Chemical ligation methods for the tagging of DNA-encoded chemical libraries

• Methods generating native phosphodiester ligation junctions.
• Methods generating modified ligation junctions that are polymerase-traversable.
• Methods generating readable modified ligation junctions that are not polymerase-traversable.
• Methods that have been used for the successful discovery of therapeutic protein target inhibitors.

The generation of DNA-encoded chemical libraries requires the unimolecular association of multiple encoding oligonucleotides with encoded chemical entities during combinatorial synthesis processes. This has traditionally been achieved using enzymatic ligation. We discuss a range of chemical ligation methods that provide alternatives to enzymatic ligation. These chemical ligation methods include the generation of modified internucleotide linkages that support polymerase translocation and other modified linkages that while not supporting the translocation of polymerases can also be used to generate individual cDNA molecules containing encoded chemical information specifying individual library members. We also describe which of these approaches have been successfully utilized for the preparation of DNA-encoded chemical libraries and those that were subsequently used for the discovery of inhibitors.