The screening of a library of flavonoids identified a family of 3-chloro-3nitroflavanones which was able to inhibit DNMT3A and DNA methylation in
zebrafish embryos (flavanone 69 (15) Fig. 3; [83]). This family of compounds
showed selectivity for the C5-DNA methyltransferases, compared to other
non-specific flavones such as epigallocatechin gallate (EGCG).
Procainamide and procaine were described to weakly bind to DNA and inhibit
DNMTs [84, 85] and were chemically modified to improve the inhibition
[86, 87]. The conjugation to diverse moieties resulted in micromolar inhibitors of
DNMT1 and Dnmt3A/3L (conjugate 12 (16), Fig. 3, [88]).
High-throughput screening campaigns against different DNMTs and use of
diverse biochemical assays resulted in the identification of miscellaneous compounds, the most potent of which are shown in Fig. 3. Among these, the anthraquinone laccaic acid (25) was described as a DNA-competitive inhibitor of DNMT1
with a weak activity in breast MCF-7 cancer cells (at 200 μM) [89]. A
naphthoquinone, diclone (19), a pesticide and fungicide, was specific of DNMT1
and Dnmt3A and inactive against the histone methyltransferase G9A. This observation opened the path to studying the impact on the epigenome of plants, animals and
human when addressing the toxicology of pesticides [90]. SW155246 (20), an
aromatic sulphonamide, showed a weak selectivity against DNMT1 vs DNMT3A
and DNMT3B and induced a weak inhibition of methylation and reactivation of
TSGs in human lung carcinoma [91]. DC_501, DC_517 (24) [92] and SID49645275
(21) [93] were identified to inhibit DNMT1 in the low micromolar level and to
inhibit cell proliferation. The mechanism of action and the selectivity still need to be
explored.
3.3 Transition State and Bisubstrate Analogues
Recently, progress has been made in the design of transition state and bisubstrate
analogues. We have shown that seven cytosine-adenosine compounds, designed as
transition state analogues of the methylation reaction of position 5 of cytosine by
DNMT1 and DNMT3, did not result in inhibitors of DNMTs but rather of histone
arginine methyltransferases PRMT4 [94].
Interestingly, based on the design of mechanism-based transition analogues,
Miletic et al. have described and evaluated a set of adenosyl-1-methyl-pyrimidin2-one derivatives in silico as leads for the synthesis of mechanism-based suicide
inhibitors of DNMT1 ([95], prototype (18) Fig. 3).
Another chemical approach we explored is the bisubstrate analogues that have
successfully been applied to inhibit adenine DNA methyltransferases. Using this
approach we have identified compounds (17) as potent inhibitor of DNMT3A able to
demethylate promoters of tumour suppressor genes and to reactivate gene expression
in cancer cells ([96], Fig. 3).
Chemical Compounds Targeting DNA Methylation and Hydroxymethylation
265
zebrafish embryos (flavanone 69 (15) Fig. 3; [83]). This family of compounds
showed selectivity for the C5-DNA methyltransferases, compared to other
non-specific flavones such as epigallocatechin gallate (EGCG).
Procainamide and procaine were described to weakly bind to DNA and inhibit
DNMTs [84, 85] and were chemically modified to improve the inhibition
[86, 87]. The conjugation to diverse moieties resulted in micromolar inhibitors of
DNMT1 and Dnmt3A/3L (conjugate 12 (16), Fig. 3, [88]).
High-throughput screening campaigns against different DNMTs and use of
diverse biochemical assays resulted in the identification of miscellaneous compounds, the most potent of which are shown in Fig. 3. Among these, the anthraquinone laccaic acid (25) was described as a DNA-competitive inhibitor of DNMT1
with a weak activity in breast MCF-7 cancer cells (at 200 μM) [89]. A
naphthoquinone, diclone (19), a pesticide and fungicide, was specific of DNMT1
and Dnmt3A and inactive against the histone methyltransferase G9A. This observation opened the path to studying the impact on the epigenome of plants, animals and
human when addressing the toxicology of pesticides [90]. SW155246 (20), an
aromatic sulphonamide, showed a weak selectivity against DNMT1 vs DNMT3A
and DNMT3B and induced a weak inhibition of methylation and reactivation of
TSGs in human lung carcinoma [91]. DC_501, DC_517 (24) [92] and SID49645275
(21) [93] were identified to inhibit DNMT1 in the low micromolar level and to
inhibit cell proliferation. The mechanism of action and the selectivity still need to be
explored.
3.3 Transition State and Bisubstrate Analogues
Recently, progress has been made in the design of transition state and bisubstrate
analogues. We have shown that seven cytosine-adenosine compounds, designed as
transition state analogues of the methylation reaction of position 5 of cytosine by
DNMT1 and DNMT3, did not result in inhibitors of DNMTs but rather of histone
arginine methyltransferases PRMT4 [94].
Interestingly, based on the design of mechanism-based transition analogues,
Miletic et al. have described and evaluated a set of adenosyl-1-methyl-pyrimidin2-one derivatives in silico as leads for the synthesis of mechanism-based suicide
inhibitors of DNMT1 ([95], prototype (18) Fig. 3).
Another chemical approach we explored is the bisubstrate analogues that have
successfully been applied to inhibit adenine DNA methyltransferases. Using this
approach we have identified compounds (17) as potent inhibitor of DNMT3A able to
demethylate promoters of tumour suppressor genes and to reactivate gene expression
in cancer cells ([96], Fig. 3).
Chemical Compounds Targeting DNA Methylation and Hydroxymethylation
265