Lipid nanoparticles (LNPs) are leading drug delivery platforms for mRNA or other nucleic-acid-based therapeutics. LNP platforms like those used in the recently FDA approved COVID-19 vaccines by Moderna and Pfizer/BioNTech are typically composed of ionizable aminolipids, phospholipids, sterols, and PEG lipids. These ionizable aminolipids are typically protonated at low pH, allowing them to encapsulate negatively charged mRNA. The fraction of charged ionizable head groups of the aminolipids when incorporated into LNPs, the apparent pK a of the LNPs, is a key factor determining efficacy of the mRNA vaccines. However, this is difficult to measure as the apparent pK a differs from the pK a of the aminolipids in bulk solution on account of the complex chemical and charge environment inside and at the surface of an LNP. In this study, we use molecular dynamics (MD) simulations with the alchemical free-energy perturbation to calculate the free energy to protonate an ionizable aminolipid in a LNP-like membrane bilayer, allowing us to calculate the apparent pK a of the system. We do this for membranes with a range of aminolipid compositions and represent various pH environments by varying the fraction of charged aminolipids to quantify the apparent pK a of the system over a wide range of physiological conditions. Our all-atom simulation protocol provides a quick means of estimating the apparent pK a of LNPs formed with both newly developed ionizable aminolipid candidates as well as new LNP compositions.
Sharma et al. (Sun,) studied this question.