DNA-encoded chemical libraries - achievements and remaining challenges

Abstract

DNA-encoded chemical libraries (DECLs) are collections of compounds, individually coupled to DNA tags serving as amplifiable identification barcodes. Since individual compounds can be identified by the associated DNA tag, they can be stored as a mixture, allowing the synthesis and screening of combinatorial libraries of unprecedented size, facilitated by the implementation of split-and-pool synthetic procedures or other experimental methodologies. In this review, we briefly present relevant concepts and technologies, which are required for the implementation and interpretation of screening procedures with DNA-encoded chemical libraries. Moreover, we illustrate some success stories, detailing how novel ligands were discovered from encoded libraries. Finally, we critically review what can realistically be achieved with the technology at the present time, highlighting challenges and opportunities for the future.

Keywords: DNA; DNA-encoded chemical libraries; combinatorial chemistry; drug discovery; high-throughput DNA sequencing.

Figure 1

Schematic representation of (a) a single-pharmacophore DNA-encoded chemical library and (b) of a dual pharmacophore DNA-encoded chemical library. In the scheme, the building blocks (triangles and circles) and the corresponding DNA-barcodes (rectangles) are depicted using the same color.

Figure 2

(a) Schematic representation of strategies for DNA-recorded synthesis. In the first reaction cycle, chemical building blocks are encoded by direct coupling with 5' amino-modified oligonucleotides containing individual coding DNA-sequences (Code “A”). After a split & pool step which introduces the second set of building blocks B the DNA-code "B" is introduced by enzymatic DNA-ligation. In the last reaction cycle, the introduced building can be encoded by annealing with a partially-complementary oligonucleotide containing code "C", followed by the fill-in of the DNA-heteroduplex by Klenow polymerase. (b) In a variation of the encoding procedures described in (a), the organic moiety is connected by a linker (termed “headpiece”) to a double-strand DNA which is extended by subsequent ligation with coding DNA heteroduplexes, in parallel with the split-and-pool based synthesis. (c) In DNA-templated synthesis, pre-formed DNA-template molecules containing coding parts are annealed with code-specific reagent oligonucleotides, which mediate the transfer of the chemical moiety by its high effective molarity. After cleavage of the chemical moiety from the reagent oligonucleotide, it can be removed and the template undergo a new round of template-based synthesis. (d) In a further implementation of this procedure, a template containing poly-inosine (poly-I) segments allows the annealing with various code-building block oligonucleotide conjugates. The building blocks are then transferred from the code-building block oligonucleotide conjugates to the main oligonucleotide template which, after hybridization, is encoded by ligation. (e) In the ESAC approach, two partially complementary sub-libraries A and B are combinatorially assembled. A Klenow fill-in reaction facilitates the transfer of code B onto the complementary strand, bearing code A. Following target-based selection, PCR amplification and DNA sequencing allows the identification of the preferentially enriched pairs of building blocks.

Figure 3

Fingerprints of Naïve libraries (left panels) composed of (a) two sets of building blocks or (b) three sets of building blocks are compared with the same libraries selected against (a) horseradish peroxidase (HRP) or (b) carbonic anhydrase (CA) IX (right panels).