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Synthesis of DNA Encoded Libraries for Drug Discovery

DNA Encoded Libraries (DELs), often referred to as DNA Encoded Chemical Libraries (DECLs), have emerged as a powerful technique for synthesizing massive collections of small molecule libraries. Libraries are synthesized with DNA tags which serve as barcodes used to identify small molecule binders against a given target. In this article, we will delve into the world of DNA Encoded Libraries, describing both their synthesis, and encoding strategies, along with innovative approaches for their use in modern drug discovery.

Introduction to DNA Encoded Libraries in Drug Discovery

Traditionally high throughput screening of large compound collections has been the starting point for many drug discovery campaigns. This method is time-consuming and can be resource intensive if robotic setups are not utilized. Furthermore, access to large compound collections is limited, and usually only large pharmaceutical companies have access to the vast number of compounds required for comprehensive screening. One solution to the challenges associated with high-throughput screening is DELs, which offer a more efficient and cost-effective approach to screening millions of compounds in parallel. 

DELs have the unique feature of combining the power of chemistry with DNA to create libraries of compounds that can easily be screened and decoded rapidly. In DELs the compounds are linked covalently to short DNA sequences, which serve as their identifiers. This allows for fast and accurate identification of hits during screening by decoding these using next-generation sequencing (NGS). 

Early History of DNA Encoded Libraries

Following the rise of combinatorial chemistry, Brenner and Lerner conceptualized DNA encoding of small molecules in 1992 (Brenner and Lerner, 1992). Soon after, in 1993 the first chemistry was developed, in which a peptide library was constructed on glass beads carrying a DNA barcode (Nielsen, 1993). Following this no significant advancements were made until around 2004, when the first methodologies for construction of DELs without the use of beads were reported:

  • David Liu’s group introduced DNA-templated synthesis (Gartner, 2004).
  • Dario Neri’s group introduced encoded self-assembling chemical libraries (Melkko, 2004).
  • Harpin and Harbury introduced DNA routed synthesis (Harpin and Harbury, 2004).

A few years after these initial discoveries Morgan and co-workers at Praecis Pharmaceuticals (now GSK) introduced the first Split-and-Pool derived DEL, which is today the most used technology for DEL synthesis (Clark, 2009). At the same time Vipergen introduced an alternative method for DEL synthesis using 3D DNA junctions to template DEL synthesis (Hansen, 2009).

Synthesis and Encoding Strategies for DNA Encoded Libraries

Multiple techniques exist to construct DELs, and novel approaches also appear in literature today. There are, however, a set of methods that have proven powerful and are used today to construct DELs both in academia as well as in pharmaceutical companies. The most prominent methods are described below.

Split-and-Pool Synthesis of DNA Encoded libraries

Split-and-Pool Synthesis is the most widely used technique for constructing DELs (Figure 1A). Here, the library is constructed stepwise by subsequent chemical reactions and DNA encoding. Following each encoding step, the library is pooled together and mixed before it is split into new fractions for the subsequent chemical step. If N building blocks are utilized in each round (R) of split-and-pool synthesis the library will consist of NR library members. Three rounds of synthesis with 100 building blocks in each round will result in a DEL containing 106 different molecules. If one additional round is added the library will have 108 different molecules. It might seem compelling to add more rounds of synthesis, but practically once the synthesis exceeds 3-4 rounds the molecules identified will have a high molecular weight which falls outside of the drug-like chemical space. 

The major pitfall of DEL synthesis by Split-and-Pool is the risk of truncated products. As the encoding (e.g. by ligation) of DNA happens independently of the chemical reaction each individual molecule will carry the DNA-tag even if the chemical reaction has not taken place. This puts limits on which chemical reaction can take place as they need to be high yielding and not generate side products. 

Encoded Self-Assembling Chemical Libraries

Encoded Self-Assembling Chemical (ESAC) Libraries rely on single stranded DNA to form duplexes when paired with a complementary strand. This allows for the construction of sub-libraries containing a constant region which has a complementary hybridization strand, which forms duplexes with the other sub-libraries. If each sub-library contains X and Y members respectively, the total number of library members will be X×Y. ESAC libraries can be utilized in many ways allowing for a flexible screening platform:

  • Two sub-libraries can be assembled allowing for identification of de novo bidentate molecules. Though this might seem appealing, the initial follow-up work needs to merge these individual ligands together, which can be challenging.
  • A non-coding oligonucleotide can be used to make a sub-library double stranded. This will give display of one of the sub-libraries which will resemble a classic DEL.
  • Pairing a known binder with a sub-library allows for the maturation of a hit compound.

Proximity-Driven Synthesis of DNA Encoded Libraries Utilizing the YoctoReactor

To circumvent truncations and poor reactivity of some building blocks, Vipergen has developed the YoctoReactor (yR) technology (Figure 1B, Hansen 2009). The yR exploits the inherent capabilities of DNA to self-assemble into complex 3D structures. Bringing chemical building blocks into proximity, directed by DNA, allows for highly efficient synthesis of DNA encoded libraries. Chemical building blocks are attached to a DNA region, which besides encoding for the building block also contains a non-coding region which directs the yR self-assembly when mixed with complimentary building blocks allows for the self-assembly of the yR. The building blocks can be attached to the DNA via either a cleavable or non-cleavable linker specified by the attachment point to the DNA.

Initially two building block-DNA conjugates self-assembles with a helper oligo to form the yR. The two chemical building blocks are brought into proximity in the DNA junction, where they can react. Following chemical reaction, the conjugates are purified, and the DNA is ligated before the linker of one building block is cleaved. Next, the third building block can be added and reacted. Again, the conjugates are purified, before the DNA is ligated and the linker is cleaved. Finally, purification followed by primer extension yields the final display product. 

By introducing a purification step after the two building blocks have reacted, but before the DNA is ligated, this allows for unreacted building blocks to be removed from the library. This ensures that any truncated products will not be part of the final library, meaning that there will be a complete match between the DNA code and the displayed product.

DNA-recorded synthesis vs DNA-templated synthesis of DELs

Where Split-and-Pool synthesis is described as DNA-recorded, utilizing the YoctoReactor can be classified as DNA-templated DEL synthesis as the DNA sequence and formation of the 3D template drive library construction. Other methods of DNA-templated DEL synthesis exist, e.g. by Halpin and Harbury, who developed hybridization columns which can capture DNA onto Sepharose resin on which the chemical reaction can be performed (Halpin and Harbury 2004). A similar technique was developed by Li and co-workers, who introduced a universal DNA template, which can hybridize with non-specific reagent DNAs containing different sequences (Li 2013). In this way, one DNA string can be used to template the entire synthesis.

Applications of DELs in Modern Drug Discovery

DNA-Encoded Libraries (DELs) have transformed the landscape of early-stage drug discovery by enabling the rapid identification of small-molecule binders across a broad range of biological targets. Beyond their utility as a screening platform, DELs have been integrated into various stages of hit identification and optimization, with growing relevance in both academic and industrial settings.

One of the key advantages of DEL technology lies in its capacity to screen billions of compounds simultaneously using minimal amounts of target protein. This has made DELs especially attractive for targets that are challenging to access using traditional high-throughput screening (HTS) methods. These include:

  • Protein–protein interactions (PPIs): DELs have been successfully applied to identify small molecules that modulate or inhibit PPIs, a target class traditionally considered undruggable.
  • Difficult or low-abundance targets: DELs can be used even when target protein is available only in small quantities, such as membrane proteins, nuclear receptors, and multi-subunit complexes.
  • Fragment-based approaches: DELs can be used to explore vast chemical space with small, fragment-like building blocks, which can be further optimized post-screening.

Advancing from Hits to Leads

Once potential binders are identified through DEL selection and decoding, off-DNA synthesis of hits enables their validation in orthogonal biochemical or biophysical assays. Many companies have incorporated DEL-derived hits into their lead optimization workflows, where these compounds undergo structure–activity relationship (SAR) exploration and pharmacological profiling.

DELs have also played a role in:

  • Allosteric modulator discovery, where hits bind to non-canonical sites
  • Covalent inhibitor development, through libraries containing reactive electrophiles

Structure-based drug design, especially when DEL hits are co-crystallized with targets

Target Class Versatility

DELs have been successfully used across various target classes, including:

  • Kinases
  • G-protein-coupled receptors (GPCRs)
  • Proteases
  • Epigenetic regulators
  • RNA-binding proteins

This versatility makes DELs a powerful complementary approach to traditional screening platforms, especially when combined with structural biology or AI-driven hit expansion.

Conclusion

DNA-Encoded Libraries (DELs) represent a transformative advancement in early-stage drug discovery, offering an efficient and scalable means to explore vast chemical space. Through diverse synthesis strategies such as split-and-pool and proximity-driven approaches like Vipergen’s YoctoReactor, DELs enable the rapid identification of small-molecule binders against a wide range of biological targets. Each method offers unique advantages—split-and-pool synthesis provides unparalleled diversity, while proximity-driven methods offer higher fidelity and reduced truncation artifacts. Together, these complementary technologies allow researchers to tailor DEL campaigns to specific targets, chemical constraints, or discovery goals. As DEL platforms continue to evolve, they are expected to play an increasingly central role in hit discovery, target validation, and the acceleration of lead optimization efforts.

References

  • Brenner, S. and Lerner, R. A. (1992), Encoded combinatorial chemistry. Proc. Natl. Acad. Sci. USA, 89, 5381-5383. doi.org/10.1073/pnas.89.12.5381
  • Gartner, Z. J. et. al. (2004), DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles. Science, 305, 1601-1605. doi.org/10.1126/science.1102629
  • Halpin, D. R. and Harbury, R. B. (2004), DNA Display I. Sequence-Encoded Routing of DNA Populations, PLoS Biology, 2 (7), 1015-1021. doi.org/10.1371/journal.pbio.0020173
  • Halpin, D. R. and Harbury, R. B. (2004), DNA Display II. Genetic Manipulation of Combinatorial Chemistry Libraries for Small-Molecule Evolution, PLoS Biology, 2 (7), 1022-1030. doi.org/10.1371/journal.pbio.0020174
  • Hansen, M. H. et. al. (2009), A Yoctoliter-Scale DNA Reactor for Small-Molecule Evolution, J. Am. Chem. Soc., 131 (3), 1322-1327. doi.org/10.1021/ja808558a
  • Li, Y., et. al. (2013), Multistep DNA-Templated Synthesis Using a Universal Template. J. Am. Chem. Soc., 135, 17727-17730. doi.org/10.1021/ja409936r
  • Melkko, S. et. al. (2004), Encoded Self Assembling Chemical Libraries. Nat. Biotechnol., 22, 568-574. doi.org/10.1038/nbt961
  • Nielsen, J., Brenner, S., Janda, K. D. (1993), Synthetic methods for the implementation of encoded combinatorial chemistry. J. Am. Chem. Soc., 115, 9812-9813. doi.org /10.1021/ja00074a063

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