ProTargetMiner is a proteome signature library of anticancer molecules for functional discovery.
Strategy and workflow:
- Nordic Preclinical Sciences AB, using ProTargetMiner, can provide valuable information in terms of mechanism of action (MoA) of an oncology drug candidate.
- ProTargetMiner is an extensive proteome signature database of anticancer molecules to identify compounds with similar MOA in multidimensional space.
- Since the response of the target and mechanistic proteins to a compound is specific, an orthogonal partial least square discriminant analysis (OPLS-DA) model contrasting the given compound with all other molecules in the database will identify the drug targets (red circles) and mechanistic proteins as specifically regulated proteins (among other proteins shown with gray circles).
- Determination of LC50 values for the library of compounds and selected cells;
- Cell treatment with panel of compounds as well as vehicle-treated control and standard treatments (e.g., methotrexate, paclitaxel and camptothecin) in at least three biological replicates;
- Lysis, digestion and labeling with TMT-10plex reagents;
- Multiplexing the 10-plexed samples and fractionation of the pooled sample to increase the proteome coverage;
- Analysis of individual fractions by LC-MS/MS;
- Protein identification and relative quantification;
- Data post-processing and deconvolution of MoA.