Biomedical Engineering Reference
In-Depth Information
In 2009, as a proof-of-concept demonstration, Vipergen applied the principles
of yR technology to generate a 100-member DNA-encoded pentapeptide library. In
a model selection conducted over two rounds of panning and library resynthesis,
>
150,000-fold enrichment of known ligand (ENK, [Leu]-enkephalin) toward the
anti-ENK antibody 3-E was reported [49,90].
In principle, yR supports DNA frameworks with higher dimensions (e.g., four-
and five-way DNA junctions) and the construction of DNA-encoded small molecule
collections comprising up to billions of different compounds [90,91]. However, to
date, there is no peer-reviewed report on the efficacy of the Vipergen's YoctoReactor
approach and of its rolling translation for the de novo discovery of small-molecule
ligands against a given biological target.
11.2.3 Self-Assembled DNA-Encoded Chemical Libraries
(Dual-Pharmacophore Libraries)
Philochem AG, in collaboration with Neri's group at ETH Z urich, has pioneered a
conceptually different approach for the construction of very large high-quality DNA-
encoded chemical libraries. This strategy, also known as
encoded self-assembling
chemical
(ESAC)
libraries
, features the combinatorial assembly of complementary
sublibraries by means of Watson-Crick base pairing to form stable heterodimers (Fig-
ure 11.19a) [92]. The methodology can be extended to a triple-pharmacophore library
by applying Hoogsteen base pairing (Figure 11.19a) [92]. Each sublibrary consists
of an oligonucleotide containing both a tagging domain, univocally encoding the
covalently linked chemical moiety (at either the 5
-or3
-etremity), and a hybridiza-
tion domain featuring self-assembling with a further sublibrary pool (Figure 11.19a)
[63,92].
In sharp contrast with single-pharmacophore methodologies, the ESAC approach
does not involve chemical reactions between building blocks to generate complex
FIGURE 11.18
(
Continued
) oligonucleotides.
a
, building block 1, and
b
, building block 2,
undergo the first DNA-directed reaction. Following encoding of building block 2 by enzymatic
ligation, cleavage of the linker enables irreversible delivery of the compound to the initial
reaction site. Iteration of the process enables incorporation of the third set of building blocks
(
c
) and corresponding DNA-coding tags. After the reactions are completed, the hairpin-DNA
reactor is converted into a linear oligonucleotide, yielding to the final library of small molecules
displayed on double-stranded DNA templates. (c) Rolling translation: PCR-amplified DNA-
coding tags selected in the first round of panning serve as yR templates for chemical trans-
lation of the next-generation library in a subsequent round of selection. Before entering
the next round of translation and selection, the double-stranded DNA templates are site-
specifically digested to expose single-stranded DNA codons, which effectively allow hybridiza-
tion with the corresponding building block conjugates. (
See insert for color representation of
the figure.
)
