Lipid Nanoparticle Database towards structure-function modeling and data-driven design for nucleic acid delivery.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41605942.
- Also identified by DOI 10.1038/s41467-026-68818-1 and PMC identifier 12992592.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Lipid nanoparticles (LNPs) are the leading nonviral nucleic acid delivery technology, but LNP structure-function data remains fragmented and nonstandardized. Unlike protein engineering which is anchored by the centralized Protein Data Bank, the LNP field lacks a unified repository for systematic analysis. To address this, we develop Lipid Nanoparticle Database (LNPDB) ( https://lnpdb.molcube.com ), an integrated database and web tool that consolidates structural and functional data for 19,528 LNPs. LNPDB standardizes LNP featurization by encoding lipid composition, experimental methods, and functional results, and generates CHARMM force field files for constituent lipids to enable molecular dynamics simulations. LNPDB also supports future data contributions for continued growth. We examine the utility of LNPDB through two applications: advancing our deep learning model for predicting LNP delivery performance, and simulating bilayer dynamics to identify structural features - bilayer stability and critical packing parameter - that correlate with LNP delivery performance. Altogether, LNPDB provides the digital framework for LNP modeling and data-driven rational design.
Medical subject headings
- Nanoparticles
- Lipids
- Nucleic Acids
- Databases, Factual