Binding of Androgen- and Estrogen-Like Flavonoids to Their Cognate (Non)Nuclear Receptors: A Comparison by Computational Prediction

Flavonoids are plant bioactives that are recognized as hormone-like polyphenols because of their similarity to the endogenous sex steroids 17β-estradiol and testosterone, and to their estrogen- and androgen-like activity. Most efforts to verify flavonoid binding to nuclear receptors (NRs) and explain their action have been focused on ERα, while less attention has been paid to other nuclear and non-nuclear membrane androgen and estrogen receptors. Here, we investigate six flavonoids (apigenin, genistein, luteolin, naringenin, quercetin, and resveratrol) that are widely present in fruits and vegetables, and often used as replacement therapy in menopause. We performed comparative computational docking simulations to predict their capability of binding nuclear receptors ERα, ERβ, ERRβ, ERRγ, androgen receptor (AR), and its variant AR^T877A and membrane receptors for androgens, i.e., ZIP9, GPRC6A, OXER1, TRPM8, and estrogens, i.e., G Protein-Coupled Estrogen Receptor (GPER). In agreement with data reported in literature, our results suggest that these flavonoids show a relevant degree of complementarity with both estrogen and androgen NR binding sites, likely triggering genomic-mediated effects. It is noteworthy that reliable protein–ligand complexes and estimated interaction energies were also obtained for some suggested estrogen and androgen membrane receptors, indicating that flavonoids could also exert non-genomic actions. Further investigations are needed to clarify flavonoid multiple genomic and non-genomic effects. Caution in their administration could be necessary, until the safe assumption of these natural molecules that are largely present in food is assured.     

Reducing the computational cost of NMR crystallography of organic powders at natural isotopic abundance with the help of 13C-13C dipolar couplings

Structure determination of functional organic compounds remains a formidable challenge when the sample exists as a powder. Nuclear magnetic resonance crystallography approaches based on the comparison of experimental and Density Functional Theory (DFT)-computed ¹H chemical shifts have already demonstrated great potential for structure determination of organic powders, but limitations still persist. In this study, we discuss the possibility of using ¹³C-¹³C dipolar couplings quantified on powdered theophylline at natural isotopic abundance with the help of dynamic nuclear polarization, to realize a DFT-free, rapid screening of a pool of structures predicted by ab initio random structure search. We show that although ¹³C-¹³C dipolar couplings can identify structures possessing long range structural motifs and unit cell parameters close to those of the true structure, it must be complemented with other data to recover information about the presence and the chemical nature of the supramolecular interactions.     

Molecular Size and Electronic Structure Combined Effects on the Electrogenerated Chemiluminescence of Sulfurated Pyrene‐Cored Dendrimers

The electrochemistry, photophysics, and electrochemically generated chemiluminescence (ECL) of a family of polysulfurated dendrimers with a pyrene core have been thoroughly investigated and complemented by theoretical calculations. The redox and luminescence properties of dendrimers are dependent on the generation number. From low to higher generation it is both easier to reduce and oxidize them and the emission efficiency increases along the family, with respect to the polysulfurated pyrene core. The analysis of such data evidences that the formation of the singlet excited state by cation–anion annihilation is an energy‐deficient process and, thus, the ECL has been justified through the triplet–triplet annihilation pathway. The study of the dynamics of the ECL emission was achieved both experimentally and theoretically by molecular mechanics and quantum chemical calculations. It has allowed rationalization of a possible mechanism and the experimental dependence of the transient ECL on the dendrimer generation. The theoretically calculated Marcus electron‐transfer rate constant compares very well with that obtained by the finite element simulation of the whole ECL mechanism. This highlights the role played by the thioether dendrons in modulating the redox and photophysical properties, responsible for the occurrence and dynamics of the electron transfer involved in the ECL. Thus, the combination of experimental and computational results allows understanding of the dendrimer size dependence of the ECL transient signal as a result of factors affecting the annihilation electron transfer.     

Effect of permodified β‐cyclodextrin on the photophysical properties of poly[2,7‐(9,9‐dioctylfluorene)‐alt‐(5,5′‐bithiophene)] main chain polyrotaxanes

The photophysical properties of two polyrotaxanes ( PFBTh?PSβCD and PFBTh?PMeβCD ) composed of fluorene and bithiophene encapsulated into permodified β‐cyclodextrin cavities have been investigated and compared with those of the reference PFBTh . Rotaxane formation results in improvements of the thermal stability, solubility in common organic solvents, as well as better film forming ability combined with a high transparency. As expected PFBTh and its encapsulated forms absorb at wavelengths beyond 510 nm, and time‐resolved photoluminescence (PL) in solution shows a well‐define vibronic structures with a predominance of the 0‐0 transitions and an energy difference of 0.16 eV. The fluorescence lifetimes follow a monoexponential decay with a value τ = 630 ± 30 ps. Atomic force microscopy, AFM, indicated a tendency of polyrotaxanes to organize into fibers. The advancing contact angles indicated higher surface hydrophobicity and lower surface free‐energy values for polyrotaxanes compared with their unthreaded analogues. The device based on PFBTh?PSβCD: PCBM in a 1/1 w/w ratio under simulated AM 1.5G illumination at 100 mW cm^?2 exhibited improved photovoltaic parameters of cells, resulted in high V_oc (0.68 V), J_sc (1.65 mA cm^?2), FF (31.6%), and PCE (0.35) values, compared with PFBTh or PFBTh?PMeβCD , respectively. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 460–471     

Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple‐scattering EXAFS analysis performed within the rigid‐body refinement scheme, non‐muffin‐tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye–Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K‐edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.