A DNA-Encoded Library, or DEL, is a technology used to accelerate the initial stages of drug discovery. It consists of a vast collection of small chemical compounds, potentially numbering in the billions or trillions. Each of these distinct molecules is physically attached to a short, unique strand of DNA that functions as an identifying barcode for its specific chemical partner. This direct linkage is the core principle of a DEL. To conceptualize this, one can imagine a library containing billions of books, where each book has a unique barcode that instantly reveals its title and contents.
Building a DNA-Encoded Library
The construction of a DNA-Encoded Library relies on a chemical strategy known as “split-and-pool” synthesis. This method allows for the creation of immense molecular diversity from a manageable number of starting materials. The process begins with a common chemical starting point, or scaffold, which is already attached to an initial DNA oligonucleotide that serves as the first part of the barcode.
This initial collection is then split into numerous separate portions, for instance, into the individual wells of a laboratory plate. In each of these wells, a distinct chemical building block is chemically attached to the scaffold. At the same time, a unique DNA tag, specific to that building block, is attached to the growing DNA strand.
After the chemical and DNA tagging reactions are complete, all the separate portions are recombined into a single pool. The mixture now contains a variety of new molecules, each with a DNA barcode reflecting its specific synthetic history. This “split-add-tag-pool” cycle is then repeated multiple times. With each cycle, the number of unique compounds in the library grows exponentially, and a process with just a few cycles can generate a library containing billions of distinct molecules.
The Affinity Screening Process
Once a library is built, it is used to find chemical compounds that interact with a specific biological target, such as a protein implicated in a disease. This search is performed through affinity-based selection, which isolates molecules based on their ability to bind to the target. The process begins by incubating the entire library with a purified version of the protein target within a single tube.
During this incubation, molecules from the library that have a natural chemical affinity for the protein target will physically bind to it. The vast majority of molecules will not have this affinity and will remain free-floating in the solution. To separate the binders from the non-binders, the mixture is subjected to a series of washing steps. These washes rinse away all molecules that failed to attach, leaving only the target and the library members bound to it.
The final stage is to identify these successful binders, or “hits.” The molecules are released from the protein target, and their DNA barcodes are analyzed. The DNA is first amplified using Polymerase Chain Reaction (PCR) to create millions of copies. These copies are then analyzed with high-throughput DNA sequencing, which reads the barcodes to reveal the chemical structure of the successful molecules.
Comparison to High-Throughput Screening
DNA-Encoded Library technology presents a different approach to drug discovery compared to High-Throughput Screening (HTS). The primary distinction is the scale of the screening effort. While HTS campaigns might test one to two million compounds, DELs allow researchers to screen billions or trillions of molecules simultaneously.
This difference in scale is enabled by the format. HTS requires each compound to be stored and tested in a separate well of a multi-well plate, necessitating extensive robotics. In contrast, a DEL screening experiment is performed with the entire collection mixed in a single tube. This single-pot approach reduces the amount of resources required, particularly the purified protein target, and is faster and more cost-effective.
The method of hit identification also differs. In HTS, a “hit” is identified directly when a desired biological activity is observed in a specific well, so scientists immediately know the compound’s structure. With DELs, the hit is identified indirectly by sequencing its DNA barcode. This means the corresponding chemical compound must be synthesized anew, without the DNA tag, to confirm its activity.
Impact on Drug Discovery
The development of DNA-Encoded Libraries has had a significant impact on modern drug discovery. The technology has been widely adopted across the pharmaceutical and biotechnology sectors, becoming a mainstream tool for finding starting points for new medicines. This expanded search increases the probability of discovering novel molecules that can interact with challenging disease targets.
The influence of this technology can be seen in its successful application by major pharmaceutical companies. For instance, early work at institutions like GlaxoSmithKline led to the identification of potent inhibitors for various protein targets, validating the technology’s utility. These successes demonstrated that DELs could provide high-quality lead compounds that could be optimized into clinical drug candidates.
By expanding the scope of chemical screening, DELs have changed the approach to early-stage discovery. This has opened new avenues for therapeutic intervention and continues to accelerate the identification of chemical probes to study biology and starting points for the development of future medicines.