Understanding the selectivity of genistein for human estrogen receptor-beta using X-ray crystallography and computational methods

A molecular docking study of phytochemical estrogen mimics from dietary herbal supplements

PURPOSE

The purpose of this study is to use a molecular docking approach to identify potential estrogen mimics or anti-estrogens in phytochemicals found in popular dietary herbal supplements.

METHODS

In this study, 568 phytochemicals found in 17 of the most popular herbal supplements sold in the United States were built and docked with two isoforms of the estrogen receptor, ERα and ERβ (a total of 27 different protein crystal structures).

RESULTS

The docking results revealed six strongly docking compounds in Echinacea, three from milk thistle (Silybum marianum), three from Gingko biloba, one from Sambucus nigra, none from maca (Lepidium meyenii), five from chaste tree (Vitex agnus-castus), two from fenugreek (Trigonella foenum-graecum), and two from Rhodiola rosea. Notably, of the most popular herbal supplements for women, there were numerous compounds that docked strongly with the estrogen receptor: Licorice (Glycyrrhiza glabra) had a total of 26 compounds strongly docking to the estrogen receptor, 15 with wild yam (Dioscorea villosa), 11 from black cohosh (Actaea racemosa), eight from muira puama (Ptychopetalum olacoides or P. uncinatum), eight from red clover (Trifolium pratense), three from damiana (Turnera aphrodisiaca or T. diffusa), and three from dong quai (Angelica sinensis). Of possible concern were the compounds from men's herbal supplements that exhibited strong docking to the estrogen receptor: Gingko biloba had three compounds, gotu kola (Centella asiatica) had two, muira puama (Ptychopetalum olacoides or P. uncinatum) had eight, and Tribulus terrestris had six compounds.

CONCLUSIONS

This molecular docking study has revealed that almost all popular herbal supplements contain phytochemical components that may bind to the human estrogen receptor and exhibit selective estrogen receptor modulation. As such, these herbal supplements may cause unwanted side effects related to estrogenic activity.

Computational polypharmacology analysis of the heat shock protein 90 interactome

The design of a single drug molecule that is able to simultaneously and specifically interact with multiple biological targets is gaining major consideration in drug discovery. However, the rational design of drugs with a desired polypharmacology profile is still a challenging task, especially when these targets are distantly related or unrelated. In this work, we present a computational approach aimed at the identification of suitable target combinations for multitarget drug design within an ensemble of biologically relevant proteins. The target selection relies on the analysis of activity annotations present in molecular databases and on ligand-based virtual screening. A few target combinations were also inspected with structure-based methods to demonstrate that the identified dual-activity compounds are able to bind target combinations characterized by remote binding site similarities. Our approach was applied to the heat shock protein 90 (Hsp90) interactome, which contains several targets of key importance in cancer. Promising target combinations were identified, providing a basis for the computational design of compounds with dual activity. The approach may be used on any ensemble of proteins of interest for which known inhibitors are available.

A structural perspective on nuclear receptors as targets of environmental compounds

Nuclear receptors (NRs) are members of a large superfamily of evolutionarily related transcription factors that control a plethora of biological processes. NRs orchestrate complex events such as development, organ homeostasis, metabolism, immune function, and reproduction. Approximately one-half of the 48 human NRs have been shown to act as ligand-regulated transcription factors and respond directly to a large variety of endogenous hormones and metabolites that are generally hydrophobic and small in size (eg, retinoic acid or estradiol). The second half of the NR family comprises the so-called orphan receptors, for which regulatory ligands are still unknown or may not exist despite the presence of a C-terminal ligand-binding domain, which is the hallmark of all NRs. Several chemicals released into the environment (eg, bisphenols, phthalates, parabens, etc) share some physicochemical properties with natural ligands, allowing them to bind to NRs and activate or inhibit their action. Collectively referred to as endocrine disruptors or endocrine-disrupting chemicals (EDCs), these environmental pollutants are highly suspected to cause a wide range of developmental, reproductive, neurological, or metabolic defects in humans and wildlife. Crystallographic studies are revealing unanticipated mechanisms by which chemically diverse EDCs interact with the ligand-binding domain of NRs. These studies thereby provide a rational basis for designing novel chemicals with lower impacts on human and animal health. In this review, we provide a structural and mechanistic view of endocrine disrupting action using estrogen receptors α and β, (ERα/β), peroxisome proliferator activated receptor γ (PPARγ), and their respective environmental ligands as representative examples.

Genistein disrupts glucocorticoid receptor signaling in human uterine endometrial Ishikawa cells

BACKGROUND

The link between environmental estrogen exposure and defects in the female reproductive tract is well established. The phytoestrogen genistein is able to modulate uterine estrogen receptor (ER) activity, and dietary exposure is associated with uterine pathologies. Regulation of stress and immune functions by the glucocorticoid receptor (GR) is also an integral part of maintaining reproductive tract function; disruption of GR signaling by genistein may also have a role in the adverse effects of genistein.

OBJECTIVE

We evaluated the transcriptional response to genistein in Ishikawa cells and investigated the effects of genistein on GR-mediated target genes.

METHODS

We used Ishikawa cells as a model system to identify novel targets of genistein and the synthetic glucocorticoid dexamethasone through whole genome microarray analysis. Common gene targets were defined and response patterns verified by quantitative real-time reverse-transcription polymerase chain reaction. The mechanism of transcriptional antagonism was determined for select genes.

RESULTS

Genistein regulated numerous genes in Ishikawa cells independently of estradiol, and the response to coadministration of genistein and dexamethasone was unique compared with the response to either estradiol or dexamethasone alone. Furthermore, genistein altered glucocorticoid regulation of GR target genes. In a select set of genes, co-regulation by dexamethasone and genistein was found to require both GR and ERα signaling, respectively.

CONCLUSIONS

Using Ishikawa cells, we observed that exposure to genistein resulted in distinct changes in gene expression and unique differences in the GR transcriptome.

Exogenous hormonal regulation in breast cancer cells by phytoestrogens and endocrine disruptors

Observations on the role of ovarian hormones in breast cancer growth, as well as interest in contraception, stimulated research into the biology of estrogens. The identification of the classical receptors ERα and ERβ and the transmembrane receptor GPER and the resolution of the structure of the ligand bound to its receptor established the principal molecular mechanisms of estrogen action. The presence of estrogen-like compounds in many plants used in traditional medicine or ingested as food ingredients, phytoestrogens, as well as the estrogenic activities of many industrial pollutants and pesticides, xenoestrogens, have prompted investigations into their role in human health. Phyto- and xenoestrogens bind to the estrogen receptors with a lower affinity than the endogenous estrogens and can compete or substitute the hormone. Xenoestrogens, which accumulate in the body throughout life, are believed to increase breast cancer risk, especially in cases of prenatal and prepuberal exposure whereas the role of phytoestrogens is still a matter of debate. At present, the application of phytoestrogens appears to be limited to the treatment of post-menopausal symptoms in women where the production of endogenous estrogens has ceased. In this review we discuss chemistry, structure and classification, estrogen signaling and the consequences of the interactions of estrogens, phytoestrogens and xenoestrogens with their receptors, the complex interactions of endogenous and exogenous ligands, the evaluation of the health risks related to xenoestrogens, and the perspectives toward the synthesis of potent third generation selective estrogen receptor modulators (SERMs).

Phytoestrogens in postmenopause: the state of the art from a chemical, pharmacological and regulatory perspective

Phytoestrogens represent a diverse group of non-steroidal natural products, which seem to have some oestrogenic effects and are often marketed as food supplements. Population exposed to phytoestrogens is potentially increasing, in part because an unfavourable risk-benefit profile of Hormone Replacement Therapy (HRT) for prolonged treatments (e.g., osteoporosis prevention) highlighted by the publication of the Women Health Initiative (WHI) trial in 2002, but also because many post-menopausal women often perceived phytoestrogens in food supplements as a safer alternative than HRT. Despite of increasing preclinical and clinical studies in the past decade, appealing evidence is still lacking to support the overall positive risk-benefit profile of phytoestrogens. Their status as food supplements seems to discourage studies to obtain new evidence, and the chance to buy them by user's initiative make it difficult to survey their prevalence and pattern of use. The aim of the present review is to: (a) outline the clinical scenario underlying the increased interest on phytoestrogens, by overviewing the evolution of the evidence on HRT and its main therapeutic goals (e.g., menopausal symptoms relief, chemoprevention, osteoporosis prevention); (b) address the chemical and pharmacological features (e.g. chemical structure, botanical sources, mechanism of action) of the main compounds (e.g., isoflavones, lignans, coumestans); (c) describe the clinical evidence on potential therapeutic applications; (d) put available evidence on their riskbenefit profile in a regulatory perspective, in light of the recent regulation on health claims of food supplements.

Versatility or promiscuity: the estrogen receptors, control of ligand selectivity and an update on subtype selective ligands

The estrogen receptors (ERs) are a group of versatile receptors. They regulate an enormity of processes starting in early life and continuing through sexual reproduction, development, and end of life. This review provides a background and structural perspective for the ERs as part of the nuclear receptor superfamily and discusses the ER versatility and promiscuity. The wide repertoire of ER actions is mediated mostly through ligand-activated transcription factors and many DNA response elements in most tissues and organs. Their versatility, however, comes with the drawback of promiscuous interactions with structurally diverse exogenous chemicals with potential for a wide range of adverse health outcomes. Even when interacting with endogenous hormones, ER actions can have adverse effects in disease progression. Finally, how nature controls ER specificity and how the subtle differences in receptor subtypes are exploited in pharmaceutical design to achieve binding specificity and subtype selectivity for desired biological response are discussed. The intent of this review is to complement the large body of literature with emphasis on most recent developments in selective ER ligands.

3D models of human ERα and ERβ complexed with coumestrol

Coumestrol, a phytoestrogen found in alfalfa, clover, and beans, has nM affinity for both estrogen receptor-α [ERα] and ERβ. Recently, a novel activity of coumestrol was reported: coumestrol binding to human ERβ represses microglia-mediated inflammation, which is associated with various neurodegenerative diseases, such as multiple sclerosis. In contrast, estradiol binding to ERβ had little or no effect on repression of microglia-mediated inflammation. Coumestrol and estradiol have several structural differences, which suggest that each ligand could induce different conformations in ERβ and, thus, different transcriptional responses in brain microglia. To begin to understand how coumestrol binds to ERβ and ERα, we constructed 3D models of coumestrol with human ERβ and ERα, which were compared to the structures of these ERs with estradiol. Of four possible orientations of coumestrol in ERα and ERβ, one orientation had the most favorable contacts with both ERs. Other phytochemicals may activate ERβ and inhibit inflammation in brain microglia and be useful therapeutics for inflammatory conditions in the brain.

Interactions of isoflavones and other plant derived estrogens with estrogen receptors for prevention and treatment of breast cancer-considerations concerning related efficacy and safety

Phytoestrogens are natural endocrine disruptors that interfere with estrogenic pathways. They insert directly within the hormone-binding domain of ERα and β, with a preference for the β isoform of which the concentration predominates in the normal mammary epithelium. Since ERβ antagonizes the growth promoting effect of ERα, which is mainly expressed in estrogen-sensitive tumor cells, a potential protective action against breast cancer incidence has been ascribed to phytoestrogens. The fact that Asian women living in far-east countries who consume isoflavone-rich food are less subjected to breast cancer emergence than their congeners in the USA as well as Caucasian women has been advocated to justify such a concept. Overview of data concerning the mechanism of action phytoestrogens reveals that such a view is an oversimplification: Such compounds interfere with a huge panel of regulatory proteins, giving rise to both promoting and antagonizing carcinogenic effects. Moreover, various physiological and pathological factors able to amplify these effects are not often sufficiently taken into account, which increases the difficulty to interpret data. Nevertheless, this overview of data established that chemical structures and concentrations modulate such effects: at the micromolar level, isoflavones activate ERα-mediated transcription and breast cancer cell proliferation while flavones fail to induce any significant promoting effects. At higher doses, both classes of compounds may display an antitumor activity. Reasons for such distinct behaviors as well as their potential impact in therapeutic applications are analyzed here. Ability of isoflavones and flavones to antagonize the association of calmodulin to ERα, which is required for its enhanced transcriptional activity is evoked to justify the antitumor activity ascribed to some flavones. Finally, a suspicion that peculiar classes of phytoestrogens may adopt a SERM-like conformation is addressed in a context of selection and synthesis of compounds with non-equivocal therapeutic value. This article is part of a Special Issue entitled "Phytoestrogens".

Probing the human estrogen receptor-α binding requirements for phenolic mono- and di-hydroxyl compounds: a combined synthesis, binding and docking study

Various estrogen analogs were synthesized and tested for binding to human ERα using a fluorescence polarization displacement assay. Binding affinity and orientation were also predicted using docking calculations. Docking was able to accurately predict relative binding affinity and orientation for estradiol, but only if a tightly bound water molecule bridging Arg394/Glu353 is present. Di-hydroxyl compounds sometimes bind in two orientations, which are flipped in terms of relative positioning of their hydroxyl groups. Di-hydroxyl compounds were predicted to bind with their aliphatic hydroxyl group interacting with His524 in ERα. One nonsteroid-based dihdroxyl compound was 1000-fold specific for ERβ over ERα, and was also 25-fold specific for agonist ERβ versus antagonist activity. Docking predictions suggest this specificity may be due to interaction of the aliphatic hydroxyl with His475 in the agonist form of ERβ, versus with Thr299 in the antagonist form. But, the presence of this aliphatic hydroxyl is not required in all compounds, since mono-hydroxyl (phenolic) compounds bind ERα with high affinity, via hydroxyl hydrogen bonding interactions with the ERα Arg394/Glu353/water triad, and van der Waals interactions with the rest of the molecule.

A fluorescence-based thermal shift assay identifies inhibitors of mitogen activated protein kinase kinase 4

Prostate cancer (PCa) is the second highest cause of cancer death in United States males. If the metastatic movement of PCa cells could be inhibited, then mortality from PCa could be greatly reduced. Mitogen-activated protein kinase kinase 4 (MAP2K4) has previously been shown to activate pro-invasion signaling pathways in human PCa. Recognizing that MAP2K4 represents a novel and validated therapeutic target, we sought to develop and characterize an efficient process for the identification of small molecules that target MAP2K4. Using a fluorescence-based thermal shift assay (FTS) assay, we first evaluated an 80 compound library of known kinase inhibitors, thereby identifying 8 hits that thermally stabilized MAP2K4 in a concentration dependent manner. We then developed an in vitro MAP2K4 kinase assay employing the biologically relevant downstream substrates, JNK1 and p38 MAPK, to evaluate kinase inhibitory function. In this manner, we validated the performance of our initial FTS screen. We next applied this approach to a 2000 compound chemically diverse library, identified 7 hits, and confirmed them in the in vitro kinase assay. Finally, by coupling our structure-activity relationship data to MAP2K4's crystal structure, we constructed a model for ligand binding. It predicts binding of our identified inhibitory compounds to the ATP binding pocket. Herein we report the creation of a robust inhibitor-screening platform with the ability to inform the discovery and design of new and potent MAP2K4 inhibitors.

Structural insights into Resveratrol's antagonist and partial agonist actions on estrogen receptor alpha

BACKGROUND

Resveratrol, a naturally occurring stilbene, has been categorized as a phytoestrogen due to its ability to compete with natural estrogens for binding to estrogen receptor alpha (ERα) and modulate the biological responses exerted by the receptor. Biological effects of resveratrol (RES) on estrogen receptor alpha (ERα) remain highly controversial, since both estrogenic and anti-estrogenic properties were observed.

RESULTS

Here, we provide insight into the structural basis of the agonist/antagonist effects of RES on ERα ligand binding domain (LBD). Using atomistic simulation, we found that RES bound ERα monomer in antagonist conformation, where Helix 12 moves away from the ligand pocket and orients into the co-activator binding groove of LBD, is more stable than RES bound ERα in agonist conformation, where Helix 12 lays over the ligand binding pocket. Upon dimerization, the agonistic conformation of RES-ERα dimer becomes more stable compared to the corresponding monomer but still remains less stable compared to the corresponding dimer in antagonist conformation. Interestingly, while the binding pocket and the binding contacts of RES to ERα are similar to those of pure agonist diethylstilbestrol (DES), the binding energy is much less and the hydrogen bonding contacts also differ providing clues for the partial agonistic character of RES on ERα.

CONCLUSIONS

Our Molecular Dynamics simulation of RES-ERα structures with agonist and antagonist orientations of Helix 12 suggests RES action is more similar to Selective Estrogen Receptor Modulator (SERM) opening up the importance of cellular environment and active roles of co-regulator proteins in a given system. Our study reveals that potential co-activators must compete with the Helix 12 and displace it away from the activator binding groove to enhance the agonistic activity.

Structural characterization of the binding interactions of various endogenous estrogen metabolites with human estrogen receptor α and β subtypes: a molecular modeling study

In the present study, we used the molecular docking approach to study the binding interactions of various derivatives of 17β-estradiol (E₂) with human estrogen receptor (ER) α and β. First, we determined the suitability of the molecular docking method to correctly predict the binding modes and interactions of two representative agonists (E₂ and diethylstilbesterol) in the ligand binding domain (LBD) of human ERα. We showed that the docked structures of E₂ and diethylstilbesterol in the ERα LBD were almost exactly the same as the known crystal structures of ERα in complex with these two estrogens. Using the same docking approach, we then characterized the binding interactions of 27 structurally similar E₂ derivatives with the LBDs of human ERα and ERβ. While the binding modes of these E₂ derivatives are very similar to that of E₂, there are distinct subtle differences, and these small differences contribute importantly to their differential binding affinities for ERs. In the case of A-ring estrogen derivatives, there is a strong inverse relationship between the length of the hydrogen bonds formed with ERs and their binding affinity. We found that a better correlation between the computed binding energy values and the experimentally determined logRBA values could be achieved for various A-ring derivatives by re-adjusting the relative weights of the van der Waals interaction energy and the Coulomb interaction energy in computing the overall binding energy values.

A plant homolog of animal glutamate receptors is an ion channel gated by multiple hydrophobic amino acids

Ionotropic glutamate receptors (iGluRs) are ligand-gated cation channels that mediate neurotransmission in animal nervous systems. Homologous proteins in plants have been implicated in root development, ion transport, and several metabolic and signaling pathways. AtGLR3.4, a plant iGluR homolog from Arabidopsis thaliana, has ion channel activity and is gated by asparagine, serine, and glycine. Using heterologous expression in Xenopus oocytes, we found that another Arabidopsis iGluR homolog, AtGLR1.4, functioned as a ligand-gated, nonselective, Ca(2+)-permeable cation channel that responded to an even broader range of amino acids, none of which are agonists of animal iGluRs. Seven of the 20 standard amino acids--mainly hydrophobic ones--acted as agonists, with methionine being most effective and most potent. Nine amino acids were antagonists, and four, including glutamate and glycine, had no effect on channel activity. We constructed a model of this previously uncharacterized ligand specificity and used knockout mutants to show that AtGLR1.4 accounts for methionine-induced membrane depolarization in Arabidopsis leaves.

A conformational study of hydroxyflavones by vibrational spectroscopy coupled to DFT calculations

The conformational preferences of a series of hydroxyflavones were studied by Raman and FTIR spectroscopies, coupled to Density Functional Theory calculations. Special attention was paid to the effect of hydroxyl substitution, due to its importance on the biological activity of these compounds. Their conformational preferences were found to be determined mainly by the orientation of the hydroxylic groups at C(7) and within the catechol moiety, leading to the occurrence of distinct conformers in the solid state. A complete assignment of the experimental spectra was carried out for these molecules, in the light of their most stable conformers and the corresponding predicted vibrational pattern.

Ligand selectivity of estrogen receptors by a molecular dynamics study

Estrogen receptors α (ERα) and β (ERβ) have different physiological functions and expression levels in different tissues. ERα and ERβ are highly homologous and have only two residue substitutions in the binding pocket. This high similarity at the active site stimulates the interests for discovering subtype selective ligands. In this study, molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method have been carried out to analyze the basis of selectivity of three ligands (659, 818 and 041). The calculated binding free energies show that all the ligands bind more tightly to ERβ than to ERα. The dominant free energy components of selectivity for 659 are similar to that for 041, but different from that for 818. The decompositions of free energy contributions and structural analysis imply that there are eight residues primarily contributing to the selectivity for 659, five residues for 041, as well as two residues for 818. The structural analysis implies that two residue substitutions in binding packet cause the position of 659 in ERβ-659 complex to shift relative to that in ERα-659 complex and also cause the conformational changes of other residues in the binding pocket. The higher selectivity for 041 is mainly caused by three residues, Ile373 (Met421), His475 (His524) and Leu476 (Leu525).

Estrogenic effect of three substituted deoxybenzoins

Deoxybenzoins (1-(2,4-dihydroxyphenyl)-2-(4-hydroxyphenyl)ethanone) are possible precursors or metabolites of isoflavanones which may have xenoestrogenic potential on estrogen receptor (ER). In this study we evaluated three 2'-substituted deoxybenzoin derivatives for their estrogenic effect based upon their ability to affect the proliferation of ERα(+) MCF7 cells, ERβ(+) PC3 cells and Hep2 cells stably transfected and expressing either ERα or ERβ. These compounds designated as CMPD3, CMPD6 and CMPD9 had -COOH, -(CH(2))(4)-CH(3) and -CH(3) substitutions, respectively on the 2'-position of the 2,4-dihydroxyphenyl ring of deoxybenzoin. We found that all three compounds increased the proliferation of ERα(+) MCF7 cells (EC(50)~1-12 μM) and ERα(+) Hep2 cells, while causing apoptosis in ERβ(+) PC3 cells (IC(50)~1-5 μM) and ERβ(+) Hep2 cells. The compounds also up-regulated the expression of estrogen sensitive genes, trefoil factor 1 (TFF1, previously known as pS2) and cathepsin-D (CTSD), in these cells. We performed in vitro ER transcription activation assays using Hep2 cells transiently co-transfected with estrogen response element driven luciferase and either ERα or ERβ vectors to ascertain the mechanism of action of these compounds through the 'classical' genomic pathway of estrogenic activity and to determine their ER subtype selectivity. Molecular docking of the compounds with the Ligand Binding Domain of ERα and ERβ showed similar docking scores (Glidescores of -6.5 to -8.5 kcal/mol) indicating that these compounds were ligands of both ERα and ERβ with similar affinity.

Nutritional flavonoids impact on nuclear and extranuclear estrogen receptor activities

Flavonoids are a large group of nonnutrient compounds naturally produced from plants as part of their defence mechanisms against stresses of different origins. They emerged from being considered an agricultural oddity only after it was observed that these compounds possess a potential protective function against several human degenerative diseases. This has led to recommending the consumption of food containing high concentrations of flavonoids, which at present, especially as soy isoflavones, are even available as overthecounter nutraceuticals. The increased use of flavonoids has occurred even though their mechanisms are not completely understood, in particular those involving the flavonoid impact on estrogen signals. In fact, most of the human health protective effects of flavonoids are described either as estrogenmimetic, or as antiestrogenic, while others do not involve estrogen signaling at all. Thus, the same molecule is reported as an endocrine disruptor, an estrogen mimetic or as an antioxidant without estrogenic effects. This is due in part to the complexity of the estrogen mechanism, which is conducted by different pathways and involves two different receptor isoforms. These pathways can be modulated by flavonoids and should be considered for a reliable evaluation of flavonoid, both estrogenicity and antiestrogenicity, and for a correct prediction of their effects on human health.

X-ray structures of progesterone receptor ligand binding domain in its agonist state reveal differing mechanisms for mixed profiles of 11β-substituted steroids

We present here the x-ray structures of the progesterone receptor (PR) in complex with two mixed profile PR modulators whose functional activity results from two differing molecular mechanisms. The structure of Asoprisnil bound to the agonist state of PR demonstrates the contribution of the ligand to increasing stability of the agonist conformation of helix-12 via a specific hydrogen-bond network including Glu(723). This interaction is absent when the full antagonist, RU486, binds to PR. Combined with a previously reported structure of Asoprisnil bound to the antagonist state of the receptor, this structure extends our understanding of the complex molecular interactions underlying the mixed agonist/antagonist profile of the compound. In addition, we present the structure of PR in its agonist conformation bound to the mixed profile compound Org3H whose reduced antagonistic activity and increased agonistic activity compared with reference antagonists is due to an induced fit around Trp(755), resulting in a decreased steric clash with Met(909) but inducing a new internal clash with Val(912) in helix-12. This structure also explains the previously published observation that 16α attachments to RU486 analogs induce mixed profiles by altering the binding of 11β substituents. Together these structures further our understanding of the steric and electrostatic factors that contribute to the function of steroid receptor modulators, providing valuable insight for future compound design.

Characterization of agonist binding to His524 in the estrogen receptor α ligand binding domain

The bioactivities of the natural steroidal estrogen 17β-estradiol (E2), the synthetic estrogen diethylstilbestrol (DES), and the phytoestrogen genistein (GEN) are intimately associated with their binding to the estrogen receptor α ligand binding domain (ERα LBD) and accordingly allostery. Molecular modeling techniques have been performed on agonists in complex with the LBD, focusing on the pivotal role of His524 modeled as the ε-tautomer and the protonated form (depending on pH). It is found that E2 binds to the active LBD with the aid of Leu525, showing existing stable patterns of an H-binding network with Glu419 via His524 in all models. The main difference seen in the effect is that the full agonists E2 and DES have higher binding energies to the protonated His524 than the partial agonists GEN and Way-169916 (W), which is in line with noted experimental transcriptional activities. In conclusion, the study demonstrates that the phytoestrogen GEN interacts differently with the LBD than what E2 and DES do, which explains the observed signaling differences.

Review of the efficacy of green tea, isoflavones and aloe vera supplements based on randomised controlled trials

We assess the evidence for health benefits of three commonly consumed plant food supplements (PFS), green tea, isoflavone and aloe vera, based on published systematic reviews of randomised controlled trials (RCTs). Whilst the potential benefits of green tea have been reported in a wide range of health areas, it is only in the area of the metabolic syndrome that the number of RCTs is approaching sufficient to judge such efficacy. Isoflavone supplements are widely used, and RCTs indicate that they affect bone resorption at lower doses in postmenopausal women undergoing estrogen-related bone loss, but this is only translated to attenuation of bone loss at higher doses of isoflavones. A systematic review on RCTs concluded that the effects of isoflavones on hot flashes in postmenopausal women were highly variable and no conclusions could be drawn. Despite the popularity of aloe vera as a PFS, the evaluation of its efficacy as a coadjuvant therapy for certain metabolic or digestive pathologies remains scarce; it constitutes a typical example of a naturally occurring ingredient whose efficacy in topical applications presupposes its efficacy in systemic applications. Nevertheless, its possible toxic effects on oral consumption call for caution in its utility as a PFS. Since 2007, efficacy evaluation of PFS in Europe has been covered by European Union Nutrition and Health Claims legislation. The European Food Safety Authority has adopted an approach relying on RCTs, while medicinal effects are accepted based on traditional use. In general, there are insufficient RCTs for claims to be made, and conclusive results on PFS should be obtained in the future by conducting studies with more homogeneous populations, by using supplements with optimised and measured bioavailability, and by conducting larger RCTs.

Lignans as food constituents with estrogen and antiestrogen activity

Phytoestrogens are plant-derived food ingredients assumed to contribute to the prevention of hormone-dependent cancers, osteoporosis, cardiovascular disease, and menopausal symptoms. Lignans occur in numerous food plants and various structures; they are common constituents of human diet, and estrogen activity has been assessed for lignan metabolites formed in the mammalian intestine. We examined natural lignans and semisynthetic norlignans for estrogen and antiestrogen activity. A transformed yeast strain (Saccharomyces cerevisiae) expressing the estrogen receptor alpha and a reporter system was applied as test system. Some plant lignans showed estrogen activity while others and the semisynthetic norlignans were moderately active antiestrogens. Docking of lignans to protein models of estrogen receptor alpha in the active and inactive form sustained the results of the yeast estrogen assay and supported the concept of plant lignans as phytoestrogens.

Genistein inhibits placental choriocarcinoma cell line JAR invasion through ERβ/MTA3/Snail/E-cadherin pathway

Genistein, the most abundant phytoestrogen in soybeans, may bind to estrogen receptors and perform anticancer activities. Choriocarcinoma is a malignant, trophoblastic and aggressive cancer of the placenta. Few studies are currently available concerning the effects of genistein on choriocarcinoma. In the present study, we investigated the effect of genistein on the invasive potential of the choriocarcinoma cell line JAR and its underlying mechanism. Our data revealed that genistein inhibited JAR cell invasion in a dose-dependent manner by a matrigel invasion assay. Moreover, genistein was found to have decreased the metastasis-associated gene MTA3 mRNA level, increased the transcriptional suppressor Snail mRNA level and upregulated the protein expression of the cell-cell adhesion molecule E-cadherin by real-time RT-PCR and Western blot analysis, respectively. ERβ siRNA was used to knock down ERβ expression in JAR cells. In the ERβ-knockdown JAR cells, genistein failed to inhibit JAR cell invasion. The effects of genistein on MTA3, Snail and E-cadherin expression were also eradicated following ERβ siRNA transfection. These results demonstrated that genistein triggered the MTA3/Snail/E-cadherin regulatory pathway by binding with ERβ, thereby inhibiting JAR cell invasion. In conclusion, our findings have significant implications for the prevention and therapy of choriocarcinoma.

5- and 4'-Hydroxylated flavonoids affect voltage gating of single alpha-hemolysin pore

Molecular mechanisms of the influence of flavonoids on the voltage gating of a single alpha-hemolysin channel in planar lipid membranes are studied. It is shown that the addition of flavonoids hydroxylated in position 5 of the A-ring and in position 4' of the B-ring into bilayer bathing solution shifts the voltage dependence of channel switching from high- to low-conductance states to voltages nearer zero. It is concluded that the effect is likely to be attributed to a specific interaction of at least three flavonoid molecules with the voltage sensor of an alpha-hemolysin pore. Possible flavonoid binding sites and identification of amino acid residues included into the voltage sensor domain of the alpha-hemolysin channel are discussed.

iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis

BACKGROUND

Pharmacological interactions are useful for understanding ligand binding mechanisms of a therapeutic target. These interactions are often inferred from a set of active compounds that were acquired experimentally. Moreover, most docking programs loosely coupled the stages (binding-site and ligand preparations, virtual screening, and post-screening analysis) of structure-based virtual screening (VS). An integrated VS environment, which provides the friendly interface to seamlessly combine these VS stages and to identify the pharmacological interactions directly from screening compounds, is valuable for drug discovery.

RESULTS

We developed an easy-to-use graphic environment, iGEMDOCK, integrating VS stages (from preparations to post-screening analysis). For post-screening analysis, iGEMDOCK provides biological insights by deriving the pharmacological interactions from screening compounds without relying on the experimental data of active compounds. The pharmacological interactions represent conserved interacting residues, which often form binding pockets with specific physico-chemical properties, to play the essential functions of a target protein. Our experimental results show that the pharmacological interactions derived by iGEMDOCK are often hot spots involving in the biological functions. In addition, iGEMDOCK provides the visualizations of the protein-compound interaction profiles and the hierarchical clustering dendrogram of the compounds for post-screening analysis.

CONCLUSIONS

We have developed iGEMDOCK to facilitate steps from preparations of target proteins and ligand libraries toward post-screening analysis. iGEMDOCK is especially useful for post-screening analysis and inferring pharmacological interactions from screening compounds. We believe that iGEMDOCK is useful for understanding the ligand binding mechanisms and discovering lead compounds. iGEMDOCK is available at http://gemdock.life.nctu.edu.tw/dock/igemdock.php.

3D models of lamprey progesterone receptor complexed with progesterone, 7α-hydroxy-progesterone and 15α-hydroxy-progesterone

Sea lamprey, a basal vertebrate, contains a progesterone receptor [PR]. An unusual property of lamprey is that gonadotropin-releasing hormone induces synthesis of 15α-hydroxy-progesterone [15α-OH-P] instead of progesterone. There also is indirect evidence for 7α-OH-P in lamprey serum. To determine if there is a structural basis for the binding of 7α-OH-P and 15α-OH-P to lamprey PR, we constructed 3D models of the lamprey PR complexed with progesterone, 7α-OH-P and 15α-OH-P. These 3D models reveal that Met-277 in lamprey PR has a specific interaction with the 15α-hydroxyl on 15α-OH-P and with Met-192, which also contacts the 15α-hydroxyl group. We also find that 7α-OH-P has favorable contacts with side-chains in lamprey PR. BLAST searches reveal that Met-277 on lamprey PR is unique among vertebrate PRs. This unique site on lamprey PR could be a target for compounds to control reproduction in sea lamprey, an environmental pest in Lake Michigan.

Characterization of the estradiol-binding site structure of human pancreas-specific protein disulfide isomerase: indispensable role of the hydrogen bond between His278 and the estradiol 3-hydroxyl group

Estradiol (E(2)), a female sex hormone, has important biological functions. Human pancreas-specific protein disulfide isomerase (PDIp), a protein folding catalyst, was recently found to be able to bind E(2). Here we report the characterization of its E(2)-binding site by using biochemical methods coupled with molecular modeling tools. Analysis of various truncated PDIp proteins showed that the b-b' fragment contains an intact E(2)-binding site that has the same binding affinity as the full-length PDIp protein, with apparent K(d) values of approximately 170 nM. Computational modeling and docking analyses revealed that the E(2)-binding site in the b-b' fragment is located in a hydrophobic pocket composed mainly of the b' domain and partially of the b domain. The hydrogen bond, formed between the 3-hydroxyl group of E(2) (donor) and PDIp's His278 (acceptor), is indispensable for its binding. By contrast, the 17β-hydroxyl group of E(2) is of negligible importance for E(2) binding. This binding model was jointly confirmed by a series of experiments, such as selective mutation of the binding site amino acid residues and selective modification of the ligand structures.

Endocrine disrupting chemicals targeting estrogen receptor signaling: identification and mechanisms of action

Many endocrine disrupting chemicals (EDCs) adversely impact estrogen signaling by interacting with two estrogen receptors (ERs): ERα and ERβ. Though the receptors have similar ligand binding and DNA binding domains, ERα and ERβ have some unique properties in terms of ligand selectivity and target gene regulation. EDCs that target ER signaling can modify genomic and nongenomic ER activity through direct interactions with ERs, indirectly through transcription factors such as the aryl hydrocarbon receptor (AhR), or through modulation of metabolic enzymes that are critical for normal estrogen synthesis and metabolism. Many EDCs act through multiple mechanisms as exemplified by chemicals that bind both AhR and ER, such as 3-methylcholanthrene. Other EDCs that target ER signaling include phytoestrogens, bisphenolics, and organochlorine pesticides, and many alter normal ER signaling through multiple mechanisms. EDCs can also display tissue-selective ER agonist and antagonist activities similar to selective estrogen receptor modulators (SERMs) designed for pharmaceutical use. Thus, biological effects of EDCs need to be carefully interpreted because EDCs can act through complex tissue-selective modulation of ERs and other signaling pathways in vivo. Current requirements by the U.S. Environmental Protection Agency require some in vitro and cell-based assays to identify EDCs that target ER signaling through direct and metabolic mechanisms. Additional assays may be useful screens for identifying EDCs that act through alternative mechanisms prior to further in vivo study.

The pros and cons of phytoestrogens

Phytoestrogens are plant derived compounds found in a wide variety of foods, most notably soy. A litany of health benefits including a lowered risk of osteoporosis, heart disease, breast cancer, and menopausal symptoms, are frequently attributed to phytoestrogens but many are also considered endocrine disruptors, indicating that they have the potential to cause adverse health effects as well. Consequently, the question of whether or not phytoestrogens are beneficial or harmful to human health remains unresolved. The answer is likely complex and may depend on age, health status, and even the presence or absence of specific gut microflora. Clarity on this issue is needed because global consumption is rapidly increasing. Phytoestrogens are present in numerous dietary supplements and widely marketed as a natural alternative to estrogen replacement therapy. Soy infant formula now constitutes up to a third of the US market, and soy protein is now added to many processed foods. As weak estrogen agonists/antagonists with molecular and cellular properties similar to synthetic endocrine disruptors such as Bisphenol A (BPA), the phytoestrogens provide a useful model to comprehensively investigate the biological impact of endocrine disruptors in general. This review weighs the evidence for and against the purported health benefits and adverse effects of phytoestrogens.

Development of a nanoparticle-based FRET sensor for ultrasensitive detection of phytoestrogen compounds

Phytoestrogens are plant compounds that mimic the actions of endogenous estrogens. The abundance of these chemicals in nature and their potential effects on health require the development of a convenient method to detect phytoestrogens. We have developed a nanoparticle (NP)-conjugated FRET probe based on the human estrogen receptor α (ER) ligand-binding domain (LBD) to detect phytoestrogens. The NP-conjugated FRET probe showed fluorescence signals for genistein, resveratrol and daidzein compounds with Δ ratios of 1.65, 2.60 and 1.37 respectively, which are approximately six times greater compared to individual FRET probes. A significantly higher signal for resveratrol versus genistein and daidzein indicates that the probe can differentiate between antagonistic phytoalexin substances and agonistic isoflavone compounds. NP-conjugated probes demonstrated a wide dynamic range, ranging from 10(-18) to 10(-1) M with EC(50) values of 9.6 × 10(-10), 9.0 × 10(-10) and 9.2 × 10(-10) M for genistein, daidzein and resveratrol respectively, whereas individual probes detected concentrations of 10(-13) to 10(-4) M for phytoestrogens compounds. The time profile revealed that the NP-conjugated probe is stable over 30 h and there is not a significant deviation in the FRET signal at room temperature. These data demonstrate that conjugation of a FRET probe to nanoparticles is able to serve as an effective FRET sensor for monitoring bioactive compounds with significantly increased sensitivity, dynamic range and stability.

Cytotoxic flavonoids as agonists of peroxisome proliferator-activated receptor gamma on human cervical and prostate cancer cells

We conducted in silico screening for human peroxisome proliferator-activated receptor gamma (hPPARgamma) by performing an automated docking study with 450 flavonoids. Among the eight flavonoids as possible agonists of hPPARgamma, only 3,6-dihydroxyflavone (4) increased the binding between PPARgamma and steroid receptor coactivator-1 (SRC-1), approximately 5-fold, and showed one order higher binding affinity for PPARgamma than a reference compound, indomethacin. The 6-hydroxy group of the A-ring of 3,6-dihydroxyflavone (4) participated in hydrogen-bonding interactions with the side chain of Tyr327, His449, and Tyr473. The B-ring formed a hydrophobic interaction with Leu330, Leu333, Val339, Ile341, and Met364. Therefore, 3,6-dihydroxyflavone is a potent agonist of hPPAR with cytotoxic effects on human cervical and prostate cancer cells.