2.1 Structures and Mechanism of DNMTs
DNMTs belong to the C5-DNA methyltransferases, which have a three-dimensionally
conserved catalytic pocket. The C-terminal contains the motifs of DNA binding and
catalysis of methyl transfer. Upon binding to DNA double helix, cytosine flips and
binds in the catalytic pocket. The catalytic cysteine in the Pro-Cys motif (PCQ or PCN)
then binds to position 6 of cytosine. Then the methyl group from the SAM is transferred
to position 5 of the cytosine, creating a steric clash that releases the 5mC by
β-elimination and resolves the DNA-DNMT complex.
In addition to the catalytic domain at the C-terminus, the DNMTs possess
regulatory N-terminal domains that include a nuclear localisation signal and domains
for protein-protein interactions to chromatin, transcriptional and replication regulators [26]. Several structures of the mammalian DNMTs have been resolved showing
the particular features of the different isoforms and some protein partners. In
particular, the three DNMT3s have a PHD (plant homeodomain)-like domain,
ADD (ATRX-DNMT3-DNMT3L domain) for the interaction with the tail of histone
H3 [26] and DNMT3A and 3B have a PWWP domain found in DNA-binding
proteins and involved in nucleosome recognition [27], interacting with H3K36me3
[26]. The N-terminus of DNMT1 is rich in protein interaction domains that localise it
to the nucleus (NLS), to replication forks (PBD, PCNA-binding domain, DMAP
domain, RFTS domain, BAH1 and 2 [28]) and to un-methylated and hemimethylated DNA (CXXC zinc finger domain; BAH1 and BAH2). These domains
are also involved in the enzymatic control of the protein, for example, its inhibition
when bound to non-methylated DNA and its switch to catalytically active form when
bound to hemi-methylated DNA [26, 29, 30].
2.2 DNMTs in Diseases
It is clearly established that aberrant DNA methylation profile is associated with
cancers [31–35]. In parallel to a global hypomethylation, hypermethylation at promoters of specific genes are observed in cancer cells. In particular, genes, such as
tumour suppressor genes, are commonly silenced by promoter hypermethylation.
These features have been exploited for the development of biomarkers for the
detection of many cancers [36, 37], including for colon cancer (ColoVantage
® and
Epi proColon
® ) and lung cancer (Epi proLung). Moreover, DNA methylation is an
anticancer therapeutic target: 5aza and 5azadC have been approved for the treatment
of certain haematological cancers. These drugs are also in clinical trials, mainly in
combination, for several solid tumours [38, 39]. However, these aberrant patterns are
not limited to cancers [40]. Alteration in DNA methylation, caused by genetic
mutations in the DNMTs or DNMTs deregulation, is involved in psychiatric,
cognition, neuronal, ageing disorders, cardiovascular diseases, bacterial and viral
infections and genetic diseases such as cystic fibrosis [41, 42]. Finally, epigenomics
Chemical Compounds Targeting DNA Methylation and Hydroxymethylation
261
DNMTs belong to the C5-DNA methyltransferases, which have a three-dimensionally
conserved catalytic pocket. The C-terminal contains the motifs of DNA binding and
catalysis of methyl transfer. Upon binding to DNA double helix, cytosine flips and
binds in the catalytic pocket. The catalytic cysteine in the Pro-Cys motif (PCQ or PCN)
then binds to position 6 of cytosine. Then the methyl group from the SAM is transferred
to position 5 of the cytosine, creating a steric clash that releases the 5mC by
β-elimination and resolves the DNA-DNMT complex.
In addition to the catalytic domain at the C-terminus, the DNMTs possess
regulatory N-terminal domains that include a nuclear localisation signal and domains
for protein-protein interactions to chromatin, transcriptional and replication regulators [26]. Several structures of the mammalian DNMTs have been resolved showing
the particular features of the different isoforms and some protein partners. In
particular, the three DNMT3s have a PHD (plant homeodomain)-like domain,
ADD (ATRX-DNMT3-DNMT3L domain) for the interaction with the tail of histone
H3 [26] and DNMT3A and 3B have a PWWP domain found in DNA-binding
proteins and involved in nucleosome recognition [27], interacting with H3K36me3
[26]. The N-terminus of DNMT1 is rich in protein interaction domains that localise it
to the nucleus (NLS), to replication forks (PBD, PCNA-binding domain, DMAP
domain, RFTS domain, BAH1 and 2 [28]) and to un-methylated and hemimethylated DNA (CXXC zinc finger domain; BAH1 and BAH2). These domains
are also involved in the enzymatic control of the protein, for example, its inhibition
when bound to non-methylated DNA and its switch to catalytically active form when
bound to hemi-methylated DNA [26, 29, 30].
2.2 DNMTs in Diseases
It is clearly established that aberrant DNA methylation profile is associated with
cancers [31–35]. In parallel to a global hypomethylation, hypermethylation at promoters of specific genes are observed in cancer cells. In particular, genes, such as
tumour suppressor genes, are commonly silenced by promoter hypermethylation.
These features have been exploited for the development of biomarkers for the
detection of many cancers [36, 37], including for colon cancer (ColoVantage
® and
Epi proColon
® ) and lung cancer (Epi proLung). Moreover, DNA methylation is an
anticancer therapeutic target: 5aza and 5azadC have been approved for the treatment
of certain haematological cancers. These drugs are also in clinical trials, mainly in
combination, for several solid tumours [38, 39]. However, these aberrant patterns are
not limited to cancers [40]. Alteration in DNA methylation, caused by genetic
mutations in the DNMTs or DNMTs deregulation, is involved in psychiatric,
cognition, neuronal, ageing disorders, cardiovascular diseases, bacterial and viral
infections and genetic diseases such as cystic fibrosis [41, 42]. Finally, epigenomics
Chemical Compounds Targeting DNA Methylation and Hydroxymethylation
261