Physical Basis Of pK a Shift For Ionizable Lipids In An LNP-like Environment
Year: 2026
Type: preprint
Abstract: ABSTRACT Lipid nanoparticles (LNPs) are a leading drug delivery platform for mRNA or other nucleic-acid based therapeutics. LNP platforms are typically composed of ionizable aminolipids, phospholipids, sterols, and PEG lipids. These ionizable aminolipids are typically cationic at low pH, allowing them to encapsulate negatively charged mRNA. The fraction of charged ionizable head groups, i.e; the apparent pK a of the LNPs, is of interest in understanding LNP characteristics. However, this is difficult to measure as the apparent pK a differs from the pK a of the aminolipids in bulk solution due to the complex chemical and charge environment. In this study, we use molecular dynamics (MD) simulations with alchemical free energy perturbation to calculate the free energy to protonate an ionizable aminolipid in a LNP-like membrane, allowing us to calculate the apparent pKa 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. We calculate the pK a shifts, and find that the pH dependent structure of the systems affects the trends in pK a shifts. We classify the structures, investigate the electrostatic environment at the surface of our systems, and draw insights into how these factors affect the pK a shifts. 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. SIGNIFICANCE This study addresses the physical driving forces behind the pK a shift of ionizable lipids in lipid nanoparticles by modeling them using membranes with an internalized neutral ionizable lipid phase. Our study provides an estimate of the pK a shift at the model surface and is the first to isolate the contributions to the pK a shift from electrostatics and the internalization equilibrium. We establish trends seen with change in composition and pH in the extent of this pK a shift.
Authors: Akshara Sharma, Sreyoshi Sur, Alan Grossfield
Institution: University of Rochester Medicine
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7221188450