Isocitrate dehydrogenases (IDHs) catalyze the oxidative decarboxylation of isocitric acid to α-ketoglutaric acid (αKG). Point mutations in IDH1 and IDH2 confer a neomorphic enzymatic activity: the reduction of αKG to D-2-hydroxyglutaric acid (2HG), which acts as an oncometabolite by inducing hypermethylation of histones and DNA. IDH1 mutations (predominantly R132H) have been found in 50-80% of grade II gliomas. To find potential IDH1-targeted therapeutics, we conducted a full small-molecule HTS and hit validation campaign using recombinant R132H IDH1. This campaign identified Compound 1, which belongs to a phenol-azole series, as a potent and selective inhibitor of mutant IDH1. We investigated the mode of inhibition of Compound 1 and a published IDH1 mutant inhibitor with a different chemical scaffold (Compound 2). Steady-state kinetics and biophysical studies showed that both inhibitors reversibly interact with both free and substrate-bound enzyme at an allosteric site. A crystal structure of Compound 1 complexed with R132H demonstrates binding of the inhibitor at the dimer interface. A competitive binding study showed that Compound 2 competes with Compound 1, suggesting that Compound 2 also binds at the dimer interface. This is contrary to a previously published statement that Compound 2 is a competitive inhibitor with respect to αKG. In cancer cell lines engineered to produce high levels of 2HG, both inhibitors penetrate cells efficiently and inhibit 2HG production with minimal cell toxicity. This study indicates that the dimer interface pocket is a druggable binding site for IDH1 inhibitors, and suggests that Compound 1 is a promising new starting point for future structure-based drug discovery efforts.
Citation Format: Gejing Deng, Stuart Licht, Junqing Shen, Ming Yin, Jessica McManus, Patricia Gee, Tim He, Giang Gao, Bailin Zhang, Magali Mathieu, Alexey Rak, Olivier Bedel, Chaomei Shi, Stefan Gross, Dietmar Hoffmann, Eamonn Rooney, Aurelie Vassort, Walter Englaro, Yi Li, Dmitri Wiederschain, Vinod Patel, Francisco Adrian, Hong Cheng. Selective inhibition of mutant IDH1 via small molecule binding to the dimer interface. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4746. doi:10.1158/1538-7445.AM2014-4746