In Silico/In Vitro Hit-to-Lead Methodology Yields SMYD3 Inhibitor That Eliminates Unrestrained Proliferation of Breast Carcinoma Cells

• Published in: International journal of molecular sciences 2020-12, Vol.21 (24), p.9549
• Main Authors: Alshiraihi, Ilham M, Jarrell, Dillon K, Arhouma, Zeyad, Hassell, Kelly N, Montgomery, Jaelyn, Padilla, Alyssa, Ibrahim, Hend M, Crans, Debbie C, Kato, Takamitsu A, Brown, Mark A
• Format: Article
• Language: English
• Subjects: Apoptosis; Apoptosis - drug effects; Binding; Breast cancer; Breast carcinoma; Breast Neoplasms - genetics; Breast Neoplasms - metabolism; Cell cycle; Cell growth; Cell Line, Tumor; Cell proliferation; Cell Survival - drug effects; Colorectal carcinoma; Drug Discovery - methods; Female; Gene expression; Genes; Hepatocellular carcinoma; Histone Deacetylase Inhibitors - chemistry; Histone Deacetylase Inhibitors - pharmacology; Histone-Lysine N-Methyltransferase - antagonists & inhibitors; Histone-Lysine N-Methyltransferase - chemistry; hit-to-lead; Humans; in silico drug development; In vitro methods and tests; Inhibitor-4; Inhibitors; Ligands; Lysine; Methyltransferase; Molecular Docking Simulation; Molecular Dynamics Simulation; Molecular Structure; Proteins; SMYD3; Structure-Activity Relationship; Tumor cell lines
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms21249549

SMYD3 is a lysine methyltransferase that regulates the expression of over 80 genes and is required for the uncontrolled proliferation of most breast, colorectal, and hepatocellular carcinomas. The elimination of SMYD3 restores normal expression patterns of these genes and halts aberrant cell proliferation, making it a promising target for small molecule inhibition. In this study, we sought to establish a proof of concept for our in silico/in vitro hit-to-lead enzyme inhibitor development platform and to identify a lead small molecule candidate for SMYD3 inhibition. We used Schrodinger software to screen libraries of small molecules in silico and the five compounds with the greatest predicted binding affinity within the SMYD3 binding pocket were purchased and assessed in vitro in direct binding assays and in breast cancer cell lines. We have confirmed the ability of one of these inhibitors, Inhibitor-4, to restore normal rates of cell proliferation, arrest the cell cycle, and induce apoptosis in breast cancer cells without affecting wildtype cell behavior. Our results provide a proof of concept for this fast and affordable small molecule hit-to-lead methodology as well as a promising candidate small molecule SMYD3 inhibitor for the treatment of human cancer.