Biomedical Engineering Reference
In-Depth Information
genotype (e.g., encoding gene) allows for PCR amplification of the genetic infor-
mation, and the consequent translation into a succeeding population of enriched
biomolecular compounds suitable for further rounds of selection (a process often
termed
biomolecular evolution
) (Figure 11.1b) [27,39,40]. After multiple cycles of
translation and selection, sequencing of the enriched genome information yields to
the final identification of the selected binding molecules (Figure 11.1b).
In this light,
selection
procedures are intimately connected with the Darwinian
evolutionary approach applied by nature to discover molecules with appropriate
functions. Indeed, nature simultaneously imposes a selection pressure on a large
population of candidate molecules. The cell that survives proliferates, and its genetic
information is amplified and translated in the next population of bioactive molecules
that will undergo the next selection process.
It is worth noting that in sharp contrast to the high-throughput
screening
approach,
in which compound libraries are screened individually (i.e., one molecule at a time),
based on a specific functional or binding assay, in selection approaches the display
libraries are interrogated simultaneously, imposing the same selection conditions on
all library members (Figure 11.1). Time and costs for selections are, in first-order
approximation, independent of library size, since all library members are interrogated
in a single experiment. Conversely, screening efforts tend to the increase linearly with
library size, due to the discrete nature of the assays required.
Over the last 20 years, display technologies have shown themselves to be enor-
mously effective for the identification of biopharmaceutical candidates [37,39,41-
43]. However, such compounds (i.e., antibodies) are often unable to interfere with
the majority of intracellular processes. Therefore, it would be conceivable to develop
conceptually analog selection methodologies (e.g., similar to phage display) for the
discovery of more target specific biologically effective low-molecular-weight com-
pounds (Figure 11.2).
As small organic molecule libraries cannot be biosynthesized by native biosyn-
thetic machineries, DNA-encoded chemical library technology emerged as the most
promising and fascinating alternative to fill such a gap, allowing for the facile linkage
of unnatural chemotypes to corresponding amplifiable genotypes (Figure 11.2).
11.1.3 Chapter Overview
In this chapter the concept of DNA encoding and the basic principles of DNA-
encoded chemistry are described, including the fundaments of DNA conjugation and
DNA-templated synthesis. Subsequently, with a focus on combinatorial synthesis,
the history of DNA-encoded chemical libraries will be retraced, from the pioneering
paper of Lerner and Brenner in 1992 to recent developments as an effective drug
discovery tool.
In the second part of the chapter, alternative strategies for the construction of
DNA-encoded chemical libraries, as well as the various selection and decoding
approaches, are thoroughly surveyed. Moreover, the latest developments in DNA-
encoded chemical libraries are reviewed, examining closely recent and future possible
implications for drug discovery programs. Finally, looking globally at the technology
