Abstract 6853: A standardized drug selectivity profiling platform with a proteome coverage of more than 5,000 proteins

Abstract Drug hunters typically rely on a combination of biophysical/biochemical binding and efficacy assays to find and prioritize hit compounds in their drug discovery efforts. These activities are pivotal for success where the right assay combination can correlate productive binding (target engagement) with a biological effect. The earlier such correlations can be established, the better, as that speeds up the prioritization process and builds confidence in the lead series that are progressed to lead optimization. Currently, at that stage, selectivity assays for specific protein classes, typically including safety panels of up to 200 proteins, are applied. However, a limited number of proteins will result in a biased selectivity assessment. Instead, an unbiased and proteome-wide selectivity profiling assay, employed early in the drug discovery process, contributes to the correct prioritization of lead compounds. Pelago Bioscience has established a standardized assay for selectivity profiling, based on the Cellular Thermal Shift Assay (CETSA) with mass spectrometry (MS) detection, which enables discrimination between selective and more promiscuous molecules at the proteome level. As an example, we have profiled over 100 different drugs and probes used in clinical oncology and tumor biology research. Investigated drug classes include antimetabolites, alkylating agents, DNA intercalating agents, epigenetic modifiers, kinase inhibitors, and microtubule inhibitors. In the work presented here, we will show how compounds with similar structures and mode of action also display similar CETSA protein shift profiles with regards to intended targets and off-targets. Such reference data allows comparison of novel chemical hits to compounds with an established mode of action. High throughput and data quality, with an assessment of more than 5, 000 proteins, enables large compound batches to be assayed also during early phases of drug discovery. This speeds up the process and increases the confidence in lead series and future lead candidates. Citation Format: Tomas Friman, Tuomas Tolvanen, Tove Boström, Ying Sun, Alexey Chernobrovkin, Yasmin Andersson, Christina Velasco, Daniel Martinez Molina. A standardized drug selectivity profiling platform with a proteome coverage of more than 5, 000 proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6853.