Enzymatic Cleavage of Double-Stranded DNA-Encoded Libraries (DELs) to Single-Stranded DELs with Compounds at the 3' End: Its Application in Photo-Crosslinking Selection

Masatoshi Niwa; Jun Hayashida; Munefumi Tokugawa; Takeshi Nanya; Masako Tanabe; Naoko Honda; Takehiko Inohana; Hajime Fukano; Yukihiro Shigeta; Takeshi Kuboyama; Shin Itoh

doi:10.1002/chem.202403233

Enzymatic Cleavage of Double-Stranded DNA-Encoded Libraries (DELs) to Single-Stranded DELs with Compounds at the 3' End: Its Application in Photo-Crosslinking Selection

Chemistry. 2024 Oct 10:e202403233. doi: 10.1002/chem.202403233. Online ahead of print.

Authors

Affiliations

¹ Chemical Research Laboratories, Nissan Chemical Corporation, 10-1 Tsuboi-Nishi 2-chome, Funabashi, Chiba, Japan.
² Biological Research Laboratories, Nissan Chemical Corporation, 1470, Shiraoka, Shiraoka, Saitama, Japan.
³ Biological Research Department, Daiichi Sankyo RD Novare Co., Ltd., 1-16-13, Kitakasai, Edogawa-ku, Tokyo, Japan.
⁴ Hit Discovery Platform Laboratories, Research Function, R&D Division, Daiichi Sankyo Co., Ltd., 1-16-13, Kitakasai, Edogawa-ku, Tokyo, Japan.
⁵ Head Office, Nissan Chemical Corporation, 5-1, Nihonbashi 2-chome, Chuo-ku, Tokyo, Japan.

PMID: 39390663
DOI: 10.1002/chem.202403233

Abstract

DNA-encoded library (DEL) technology is a crucial tool in pharmaceutical research, rapidly identifying compounds that bind to a target of interest from an extensive pool of compounds. In this study, we propose a new method for generating single-stranded DELs (ssDELs) with compounds at the 3' end. The introduction of uniquely designed hairpin-shaped headpieces containing deoxyuridine (NC-HP) and the use of a cleavage enzyme facilitate the conversion from double-stranded DELs (dsDELs) to such ssDELs. Moreover, Klenow fill-in provides the dsDELs with photo-crosslinkers covalently linked to the coding region, which exhibit durability even under stringent washing conditions and enable photo-crosslinking with a high signal-to-noise ratio, as also confirmed in cell-based photo-crosslinking selections.

Keywords: DNA-encoded libraries; Drug discovery; Photoaffinity labeling; USERTM enzyme; dsDELs to ssDELs.