PharmaQA: Prompt-Based Molecular Representation Learning via Pharmacophore-Oriented Question Answering

Abstract Molecular representation plays a central role in computational drug discovery. Pharmacophores, functional groups responsible for molecular bioactivity, have been widely studied in cheminformatics. However, their incorporation into molecular representation learning, particularly in a context reasoning or generalization, remains relatively limited. To address this gap, we propose PharmaQA, a pharmacophore oriented question answering framework that formulates tailored prompts to extract context-aware molecular semantics. Rather than encoding pharmacophore features, PharmaQA learns to answer pharmacophore related queries. This design enables flexible reasoning across diverse tasks, including molecular property prediction, compound-target interaction prediction, and binding affinity estimation. Experimental results on benchmark datasets demonstrate that PharmaQA achieves competitive performance. In a ligand discovery case study using FDA-approved compounds, the framework identified potential inhibitors for three therapeutic targets, with strong docking performance. As a generalizable and modular solution, PharmaQA incorporates pharmacophoric knowledge into molecular embeddings, enhancing both predictive accuracy and interpretability in drug discovery applications.