Discovery of Novel Ionizable Lipids for Lipid Nanoparticles: Lipophilicity as a Predictor of Squaramide Head Group Lipid Clearance

Ionizable lipids are a critical component of lipid nanoparticles (LNPs) for messenger RNA (mRNA) delivery, driving cellular uptake, endosomal escape, and tolerability. It is well-known that chemical modifications to ionizable lipids profoundly affect both potency and safety profiles. However, the lack of reliable predictive tools, limited understanding of lipid behavior, and the intrinsic complexity of LNPs remain major challenges in LNP development. Among these, in vivo lipid clearance is a critical yet poorly understood factor influencing long-term safety of mRNA loaded LNPs, particularly with respect to their accumulation. Impaired clearance leading to lipid accumulation can pose safety liabilities and contribute to long-term toxicity. To address this, we investigated lipophilic properties of squaramide head group ionizable lipids with ester linkers as surrogates for in vivo clearance. We demonstrate that lipid clearance can be tuned by chemical modification and is predictable from simple lipophilicity calculation. To our knowledge, this represents the first computationally driven approach predicting lipid properties relevant to both efficacy and long-term safety within the current competitive landscape.