Biomedical Engineering Reference
In-Depth Information
a proper synthetic route can be designed to facilitate achieving the synthesis. Over
the past 20 years, many efficient library synthetic approaches, such as diversity-
oriented synthesis and fragment-based methods, have been developed to facilitate the
production of small-molecule libraries. In the following sections we explore these
approaches in greater detail.
13.2.1 Diversity-Oriented Synthesis
Diversity-oriented synthesis (DOS) was devised by Schreiber in 2000 [17]. It estab-
lished a milestone as an innovative strategy to create diverse libraries for probing
biological mechanisms. Through this ingenious method, synthetic chemists are able
to generate compound collections with rapidly both skeletal and stereochemical diver-
sity. These molecules can be screened to unravel novel lead compounds for multiple
protein targets by exploiting a variety of biological assays, including protein-binding
assay and cell-based phenotypic assay. On the other hand, the DOS approach has also
posed several challenges to synthetic chemists. For example, DOS synthetic libraries
require products with skeletal diversity and high purity. To implement the DOS
approach appropriately, the chemistry employed must be highly efficient because it
is performed on a solid support and involves multiple steps of synthesis. The syn-
thetic route designed must also meet the requirement to provide complex and diverse
structures with accessible building blocks. Furthermore, the planned reaction at each
step must be compatible with various intermediates generated during the synthe-
sis. Last but not least, stereoselectivity is also a key parameter for a DOS library.
Stereoselective reactions should be chosen carefully in the design.
In 2002, a group led by Schreiber applied the DOS methodology to construct a
3780-member small-molecule library using a “one bead-one stock solution” approach
[11]. As shown in Figure 13.2a, the overall design of this small-molecule library was
based on the 1,3-dioxane scaffold because of its rigidity, which is an important
parameter of a drug candidate. The scaffold could be synthesized in a stereoselective
manner. After stepwise solid-phase synthesis, the 1,3-dioxanes were released from
solid support and immobilized onto a chlorinated glass slide through a hydroxyl
group handle. The fabricated array was then incubated with fluorescently labeled
yeast transcription inhibitor Ure2p. Eight compounds were identified as Ure2p binder,
and one of the compounds, uretupamine A, was found capable of inhibiting Ure2p
activity with excellent selectivity in vivo. Subsequent SAR analysis revealed a more
potent analog, uretupamine B (
K
d
=
M). The result offers indisputable evidence
that it is possible to combine DOS strategy and microarray platform to discover new
small molecules, which are capable of selectively modulating protein functions.
In the following years, the Schreiber group led this research further by synthesizing
a library containing 12,396 compounds using three different DOS pathways [18].
The libraries were generated through 1,3-dioxane, biaryl, and Diels-Alder synthetic
pathways, respectively. The group printed these compounds onto chlorinated glass
slides as before, and screened them by sandwich assay with Hap3p, a subunit of yeast
transcription factor complex (Figure 13.2b). The three microarrays were probed
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