Agentic Literature Extraction Augments Targeted Protein Degradation Databases

arXiv:2605.11221v2 Announce Type: replace-cross Abstract: Predictive models in medicinal chemistry depend on structured assay data locked in primary publications. This bottleneck is acute in targeted protein degradation (TPD), where each assay record must combine compound identity, degradation target, recruiter, assay context, and endpoint values reported across sections, tables, and supplementary files. Existing TPD databases are manually curated and often lack assay context. We present an expert-in-the-loop large language model workflow in which a cross-validated prompt-refinement module adapts extraction instructions from scarce expert annotations. With only seven annotated molecular glue publications, the workflow achieved record-level $F_1 = 0.98$ and transferred to proteolysis-targeting chimeras (PROTACs) by terminology substitution alone ($F_1 \geq 0.93$). The resulting database, AutoTPD, contained 81% and 92% more molecular glue and PROTAC records than standardized reference datasets; expert audits found 92/100 and 33/40 new records to be correct. Applying the workflow to eligible PubMed Central open-access literature added 4,483 records from 598 publications, yielding AutoTPD+, a public, versioned database of 7,622 TPD records, including degradation assay measurements, designed for monthly updates. In a controlled surrogate model comparison, PROTAC degradation activity models trained on AutoTPD+ saw a 8.9-18.2% error reduction relative to models trained on the original PROTAC-DB data.