Rational Design of Broad-Spectrum Antimicrobial Peptides Derived from the Dengue Virus Capsid Alpha2 Sequence

Antimicrobial peptides (AMP) offer an attractive alternative to antibiotics in the global fight against antibiotic resistance. AMPs can impose fast structural disruptions to microbial membranes and kill pathogens by causing the leakage of their internal contents, making it less likely for pathogens to develop resistance. However, current AMPs still suffer from various drawbacks including weak efficacy, unacceptable toxicity, and side effects. This work seeks to design a group of amphiphilic AMPs based on the α2 sequence of a Dengue viral capsid protein to address the challenge of ineffective membrane disruptions of AMPs. The design was also inspired by well-studied G(IIKK)₃I-NH₂ (G₃) for broad-spectrum antimicrobial actions. All designed Dengue viral-inspired peptides displayed lower minimum inhibition concentrations and faster time-dependent killing than G₃, with the fastest DVP-3 (RIFRAIRRIARFIR) achieving complete killing within 10 min. Fluorescence assays of AMP binding to bacterial membranes revealed varying degrees of membrane permeability change, depolarization, and leakage. Model inner membrane (IM) and outer membrane (OM) of Gram-negative bacteria facilitated leakage assay and neutron reflection, linking membrane binding and disruptions with antimicrobial behaviors. The findings reveal that DVP-3 could cause more effective disruptions to the bacterial OM than to the IM, consistent with its potent antimicrobial efficacy and rapid dynamic killing. This work offers new insights into how the newly designed AMPs destabilize bacterial membranes to improve antimicrobial performance and the combined approach allows effective in vitro AMP evaluation to overcome bacterial resistance.