Lipid nanoparticles (LNPs) represent a promising platform for advanced drug and gene delivery, yet optimizing these particles for specific cargos and cell targets poses a complex multifaceted challenge. Furthermore, there is a pressing need for a more comprehensive understanding of the underlying technology. Experimental studies are costly and often provide low-resolution information. Molecular dynamics (MD) simulations allow us to study these particles at a higher resolution, enhancing our understanding. However, studying these systems at atomic resolutions is both challenging and computationally expensive as well as time-consuming. Coarse-grained (CG) models, such as Martini 3, are positioned as promising tools for studying LNPs. To enable CG-MD studies of LNPs, accurate and validated models of their components are needed. Here, we present a substantial extension of the Martini 3 lipid library, introducing over one hundred ionizable lipid models, natural sterols, and PEGylated lipids, covering the key components of LNP formulations. This expanded library brings an essential toolset to simulate LNPs at Martini coarse-grained resolution. We furthermore introduce initial protocols for screening fusion efficacy across lipid formulations and for constructing full LNPs and show how these tools can provide new insights into the LNP structure, dynamics, and efficiency. Altogether, this work introduces a practical and scalable approach for advancing the mechanistic understanding of LNPs and guiding their future development.

Centre Blaise Pascal de Simulation et de Modélisation Numérique Ecole Normale Supérieure de Lyon 47 Allée d'Italie 69364 Lyon France

Departamento de Quimica Facultad de Ciencias Universidad de Tarapacá Av Gral Velasquez 1775 Arica Chile

Department of Physics Pukyong National University 48513 Busan Republic of Korea

Department of Physics University of Helsinki P O Box 64 FI 00014 Helsinki Finland

Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen 9712 CP Groningen The Netherlands

Heidelberg Institute for Theoretical Studies 69118 Heidelberg Germany

IT4Innovations VŠB─Technical University of Ostrava 17 listopadu 2172 15 708 00 Ostrava Poruba Czech Republic

Laboratoire de Biologie et Modélisation de la Cellule CNRS UMR 5239 Inserm U1293 Universite Claude Bernard Lyon 1 Ecole Normale Supérieure de Lyon 46 Allée d'Italie 69364 Lyon France

Laboratorio de Simulación Molecular y Bioinformática Centro de Investigación en Ciencias de la Vida Universidad Simón Bolívar Carrera 59 59 65 080002 Barranquilla Colombia

Molecular Microbiology and Structural Biochemistry CNRS and University of Lyon 69000 Lyon France

PharmCADD 1102 ho 60 Centum jungang ro Haeundae gu 48059 Busan Republic of Korea

Regional Centre of Advanced Technologies and Materials Czech Advanced Technology and Research Institute Palacký University Olomouc Šlechtitelů 27 779 00 Olomouc Czech Republic

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