DNA‐Encoded Dynamic Combinatorial Chemical Libraries

Abstract

Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions.

Dynamic Combinatorial Chemistry: A New Methodology Comes of Age

“…In addition, innovative workup procedures should be explored further, for example involving the separation of unbound and target‐bound ligand fractions ,,. Also, the combination of DCC with DNA‐encoded approaches or the integration of tdDCC into broader drug discovery strategies might be of value. In summary, to exploit the full potential of tdDCC for drug discovery, the future focus should aim on method development, that is, a more detailed account of sample preparation, evaluation, and overall rationale.…”

Protein‐Templated Dynamic Combinatorial Chemistry: Brief Overview and Experimental Protocol

“…Table 1. [28] Therefore, only articles using an adaptive approach are listed, pre-equilibrated DCC examples are omitted.…”

“…[28] In this method, the protein is incubated together with a lipophilic dye, for example sypro orange. [28] In this method, the protein is incubated together with a lipophilic dye, for example sypro orange.…”

Screening of Three Transition Metal‐Mediated Reactions Compatible with DNA‐Encoded Chemical Libraries

“…[1 -11] Libraries containing billions of compounds from a relatively small number of building blocks (e. g., few thousand chemical compounds) can be constructed using a variety of different experimental approaches, such as pool-and-split methodologies, [12] DNA-templated chemical reactions with preformed oligonucleotide derivatives, [13 -15] or the use of encoded self-assembling strategies. [16][17][18][19][20][21] The attractiveness of encoding chemical compounds with DNA fragments relate to the possibility of constructing and storing large libraries as a mixture, that can be interrogated by affinity capture procedures on immobilized proteins of interest, followed by decoding, using high-throughput DNA sequencing. [12,22,23] Indeed, the identity and relative frequency of each compound in the library (e. g., before and after a screening experiment) can be directly retrieved from the results of a DNA sequencing experiment, since each library member is encoded by a distinctive DNA fragment.…”