The antimicrobial peptide database is 20 years old: Recent developments and future directions.

Area of Science:

• Biochemistry and Molecular Biology
• Computational Biology
• Drug Discovery

Background:

• The Antimicrobial Peptide Database (APD) has been a key resource for 20 years, cataloging antimicrobial peptides (AMPs).
• Previous work detailed the APD's expansion in peptide entries, classification, and functional annotations.
• Combating drug-resistant pathogens requires continuous development of novel antimicrobial agents.

Purpose of the Study:

• To highlight new additions and findings within the APD, focusing on recent data re-annotations and new peptide categories.
• To facilitate the development of antimicrobial peptides (AMPs) by providing enhanced data for combating drug-resistant pathogens.
• To enable new insights into peptide design through comparative analysis of desired and undesired AMP characteristics.

Main Methods:

• Re-annotation of existing APD data for antibacterial activity, toxicity (hemolytic potential), and salt tolerance.
• Creation of a new 'predicted' peptide group to include machine learning-derived peptide candidates.
• Comparative analysis of amino acid composition between natural AMPs, predicted peptides, and synthetic peptides.

Main Results:

• Re-annotated data provides clearer distinctions for antibacterial activity, toxicity, and salt tolerance, aiding in the selection of effective and safe AMPs.
• The 'predicted' peptide group, informed by machine learning, shows an amino acid composition intermediate between natural and synthetic peptides.
• Natural AMPs exhibit higher abundance of cysteine, glycine, and lysine compared to globular proteins, attributed to their amphipathic helical and disulfide-linked structures.

Conclusions:

• The APD's 20-year accumulation of natural AMP data provides a crucial foundation for machine learning-based peptide prediction.
• Comparative analysis of AMP groups yields valuable knowledge for optimizing the design of novel antimicrobial peptides.
• The APD is expected to remain a vital resource for research and education in antimicrobial peptide discovery and development.