A Unified Hierarchical Multiscale Fusion Framework for Drug–Target Affinity Prediction: From Benchmark Performance to Nanomolar Inhibitor Discovery

ABSTRACT Accurately predicting drug–target affinity (DTA) is crucial for accelerating virtual screening and guiding lead optimization in drug discovery. However, current computational approaches face a critical trade‐off: interaction‐free models lack fine‐grained binding details, while interaction‐based models overlook higher‐order contextual and functional patterns. This limitation hinders both prediction performance and real‐world generalization. To overcome this, we propose MF‐Net, a unified hierarchical multiscale fusion framework that integrates sequence‐, atomic‐, and fragment‐level representations to model drug–target interactions across complementary scales. MF‐Net achieves state‐of‐the‐art performance on the PDBBind v2016 benchmark and demonstrates strong early enrichment across multiple virtual screening datasets. Additionally, ADP‐Glo assays confirm that the MF‐Net‐guided virtual screening pipeline identifies seven novel nanomolar inhibitors targeting hematopoietic progenitor kinase 1 (HPK1). Among them, one compound achieves sub‐nanomolar activity (IC 50 = 0.41 nM), outperforming the positive control inhibitor Sunitinib. These results demonstrate that MF‐Net not only excels on standard benchmarks but also delivers tangible lead discovery outcomes, underscoring its practical value for structure‐based drug design.