CAMPER: mechanistic artificial intelligence for designing peptides that target MRSA persisters

Area of Science:

• Biochemistry
• Computational Biology
• Infectious Diseases

Background:

• Antimicrobial resistance (AMR) necessitates novel therapeutic strategies.
• Short, stable, and potent antimicrobial peptides (AMPs) show promise against resistant bacteria.
• Targeting persister and biofilm forms of bacteria like methicillin-resistant Staphylococcus aureus (MRSA) is crucial.

Purpose of the Study:

• To develop an artificial intelligence (AI) framework for designing effective antimicrobial peptides.
• To identify novel membrane-targeting peptides with activity against MRSA persister and biofilm cells.
• To evaluate the efficacy of identified peptides in preclinical infection models.

Main Methods:

• Developed CAMPER (Constraint-driven AMP Engineering with Ranking), an AI framework integrating machine learning and biophysical ranking.
• Applied CAMPER to identify and design novel antimicrobial peptides.
• Tested peptide efficacy against Staphylococcus aureus (S. aureus) strains, including MRSA.
• Utilized murine models for prophylactic skin, established biofilm, and deep-seated thigh infections.
• Employed single-cell analysis via high-throughput microfluidics to study peptide effects on bacterial persisters.

Main Results:

• Identified WP-CAMPER1 (12mer) with a minimal inhibitory concentration (MIC) of 4 µg/mL against S. aureus MW2.
• Demonstrated significant reduction in S. aureus MW2 burden (2.5 log10) in a murine skin infection model using a 2% topical WP-CAMPER1 formulation.
• Showed WP-CAMPER1-d reduced S. aureus MW2 burden by 1.37 log10 in an established biofilm model.
• Confirmed WP-CAMPER1-d reduced S. aureus persisters in both exponential and stationary phases in vitro and in vivo (1.6 log10 reduction in thigh infection model).

Conclusions:

• CAMPER is an effective AI framework for designing potent antimicrobial peptides.
• WP-CAMPER1 and its D-enantiomer show significant potential as therapeutics against MRSA, including persister and biofilm forms.
• These findings offer a promising strategy to combat antibiotic resistance and persistence.