Abstract：
The equilibrium of cellular protein levels is pivotal for maintaining normal physiological functions. USP5 belongs to the deubiquitination enzyme (DUBs) family, controlling protein degradation and preserving cellular protein homeostasis. Aberrant expression of USP5 is implicated in a variety of diseases, including cancer, neurodegenerative diseases, and inflammatory diseases. In this paper, a multi-level virtual screening (VS) approach was employed to target the zinc finger ubiquitin-binding domain (ZnF-UBD) of USP5, leading to the identification of a highly promising candidate compound 0456-0049. Molecular dynamics (MD) simulations were then employed to assess the stability of complex binding and predict hotspot residues in interactions. The results indicated that the candidate stably binds to the ZnF-UBD of USP5 through crucial interactions with residues ARG221, TRP209, GLY220, ASN207, TYR261, TYR259, and MET266. Binding free energy calculations, along with umbrella sampling (US) simulations, underscored a superior binding affinity of the candidate relative to known inhibitors. Moreover, US simulations revealed conformational changes of USP5 during ligand dissociation. These insights provide a valuable foundation for the development of novel inhibitors targeting USP5.
摘要：
细胞蛋白质水平的平衡是维持正常生理功能的关键。USP5属于去泛素化酶（DUBs）家族，控制蛋白质降解和保持细胞蛋白质稳态。USP5的异常表达与多种疾病有关。包括癌症,神经退行性疾病，和炎症性疾病。在本文中,采用多水平虚拟筛选(VS)方法靶向USP5的锌指泛素结合域(ZnF-UBD),从而鉴定出极具前景的候选化合物0456-0049.然后采用分子动力学（MD）模拟来评估复合物结合的稳定性并预测相互作用中的热点残基。结果表明，候选物通过与残基ARG221，TRP209，GLY220，ASN207，TYR261，TYR259和MET266的关键相互作用稳定地结合USP5的ZnF-UBD。结合自由能计算，随着伞式采样(美国)模拟，强调了候选物相对于已知抑制剂的优异结合亲和力。此外，US模拟揭示了配体解离过程中USP5的构象变化。这些见解为开发靶向USP5的新型抑制剂提供了有价值的基础。
