inhibition, providing promising opportunities for ‘target-hopping’ for histone
substrate-mimicking inhibitors. It is worth noting that inhibitor chemotypes targeting
other epigenetic proteins have successfully been designed to inhibit the JmjC-KDMs.
Filgastat (25), derived from methyllysine reader domain inhibitor (26), is a potent and
selective inhibitor of KDM2/7 [79]. It does not compete with 2OG nor histone H3
peptide, and the mode of inhibition is unclear; however, it demonstrates that selective
allosteric inhibition of JmjC-domain is possible.
4 Conclusions
The JmjC-KDMs are a protein family rich in links to disease pathology and are an
exciting new hunting ground of epigenetic targets for drug discovery. This family of
enzymes has been extensively characterised by structural biology to explain their
function and enable inhibitor design. The KMDs all share a similar mechanism of
action and conserved features – Fe(II) chelation, salt bridging and hydrogen bonding
to 2OG – but differences in their active sites, substrate-binding surface and domain
organisation allow selectivity for similar methylated lysine substrates.
Initial efforts at inhibitor discovery yielded nonselective compounds by relying
primarily on iron chelation and salt bridging for potency such as NOG, 8HQ and
Bpy (Fig. 3). Since those initial inhibitor reports, much effort at inhibitor discovery,
aided by thorough characterisation of the family with X-ray crystal structures, has
yielded new chemotypes that still rely on iron chelation and ionic interactions with
the KDMs but achieve selectivity by exploiting differences in the active sites’ first
sphere of residues. This led to compounds selective for KDM5 and KDM6 subfamilies such as KDOAM25 (10), CPI-455 (11) and GSK-J1 (15). Selectivity for
KDM members with similar active sites was then achieved by taking into account
subtle differences in active site residues such as CPI-455 (11) which is selective for
KDM5 members over KDM4 due to the propensity of an active site Tyr to shift more
readily in KDM5 than KDM4. Single KDM selectivity is still elusive, although this
may be acceptable and even desirable in drug development as many KDM subfamily
members, i.e. KDM5A/B/C/D, have identical substrates and redundant function.
A second class of KDM inhibitors are peptide-competitive and achieve selectivity
at the methyllysine binding groove and enzyme surface. CP2 is a cyclic peptide that
has no homology to histone H3 yet is a potent and selective inhibitor of KDM4s
(Fig. 16). The HMT inhibitors BIX01294 and E67-2 bind at the peptide site and are
selective for KDM7, and the related Filgerstat is KDM2A/7A selective although its
binding is not well understood.
The future of KDM drug discovery will involve developing a deeper understanding
of KDM biology using the inhibitors described herein. To be successful, it will also be
necessary to discover new inhibitor chemotypes to continue to improve the potency,
selectivity and cellular activity of this important class of epigenetic enzymes.
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M. Wright et al.
substrate-mimicking inhibitors. It is worth noting that inhibitor chemotypes targeting
other epigenetic proteins have successfully been designed to inhibit the JmjC-KDMs.
Filgastat (25), derived from methyllysine reader domain inhibitor (26), is a potent and
selective inhibitor of KDM2/7 [79]. It does not compete with 2OG nor histone H3
peptide, and the mode of inhibition is unclear; however, it demonstrates that selective
allosteric inhibition of JmjC-domain is possible.
4 Conclusions
The JmjC-KDMs are a protein family rich in links to disease pathology and are an
exciting new hunting ground of epigenetic targets for drug discovery. This family of
enzymes has been extensively characterised by structural biology to explain their
function and enable inhibitor design. The KMDs all share a similar mechanism of
action and conserved features – Fe(II) chelation, salt bridging and hydrogen bonding
to 2OG – but differences in their active sites, substrate-binding surface and domain
organisation allow selectivity for similar methylated lysine substrates.
Initial efforts at inhibitor discovery yielded nonselective compounds by relying
primarily on iron chelation and salt bridging for potency such as NOG, 8HQ and
Bpy (Fig. 3). Since those initial inhibitor reports, much effort at inhibitor discovery,
aided by thorough characterisation of the family with X-ray crystal structures, has
yielded new chemotypes that still rely on iron chelation and ionic interactions with
the KDMs but achieve selectivity by exploiting differences in the active sites’ first
sphere of residues. This led to compounds selective for KDM5 and KDM6 subfamilies such as KDOAM25 (10), CPI-455 (11) and GSK-J1 (15). Selectivity for
KDM members with similar active sites was then achieved by taking into account
subtle differences in active site residues such as CPI-455 (11) which is selective for
KDM5 members over KDM4 due to the propensity of an active site Tyr to shift more
readily in KDM5 than KDM4. Single KDM selectivity is still elusive, although this
may be acceptable and even desirable in drug development as many KDM subfamily
members, i.e. KDM5A/B/C/D, have identical substrates and redundant function.
A second class of KDM inhibitors are peptide-competitive and achieve selectivity
at the methyllysine binding groove and enzyme surface. CP2 is a cyclic peptide that
has no homology to histone H3 yet is a potent and selective inhibitor of KDM4s
(Fig. 16). The HMT inhibitors BIX01294 and E67-2 bind at the peptide site and are
selective for KDM7, and the related Filgerstat is KDM2A/7A selective although its
binding is not well understood.
The future of KDM drug discovery will involve developing a deeper understanding
of KDM biology using the inhibitors described herein. To be successful, it will also be
necessary to discover new inhibitor chemotypes to continue to improve the potency,
selectivity and cellular activity of this important class of epigenetic enzymes.
248
M. Wright et al.