Identifying USP1 Inhibitors with Allosteric Effect on Its Triple Catalytic Center through Virtual Screening

Previous studies have shown that downregulation of ubiquitin-specific protease 1 (USP1) can inhibit cell proliferation and promote apoptosis, indicating that targeting USP1 with drugs is a potential treatment for cancer, especially breast and ovarian cancer. In this study, we performed virtual screening on a database containing about 1.37 million molecules using the pharmacophore model, multiple precision molecular docking algorithms, molecular mechanics/generalized born surface area (MM/GBSA), strain energy, and ADMET screening methods. We found that Z28551960, Z423064076, Z1037335610, and Z1129923146 compounds showed excellent performance in terms of binding energy with USP1, ADMET property evaluation, and binding dynamics with USP1, had high potential as USP1 inhibitors, and were identified as hits in virtual screening. In addition, we demonstrated for the first time through molecular dynamics simulations that those molecules can enhance the structural flexibility of the USP1 protein and reduce its structural compactness, providing a basis for protein conformational changes. In summary, our discovery of potential USP1 inhibitors with novel scaffolds provides a theoretical basis for further development of USP1 inhibitors.