Inhibitor potency varies widely among tumor-relevant human isocitrate dehydrogenase 1 mutants

Abstract

Mutations in isocitrate dehydrogenase 1 (IDH1) drive most low-grade gliomas and secondary glioblastomas and many chondrosarcomas and acute myeloid leukemia cases. Most tumor-relevant IDH1 mutations are deficient in the normal oxidization of isocitrate to α-ketoglutarate (αKG), but gain the neomorphic activity of reducing αKG to D-2-hydroxyglutarate (D2HG), which drives tumorigenesis. We found previously that IDH1 mutants exhibit one of two reactivities: deficient αKG and moderate D2HG production (including commonly observed R132H and R132C) or moderate αKG and high D2HG production (R132Q). Here, we identify a third type of reactivity, deficient αKG and high D2HG production (R132L). We show that R132Q IDH1 has unique structural features and distinct reactivities towards mutant IDH1 inhibitors. Biochemical and cell-based assays demonstrate that while most tumor-relevant mutations were effectively inhibited by mutant IDH1 inhibitors, R132Q IDH1 had up to a 16 300-fold increase in IC50 versus R132H IDH1. Only compounds that inhibited wild-type (WT) IDH1 were effective against R132Q. This suggests that patients with a R132Q mutation may have a poor response to mutant IDH1 therapies. Molecular dynamics simulations revealed that near the NADP+/NADPH-binding site in R132Q IDH1, a pair of α-helices switches between conformations that are more wild-type-like or more mutant-like, highlighting mechanisms for preserved WT activity. Dihedral angle changes in the dimer interface and buried surface area charges highlight possible mechanisms for loss of inhibitor affinity against R132Q. This work provides a platform for predicting a patient’s therapeutic response and identifies a potential resistance mutation that may arise upon treatment with mutant IDH inhibitors.

Targeting Mitochondrial Oncometabolites: A New Approach to Overcome Drug Resistance in Cancer

“…One of the most promising dual inhibitors is vorasidenib, and has been proposed for the treatment of GBM since it is able to cross the blood brain barrier [71]. Importantly, the response to IDH inhibitors is affected by the type of mutations [72]. Indeed, it has been demonstrated that R132Q mutation alters the catalytic site structure in such a way that the IDH1 inhibitors ML309, AGI-5198 and GSK864 are less potent.…”

“…Indeed, it has been demonstrated that R132Q mutation alters the catalytic site structure in such a way that the IDH1 inhibitors ML309, AGI-5198 and GSK864 are less potent. By contrast they are instead more active against R132H-IDH1 or wild-type IDH1 expressing cells [72]. This aspect must be carefully considered in choosing the right inhibitor for the right mutant tumor.…”

Evaluating Mechanisms of IDH1 Regulation through Site-Specific Acetylation Mimics

“…All proteins were expressed and purified using conditions published previously [ 3 , 33 ]. Purity (≥ 90%) was confirmed by SDS-PAGE, and IDH1 was flash frozen in liquid nitrogen and stored at 80 °C for no longer than 1.5 months.…”

2-Hydroxyglutarate in Cancer Cells

“…Three phenotypes were characterized: The first phenotype involved depleted 2OG but moderate r -2HG and was associated with the most common R132H and R132C IDH1 mutations; the second exhibited moderate 2OG levels and high r -2HG levels and was associated with IDH1 R132Q ; the third phenotype was characterized by depleted 2OG but again high r -2HG levels, being associated with R132L ( 108 ).…”

“…It seems that specific inhibitors should be designed for each mutation. For example, the mutant IDH1 R132Q was 10 5 -less sensitive to mutant inhibitors than IDH1 R132H ( 108 ). This was explained by the conformation of α-helices more closely resembling the wt enzyme.…”