Selective inhibition of mutant isocitrate dehydrogenase 1 (IDH1) via disruption of a metal binding network by an allosteric small molecule.
Cancer-associated point mutations in isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) confer a neomorphic enzymatic activity: the reduction of α-ketoglutarate to d-2-hydroxyglutaric acid, which is proposed to act as an oncogenic metabolite by inducing hypermethylation of histones and DNA. Although selective inhibitors of mutant IDH1 and IDH2 have been identified and are currently under investigation as potential cancer therapeutics, the mechanistic basis for their selectivity is not yet well understood. A high throughput screen for selective inhibitors of IDH1 bearing the oncogenic mutation R132H identified compound 1, a bis-imidazole phenol that inhibits d-2-hydroxyglutaric acid production in cells. We investigated the mode of inhibition of compound 1 and a previously published IDH1 mutant inhibitor with a different chemical scaffold. Steady-state kinetics and biophysical studies show that both of these compounds selectively inhibit mutant IDH1 by binding to an allosteric site and that inhibition is competitive with respect to Mg(2+). A crystal structure of compound 1 complexed with R132H IDH1 indicates that the inhibitor binds at the dimer interface and makes 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 for the mutant enzyme.
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139, gejing.deng@sanofi.com.
Gejing
G
Deng
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Junqing
J
Shen
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Ming
M
Yin
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Jessica
J
McManus
Division of Lead Generation & Compound Realization, Sanofi, Vitry 94403, France.
Magali
M
Mathieu
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Patricia
P
Gee
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Timothy
T
He
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Chaomei
C
Shi
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Olivier
O
Bedel
Division of Lead Generation & Compound Realization, Sanofi, Waltham, Massachusetts 02452, and.
Larry R
LR
McLean
Department of Disposition, Safety & Animal Research, Sanofi, Chilly-Mazarin 91385, France.
Frank
F
Le-Strat
Division of Lead Generation & Compound Realization, Sanofi, Waltham, Massachusetts 02452, and.
Ying
Y
Zhang
Division of Lead Generation & Compound Realization, Sanofi, Vitry 94403, France.
Jean-Pierre
JP
Marquette
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Qiang
Q
Gao
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Bailin
B
Zhang
Division of Lead Generation & Compound Realization, Sanofi, Vitry 94403, France.
Alexey
A
Rak
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Dietmar
D
Hoffmann
Division of Lead Generation & Compound Realization, Sanofi, Vitry 94403, France.
Eamonn
E
Rooney
Division of Lead Generation & Compound Realization, Sanofi, Vitry 94403, France.
Aurelie
A
Vassort
Division of Lead Generation & Compound Realization, Sanofi, Vitry 94403, France.
Walter
W
Englaro
Division of Lead Generation & Compound Realization, Sanofi, Waltham, Massachusetts 02452, and.
Yi
Y
Li
Division of Lead Generation & Compound Realization, Sanofi, Waltham, Massachusetts 02452, and.
Vinod
V
Patel
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Francisco
F
Adrian
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Stefan
S
Gross
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Dmitri
D
Wiederschain
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Hong
H
Cheng
From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.
Stuart
S
Licht
D000495:Allosteric Site; D018360:Crystallography, X-Ray; D019175:DNA Methylation / Q000235:genetics; D055808:Drug Discovery; D004791:Enzyme Inhibitors / Q000138:chemical synthesis / Q000737:chemistry* / Q000627:therapeutic use; D004926:Escherichia coli; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007521:Isocitrate Dehydrogenase / Q000037:antagonists & inhibitors / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics; D008274:Magnesium / Q000737:chemistry; D050505:Mutant Proteins / Q000737:chemistry / Q000235:genetics; D009369:Neoplasms / Q000188:drug therapy* / Q000235:genetics / Q000473:pathology; D011487:Protein Conformation
D004791:Enzyme Inhibitors; D050505:Mutant Proteins; C538784:IDH2 protein, human; D007521:Isocitrate Dehydrogenase; C543588:IDH1 protein, human; D008274:Magnesium
Anticancer Drug; Cancer Metabolism; Drug Action; Drug Discovery; Enzyme Inhibitor; IDH1 Inhibitor; Mechanism of Inhibition; Metalloenzyme