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Published on: December 1, 2020
ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides.
Hongfang Wu1,2, Rongxian Chen1,2, Xuejian Li1,2,3
1National Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan 430070, China.
Superbugs, including ESKAPE bacteria, cause millions of deaths. Researchers identified over 12 million antimicrobial peptides from phages and phage peptidoglycan hydrolases (PGHs) to combat these resistant bacteria.
Area of Science:
- Microbiology
- Bioinformatics
- Drug Discovery
Background:
- ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) are a major cause of multidrug-resistant infections, leading to over 1.27 million deaths in 2019.
- Phage peptidoglycan hydrolases (PGHs)-derived antimicrobial peptides are emerging as promising agents against multidrug-resistant bacteria.
- Current methods for mining antimicrobial peptides from phages or phage PGHs are limited.
Purpose of the Study:
- To systematically identify and mine antimicrobial peptides from phages and their PGHs targeting ESKAPE bacteria.
- To develop a user-friendly tool for predicting phage PGHs-derived antimicrobial peptides and analyzing their properties.
- To create an accessible database (ESKtides) for browsing, searching, and downloading these antimicrobial peptides.
Main Methods:
- Genome-wide analysis of 6809 ESKAPE isolate genomes and their corresponding phages from public databases.
- Unified annotation process to identify PGHs and mine derived peptides.
- Development of a prediction tool incorporating phylogeny, physicochemical properties, and secondary structure analysis.
- Creation of the ESKtides database for data management and access.
Main Results:
- Identification and mining of 12,067,248 peptides with high antibacterial activity from ESKAPE-associated phages.
- Development of a functional tool for predicting and characterizing phage PGHs-derived antimicrobial peptides.
- Establishment of the ESKtides database, offering a comprehensive resource for these peptides.
Conclusions:
- This study provides a substantial library of potential antimicrobial peptides derived from phages targeting ESKAPE bacteria.
- The developed tool and ESKtides database facilitate the discovery and utilization of novel antibacterial agents against multidrug-resistant pathogens.
- This work contributes to the fight against antimicrobial resistance by offering new therapeutic strategies.
