GenShin: Guiding Rational Liposome Design by Ranking Liposomal Protein Corona through a Docking-Pose-Free GNN
Authors: Pingfei Zhu, Hongyi Liu, Xueyan Liu, Zhenjun Yang, Bo Yang
Abstract
Rational design of lipid nanoparticles (LNPs) for tissue-specific delivery critically depends on predicting the composition of the protein corona that forms on the lipid surface after intravenous administration. However, conventional characterization of the protein corona relies on costly and time-consuming mass spectrometry experiments, which require physically prepared liposome samples and therefore cannot serve as a pre-synthesis screening strategy for large candidate lipid spaces. The adsorption of plasma proteins onto liposomal surfaces is shaped by lipid chemical structures, protein properties and the biological environment, making this process difficult to simulate directly. In this work, we propose that scoring lipid-plasma protein pairs and ranking the resulting scores can provide a practical signal for revealing the relative composition of the liposomal surface protein corona.Here we introduce GenShin, a geometry-enhanced pose-free graph neural network designed to score lipid-plasma protein pairs. GenShin is pretrained on compound-protein affinity data to initialize a generalizable scoring function and is then fine-tuned on a rank fine-tuning dataset constructed from liposomal protein-corona abundance measurements to adapt the model to lipid-plasma protein pair scoring. Before fine-tuning, GenShin achieves competitive pose-free affinity prediction on the PDBbind v2016 benchmark compared with representative pose-dependent models. CASF-2016 perturbation experiments using the pretrained GenShin model further show that pose-dependent inference substantially degrades when intermolecular poses are unreliable, whereas GenShin remains stable without requiring such poses. This supports the practical advantage of GenShin for large-scale lipid-protein scoring.
Lipid nanoparticles (LNPs) are among the most clinically mature platforms for nucleic acid delivery, yet designing lipids that are both effective and biologically safe remains a major bottleneck. In practical screening, toxicity is a decision-level constraint: if a lipid is toxic, its efficiency prediction is clinically irrelevant. We propose LipoAgent, a safety-aware multi-agent LLM framework for lipid discovery. LipoAgent combines domain-specific finetuning with a conditional prediction objective that enforces toxicity as a prerequisite for efficiency prediction, and further improves reliability via multi-agent verification with lightweight human oversight when disagreement persists. Across multiple foundation models, LipoAgent achieves an average 32% relative improvement in mRNA transfection efficiency prediction compared with other reported models for lipid design. Wet-lab validation confirms that virtual screening rankings reliably translate to biological transfection outcomes. The code is publicly available at https://github.com/SAI-Lab-NYU/LipoAgent.git.
The discovery of new ionizable lipids for efficient lipid nanoparticle (LNP)-mediated RNA delivery remains a major bottleneck in RNA therapeutics development. Recent advances demonstrate the potential of machine learning (ML) models to predict transfection efficiency directly from lipid structure, enabling high-throughput virtual screening and accelerating lead identification. However, as new models for LNP transfection prediction continue to emerge, the lack of rigorous and standardized benchmarking poses a significant risk and may undermine confidence in their reliability for discovery. Here, we present a robust ML benchmarking framework for evaluating transfection prediction models based on ionizable lipid structures. This framework systematically benchmarks diverse molecular representations paired with a broad range of ML architectures spanning traditional models, feedforward neural networks, and state-of-the-art graph-based methods. In addition, the presented framework supports assessment of model generalization and evaluates prediction reliability beyond standard regression metrics. Using a curated dataset of 1,100 unique ionizable lipid structures derived from the HeLa transfection dataset originally reported by Xu et al., we show that within this framework, models leveraging explicit molecular substructure encoding consistently achieve the highest predictive accuracy and should serve as essential baselines for the development of new, more sophisticated models. In contrast, some current graph-based models, including AGILE, Chemprop, and KPGT, tend to show comparatively lower accuracy. The presented framework provides a standardized, transparent, and comprehensive benchmarking resource that enables meaningful comparison of emerging architectures and establishes strong baselines for future development of predictive models in lipid-based RNA delivery.
Asal Mehradfar, Mohammad Shahab Sepehri, Jose Miguel Hernandez-Lobato +4
Lipid nanoparticles (LNPs) are efficient delivery systems for negatively charged nucleic acids. Their multi-component architecture yields a core-shell structure. Small-angle X-ray scattering (SAXS) is an important characterization technique for LNPs, but recovering internal structure and size distribution from SAXS is an inverse problem with non-unique solutions. Realistic models are often too expensive for systematic exploration. We introduce a machine-learning-accelerated, differentiable framework for SAXS analysis of heterogeneous, polydisperse LNPs. The forward model combines a core-shell particle with a Gaussian random-field interior, a neural surrogate for the monodisperse SAXS map, and a differentiable layer integrating over particle-size distributions. The surrogate reduces prediction cost by four orders of magnitude, while differentiability enables large-scale multi-start fitting and ensemble identifiability analysis. Applied to synthetic and experimental MC3 LNP data, the framework shows that near-identical SAXS fits can arise from distinct parameter modes, with the experimental fits dominated by a trade-off between size-distribution and interior-structure parameters.