Coarse-Grained Simulations of RNA-Loaded Lipid Nanoparticles: Implications on RNA Stability and Antigenic Protein Expression in mRNA Vaccines

, an mRNA molecule requires a safe, effective, and stable delivery system that protects it from degradation, that allows cellular uptake, and the mRNA release in the cytoplasm. This is achieved in the commercial mRNA vaccines against COVID-19 by using a specific class of molecules called cationic lipids (CLs) or ionizable lipids (ILs) as one of the main components of the LNPs. In this article, we perform coarse-grained simulations using the Martini force field for large systems, encompassing all constituents of the LNP (RNA, IL, cholesterol, PEGylated lipids, and water), and we highlight the strategic role at different pHs of the DLin-MC3-DMA (MC3) molecule, which is commercially used as an RNA delivery vehicle. Then, we discuss the role of MC3 in the shaping, internal organization, and water content of the LNP. Finally, we investigate the role of MC3 as an IL during the endosomal fusion, and we describe its behavior at different pHs. Our results illustrate the challenges associated with the selection of an IL in the design of an RNA-LNP system, and IL's potential role in the RNA's stability and efficiency. This work can serve as a useful resource for the future development of new RNA-LNP carriers and mRNA-based vaccines.