Reversible Covalent Headpiece Enables Interconversion between Double‐ and Single‐Stranded DNA‐Encoded Chemical Libraries

Abstract

The use of a proper encoding methodology is one of the most important aspects when practicing DEL technology. A "headpiece"-based double-stranded DEL encoding method is currently the most widely used for productive DEL. However, the robustness of double-stranded DEL construction conflicts with the versatility presented by singlestranded DEL applications. We here report a novel encoding method, which is based on a "reversible covalent headpiece (RCHP)". The RCHP allows reversible interconversion between double-and single-stranded DNA formats, providing an avenue to robust synthesis and allowing for the applications in distinct setups. We have validated the versatility of this encoding method with encoded self-assembled chemical library and DNA-encoded dynamic library technology. Notably, based on the RCHP-settled library construction, a unique "ternary covalent complex" mediating ligand isolation methodology against non-immobilized targets was developed.

DNA-Compatible Suzuki-Miyaura Cross-Coupling Reaction of Aryl Iodides With (Hetero)Aryl Boronic Acids for DNA-Encoded Libraries

“…During the past decade, the use of DEL technology provided a great opportunity to identify drug-like compounds that can bind selectively to a variety of target proteins ( Deng et al, 2012 ; Gentile et al, 2012 ; Disch et al, 2013 ; Samain et al, 2015 ; Seigal et al, 2015 ; Harris et al, 2016 ; Belyanskaya et al, 2017 ; Dawadi et al, 2020 ; Chamakuri et al, 2021 ). More recently, a number of different powerful applications leveraging the DEL technology have been proposed ( Huang et al, 2022 ; Sunkari et al, 2022 ; Zhao et al, 2022 ). To expand the chemical space of these DNA-Encoded Libraries, a greater variety of DNA-Compatible reactions is required.…”

3CLpro inhibitors: DEL-based molecular generation

“…This is the main reason for molecular generation, and even AIDD is still challenging to apply to the structure optimization of hit compounds for new targets. DNAencoded library (DEL) (Dickson et al, 2019;Nie et al, 2022;Song et al, 2020;Yang et al, 2022;Zhao et al, 2019;Zhao et al, 2022) Frontiers in Pharmacology frontiersin.org economically generate a large amount of affinity data for specific targets, including new target data (hundreds of billions scale) (Buller et al, 2010;Kalliokoski, 2015). Therefore, using the DEL dataset, mainly the structure-affinity relationship, for molecular generation could be a reasonable solution to the problem of efficient structural optimization for new target drug development.…”

Quantitative Validation and Application of the Photo-Cross-Linking Selection for Double-Stranded DNA-Encoded Libraries

“…The dsDELs is more stable in structure and compatible with many on-DNA chemical reactions. In dsDELs construction, encoded tags are elongated through sticky end ligation under the catalysis of T4 DNA ligase, which exhibits a high conversion rate on both solution- and solid-phase synthesis, ensuring the tag encoding efficiency and hit-decoding accuracy . Krusemark and co-workers applied photo-cross-linking to dsDELs by appending a piece of ssDNA linker to the dsDNA tag so that the photoactive group could be connected via complementary DNA pairing .…”

“…In dsDELs construction, encoded tags are elongated through sticky end ligation under the catalysis of T4 DNA ligase, which exhibits a high conversion rate on both solution-and solid-phase synthesis, ensuring the tag encoding efficiency and hit-decoding accuracy. 18 Krusemark and co-workers applied photo-cross-linking to dsDELs by appending a piece of ssDNA linker to the dsDNA tag so that the photoactive group could be connected via complementary DNA pairing. 19 This photo-cross-linking method has been applied to DEL cell selection in targeting proteins both within the cytosol and on the cell surface.…”