Binding of Genistein to the Estrogen Receptor Based on an Experimental Electron Density Study

Estrogenic flavonoids and their molecular mechanisms of action

Flavonoids are a major group of phytoestrogens associated with physiological effects, and ecological and social impacts. Although the estrogenic activity of flavonoids was reported by researchers in the fields of medical, environmental and food studies, their molecular mechanisms of action have not been comprehensively reviewed. The estrogenic activity of the respective classes of flavonoids, anthocyanidins/anthocyanins, 2-arylbenzofurans/3-arylcoumarins/α-methyldeoxybenzoins, aurones/chalcones/dihydrochalcones, coumaronochromones, coumestans, flavans/flavan-3-ols/flavan-4-ols, flavanones/dihydroflavonols, flavones/flavonols, homoisoflavonoids, isoflavans, isoflavanones, isoflavenes, isoflavones, neoflavonoids, oligoflavonoids, pterocarpans/pterocarpenes, and rotenone/rotenoids, was summarized through a comprehensive literature search, and their structure-activity relationship, biological activities, signaling pathways, and applications were discussed. Although the respective classes of flavonoids contained at least one chemical mimicking estrogen, the mechanisms varied, such as those with estrogenic, anti-estrogenic, non-estrogenic, and biphasic activities, and additional activities through crosstalk/bypassing, which exert biological activities through cell signaling pathways. Such mechanistic variations of estrogen action are not limited to flavonoids and are observed among other broad categories of chemicals, thus this group of chemicals can be termed as the "estrogenome". This review article focuses on the connection of estrogen action mainly between the outer and the inner environments, which represent variations of chemicals and biological activities/signaling pathways, respectively, and form the basis to understand their applications. The applications of chemicals will markedly progress due to emerging technologies, such as artificial intelligence for precision medicine, which is also true of the study of the estrogenome including estrogenic flavonoids.

Switching from Aromatase Inhibitors to Dual Targeting Flavonoid-Based Compounds for Breast Cancer Treatment

Despite the significant outcomes attained by scientific research, breast cancer (BC) still represents the second leading cause of death in women. Estrogen receptor-positive (ER+) BC accounts for the majority of diagnosed BCs, highlighting the disruption of estrogenic signalling as target for first-line treatment. This goal is presently pursued by inhibiting aromatase (AR) enzyme or by modulating Estrogen Receptor (ER) α. An appealing strategy for fighting BC and reducing side effects and resistance issues may lie in the design of multifunctional compounds able to simultaneously target AR and ER. In this paper, previously reported flavonoid-related potent AR inhibitors were suitably modified with the aim of also targeting ERα. As a result, homoisoflavone derivatives 3b and 4a emerged as well-balanced submicromolar dual acting compounds. An extensive computational study was then performed to gain insights into the interactions the best compounds established with the two targets. This study highlighted the feasibility of switching from single-target compounds to balanced dual-acting agents, confirming that a multi-target approach may represent a valid therapeutic option to counteract ER+ BC. The homoisoflavone core emerged as a valuable natural-inspired scaffold for the design of multifunctional compounds.

Real-Space Interpretation of Interatomic Charge Transfer and Electron Exchange Effects by Combining Static and Kinetic Potentials and Associated Vector Fields

Intricate behaviour of one-electron potentials from the Euler equation for electron density and corresponding gradient force fields in crystals was studied. Channels of locally enhanced kinetic potential and corresponding saddle Lagrange points were found between chemically bonded atoms. Superposition of electrostatic ϕ e s r and kinetic ϕ k r potentials and electron density ρ r allowed partitioning any molecules and crystals into atomic ρ - and potential-based ϕ -basins; ϕ k -basins explicitly account for the electron exchange effect, which is missed for ϕ e s -ones. Phenomena of interatomic charge transfer and related electron exchange were explained in terms of space gaps between zero-flux surfaces of ρ - and ϕ -basins. The gap between ϕ e s - and ρ -basins represents the charge transfer, while the gap between ϕ k - and ρ -basins is a real-space manifestation of sharing the transferred electrons caused by the static exchange and kinetic effects as a response against the electron transfer. The regularity describing relative positions of ρ -, ϕ e s -, and ϕ k - basin boundaries between interacting atoms was proposed. The position of ϕ k -boundary between ϕ e s - and ρ -ones within an electron occupier atom determines the extent of transferred electron sharing. The stronger an H⋅⋅⋅O hydrogen bond is, the deeper hydrogen atom's ϕ k -basin penetrates oxygen atom's ρ -basin, while for covalent bonds a ϕ k -boundary closely approaches a ϕ e s -one indicating almost complete sharing of the transferred electrons. In the case of ionic bonds, the same region corresponds to electron pairing within the ρ -basin of an electron occupier atom.

IRMPD Spectroscopy of Bare Monodeprotonated Genistein, an Antioxidant Flavonoid

Genistein is a naturally occurring polyphenol belonging to the family of flavonoids with estrogenic properties and proven antioxidant, anti-inflammatory, and hormonal effects. Genistein and its derivatives are involved in radical scavenging activity by way of mechanisms based on sequential proton-loss electron transfer. In view of this role, a detailed structural characterization of its bare deprotonated form, [geni-H]^-, generated by electrospray ionization, has been performed by tandem mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy in the 800-1800 cm^-1 spectral range. Quantum chemical calculations at the B3LYP/6-311+G(d,p) level of theory were carried out to determine geometries, thermochemical data, and anharmonic vibrational properties of low-lying isomers, enabling to interpret the experimental spectrum. Evidence is gathered that the conjugate base of genistein exists as a single isomeric form, which is deprotonated at the most acidic site (7-OH) and benefits from a strong intramolecular H-bond interaction between 5-OH and the adjacent carbonyl oxygen in the most stable arrangement.

Comparative Study of Natural Antioxidants from Glycine max, Anethum graveolensand Pimpinella anisum Seed and Sprout Extracts Obtained by Ultrasound-Assisted Extraction

The study aimed to evaluate the antioxidant potential of sprout and seed extracts from three species of plants, namely Glycine max (GMsp-sprouts, GMsd-seeds), Anethum graveolens (AGsp-sprouts, AGsd-seeds) and Pimpinella anisum (PAsp-sprouts, PAsd-seeds), which are widely accepted by consumers and have various applications in food flavoring, and also in natural medical treatments in the pharmaceutical industries. These plants are rich in valuable compounds that show a remarkable antioxidant power and are associated with many health benefits. Ethanol extracts were obtained by ultrasound-assisted extraction and they were comparatively evaluated for their in vitro antioxidant properties. The extracts were characterized by HPTLC, HPLC-DAD, total phenol content (TPC), total flavonoid content (TFC) analysis and antioxidant activities with different assays, such as total antioxidant capacity (TAC), 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) radical cation decolorization assay (ABTS), 1,1-diphenyl 1-2-picryl-hydrazyl (DPPH) and iron binding ability of chelators. Our results showed that the sprout and seed extracts of the studied plants exhibited a high content of phytochemicals and promising antioxidant properties. The highest polyphenols content was detected for AGsd (53.02 ± 0.57 mg/g DW), PAsd (48.75 ± 0.34 mg/g DW) and the highest flavonoids content for PAsp (26.84 ± 0.57 mg/g DW). Moreover, the presence of valuable compounds was demonstrated by using HPTLC, FT-IR and HPLC-DAD techniques. In order to have a better understanding of the relationship between the biological properties and the electronic structure, a molecular modelling study of genistein was also conducted. Our approach to the comparative assessment of these three plant species was based on a priori knowledge from literature data; however, this study demonstrated that these plant extracts of seeds and also sprouts are excellent sources of natural antioxidants. Significant additional differences that were found in the phytochemical composition could be exploited in future research for pharmaceutical purposes.

The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals

The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

Estimating electron density at the bond critical point through atomic Hirshfeld surfaces

Interatomic surfaces often carry information related to the electron distribution in a molecule or crystal, not only being a visual aid but also enabling quantitative analyses. Under certain conditions, atomic Hirshfeld surfaces present a high resemblance to the interatomic surfaces obtained through the quantum theory of atoms in molecules (QTAIM), with the advantage of being easily calculated, even for crystal structures determined at low resolutions (i.e. when a charge-density refinement is not performed). Here an empirical relation between the curvedness property of the Hirshfeld surfaces and the electron density at the bond critical point for certain types of covalent and coordination interactions involving carbon atoms has been obtained. The exponential function was tested to estimate the electron density in different crystalline systems, and the highest deviation from reference values obtained through QTAIM was just 16%. Additionally, fine details of this fit may be salient to the difference in electronegativity of the atoms involved in the bond.

Real-Time Analysis of Polyphenol-Protein Interactions by Surface Plasmon Resonance Using Surface-Bound Polyphenols

A selection of bioactive polyphenols of different structural classes, such as the ellagitannins vescalagin and vescalin, the flavanoids catechin, epicatechin, epigallocatechin gallate (EGCG), and procyanidin B2, and the stilbenoids resveratrol and piceatannol, were chemically modified to bear a biotin unit for enabling their immobilization on streptavidin-coated sensor chips. These sensor chips were used to evaluate in real time by surface plasmon resonance (SPR) the interactions of three different surface-bound polyphenolic ligands per sensor chip with various protein analytes, including human DNA topoisomerase IIα, flavonoid leucoanthocyanidin dioxygenase, B-cell lymphoma 2 apoptosis regulator protein, and bovine serum albumin. The types and levels of SPR responses unveiled major differences in the association, or lack thereof, and dissociation between a given protein analyte and different polyphenolic ligands. Thus, this multi-analysis SPR technique is a valuable methodology to rapidly screen and qualitatively compare various polyphenol-protein interactions.

Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules

The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.

Antibacterial and cytotoxic prenylated dihydrochalcones from Eriosema montanum

Two new prenylated dihydrochalcones (1,2) and eighteen known secondary metabolites (3-20) were isolated from the CH₂Cl₂-MeOH (1:1) extracts of the roots, the stem bark and the leaves of Eriosema montanum Baker f. (Leguminosae). The structures of the isolated compounds were characterized by NMR, IR, and UV spectroscopic and mass spectrometric analyses. The structures of compounds 5, 10, 11 and 13 were confirmed by single crystal X-ray diffraction. The antibacterial activity of the crude extracts and the isolated constituents were established against Gram-positive and Gram-negative bacteria. Among the tested compounds, 1-4 and 10 showed strong activity against the Gram-positive bacterium Bacillus subtilis with minimum inhibitory concentration (MIC) ranging from 3.1 to 8.9 μM, as did the leaf crude extract with an MIC of 3.0 μg/mL. None of the crude extracts nor the isolated compounds were active against Escherichia coli. Compounds 1, 3 and 4 showed higher cytotoxicity, evaluated against the human breast cancer cell line MCF-7, with EC₅₀ of 7.0, 18.0 and 18.0 μM, respectively. These findings contribute to the phytochemical understanding of the genus Eriosema, and highlight the pharmaceutical potential of prenylated dihydrochalcones.

Effects of Hydroxyl Group on the Interaction of Carboxylated Flavonoid Derivatives with S. Cerevisiae α-Glucosidase

Introduction

Carboxyalkyl flavonoids derivatives are considered as effective inhibitors in reducing post-prandial hyperglycaemia.

Methods

Combined with Density Functional Theory (DFT) and the theory of Atoms in Molecules (AIM), molecular docking and charge density analysis are carried out to understand the molecular flexibility, charge density distribution and the electrostatic properties of these carboxyalkyl derivatives.

Results

Results show that the electron density of the chemical bond C14-O17 on B ring of molecule II increases while O17-H18 decreases at the active site, suggesting the existence of weak non-covalent interactions, most prominent of which are H-bonding and electrostatic interaction. When hydroxyl groups are introduced, the highest positive electrostatic potentials are distributed near the B ring hydroxyl hydrogen atom and the carboxyl hydrogen atom on the A ring. It was reported that quercetin has a considerably inhibitory activity to S. cerevisiae α-glucosidase, from the binding affinities, it is suggested that the position and number of hydroxyl groups on the B and C rings are also pivotal to the hypoglycemic activity when the long carboxyalkyl group is introduced into the A ring.

Conclusion

It is concluded that the presence of three well-defined zones in the structure, both hydrophobicity alkyl, hydrophilicity carboxyl and hydroxyl groups are necessary.

Randomized double-blind placebo-controlled trial of the effect of Morus nigra L. (black mulberry) leaf powder on symptoms and quality of life among climacteric women

OBJECTIVE

To test the efficacy of Morus nigra L. (MN) leaf powder for treating climacteric symptoms by comparison with hormone therapy (HT) and placebo.

METHODS

A randomized controlled trial among 62 climacteric women attending Hospital of the Federal University of Maranhão, Brazil. Women were divided into MN, HT, and placebo groups, and received 250 mg of MN leaf powder, 1 mg of estradiol, or placebo for 60 days. Primary outcomes were the Blatt-Kupperman index (BKI) for climacteric symptoms and SF-36 health questionnaire scores.

RESULTS

Baseline sociodemographic variables, BKI scores, symptoms, and SF-36 domains did not differ among the groups. There was a reduction in mean BKI in the MN (17.5 vs 9.7, P<0.001), HT (15.4 vs 8.6, P=0.001), and placebo (16.1 vs 12.4, P=0.040) groups. Analysis of quality of life (QoL) showed that functional capacity (P=0.006), vitality (P=0.031), mental health (P=0.017), and social aspect (P<0.01) improved after treatment in the MN group. The HT group showed improvement in emotional limitation (P=0.040), and the placebo group showed better functional capacity (P=0.030) after treatment.

CONCLUSIONS

Climacteric symptoms and QoL improved after administration of 250 mg of MN leaf powder for 60 days, similar to the effects of HT. The trial is registered in the Brazilian Registry of Clinical Trials (REBEC) under registration number RBR-9t4xxk.

Exploring the different environments effect of piperine via combined crystallographic, QM/MM and molecular dynamics simulation study

Piperine is a pungent alkaloid, largely present in the skin of pepper. It is the most active component of pepper and being used as a medicine in many Asian countries. The effect of piperine on memory impairment and neurodegeneration in Alzheimer's disease model has been investigated. In the present study, we aim to investigate the effect of piperine molecule in different environments (crystal and active site of proteins) from crystallography, molecular docking, QM/MM based charge density analysis and molecular dynamic simulation. The crystal structure of piperine has been used to determine the topological electron density of intermolecular interactions. The O-atoms of piperine is forming C-H⋅⋅⋅O interactions with the neighboring molecules in the crystal, these interactions also confirmed from the Hirshfeld surface. Further, to understand the nature of interactions and the conformational flexibility of piperine in the active site of recombinant human acetylcholinesterase (rhAChE), molecular docking analysis has been performed. The selected docked complex suggests favorable hydrogen bonding and hydrophobic interactions with rhAChE enzyme; notably, the O3 atom of piperine molecule forms strong hydrogen bonding interaction with Glu202 at 1.8 Å. To determine the charge density distribution and the electrostatic properties of piperine molecule in the active site of rhAChE, the piperine-rhAChE complex was minimized at QM/MM energy level; in which, the binding pocket with piperine was considered as QM region. The charge density analysis of piperine and the interacting amino acid groups have been carried out. The topological analysis of O3⋯H-O/Glu202 hydrogen bonding interaction exhibits strong interactions and the electron density ρ_cp(r): 0.242 eÅ^-3 and the Laplacian ∇²ρ_cp(r): 3.176 eÅ^-5 respectively. These results were compared with the corresponding molecule present in the crystal and gas phase environments of piperine. The comparison of active site structure with the corresponding crystal phase and gas phase structures reveal that piperine exhibits large conformational modification in the active site. The molecular dynamics simulation and binding free energy calculations were performed, this gives the stability, binding affinity of the molecule in the active site of rhAChE. The O3⋯H-O/Glu202 interaction shows the high stability (89.2%), this was confirmed from the stability of hydrogen bond analysis. The binding free energy was used to measure the rate of inhibition of enzyme in the presence of ligand molecule. The comparative study allows to understand the nature of piperine molecule in the gas and crystal phases, and amino acids environment.

Experimental and theoretical charge-density analysis of hippuric acid: insight into its binding with human serum albumin

In order to comprehend the binding of an important metabolite, hippuric acid, with human serum albumin and to understand its chemical and electronic nature, an experimental charge-density analysis has been carried out using high-resolution diffraction data collected under cryogenic conditions, and all the results have been compared with theoretical findings using the B3LYP/6-311++g(2d,2p) level of theory. The structure displays very strong classical hydrogen bonds as well as other noncovalent interactions, which have been fully characterized using Hirshfeld surface analysis and Bader's quantum theory of atoms in molecules. Contact analysis on the Hirshfeld surfaces shows that the O...H, C...H and C...N intermolecular interactions are enriched and gives their relative strengths. Topological analysis of the electron density shows the charge concentration/depletion of hippuric acid bonds in the crystal structure. Electrostatic parameters such as atomic charges and dipole moments were calculated. The mapping of atomic basins and the calculation of respective charges show the atomic volumes of each atom as well as their charge contributions in the hippuric acid crystal structure. The dipole-moment calculations show that the molecule is very polar in nature. Calculations of the electrostatic potential show that the chain part of the molecule has a higher concentration of negative charge than the ring, which might be instrumental in its strong binding with the polar residues of site II of human serum albumin.

Molecular interaction between MeOH and genistein during soy extraction

Genistein has received great attention due to its possible anti-oxidant properties. The interaction between genistein and the extraction solvent helps in understanding the extraction efficiency. Hydrogen bonding plays a crucial role in liquid systems. Density functional theory quantum chemical computations in both gas phase and solution were performed to investigate the molecular interaction between genistein and methanol. All the resulting complexes (MeOH : genistein = 1 : 1, 2 : 1, 3 : 1, 6 : 1) were studied using the B3LYP-D3 computational level and the cc-pVTZ basis set. Binding energies demonstrate that more MeOH molecules surrounding genistein could stabilize the system more. Geometry optimizations show that there are strong O–H⋯O interactions between MeOH and genistein. The electron density and the corresponding Laplacian of charge density at bond critical points were also calculated using AIM theory, and the results are in line with the structural and energetic analysis of the studied system. Moreover, energy decomposition analysis shows that the exchange energy term has the largest contribution to the attraction interaction energy as compared with other energy terms. Meanwhile, this study shows that the MeOH–genistein system is more stable under basic conditions. This study could help increase the efficiency of extraction.

The interaction between genistein and extraction solvent helps in understanding the extraction efficiency.

Probing the "fingers" domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking, molecular dynamics simulation and binding free energy calculations

The NS5B RdRp polymerase is a prominent enzyme for the replication of Hepatitis C virus (HCV). During the HCV replication, the template RNA binding takes place in the "fingers" sub-domain of NS5B. The "fingers" domain is a new emerging allosteric site for the HCV drug development. The inhibitors of the "fingers" sub-domain adopt a new antiviral mechanism called RNA intervention. The details of essential amino acid residues, binding mode of the ligand, and the active site intermolecular interactions of RNA intervention reflect that this mechanism is ambiguous in the experimental study. To elucidate these details, we performed molecular docking analysis of the fingers domain inhibitor quercetagetin (QGN) with NS5B polymerase. The detailed analysis of QGN-NS5B intermolecular interactions was carried out and found that QGN interacts with the binding pocket amino acid residues Ala97, Ala140, Ile160, Phe162, Gly283, Gly557, and Asp559; and also forms π⋯π stacking interaction with Phe162 and hydrogen bonding interaction with Gly283. These are found to be the essential interactions for the RNA intervention mechanism. Among the strong hydrogen bonding interactions, the QGN⋯Ala140 is a newly identified important hydrogen bonding interaction by the present work and this interaction was not resolved by the previously reported crystal structure. Since D559G mutation at the fingers domain was reported for reducing the inhibition percentage of QGN to sevenfold, we carried out molecular dynamics (MD) simulation for wild and D559G mutated complexes to study the stability of protein conformation and intermolecular interactions. At the end of 50 ns MD simulation, the π⋯π stacking interaction of Phe162 with QGN found in the wild-type complex is altered into T-shaped π stacking interaction, which reduces the inhibition strength. The origin of the D559G resistance mutation was studied using combined MD simulation, binding free energy calculations and principal component analysis. The results were compared with the wild-type complex. The mutation D559G reduces the binding affinity of the QGN molecule to the fingers domain. The free energy decomposition analysis of each residue of wild-type and mutated complexes revealed that the loss of non-polar energy contribution is the origin of the resistance. Communicated by Ramaswamy H. Sarma.

Isoflavones, their Glycosides and Glycoconjugates. Synthesis and Biological Activity

Glycosylation of small biologically active molecules, either of natural or synthetic origin, has a profound impact on their solubility, stability, and bioactivity, making glycoconjugates attractive compounds as therapeutic agents or nutraceuticals. A large proportion of secondary metabolites, including flavonoids, occur in plants as glycosides, which adds to the molecular diversity that is much valued in medicinal chemistry studies. The subsequent growing market demand for glycosidic natural products has fueled the development of various chemical and biotechnological methods of glycosides preparation. The review gives an extensive overview of the processes of the synthesis of isoflavones and discusses recently developed major routes towards isoflavone-sugar formation processes. Special attention is given to the derivatives of genistein, the main isoflavone recognized as a useful lead in several therapeutic categories, with particular focus on anticancer drug design. The utility of chemical glycosylations as well as glycoconjugates preparation is discussed in some theoretical as well as practical aspects. Since novel approaches to chemical glycosylations and glycoconjugations are abundant and many of them proved suitable for derivatization of polyphenols a new body of evidence has emerged, indicating that sugar moiety can play a much more significant role, when attached to a pharmacophore, then being a mere “solubilizer”. In many cases, it has been demonstrated that semisynthetic glycoconjugates are much more potent cytostatic and cytotoxic agents than reference isoflavones. Moreover, the newly designed glycosides or glycoside mimics can act through different mechanisms than the parent active molecule.

Comparative analysis of interactions between the hydropyridine dicarboxylate derivatives and different proteins by molecular docking and charge density analysis

Molecular docking and charge density analysis were carried out to understand the geometry, charge density distribution and electrostatic properties of one of newly synthesized 4-substituted-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylates (PDE), which is regarded as the best [Formula: see text]-Glucosidase inhibitor among the hydropyridine dicarboxylate derivatives. The different bonding models of the PDE molecule in the active sites of proteins Human serum albumin (HSA) and Saccharomyces cerevisiae [Formula: see text]-glucosidase (SAG) are firstly compared, which is important to understand the different intermolecular interactions between drug-transport protein and drug-target protein. The deformation density maps suggest that the electron densities of the PDE molecule are redistributed when it presents in the active sites. When the molecule presents in the active site of the SAG, it is evident to find that the negative region does not appear at the vicinity of the oxygen atoms on one of the carboxylic acid dimethyl ester group. Frontier molecular orbital density distributions for the PDE molecule are similar in all forms. The highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) energy gaps in the active sites are higher than that of the molecule in pure solution phase. It is generally noticed that all of the orientations of the dipole moment vectors are reoriented in both active sites. These fine details at electronic level allow to better understand the exact drug-transport protein and drug-target protein interactions.

Synthesis and characterization of genistein conjugated with gold nanoparticles and the study of their cytotoxic properties

Gold nanoparticles conjugated with drug substances are used in diagnostics and therapies. Apart from the combinations involving gold nanoparticles conjugated with drug substances through linkers, a direct bonding is also known. In our paper the example of such a direct bonding between gold nanoparticles and genistein (AuNPs-GE) is presented. This conjugate was obtained in a one-pot synthesis and the formation of AuNPs-GE was monitored in terms of color change and UV-Vis spectroscopy. It has been shown that genistein reduces Au³⁺ ions to spherical Au⁰ nanocrystallites and acts as a stabilizing agent. The efficiency of the purification of the conjugate from free genistein was controlled by the capillary electrophoresis. Gold nanoparticles are homogeneously shaped and have a narrow range of size from 14 to 33nm and the size of the nanoparticles modified with genistein is around 64.64±0.41nm, as measured by the TEM and DSL techniques, respectively. The zeta potential of the gold nanoparticles modified with genistein is -19.32±0.82mV and suggests a high stability of the nanoparticles and lower toxicity for the normal cells. The identity of genistein on the gold nanoparticles was proved by the electrochemistry, NMR and Raman spectroscopy. The mechanism of the conjugate forming has been proposed. The coverage of gold nanoparticles with genistein 5.09% (m/m) has been calculated from the TGA analysis. Moreover, it has been proved that the obtained conjugate is characterized by a high cytotoxic activity towards cancer cells, as observed in the cell line test.

Charge Density and Electrostatic Potential Study of 16α,17β-Estriol and the Binding of Estrogen Molecules to the Estrogen Receptors ERα and ERβ

An accurate X-ray diffraction study at 20 K combined with DFT theoretical calculations has been performed for the estriol crystal with two conformationally different molecules in the asymmetric unit. The electron density has been modeled via a multipole expansion, using both experimental and theoretical structure factors, and a topological analysis has been performed. The experimental molecular geometry, hydrogen bonding, atomic charges, dipole moments, and other topological characteristics are compared with those calculated theoretically. In particular, the molecular electrostatic potential has been extracted and compared with those reported for other estrogen molecules exhibiting different binding affinities to the estrogen receptors (ERα and ERβ).

Contributions of charge-density research to medicinal chemistry

This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max= 1.1 Å−1] measured at 100 (2) K. The structure was solved by direct methods usingSHELXS97 and refined bySHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen–Coppens multipole formalism implemented in theXDsoftware. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained fromCRYSTAL09at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N—H...N and N—H...O hydrogen bonds, in which the N3—H3B...N1 and N3—H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.

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".

Molecular flexibility and the electrostatic moments of curcumin and its derivatives in the active site of p300: a theoretical charge density study

A molecular docking analysis and quantum chemical calculation coupled with the charge density analysis have been carried out to understand the conformational change, charge density distribution and the electrostatic properties of HAT inhibitors curcumin and its derivatives (cinnamoyl compounds) in the active site of p300. The nearest neighbours, the shortest intermolecular contacts between the inhibitors and receptor p300; their binding energies were calculated from molecular docking analysis. A high level quantum chemical calculations were performed using density functional theory (DFT-B3LYP) with the basis set 6-311G(∗∗) combined with the theory of atoms in molecules (AIM) for the inhibitors in gas phase and in the active site of p300. It is observed that, when the molecules present in the active site of p300, relatively, their geometrical, bond topological and the electrostatic properties are significantly altered. The comparative study on the geometrical and electrostatic properties of these three inhibitors in gas phase and amino acid environment gives an insight on the molecular flexibility and the exact modification of electrostatic interaction of the inhibitor in the active site of p300. These fine details at electronic level allow to understand the exact drug-receptor interaction.

Summation Solute Hydrogen Bonding Acidity Values for Hydroxyl Substituted Flavones Determined by NMR Spectroscopy

The flavonoids are a structurally diverse class of natural products that exhibit a broad spectrum of biochemical activities. The flavones are one of the most studied flavonoid subclasses due to their presence in dietary plants and their potential to protect human cells from reactive oxygen species (ROS). Several flavone compounds also mediate beneficial actions by direct binding to protein receptors and regulatory enzymes. There is current interest in using Quantitative Structure Activity Relationships (QSARs) to guide drug development based on flavone lead structures. This approach is most informative when it involves the use of accurate physical descriptors. The Abraham summation solute hydrogen bonding acidity ( A) is a descriptor in the general solvation equation. It defines the tendency of a molecule to act as a hydrogen bond donor, or acid, when surrounded by solvent molecules that are hydrogen bonding acceptors, or bases. As a linear free energy relationship, it is useful for predicting the absorption and uptake of drug molecules. A previously published method, involving nuclear magnetic resonance (NMR) spectroscopy, was used to evaluate A for the monohydroxyflavones (MHFs). Values of A ranged from 0.02, for 5-hydroxyflavone, to 0.69 for 4′-hydroxyflavone. The ability to examine separate NMR signals for individual hydroxyl groups allowed the investigation of intramolecular interactions between functional groups. The value of A for the position 7 hydroxyl group of 7-hydroxyflavone was 0.67. The addition of a position 5 hydroxyl group (in 5,7-dihydroxyflavone) increased the value of A for the position 7 hydroxyl group to 0.76. Values of A for MHFs were also calculated by the program ACD-Absolve and these agreed well with values measured by NMR. These results should facilitate more accurate estimation of the values of A for structurally complex flavones with pharmacological activities.

Advances in understanding of chemical bonding: inputs from experimental and theoretical charge density analysis

The development of charge density analysis has undergone a major renaissance in the last two decades. In recent years, the characterization of bonding features associated with atoms in molecules and in crystals has been explored using high-resolution X-ray diffraction data (laboratory or synchrotron) complemented by high level ab initio theoretical calculations. The extraction of one electron topological properties, namely, electrostatic charges, dipole moment and higher moments, electrostatic potential, electric field gradients, in addition to evaluation of the local kinetic and potential energy densities, have contributed toward an understanding of the electron density distributions in molecular solids. New topological descriptors, namely, the source function (SF) and electron localization function (ELF) provide additional information as regards characterization of the topology of the electron density. In addition, delocalization indices have also been developed to account for bonding features pertinent to M-M bonds. The evaluation of these properties have contributed significantly toward the understanding of intra- and intermolecular bonding features in organic, inorganic, and biomolecules in the crystalline phase, with concomitant applications in the understanding of chemical reactivity and material/biological properties. In recent years, the focus has strongly shifted toward the understanding of structure-property relationships in organometallic complexes containing labile M-C bonds in the crystal structure with subsequent implications in catalysis. This perspective aims to highlight the major developments in electron density measurements in the past few years and provides pointers directed toward the potential use of this technique in future applications for an improved understanding of chemical bonding in systems that have been unexplored.

Probing the effect of intermolecular interaction and understanding the electrostatic moments of anacardic acid in the active site of p300 enzyme via DFT and charge density analysis

A charge density analysis has been performed on gas phase and docked forms of anacardic acid molecule to understand its charge density distribution, electrostatic moments and the conformation in the active site of p300 enzyme. Here, we report the binding affinity of anacardic acid with the p300 enzyme calculated from docking analysis. The charge density distribution of anacardic acid molecule in the gas phase as well as the docked form has been determined from the high level quantum chemical calculations using HF and DFT methods coupled with AIM theory. The charge density study on both forms of anacardic acid differentiates its structural and the electrostatic properties in different environments. When the molecule enters into the active site of p300 its conformation, charge density distribution, dipole moment and electrostatic potential are significantly altered in comparison to its gas phase structure. In the active site, the molecule adopts different conformations, its pentadecyl chain is found to be highly twisted; the charges are redistributed and the dipole moment increases from 2.37 to 3.17D. Due to the charge redistribution, the electronegative region of carboxyl group increased as it is found small in the gas phase. The comparisons between both forms reveal the flexibility of anacardic acid in the active site.

Plant polyphenols: chemical properties, biological activities, and synthesis

Eating five servings of fruits and vegetables per day! This is what is highly recommended and heavily advertised nowadays to the general public to stay fit and healthy! Drinking green tea on a regular basis, eating chocolate from time to time, as well as savoring a couple of glasses of red wine per day have been claimed to increase life expectancy even further! Why? The answer is in fact still under scientific scrutiny, but a particular class of compounds naturally occurring in fruits and vegetables is considered to be crucial for the expression of such human health benefits: the polyphenols! What are these plant products really? What are their physicochemical properties? How do they express their biological activity? Are they really valuable for disease prevention? Can they be used to develop new pharmaceutical drugs? What recent progress has been made toward their preparation by organic synthesis? This Review gives answers from a chemical perspective, summarizes the state of the art, and highlights the most significant advances in the field of polyphenol research.

Through-Space Effects of Substituents Dominate Molecular Electrostatic Potentials of Substituted Arenes

Model systems have been studied using density functional theory to assess the contributions of π-resonance and through-space effects on electrostatic potentials of substituted arenes. The results contradict the widespread assumption that changes in molecular ESPs reflect only local changes in the electron density. Substituent effects on the ESP above the molecular plane are commonly attributed to changes in the aryl π-system. We show that ESP changes for a collection of substituted benzenes and more complex aromatic systems can be accounted for mostly by through-space effects, with no change in the aryl π-electron density. Only when π-resonance effects are substantial do they influence changes in the ESP above the aromatic ring to any extent. Examples of substituted arenes studied here are taken from the fields of drug design, host-guest chemistry, and crystal engineering. These findings emphasize the potential pitfalls of assuming ESP changes reflect changes in the local electron density. Since ESP changes are frequently used to rationalize and predict intermolecular interactions, these findings have profound implications for our understanding of substituent effects in countless areas of chemistry and molecular biology. Specifically, in many non-covalent interactions there are significant, often neglected, through-space interactions with the substituents. Finally, the present results explain the perhaps unexpectedly good performance of many molecular mechanics force-fields applied to supramolecular assembly phenomena and π-π interactions in biological systems despite the neglect of the polarization of the aryl π-system by substituents.