Bahcesehir University School of Medicine, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey.
Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, Bahcesehir University School of Medicine, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey.
ChemMedChem. 2021 Feb 4;16(3):555-567. doi: 10.1002/cmdc.202000675. Epub 2020 Nov 12.
The ubiquitin-specific protease 7 (USP7) is a highly promising well-validated target for a variety of malignancies. USP7 is critical in regulating the tumor suppressor p53 along with numerous epigenetic modifiers and transcription factors. Previous studies showed that USP7 inhibitors led to increased levels of p53 and anti-proliferative effects in hematological and solid tumor cell lines. Thus, this study aimed to identify potent and safe USP7 hit inhibitors as potential anti-cancer therapeutics via an integrated computational approach that combines pharmacophore modeling, molecular docking, molecular dynamics (MD) simulations and post-MD free energy calculations. In this study, the crystal structure of USP7 has been extensively investigated using a combination of three different chemical pharmacophore modeling approaches. We then screened ∼220.000 drug-like small molecule library and the hit ligands predicted to be nontoxic were evaluated further. The identified hits from each pharmacophore modeling study were further examined by 1-ns short MD simulations and MM/GBSA free energy analysis. In total, we ran 1 ns MD simulations for 1137 selected on small compounds. Based on their average MM/GBSA scores, 18 ligands were selected for 50 ns MD simulations along with one highly potent USP7 inhibitor used as a positive control. The in vitro enzymatic inhibition assay testing of our lead 18 molecules confirmed that 7 of these molecules were successful in USP7 inhibition. Screening results showed that within the used screening approaches, the most successful one was structure-based pharmacophore modeling with the success rate of 75 %. The identification of potent and safe USP7 small molecules as potential inhibitors is a step closer to finding appropriate effective therapies for cancer. Our lead ligands can be used as a scaffold for further structural optimization and development, enabling further research in this promising field.
泛素特异性蛋白酶 7（USP7）是一个极具潜力和经过充分验证的多种恶性肿瘤的靶点。USP7 在调节肿瘤抑制因子 p53 以及许多表观遗传修饰剂和转录因子方面起着关键作用。先前的研究表明，USP7 抑制剂可导致血液系统和实体肿瘤细胞系中 p53 水平升高和抗增殖作用。因此，本研究旨在通过结合药效团建模、分子对接、分子动力学（MD）模拟和 MD 后自由能计算的综合计算方法，鉴定有效的 USP7 高活性抑制剂，作为潜在的抗癌治疗药物。在这项研究中，USP7 的晶体结构已通过三种不同的化学药效团建模方法进行了广泛研究。然后，我们筛选了约 220,000 种药物样小分子库，并进一步评估了预测为非毒性的命中配体。从每个药效团建模研究中识别出的命中化合物通过 1 ns 短 MD 模拟和 MM/GBSA 自由能分析进一步检查。总共，我们对 1137 种选定的小分子化合物进行了 1 ns MD 模拟。根据它们的平均 MM/GBSA 评分，选择了 18 个配体进行 50 ns MD 模拟，同时选择了一个高效的 USP7 抑制剂作为阳性对照。我们的先导化合物 18 个分子的体外酶抑制测定证实，其中 7 个分子成功抑制了 USP7。筛选结果表明，在所使用的筛选方法中，最成功的是基于结构的药效团建模，成功率为 75%。鉴定有效的和安全的 USP7 小分子作为潜在抑制剂是朝着寻找合适的癌症有效治疗方法迈出的一步。我们的先导配体可以用作进一步结构优化和开发的支架，为这一有前途的领域的进一步研究提供了可能。
