ADAPT-M: a workflow for rapid, quantitative in vitro measurements of enriched protein libraries.

Abstract

Protein-protein interactions underpin most cellular processes, and engineered binders present powerful tools for probing biology and developing novel therapeutics. However, scalable, quantitative characterization of large numbers of candidates remains a major bottleneck. Here we show that ADAPT-M (Affinity Determination by Adaptation of ProTein binders for Microfluidics) enables rapid, parallel measurement of binding affinities and dissociation behavior directly from enriched display libraries in under one week, without requiring gene synthesis or hands-on protein purification. Applied to a computationally designed library targeting the SARS-CoV-2 Omicron BA.1 receptor binding domain, ADAPT-M recovered most highly enriched variants and revealed that many display-enriched binders lacked measurable binding in vitro, highlighting limitations of screening alone. ADAPT-M enabled quantitative characterization of dozens of binders in parallel and selection of lead candidates for structural analysis. Unexpectedly, structural and mutational studies revealed that designed binding interfaces were preserved despite engaging alternative epitopes. By bridging screening and scalable in vitro validation, ADAPT-M accelerates protein binder discovery and supports data-driven protein engineering.