enantiomer, while the (S)-enantiomer was relatively inactive. Compound 3 was
identified as the most potent inhibitor against KDM4C (IC 50 ¼ 35 nM) and showed
cell activity against KYSE-150 cells with an EC 50 of 3.5 nM. Cellular on-target
engagement using the same cell line was determined by measuring the increase in
H3K9me3 and H3K36me3 through time-resolved fluorescence assay and mass
spectroscopy detection to give a H3K36me3 mechanism of action (MOA) EC 50 of
1.3 nM. The significant improvement in cellular potency from previously reported
pyridine carboxylic acids could be attributed to the greater cell permeability from the
addition of the lipophilic tetrahydronaphthalene and phenyl rings.
Good selectivity (>1,000-fold) was achieved over other KDM families such as
KDM2B, KDM3, KDM6B and KDM7B. However, selectivity over KDM5B was
moderate (IC 50 ¼ 750 nM), so some cellular activity may be contributed to KDM5B
inhibition. 3 was also efficacious in vivo in breast and colon cancer PDX models
showing a reduction in the rate of tumour growth.
A co-crystal structure of 3 with KDM4A (PDB:5VGI) revealed a similar binding
mode involving pyridyl N coordinating to Ni(II). Key hydrogen bonding interactions
of carboxylic acid with Y132 and K206 were observed (Fig. 8b). The methyl group
of the methylaniline pointed towards N86 and carbonyl of H240, while the phenyl
group is positioned in the R239/H240 loop.
An analogue of 2,4-PDCA, 4 (KDM5-C49), in which the 2-position is substituted
with an amino methyl group, was identified as a potent nanomolar inhibitor of
KDM5 family (KDM5A/B/C/D IC 50 7/4/13/15 nM) with ~50-fold selectivity
over closely related KDM4C and >50-fold selectivity over KDM2, 3 and
6 [63, 64]. 5 (KDM5-C70) was designed as an ester pro-drug to permeate the cell
and be hydrolysed in the cell to the active carboxylic acid. This compound showed
growth inhibition in several breast cancer cell lines and also exhibited increased
expression of MTIF and MT1H genes in comparable levels observed upon KDM5B
knockdown [65].
4 binds to KDM5B (PDB:5A3T) in the 2OG binding site with bidentate coordination of pyridine N and aminomethyl N to the metal (Fig. 8c). As with other
pyridine carboxylate derivatives, there are key hydrogen bonding interactions with
K517 and Y425. Extensive polar interactions are observed with K517, Y425, N509,
E509, R98 and Y488 as well as hydrophobic interactions with W486, V99 and F496.
Similar key binding interactions were observed when 4 was crystallised in KDM4
(PDB:5FPV) which resulted in only moderate selectivity.
Chiral enantiomers (R)- and (S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)
methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid, (R)-6 and (S)-6, were active
inhibitors of KDM5A with binding affinities of 220 nM and 60 nM, respectively,
and greater than 20-fold selectivity over KDM4A [53]. Cellular activity was not
observed, even at high concentrations, with the methyl ester cell-permeable
pro-drugs of the racemic compound. The compounds were 2OG competitive with
the carboxylic acid ring interacting with K501, N575 and Y409 and pyridine
nitrogen coordinating to the metal.
Inhibitors of JmjC-Containing Histone Demethylases
237
identified as the most potent inhibitor against KDM4C (IC 50 ¼ 35 nM) and showed
cell activity against KYSE-150 cells with an EC 50 of 3.5 nM. Cellular on-target
engagement using the same cell line was determined by measuring the increase in
H3K9me3 and H3K36me3 through time-resolved fluorescence assay and mass
spectroscopy detection to give a H3K36me3 mechanism of action (MOA) EC 50 of
1.3 nM. The significant improvement in cellular potency from previously reported
pyridine carboxylic acids could be attributed to the greater cell permeability from the
addition of the lipophilic tetrahydronaphthalene and phenyl rings.
Good selectivity (>1,000-fold) was achieved over other KDM families such as
KDM2B, KDM3, KDM6B and KDM7B. However, selectivity over KDM5B was
moderate (IC 50 ¼ 750 nM), so some cellular activity may be contributed to KDM5B
inhibition. 3 was also efficacious in vivo in breast and colon cancer PDX models
showing a reduction in the rate of tumour growth.
A co-crystal structure of 3 with KDM4A (PDB:5VGI) revealed a similar binding
mode involving pyridyl N coordinating to Ni(II). Key hydrogen bonding interactions
of carboxylic acid with Y132 and K206 were observed (Fig. 8b). The methyl group
of the methylaniline pointed towards N86 and carbonyl of H240, while the phenyl
group is positioned in the R239/H240 loop.
An analogue of 2,4-PDCA, 4 (KDM5-C49), in which the 2-position is substituted
with an amino methyl group, was identified as a potent nanomolar inhibitor of
KDM5 family (KDM5A/B/C/D IC 50 7/4/13/15 nM) with ~50-fold selectivity
over closely related KDM4C and >50-fold selectivity over KDM2, 3 and
6 [63, 64]. 5 (KDM5-C70) was designed as an ester pro-drug to permeate the cell
and be hydrolysed in the cell to the active carboxylic acid. This compound showed
growth inhibition in several breast cancer cell lines and also exhibited increased
expression of MTIF and MT1H genes in comparable levels observed upon KDM5B
knockdown [65].
4 binds to KDM5B (PDB:5A3T) in the 2OG binding site with bidentate coordination of pyridine N and aminomethyl N to the metal (Fig. 8c). As with other
pyridine carboxylate derivatives, there are key hydrogen bonding interactions with
K517 and Y425. Extensive polar interactions are observed with K517, Y425, N509,
E509, R98 and Y488 as well as hydrophobic interactions with W486, V99 and F496.
Similar key binding interactions were observed when 4 was crystallised in KDM4
(PDB:5FPV) which resulted in only moderate selectivity.
Chiral enantiomers (R)- and (S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)
methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid, (R)-6 and (S)-6, were active
inhibitors of KDM5A with binding affinities of 220 nM and 60 nM, respectively,
and greater than 20-fold selectivity over KDM4A [53]. Cellular activity was not
observed, even at high concentrations, with the methyl ester cell-permeable
pro-drugs of the racemic compound. The compounds were 2OG competitive with
the carboxylic acid ring interacting with K501, N575 and Y409 and pyridine
nitrogen coordinating to the metal.
Inhibitors of JmjC-Containing Histone Demethylases
237