John P Burdick, Erika M Cerna Arroyo, Samantha R Levine, Brian M Paegel

Journal of Medicinal Chemistry

DOI: 10.1021/acs.jmedchem.6c01339

Abstract

One-bead-one-compound DNA-encoded library (OBOC-DEL) technology enables synthesis and activity-based screening of diverse compound collections but requires complex microfluidic instrumentation and laborious manual bead handling. Here, we execute DEL synthesis on 2.8-μm-dia magnetic beads and encapsulate them in a functionalized polyacrylamide hydrogel to support in-gel activity assays. Magnetic-bead loading capacity was ∼10 amol of small molecule and ∼104 DNA encoding tags per bead. We developed a fully automated magnetic solid-phase synthesis using a KingFisher instrument. Bulk emulsification of DEL beads with assay reagents eliminated the need for microfluidics. Activity-based screening against Factor Xa identified enzyme inhibitors, including the positive control (rivaroxaban, incorporated into the library), which was recovered as the most abundant hit (replicate k class = 14). This ultraminiaturized platform uses commercially available automation and flow cytometry, making OBOC-DEL technology broadly accessible and distributable.