Automated screening for small organic ligands using DNA-encoded chemical libraries

Decurtins, Willy; Wichert, Moreno; Franzini, Raphael M.; Buller, Fabian; Stravs, Michael A.; Zhang, Yixin; Neri, Dario; Scheuermann, Jörg

doi:10.1038/nprot.2016.039

Cited by 111 publications

(123 citation statements)

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“…The three CAIX ligands were chemically coupled to one amino‐tagged DNA fragment (96 bp) and mixed with a different DNA fragment in a 1:1 ratio and at various concentrations, to assess experimental recovery rates (Figure ). Ligand capture procedures were performed by using both biotinylated CAIX on streptavidin‐coated supports or His‐tagged protein preparations on metal‐based supports, with suitable washing procedures . After selection, the DNA fragments were eluted and quantified by means of qPCR (Figure ).…”

Section: Resultsmentioning

confidence: 99%

“…Most commonly, a protein target of interest is immobilized onto magnetic beads or resins. Libraries are incubated with the affinity support and preferential binders are recovered after a series of washing steps . The performance (in terms of recovery and selectivity) of antibody phage display library selections has been systematically investigated in model systems .…”

Section: Introductionmentioning

confidence: 99%

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Quantitative Assessment of Affinity Selection Performance by Using DNA‐Encoded Chemical Libraries

et al. 2019

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DNA‐encoded chemical libraries are often used for the discovery of ligands against protein targets of interest. These large collections of DNA‐barcoded chemical compounds are typically screened by using affinity capture methodologies followed by PCR amplification and DNA sequencing procedures. However, the performance of individual steps in the selection procedures has been scarcely investigated, so far. Herein, the quantitative analysis of selection experiments, by using three ligands with different affinity to carbonic anhydrase IX as model compounds, is described. In the first set of experiments, quantitative PCR (qPCR) procedures are used to evaluate the recovery and selectivity for affinity capture procedures performed on different solid‐phase supports, which are commonly used for library screening. In the second step, both qPCR and analysis of DNA sequencing results are used to assess the recovery and selectivity of individual carbonic anhydrase IX ligands in a library, containing 360 000 compounds. Collectively, this study reveals that selection procedures can be efficient for ligands with sub‐micromolar dissociation constants to the target protein of interest, but also that selection performance dramatically drops if 104 copies per library member are used as the input.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Quantitative Assessment of Affinity Selection Performance by Using DNA‐Encoded Chemical Libraries

et al. 2019

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“…

are encoded by unique DNA sequences as identification "barcodes," and are assembled combinatorial using split-andpool strategy or alternative procedures via DNA-compatible reactions. [10,11] To date, a large number of high-quality hits have been identified by the DEL technology for various therapeutically relevant targets, such as kinases, [12] phosphatases, [13] and G-protein coupled receptors. In a typical affinity-based selection experiment, when non-and low-affinity binders are washed away, the DNA tag of the remaining compounds can be amplified using polymerase chain reaction and the relative frequency of the remaining compounds before and after selection is determined by counting the number of DNA tags in high-throughput DNA sequencing experiments.

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confidence: 99%

DNA‐Encoded Libraries: Aryl Fluorosulfonates as Versatile Electrophiles Enabling Facile On‐DNA Suzuki, Sonogashira, and Buchwald Reactions

Wang

et al. 2019

Advanced Science

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are encoded by unique DNA sequences as identification "barcodes," and are assembled combinatorial using split-andpool strategy or alternative procedures via DNA-compatible reactions. [7][8][9] DELs comprising millions or even billions of DNA-tagged druglike molecules can be effectively synthesized via this technology and screened against various protein targets of interest in a single pooled assay. In a typical affinity-based selection experiment, when non-and low-affinity binders are washed away, the DNA tag of the remaining compounds can be amplified using polymerase chain reaction and the relative frequency of the remaining compounds before and after selection is determined by counting the number of DNA tags in high-throughput DNA sequencing experiments. [10,11] To date, a large number of high-quality hits have been identified by the DEL technology for various therapeutically relevant targets, such as kinases, [12] phosphatases, [13] and G-protein coupled receptors. [14] Several drug candidates derived from their corresponding DEL hits, such as soluble epoxide hydrolase inhibitor GSK2256294, and death domain receptor-associated adaptor kinase RIP1 inhibitor GSK2982772 have progressed to latestage clinical development, [15,16] further emphasizing DEL as a powerful technology for small molecular drug discovery.Despite these successes, the great potential of DEL technology in drug discovery has not yet been fully realized. One of the most fundamental challenges is the synthesis of high-quality libraries with more structural diversity, which in turn depends on the development of new and robust DNA-compatible reactions that allow more flexibility in DEL's design and synthesis. Among various DNA-compatible reactions developed in recent years, transition-metal-promoted reactions such as Suzuki-Miyaura coupling, [17][18][19][20][21][22][23] Sonogashira coupling, and Buchwald-Hartwig amination using DNA-conjugated aryl halides as electrophiles have been elegantly developed (Figure 1), [24][25][26] and some of them have been developed for DEL synthesis. However, the environmental toxicity and high costs of aryl halides have hindered their large-scale applications in industry. Thus, much attention has been paid to phenol-derived electrophiles recently, [27] which, as compared to aryl halides, offer a more sustainable starting material because most of them are readily available from biomass. [28] In addition, phenol modules are also important components of natural products (NPs), bioactive molecules, and pharmaceutical drugs. Coupling reactions with Using (hetero)aryl fluorosulfonates as versatile electrophiles, facile on-DNA cross-coupling reactions of Suzuki, Sonogashira, and Buchwald are reported here. Notably, all of these reactions show excellent functional group tolerance, mild reaction conditions (relative low temperature and open to air), rich heterocyclic coupling partners, and more importantly, DNA-compatibility. Thus, these new reactions based on efficient formation of C(sp 2 )-C(sp 2 ), C(sp 2 )-C(sp), and C(s...

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“…Several approaches have been used to generate DECLs with different library-encoding methods and assembly of chemical building blocks [45••,46••]. As all compounds in the library can be identified by their DNA tags, a very large number of compounds (up to billions of molecules) can be screened simultaneously in mixture in affinity-capture experiments on target proteins.…”

Section: Screening Of Combinatorial Librariesmentioning

confidence: 99%

Combinatorial chemistry in drug discovery

Liu

Lam

2017

Current Opinion in Chemical Biology

249

131

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Several combinatorial methods have been developed to create focused or diverse chemical libraries with a wide range of linear or macrocyclic chemical molecules: peptides, non-peptide oligomers, peptidomimetics, small-molecules, and natural product-like organic molecules. Each combinatorial approach has its own unique high-throughput screening and encoding strategy. In this article, we provide a brief overview of combinatorial chemistry in drug discovery with emphasis on recently developed new technologies for design, synthesis, screening and decoding of combinatorial library. Examples of successful application of combinatorial chemistry in hit discovery and lead optimization are given. The limitations and strengths of combinatorial chemistry are also briefly discussed. We are now in a better position to truly leverage the power of combinatorial technologies for the discovery and development of next-generation drugs.

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Automated screening for small organic ligands using DNA-encoded chemical libraries

Cited by 111 publications

References 80 publications

Quantitative Assessment of Affinity Selection Performance by Using DNA‐Encoded Chemical Libraries

Quantitative Assessment of Affinity Selection Performance by Using DNA‐Encoded Chemical Libraries

DNA‐Encoded Libraries: Aryl Fluorosulfonates as Versatile Electrophiles Enabling Facile On‐DNA Suzuki, Sonogashira, and Buchwald Reactions

Combinatorial chemistry in drug discovery

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