Atomic Insights into pH-Dependent and Water Permeation of mRNA-Lipid Nanoparticles

The exposure of mRNA to water is likely to contribute to the instability of RNA vaccines upon storage under nonfrozen conditions. Using atomistic molecular dynamics (MD) simulations, we investigated the pH-dependent structural transition and water penetration behavior of mRNA-lipid nanoparticles (LNPs) with the compositions of Moderna and Pfizer vaccines against COVID-19 in an aqueous solution. It was revealed that the ionizable lipid (IL) membranes of LNPs were extremely sensitive to pH, and the increased acidity could cause a rapid membrane collapse and hydration swelling of LNP, confirming the high releasing efficiency of both LNP vaccines. The free energy profiles of water penetration showed that the conical structure of IL played a key role in obstructing water from entering the inner core of LNPs: the molecular geometry with more tail chains, lower linearity, and looser packing structure resulted in higher water permeability, leading to lower stability in nonfrozen liquid environment. On the other hand, the geometry of IL also dominated the fusion behavior of LNP with endosomal membrane during the endosomal escape. Thus, for LNP-based vaccines with both high release efficiency and high stability, a suitable molecular structure of ILs should be selected to seek a balance between the packing tightness and fusion rate of membranes.