Discovery of ERα‐Targeting Phytochemicals With In Vitro Cytotoxicity and Computational Prediction of Y537S Mutant Inhibition

Abstract

Breast cancer is known as a frequently diagnosed malignancy in women. Over 70% of cases express estrogen receptor α (ERα). The activation of ERα promotes tumor proliferation and progression. Furthermore, mutations in ERα lead to acquired resistance against standard endocrine therapies such as tamoxifen. The induced resistance posed a significant clinical challenge in metastatic breast cancer. In this study, research for identifying novel, naturally derived compounds to inhibit the Y537S‐mutated ERα was conducted using in silico methods supported by an in vitro cytotoxicity screen. Molecular docking and molecular dynamics simulations served as the primary in silico screening strategies. The top 2% of candidates were filtered from a docking screen of the IBS natural library composed of over 15,000 chemicals. From this group, 11 compounds were purchased and tested using a cell‐based cytotoxicity assay in MCF‐7 before advancing to detailed simulations. Five candidates were then advanced to 150 ns MD simulations. A post‐MD analysis followed, including MM‐PBSA binding free energy calculations and principal component analysis (PCA). The phytochemical ibs‐04156 was identified as the most promising overall candidate, predicted to maintain consistent stability across both the wild‐type and Y537S‐mutated ERα, while ibs‐18821 demonstrated potent mutant‐specific inhibition via an allosteric mechanism involving spatial deviations in distal helices H3 and H11. This result shows that mutated ERα can be potentially targeted by bioactive phytochemical scaffolds found through molecular modeling, presenting a potential therapeutic strategy for metastatic breast cancer resistant to therapies such as tamoxifen.