Building a State-of-the-Art Automation Platform to Support High-Throughput 96-Well Caco-2 Permeability Assay

Abstract

Automation plays a crucial role in enhancing efficiency and increasing capacity for in vitro absorption, distribution, metabolism, and excretion profiling in early drug discovery. Building an automation platform requires a careful balance of innovation and practical considerations to align assay needs with technological capabilities. In this study, we present a state-of-the-art automation system designed to support the miniaturization of the Caco-2 permeability assay from the 24-well to the 96-well format. This platform integrates advanced infrastructure for cell culture and assay execution, along with several key features, including innovative cleaning protocols, cutting-edge plate tracking, and dynamic scheduling capabilities. The fully automated 96-well platform delivers significant efficiency gains, increased capacity, and faster turnaround for permeability assay support while maintaining high predictive accuracy. It correctly classified 94% of 50 literature compounds, demonstrating strong concordance with the established 24-well format. Moreover, the platform enables large-scale permeability data generation, advancing our “predict-first” modeling paradigm, in which predictive models guide experimental design and compound prioritization.