NECEEM-Based technology for selection of drug leads from libraries of DNA-Encoded small molecules

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Regulatory proteins are major therapeutic targets; finding small molecules which bind those proteins is the mainstream in modern drug discovery. Selection of protein binders from combinatorial libraries of small molecules is a promising addition to slow and expensive rational drug design. Since such selection relies on a random chance, its success improves with increasing diversity of the library. Libraries of small molecules with practically an unlimited number of unique structures can be synthesized by a split-and-pool method. However, selection of protein binders from highly-diverse libraries of small molecules is challenging due to the lack of compatible structure-identification tools. A solution was recently found through the creation of libraries of DNA-encoded small molecules (LDESMs) in which the DNA tag is used to identify the small-molecule structure. LDESMs of more than ten billion unique compounds have been successfully synthesized. In a currently used selection method using LDESMs, a target protein is immobilized on the surface and the surface is exposed to contact with a LDESM. After binding equilibrium is approached, the compounds that do not bind the surface are washed out and the ones that are bound to the surface are collected and their structures are identified through sequencing the DNA tags. The efficiency of this approach is, however, dramatically affected by non-specific binding of compounds to the surface leading to unacceptably-high "chemical noise". We recently invented a solution-based (rather than surface-based) approach for selection of protein binders from highly-diverse libraries. Our approach is called non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM). We hold 3 patents for practical applications of NECEEM for drug development. Here we propose to reduce to practice the application of NECEEM for selection of protein binders from LDESMs. All commercially unavailable materials, including LDESMs and targets, will be provided by an industrial collaborator. We will conduct a series of tests to demonstrate outstanding performance of NECEEM in application to LDESMs. This work is necessary for our efforts to commercialize the NECEEM technology.