Identification of Structure–Activity Relationships from Screening a Structurally Compact DNA‐Encoded Chemical Library

Abstract

Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA-encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL-100K, a DNA-encoded chemical library containing 103 200 structurally compact compounds. Affinity screening experiments and DNA-sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate-specific membrane antigen and tankyrase 1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small-molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding. DNA-encoded chemical libraries (DECLs) are promisingtools for pharmaceutical hit discovery.[1] DECLs are compound collections in which each molecule is uniquely encoded by an appended DNA sequence, serving as amplifiable identification barcodes. Affinity screening of DECLs against proteins of interest enriches target-binding molecules, which are identified by high-throughput sequencing of the corresponding DNA tags. [2] DECL technology allows for the rapid screening of smallmolecule libraries of unprecedented size in a one-pot protocol, requiring only microgram quantities of the target proteins. Several groups have described DECLs of various designs and modes of preparation [3] and selections performed with DECLs have yielded ligands for diverse proteins of biological and pharmacological interest.

DNA‐encoded chemical libraries – achievements and remaining challenges

“…After a further suitable pool-andsplit procedure, a third set of chemical transformations can be performed (with building blocks depicted in green), thus generating the final compounds, consisting of three sets of building blocks. The chemical identity of the third reaction can be encoded by annealing with a set of partially complementary oligonucleotides, followed by a Klenow polymerization step [21,29,32,33]. This procedure is efficient as it makes use of one oligonucleotide for each building block used for library construction.…”

“…A comparison of Illumina and 454 sequencing technologies has been reported [39]. In some cases, it may be preferable to incubate the library with a suitably tagged protein (e.g., a biotinylated protein) in solution, with a subsequent capture step on an affinity support (e.g., streptavidin-coated solid support) [17,[31][32][33]40].…”

“…The first example described in Table 1 (entry a) derives from a structurally compact two building block single-pharmacophore DNAencoded chemical library [33]. The library contained 103'200 members formed from two sets of carboxylic acids (240 9 430).…”

DNA Encoded Library Selections and Insights Provided by Computational Simulations

“…This assumption is basic to how practitioners in the field currently triage their data. [6][7][8]19 However, the actual relationship between the counts of a particular library member and its equilibrium association constant with the target has never been explicitly described.…”

“Cap-and-Catch” Purification for Enhancing the Quality of Libraries of DNA Conjugates

“…For instance, conserved structural features were observed among series of hit compounds, 3−6 and simple structure−activity patterns could be identified from DECL screening experiments. 7 Indeed, a correlation between sequence enrichment and binding affinity may provide valuable guidance for subsequent lead optimization. However, the identification of semiquantitative structure−activity relationships using DECLs requires libraries of good quality.…”