An Integrated in silico Approach and in vitro Study for the Discovery of Small‐Molecule USP7 Inhibitors as Potential Cancer Therapies

• Published in: ChemMedChem 2021-02, Vol.16 (3), p.555-567
• Main Authors: Kanan, Duaa, Kanan, Tarek, Dogan, Berna, Orhan, Muge Didem, Avsar, Timucin, Durdagi, Serdar
• Format: Article
• Language: English
• Subjects: Cancer; Cancer therapies; Computer applications; Crystal structure; drug design; Epigenetics; Free energy; Hematology; Inhibitors; Lead; Ligands; Molecular docking; Molecular dynamics; Optimization; Pharmacology; pharmacophores; Screening; Simulation; Solid tumors; Transcription factors; Tumor cell lines; Tumor suppressor genes; Tumors; Ubiquitin; ubiquitin specific protease 7 (USP7)
• ISSN: 1860-7179; 1860-7187
• DOI: 10.1002/cmdc.202000675

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. Seven for 7: The search for potent and nontoxic ubiquitin‐specific protease 7 (USP7) inhibitors is critical for cancer drug discovery. In this study, we used three different pharmacophore modelling strategies as tools to investigate the binding pocket of USP7 for drug‐like library screening. Eighteen hit ligands were identified and tested in biochemical assays, of which seven compounds (∼40 %) were successful at inhibiting the activity of USP7.