From genotype-selective small molecules to novel clinical candidates and novel drug targets in cancer: Chemi-proteomics approach
Authors: Sudhir Sahasrabudhe, Paul Robbins, Tracy Erkkila, Rob Becklin, Michael Pierce, Justin Savage, Brent Stockwell
Journal: Clinical Cancer Research (2008)

A1   Traditional drug discovery process involves identification of candidate targets, followed by target validation, assay development, assay adaptation, high-throughput screening followed by the identification of hits and leads. This process can easily take 5 to 7 years before the pre-clinical studies are completed and the human clinical trials can begin. At times this approach has resulted in the identification of drugs that exert the therapeutic benefit via a protein target which is separate and distinct from the target against which the drug was optimized. It is therefore important to explore additional alternative paths that lead to rapid identification of novel therapeutic anti-cancer agents.  Our strategy involves searching for genotype-selective, or tumor cell selective agents that become lethal to tumor cells only in the presence of specific oncoproteins. Such genotype-selective compounds may serve as: 1) small molecule hits for development of clinically effective drugs with a favorable therapeutic index and desirable pharmaceutical properties; 2) molecular probes for tumor-relevant biological networks; or 3) identification of novel candidate drug targets. The direct identification of a small molecule lead may provide a cost-effective and time-effective strategy to test novel therapeutic agents in the clinic. Parallel efforts geared towards identification of the drug’s molecular target can significantly advance our understanding of the mechanism-of-action of the candidate drug and permit identification of the potential pharmacodynamic marker(s), and additional drug targets. This small molecule-based approach may lead to the identification of novel proteins that may otherwise escape traditional methods of identifying a candidate therapeutic target.  We have developed a chemiproteomics approach in which a drug is immobilized to a solid support and the direct or indirect interaction between it and one or more cellular target protein(s) can aid in the elucidation of drug targets. Successful target identification is dependent upon several factors, such as the drug’s affinity for target proteins in its immobilized form, target protein expression levels, chromatography methods powerful enough to separate many hundreds of peptides, and the ability of tandem mass spectrometry to identify target proteins, even if those proteins exist as isomers. We have identified protein interactions that are specific to Erastin, a small molecule that induces cell death in engineered human tumor cells (BJ-TERT/LT/ST/RASV12; Yagoda et al., Nature 447:864-868, 2007). PRLX 93936, a structural analog of Erastin, shows potent anti-tumor activity against a wide variety of tumor cells in vitro and in vivo. Interestingly, PRLX 93936 shows selective anti-tumor activity by a mode of action that is distinct from that of Erastin. In this presentation we will discuss the chemiproteomics data obtained with the analogs of Erastin and PRLX 93936.