Open AccessDNA-Encoded Library Hit Confirmation: Bridging the Gap Between On-DNA and Off-DNA Chemistry
Author(s) -
Bing Xia,
G Joseph Franklin,
Xiaojie Lu,
Katie L Sargent Bedard,
LaShadric C. Grady,
Jennifer Summerfield,
Eric X Shi,
Bryan W. King,
Kenneth Lind,
Cynthia H. Chiu,
Eleanor Watts,
Vera Q. Bodmer,
Xiaopeng Bai,
Lisa A. Marcaurelle
Publication year - 2021
Publication title -
acs medicinal chemistry letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.065
H-Index - 66
ISSN - 1948-5875
DOI - 10.1021/acsmedchemlett.1c00156
Subject(s) - linker , dna , combinatorial chemistry , chemistry , dna sequencing , computational biology , drug discovery , computer science , biochemistry , biology , operating system
DNA-encoded library (DEL) technology is a powerful platform for hit identification in academia and the pharmaceutical industry. When conducting off-DNA resynthesis hit confirmation after affinity selection, PCR/sequencing, and data analysis, one typically assumes a "one-to-one" relationship between the DNA tag and the chemical structure of the attached small-molecule it encodes. Because library synthesis often yields a mixture, this approximation increases the risk of overlooking positive discoveries and valuable information. To address this issue, we apply a library synthesis "recipe" strategy for on-DNA resynthesis using a cleavable linker, followed by direct affinity selection mass spectrometry (AS-MS) evaluation and identification of binder(s) from the released small-molecule mixture. We validate and showcase this approach employing the receptor-interacting-protein kinase 2 (RIP2) DEL campaign. We also designed and developed two cleavable linkers to enable this method, a photocleavable linker (nitrophenyl-based) and acid-labile linker (tetrahydropyranyl ether). The strategy provides an effective means of hit identification and rapid determination of key active component(s) of the mixture.