Activity-Based DNA-Encoded Library Screening

Abstract

Robotic high-throughput compound screening (HTS) and, increasingly, DNA-encoded library (DEL) screening are driving bioactive chemical matter discovery in the post-genome era. HTS enables activity-based investigation of highly complex targets using static compound libraries. Conversely, DEL grants efficient access to novel chemical diversity, although screening is limited to affinity-based selections. Here, we describe an integrated droplet-based microfluidic circuit that directly screens solid-phase DELs for activity. An example screen of a 67,100-member library for inhibitors of the phosphodiesterase autotaxin yielded 35 high-priority structures for nanomolescale synthesis and validation (20 active), guiding candidate selection for synthesis at scale (5/5 compounds with IC50s 4-10 μM). We further compared activity-based hits with those of an analogous affinity-based DEL selection. This miniaturized screening platform paves the way toward applying DELs to more complex targets (signaling pathways, cellular response), and represents a distributable approach to small molecule discovery.

Mass Activated Droplet Sorting (MADS) Enables High‐Throughput Screening of Enzymatic Reactions at Nanoliter Scale

“…Droplet microfluidics enables experiments to be performed at nanoliter to femtoliter scale, increasing throughput and decreasing unit costs of chemical and biological experimentation . A decade of research in the field has demonstrated the utility of droplet systems for a range of applications, including single cell gene expression profiling, small molecule screening, and diagnostics . Dielectrophoretic (DEP) droplet sorting has made possible the rapid recovery of selected samples for analysis .…”

DNA Encoded Libraries: A Visitor's Guide

“…Recently, Paegel and coworkers reported a microfluidics-based system that allows a one-bead-one-compound (OBOC) DEL to be selected for activity instead of merely binding ( Figure 3C). [41,42] In this system, a 67,100 member OBOC library was assembled on a bifunctional TentaGel Rink Amide support by standard split and pool methods. The library member (small molecule) is attached to the bead through a photocleavable linker and the DNA barcode is separately attached through an orthogonal linker.…”

“…To this end, activity‐based DEL selections that rely on more complex biochemical assays would be a powerful tool. Recently, Paegel and coworkers reported a microfluidics‐based system that allows a one‐bead‐one‐compound (OBOC) DEL to be selected for activity instead of merely binding (Figure C) . In this system, a 67,100 member OBOC library was assembled on a bifunctional TentaGel Rink Amide support by standard split and pool methods.…”

Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery

“…For small molecules, the Paegel group reported the combination of DNA-encoded small molecule on bead libraries with microdroplet-based sorting to enrich for ligands with the desired biochemical activity. After an initial model experiment [103] the group recently reported the identification of novel inhibitors of autotaxin in an activity based DEL screen [104]. Since microfluidic devices are also compatible with cellular systems [105,106], such functional selections can be expanded to the identification of cellular active compounds from both encoded technologies.…”