incorporation into RNA and DNA, and also by the formation of suicide complexes.
Indeed, the nucleoside analogues are incorporated into DNA (and 5azaC also in
RNA) instead of C, but not only at CpG sites. They then induce the formation of a
suicide substrate with DNMT that is processed by the proteasome and the DNA
repair machinery. Because of their mode of action, they are not selective for an
isoform of DNMTs and induce effects other than just DNA demethylation. To
overcome this, several studies have focused on the identification of DNMT inhibitors that are not nucleoside analogues.
3.2 Non-nucleoside Analogues
The family of non-nucleoside inhibitors has been largely reviewed [24, 42, 59], so
this section will focus on a selection of inhibitors that have shown effects on cellular
phenotypes and on gene expression or have provided new concepts for the discovery
of new inhibitors (Fig. 3). We have chosen to omit most of the compounds that act by
binding to DNA, such as intercalators (i.e. acridine derivatives [63]) or minor groove
binders (i.e. bisbenzimidazoles [64]), that lack specificity for CpG sites. Natural
products have also been excluded since they have been reviewed recently and show
little specificity for the DNMT enzymes [65]. Importantly direct comparisons of
inhibition properties of these compounds cannot be made, because the assays and
conditions used for each study are very different, as well as the choice of the enzyme
used (reviewed in [66]), which can have an important impact on the inhibition [67].
The first synthetic non-nucleoside inhibitor, N-phthaloyl-l-tryptophan RG108,
was identified by in silico screening against a model of DNMT1 and showed
reactivation of tumour suppressor genes in different cancer models [68, 69]. It is
worth noting that the compound is not active in enzymatic studies against mammalian DNMT1 and DNMT3A [70–72]. However, it is of interest from the perspective
of inhibiting DNA methylation since several groups have shown that it leads to
demethylation of genes in cellular models [73–77] and in vivo [75, 78]. Modifications
on RG108 resulted in compounds with improved activity against the mammalian
DNMTs (maleimide 5, (10), (12) and RG119-1 (11) [70, 71, 79] (Fig. 3)) and
highlighted the interactions of the compound within the catalytic pocket. These
studies provide new potential for improving this chemotype.
By modulation of DNA minor groove binders, Datta et al. identified SGI-1027
(13) [80] which interacts weakly with DNA and inhibits DNMT3A and DNMT1 in
the micromolar range [81]. Further modifications by Valente et al. resulted in a more
active meta-meta analogue Cpd5 (14) ([82] Fig. 3), which shows a stronger interaction with DNA at CG-rich regions [81]. Chemical modifications to better characterise the structure-activity relationships and increase the cellular potency are ongoing.
264
R. Belle et al.
Indeed, the nucleoside analogues are incorporated into DNA (and 5azaC also in
RNA) instead of C, but not only at CpG sites. They then induce the formation of a
suicide substrate with DNMT that is processed by the proteasome and the DNA
repair machinery. Because of their mode of action, they are not selective for an
isoform of DNMTs and induce effects other than just DNA demethylation. To
overcome this, several studies have focused on the identification of DNMT inhibitors that are not nucleoside analogues.
3.2 Non-nucleoside Analogues
The family of non-nucleoside inhibitors has been largely reviewed [24, 42, 59], so
this section will focus on a selection of inhibitors that have shown effects on cellular
phenotypes and on gene expression or have provided new concepts for the discovery
of new inhibitors (Fig. 3). We have chosen to omit most of the compounds that act by
binding to DNA, such as intercalators (i.e. acridine derivatives [63]) or minor groove
binders (i.e. bisbenzimidazoles [64]), that lack specificity for CpG sites. Natural
products have also been excluded since they have been reviewed recently and show
little specificity for the DNMT enzymes [65]. Importantly direct comparisons of
inhibition properties of these compounds cannot be made, because the assays and
conditions used for each study are very different, as well as the choice of the enzyme
used (reviewed in [66]), which can have an important impact on the inhibition [67].
The first synthetic non-nucleoside inhibitor, N-phthaloyl-l-tryptophan RG108,
was identified by in silico screening against a model of DNMT1 and showed
reactivation of tumour suppressor genes in different cancer models [68, 69]. It is
worth noting that the compound is not active in enzymatic studies against mammalian DNMT1 and DNMT3A [70–72]. However, it is of interest from the perspective
of inhibiting DNA methylation since several groups have shown that it leads to
demethylation of genes in cellular models [73–77] and in vivo [75, 78]. Modifications
on RG108 resulted in compounds with improved activity against the mammalian
DNMTs (maleimide 5, (10), (12) and RG119-1 (11) [70, 71, 79] (Fig. 3)) and
highlighted the interactions of the compound within the catalytic pocket. These
studies provide new potential for improving this chemotype.
By modulation of DNA minor groove binders, Datta et al. identified SGI-1027
(13) [80] which interacts weakly with DNA and inhibits DNMT3A and DNMT1 in
the micromolar range [81]. Further modifications by Valente et al. resulted in a more
active meta-meta analogue Cpd5 (14) ([82] Fig. 3), which shows a stronger interaction with DNA at CG-rich regions [81]. Chemical modifications to better characterise the structure-activity relationships and increase the cellular potency are ongoing.
264
R. Belle et al.