Development of the first label-free and high-throughput, cell-based assay that reports on specific enzyme activities

Project Summary / Abstract Cell-based assays that quantitate the effect of small molecules on cellular behavior are powerful tools in cancer research. The ability to assess small molecules in a physiologically relevant environment is informative, as the assays simultaneously evaluate compound permeability, toxicity, and potency. To date, cell-based assays are largely limited to measure global changes such as phenotype, proliferation, or gene expression. The current challenge is to develop cell-based assays for specific enzyme activities to augment and accelerate drug discovery campaigns. Notably, the most common strategies for measuring enzyme activities, such as radioactivity, absorbance, and fluorescent labels, often cannot be delivered to the appropriate target within the cellular environment and they are susceptible to high rates of false positives. This proposal describes the continued development and validation of a novel label-free methodology that combines cell culture and lysis on customized surface chemistries to allow a mass spectrometry readout for distinct enzyme activities. The approach uses functionalized self-assembled monolayers (SAMs) that present cell adhesion ligands along with substrates for the relevant cellular enzyme targets. Cells are cultured on the monolayers in the presence of small molecules, and then lysed such that enzymes within the lysate have immediate access to convert the immobilized substrate to a product. An advantage of using SAMs on gold is their compatibility with matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS), an approach termed “SAMDI”, that records the activity of specific enzymes within the lysate. This technique, termed Tandem Culture and Lysis (TCAL)-SAMDI, offers a novel, powerful tool for a quantitative readout of virtually any cellular enzyme activity and represents new capabilities for high-throughput and label-free, cell- based screens for drug discovery.Project Narrative This proposal addresses the lack of label-free, high-throughput cell-based assays that report on specific enzyme activities suitable for drug discovery. The project aims to advance the development of our novel approach that combines cell culture and lysis on customized surface chemistries that allows, for the first time, a mass spectrometry readout for distinct cellular enzyme activities. We will highlight the value and flexibility of this disruptive methodology by profiling substrate specificities using high density biochip arrays, developing novel assays for epigenetic enzyme activities implicated in cancer, and performing a multiplex high-throughput screen of 100,000 compounds to identify novel epigenetic modulators. Moreover, we will benchmark our technology against the current state-of-the-art cell-based high-throughput screening assay. Our proposal aims to highlight that our technology, which we intend to offer on a fee-for-service basis starting in 2022, will generate more relevant data, save companies tens of millions of dollars, and can expedite drug discovery by two years.