Mutations in IDH induce epigenetic and transcriptional reprogramming, differentiation bias, and susceptibility to mitochondrial inhibitors in cancer cells. Here, we first show that cell lines, PDXs, and patients with acute myeloid leukemia (AML) harboring an IDH mutation displayed an enhanced mitochondrial oxidative metabolism. Along with an increase in TCA cycle intermediates, this AML-specific metabolic behavior mechanistically occurred through the increase in electron transport chain complex I activity, mitochondrial respiration, and methylation-driven CEBPα-induced fatty acid β-oxidation of IDH1 mutant cells. While IDH1 mutant inhibitor reduced 2-HG oncometabolite and CEBPα methylation, it failed to reverse FAO and OxPHOS. These mitochondrial activities were maintained through the inhibition of Akt and enhanced activation of peroxisome proliferator-activated receptor-γ coactivator-1 PGC1α upon IDH1 mutant inhibitor. Accordingly, OxPHOS inhibitors improved anti-AML efficacy of IDH mutant inhibitors in vivo. This work provides a scientific rationale for combinatory mitochondrial-targeted therapies to treat IDH mutant AML patients, especially those unresponsive to or relapsing from IDH mutant inhibitors.

SummaryThere are numerous applications that use the structures of protein-ligand complexes from the PDB, such as 3D pharmacophore identification, virtual screening, and fragment-based drug design. The structures underlying these applications are potentially much more informative if they contain biologically relevant bound ligands, with high similarity to the cognate ligands. We present a study of ligand-enzyme complexes that compares the similarity of bound and cognate ligands, enabling the best matches to be identified. We calculate the molecular similarity scores using a method called PARITY (proportion of atoms residing in identical topology), which can conveniently be combined to give a similarity score for all cognate reactants or products in the reaction. Thus, we generate a rank-ordered list of related PDB structures, according to the biological similarity of the ligands bound in the structures.

Phone: +33 582 74 16 32 51 52 Running Title: IDH and OxPHOS inhibitors 53 54 55 3 Isocitrate dehydrogenases (IDH) are involved in redox control and central metabolism. 56Mutations in IDH induce epigenetic and transcriptional reprogramming, differentiation 57 bias, BCL-2 dependence and susceptibility to mitochondrial inhibitors in cancer cells. 58Here we show that high sensitivity to mitochondrial oxidative phosphorylation 59 (OxPHOS) inhibitors is due to an enhanced mitochondrial oxidative metabolism in cell 60 lines, PDX and patients with acute myeloid leukemia (AML) harboring IDH mutation. 61Along with an increase in TCA cycle intermediates, this AML-specific metabolic 62 behavior mechanistically occurs through the increase in methylation-driven CEBPα-63 and CPT1a-induced fatty acid oxidation, electron transport chain complex I activity and 64 mitochondrial respiration in IDH1 mutant AML. Furthermore, an IDH mutant 65 inhibitor that significantly and systematically reduces 2-HG oncometabolite transiently 66 reverses mitochondrial FAO and OxPHOS gene signature and activities in patients who 67 responded to the treatment and achieved the remission. However, at relapse or in 68 patients who did not respond, IDH mutant inhibitor failed to block these mitochondrial 69properties. Accordingly, OxPHOS inhibitors such as IACS-010759 improve anti-AML 70 efficacy of IDH mutant inhibitors alone and in combination with chemotherapy in vivo. 71This work provides a scientific rationale for combinatory mitochondrial-targeted 72 therapies to treat IDH mutant-positive AML patients, especially those unresponsive to 73 or relapsing from IDH mutant-specific inhibitors. 74 75 76 4Changes in intermediary and energy metabolism provide the flexibility for cancer cells to 77 adapt their metabolism to meet energetic and biosynthetic requirements for proliferation [1][2][3][4] . 78Manipulating glycolysis, glutaminolysis, fatty acid β-oxidation (FAO) or oxidative 79 phosphorylation (OxPHOS) markedly reduces cell growth in vitro and in vivo and sensitizes 80 acute myeloid leukemia (AML) cells to chemotherapeutic drugs [5][6][7][8][9][10][11][12][13] . The importance of the 81 metabolic reprogramming in this disease is further illustrated by recurrent mutations in genes 82 of two crucial metabolic enzymes, isocitrate dehydrogenases (IDH) 1 and 2, present in more 83 than 15% of AML patients [14][15][16][17] . 84The impact of IDH mutation and the related accumulation of the oncometabolite (R)-2-85 hydroxyglutarate (2-HG) have been well documented in leukemic transformation and AML 86 biology 18-28 . As IDH mutations are early events in oncogenesis and are systematically 87 conserved at relapse 29-31 , IDH1/2 mutated (IDHm) enzymes represent attractive therapeutic 88 targets and small molecules specifically inhibiting the mutated forms of these enzymes have 89 been developed and recently approved by the FDA 32-41 . Both the IDH2m-and IDH1m-90 inhibitors promote differentiation and reduce methylation levels as well as significantly 91 decrease 2...