α‑Helical Peptides Encoded in Collagen Exhibit Antimicrobial Activity with Low Cytotoxicity

TL;DR

Collagen proteins contain hidden antimicrobial peptides that are effective against pathogens and safe for human cells.

Contribution

Collagen's nonfibrous domains are identified as a new source of antimicrobial peptides with low cytotoxicity.

Findings

Three collagen-derived peptides showed broad-spectrum antimicrobial activity comparable to LL-37 and melittin.

Collagen peptides disrupted bacterial membranes but had low toxicity to human cells.

Machine learning-predicted peptides showed reduced or no antimicrobial activity compared to the targeted approach.

Abstract

Endogenous antimicrobial peptides
(AMPs) derived from host proteins
represent a largely underexplored class of natural products tied to
innate immunity. Here, we investigated collagen proteins as a source
of latent α-helical AMPs encoded within nonfibrous extracellular
matrix domains. Using a targeted in silico approach,
verified collagen sequences were mined and prioritized based on secondary
structure and three essential physicochemical properties: net charge,
Boman index, and hydrophobic moment, yielding 107 predicted α-helical
AMP candidates. The highest ranked peptides were synthesized and experimentally
evaluated alongside benchmark AMPs and peptides prioritized by machine
learning-based prediction tools. Three collagen-derived peptides identified
by the targeted physicochemical approach exhibited broad-spectrum
bioactivity against bacterial and fungal pathogens with minimum inhibitory
concentrations comparable to those of LL-37 and melittin. In contrast,
peptides ranked highly by machine learning predictors showed reduced
or no activity. Collagen-derived peptides disrupted bacterial mimicking
lipid membranes yet displayed markedly reduced cytotoxicity toward
human cells, maintaining high viability at concentrations well above
their antimicrobial MICs. These findings demonstrate that nonfibrous
domains of extracellular matrix collagens constitute a previously
underexplored reservoir of endogenous antimicrobial peptides with
favorable biocompatibility, expanding the natural product space of
host defense peptides and identifying collagen-derived AMPs as promising
scaffolds for future antimicrobial discovery.

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