Single-display DEL technology
The most commonly used strategy for encoding single-pharmacophore (SP) libraries is called “DNA-recorded synthesis” and relies on the use of split-and-pool synthesis which (first described for DEL construction by our lab [1] and by Praecis/GSK). Due to the ease of synthesis, such single-pharmacophore (SP) DELs are now widely used by the pharmaceutical industry and we have produced several SP DELs over the years, most currently a SP DEL of 670,752 derivatives based on 2-azido-3-iodophenylpropionic acids yielding stereo- and regiodefined compounds [2]. The scheme below illustrates the split-and-pool procedure of this recent SP DEL: We synthesized a DNA-encoded library of 670,752 derivatives (termed NF-DEL) based on 2-azido-3-iodophenylpropionic acids, with structural diversity both in terms of amino acid stereochemistry and of the regiochemistry of the phenyl ring functionalization (that is, using substituents in the ortho, meta or para positions). The scaffold was chosen based on the availability of DNA-compatible reaction conditions, which had been optimized for the uniform reactivity of different regioisomers using hundreds of different building blocks [3].
Schematic representation of the strategy used for the synthesis of a single-pharmacophore DEL, using regio- and stereoisomers of 2-azido-3-iodophenylpropionic acid. The chemical building blocks A and B and the corresponding encoding DNA portions are colour-coded in red and blue, respectively. The first set of building blocks was conjugated to the central scaffold through a triazole ring or amide bond (*), and the second set of building blocks was connected by either Suzuki or Sonogashira coupling. [2]
The NF-DEL library was screened against multiple protein targets and produced specific hits, often with Kd values in the submicromolar range. The selection fingerprints obtained for a set of protein targets of pharmaceutical relevance clearly showed the preferential enrichment of ortho-, meta- or para-regioisomers, and the respective hits were experimentally verified by affinity measurements in the absence of DNA. The discovered ligands included novel selective enzyme inhibitors and, importantly, binders to tumor-associated antigens, which enabled conditional chimeric antigen receptor T-cell activation and tumor targeting. [2]
[1] Mannocci, L., Zhang, Y., Scheuermann, J., Leimbacher, M., De Bellis, G., Rizzi, E., Dumelin, C., Melkko, S. & Neri, D.
Proc. Natl. Acad. Sci. U.S.A. 105, 17670-5. (2008).
external page https://doi.org/10.1073/pnas.0805130105
[2] Favalli, N., Bassi, G., Pellegrino, C., Millul, J., De Luca, R., Cazzamalli, S., Yang, S.,Trenner, A., Mozaffari, N.L., Myburgh, R., Moroglu, M., Conway, S.J., Sartori, A.A., Manz, M.G., Lerner, R.A., Vogt, P.K., Scheuermann, J.* , Neri, D.*
Nat. Chem. 13, 540–548 (2021).
external page https://doi.org/10.1038/s41557-021-00660-y
[3] Favalli, N., Bassi, G., Bianchi, D., Scheuermann, J.*, Neri, D.*
Bioorg. Med. Chem. 41, 116206 (2021).
external page https://doi.org/10.1016/j.bmc.2021.116206