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PreprintCited by 9Antimicrobial Peptides and ActivitiesMicrobial Natural Products and BiosynthesisComputational Drug Discovery Methods

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides

Open access
Li, Chenkai, Sutherland, Darcy, Salehi, Ali, Richter, Amelia, Lin, Diana, Aninta, Sambina Islam, Ebrahimikondori, Hossein, Yanai, Anat, Coombe, Lauren, Warren, René L., Kotkoff, Monica, Hoang, Linda M.N., Helbing, Caren C., Birol, Inanc·2024·Protein Science
DOI 10.1101/2024.05.24.595811PMC PMC11917140

Preprint — published as 10.1002/pro.70083 · Paper page

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Abstract

The ever-growing global health threat of antibiotic resistance is compelling researchers to explore alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are emerging as a promising solution to fill this need. Naturally occurring AMPs are produced by all forms of life as part of the innate immune system. High-throughput bioinformatics tools have enabled fast and large-scale discovery of AMPs from genomic, transcriptomic, and proteomic resources of selected organisms. Public protein sequence databases, comprising over 200 million records and growing, serve as comprehensive compendia of sequences from a broad range of source organisms. Yet, large-scale in silico probing of those databases for novel AMPs has never been reported. In the present study, we propose an AMP mining workflow to predict novel AMPs from the UniProtKB/Swiss-Prot database using the AMP prediction tool, AMPlify, as its discovery engine. Using this workflow, we identified 8,008 novel putative AMPs from all eukaryotic sequences in the database. Focusing on the practical use of AMPs as suitable antimicrobial agents with applications in the poultry industry, we prioritized 40 of those AMPs based on their similarities to known chicken AMPs in predicted structures. In our tests, 13 out of the 38 successfully synthesized peptides showed antimicrobial activity against Escherichia coli and/or Staphylococcus aureus .

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Research works printed but not linked: 52

  1. 10.1038/509141a · DOI
  2. 10.1016/S0140-6736(21)02724-0 · DOI · Paper page
  3. 10.1016/S1473-3099(13)70318-9 · DOI · Paper page
  4. 10.1002/pep2.24122 · DOI
  5. 10.3390/molecules26092671 · DOI
  6. 10.1007/978-981-13-3588-4_10 · DOI
  7. 10.1016/j.cub.2015.11.017 · DOI
  8. 10.2174/092986608784567618 · DOI
  9. 10.1093/nar/gkv1278 · DOI
  10. 10.1128/AAC.43.1.1 · DOI
  11. 10.1038/nri1860 · DOI · Paper page
  12. 10.1016/j.tibtech.2011.05.001 · DOI
  13. 10.1046/j.1365-2796.2003.01228.x · DOI
  14. 10.2174/1568026619666190122151634 · DOI
  15. 10.1016/j.ab.2013.01.019 · DOI
  16. 10.1038/srep42362 · DOI
  17. 10.1093/bioinformatics/bty179 · DOI
  18. 10.1186/s12864-022-08310-4 · DOI
  19. 10.1186/s13104-023-06279-1 · DOI
  20. Vaswani A , Shazeer N , Parmar N , Uszkoreit J , Jones L , Gomez AN , et al. Attention Is All You Need. Advances in Neural Information Processing Systems. 2017.
  21. 10.18653/v1/N16-1174 · DOI
  22. 10.3390/antibiotics11070952 · DOI
  23. 10.3390/antibiotics11121710 · DOI
  24. 10.1016/j.peptides.2012.07.021 · DOI
  25. 10.3390/md19060328 · DOI
  26. 10.5772/intechopen.76631 · DOI
  27. 10.3390/proteomes7040032 · DOI
  28. 10.1093/nar/gky1049 · DOI · Paper page
  29. 10.3390/ijms21124310 · DOI
  30. 10.1016/j.jsps.2016.04.027 · DOI
  31. 10.3923/ijps.2009.404.408 · DOI
  32. 10.1093/protein/gzh013 · DOI
  33. 10.1093/bioinformatics/bts141 · DOI
  34. 10.1038/s41598-018-38442-1 · DOI
  35. Alberts B , Johnson A , Lewis J , Raff M , Roberts K , Walter P . Analyzing protein structure and function. Molecular Biology of the Cell, 4th edition. New York: Garland Science; 2002.
  36. 10.1038/s41592-022-01488-1 · DOI · Paper page
  37. 10.1002/prot.20264 · DOI · Paper page
  38. 10.1093/nar/gki524 · DOI · Paper page
  39. 10.1016/j.vetimm.2005.03.003 · DOI
  40. 10.1074/jbc.M507180200 · DOI
  41. 10.1101/2021.09.28.462162 · DOI
  42. 10.1016/j.ymeth.2019.04.008 · DOI · Paper page
  43. 10.3389/fmicb.2016.00381 · DOI
  44. 10.1038/s41467-019-13618-z · DOI
  45. 10.1021/acsinfecdis.9b00073 · DOI
  46. 10.1371/journal.ppat.1000857 · DOI
  47. 10.1186/rr25 · DOI
  48. 10.1038/nbt.3988 · DOI · Paper page
  49. 10.1002/prot.21123 · DOI
  50. 10.1038/nprot.2007.521 · DOI · Paper page
  51. 10.1006/bbrc.1998.9362 · DOI
  52. 10.1007/s00726-017-2402-9 · DOI

Metadata

Authors
Li, C., Sutherland, D., Salehi, A., Richter, A., Lin, D., Aninta, S. I., Ebrahimikondori, H., Yanai, A., Coombe, L., Warren, R. L., Kotkoff, M., Hoang, L. M. N., Helbing, C. C., & Birol, I.
Affiliations
  • BC Cancer Agency (CA)
  • University of British Columbia (CA)
  • University of Victoria (CA)
ORCID
Venue
Protein Science
Publisher
openRxiv
Published
2024-05-29
Volume
34
Issue
4
Pages
e70083-e70083
ISSN
0961-8368 (ISSN-L)
DOI
10.1101/2024.05.24.595811
PMC
PMC11917140
OpenAlex
W4408538820
Cited by
9
References
1
Citations by year
2026: 5 · 2025: 3 · 2024: 1
FWCI
4.38
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Protein Science (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Genome Canada (291PEP)
  • Genome British Columbia (291PEP)
  • Investment Agriculture Foundation (INV106)
Topics
  • Life Sciences › Immunology and Microbiology › Microbiology › Antimicrobial Peptides and Activities
  • Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Microbial Natural Products and Biosynthesis
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Keywords
antimicrobial peptides, UniProtKB/Swiss-Prot, antibiotic resistance, eukaryotic proteins, poultry, Escherichia coli, Staphylococcus aureus, peptide synthesis, innate immunity
MeSH terms
Antimicrobial Peptides, Animals, Anti-Bacterial Agents, Chickens, Staphylococcus aureus, Computational Biology, Databases, Protein, Data Mining

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