Objective

Antimicrobial peptides (AMPs) are part of the innate defense system. They demonstrate antimicrobial, anticancer, anti-HIV, etc. activities, and thus pose as prominent future drug candidates. Understanding the mechanism behind the activity is certainly vital for designing AMPs into drugs of the right efficacy. There are many proposed modes of action that are mostly addressing the pathogen membrane disruption by AMPs. However, the understanding of underlying mechanisms at atomistic level is still incomplete to support hypotheses and clarify experimental observations, and experiments cannot, e.g. capture the onset of the pore formation, MD simulations may be instrumental in filling up the knowledge gap.

We performed all-atom MD study as well as free energy explorations starting with cecropin B. Cecropins from the Cecropia moth (Hyalophoru cecropia) form a family of AMPs and demonstrate a broad spectrum antibacterial activity on both Gram-negative and Gram-positive bacteria. By gaining understanding on mechanism of cecropin B (and maybe more AMPs) interacting with membrane, we aim to put forward designing ideas for AMPs.