OmniBind: Proteome-Wide Promiscuity Predictions for Early-Stage Drug Screening

Abstract

Off-target binding remains a leading cause of drug attrition, yet no method exists for rapidly quantifying small-molecule promiscuity across the human proteome. Here, we define promiscuity as the mean predicted binding affinity over 15,405 human proteins and derive a specificity score combining target affinity with this proteome-wide distribution. To make this assessment tractable at scale, we introduce OmniBind, a message-passing neural network that predicts promiscuity directly from a SMILES string at about a thousand compounds per second, several orders of magnitude faster than proteome-wide profiling. OmniBind promiscuity scores correlate with experimental binding data near assay reproducibility limits. Ranking candidates by specificity rather than affinity alone improves enrichment of approved drugs across all thresholds tested, an advantage robust to the choice of affinity predictor. OmniBind fills an unoccupied niche in the early-stage screening landscape as a fast, proteome-scale complement to traditional safety panels, with accuracy that will scale as the underlying affinity predictors continue to improve.