DNA-encoded
chemical libraries (DELs) represent a versatile and
powerful technology platform for the discovery of small-molecule ligands
to protein targets of biological and pharmaceutical interest. DELs
are collections of molecules, individually coupled to distinctive
DNA tags serving as amplifiable identification barcodes. Thanks to
advances in DNA-compatible reactions, selection methodologies, next-generation
sequencing, and data analysis, DEL technology allows the construction
and screening of libraries of unprecedented size, which has led to
the discovery of highly potent ligands, some of which have progressed
to clinical trials. In this Review, we present an overview of diverse
approaches for the generation and screening of DEL molecular repertoires.
Recent success stories are described, detailing how novel ligands
were isolated from DEL screening campaigns and were further optimized
by medicinal chemistry. The goal of the Review is to capture some
of the most recent developments in the field, while also elaborating
on future challenges to further improve DEL technology as a therapeutic
discovery platform.
DNA-encoded library technology (ELT) has emerged in the pharmaceutical industry as a powerful tool for hit and lead generation. Over the last 10 years, a number of DNA-compatible chemical reactions have been published and used to synthesize libraries. Among the most commonly used reactions in medicinal chemistry is the C−N bond formation, and its application to DNA-encoded library technology affords an alternative approach to identify high-affinity binders for biologically relevant protein targets. Herein we report a newly developed Pd-promoted C−N cross coupling reaction between DNA-conjugated aryl bromides and a wide scope of arylamines in good to excellent yields. The mild reaction conditions should facilitate the synthesis of novel DNA-encoded combinatorial libraries.
The
growing importance of DNA-encoded chemical libraries (DECLs) as tools
for the discovery of protein binders has sparked an interest for the
development of efficient screening methodologies, capable of discriminating
between high- and medium-affinity ligands. Here, we present a systematic
investigation of selection methodologies, featuring a library displayed
on single-stranded DNA, which could be hybridized to a complementary
oligonucleotide carrying a diazirine photoreactive group. Model experiments,
performed using ligands of different affinity to carbonic anhydrase
IX, revealed a recovery of preferential binders up to 10%, which was
mainly limited by the highly reactive nature of carbene intermediates
generated during the photo-cross-linking process. Ligands featuring
acetazolamide or p-phenylsulfonamide exhibited a higher recovery compared
to their counterparts based on 3-sulfamoyl benzoic acid, which had
a lower affinity toward the target. A systematic evaluation of experimental
parameters revealed conditions that were ideally suited for library
screening, which were used for the screening of a combinatorial DECL
library, featuring 669 240 combinations of two sets of building
blocks. Compared to conventional affinity capture procedures on protein
immobilized on solid supports, photo-cross-linking provided a better
discrimination of low-affinity CAIX ligands over the background signal
and therefore can be used as a tandem methodology with the affinity
capture procedures.
DNA-encoded chemical libraries (DECLs) are increasingly employed in hit discovery toward proteins of pharmaceutical interest. Protected amino acids are the most commonly used building blocks for the construction of DECLs; therefore, the expansion of reaction scope with the subsequent free amine is highly desired. Here, we developed a robust DNA-compatible diazo-transfer reaction using imidazole-1-sulfonyl azide tetrafluoroborate salt converting a wide range of primary amines into their corresponding azides in good to excellent yields.
Interleukin-2 (IL2) is a pro-inflammatory cytokine that plays a
crucial role in immunity, which is increasingly being used for therapeutic
applications. There is growing interest in developing IL2-based therapeutics
which do not interact with the alpha subunit of the IL2 receptor (CD25)
as this protein is primarily found on immunosuppressive regulatory
T cells (Tregs). Screenings of a new DNA-encoded library,
comprising 669,240 members, provided a novel series of IL2 ligands,
subsequently optimized by medicinal chemistry. One of these molecules
(compound 18) bound to IL2 with a dissociation constant
of 0.34 μM was able to form a kinetically stable complex with
IL2 in size-exclusion chromatography and recognized the CD25-binding
site as evidenced by competition experiments with the NARA1 antibody.
Compound 18 and other members of the series may represent
the starting point for the discovery of potent small-molecule modulators
of IL2 activity, abrogating the binding to CD25.
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