Decoding pH‐Driven Phase Transition of Lipid Nanoparticles

ABSTRACT The functionality of lipid nanoparticles (LNPs) as delivery systems in mRNA‐based therapeutics is intricately linked to the protonation behavior of their aminolipid components. This study employs large‐scale constant‐pH molecular dynamics (CpHMD) simulations to decode the environment‐dependent of aminolipids in the Comirnaty lipid formulation, providing a detailed view of their pH‐dependent structural dynamics. Our results reveal a significant shift in the apparent of the aminolipid ALC‐0315, from an intrinsic value of 9.3 in water to 4.9 within the LNP environment. This shift arises from the interplay between lipid reorganization and local electrostatic interactions, resulting in distinct protonation states across the LNP core and surface. At low pH, protonated aminolipids dominate the LNP surface, promoting efficient mRNA encapsulation, whereas at neutral pH, deprotonated aminolipids migrate to the hydrophobic core, driving structural stabilization. Notably, the localized of aminolipids varies significantly with their position, decreasing from near‐surface regions (7 to 8) to the hydrophobic core (4). These findings elucidate the molecular mechanisms underpinning LNP phase transitions and highlight the key role of shifts for the design of aminolipids and for optimizing LNP compositions for enhanced therapeutic delivery. This study bridges experimental observations with molecular‐level insights, advancing the rational development of next‐generation lipid‐based nanocarriers.