SUMMARY Protein kinases are therapeutic targets for human cancer. However, “gatekeeper” mutations in tyrosine kinases cause acquired clinical resistance, limiting long-term treatment benefits. mTOR is a key cancer driver and drug target. Numerous small molecule mTOR kinase inhibitors have been developed, with some already in human clinical trials. Given our clinical experience with targeted therapeutics, acquired drug resistance in mTOR is thought likely but not yet documented. Herein, we describe identification of a hotspot (L2185) for drug-resistant mutations, which is distinct from the “gatekeeper” site, and a chemical scaffold refractory to drug-resistant mutations. We also provide new insights into mTOR kinase structure and function. The hotspot mutations are potentially useful as surrogate biomarkers for acquired drug resistance in ongoing clinical trials and future treatments, and to facilitate design of the next generation of mTOR-targeted drugs. Our study provides a foundation for further research on mTOR kinase function and targeting.

The mammalian target of rapamycin (mTOR) is the major regulator of cell growth, metabolism and survival. The anti-cancer effect of allosteric mTOR-inhibitors, rapamycin and its analogs (rapalogs), has been tested extensively in different types of cancer cells. However, there is only limited clinical efficacy observed by treatment of these traditional mTOR inhibitors, partly due to the occurring of acquired rapamycin resistance (ARR). Several new mTOR inhibitors have been developed which specifically target to the catalytic sites of mTOR by competing with ATP binding, and are suggested to be more effective in inhibiting mTOR signaling and cell growth. However, their effect and mechanisms in ARR cells are not clear yet. In the present study, we used an in vitro model of acquired rapamycin-resistant (ARR) breast cancer cells to evaluate the efficacy of two major classes of ATP-competitive mTOR inhibitors, PI3K/mTOR dual and mTORC1/mTORC2 inhibitors. We found that ATP-competitive mTOR inhibitors acutely suppress the proliferation and prominently inhibit PI3K/mTOR signaling of ARR breast cancer cells. In contrast to the cytostatic effect of rapamycin, the ATP-competitive mTOR inhibitors induced apoptosis in ARR breast cancer cells. Unexpectedly, one of PI3K/mTOR dual inhibitors we tested, PI-103, only transiently inhibits its proposed signaling targets and the anti-proliferation effects are possibly mediated through the off-target mechanism. Our results support the rationale to use ATP-competitive mTOR inhibitors to treat rapamycin-resistant breast cancer cells and highlight the putative off-target effect of the new generation of mTOR inhibitor on cancer cells.