Bing Xia; G. Joseph Franklin; Xiaojie Lu; Katie L. Bedard; LaShadric C. Grady; Jennifer D. Summerfield; Eric X. Shi; Bryan W. King; Kenneth E. Lind; Cynthia Chiu; Eleanor Watts; Vera Bodmer; Xiaopeng Bai; Lisa A. Marcaurelle
ACS Med. Chem. Lett., 2021, 12(7), 1166-1172
https://doi.org/10.1021/acsmedchemlett.1c00156

Abstract

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.