Advances in molecular dynamics approaches for investigating cell-penetrating peptides

Abstract Membrane active peptides (MAPs) are short, cationic peptides capable of interacting with biological membranes, often altering their structure or function. Two of the most important classes of MAPs are cell-penetrating peptides (CPPs), which can translocate cellular membranes without causing cytotoxicity, and antimicrobial peptides (AMPs), peptides that can disrupt microbial membranes through pore formation or membrane lysis. Despite extensive experimental research, a comprehensive understanding of CPPs’ mechanism at the molecular level remains elusive. Molecular dynamics (MD) simulations offer a powerful approach to investigate protein-lipid interactions and the dynamic behavior of peptide-membrane systems at atomic resolution. Nonetheless, capturing these complex processes through conventional MD simulations is computationally demanding. To address this, a range of enhancing sampling techniques has been developed. In this review, we discuss the MD methodologies available for studying CPPs’ interactions with membranes, focusing on the techniques introduced by our group. Our aim is to provide a useful reference for future investigations into peptide-membrane interactions, ultimately advancing molecular-level insight into these biologically significant systems.