Driving forces in the assembly of lipid nanoparticles containing mRNA revealed by molecular dynamics simulations at acidic and physiological pH

Abstract This study utilized all-atom molecular dynamics (MD) simulations to investigate the interactions and driving forces involved in the formation of mRNA-containing lipid nanoparticles (LNPs) at acidic pH (4.5) and physiological pH. Under the acidic condition, the LNP comprises mRNA, positively charged ionizable lipid (SM-102P), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), cholesterol, 1,2-dimyristoyl-rac-glycero-3-methoxypolyethylene glycol-2000 (DMG-PEG2000), and citrate ions with a charge of − 1. At physiological pH, it includes mRNA, both positively and neutrally charged ionizable lipids (SM-102P and SM-102N, respectively), DSPC, cholesterol, DMG-PEG2000, and citrate ions at − 1 and − 3 charges. MD analyses suggest that electrostatic forces play a significant role in mRNA and SM-102P interactions, which are crucial for mRNA encapsulation. Moreover, van der Waals forces are vital in the interactions between lipids during LNP formation, where at physiological pH, the lower polarity of SM-102N leads to stronger lipid interactions. Differences in the protonation states of ionizable lipids affect the hydrophobic interactions between lipid components in the LNP. Meanwhile, MD simulations in which all ionizable lipids are neutrally charged result in the mRNA not being encapsulated. Our finding offers insight into the self-assembly process of LNP, highlighting the crucial influence of pH and ionic strength on the encapsulation of mRNA by LNP.