Chemi-Proteome Language Attention Network Empowers Fragment-Based Ligand Interactome and Binding Sites Discovery with Evidence

Abstract

Deep learning has accelerated drug discovery, yet most existing models are trained using in vitro affinity datasets and consequently remain disconnected from the cellular context in which functional ligand-protein interactions occur. This limitation hinders the ability to reflect the complexity of native interactomes and characterize biological responses to molecular perturbation. Here we introduce C-PLANK (Chemi-Proteome Language Attention NetworK), a deep learning framework trained on fragment-protein interactions profiled directly in living cells using fully functionalized fragment (FFF) chemoproteomics. C-PLANK combines physicochemical embeddings with a bilinear attention network (BAN) to model both global cellular context and local residue-atom interactions, generating interpretable interaction fingerprints. Particularly, C-PLANK incorporates Cellular Interaction State Index (CISI), a systems-level evidential metric that contextualizes the biological plausibility of each predicted interaction against the global cellular interaction landscape. Across 431 ligand interactomes curated from eight independent chemoproteomic studies, C-PLANK consistently outperformed current state-of-the-art interaction prediction frameworks under both random and cold-protein evaluation settings. The inferred interaction fingerprints aligned with orthogonal evidence from structure-based pocket predictions, co-crystal structures, and cellular binding-site annotations. C-PLANK further generalized to unseen ligands. In a cellular target-focused discovery campaign, C-PLANK identified a previously unrecognized ligand that was subsequently advanced into an active chemical probe acting as a SIRT3 agonist in cellular assays. By learning directly from cellular chemoproteomics, C-PLANK moves beyond isolated interaction prediction toward cellular interaction-state modelling, establishing a computational foundation for future digital-twin frameworks in drug discovery.