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Letters in Drug Design & Discovery

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*

DOI: 10.2174/1570180820666230607102138

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

Page: [2352 - 2358] Pages: 7

  • * (Excluding Mailing and Handling)

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.

[1]
Wang, Z.; Kang, W.; You, Y.; Pang, J.; Ren, H.; Suo, Z.; Liu, H.; Zheng, Y. USP7: Novel Drug Target in Cancer Therapy. Front. Pharmacol., 2019, 10, 427.
[http://dx.doi.org/10.3389/fphar.2019.00427] [PMID: 31114498]
[2]
Nininahazwe, L.; Liu, B.; He, C.; Zhang, H.; Chen, Z.S. The emerging nature of Ubiquitin-specific protease 7 (USP7): a new target in cancer therapy. Drug Discov. Today, 2021, 26(2), 490-502.
[http://dx.doi.org/10.1016/j.drudis.2020.10.028] [PMID: 33157193]
[3]
Brooks, C.L.; Li, M.; Hu, M.; Shi, Y.; Gu, W. The p53–Mdm2–HAUSP complex is involved in p53 stabilization by HAUSP. Oncogene, 2007, 26(51), 7262-7266.
[http://dx.doi.org/10.1038/sj.onc.1210531] [PMID: 17525743]
[4]
Morotti, A.; Panuzzo, C.; Crivellaro, S.; Pergolizzi, B.; Familiari, U.; Berger, A.H.; Saglio, G.; Pandolfi, P.P. BCR-ABL disrupts PTEN nuclear-cytoplasmic shuttling through phosphorylation-dependent activation of HAUSP. Leukemia, 2014, 28(6), 1326-1333.
[http://dx.doi.org/10.1038/leu.2013.370] [PMID: 24317448]
[5]
Qi, S.M.; Cheng, G.; Cheng, X.D.; Xu, Z.; Xu, B.; Zhang, W.D.; Qin, J.J. Targeting USP7-mediated deubiquitination of MDM2/MDMX-p53 pathway for cancer therapy: Are we there yet? Front. Cell Dev. Biol., 2020, 8, 233.
[http://dx.doi.org/10.3389/fcell.2020.00233] [PMID: 32300595]
[6]
van der Horst, A.; de Vries-Smits, A.M.M.; Brenkman, A.B.; van Triest, M.H.; van den Broek, N.; Colland, F.; Maurice, M.M.; Burgering, B.M.T. FOXO4 transcriptional activity is regulated by monoubiquitination and USP7/HAUSP. Nat. Cell Biol., 2006, 8(10), 1064-1073.
[http://dx.doi.org/10.1038/ncb1469] [PMID: 16964248]
[7]
Colland, F.; Formstecher, E.; Jacq, X.; Reverdy, C.; Planquette, C.; Conrath, S.; Trouplin, V.; Bianchi, J.; Aushev, V.N.; Camonis, J.; Calabrese, A.; Borg-Capra, C.; Sippl, W.; Collura, V.; Boissy, G.; Rain, J.C.; Guedat, P.; Delansorne, R.; Daviet, L. Small-molecule inhibitor of USP7/HAUSP ubiquitin protease stabilizes and activates p53 in cells. Mol. Cancer Ther., 2009, 8(8), 2286-2295.
[http://dx.doi.org/10.1158/1535-7163.MCT-09-0097] [PMID: 19671755]
[8]
Chen, C.; Song, J.; Wang, J.; Xu, C.; Chen, C.; Gu, W.; Sun, H.; Wen, X. Synthesis and biological evaluation of thiazole derivatives as novel USP7 inhibitors. Bioorg. Med. Chem. Lett., 2017, 27(4), 845-849.
[http://dx.doi.org/10.1016/j.bmcl.2017.01.018] [PMID: 28108249]
[9]
Gavory, G.; O’Dowd, C.R.; Helm, M.D.; Flasz, J.; Arkoudis, E.; Dossang, A.; Hughes, C.; Cassidy, E.; McClelland, K.; Odrzywol, E.; Page, N.; Barker, O.; Miel, H.; Harrison, T. Discovery and characterization of highly potent and selective allosteric USP7 inhibitors. Nat. Chem. Biol., 2018, 14(2), 118-125.
[http://dx.doi.org/10.1038/nchembio.2528] [PMID: 29200206]
[10]
Hu, M.; Li, P.; Li, M.; Li, W.; Yao, T.; Wu, J.W.; Gu, W.; Cohen, R.E.; Shi, Y. Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell, 2002, 111(7), 1041-1054.
[http://dx.doi.org/10.1016/S0092-8674(02)01199-6] [PMID: 12507430]
[11]
Yuan, H.; Ma, Q.; Ye, L.; Piao, G. The traditional medicine and modern medicine from natural products. Molecules, 2016, 21(5), 559.
[http://dx.doi.org/10.3390/molecules21050559] [PMID: 27136524]
[12]
Yuan, Y.; Miao, Y.; Zeng, C.; Liu, J.; Chen, X.; Qian, L.; Wang, X.; Qian, F.; Yu, Z.; Wang, J.; Qian, G.; Fu, Q.; Lv, H.; Zheng, H. Small‐molecule inhibitors of ubiquitin‐specific protease 7 enhance type‐I interferon antiviral efficacy by destabilizing SOCS1. Immunology, 2020, 159(3), 309-321.
[http://dx.doi.org/10.1111/imm.13147] [PMID: 31691271]
[13]
Das, S.K.; Mahanta, S.; Tanti, B.; Tag, H.; Hui, P.K. Identification of phytocompounds from Houttuynia cordata Thunb. as potential inhibitors for SARS-CoV-2 replication proteins through GC–MS/LC–MS characterization, molecular docking and molecular dynamics simulation. Mol. Divers., 2022, 26(1), 365-388.
[http://dx.doi.org/10.1007/s11030-021-10226-2] [PMID: 33961167]
[14]
Li, X.; Zhang, X.X.; Lin, Y.X.; Xu, X.M.; Li, L.; Yang, J.B. Virtual screening based on ensemble docking targeting wild‐type p53 for anticancer drug discovery. Chem. Biodivers., 2019, 16(7), e1900170.
[http://dx.doi.org/10.1002/cbdv.201900170] [PMID: 31134745]
[15]
Ioakimidis, L.; Thoukydidis, L.; Mirza, A.; Naeem, S.; Reynisson, J. Benchmarking the reliability of qikprop. correlation between experimental and predicted values. QSAR Comb. Sci., 2008, 27(4), 445-456.
[http://dx.doi.org/10.1002/qsar.200730051]
[16]
Zhang, S.; Wang, Y.; Liu, L.; Zhao, G.; Sun, Y.; Wang, J.; Liu, F.; Wang, P.; Xu, X. Virtual screening inhibitors of ubiquitin‐specific protease 7 combining pharmacophore modeling and molecular docking. Mol. Inform., 2022, 41(7), 2100273.
[http://dx.doi.org/10.1002/minf.202100273] [PMID: 35037416]
[17]
Lu, J.; Zhao, H.; Yu, C.; Kang, Y.; Yang, X. Targeting Ubiquitin-Specific Protease 7 (USP7) in cancer: A new insight to overcome drug resistance. Front. Pharmacol., 2021, 12, 648491.
[http://dx.doi.org/10.3389/fphar.2021.648491] [PMID: 33967786]
[18]
Zhou, J.; Jinzheng, W.; Chen, C.; Yuan, H.; Wen, X.; Sun, H. USP7: Target validation and drug discovery for cancer therapy. Med. Chem., 2017, 14(1), 3-18.
[http://dx.doi.org/10.2174/1573406413666171020115539]
[19]
Qin, J.J.; Li, X.; Hunt, C.; Wang, W.; Wang, H.; Zhang, R. Natural products targeting the p53-MDM2 pathway and mutant p53: Recent advances and implications in cancer medicine. Genes Dis., 2018, 5(3), 204-219.
[http://dx.doi.org/10.1016/j.gendis.2018.07.002] [PMID: 30320185]
[20]
Qin, J.J.; Nag, S.; Voruganti, S.; Wang, W.; Zhang, R. Natural product MDM2 inhibitors: anticancer activity and mechanisms of action. Curr. Med. Chem., 2012, 19(33), 5705-5725.
[http://dx.doi.org/10.2174/092986712803988910] [PMID: 22830335]
[21]
Cabrera, J.; Saavedra, E.; del Rosario, H.; Perdomo, J.; Loro, J.F.; Cifuente, D.A.; Tonn, C.E.; García, C.; Quintana, J.; Estévez, F. Gardenin B-induced cell death in human leukemia cells involves multiple caspases but is independent of the generation of reactive oxygen species. Chem. Biol. Interact., 2016, 256, 220-227.
[http://dx.doi.org/10.1016/j.cbi.2016.07.016] [PMID: 27423764]