compounds incorporated a dichloro-phenylpiperidine moiety 8 and showed an IC 50
of <50 nM against KDM4B and KDM5B. Some cellular inhibition of H3K9me3
and H3K4me3 demethylation was observed but only at high compound
concentrations.
A crystal structure of dichloro-phenylpiperidine 8 bound in KDM4A was
obtained (PDB:5F3I) (Fig. 8e). The compound bound in the 2OG binding site and
engaged in a bidentate coordination to the active site metal via the pyridine nitrogen
and pyrazole N2 nitrogen. The carboxylate engaged in favourable interactions with
K206 and Y132, and extending the pyrazole with a phenylpiperidine linker resulted
in access to the histone peptide binding pocket for interactions with D135 and Y175.
The piperidine ring had an important role in rigidifying the pyrazole substituent from
different rotational conformations and ensuring good selectivity over KDM2,
KDM3 and KDM6. A hydrophobic interaction was observed between the chlorine
and V313 in the m-dichlorophenyl analogue which could explain the improved
KDM4A/B inhibition compared with the p-chlorophenyl analogue in which the
chlorine was too distal for an interaction.
Pyrazolylpyridines were designed based on structural information from the
known KDM inhibitors [68]. The best compound in this series, 9, showed nanomolar
activity against KDM5 (IC 50 KDM5A/B ¼ 13/2 nM) as well as KDM4C
(IC 50 ¼ 41 nM) but did exhibit good selectivity across the other KDM families.
An increase in H3K4me3 was observed in a breast cancer cell line, ZR-75-1, and
in vivo, in a MCF7-breast cancer xenograft PK/PD model upon treatment with 9.
9 was co-crystallised with KDM5A (PDB:5IW0) confirming bidentate coordination of pyrazolyl and pyridyl nitrogens with the metal centre (Fig. 8f). As previously
observed, the carboxylate group interacts with K501 and Y409 while the pyridyl
group π-stacks with F480. The benzyl ether also engaged in π-stacking interactions
with Y409 resulting in improved selectivity over the other KDMs.
3.1.2 Selective KDM5 Inhibitors
More recently, compounds have been designed that are more potent and selective
towards KDM5 using structural information from crystal structures of known
KDM5 inhibitors (Fig. 10).
Aminomethylpyridine 10 (KDOAM-25), in which the carboxylic acid of KDM5C49 was replaced with a primary amide, showed excellent activity on KDM5B
(IC 50 ¼ 19 nM) and also showed improved selectivity (>1,000-fold) over KDM4C
as well as other 2OG oxygenases [64]. The compound was partially competitive with
2OG which may explain the low cellular activity (~50 μM) observed in an immunofluorescence assay measuring the increase in H3K4me3 levels upon incubation
with 10.
KDOAM-25 binds to KDM5B (PDB: 5A3N) in a similar pose to KDM5-C49 via
metal chelation of the pyridine nitrogen (Fig. 11a). The main difference is the
displacement of Y425 to become a hydrogen bond acceptor with the carboxamide
rather than a hydrogen bond donor with the carboxylate. A water molecule can
Inhibitors of JmjC-Containing Histone Demethylases
239
of <50 nM against KDM4B and KDM5B. Some cellular inhibition of H3K9me3
and H3K4me3 demethylation was observed but only at high compound
concentrations.
A crystal structure of dichloro-phenylpiperidine 8 bound in KDM4A was
obtained (PDB:5F3I) (Fig. 8e). The compound bound in the 2OG binding site and
engaged in a bidentate coordination to the active site metal via the pyridine nitrogen
and pyrazole N2 nitrogen. The carboxylate engaged in favourable interactions with
K206 and Y132, and extending the pyrazole with a phenylpiperidine linker resulted
in access to the histone peptide binding pocket for interactions with D135 and Y175.
The piperidine ring had an important role in rigidifying the pyrazole substituent from
different rotational conformations and ensuring good selectivity over KDM2,
KDM3 and KDM6. A hydrophobic interaction was observed between the chlorine
and V313 in the m-dichlorophenyl analogue which could explain the improved
KDM4A/B inhibition compared with the p-chlorophenyl analogue in which the
chlorine was too distal for an interaction.
Pyrazolylpyridines were designed based on structural information from the
known KDM inhibitors [68]. The best compound in this series, 9, showed nanomolar
activity against KDM5 (IC 50 KDM5A/B ¼ 13/2 nM) as well as KDM4C
(IC 50 ¼ 41 nM) but did exhibit good selectivity across the other KDM families.
An increase in H3K4me3 was observed in a breast cancer cell line, ZR-75-1, and
in vivo, in a MCF7-breast cancer xenograft PK/PD model upon treatment with 9.
9 was co-crystallised with KDM5A (PDB:5IW0) confirming bidentate coordination of pyrazolyl and pyridyl nitrogens with the metal centre (Fig. 8f). As previously
observed, the carboxylate group interacts with K501 and Y409 while the pyridyl
group π-stacks with F480. The benzyl ether also engaged in π-stacking interactions
with Y409 resulting in improved selectivity over the other KDMs.
3.1.2 Selective KDM5 Inhibitors
More recently, compounds have been designed that are more potent and selective
towards KDM5 using structural information from crystal structures of known
KDM5 inhibitors (Fig. 10).
Aminomethylpyridine 10 (KDOAM-25), in which the carboxylic acid of KDM5C49 was replaced with a primary amide, showed excellent activity on KDM5B
(IC 50 ¼ 19 nM) and also showed improved selectivity (>1,000-fold) over KDM4C
as well as other 2OG oxygenases [64]. The compound was partially competitive with
2OG which may explain the low cellular activity (~50 μM) observed in an immunofluorescence assay measuring the increase in H3K4me3 levels upon incubation
with 10.
KDOAM-25 binds to KDM5B (PDB: 5A3N) in a similar pose to KDM5-C49 via
metal chelation of the pyridine nitrogen (Fig. 11a). The main difference is the
displacement of Y425 to become a hydrogen bond acceptor with the carboxamide
rather than a hydrogen bond donor with the carboxylate. A water molecule can
Inhibitors of JmjC-Containing Histone Demethylases
239