25% glycerol was added as a cryo-protecting agent prior to freezing

25% glycerol was added as a cryo-protecting agent prior to freezing. For co-crystallization of R132H IDH1 and compound 1, the protein was concentrated to 8 mg/ml in 50 mm Tris, pH 7.5, 200 mm NaCl, 5 mm DTT, and 10% glycerol and incubated with 1 mm compound 1 overnight. direct contact with a residue involved in binding of the catalytically essential divalent cation. These results show that targeting a divalent cation binding residue can enable selective inhibition of mutant IDH1 and suggest that differences in magnesium binding between wild-type and mutant enzymes may contribute to the inhibitors’ selectivity DNM1 for the mutant enzyme. characterization of the enzymatic activity of this IDH1 mutant led to the surprising discovery that the oncogenic mutation, in addition to causing a loss of normal enzymatic function (7, 11), also enabled a neomorphic enzymatic activity: the NADPH-dependent reduction of KG to d-2-hydroxyglutarate (2HG) (12). The mutations associated with the neomorphic activity are also associated with other changes in catalytic active site function: values for both isocitrate and Mg2+ in the residual isocitrate dehydrogenase reaction of the mutant enzyme are much higher than the corresponding values for the wild-type enzyme (300-fold higher in the case of Mg2+) (12). The observation Oritavancin (LY333328) of the neomorphic activity, together with the oncogene-like genetics of the IDH mutations, led to the Oritavancin (LY333328) hypothesis that 2HG acts as an oncometabolite. Subsequent experiments demonstrated that 2HG is an inhibitor of histone demethylases and TET family 5-methylcytosine hydroxylases at the high (10 mm) concentrations observed in tumors (13,C15), suggesting that 2HG induces dysregulation of methylation, with possible oncogenic effects. 2HG has also been proposed to promote oncogenic transformation by activating EGLN, an -ketoglutarate-dependent prolyl hydroxylase involved in the hypoxia-inducible factor signaling pathway (16). experiments using small molecule inhibitors of mutant IDH1 and IDH2 also support a role for 2HG in maintenance of undifferentiated tumor phenotypes and the potential clinical utility of mutant IDH inhibitors (17, 18). The IDH2 allosteric inhibitor AGI-6780 relieves the differentiation block in TF-1 erythroleukemia cells expressing an IDH2 mutant enzyme, and it stimulates the differentiation of primary acute myeloid anemia blasts (18). AGI-5198, an IDH1 inhibitor that has been reported to inhibit competitively with respect to KG and noncompetitively with respect to NADPH (19), acts on IDH1 mutant glioma cells to inhibit 2HG accumulation (17) and to reverse histone methylation and induce the expression of genes associated with astrocytic differentiation (20). The IDH2 inhibitor AG-221, developed by Agios Pharmaceuticals, is currently in clinical trials as a therapy for hematological Oritavancin (LY333328) malignancies (ClinicalTrials.gov NCT 01915 498). Because of the potential of IDH1/2 inhibitors as anticancer therapeutics, a number of groups have investigated the structural and mechanistic aspects of IDH inhibition. Kinetic and/or structural studies suggest that some inhibitors may bind at the KG/isocitrate binding site (17, 19, 21), whereas others, such as the IDH2 inhibitor AGI-6780, bind allosterically to the interface between the two protomers of the IDH dimer (18). Based on the structure of AGI-6780-bound IDH2 (18), this inhibitor has been hypothesized to prevent catalysis by locking IDH2 in an open, precatalytic, inactive conformation that is similar to that observed in the absence of KG or isocitrate (22, 23) and distinct from the closed conformation observed when the KG/isocitrate site is occupied (12, 24). Because of the importance of wild-type IDH in primary metabolism, achieving selective inhibition of the mutant enzyme over the wild-type is Oritavancin (LY333328) a critical issue in designing IDH inhibitors for therapeutic use. The IDH inhibitors reported to date achieve moderate to high mutant selectivity, but the structural/mechanistic basis for this selectivity remains an important unsolved question. In the case of allosteric IDH inhibitors in particular, the dimer interface is well separated from the residues mutated in cancer, suggesting that direct interactions between the mutated residue and allosteric inhibitors do not account for mutant selectivity. The current study demonstrates that small molecules from two unrelated structural classes act as selective allosteric inhibitors of mutant IDH1 and act by the unusual mechanism of competing with the catalytically essential magnesium ion. Inhibitor binding thereby prevents the assembly of a catalytically competent magnesium binding site. Competitive binding with magnesium may contribute to the mutant selectivity of the inhibitor, because Mg2+.