(1196-A) TracerDB: A comprehensive database of validated fluorescent probes to quantify small molecule-protein interaction in vitro and in live cells
Monday, February 5, 2024
12:00 PM – 1:00 PM EST
Location: Exhibit Halls AB
Abstract: In the field of chemical biology and drug discovery, the characterization of compound-protein interactions is a crucial step in understanding the mechanism of action of drug molecules and chemical probes. To quantify target affinity, two major methods are commonly used: (I) Direct binding assays using purified protein either in solution (e.g. NMR or ITC) or through immobilization (e.g. SPR), or (II) competitive displacement measurements with the goal of Ki determination using either purified proteins (eg Fluorescence polarization or TR-FRET) or cellular systems (e.g. NanoBRET). Using competitive displacement assays, a well-characterized ligand binding to a distinct site on the target is always required. These bifunctional “tracer” ligands may comprise a peptide or a small molecule attached to a detection reagent such as a fluorophore. The development of tracer molecules can require significant SAR and protein preknowledge, which may not be resident to all chemical biology labs. To organize tracer development efforts and facilitate an open community of knowledge on such assay reagents, we have established a database called “TracerDB”. This project describes development of an open access database to provide reviewed tracer molecules for especially therapeutically relevant targets across the human proteome and to increase dissemination of these data in the community. The TracerDB not only contains crucial information about the tracers themselves as structure and fluorophore properties, but also experimental data for tracer affinity determination and displacement data to ensure reproducibility and certain assay standards. Additionally, we enable accessibility to the described tracers by either reporting the synthetic route or directing users to possible commercial vendors. By establishing the TracerDB, we build the foundation for the development of standardized displacement assays for the generation of comparable, high quality binding data across different labs and also enable easy access to assay systems for so far understudied targets.