Energetic analysis of binding of progesterone and 5{beta}-androstane-3,17-dione to anti-progesterone antibody DB3 using molecular dynamics and free energy calculations

Molecular dynamics simulations and molecular mechanics–Poisson–Boltzmannsurface area (MM-PBSA) free energy calculations were used tostudy the energetics of the binding of progesterone (PRG) and5ß-androstane-3,17-dione (5AD) to anti-PRG antibodyDB3. Although the two steroids bind to DB3 in different orientations,their binding affinities are of the same magnitude, 1 nM forPRG and 8 nM for 5AD. The calculated relative binding free energyof the steroids, 8.8 kJ/mol, is in fair agreement with the experimentalenergy, 5.4 kJ/mol. In addition, computational alanine scanningwas applied to study the role of selected amino acid residuesof the ligand-binding site on the steroid cross-reactivity.The electrostatic and van der Waals components of the totalbinding free energies were found to favour more the bindingof PRG, whereas solvation energies were more favourable forthe binding of 5AD. The differences in the free energy componentsare due to the binding of the A rings of the steroids to differentbinding pockets: PRG is bound to a pocket in which electrostaticantibody–steroid interactions are dominating, whereas5AD is bound to a pocket in which van der Waals and hydrophobicinteractions dominate.     

Nonspecific and metabolic interactions between steroid hormones and human plasma lipoproteins

Previous observations demonstrated that steroid hormones associate with plasma lipoproteins. The objective of this study was to estimate the relative importance of lipoproteins as steroid hormone binding agents in comparison to sex hormone binding globulin, corticosteroid binding globulin, and albumin in both normal and hyperlipidemic human plasma. The 16 steroid hormones and related metabolites included in the study were: androstanediol, androstenediol, androstenedione, androsterone, corticosterone, cortisol, dehydroepiandrosterone, deoxycorticosterone, dihydrotestosterone, estradiol, estriol, estrone, 17α-hydroxyprogesterone, pregnenolone, progesterone, and testosterone. The binding activity of these 16 steroid hormones with purified high density lipoprotein (HDL), low density lipoprotein and very low density lipoprotein were separately evaluated by equilibrium dialysis incubations to yield 48 steroid hormone-lipoprotein combinations for further study. In incubations with HDL, six steroid hormones (androstenediol, dehydroepiandrosterone, dihydrotestosterone, estradiol, pregnenolone, and progesterone) were identified as non-equilibrium, apparently due to metabolic conversion of the steroid hormones. The metabolic activity for the three Δ⁵-3β hydroxy steroids and estradiol appears to be fatty acid esterification by lecithin:cholesterol acyltransferase. The computer program TRANSPORT, which was used to evaluate only the nonspecific steroid hormone-lipoprotein association levels in a 16×6 matrix at simultaneous equilibrium, indicated that lipoprotein-bound steroid hormones ranged from 1% for cortisol to 56% for pregnenolone in normal human blood. Simulated projections of the increase in nonspecific steroid hormone association with lipoproteins during hyperlipidemia are also presented. These results demonstrate how lipoproteins are likely to be important in the transport and metabolism of steroid hormones in human plasma.     

Molecular dynamics studies of AChBP with nicotine and carbamylcholine: the role of water in the binding pocket

The acetylcholine-binding protein (AChBP) is homologous to the ligand-binding domain of the nicotinic acetylcholine receptor (nAChR) and other members of the Cys-loop family of neurotransmitter receptors. The high-resolution X-ray structures of AChBP mean it has been used as a model from which to understand agonist and antagonist binding to nAChRs. We present here a molecular dynamics (MD) study of AChBP with nicotine and carbamylcholine bound. Our results suggest that the ligand imposes rigidity on the binding pocket residues. The simulations also suggest that the protein undergoes breathing motions with respect to the five-fold axis, a motion that has been postulated to be related to gating in the nAChR. We analyzed the behaviour of the water molecules in and around the binding site and found that they occupied five distinct sites within the binding pocket. Water occupied these sites in the absence of ligand, but the presence of ligand increased the probability that a water molecule would be found in these sites. Finally, we demonstrate how the positions of these waters might be used in the design of new ligands by comparing the positions of these sites with other recent structures.     

Key to Life: Physiological Role and Clinical Implications of Progesterone

The most recent studies of progesterone research provide remarkable insights into the physiological role and clinical importance of this hormone. Although the name progesterone itself means “promoting gestation”, this steroid hormone is far more than a gestational agent. Progesterone is recognized as a key physiological component of not only the menstrual cycle and pregnancy but also as an essential steroidogenic precursor of other gonadal and non-gonadal hormones such as aldosterone, cortisol, estradiol, and testosterone. Based on current findings, progesterone and novel progesterone-based drugs have many important functions, including contraception, treatment of dysfunctional uterine bleeding, immune response, and prevention of cancer. Considering the above, reproduction and life are not possible without progesterone; thus, a better understanding of this essential molecule could enable safe and effective use of this hormone in many clinical conditions.     

Relationships Between Sex and Stress Hormone Levels in Feces and Marking Behavior in a Wild Population of Iberian Wolves (Canis lupus signatus)

Feces deposited by the breeding alpha pair on exposed substrates and/or zones may act as visual and olfactory marks associated with social dominance in wolves. The aim of this study was to determine if there was a correlation between marking behavior, sex hormone levels, and physiological stress in a wild population of Iberian wolves in Northwest Spain. The glucocorticoid and sex hormone levels were measured in feces collected as a function of exposure (conspicuous/inconspicuous), height (above ground level/at ground level), and strategic location in the habitat (at crossroads/off crossroads), as well as the frequency of re-marking. The feces, believed to serve as marking cues, had higher glucocorticoid levels (cortisol) and sex hormones (testosterone, progesterone, and estradiol). The results suggest that in Iberian wolves, the alpha pair is subject to higher social stress than subordinate individuals, and that the reproductive suppression of subordinates is not mediated by chronic glucocorticoid elevation.     

Sex pheromones of the sea lamprey (Petromyzon marinus): Steroid studies

Pheromone-containing and pheromone-devoid samples of male sea lamprey (Petromyzon marinus) urine were analyzed for the concentrations of nine steroids [dehydroepiandrosterone (DHEA), testosterone (T), dihydrotestosterone (DHT), progesterone (P), androstenedione (A), estrone (E₁), estradiol (E₂), corticosterone (B), and cortisol (F)] by radioimmunoassay (RIA). Samples analyzed included native urine that had been enzymatically hydrolyzed with mixed -glucuronidase/sulfatase. Values of the analyses were used to prepare solutions of the individual steroids for bioassay at concentrations which bracketed the urinary concentrations. Results show that only testosterone elicited a preference response in spawning-run female sea lampreys, and in concentrations three to four orders of magnitude greater than those found in active, unhydrolyzed male urine. The possibility that testosterone acts as a pheromone in this species is discussed.     

Effects of free fatty acids on the binding of steroid hormones to bovine serum albumin

The effects of binding of free fatty acids (FFA) to bovine serum albumin (BSA) on steroid hormone binding to BSA were examined. The FFA studied included myristic, palmitic, stearic, oleic and linoleic acids. The binding coefficient K was estimated from the changes in the equilibrium partition coefficient between the aqueous and the hexane phase caused by the addition to BSA to the aqueous phase. A noticeable effect of FFA binding (molar ratio FFA/BSA, 2∶1) on the affinities of α-estradiol, ethynylestradiol and dehydroisoandrosterone to BSA was not observed: however, the affinities of progesterone, androsterone and testosterone were distinctly enhanced by FFA binding. Furthermore, the elution profiles of gel filtration chromatography clearly showed that progesterone and testosterone are easily liberated from the hormone/BSA complexes and that stronger binding of these hormones to BSA is caused by binding of FFA to BSA. The affinity of ethynylestradiol to BSA is stronger than that of progesterone and testosterone and is not affected by palmitic acid binding to BSA.     

Creation of GPCR-based chemical sensors by directed evolution in yeast

G protein-coupled receptors (GPCRs) form a class of biological chemical sensors with an enormous diversity in ligand binding and sensitivity. To explore structural aspects of ligand recognition, we subjected the human UDP-glucose receptor (P2Y14) functionally expressed in the yeast Saccharomyces to directed evolution. We sought to generate new receptor subtypes with ligand-binding properties that would be useful in the development of practical biosensors. Mutagenesis of the entire UDP-glucose receptor gene yielded receptors with increased activity but similar ligand specificities, while random mutagenesis of residues in the immediate vicinity of the ligand-binding pocket yielded mutants with altered ligand specificity. By first sensitizing the P2Y14 receptor and then redirecting ligand specificity, we were able to create mutant receptors suitable for a simple biosensor. Our results demonstrate the feasibility of altering receptor ligand-binding properties via a directed evolution strategy, using standard yeast genetic techniques. The novel receptor mutants can be used to detect chemical ligands in complex mixtures and to discriminate among chemically or stereochemically related compounds. Specifically, we demonstrate how engineered receptors can be applied in a pairwise manner to differentiate among several chemical analytes that would be indistinguishable with a single receptor. These experiments demonstrate the feasibility of a combinatorial approach to detector design based on the principles of olfaction.     

Mapping the Binding Sites of UDP and Prostaglandin E2 Glyceryl Ester in the Nucleotide Receptor P2Y6

Cyclooxygenase-2 catalyzes the biosynthesis of prostaglandins from arachidonic acid and the biosynthesis of prostaglandin glycerol esters (PG-Gs) from 2-arachidonoylglycerol. PG-Gs are mediators of several biological actions such as macrophage activation, hyperalgesia, synaptic plasticity, and intraocular pressure. Recently, the human UDP receptor P2Y₆ was identified as a target for the prostaglandin E2 glycerol ester (PGE₂-G). Here, we show that UDP and PGE₂-G are evolutionary conserved endogenous agonists at vertebrate P2Y₆ orthologs. Using sequence comparison of P2Y₆ orthologs, homology modeling, and ligand docking studies, we proposed several receptor positions participating in agonist binding. Site-directed mutagenesis and functional analysis of these P2Y₆ mutants revealed that both UDP and PGE₂-G share in parts one ligand-binding site. Thus, the convergent signaling of these two chemically very different agonists has already been manifested in the evolutionary design of the ligand-binding pocket.     

The binding mode of progesterone to its receptor deduced from molecular dynamics simulations

An unambiguous understanding of the binding mode of human progesterone to its receptor still eludes experimental search. According to the X-ray structure of the ligand-binding domain, only one (O3) of the two keto groups at the ligand ends (O3 and O20) should play a role. This result is in conflict with chemical intuition and the results of site-directed mutagenesis experiments. Herein, we report classical molecular dynamics simulations that reveal the dynamic nature of the binding in solution, elucidate the reasons why X-ray studies failed to determine the role of O20, and clarify the effects of the mutations. The predictive power of the force field is ensured by the consistent introduction of a first-principles representation of the ligand.     

Synthesis, 3D‐QSAR,and Structural Modeling of Benzolactam Derivatives with Binding Affinity for the D2 and D3 Receptors

A series of 37 benzolactam derivatives were synthesized, and their respective affinities for the dopamine D₂ and D₃ receptors evaluated. The relationships between structures and binding affinities were investigated using both ligand‐based (3D‐QSAR) and receptor‐based methods. The results revealed the importance of diverse structural features in explaining the differences in the observed affinities, such as the location of the benzolactam carbonyl oxygen, or the overall length of the compounds. The optimal values for such ligand properties are slightly different for the D₂ and D₃ receptors, even though the binding sites present a very high degree of homology. We explain these differences by the presence of a hydrogen bond network in the D₂ receptor which is absent in the D₃ receptor and limits the dimensions of the binding pocket, causing residues in helix 7 to become less accessible. The implications of these results for the design of more potent and selective benzolactam derivatives are presented and discussed.     

Effect of various steroids on the biosynthesis of arachidonic acid in isolated hepatocytes and HTC cells

The effect of various steroids on the incorporation and desaturation of eicosa-8,11,14-trienoic acid in normal hepatocytes and HTC cells was investigated. After 3 hr incubation with 11-deoxycorticosterone, both kinds of cells showed an increase in the incorporation of eicosatrienoic acid. In contrast, progesterone, cortexolone, 17-β-estradiol, testosterone, estriol, aldosterone, corticosterone, dexamethasone, dehydroepiandrosterone, 11-β-hydroxyandrosterone, 11-ketoaetiocholanolone, epiaetiocholanolone and 5-β-pregnane-3α,20α-diol, provoked no significant changes in the uptake of the exogenous acid. Of all the steroids tested, only 11-dexycorticosterone, dexamethasone and 17-β-estradiol evoked a significant inhibition on the arachidonate biosynthesis in both kinds of cells. Testosterone, estriol, aldosterone and corticosterone provoked a significant inhibition of Δ5-desaturase in HTC cells. In dexamethasone, this effect was dose-dependent (0 to 10⁻⁴ M). Simultaneous incubation with 17-β- estradiol or 11-deoxycorticosterone with dexamethasone led to an extent of inhibition on arachidonate biosynthesis that did not surpass the effect of each drug. Pretreatment of isolated hepatocytes with the antiglucocorticoid, cortexolone, prevented the dexamethasone-induced inhibition of arachidonate biosynthesis. Normal rat liver microsomes preincubated in vitro with dexamethasone, 11-deoxycorticosterone, 17-β-estradiol, corticosterone or estriol (10⁻⁶ or 10⁻⁴ M concentration), showed no significant changes in the Δ5-desaturase activity. The results obtained suggest that the effect of the steroids on arachidonic acid biosynthesis in normal hepatocytes and HTC cells requires receptor occupancy and probably is mediated through a common biochemical mechanism.     

Partial Agonistic Actions of Sex Hormone Steroids on TRPM3 Function

Sex hormone steroidal drugs were reported to have modulating actions on the ion channel TRPM3. Pregnenolone sulphate (PS) presents the most potent known endogenous chemical agonist of TRPM3 and affects several gating modes of the channel. These includes a synergistic action of PS and high temperatures on channel opening and the PS-induced opening of a noncanonical pore in the presence of other TRPM3 modulators. Moreover, human TRPM3 variants associated with neurodevelopmental disease exhibit an increased sensitivity for PS. However, other steroidal sex hormones were reported to influence TRPM3 functions with activating or inhibiting capacity. Here, we aimed to answer how DHEAS, estradiol, progesterone and testosterone act on the various modes of TRPM3 function in the wild-type channel and two-channel variants associated with human disease. By means of calcium imaging and whole-cell patch clamp experiments, we revealed that all four drugs are weak TRPM3 agonists that share a common steroidal interaction site. Furthermore, they exhibit increased activity on TRPM3 at physiological temperatures and in channels that carry disease-associated mutations. Finally, all steroids are able to open the noncanonical pore in wild-type and DHEAS also in mutant TRPM3. Collectively, our data provide new valuable insights in TRPM3 gating, structure-function relationships and ligand sensitivity.     

Molecular Recognition of Two 2,4‐syn‐Functionalized (S)‐Glutamate Analogues by the Kainate Receptor GluK3 Ligand Binding Domain

The kainate receptors are the least studied subfamily of ionotropic glutamate receptors. These receptors are thought to have a neuromodulatory role and have been associated with a variety of disorders in the central nervous system. This makes kainate receptors interesting potential drug targets. Today, structures of the ligand binding domain (LBD) of the kainate receptor GluK3 are only known in complex with the endogenous agonist glutamate, the natural product kainate, and two synthetic agonists. Herein we report structures of GluK3 LBD in complex with two 2,4‐syn‐functionalized (S)‐glutamate analogues to investigate their structural potential as chemical scaffolds. Similar binding affinities at GluK3 were determined for the 2‐(methylcarbamoyl)ethyl analogue (K_i=4.0 μM ) and the 2‐(methoxycarbonyl)ethyl analogue (K_i=1.7 μM ), in agreement with the similar positioning of the compounds within the binding pocket. As the binding affinity is similar to that of glutamate, this type of Cγ substituent could be used as a scaffold for introduction of even larger substituents reaching into unexplored binding site regions to achieve subtype selectivity.     

CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations

Because of the large flexibility and malleability of Cytochrome P450 enzymes (CYPs), in silico prediction of CYP binding affinities to drugs and other xenobiotic compounds is a true challenge. In the current work, we use an iterative linear interaction energy (LIE) approach to compute CYP binding affinities from molecular dynamics (MD) simulation. In order to improve sampling of conformational space, we combine results from simulations starting with different relevant protein-ligand geometries. For calculated binding free energies of a set of thiourea compounds binding to the flexible CYP 2D6 isoform, improved correlation with experiment was obtained by combining results ofMDruns starting from distinct protein conformations and ligand-binding orientations. This accuracy was obtained from relatively short MD simulations, which makes our approach computationally attractive for automated calculations of ligand-binding affinities to flexible proteins such as CYPs.     

Discovering small-molecule estrogen receptor α/coactivator binding inhibitors: high-throughput screening, ligand development, and models for enhanced potency

Small molecules, namely coactivator binding inhibitors (CBIs), that block estrogen signaling by directly inhibiting the interaction of the estrogen receptor (ER) with coactivator proteins act in a fundamentally different way to traditional antagonists, which displace the endogenous ligand estradiol. To complement our prior efforts at CBI discovery by de?novo design, we used high-throughput screening (HTS) to identify CBIs of novel structure and subsequently investigated two HTS hits by analogue synthesis, finding many compounds with low micromolar potencies in cell-based reporter gene assays. We examined structure-activity trends in both series, using induced-fit computational docking to propose binding poses for these molecules in the coactivator binding groove. Analysis of the structure of the ER-steroid receptor coactivator (SRC) complex suggests that all four hydrophobic residues within the SRC nuclear receptor box sequence are important binding elements. Thus, insufficient water displacement upon binding of the smaller CBIs in the expansive complexation site may be limiting the potency of the compounds in these series, which suggests that higher potency CBIs might be found by screening compound libraries enriched with larger molecules.     

A new test to identify endocrine disruptors using sex hormone‐binding globulins from human serum

Based on the concept in clinical diagnostics that the principal binding protein in blood for estrogens and androgens, sex hormone‐binding globulin (SHBG), determines the estrogenic/androgenic status of humans, a new assay was developed. The format of this assay was similar to a competitive radioimmuno assay, wherein SBHG as capture protein was coupled to microtiter plates coated with anti‐SHBG antibody and tritiated estradiol was used as a tracer. Due to its affinity for SHBG relative to estradiol, testosterone was selected as sensitive reference compound to assess any estrogenic activity of environmental contaminants and a reference curve was established. Test compounds included endogenous steroids, pharmaceutical substances, pesticides and industrial pollutants. For each test compound a competition curve of similar shape was obtained and compared to that of testosterone. Displacement of tritiated estradiol indicated an affinity of a certain substance for SHBG and, consequently, an estrogenic activity. Among the compounds tested, strong displacement was demonstrated for estradiol, diethylstilbestrol (DES), norgestrel, permithrin, nonylphenol and bisphenol‐A; followed by dehydro‐isoandrosterone, 6a‐methylprednisolone, androsterone, 2,4‐D, dichlofluanid, vinclozolin, and malathion. No affinity could be observed for atrazin, simazin, hexaconazole, tebuconazole, glyphosate, and aldicarb. Further, combinations of some of the compounds tested showed no additive or synergistic effects. Our data are discussed in relation to those reported in the literature. Other hormone‐binding proteins from human blood are proposed for further research on hormone‐disrupting xenobiotics.