Gardenin B, A Natural Inhibitor for USP7: In vitro Evaluation and In silico Identification

Title:Gardenin B, A Natural Inhibitor for USP7: In vitro Evaluation and In silico Identification

Volume: 20

Author(s): Siyu Zhang, Yujie Sun, Zhongyue Bai, Yifan Wang, Guangjian Zhao, Fengli Yao, Yacong Yang, Yu Hu, Xionghao Li, Fang Liu, Peng Wang and Ximing Xu*

Affiliation:

• School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, Shandong, China
• Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
• Marine Biomedical Research Institute of Qingdao, Qingdao, Shandong 266071, China

Keywords: USP7 inhibitor, natural product, enzyme activity screening, molecular docking, molecular dynamics, gardenin B.

Abstract: Background: Ubiquitin-specific protease 7 (USP7) is one of the most widely studied deubiquitin enzymes (DUBs). The protein level of USP7 is highly expressed in a variety of malignant cancers, which suggests that it is a prognostic marker of cancers and a potential drug target for oncotherapy.

Objective: The aim of this study was to identify natural and effective USP7 inhibitors, in order to understand the activation of the USP7/p53 pathway by natural inhibitors.

Methods: In this study, USP7 enzyme activity screening assay system and p53 luciferase reporter assay system have been applied for the discovery of natural USP7 inhibitors targeting the catalytic active site. Molecular docking and molecular dynamics (MD) simulation revealed the combined mechanism between USP7 with gardenin B.

Results: The gardenin B was screened from our home-lab natural products (160 flavonoids) and had cytotoxicity in HCT116 cells (IC50 = 46.28 ± 2.16 μM). Preliminary in vitro studies disclosed its antiproliferative activity and activated p53 signaling pathway in HCT116 cells. We found that the complex formed by gardenin B and 5vsk (Ledock score = -6.86, MM/GBSA score = -53.35) had the optimal binding conformation. Moreover, the MD simulation showed that the π-π interactions between gardenin B with His461 and Phe409, and the hydrogen bonds interaction between gardenin B with Leu406 played an important role in maintaining the close binding of the complexes.

Conclusion: In conclusion, gardenin B could be used as a natural product inhibitor of USP7 for further optimized design and development potential.

Cite this article as:

Zhang Siyu, Sun Yujie, Bai Zhongyue, Wang Yifan, Zhao Guangjian, Yao Fengli, Yang Yacong, Hu Yu, Li Xionghao, Liu Fang, Wang Peng and Xu Ximing*, Gardenin B, A Natural Inhibitor for USP7: In vitro Evaluation and In silico Identification, Letters in Drug Design & Discovery 2023; 20 () . https://dx.doi.org/10.2174/1570180820666230607102138