p-Hydroxyphenyl-pyranoanthocyanins: An Experimental and Theoretical Investigation of Their Acid-Base Properties and Molecular Interactions

The physicochemical properties of the wine pigments catechyl-pyranomalvidin-3-O-glucoside (PA1) and guaiacyl-pyranomalvidin-3-O-glucoside (PA2) are extensively revisited using ultraviolet (UV)-visible spectroscopy, dynamic light scattering (DLS) and quantum chemistry density functional theory (DFT) calculations. In mildly acidic aqueous solution, each cationic pigment undergoes regioselective deprotonation to form a single neutral quinonoid base and water addition appears negligible. Above pH = 4, both PA1 and PA2 become prone to aggregation, which is manifested by the slow build-up of broad absorption bands at longer wavelengths (λ ≥ 600 nm), followed in the case of PA2 by precipitation. Some phenolic copigments are able to inhibit aggregation of pyranoanthocyanins (PAs), although at large copigment/PA molar ratios. Thus, chlorogenic acid can dissociate PA1 aggregates while catechin is inactive. With PA2, both chlorogenic acid and catechin are able to prevent precipitation but not self-association. Calculations confirmed that the noncovalent dimerization of PAs is stronger with the neutral base than with the cation and also stronger than π–π stacking of PAs to chlorogenic acid (copigmentation). For each type of complex, the most stable conformation could be obtained. Finally, PA1 can also bind hard metal ions such as Al³⁺ and Fe³⁺ and the corresponding chelates are less prone to self-association.

Unravelling the immunopathological mechanisms of heavy chain deposition disease with implications for clinical management

Randall-type heavy chain deposition disease (HCDD) is a rare disorder characterized by tissue deposition of a truncated monoclonal immunoglobulin heavy chain lacking the first constant domain. Pathophysiological mechanisms are unclear and management remains to be defined. Here we retrospectively studied 15 patients with biopsy-proven HCDD of whom 14 presented with stage 3 or higher chronic kidney disease, with nephrotic syndrome in 9. Renal lesions were characterized by nodular glomerulosclerosis, with linear peritubular and glomerular deposits of γ-heavy chain in 12 patients or α-heavy chain in 3 patients, without concurrent light chain staining. Only 2 patients had symptomatic myeloma. By serum protein electrophoresis/immunofixation, 13 patients had detectable monoclonal gammopathy. However, none of these techniques allowed detection of the nephrotoxic truncated heavy chain, which was achieved by immunoblot and/or bone marrow heavy chain sequencing in 14 of 15 patients. Serum-free kappa to lambda light chain ratio was abnormal in 11 of 11 patients so examined. Immunofluorescence studies of bone marrow plasma cells showed coexpression of the pathogenic heavy chain with light chain matching the abnormal serum-free light chain in all 3 tested patients. Heavy chain sequencing showed first constant domain deletion in 11 of 11 patients, with high isoelectric point values of the variable domain in 10 of 11 patients. All patients received chemotherapy, including bortezomib in 10 cases. Renal parameters improved in 11 patients who achieved a hematological response, as assessed by normalization of the free light chain ratio in 8 cases. Tissue deposition in HCDD relates to physicochemical peculiarities of both variable and constant heavy chain domains. Early diagnosis and treatment with bortezomib-based combinations appear important to preserve renal prognosis. Thus, monitoring of serum-free light chain is an indirect but useful method to evaluate the hematological response.

Dimerization of quercetin, Diels-Alder vs. radical-coupling approach: a joint thermodynamics, kinetics, and topological study

Quercetin is a prototypical antioxidant and prominent member of flavonoids, a large group of natural polyphenols. The oxidation of quercetin may lead to its dimerization, which is a paradigm of the more general polyphenol oligomerization. There exist two opposing mechanisms to describe the dimerization process, namely radical-coupling or Diels-Alder reactions. This work presents a comprehensive rationalization of this dimerization process, acquired from density functional theory (DFT) calculations. It is found that the two-step radical-coupling pathway is thermodynamically and kinetically preferred over the Diels-Alder reaction. This is in agreement with the experimental results showing the formation of only one isomer, whereas the Diels-Alder mechanism would yield two isomers. The evolution in bonding, occurring during these two processes, is investigated using the atoms in molecules (AIM) and electron localization function (ELF) topological approaches. It is shown that some electron density is accumulated between the fragments in the transition state of the radical-coupling reaction, but not in the transition state of the Diels-Alder process. Graphical Abstract Quantum chemistry calculations of the dimerization process of quercetin show that a radical coupling approach is preferred to a Diels-Alder type reaction, in agreement with experimental results. Analysis of the bonding evolution highlights the reaction mechanism.

In silico pharmacology: Drug membrane partitioning and crossing

Over the past decade, molecular dynamics (MD) simulations have become particularly powerful to rationalize drug insertion and partitioning in lipid bilayers. MD simulations efficiently support experimental evidences, with a comprehensive understanding of molecular interactions driving insertion and crossing. Prediction of drug partitioning is discussed with respect to drug families (anesthetics; β-blockers; non-steroidal anti-inflammatory drugs; antioxidants; antiviral drugs; antimicrobial peptides). To accurately evaluate passive permeation coefficients turned out to be a complex theoretical challenge; however the recent methodological developments based on biased MD simulations are particularly promising. Particular attention is paid to membrane composition (e.g., presence of cholesterol), which influences drug partitioning and permeation. Recent studies concerning in silico models of membrane proteins involved in drug transport (influx and efflux) are also reported here. These studies have allowed gaining insight in drug efflux by, e.g., ABC transporters at an atomic resolution, explicitly accounting for the mandatory forces induced by the surrounded lipid bilayer. Large-scale conformational changes were thoroughly analyzed.

A Blue-Light-Emitting BODIPY Probe for Lipid Membranes

Here we describe a new BODIPY-based membrane probe (1) that provides an alternative to dialkylcarbocyanine dyes, such as DiI-C18, that can be excited in the blue spectral region. Compound 1 has unbranched octadecyl chains at the 3,5-positions and a meso-amino function. In organic solvents, the absorption and emission maxima of 1 are determined mainly by solvent acidity and dipolarity. The fluorescence quantum yield is high and reaches 0.93 in 2-propanol. The fluorescence decays are well fitted with a single-exponential in pure solvents and in small and giant unilamellar vesicles (GUV) with a lifetime of ca. 4 ns. Probe 1 partitions in the same lipid phase as DiI-C18(5) for lipid mixtures containing sphingomyelin and for binary mixtures of dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC). The lipid phase has no effect on the fluorescence lifetime but influences the fluorescence anisotropy. The translational diffusion coefficients of 1 in GUVs and OLN-93 cells are of the same order as those reported for DiI-C18. The directions of the absorption and emission transition dipole moments of 1 are calculated to be parallel. This is reflected in the high steady-state fluorescence anisotropy of 1 in high ordered lipid phases. Molecular dynamic simulations of 1 in a model of the DOPC bilayer indicate that the average angle of the transition moments with respect to membrane normal is ca. 70°, which is comparable with the value reported for DiI-C18.

Flavonolignans As a Novel Class of Sodium Pump Inhibitors

We examined the inhibitory effects of three flavonolignans and their dehydro- derivatives, taxifolin and quercetin on the activity of the Na⁺/K⁺-ATPase (NKA). The flavonolignans silychristin, dehydrosilychristin and dehydrosilydianin inhibited NKA with IC₅₀ of 110 ± 40 μM, 38 ± 8 μM, and 36 ± 14 μM, respectively. Using the methods of molecular modeling, we identified several possible binding sites for these species on NKA and proposed the possible mechanisms of inhibition. The binding to the extracellular- or cytoplasmic C-terminal sites can block the transport of cations through the plasma membrane, while the binding on the interface of cytoplasmic domains can inhibit the enzyme allosterically. Fluorescence spectroscopy experiments confirmed the interaction of these three species with the large cytoplasmic segment connecting transmembrane helices 4 and 5 (C45). The flavonolignans are distinct from the cardiac glycosides that are currently used in NKA treatment. Because their binding sites are different, the mechanism of inhibition is different as well as the range of active concentrations, one can expect that these new NKA inhibitors would exhibit also a different biomedical actions than cardiac glycosides.

Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment

Natural anthocyanin pigments/dyes and phenolic copigments/co-dyes form noncovalent complexes, which stabilize and modulate (in particular blue, violet, and red) colors in flowers, berries, and food products derived from them (including wines, jams, purees, and syrups). This noncovalent association and their electronic and optical implications constitute the copigmentation phenomenon. Over the past decade, experimental and theoretical studies have enabled a molecular understanding of copigmentation. This review revisits this phenomenon to provide a comprehensive description of the nature of binding (the dispersion and electrostatic components of π-π stacking, the hydrophobic effect, and possible hydrogen-bonding between pigment and copigment) and of spectral modifications occurring in copigmentation complexes, in which charge transfer plays an important role. Particular attention is paid to applications of copigmentation in food chemistry.

Synergism of antioxidant action of vitamins E, C and quercetin is related to formation of molecular associations in biomembranes

Vitamins E, C and polyphenols (flavonoids and non-flavonoids) are major natural antioxidants capable of preventing damage generated by oxidative stress. Here we show the capacity of these antioxidants to form non-covalent association within lipid bilayers close to the membrane/cytosol interface. Antioxidant regeneration is significantly enhanced in these complexes.

Synthesis and conformation of a novel fluorescein–Zn-porphyrin dyad and intramolecular energy transfer

Modulations of the optical properties of a new porphyrin–fluorescein dyad were elucidated using experimental and theoretical techniques, with conformational rearrangements being studied.

Flavonolignan 2,3-dehydroderivatives: Preparation, antiradical and cytoprotective activity

The protective constituents of silymarin, an extract from Silybum marianum fruits, have been extensively studied in terms of their antioxidant and hepatoprotective activities. Here, we explore the electron-donor properties of the major silymarin flavonolignans. Silybin (SB), silychristin (SCH), silydianin (SD) and their respective 2,3-dehydroderivatives (DHSB, DHSCH and DHSD) were oxidized electrochemically and their antiradical/antioxidant properties were investigated. Namely, Folin-Ciocalteau reduction, DPPH and ABTS(+) radical scavenging, inhibition of microsomal lipid peroxidation and cytoprotective effects against tert-butyl hydroperoxide-induced damage to a human hepatocellular carcinoma HepG2 cell line were evaluated. Due to the presence of the highly reactive C3-OH group and the C-2,3 double bond (ring C) allowing electron delocalization across the whole structure in the 2,3-dehydroderivatives, these compounds are much more easily oxidized than the corresponding flavonolignans SB, SCH and SD. This finding was unequivocally confirmed not only by experimental approaches, but also by density functional theory (DFT) calculations. The hierarchy in terms of ability to undergo electrochemical oxidation (DHSCH~DHSD>DHSB>>SCH/SD>SB) was consistent with their antiradical activities, mainly DPPH scavenging, as well as in vitro cytoprotection of HepG2 cells. The results are discussed in the context of the antioxidant vs. prooxidant activities of flavonolignans and molecular interactions in complex biological systems.

Unraveling the performance of dispersion-corrected functionals for the accurate description of weakly bound natural polyphenols

Long-range non-covalent interactions play a key role in the chemistry of natural polyphenols. We have previously proposed a description of supramolecular polyphenol complexes by the B3P86 density functional coupled with some corrections for dispersion. We couple here the B3P86 functional with the D3 correction for dispersion, assessing systematically the accuracy of the new B3P86-D3 model using for that the well-known S66, HB23, NCCE31, and S12L datasets for non-covalent interactions. Furthermore, the association energies of these complexes were carefully compared to those obtained by other dispersion-corrected functionals, such as B(3)LYP-D3, BP86-D3 or B3P86-NL. Finally, this set of models were also applied to a database composed of seven non-covalent polyphenol complexes of the most interest. Graphical abstract Weakly bound natural polyphenolsᅟ.

Oligostilbenoids from the heartwood of N. Heimii: role of non-covalent association in their biogenesis

Four new oligostilbenes, including one dimer and three tetramers of resveratrol, that is, heimiols B-E (1-4) were isolated from the heartwood of Neobalanocarpus heimii (Dipterocarpaceae), together with thirteen known resveratrol oligomers (5-17). Examination of the structural diversity of the isolated oligostilbenes led to hypothesis of their biogenetic origin through a small number of versatile chemical pathways. These hypotheses are strongly supported by computational calculations (based on the density functional theory, DFT) that were performed to rationalize conformational re-arrangements and thus provide insights into the mechanism of oligostilbenoid biosynthesis. Non-covalent complexes are believed to drive the regio- and stereoselectivity of the oligomerization reactions.

Elucidation of antioxidant properties of wood bark derived saturated diarylheptanoids: a comprehensive (DFT-supported) understanding

A series of diarylheptanoids, namely 1,7-bis-(3,4-dihydroxyphenyl)-heptan-3-one-5-O-D-xylopyranoside (oregonin), 1,7-bis-(3,4-dihydroxyphenyl)-3-hydroxyheptane-5-O-β-D-xylopyranoside and 1,7-bis-(4-hydroxyphenyl)-heptane-3-one-5-O-β-D-glucopyranoside (platyphylloside), were isolated from the bark of alder family trees, a species widely spread over in Europe. As antioxidants, these natural polyphenols have a promising potential in various fields of application, but their redox reactivity is insufficiently characterized. In this work, their antioxidant activity is described using assays based on DPPH and ABTS(+) radical scavenging, oxygen anion radicals (O2(-)) quenching. The standardized ORAC assay was also achieved, which measures the capacity to protect fluorescent molecules against oxidative degradation. The measured antioxidant activity was higher than that of the well-known antioxidant and biologically active diarylheptanoid curcumin. Molecular modeling was used to rationalize the differences in activity and the mechanisms of action. Thermodynamic descriptors mainly O-H bond dissociation enthalpies (BDEs) establish a clear structure-activity relationship.

Application of recent double-hybrid density functionals to low-lying singlet-singlet excitation energies of large organic compounds

The present work assesses some recently developed double-hybrid density functionals (B2π-PLYP, PBE0-DH, and PBE0-2) using linear-response Tamm-Dancoff Time-Dependent Density Functional Theory. This assessment is achieved against experimentally derived low-lying excitation energies of large organic dyes of recent interest, including some excitations dominated by charge-transfer transitions. Comparisons are made with some of the best-performing methods established from the literature, such as PBE0 or B3LYP hybrid or the recently proposed B2-PLYP and B2GP-PLYP double-hybrid models, to ascertain their quality and robustness on equal footing. The accuracy of parameter-free or empirical forms of double-hybrid functionals is also briefly discussed. Generally speaking, it turns out that double-hybrid expressions always provide more accurate estimates than corresponding hybrid methods. Double-hybrid functionals actually reach averaged accuracies of 0.2 eV, that can be admittedly considered close to any intended accuracy limit within the present theoretical framework.

cis-trans Isomerization of silybins A and B

Methods were developed and optimized for the preparation of the 2,3-cis- and the 10,11-cis-isomers of silybin by the Lewis acid catalyzed (BF3∙OEt2) isomerization of silybins A (1a) and B (1b) (trans-isomers). The absolute configuration of all optically pure compounds was determined by using NMR and comparing their electronic circular dichroism data with model compounds of known absolute configurations. Mechanisms for cis-trans-isomerization of silybin are proposed and supported by quantum mechanical calculations.