Abstract PD10-05: (z)-endoxifen maintains erα antagonist function against esr1 mutants via inactive conformation stabilization and reversal of mutant esr1-associated transcriptional signatures

Abstract Background: Mutations in the estrogen receptor gene (ESR1), particularly Y537S and D538G, are key drivers of resistance in estrogen receptor-positive (ER+) metastatic breast cancer (MBC) following aromatase inhibitor therapy. These mutations promote ligand-independent ER activation. In this in silico modeling study, we examined the biophysical behavior and downstream transcriptional impacts of (Z)-endoxifen, an active tamoxifen metabolite, a selective estrogen receptor modulator (SERM), across ESR1 variants to further elucidate its mechanism of action and therapeutic potential. Methods: We conducted full-atom molecular dynamics (MD) and metadynamics simulations of ERα-ligand complexes (wild-type and mutant) to assess conformational dynamics and antagonist state probability. Alchemical Non-Equilibrium Switching (NES) simulations compared binding affinities of (Z)-endoxifen vs. 4-hydroxy-tamoxifen (4-OHT). Luciferase reporter assays and 2D growth assays were performed in 293T and MCF-7 cells expressing ESR1-WT or D538G. Transcriptomic data were analyzed from public datasets, including RNA-seq and microarray profiles from ESR1 mutant tumors (n=56) and drug-treated breast cancer cells (n=27 for (Z)-endoxifen; n=5 for elacestrant). Differential expression and enrichment analyses (gene sets, pathways, TFs) were conducted using the limma and gseapy packages. Results- Biophysical Modeling: MD simulations (4 μs) showed stable (Z)-endoxifen binding across WT and mutant ERα, with no spontaneous receptor reactivation. Alchemical free energy calculations revealed favorable or equivalent binding of (Z)-endoxifen vs. 4-OHT (ΔΔG = 0.09 kcal/mol for WT; 1.30 kcal/mol for D538G). Metadynamic simulations on apo ERα indicated that mutations skewed toward the active state but did not prevent (Z)-endoxifen from stabilizing the antagonist conformation (antagonist state probability: WT 93.5%, Y537S 35.4%, D538G 46.9%). Functional Assays: (Z)-endoxifen potently suppressed ER-Luc activity (>70% inhibition) in 293T cells expressing ESR1-WT and all tested mutants (Y537S, Y537N, D538G, K303R), showing comparable potency across constructs. In MCF-7 cells, (Z)-endoxifen significantly reduced proliferation in both parental and ESR1-D538G lines. D538G expression did not rescue growth; a 60% reduction in 2D proliferation was observed with treatment. Transcriptomic Analysis: Gene expression analyses identified numerous transcripts with reversed regulation between ESR1 mutant tumors and (Z)-endoxifen-treated cells, indicating a functional reversal of mutant-driven expression patterns. Pathways upregulated in ESR1 mutant tumors and downregulated by (Z)-endoxifen included estrogen response, E2F targets, and Myc targets. Conversely, oxidative phosphorylation and p53 signaling were suppressed in ESR1 mutants and upregulated by (Z)-endoxifen (FDR < 0.05).(Z)-endoxifen also reactivated suppressed TF target networks (e.g., AHRR, GLIS2, NFATC4) in mutant tumors. In contrast, elacestrant had minimal transcriptional impact in ESR1 mutant MCF-7 cells, suggesting a narrower effect on disease-relevant pathways. Conclusion: (Z)-Endoxifen demonstrates robust biophysical and functional activity against ESR1 mutations. It stabilizes inactive ERα conformations and reverses mutant-driven transcriptional programs, showing greater transcriptional breadth than next-generation SERDs like elacestrant. These findings support (Z)-endoxifen’s potential as a precision therapy for ESR1-mutant ER+ MBC and justify further clinical investigation in endocrine-resistant settings. Citation Format: S. S. Hammer, E. Kirilin, H. de Almeida, V. Aladinskiy, A. Ustiugova, A. Shneyderman, A. Veviorskiy, M. Korzinkin, S. C. Quay. (z)-endoxifen maintains erα antagonist function against esr1 mutants via inactive conformation stabilization and reversal of mutant esr1-associated transcriptional signatures [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PD10-05.