Tales of 1,008 Small Molecules: Phenomic Profiling through Live-cell Imaging in a Panel of Reporter Cell Lines

To devise an economical set of phenomic profiling assays, we assembled a library of 1,008 approved drugs and tool compounds manually annotated to 218 unique MoAs and an additional 169 natural products, and we profiled each compound at four concentrations in live-cell, high-content imaging screens against a panel of 15 reporter cell lines, which expressed a diverse set of fluorescent organelle and pathway markers in three distinct cell lineages. Phenomic profiling can be used for compound target identification or mechanism of action (MoA) prediction and other applications in drug discovery. For 41 of 83 MoAs with sufficiently many active compounds, phenomic profiles accurately ranked the reference compounds (AUC-ROC ≥0.9) in at least one of our cell lines.