Moving beyond the genome to fight cancer

The first total synthesis of the complex natural product chaetocin
expands the tools to reverse lethal gene expressions

Unlocking our genetic blueprint is well underway with the sequencing of the
human genome, but a secondary layer of structure on the genome that
affects gene expression, the ‘epigenome,’ remains largely unmapped.
The packing structure of the epigenome can be altered by chemically modifying
histones, spool-like proteins around which DNA strands are wrapped within our
cells. Histones physically control access to genes, and adding small functional
groups such as acetyl or methyl units to them can selectively switch certain genes
on and off.
Recent developments in methods that can controllably influence these DNA
architectures have focused on the methylation of histone proteins. Now, a research
team led by Mikiko Sodeoka from the RIKEN Advanced Science Institute in Wako,
Japan, has produced the first total synthesis of chaetocin1, a natural product that
inhibits the activity of histone methyltransferases—enzymes that play critical roles
in gene expression (Fig. 1). The results of this work could enable new therapeutics
for destructive diseases such as cancer.
A ‘tail’ of influence
Histones contain floppy ‘tail’ regions, terminated by an amino acid with a free amine
group, that extend from the body of the protein. These tails can influence the epigenome
structure and serve as extremely active sites for chemical modification. Histone
methyltransferase enzymes catalyze the addition of methyl units to lysine and arginine
amino acid side chains in this tail, forming strong bonds in the process. This reaction
does not change the genetic code of the protein, but radically influences transcription
processes—giving histone methylation an influential role in inherited gene expression
.Normally, the levels of histone methylation are delicately balanced within our cells.
However, dysfunction of histone methyltransferases can alter the epigenome and
lead to abnormalities—notably, the loss of expression of tumor-suppressing genes.
Therapies that can selectively control the activity of these enzymes hold great potential
for new cancer therapeutics without the dangerous side effects of chemotherapy.
Natural guides
The number of chemicals that can modulate histone methyltransferase enzymes is
limited. According to team-member Yoshitaka Hamashima, also from RIKEN, only
a few compounds that can selectively inhibit these enzymes have been reported to date.
He says, “it is only chaetocin that comes from natural sources.”
Chaetocin is a natural alkaloid produced by Chaetomium minutum, a form of wood
mold. The complex and elegantly symmetric structure of this molecule features eight rings
and several functional groups, most notably a pair of disulfide bridges attached to two
terminal rings. Chaetocin has been extensively investigated for its antibacterial behavior
and ability to suppress cell growth, and has the potential to play an important role in
modifying the epigenome.
Several research groups have produced related analogues of chaetocin, but the total
synthesis of this molecule has eluded organic chemists since its discovery forty years
ago—setting up a significant test to the synthetic skills of Sodeoka and her team. “The fact
that no one had succeeded in the total synthesis after its isolation in 1970 drove us to
embark on this formidable challenge,” says Hamashima.
Risk and reward
The final part of the reaction—construction of the disulfide bridges—involved some
risky chemistry, Hamashima notes. “In our initial plan, we expected that the
double-decker structure of chaetocin might control the approach of hydrogen sulfide
from the outer side. But nobody was convinced that it would work well.” The team was
extremely gratified when the final step in the reaction, which involved ten bond-forming
and -cleaving events, generated chaetocin with the correct geometrical structure.
Overall, the team’s method demonstrates a highly efficient way to produce chaetocin,
because the total synthesis required only nine chemical transformations.
Bridging differences
With the chemical synthesis of chaetocin complete, Sodeoka and colleagues prepared
various analogues of the molecule—two optical isomers of chaetocin, and a version
missing the disulfide bridges. The latter allowed them to examine the structure–activity
relationship between this natural product and a particular histone methyltransferase
enzyme called G9a, in collaboration with Minoru Yoshida’s group also from RIKEN
Advanced Science Institute. Although both chaetocin isomers showed strong inhibitory
activity, the molecule without the sulfur bridges was inactive—demonstrating the critical
role of this functionality.
Hamashima says that the target enzyme has a domain, close to chaetocin’s binding site,
which is full of amino acids called cysteines. Cysteines have a thiol (-SH) side chain
that may be able to form transitory bonds with the critical disulfide bridges of chaetocin.
“While the exact mechanism is still unclear,” he says, “we speculate that such chemical
bond formations are responsible for the inhibition of G9a.”
The researchers believe that further studies into the molecular mechanisms of chaetocin
should deliver a new generation of enzyme-specific pharmaceuticals that can control gene
expression patterns—an important step in the treatment of cancerous diseases.
“Contributing to human health by creating new drugs is our goal,” says Hamashima.
“In the future, the day will come when we can wake up silent genes in cells at will by
simply adding chemical modulators.”