Roles of metal ions in the selective inhibition of oncogenic variants of isocitrate dehydrogenase 1

Abstract

Cancer linked isocitrate dehydrogenase (IDH) 1 variants, notably R132H IDH1, manifest a ‘gain-of-function’ to reduce 2-oxoglutarate to 2-hydroxyglutarate. High-throughput screens have enabled clinically useful R132H IDH1 inhibitors, mostly allosteric binders at the dimer interface. We report investigations on roles of divalent metal ions in IDH substrate and inhibitor binding that rationalise this observation. Mg2+/Mn2+ ions enhance substrate binding to wt IDH1 and R132H IDH1, but with the former manifesting lower Mg2+/Mn2+KMs. The isocitrate-Mg2+ complex is the preferred wt IDH1 substrate; with R132H IDH1, separate and weaker binding of 2-oxoglutarate and Mg2+ is preferred. Binding of R132H IDH1 inhibitors at the dimer interface weakens binding of active site Mg2+ complexes; their potency is affected by the Mg2+ concentration. Inhibitor selectivity for R132H IDH1 over wt IDH1 substantially arises from different stabilities of wt and R132H IDH1 substrate-Mg2+ complexes. The results reveal the importance of substrate-metal ion complexes in wt and R132H IDH1 catalysis and the basis for selective R132H IDH1 inhibition. Further studies on roles of metal ion complexes in TCA cycle and related metabolism, including from an evolutionary perspective, are of interest.

Resistance to the isocitrate dehydrogenase 1 mutant inhibitor ivosidenib can be overcome by alternative dimer-interface binding inhibitors

“…Consistent with prior studies on IDH1 R132H and R132C, all the recombinant proteins were predominantly dimeric in solution (Supplementary Fig. 1d–f ) and likely copurify with two NADPH molecules (as reported for IDH1 wt and R132H 18 , and shown for IDH1 R132C, Supplementary Fig. 1g/h ).…”

“…To investigate the mechanism of IDH1 S280F mediated inhibitor resistance, we used established protocols 17 , 18 to produce highly purified forms of recombinant IDH1 R132C/S280F and R132H/S280F and, for comparison, IDH1 R132C, IDH1 R132H, IDH1 wildtype (wt), IDH1 S280F (without IDH1 R132C or R132H) and IDH1 R132H/Q277E (Supplementary Fig. 1a ).…”

Metabolic adaptations in cancers expressing isocitrate dehydrogenase mutations

“… 7 , 8 Kinetic and structural analyses of the mutIDH1s have revealed that substitution of an active-site arginine (R132 IDH1) correlates with a lowered affinity for isocitrate and the NADPH-dependent ability to reduce 2-OG to R -2-HG. 6 , 7 , 8 , 162 However, it has been shown that, when observed with NMR-based enzyme assays 163 rather than a fluorescence-based assay, 164 mutIDH1 R132H is capable of producing R -2-HG from isocitrate. 163 At least in studied cases, mutIDH2 does not appear to bind to or dominantly inhibit WT IDH2 165 and does not require WT IDH2 or IDH3 to produce R -2-HG.…”

“… 6 , 7 , 8 , 162 However, it has been shown that, when observed with NMR-based enzyme assays 163 rather than a fluorescence-based assay, 164 mutIDH1 R132H is capable of producing R -2-HG from isocitrate. 163 At least in studied cases, mutIDH2 does not appear to bind to or dominantly inhibit WT IDH2 165 and does not require WT IDH2 or IDH3 to produce R -2-HG. 166 Cytosolic mutIDH1, however, has been reported to rely on co-expression with WT IDH1 to elevate intracellular 2-HG, 166 , 167 , 168 but that substrate (2-OG and NADPH) is likely not channeled from WT IDH1 to mutIDH1 in a heterodimer.…”

Spectroscopic studies reveal details of substrate-induced conformational changes distant from the active site in isopenicillin N synthase

“…allosteric) inhibition mechanisms have been identified, e.g. in recent work on allosteric isocitrate dehydrogenase inhibitors, (52,53) have emerged from empirical screens rather than detailed knowledge of the roles of the overall protein fold in enzyme catalysis.…”