Unconventional Isoquinoline-Based SERMs Elicit Fulvestrant-Like Transcriptional Programs in ER+ Breast Cancer Cells

Abstract Estrogen receptor alpha (ERα) is a ligand-dependent master transcriptional regulator and key driver of breast cancer pathology. Small molecule hormones and competitive antagonists favor unique ERα conformational ensembles that elicit ligand-specific transcriptional programs in breast cancer and other hormone-responsive tissues. By affecting disparate ligand binding domain structural features, unconventional ligand scaffolds can redirect ERα genomic binding patterns to engage novel therapeutic transcriptional programs. To improve our understanding of these ERα structure-transcriptional relationships, we have developed a series of chemically unconventional antagonists based on the antiestrogens RAD1901 and lasofoxifene. High-resolution x-ray co-crystal structures show that these molecules affect both classical and unique structural motifs within the ERα ligand binding pocket. They show moderately reduced antagonistic potencies on ERα genomic activities but are effective anti-proliferative agents in luminal breast cancer cells. Interestingly, they show SERM-like ERα accumulation in breast cancer cells but lack uterotrophic activities in an endometrial cell line. RNA sequencing shows that the lead molecules mediate transcriptional pathways similar to fulvestrant and other SERDs in these cells. This advance shows that fulvestrant-like genomic activities can be achieved without affecting ERα accumulation in breast cancer cells.