DNA-encoded libraries technology (DELT), also referred to as DNA-encoded chemical libraries, are valuable pharmaceutical tools for drug discovery.
The technique enables the screening of thousands of potential drugs against a target protein. These targets are chosen for their therapeutic potential. DELT identifies chemicals that interact with the target molecule, highlighting them for investigation as future drugs.
How does DELT work?
DELT works by tagging each different chemical complex with a unique DNA barcode. These complexes are kept in large libraries which, when exposed to a protein of interest, provides the opportunity for any chemicals to bind to this protein of interest.
The protein of interest is then isolated, and the DNA tags of any bound chemicals are read. Therefore, many potential chemicals can be tested against a particular molecule of interest at the same time, speeding up the process of drug discovery.
The creation of DELTs
In essence, DELT are libraries of small chemicals each attached to a unique DNA sequence that acts as a barcode. A library is made up of thousands of different small DNA barcoded chemicals. This diversity is established through the split pool method, after each round of synthesis the library is split and combined with other libraries increasing diversity. There are several methods of synthesis with the two fundamentally different methods being single-pharmacophore or dual-pharmacophore.
Single-pharmacophore libraries
Single-pharmacophore DELT libraries are created through the addition of new chemical building blocks and their attached short identifying oligonucleotides in over successive rounds of synthesis. Each chemical building block binds to the previous block and the accompanying oligonucleotides bind to the growing DNA barcode.
Within this technique, there are different methods, either recorded or templated. In the recorded method, each new chemical block and attached DNA barcode is introduced in a stepwise manner. The new chemicals bind while the barcode extends, thus creating a record of the chemical structure. Whereas in templated methods a DNA template or poly-I containing template, is used to guide the chemicals into binding in the correct order.
Dual-pharmacophore libraries
Another method of creating DNA encoded libraries is dual-pharmacophore libraries or encoded self-assembled chemical (ESAC) libraries. In this method, the library is created by hybridization between chemicals.
Each DNA barcode contains the unique oligonucleotides that identify the chemical building blocks alongside a partially complementary DNA sequence. These partially complementary DNA sequences form stable DNA-heteroduplexes with other chemical building blocks thereby creating pairs of chemical building blocks that can be identified by the two unique DNA barcodes attached.
Incubation Phase
The incubation phase is where the potential drugs bind to the protein of interest. During the incubation stage, the method the library was created with does not matter. Incubation can be accomplished in one of two ways, either as a solid or in solution. In a solid incubation, the molecule of interest is immobilized on a scaffold then immersed in the library solution. These scaffolds can be magnetic beads or resin-filled tips.
After incubation, the library solution is washed away leaving only the bound chemicals which can then be identified. In this method, the washing agent has to be carefully selected because it can interfere with the bound molecules.
Alternatively, a solution based incubation method can be used. In this method, the molecule of interest is added in solution and only the DNA barcodes that are attached to bound chemicals are amplified.
This is enabled through protein-oligonucleotide conjugates that act as a primer for bound molecules, these stabilize the DNA heteroduplex formation and facilitates the initiation of a PCR amplification step. Thereby ensuring only the DNA barcodes of the bound chemicals are amplified.
Reading the DNA barcode
To identify the chemical that is bound to the protein of interest the barcode is amplified by PCR and read by high-throughput DNA sequencing. These barcodes are then compared to the data recorded in the creation of the libraries and matched to the chemical composition.
Limitations
One major limitation is that this DELT does not select for how the chemicals interact with the protein of interest.
DELT cannot discriminate between chemicals inducing different conformational changes to the protein of interest, it can only establish that it binds. Therefore, this process can only highlight molecules for further research concerning the protein of interest.
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Conclusions
DELT is a method of screening of many potential drugs against a target protein of interest. The creation of the pharmacophore library can be by either the single or dual method, although they both create a pool of different chemicals each with their own unique DNA barcode.
By reading the DNA barcodes of the chemicals that bind to the protein of interest, the structure of the chemical can be identified. DELT can only be used to speed up the identification of potential drugs for further research as it does not differentiate between the effects the bound molecule has on the target protein, it only notes that it binds.
Despite this drawback, DELT still provides a powerful tool in drug discovery by enabling high throughput screening of potential drugs.
References
- Favalli, N., Bassi, G., Scheuermann, J., & Neri, D. (2018). DNA-Encoded Chemical Libraries: Achievements and Remaining Challenges. FEBS Letters, 592(12), 2168–2180. https://doi.org/10.1002/1873-3468.13068
- Brenner, S., & Lerner, R. A. (1992). Encoded combinatorial chemistry. Proceedings of the National Academy of Sciences of the United States of America, 89, 5381–5383.
- Castañón, J., Román, J. P., Jessop, T. C., De Blas, J., & Haro, R. (2018). Design and Development of a Technology Platform for DNA-Encoded Library Production and Affinity Selection. SLAS Discovery, 23(5), 387–396. https://doi.org/10.1177/2472555217752091
- Favalli, N., Bassi, G., Scheuermann, J., & Neri, D. (2018). DNA-Encoded Chemical Libraries: Achievements and Remaining Challenges. FEBS Letters, 592(12), 2168–2180. https://doi.org/10.1002/1873-3468.13068
- Goodnow Jr, R. (2018). DNA-Encoded Library Technology (DELT) After a Quarter Century. SLAS Discovery, 23(5), 385–386. https://doi.org/10.1177/2472555218766250
- Zimmermann, G., Rieder, U., Bajic, D., Vanetti, S., Chaikuad, A., Knapp, S., Scheuermann, J., Mattarella, M., & Neri, D. (2017). A specific and covalent JNK-1 ligand selected from an encoded self-assembling chemical library. Chemistry, 23(34), 8152–8155. https://doi.org/10.1002/chem.201701644
Further Reading