Simulations reveal increased fluctuations in estrogen receptor-alpha conformation upon antagonist binding

Study of potential inhibition of the estrogen receptor α by cannabinoids using an in silico approach: Agonist vs antagonist mechanism

Breast cancer is the main cancer type with more than 2.2 million cases in 2020, and is the principal cause of death in women; with 685000 deaths in 2020 worldwide. The estrogen receptor is involved at least in 70% of breast cancer diagnoses, and the agonist and antagonist properties of the drug in this receptor play a pivotal role in the control of this illness. This work evaluated the agonist and antagonist mechanisms of 30 cannabinoids by employing molecular docking and dynamic simulations. Compounds with docking scores < -8 kcal/mol were analyzed by molecular dynamic simulation at 300 ns, and relevant insights are given about the protein's structural changes, centered on the helicity in alpha-helices H3, H8, H11, and H12. Cannabicitran was the cannabinoid that presented the best relative binding-free energy (-34.96 kcal/mol), and based on rational modification, we found a new natural-based compound with relative binding-free energy (-44.83 kcal/mol) better than the controls hydroxytamoxifen and acolbifen. Structure modifications that could increase biological activity are suggested.

A molecular dynamics perspective into estrogen receptor inhibition by selective flavonoids as alternative therapeutic options

Zearalenone is an estrogenic mycotoxin which is a common food contaminant and has been implicated in increasing the incidence of carcinogenesis and other reproductive health ailments through the estrogen receptor alpha (ERα) pathway. Competitive ERα blockers such as 4-Hydroxytamoxifen (OHT), are synthetic FDA approved drugs which, albeit being an effective anticancer agent, induces life altering side effects. For this reason, there is an increased interest in the use of naturally occurring medicinal plant products such as flavonoids. This study aimed to identity flavonoid ERα inhibitors and provide insights into the mechanism of inhibition using computational techniques. The Molecular Mechanics/Generalized Born Surface Area calculations revealed that quercetrin, hesperidin, epigallocatechin 3-gallate and kaempferol 7-O-glucoside out of 14 flavonoids had higher binding affinity for ERα than OHT. The structural analysis revealed that the binding of the compounds to the receptor lead to dynamic alterations, which induced conformational shift in the structure and orientation of the receptor resulting in stabilised, compact and low energy systems. The results of this study provide imperative information that supports the use of flavonoids in the inhibition of ERα to prevent or ameliorate the consequential adverse effects associated with zearalenone exposure.Communicated by Ramaswamy H. Sarma.

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

Exploring the conformational space of a receptor for drug design: An ERα case study

Protein flexibility is challenging for both experimentalists and modellers, especially in the field of drug design. Estrogen Receptor alpha (ERα) is an extensively studied Nuclear Receptor (NR) and a well-known therapeutic target with an important role in development and physiology. It is also a frequent off-target in standard toxicity tests for endocrine disruption. Here, we aim to evaluate the degree to which the conformational space and macromolecular flexibility of this well-characterized drug target can be described. Our approach exploits hundreds of crystallographic structures by means of molecular dynamics simulations and of virtual screening. The analysis of hundreds of crystal structures confirms the presence of two main conformational states, known as 'agonist' and 'antagonist', that mainly differ by the orientation of the C-terminal helix H12 which serves to close the binding pocket. ERα also shows some loop flexibility, as well as variable side-chain orientations in its active site. We scrutinized the extent to which standard molecular dynamics simulations or crystallographic refinement as ensemble recapitulate most of the variability features seen by the array of available crystal structures. In parallel, we investigated on the kind and extent of flexibility that are required to achieve convincing docking for all high-affinity ERα ligands present in BindingDB. Using either only one conformation with a few side-chains set flexible, or static structure ensembles in parallel during docking led to good quality and similar pose predictions. These results suggest that the several hundreds of crystal structures already known can properly describe the whole conformational universe of ERα's ligand binding domain. This opens the road for better drug design and affinity computation.

RORγ Structural Plasticity and Druggability

Retinoic acid receptor-related orphan receptor γ (RORγ) is a transcription factor regulating the expression of the pro-inflammatory cytokine IL-17 in human T helper 17 (Th17) cells. Activating RORγ can induce multiple IL-17-mediated autoimmune diseases but may also be useful for anticancer therapy. Its deep immunological functions make RORɣ an attractive drug target. Over 100 crystal structures have been published describing atomic interactions between RORɣ and agonists and inverse agonists. In this review, we focus on the role of dynamic properties and plasticity of the RORɣ orthosteric and allosteric binding sites by examining structural information from crystal structures and simulated models. We discuss the possible influences of allosteric ligands on the orthosteric binding site. We find that high structural plasticity favors the druggability of RORɣ, especially for allosteric ligands.

Computer-Aided Ligand Discovery for Estrogen Receptor Alpha

Breast cancer (BCa) is one of the most predominantly diagnosed cancers in women. Notably, 70% of BCa diagnoses are Estrogen Receptor α positive (ERα+) making it a critical therapeutic target. With that, the two subtypes of ER, ERα and ERβ, have contrasting effects on BCa cells. While ERα promotes cancerous activities, ERβ isoform exhibits inhibitory effects on the same. ER-directed small molecule drug discovery for BCa has provided the FDA approved drugs tamoxifen, toremifene, raloxifene and fulvestrant that all bind to the estrogen binding site of the receptor. These ER-directed inhibitors are non-selective in nature and may eventually induce resistance in BCa cells as well as increase the risk of endometrial cancer development. Thus, there is an urgent need to develop novel drugs with alternative ERα targeting mechanisms that can overcome the limitations of conventional anti-ERα therapies. Several functional sites on ERα, such as Activation Function-2 (AF2), DNA binding domain (DBD), and F-domain, have been recently considered as potential targets in the context of drug research and discovery. In this review, we summarize methods of computer-aided drug design (CADD) that have been employed to analyze and explore potential targetable sites on ERα, discuss recent advancement of ERα inhibitor development, and highlight the potential opportunities and challenges of future ERα-directed drug discovery.

Estrogen receptor-positive (ER+) breast cancer treatment: Are multi-target compounds the next promising approach?

Endocrine therapy is currently the main therapeutic approach for estrogen receptor-positive (ER⁺) breast cancer, the most frequent subtype of breast cancer in women worldwide. For this subtype of tumors, the current clinical treatment includes aromatase inhibitors (AIs) and anti-estrogenic compounds, such as Tamoxifen and Fulvestrant, being AIs the first-line treatment option for post-menopausal women. Moreover, the recent guidelines also suggest the use of these compounds by pre-menopausal women after suppressing ovaries function. However, besides its therapeutic efficacy, the prolonged use of this type of therapies may lead to the development of several adverse effects, as well as, endocrine resistance, limiting the effectiveness of such treatments. In order to surpass this issues and clinical concerns, during the last years, several studies have been suggesting alternative therapeutic approaches, considering the function of aromatase, ERα and ERβ. Here, we review the structural and functional features of these three targets and their importance in ER⁺ breast cancer treatment, as well as, the current treatment strategies used in clinic, emphasizing the importance of the development of multi-target compounds able to simultaneously modulate these key targets, as a novel and promising therapeutic strategy for this type of cancer.

Computational investigations of the binding mechanism of novel benzophenone imine inhibitors for the treatment of breast cancer

4-Hydroxytamoxifen (4-OHT), the most common hormone used for the treatment of breast cancer, is a selective estrogen receptor modulator (SERM) inhibitor that acts as an antagonist in breast tissue and a partial agonist in the endometrium. However, the detailed molecular mechanism of 4-OHT structure modification has not been well investigated to date. Herein, molecular docking, molecular dynamics simulations and free energy calculations were performed to explore the mechanisms of the molecular interactions between newly designed benzophenone imines (BIs) and the three forms apo, antagonist and agonist of the human estrogen receptor hERα. The proposed inhibitors were designed by replacing the triarylethylene estrogenic scaffold found in 4-OHT with Schiff base triarylimine derivatives. The antiestrogen scaffold i.e. the O-alkyl side chain in 4-OHT was developed by incorporating an alanine amino acid side chain functionality into the triarylimine scaffold. Docking results reveal that the newly designed BIs bind to the hydrophobic open pocket of the apo and antagonist hERα conformations with higher affinity as compared to the natural and synthetic estrogen estradiol (E2) and 4-OHT. The analysis of the molecular dynamics simulation results based on six different systems of the best docked BI (5c) with hERα receptors demonstrates stable interactions, and the complex undergoes fewer conformational fluctuations in the open apo/antagonist hERα receptors as compared to the case of the closed agonist. In addition, the calculated binding free energies indicate that the main factor that contributes to the stabilization of the receptor-inhibitor complexes is hydrophobic interactions. This study suggests that the development of these Schiff base derivatives may be worth exploring for the preparation of new 4-OHT analogues.

ERE-dependent transcription and cell proliferation: Independency of these two processes mediated by the introduction of a sulfone function into the weak estrogen estrothiazine

The synthetic coumestrol derivative 6,12-dihydro-3-methoxy-1-benzopyrano[3,4-b][1,4]benzothiazin-6-one (estrothiazine, ESTZ) has been identified as a weak estrogen receptor α (ERα) ligand unable to compete with tritiated estradiol. The biological activity of this compound, supported by a methoxy group in position 3, seems mainly to result from its capacity to activate ERα dimerization without any participation of coactivators. In support of this view and referring to conventional estrogens, an ESTZ metabolism study conducted with hepatic human microsomes failed to provide any argument in favour of an estrogenic activity dependent on a metabolic conversion of the compound into hydroxylated metabolites with strong receptor activation ability. Interestingly, we failed to detect any oxidation of the sulfur atom of the compound. In the light of pharmacological literature data concerning sulfonylation, we assessed ERα-mediated activities generated by two sulfonylated ESTZ derivatives in which the methoxy group that plays a key role in its mechanism of action was maintained or removed. Sulfonylated ESTZ, even in its demethoxylated form, induced ERE-mediated transcriptions in MCF-7 breast cancer cells, without affecting the ERα turnover rate. In contrast to ESTZ, this compound failed to enhance the proliferation of ERα-positive breast cancer cells, suggesting that its sulfone function confers upon the receptor a capacity to elicit some of the known characteristics associated with estrogenic responses. Moreover, we demonstrated that this sulfone may contribute to ERα dimerization without any requirement of the methoxy group. Nevertheless, it seems to cooperate with this group, as reflected by a weak ability of the sulfonylated form of ESTZ to compete with tritiated estradiol for ERα-binding. Assessment of the docking of this compound within the ligand-binding domain of the receptor by molecular dynamics provided an explanation for this observation since the sulfone is engulfed in a small hydrophobic pocket involving the residues Leu-346, Leu-349, Ala-350 and Leu-384, also known to recruit coactivators. This work not only reports the sulfone functional group as a pharmacophore for estrogenic activity, but also opens new perspectives for the development of estrogenic molecules with therapeutic purpose and devoid of proliferative side effects.