Descriptor-Guided Selection of Extracellular Vesicle Loading Strategies for Small-Molecule Drug Delivery: A Mechanistically Interpretable Decision-Support Framework

Background: Extracellular vesicles (EVs) are increasingly explored as nanocarriers in drug delivery; however, selecting an appropriate loading strategy for a given small-molecule cargo still relies largely on empirical, resource-intensive parallel screening within EV formulation workflows. Despite the widespread application of passive incubation, electroporation, saponin-mediated permeabilization, freeze–thaw cycling, and sonication, there is currently no mechanistically grounded, descriptor-informed framework that enables rational prioritization of loading methods during the early design stage of EV-based dosage forms, leading to inefficient trial-and-error experimentation. Methods: We assembled a chemically diverse dataset of 21 compounds with experimentally determined loading efficiencies across five EV loading methods and calculated seven mechanistically motivated physicochemical descriptors (LogP, molecular weight, aqueous solubility, hydrogen bond donors/acceptors, polar surface area, and formal charge) for each drug. Separate Elastic Net regression models were trained for each loading strategy. Model performance was evaluated using leave-one-out cross-validation, a predefined external validation set (n = 4), and 50 repeated random train–test splits. The analysis emphasized decision-level ranking of loading methods rather than the precise prediction of absolute efficiencies. The applicability domain was assessed via leverage analysis to define the supported chemical space for prospective implementation in EV-based formulation development. Results: As anticipated for biologically heterogeneous EV systems, continuous regression performance remained modest (LOOCV R2 = 0.06–0.41). In contrast, decision-level accuracy for identifying the experimentally optimal loading method was consistently high across validation schemes (internal: 76.5%; predefined external: 75%; repeated random validation: 80.5 ± 16.8%). Mechanical disruption methods (freeze–thaw and sonication) demonstrated comparatively greater predictive stability, while misclassification patterns suggested potential nonlinear behavior for highly polar, ionizable cargos. All compounds resided within the leverage-defined applicability domain, confirming adequate descriptor-space representation. Conclusions: This study establishes a mechanistically interpretable, descriptor-based decision-support framework capable of reliably prioritizing EV loading strategies for small-molecule cargos beyond empirical chance without altering standard protocols. By reframing the modeling objective from high-precision efficiency prediction to robust ranking of candidate methods, the approach offers a practical tool to triage between commonly used techniques, thereby reducing experimental burden in early-stage EV formulation development. The framework provides a quantitative basis for integrating molecular-descriptor-guided method selection into rational EV-based drug delivery design and can be expanded with membrane-specific descriptors and larger datasets.