Development of novel analytical and synthetic method for DNA-encoded library synthesis

Abstract

DNA-encoded library (DEL) technology is a powerful platform for the discovery of drugs in biological and pharmaceutical interest. In DEL synthesis, DNA tags must be exposed to various conditions, which can unexpectedly modify or destroy encoded chemical information. In this study, the fluorescence-based DNA damage assay method was developed for the DEL synthesis. The fluorescence change of PicoGreen, which is widely used a fluorescent nucleic acid stain for quantitating dsDNA, in respond to dsDNA enable quantification of that, it allowed easy access to overall integrity of DNA. For the various DEL synthesis conditions, the assay was validated through cross-checking with HPLC analysis. Especially, the fact which is not previously well known, the usage of specific ratio of organic solvent could critically induce the DNA damage was confirmed. Furthermore, the applicability of this assay was confirmed through the screening of DNA-damaging condition of on-DNA amide coupling and Pd-catalyzed on-DNA N-arylation reaction. Given its simplicity, and assay speed, this assay could be applicable in the high-throughput screening of multiple reaction conditions at an early stage in DEL synthesis. Additionally, DEL synthesis has only a few reactions show direct or potential applicability to on-DNA reactions because of DNA stability or functionally. To overcome this issue, we designed and synthesized detergent type-based novel molecules in which a PEG group was introduced into DNA intercalators such as naphthalimide and phenanthridine. We assumed the PEG-intercalator could be combined the base pairs of DNA and 1) the protection of DNA is allowed steric hindrance to prevent the reactant from accessing the DNA and 2) DNA could be soluble in the organic solvents. This strategy is expected development of useful on-DNA reactions will continue to future drug discovery.