3 research outputs found
“Cap-and-Catch” Purification for Enhancing the Quality of Libraries of DNA Conjugates
The potential of DNA-encoded combinatorial
libraries (DECLs) as
tools for hit discovery crucially relies on the availability of methods
for their synthesis at acceptable purity and quality. Incomplete reactions
in the presence of DNA can noticeably affect the purity of DECLs and
methods to selectively remove unreacted oligonucleotide-based starting
products would likely enhance the quality of DECL screening results.
We describe an approach to selectively remove unreacted oligonucleotide
starting products from reaction mixtures and demonstrate its applicability
in the context of acylation of amino-modified DNA. Following an amide
bond forming reaction, we treat unreacted amino-modified DNAs with
biotinylating reagents and isolate the corresponding biotinylated
oligonucleotides from the reaction mixture by affinity capture on
streptavidin-coated sepharose. This approach, which yields the desired
DNA-conjugate at enhanced purity, can be applied both to reactions
performed in solution and to procedures in which DNA is immobilized
on an anion exchange solid support
Systematic Evaluation and Optimization of Modification Reactions of Oligonucleotides with Amines and Carboxylic Acids for the Synthesis of DNA-Encoded Chemical Libraries
DNA-encoded chemical libraries are
collections of small molecules,
attached to DNA fragments serving as identification barcodes, which
can be screened against multiple protein targets, thus facilitating
the drug discovery process. The preparation of large DNA-encoded chemical
libraries crucially depends on the availability of robust synthetic
methods, which enable the efficient conjugation to oligonucleotides
of structurally diverse building blocks, sharing a common reactive
group. Reactions of DNA derivatives with amines and/or carboxylic
acids are particularly attractive for the synthesis of encoded libraries,
in view of the very large number of building blocks that are commercially
available. However, systematic studies on these reactions in the presence
of DNA have not been reported so far. We first investigated conditions
for the coupling of primary amines to oligonucleotides, using either
a nucleophilic attack on chloroacetamide derivatives or a reductive
amination on aldehyde-modified DNA. While both methods could be used
for the production of secondary amines, the reductive amination approach
was generally associated with higher yields and better purity. In
a second endeavor, we optimized conditions for the coupling of a diverse
set of 501 carboxylic acids to DNA derivatives, carrying primary and
secondary amine functions. The coupling efficiency was generally higher
for primary amines, compared to secondary amine substituents, but
varied considerably depending on the structure of the acids and on
the synthetic methods used. Optimal reaction conditions could be found
for certain sets of compounds (with conversions >80%), but multiple
reaction schemes are needed when assembling large libraries with highly
diverse building blocks. The reactions and experimental conditions
presented in this article should facilitate the synthesis of future
DNA-encoded chemical libraries, while outlining the synthetic challenges
that remain to be overcome
Tankyrase 1 Inhibitors with Drug-like Properties Identified by Screening a DNA-Encoded Chemical Library
We
describe the synthesis and screening of a DNA-encoded chemical
library containing 76230 compounds. In this library, sets of amines
and carboxylic acids are directly linked producing encoded compounds
with compact structures and drug-like properties. Affinity screening
of this library yielded inhibitors of the potential pharmaceutical
target tankyrase 1, a poly(ADP-ribose) polymerase. These compounds
have drug-like characteristics, and the most potent hit compound (X066/Y469)
inhibited tankyrase 1 with an IC<sub>50</sub> value of 250 nM