated for a total of 96 novel peptide variants of a single bacteriocin candidate. Using this method, we identified nine synthetic safencin (syn-safencin) variants with broad and potent antimicrobial activities with minimal inhibitory concentrations (MIC) as low as 250 nM against E. coli, P. aeruginosa, X. axonopodis, and S. pyogenes with minimal cytotoxicity to mammalian cells. It is anticipated that the strategies we have developed will serve as general guides for tuning the specificity of a given natural bacteriocin compound for therapeutic specificity.

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References

  1. CDC. Antibiotic resistance threats in the United States. United States Department of Health and Human Services, Centers for Disease Control and Prevention. 2013 (http://www.cdc.gov/drugresistance/threat-report-2013/).

  2. Ageitos JM, Sánchez-Pérez A, Calo-Mata P, Villa TG. Antimicrobial peptides (AMPs): ancient compounds that represent novel weapons in the fight against bacteria. Biochem Pharmacol. 2017;133:117–38.

    CAS  Article  PubMed  Google Scholar 

  3. Uggerhøj LE, et al. Rational design of alpha-helical antimicrobial peptides: do’s and don’ts. ChemBioChem. 2015;16:242–53.

    Article  PubMed  Google Scholar 

  4. Fjell CD, Hiss JA, Hancock REW, Schneider G. Designing antimicrobial peptides: form follows function. Nat Rev Drug Discov. 2012;11:37–51.

    CAS  Article  Google Scholar 

  5. Lv Y, et al. Antimicrobial properties and membrane-active mechanism of a potential α-helical antimicrobial derived from cathelicidin PMAP-36. PLoS ONE. 2014;9:e86364.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Ong ZY, Wiradharma N, Yang YY. Strategies employed in the design and optimization of synthetic antimicrobial peptide amphiphiles with enhanced therapeutic potentials. Adv Drug Deliv Rev. 2014;78:28–45.

    CAS  Article  PubMed  Google Scholar 

  7. Alvarez-Sieiro P, Montalbán-López M, Mu D, Kuipers OP. Bacteriocins of lactic acid bacteria: extending the family. Appl Microbiol Biotechnol. 2016;100:2939–51.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Cotter PD, Ross RP, Hill C. Bacteriocins—a viable alternative to antibiotics? Nat Rev Microbiol. 2013;11:95–105.

    CAS  Article  PubMed  Google Scholar 

  9. Arnison PG, et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep. 2013;30:108–60.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. Field D, et al. A bioengineered nisin derivative to control biofilms of Staphylococcus pseudintermedius. PLoS ONE. 2015;10:e0119684.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Field D, Cotter PD, Hill C, Ross RP. Bioengineering lantibiotics for therapeutic success. Front Microbiol. 2015;6:1–6.

    Article  Google Scholar 

  12. Murinda SE, Rashid KA, Roberts RF. In vitro assessment of the cytotoxicity of nisin, pediocin, and selected colicins on simian virus 40-transfected human colon and Vero monkey kidney cells with trypan blue staining viability assays. J Food Prot. 2003;66:847–53.

    CAS  Article  PubMed  Google Scholar 

  13. Field D, Cotter PD, Ross RP, Hill C. Bioengineering of the model lantibiotic nisin. Bioengineered. 2015;5979:37–41.

    Google Scholar 

  14. Lamarche MJ, et al. Discovery of LFF571: an investigational agent for Clostridium difficile infection. J Med Chem. 2012;55:2376–87.

    CAS  Article  PubMed  Google Scholar 

  15. Mullane K, et al. Multicenter, randomized clinical trial to compare the safety and efficacy of LFF571 and vancomycin for Clostridium difficile infections. Antimicrob Agents Chemother. 2015;59:1435–40.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. Burgos MJG, Aguayo MCL, Pulido RP, Gálvez A, López RL. Inactivation of Staphylococcus aureus in oat and soya drinks by enterocin AS-48 in combination with other antimicrobials. J Food Sci. 2015;80:2030–4.

    CAS  Article  Google Scholar 

  17. Caballero Gómez N, Abriouel H, José Grande M, Pérez Pulido R, Gálvez A. Combined treatments of enterocin AS-48 with biocides to improve the inactivation of methicillin-sensitive and methicillin-resistant Staphylococcus aureus planktonic and sessile cells. Int J Food Microbiol. 2013;163:96–100.

    Article  PubMed  Google Scholar 

  18. Gómez NC, Abriouel H, Grande J, Pulido RP, Gálvez A. Effect of enterocin AS-48 in combination with biocides on planktonic and sessile Listeria monocytogenes. Food Microbiol. 2012;30:51–8.

    Article  PubMed  Google Scholar 

  19. Sánchez-Hidalgo M, et al. AS-48 bacteriocin: close to perfection. Cell Mol Life Sci. 2011;68:2845–57.

    Article  PubMed  Google Scholar 

  20. Montalbán-López M, Martínez-Bueno M, Valdivia E, Maqueda M. Expression of linear permutated variants from circular enterocin AS-48. Biochimie. 2011;93:549–55.

    Article  PubMed  Google Scholar 

  21. Angeles Jiménez M, Barrachi-Saccilotto AC, Valdivia E, Maqueda M, Rico M. Design, NMR characterization and activity of a 21-residue peptide fragment of bacteriocin AS-48 containing its putative membrane interacting region. J Pept Sci. 2005;11:29–36.

    Article  PubMed  Google Scholar 

  22. Montalbán-López M, et al. Characterization of linear forms of the circular enterocin AS-48 obtained by limited proteolysis. FEBS Lett. 2008;582:3237–42.

    Article  PubMed  Google Scholar 

  23. Thévenet P, et al. PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res. 2012;40:W288–93.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Maupetit J, Derreumaux P, Tuffery P. PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res. 2009;37:W498–503.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. Fimland G, Eijsink VGH, Nissen-Meyer J. Mutational analysis of the role of tryptophan residues in an antimicrobial peptide. Biochemistry. 2002;41:9508–15.

    CAS  Article  PubMed  Google Scholar 

  26. Nguyen, LT, et al. Serum stabilities of short tryptophan-and arginine-rich antimicrobial peptide analogs. PLoS ONE. 2010;5:1–8.

  27. Aurell CA, Wistrom AO. Critical aggregation concentrations of gram-negative bacterial lipopolysaccharides (LPS). Biochem Biophys Res Commun. 1998;253:119–23.

    CAS  Article  PubMed  Google Scholar 

  28. Avitabile C, D’Andrea LD, Romanelli A. Circular dichroism studies on the interactions of antimicrobial peptides with bacterial cells. Sci Rep. 2014;4:4293.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Sreerama N, Woody RW. Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal Biochem. 2000;287:252–60.

    CAS  Article  PubMed  Google Scholar 

  30. Yadavalli SS, et al. Antimicrobial peptides trigger a division block in Escherichia coli through stimulation of a signalling system. Nat Commun. 2016;7:12340.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. Deslouches B, et al. Rational design of engineered cationic antimicrobial peptides consisting exclusively of arginine and tryptophan, and their activity against multidrug-resistant pathogens. Antimicrob Agents Chemother. 2013;57:2511–21.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. Mikut R, et al. Improving short antimicrobial peptides despite elusive rules for activity. BBA Biomembr. 2016;1858:1024–33.

    CAS  Article  Google Scholar 

  33. Mojsoska B, Carretero G, Larsen S, Mateiu RV, Jenssen H. Peptoids successfully inhibit the growth of gram negative E. coli causing substantial membrane damage. Sci Rep. 2017;7:42332.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Cebrián R, et al. The bacteriocin AS-48 requires dimer dissociation followed by hydrophobic interactions with the membrane for antibacterial activity. J Struct Biol. 2015;190:162–72.

    Article  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA

    Francisco R. Fields, Katelyn E. Carothers & Shaun W. Lee

  2. Eck Institute for Global Health, Notre Dame, IN, 46556, USA

    Francisco R. Fields, Katelyn E. Carothers & Shaun W. Lee

  3. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA

    Rashna D. Balsara, Victoria A. Ploplis & Francis J. Castellino

  4. W.M Keck Center for Transgene Research, Notre Dame, IN, 46556, USA

    Rashna D. Balsara, Victoria A. Ploplis & Francis J. Castellino

  5. Chemistry-Biochemistry-Biology Interface Program, Notre Dame, IN, 46556, USA

    Shaun W. Lee

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  1. Francisco R. Fields
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Correspondence to Francisco R. Fields or Shaun W. Lee.

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Fields, F.R., Carothers, K.E., Balsara, R.D. et al. Rational design of syn-safencin, a novel linear antimicrobial peptide derived from the circular bacteriocin safencin AS-48. J Antibiot 71, 592–600 (2018). https://doi.org/10.1038/s41429-018-0032-4

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  • DOI: https://doi.org/10.1038/s41429-018-0032-4

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