Huiyong Ma; James B. Murray; Huadong Luo; Xuemin Cheng; Qiuxia Chen; Chao Song; Cong Duan; Ping Tan; Lifang Zhang; Jian Liu; Barry A. Morgan; Jin Li; Jinqiao Wan; Lisa M. Baker; William Finnie; Lucie Guetzoyan; Richard Harris; Nicole Hendrickson; Natalia Matassova; Heather Simmonite; Julia Smith; Roderick E. Hubbard; Guansai Liu
RSC Med. Chem., 2022, 13, 1341-1349
https://doi.org/10.1039/D2MD00197G

Abstract

We describe a novel approach for screening fragments against a protein that combines the sensitivity of DNA-encoded library technology with the ability of fragments to explore what will bind. Each of the members of the library consists of a fragment which is linked to a photoactivatable diazirine moiety. Split and pool synthesis combines each fragment with a set of linkers with the version of the library reported here containing some 70k different compounds, each with an individual DNA code. Incubation of the library with a protein sample is followed by photoactivation, washing and subsequent PCR and sequencing which allows the individual fragment hits to be identified. We illustrate how the approach allows successful hit fragment identification using only microgram quantities of material for two targets. PAK4 is a kinase for which conventional fragment screening has generated many advance leads. The as yet undrugged target, 2-epimerase, presents a more challenging active site for identification of hit compounds. In both cases, PAC-FragmentDEL identified fragments validated as hits by ligand-observed NMR measurements and crystal structure determination of off-DNA sample binding to the proteins.