Endosomal Escape of siRNA Polyplexes: A Molecular Dynamics Perspective on Underlying Mechanisms

ABSTRACT To achieve a therapeutic effect, nanoparticles delivering nucleic acids must facilitate endosomal escape (EE) of their cargo. Despite extensive research, the mechanisms that lead to an effective EE are not sufficiently understood. Herein, we compare the EE behavior of four polymeric formulations (polyplexes) and one lipid nanoparticle (LNP) in vitro. Simultaneously, we utilized molecular dynamics (MD) simulations in all atom (AA) and coarse grained (CG) resolutions to differentiate the interaction of those formulations with endosomal membranes. The identified interaction patterns were discussed in perspective with the in vitro performance of the formulations: On the one hand, the results emphasize the benefit of hydrophobic residues in the nanoparticles. On the other hand, the role of anionic lipids in the biological membranes is demonstrated by MD. Different interaction modes of polyplex formulations with endosomal membranes are visualized in simulation with the aim to distinguish potential EE mechanisms from one another. This work highlights the power of MD simulations for taking a big step toward explaining differences observed in vitro on a molecular level and toward better understanding EE efficiency.