Chemistry Reference
In-Depth Information
molecules, from organic dyes to proteins. Some oligonucleotides (25-40 bases in
length), called aptamers, show a highly organized tertiary structure that enables
them to bind specifi cally to their target (generally a protein) with high affi nity
(Figure 9.1). Aptamers, which can be selected from combinatorial nucleic acid librar-
ies through an iterative
in vitro
process (SELEX, systematic evolution of ligands by
e xponential e nrichment),
23,24
can, in principle, target virtually any protein. Among
the many aptamers reported, only Macugen
TM
, a polyethylene glycol-engrafted oli-
gonucleotide that specifi cally binds the vascular endothelial grown factor-165 isoform,
has been approved for treating age-related macular degeneration.
25
Although many
aspects such as delivery must be improved to develop new effi cient aptamer - based
drugs, aptamer technology is emerging as a powerful and versatile tool in various
fi elds of biotechnology, target validation, bioanalysis, diagnostics and imaging.
26,27
9.2 Platination as a Tool to Enhance Biological Effects
As stated above, one of the requirements for making drugs out of synthetic oligo-
nucleotides is that they effi ciently recognize and interact with their targets. Only
suffi ciently stable complexes can prevent the ribosome machinery from translating
the mRNA code into a polypeptide sequence, stop replication or transcription, or
block the function of a protein.
28
Chemical modifi cation of the chain modulates the affi nity of synthetic oligo-
nucleotides for their targets. Substitution of sulfur for one of the oxygens of the
phosphodiester bridge (phosphorothioate or S-oligonucleotides),
29
which is the
modifi cation introduced in the only antisense oligonucleotide approved for thera-
peutic use,
4
slightly decreases the stability of the modifi ed - oligonucleotide - mRNA
duplex.
30
Conversely, the stability of the duplex can be improved, for instance, by
the introduction of a methylene bridge that links the 4
-
O
and freezes the
North conformation of the ribose ring (locked nucleic acids or LNAs),
31
or by
replacement of the charged sugar-phosphate backbone with noncharged ones, as in
peptide nucleic acids (PNAs)
32
or morpholino oligonucleotides.
33
The stability of the fi nal complex, either duplex or triplex, can also be improved
by forming a crosslink between the oligonucleotide and the target. Duplexes can be
stabilized by covalently linking their ends. This covalent union has been chemically
established by a short oligonucleotide sequence, as in naturally occurring hairpin
duplexes, or by nonoligonucleotide linkages (Figure 9.2) such as disulfi de bridges,
34
alkyl chains,
35,36
aromatic moieties such as stilbenes
37
or phenanthrenes,
38
and metal
complexes.
39,40
Nevertheless, if oligonucleotides are to be used as therapeutic agents, and rec-
ognize and link to their targets, only the synthetic chain can be modifi ed. In that
case, a group attached or appended to the synthetic oligonucleotide is expected to
give rise to the desired covalent union upon hybridization. Examples of this approach
are the use of 2-arylthioethyl- or quinone methide-modifi ed oligonucleotides, as
described by Sasaki
41
and Rokita,
42
respectively (Figures 9.3A and B). In both cases,
the target is alkylated upon duplex formation, yielding the interchain crosslink.
′
-
C
and 2
′
