Abstract: The disclosed method directly conjugates one of a DNA-based barcode, a peptide-based barcode, or a fluorescent bead based-barcode onto small molecule whereby existing libraries of chemical entities may be modified through the barcoding of small molecules. The process utilizes a linker to link any molecule with an aminated molecule. A barcoded small molecule library is created through the combination of diazirine used to attach small molecules to DNA, peptide, and fluorescent microspheres followed by radiation. The exposed molecules are then photo-linked resulting in immobilization to the barcodes followed by complementary sequencing. This tri-modal barcoding system integrates with phage display and imaging-based analyzers to accelerate drug discovery by identifying novel protein-ligand interactions efficiently. The resulting barcoded library may be bound with biotin through the use of an inert substrate followed by incubation and then washing to remove unbound material.

Abstract: A system and method for the high throughput screening of small molecule-protein interactions includes first immobilizing selected small molecules on a solid matrix. Immobilization is preferably made by photo affinity labelling in which a linker used to bind the small molecule to the matrix. A cDNA library is established from a broad array of human tissues. The tissue mRNA is converted to cDNA and transferred to a phage genome to make a phage display library which is mixed with small molecules coupled to the beads and incubated. The incubation mixture is washed to remove unbound phage including non-specific and weak binders. The bound phage are amplified and are used in the next round of biopanning. The biopanning cycles are repeated followed by PCR of individual plaques selected from the final biopanning round. The PCR products are barcoded from each small molecule experiment and are pooled followed by Nextgen sequencing.