CPDP: Contrastive Protein–Drug Pre-Training for Novel Drug Discovery

Novel drug discovery and repositioning remain critical challenges in biomedical research, requiring accurate prediction of drug-target interactions (DTIs). We propose the CPDP framework, which builds upon existing biomedical representation models and integrates contrastive learning with multi-dimensional representations of proteins and drugs to predict DTIs. By aligning the representation space, CPDP enables GNN-based methods to achieve zero-shot learning capabilities, allowing for accurate predictions of unseen drug data. This approach enhances DTI prediction performance, particularly for novel drugs not included in the BioHNs dataset. Experimental results demonstrate CPDP's high accuracy and strong generalization ability in predicting novel biological entities while maintaining effectiveness for traditional drug repositioning tasks.