Highly effective identification of drug targets at the proteome level by pH-dependent protein precipitation

Fully understanding the target spaces of drugs is essential for investigating the mechanism of drug action and side effects, as well as for drug discovery and repurposing. In this study, we present an energetics-based approach, termed pH-dependent protein precipitation (pHDPP), to probe the ligand-induced protein stability shift for proteome-wide drug target identification. We demonstrate that pHDPP works for a diverse array of ligands, including a folate derivative, an ATP analog, a CDK inhibitor and an immunosuppressant, enabling highly specific identification of target proteins from total cell lysates. This approach is compared to thermal and solvent-induced denaturation approaches with a pan-kinase inhibitor as the model drug, demonstrating its high sensitivity and high complementarity to other approaches. Dihydroartemisinin (DHA), a dominant derivative of artemisinin to treat malaria, is known to have an extraordinary effect on the treatment of various cancers. However, the anti-tumor mechanisms remain unknown. pHDPP was applied to reveal the target space of DHA and 45 potential target proteins were identified. Pathway analysis indicated that these target proteins were mainly involved in metabolism and apoptosis pathways. Two cancer-related target proteins, ALDH7A1 and HMGB1, were validated by structural simulation and AI-based target prediction methods. And they were further validated to have strong affinity to DHA by using cellular thermal shift assay (CETSA). In summary, pHDPP is a powerful tool to construct the target protein space to reveal the mechanism of drug action and would have broad application in drug discovery studies.

Automated summary

Understanding the target spaces of drugs is crucial in drug research and discovery. This study introduces a new energetics-based approach, pHDPP, to investigate ligand-induced protein stability shifts. The results demonstrate that pHDPP has high specificity for various ligands and can identify target proteins from cell lysates. The approach is highly sensitive and complementary to other methods. Using pHDPP, the target space of the anti-malarial drug derivative DHA was revealed, and several potential target proteins were identified. ALDH7A1 and HMGB1, two cancer-related target proteins, were validated to have strong affinity to DHA. pHDPP is a powerful tool for elucidating drug mechanisms and has broad applications in drug discovery studies.