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

Ilham M Alshiraihi; Dillon K Jarrell; Zeyad Arhouma; Kelly N Hassell; Jaelyn Montgomery; Alyssa Padilla; Hend M Ibrahim; Debbie C Crans; Takamitsu A Kato; Mark A Brown

doi:10.3390/ijms21249549

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

Int J Mol Sci. 2020 Dec 15;21(24):9549. doi: 10.3390/ijms21249549.

Authors

Ilham M Alshiraihi^{1

2}, Dillon K Jarrell³, Zeyad Arhouma^{1

4}, Kelly N Hassell¹, Jaelyn Montgomery⁵, Alyssa Padilla⁵, Hend M Ibrahim^{6

7

8}, Debbie C Crans^{1

4}, Takamitsu A Kato^{1

7}, Mark A Brown^{1

8

9

10

11}

Affiliations

¹ Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA.
² Department of Biology, University of Tabuk, Tabuk 47713, Saudi Arabia.
³ Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045-7109, USA.
⁴ Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA.
⁵ Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA.
⁶ Department of Medical Biochemistry, Zagazig University, Zagazig 44511, Egypt.
⁷ Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523-1618, USA.
⁸ Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523-1678, USA.
⁹ Epidemiology Section, Colorado School of Public Health, Fort Collins, CO 80523-1612, USA.
¹⁰ Institute for Learning and Teaching, Colorado State University, Fort Collins, CO 80523-1052, USA.
¹¹ Department of Ethnic Studies, Colorado State University, Fort Collins, CO 80523-1790, USA.

Abstract

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.

Keywords: Inhibitor-4; SMYD3; apoptosis; breast cancer; cell cycle; cell proliferation; hit-to-lead; in silico drug development; methyltransferase.

MeSH terms

Apoptosis / drug effects
Breast Neoplasms / genetics
Breast Neoplasms / metabolism
Cell Line, Tumor
Cell Survival / drug effects
Drug Discovery* / methods
Female
Histone Deacetylase Inhibitors / chemistry*
Histone Deacetylase Inhibitors / pharmacology
Histone-Lysine N-Methyltransferase / antagonists & inhibitors
Histone-Lysine N-Methyltransferase / chemistry*
Humans
Molecular Docking Simulation*
Molecular Dynamics Simulation*
Molecular Structure
Structure-Activity Relationship

Substances

Histone Deacetylase Inhibitors
Histone-Lysine N-Methyltransferase
SMYD3 protein, human