Aggregation-prone antimicrobial peptides target gram-negative bacterial nucleic acids and protein synthesis

Area of Science:

• Biochemistry
• Microbiology
• Drug Discovery

Background:

• Antimicrobial peptides (AMPs) are crucial in innate immunity, but their discovery is often limited to known gene families.
• Organisms like Octopus lack classical AMP gene families, necessitating alternative discovery methods.
• Aggregation of AMPs can enhance their antimicrobial efficacy.

Purpose of the Study:

• To identify novel aggregation-prone antimicrobial peptides (AMPs) from protein fragments of Octopus bimaculoides using artificial intelligence.
• To investigate the mechanism of action of identified AMPs against bacterial pathogens.
• To explore a new strategy for discovering AMPs from non-traditional sources to combat antibiotic resistance.

Main Methods:

• Artificial intelligence (AI) tools were employed to predict AMPs from Octopus bimaculoides protein fragments.
• Peptide aggregation propensity was assessed to identify candidate AMPs.
• Antibacterial activity was evaluated against Escherichia coli and Staphylococcus aureus using cell viability assays, confocal laser scanning microscopy, and scanning electron microscopy.
• Mechanism of action was investigated through DNA aggregation assays, knockout mutants, aggregation-induced emission assays, and molecular dynamics simulations.

Main Results:

• Four aggregation-prone peptides (Oct-P1, Oct-P2, Oct-P3, Oct-P4) were identified from Octopus protein fragments.
• Oct-P2 demonstrated significant reduction (up to 90%) in the viability of E. coli and S. aureus.
• Oct-P2 was internalized into bacterial cells and aggregated with transcription promoter DNA, inhibiting transcription and translation.
• Extracellular DNA presence reduced Oct-P2's antibacterial activity, suggesting DNA interaction is key.

Conclusions:

• Protein fragments from organisms lacking classical AMP gene families are a viable source for novel AMP discovery.
• Oct-P2 exhibits a dual-target mechanism, disrupting bacterial cell integrity and inhibiting intracellular transcription and translation.
• Oct-P2 serves as a promising lead template for developing new antimicrobial agents to address antibiotic resistance.