Abstract 1222: Developing kinase inhibitors with polypharmacological profiles for the treatment of resistant cancers

Small molecule kinase inhibitors targeting a specific oncoprotein driving cancer cells have shown great clinical success in the past (e.g. imatinib against leukemia). However, resistance to targeted therapies quickly arises due to plasticity associated with cancer cell signaling and tumor heterogeneity. One way to overcome this problem is to rationally design drugs with polypharmacology that can target multiple signaling pathways engaging in cancer cell proliferation and survival. To this end, we have developed a strategy based on combining phenotypic screens of small molecule inhibitors and affinity-based mass spectrometry to identify drugs with multi-targeted properties and piloted this approach using the highly resistant KRAS mutant non-small cell lung cancer cell lines. We began this study by screening kinase inhibitors targeting MEK, ERK, PI3K, Akt and mTOR and found that the lung cancer cells were largely resistant to single drugs but showed enhanced sensitivity towards triple inhibition of MEK, ERK and PI3K. These cell lines were then screened with a library of covalent and non-covalent kinase inhibitors in an attempt to identify a small molecule inhibitor that could mimic the activity of the triple drug combination. This led to the discovery of SM1-71 that not only recapitulated the growth inhibitory activity of MEK+ERK+PI3K inhibition, but also blocked phosphorylation of ERK, Akt, mTOR and S6K in cells. Target profiling of the drug was carried out using chemoproteomics, which revealed that SM1-71 inhibited 55 kinases at a 1μM concentration. Dose-dependent evaluation further determined the IC50 of inhibition across the 55 kinases and rank ordered them based on binding affinity. Top hits including MEK1, MEK2, ERK1, ERK2, AURKA, SRC and RPS6KA3 were confirmed using alternate kinase screens and cellular assays. Growth factor receptors such as IGF1R, MET and EGFR were also identified and further validated using cell-based assays. Taken together, these results elucidated the polypharmacology associated with SM1-71 and uncovered key targets responsible for inducing strong cytotoxicity in KRAS mutant lung cancer cells. Through the combination of phenotypic screens and mass spectrometry-based target identification, we have demonstrated the proof of principle for developing kinase inhibitors with polypharmacology targeting resistant cancers. Citation Format: Suman Rao, Tan Li, Robert Everley, Guangyan Du, Peter Sorger, Nathanael Gray. Developing kinase inhibitors with polypharmacological profiles for the treatment of resistant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1222. doi:10.1158/1538-7445.AM2017-1222