Dynamic and Electronic Determinants of Fulvestrant Antagonism in Estrogen Receptor α: A Comparative Study with Estradiol

Breast cancer remains one of the leading causes of cancer-related mortality worldwide. Fulvestrant is an advanced therapeutic agent characterized by a unique chemical structure and mechanism of action targeting the estrogen receptor (ER). In this study, estradiol was used as a reference ligand to establish a direct comparison between the endogenous hormone involved in estrogen-dependent signaling in ER-positive breast cancer and the antagonist drug designed to inhibit receptor activation. The investigation was conducted using conformational search, quantum-chemical calculations, molecular docking, and molecular dynamics simulations to elucidate differences in the molecular behavior of estradiol and fulvestrant, with particular emphasis on the ligand-binding domain and the AF-2 region of the estrogen receptor. Docking results revealed that fulvestrant exhibits a docking score of −9.34 kcal/mol using the Vina scoring function, whereas estradiol showed a more favorable score of −11.34 kcal/mol. Owing to the conformational flexibility of fulvestrant, a conformational search was performed using CREST prior to the DFT analysis, and the lowest-energy CREST conformer remained the lowest-energy structure among the selected conformers after DFT reoptimization. The reactivity properties of the ligands were evaluated within the framework of density functional theory (DFT) employing the M06-2X functional and the 6-311+G(d,p) basis set. Furthermore, charge-transfer values (ΔN) calculated between the ligands and amino acid models of the receptor binding site were used to qualitatively characterize relative electron-density transfer tendencies. Molecular docking predictions were complemented by two independent molecular dynamics simulations for each ligand performed using the GROMACS 2026.1 software package, allowing the evaluation of receptor–ligand stability under solvated conditions.