Quantitative structure-activity relationship (QSAR) and drug-target interaction (DTI) prediction are both commonly used in drug discovery. Collaboration among pharmaceutical institutions can lead to better performance in both QSAR and DTI prediction. However, the drug-related data privacy and intellectual property issues have become a noticeable hindrance for inter-institutional collaboration in drug discovery.We have developed two novel algorithms under secure multiparty computation (MPC), including QSARMPC and DTIMPC, which enable pharmaceutical institutions to achieve high-quality collaboration to advance drug discovery without divulging private drug-related information. QSARMPC, a neural network model under MPC, displays good scalability and performance, and is feasible for privacy-preserving collaboration on large-scale QSAR prediction. DTIMPC integrates drug-related heterogeneous network data and accurately predicts novel DTIs, while keeping the drug information confidential. Under several experimental settings that reflect the situations in real drug discovery scenarios, we have demonstrated that DTIMPC possesses significant performance improvement over the baseline methods, generates novel DTI predictions with supporting evidence from the literature, and shows the feasible scalability to handle growing DTI data. All these results indicate that QSARMPC and DTIMPC can provide practically useful tools for advancing privacy-preserving drug discovery.The source codes of QSARMPC and DTIMPC are available on the GitHub: https://github.com/rongma6/QSARMPC_DTIMPC.git.Supplementary data are available at Bioinformatics online.