Conformational diversity of the quercetin molecule: a quantum-chemical view

Enhanced urease inhibitory activity of quercetin via conjugation with silver nanoparticles: synthesis, characterization, and DFT study

Urease plays a crucial role in the survival and colonization of Helicobacter pylori (H. pylori). Consequently, urease inhibitors are important in managing various diseases associated with H. pylori infection. Given the widespread use of silver nanoparticles (AgNPs) as antibacterial agents and quercetin's known urease inhibitory properties, we sought to develop a potent urease inhibitor by conjugating quercetin onto AgNPs. In fact, this study aimed to enhance the urease inhibitory activity of quercetin through its conjugation with AgNPs. Quercetin-loaded silver nanoparticles (Ag@QNPs) were successfully synthesized using the Frens method and characterized using various techniques, including UV-Vis spectroscopy, FT-IR spectroscopy, XRD analysis, DLS, and TEM. The urease inhibitory activity of Ag@QNPs was significantly higher (approximately 250 times) than that of pure quercetin, demonstrating a synergistic effect. In contrast, AgNPs alone exhibited minimal inhibitory activity against urease. Density functional theory (DFT) calculations revealed a favorable interaction energy between quercetin and the silver surface. These findings suggest the potential of Ag@QNPs as promising nanomaterials for applications in urease-related diseases.

Biodegradation of flavonoids - Influences of structural features

Flavonoids, a class of natural products with a variety of applications in nutrition, pharmacy and as biopesticides, could substitute more harmful synthetic chemicals that persist in the environment. To gain a better understanding of the biodegradability of flavonoids and the influence of structural features, firstly, the ultimate biodegradation of 19 flavonoids was investigated with the Closed Bottle Test according to the OECD guideline 301 D. Secondly, regarding the fast abiotic degradation reported for several flavonoids with severe concentration decrease within hours and its possible impacts on the processes behind the ultimate biodegradation, primary degradation of 4 selected flavonoids was compared at conditions representing biodegradation, abiotic degradation, and mixed substrates by monitoring the flavonoids' concentrations with HPLC-UV/vis. Our results showed that 17 out of the 19 tested flavonoids were readily biodegradable. Structural features like a hydroxy group at C3, the C2-C3 bond order, a methoxy group in the B ring, and the position of the B ring in regard to the chromene core did not affect biodegradation of the tested flavonoids. Only flavone without any hydroxy groups and morin with an uncommon 2',4' pattern of hydroxy groups were non-readily biodegradable. Monitoring the concentration of 4 selected flavonoids by HPLC-UV/vis revealed that biodegradation occurred faster than abiotic degradation at CBT conditions with no other carbon sources present. The presence of an alternative carbon source tends to increase lag phases and decrease biodegradation rates. At this condition, abiotic degradation contributed to the degradation of unstable flavonoids. Overall, as a first tier to assess the environmental fate, our results indicate low risks for persistence of most flavonoids. Thus, flavonoids could represent benign substitutes for persistent synthetic chemicals.

Advance in the pharmacological effects of quercetin in modulating oxidative stress and inflammation related disorders

Numerous pharmacological effects of quercetin have been illustrated, including antiinflammation, antioxidation, and anticancer properties. In recent years, the antioxidant activity of quercetin has been extensively reported, in particular, its impacts on glutathione, enzyme activity, signaling transduction pathways, and reactive oxygen species (ROS). Quercetin has also been demonstrated to exert a striking antiinflammatory effect mainly by inhibiting the production of cytokines, reducing the expression of cyclooxygenase and lipoxygenase, and preserving the integrity of mast cells. By regulating oxidative stress and inflammation, which are regarded as two critical processes involved in the defense and regular physiological operation of biological systems, quercetin has been validated to be effective in treating a variety of disorders. Symptoms of these reactions have been linked to degenerative processes and metabolic disorders, including metabolic syndrome, cardiovascular, neurodegeneration, cancer, and nonalcoholic fatty liver disease. Despite that evidence demonstrates that antioxidants are employed to prevent excessive oxidative and inflammatory processes, there are still concerns regarding the expense, accessibility, and side effects of agents. Notably, natural products, especially those derived from plants, are widely accessible, affordable, and generally safe. In this review, the antioxidant and antiinflammatory abilities of the active ingredient quercetin and its application in oxidative stress-related disorders have been outlined in detail.

Manifestations of intramolecular H-bonds of CH… O and OH… C type in quercetin molecule: Analysis of IR spectra by mean of density functional theory

The IR spectra of 48 conformers of quercetin which represent full conformation space of its tautomers have been modeled at B3LYP/6-311++G(d,p) level of the density functional theory. The presence of intramolecular H-bonds C2'H/C6'H…O3 and O3H…C2'/C6' was characterized by their spectral manifestations. The C2'H/C6'H…O3 contacts were found to have a spectral blue-shift. The O3H…C2'/C6' contacts were mostly red-shifted. The stretching vibrations of H-bonds C2'H/C6'H…O3 demonstrate an increase in the intensity of the modes of stretching vibrations ν(C2'H)/ν(C6'H) and an increase in the frequency of their out-of-plane vibrations γ(C2'H)/γ(C6'H). Most of the spectral parameters correlate a little with the energy of the H-bonds.

Natural dihydroisobenzofuran derivatives as a template for promising radical scavengers: theoretical insights into structure–activity relationships, thermochemistry and kinetics

Dihydroisobenzofuran heterocycle is a structural motif found in a number of medications with anti-tumour, anti-diabetic, and antibacterial activities. It is also found in a slew of natural substances, most notably fungus metabolites, which have been shown to possess credible radical scavenging activity. Density functional theory studies on three different derivatives were conducted to investigate their electronic structures as well as thermochemical and kinetic behaviour against ·OOH, ·OH, and ·OCH3 in biologically relevant solvents, with the goal of elucidating structure–activity relationships and discussing the potential role of the scaffolds as a template for new semisynthetic antioxidants. The importance of resonance and inductive effects, and also hydrogen bonding, has been underlined, but most importantly, it has been demonstrated that all structures have considerable scavenging potential against all studied radicals, with reactions rates close to the diffusion limit.

Modeling Tracer Diffusion Coefficients of Any Type of Solutes in Polar and Non-Polar Dense Solvents

In this work, a simple two-parameters correlation based on the Rice and Gray, Lennard-Jones, and Stockmayer theories was devised for the calculation of binary diffusion coefficients (D12) of any type of solutes at infinite dilution in polar and non-polar solvents. This equation can be relevant for systems with polar solvents, since most models in the literature fail when strong intermolecular forces predominate in solution. The new correlation embodies the Stockmayer potential without requiring the dipole moments of any component, which significantly enlarges its application. It was validated with the largest D12 database of polar and non-polar dense systems, with 8812 data points (NDP) spanning 553 systems, of which 133 have water as solvent (NDP = 1266), 89 contain polar solvents excluding water (NDP = 1405), 177 have supercritical carbon dioxide (SC-CO2) as solvent (NDP = 5028), and 154 have non-polar or weakly polar solvents excluding SC-CO2 (NDP = 1113). Overall, the model achieved an average deviation of only 3.43%, with accurate and unbiased behavior even for polar systems.

The potential biological effects of quercetin based on pharmacokinetics and multi-targeted mechanism in vivo

Quercetin is a plant-derived polyphenol flavonoid that has been proven to be effective for many diseases. However, the mechanism and in vivo metabolism of quercetin remains to be clarified. It achieves a wide range of biological effects through various metabolites, gut microbiota and its metabolites, systemic mediators produced by inflammation and oxidation, as well as by multiple mechanisms. The all-round disease treatment of quercetin is achieved through the organic combination of multiple channels. Therefore, this article clarifies the metabolic process of quercetin in the body, and explores the new pattern of action of quercetin in the treatment of diseases.

Current Trends in Computational Quantum Chemistry Studies on Antioxidant Radical Scavenging Activity

The antioxidative nature of chemicals is now routinely studied using computational quantum chemistry. Scientists are constantly proposing new approaches to investigate those methods, and the subject is evolving at a rapid pace. The goal of this review is to collect, consolidate, and present current trends in a clear, methodical, and reference-rich manner. This paper is divided into several sections, each of which corresponds to a different stage of elaborations: preliminary concerns, electronic structure analysis, and general reactivity (thermochemistry and kinetics). The sections are further subdivided based on methodologies used. Concluding remarks and future perspectives are presented based on the remaining elements.

Comparative analysis of molecular properties and reactions with oxidants for quercetin, catechin, and naringenin

Flavonoids, a large group of secondary plant phenolic metabolites, are important natural antioxidants and regulators of cellular redox balance. The present study addressed evaluation of the electronic properties of some flavonoids belonging to different classes such as quercetin (flavonols), catechin (flavanols), and naringenin (flavanones) and their interactions with oxidants in model systems of DPPH reduction, flavonoid autoxidation, and chlorination. According to our ab initio calculations, the high net negative excess charges of the C rings and the small positive excess charges of the B rings of quercetin, catechin, and naringenin make these parts of flavonoid molecules attractive for electrophilic attack. The 3'-OH group of the B ring of quercetin has the highest excess negative charge and the lowest energy of hydrogen atom abstraction for the flavonoids studied. The apparent reaction rate constants (s-1, 20 °C) and the activation energies (kJ/mol) of DPPH reduction were 0.34 ± 0.06 and 23.0 ± 2.5 in the case of quercetin, 0.09 ± 0.02 and 32.5 ± 2.5 in the case of catechin, respectively. The stoichiometry of the DPPH-flavonoid reaction was 1:1. The activation energies (kJ/mol) of quercetin and catechin autoxidations were 50.8 ± 6.1 and 58.1 ± 7.2, respectively. Naringenin was not oxidized by the DPPH radical and air oxygen (autoxidation) and the flavonoids studied effectively prevented HOCl-induced hemolysis due to direct scavenging of hypochlorous acid (flavonoid chlorination). The best antioxidant quercetin had the highest value of HOMO energy, a planar structure and optimal electron orbital delocalization on all the phenolic rings due to the C2=C3 double bond in the C ring (absent in catechin and naringenin).

The subgroup of 2'-hydroxy-flavonoids: Molecular diversity, mechanism of action, and anticancer properties

Flavonoids are abundant in nature, structurally very diversified and largely investigated. However, the subgroup of 2'-hydroxyflavonoids is much less known and not frequently studied. The present review identifies the major naturally-occurring and synthetic 2'-hydroxyflavonoid derivatives and discusses their structural characteristics and biological properties, with a focus on anticancer activities. The pharmacological properties of 2'-hydroxyflavone (2'-HF) and 2'-hydroxyflavanone (2'-HFa) are detailed. Upon binding to the Ral-interacting protein Rlip implicated in the transport of glutathione conjugates, 2'-HFa inhibits tumor cell proliferation and restrict tumor growth, in particular in breast cancer models. Among the synthetic derivatives, the characteristics of the anticancer product 2D08 (2',3',4'-trihydroxy flavone) are detailed to shed light on the molecular mechanism of action of this compound, as a regulator of protein SUMOylation. Inhibition of protein SUMOylation by 2D08 blocks cancer cell migration and invasion, and the compound greatly enhances the anticancer effects of conventional cytotoxic drugs like etoposide. The structural role of the 2'-hydroxyl group on the phenyl C-ring of the flavonoid is discussed, notably the capacity to engage intramolecular H-bonding interactions with the O1 atom on the B-ring of the chromone unit (or the oxygen of a 3-OH group when it is presents). The 2'-hydroxyl group of flavonoid appears as a regulator of the conformational freedom between the bicyclic A-B unit and the appended phenyl C-ring, favoring the planarity of the molecule. It is an essential group accounting for the biological properties of 2'-HF, 2'-HFa and structurally related compounds. This review shed light on 2'-hydroxyflavonoids to encourage their use and chemical development.

A Never-Ending Conformational Story of the Quercetin Molecule: Quantum-Mechanical Investigation of the O3′H and O4′H Hydroxyl Groups Rotations

The quercetin molecule is known to be an effective pharmaceutical compound of a plant origin. Its chemical structure represents two aromatic A and B rings linked through the C ring containing oxygen and five OH hydroxyl groups attached to the 3, 3′, 4′, 5, and 7 positions. In this study, a novel conformational mobility of the quercetin molecule was explored due to the turnings of the O3′H and O4′H hydroxyl groups, belonging to the B ring, around the exocyclic C-O bonds. It was established that the presence of only three degrees of freedom of the conformational mobility of the O3′H and O4′H hydroxyl groups is connected with their concerted behavior, which is controlled by the non-planar (in the case of the interconverting planar conformers) or locally non-planar (in other cases) TSsO3′H/O4′H transition states, in which O3′H and O4′H hydroxyl groups are oriented by the hydrogen atoms towards each other. We also explored the number of the physico-chemical and electron-topological characteristics of all intramolecular-specific contacts—hydrogen bonds and attractive van der Waals contacts at the conformers and also at the transition states. Long-terms perspectives for the investigations of the structural bases of the biological activity of this legendary molecule have been shortly described.

A Hidden Side of the Conformational Mobility of the Quercetin Molecule Caused by the Rotations of the O3H, O5H and O7H Hydroxyl Groups: In Silico Scrupulous Study

In this study at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of quantum-mechanical theory it was explored conformational variety of the isolated quercetin molecule due to the mirror-symmetrical hindered turnings of the O3H, O5H and O7H hydroxyl groups, belonging to the A and C rings, around the exocyclic C–O bonds. These dipole active conformational transformations proceed through the 72 transition states (TSs; C1 point symmetry) with non-orthogonal orientation of the hydroxyl groups relatively the plane of the A or C rings of the molecule (HO7C7C8/HO7C7C6 = ±(89.9–93.3), HO5C5C10 = ±(108.9–114.4) and HO3C3C4 = ±(113.6–118.8 degrees) (here and below signs ‘±’ corresponds to the enantiomers)) with Gibbs free energy barrier of activation ΔΔGTS in the range 3.51–16.17 kcal·mol−1 under the standard conditions (T = 298.1 K and pressure 1 atm): ΔΔGTSO7H (3.51–4.27) < ΔΔGTSO3H (9.04–11.26) < ΔΔGTSO5H (12.34–16.17 kcal mol−1). Conformational dynamics of the O3H and O5H groups is partially controlled by the intramolecular specific interactions O3H…O4, C2′/C6′H…O3, O3H…C2′/C6′, O5H…O4 and O4…O5, which are flexible and cooperative. Dipole-active interconversions of the enantiomers of the non-planar conformers of the quercetin molecule (C1 point symmetry) is realized via the 24 TSs with C1 point symmetry (HO3C3C2C1 = ±(11.0–19.1), HC2′/C6′C1′C2 = ±(0.6–2.9) and C3C2C1′C2′/C3C2C1′C6′ = ±(1.7–9.1) degree; ΔΔGTS = 1.65–5.59 kcal·mol−1), which are stabilized by the participation of the intramolecular C2′/C6′H…O1 and O3H…HC2′/C6′ H-bonds. Investigated conformational rearrangements are rather quick processes, since the time, which is necessary to acquire thermal equilibrium does not exceed 6.5 ns.

Intramolecular tautomerization of the quercetin molecule due to the proton transfer: QM computational study

Quercetin molecule (3, 3', 4', 5, 7-pentahydroxyflavone, C15H10O7) is an important flavonoid compound of natural origin, consisting of two aromatic A and B rings linked through the C ring with endocyclic oxygen atom and five hydroxyl groups attached to the 3, 3', 4', 5 and 7 positions. This molecule is found in many foods and plants, and is known to have a wide range of therapeutic properties, like an anti-oxidant, anti-toxic, anti-inflammatory etc. In this study for the first time we have revealed and investigated the pathways of the tautomeric transformations for the most stable conformers of the isolated quercetin molecule (Brovarets' & Hovorun, 2019) via the intramolecular proton transfer. Energetic, structural, dynamical and polar characteristics of these transitions, in particular relative Gibbs free and electronic energies, characteristics of the intramolecular specific interactions-H-bonds and attractive van der Waals contacts, have been analysed in details. It was demonstrated that the most probable process among all investigated is the proton transfer from the O3H hydroxyl group of the C ring to the C2' carbon atom of the C2'H group of the B ring along the intramolecular O3H…C2' H-bond with the further formation of the C2'H2 group. It was established that the proton transfer from the hydroxyl groups to the carbon atoms of the neighboring CH groups is assisted at the transition states by the strong intramolecular HCH…O H-bond (~28.5 kcal∙mol-1). The least probable path of the proton transfer-from the C8H group to the endocyclic O1 oxygen atom-causes the decyclization of the C ring in some cases. It is shortly discussed the biological importance of the obtained results.