Label-Free High-Throughput Screening of CYP3A4 Inhibitors Using Acoustic Ejection Mass Spectrometry

Label-free high-throughput screening (HTS) technologies have greatly accelerated early drug discovery by allowing direct measurement of biochemical activity without the need for chemical labels. Techniques like MALDI-TOF, RapidFire, desorption electrospray ionization, and acoustic-mist ionization mass spectrometry have shown strong analytical performance. More recently, acoustic droplet ejection mass spectrometry (AEMS) has emerged as a next-generation platform capable of analyzing over a thousand data points per hour. In this study, we thoroughly evaluated an AEMS workflow using cytochrome P450 3A4 (CYP3A4) as a model enzyme. Screening a library of 9702 compounds, this work represents the first successful label-free HTS campaign for CYP3A4 inhibitors in a 384-well format using AEMS. The result using nifedipine as a substrate was comparable to the widely used P450-Glo luminescence assay but with fewer inhibitor hits identifications. To further compare and parse differences between the methods and the substrates, 819 hits were retested using AEMS with luciferin isopropyl acetal, the same substrate used in the luminescence assay. The findings confirmed that both the assay method and the substrate influence which inhibitors were detected. Overall, this study established AEMS as a robust and reliable tool for CYP3A4 inhibitor screening. It offers high analytical precision, fewer false positives, compatibility with multiple substrates, and direct detection of metabolites, providing a practical way to validate hits and improve confidence in early drug discovery efforts.