occupy the space created by Y425. The flexibility of Y425 in KDM5B explains the
selectivity over KDM4 which has a more rigid tyrosine.
11 (CPI-455) was identified by Genentech and Constellation as a potent inhibitor
of the KDM5 subfamily with IC 50 of 10 nM against KDM5A in enzymatic assays.
The compounds were 200-fold selective over KDM4C and 700-fold selective over
KDM7B and showed no inhibition against KDM2B, KDM3B or KDM6A. A
cellular assay measuring global increase in levels of H3K4me3 in PC9 cells after
incubation with the compound resulted an EC 50 of 5.2 μM [41].
Crystallisation of 11 in KDM5A (PDB:5CEH) identified a monodentate interaction
between the nitrile and the active site metal and a hydrogen bond between carbonyl
oxygen and N575 (Fig. 11b). A π–π stacking interaction was observed between the core
and Y472 and F480 aromatic side chains as well as an edge-face interaction with W503.
Although K501 and partially charged N1 of CPI-455 are positioned in close proximity,
hydrogen bonding distance was not observed. As with other KDM inhibitors, an acidic
hydrogen was required which was demonstrated by the loss of activity upon alkylation
of 4-nitrogen or replacement of pyrimidine with triazene. 5-Phenyl substituent
interacted through an edge-face contact with Y409 but otherwise was solvent exposed.
Substitution of the isopropyl group was not tolerated due to its tight binding pocket
defined by Y409 and S478. CPI-455 binds in the 2OG binding site and demonstrated
competitive inhibition with 2OG in biochemical assays.
This compound showed no selectivity over other KDM5 isoforms due to identical
amino acids in its binding site. Selectivity over KDM6B could be explained through
collisions between the isopropyl and phenyl substituents and K1381, F1328 and
T1387 residues. Y409 in KDM5A has conformation freedom to rotate out of the
pocket to allow CPI-455 binding, whereas F1328, on a β-sheet next to ARID and
PHD1 domains in KDM5A, projects into the pocket in KDM6B. The residues in
KDM4C only differ in the second sphere of amino acids that do not directly interact
N
O
NH 2
NH
N
O
N
10
IC 50 (KDM5B) = 19 nM
N
N
H
N
O
N
11 (CPI-455)
IC 50 (KDM5A) = 10 nM
IC 50 (KDM5B) = 3 nM
IC 50 (KDM5C) = 14 nM
N
N
H
OH
N
H
O
O
13
IC 50 (KDM5A) = 50 nM
N
N
H
N
O
N
12
IC 50 (KDM5A) = 15.1 nM
IC 50 (KDM5B) = 4.7 nM
IC 50 (KDM5C) = 65.5 nM
N
N
N
O
NH
O
HN
N
14
IC 50 (KDM5A) = 45 nM
Fig. 10 KDM5 selective inhibitors
240
M. Wright et al.
selectivity over KDM4 which has a more rigid tyrosine.
11 (CPI-455) was identified by Genentech and Constellation as a potent inhibitor
of the KDM5 subfamily with IC 50 of 10 nM against KDM5A in enzymatic assays.
The compounds were 200-fold selective over KDM4C and 700-fold selective over
KDM7B and showed no inhibition against KDM2B, KDM3B or KDM6A. A
cellular assay measuring global increase in levels of H3K4me3 in PC9 cells after
incubation with the compound resulted an EC 50 of 5.2 μM [41].
Crystallisation of 11 in KDM5A (PDB:5CEH) identified a monodentate interaction
between the nitrile and the active site metal and a hydrogen bond between carbonyl
oxygen and N575 (Fig. 11b). A π–π stacking interaction was observed between the core
and Y472 and F480 aromatic side chains as well as an edge-face interaction with W503.
Although K501 and partially charged N1 of CPI-455 are positioned in close proximity,
hydrogen bonding distance was not observed. As with other KDM inhibitors, an acidic
hydrogen was required which was demonstrated by the loss of activity upon alkylation
of 4-nitrogen or replacement of pyrimidine with triazene. 5-Phenyl substituent
interacted through an edge-face contact with Y409 but otherwise was solvent exposed.
Substitution of the isopropyl group was not tolerated due to its tight binding pocket
defined by Y409 and S478. CPI-455 binds in the 2OG binding site and demonstrated
competitive inhibition with 2OG in biochemical assays.
This compound showed no selectivity over other KDM5 isoforms due to identical
amino acids in its binding site. Selectivity over KDM6B could be explained through
collisions between the isopropyl and phenyl substituents and K1381, F1328 and
T1387 residues. Y409 in KDM5A has conformation freedom to rotate out of the
pocket to allow CPI-455 binding, whereas F1328, on a β-sheet next to ARID and
PHD1 domains in KDM5A, projects into the pocket in KDM6B. The residues in
KDM4C only differ in the second sphere of amino acids that do not directly interact
N
O
NH 2
NH
N
O
N
10
IC 50 (KDM5B) = 19 nM
N
N
H
N
O
N
11 (CPI-455)
IC 50 (KDM5A) = 10 nM
IC 50 (KDM5B) = 3 nM
IC 50 (KDM5C) = 14 nM
N
N
H
OH
N
H
O
O
13
IC 50 (KDM5A) = 50 nM
N
N
H
N
O
N
12
IC 50 (KDM5A) = 15.1 nM
IC 50 (KDM5B) = 4.7 nM
IC 50 (KDM5C) = 65.5 nM
N
N
N
O
NH
O
HN
N
14
IC 50 (KDM5A) = 45 nM
Fig. 10 KDM5 selective inhibitors
240
M. Wright et al.