High-throughput screening (HTS) for compound libraries is an essential element for drug discovery, disease biomarker identification, etc. One of the key challenges in HTS bioassays is to establish a reliable and efficient encoding technique for identifying a leading compound among a large compound library. In this context, there are still some challenges to establish a simple and efficient encoding method for HTS bioassays. First of all, a practically sufficient number of unique codes must be generated to encode a huge number of compound candidates.[1,2] Moreover, the encoding and decoding process needs to be easy and straightforward.
We developed a ready-to-read on-bead peptide encoding method for high-throughput screening bioassays. With two-dimensional surface-enhanced Raman scattering nano-identifiers (2D-SERS IDs) which are concurrently labelled with two SERS codes (coupling steps and kinds of amino acid), we could possibly generate more than 10 trillion codes with only 30 Raman label compounds. The proposed encoder uses two-dimensional surface enhanced Raman scattering (SERS) nano-identifiers (2D-SERS IDs). The 2D-SERS IDs were concurrently labelled with two kinds of Raman label compounds (RLCs) having well separated spectral bands each other; one is for a coupling step code and another is for a code of amino acid (AA) at that coupling step. On the basis of this 2D-SERS encoding strategy, in theory, by using only 30 kinds of RLCs (20 AA codes and 10 coupling step codes), all possible combinations of decamer peptide (over 10 trillion peptides) could be completely and uniquely encoded. After synthesis of a compound library with this encoding process, conducting bioassays and decoding for screening leads an easy identification of each peptide sequence on the beads with an only single Raman scanning on the surface of 2D-SERS IDs encoded polymer micro-bead without a prior preparation. As a proof of concept, the HTS bioassay for a peptide library on solid supports which was encoded with 2D-SERS IDs was performed to identify on-bead ligand-binding affinities against streptavidin.