Electronic description of four flavonoids revisited by DFT method

Pyrazolone-type compounds (part II): in vitro and in silico evaluation of antioxidant potential; structure-activity relationship

The pyrazolone class comprises a variety of hybrid compounds displaying diverse biological actions. Although studied for decades, these compounds are still of interest due to their facile chemical transformations. In our previous work, we presented the synthetic route of functionalised pyrazolone derivatives. The presence of pyrazolone structural motif in many drugs, such as edaravone, prompted us to investigate the antioxidant features of the selected compounds. In this paper, we provide an extensive in vitro and in silico description of the antioxidant properties of selected pyrazolone analogues. The obtained in vitro results revealed their great antiradical potency against the DPPH radical (IC₅₀ values in the 2.6-7.8 μM range), where the best results were obtained for analogues bearing a catechol moiety. Density functional theory (DFT) was used to assess their antioxidant capacity from the thermodynamic aspect. Here, good agreement with in vitro results was achieved. DFT was employed for the prediction of the most preferable radical scavenging pathway, also. In polar solvents, the SPLET mechanism is a favourable scavenging route, whereas in nonpolar solvents the HAT is slightly predominant. Furthermore, antioxidant mechanisms were studied in the presence of relevant reactive oxygen species. The obtained values of the reaction enthalpies with the selected radicals revealed that HAT is slightly prevailing in polar solvents, while the SPLET mechanism is dominant in nonpolar solvents. Regarding the well-known antioxidant features of the drug edaravone, these findings represent valuable data for this pyrazolone class and could be used as the basis for further investigations.

Evaluation of antioxidant and cytotoxic properties of phenolic N-acylhydrazones: structure-activity relationship

Cancer is still a relentless public health issue. Particularly, colorectal cancer is the third most prevalent cancer in men and the second in women. Moreover, cancer development and growth are associated with various cell disorders, such as oxidative stress and inflammation. The quest for efficient therapeutics is a challenging task, especially when it comes to achieving both cytotoxicity and selectivity. Herein, five series of phenolic N-acylhydrazones were synthesized and evaluated for their antioxidant potency, as well as their influence on HCT-116 and MRC-5 cells viability. Among 40 examined analogues, 20 of them expressed antioxidant activity against the DPPH radical. Furthermore, density functional theory was employed to estimate the antioxidant potency of the selected analogues from the thermodynamical aspect, as well as the preferable free-radical scavenging pathway. Cytotoxicity assay exposed enhanced selectivity of a number of analogues toward cancer cells. The structure-activity analysis revealed the impact of the type and position of the functional groups on both cell viability and selectivity toward cancer cells.

Antioxidant and cytotoxic activities of selected salicylidene imines: experimental and computational study

Selected salicylidene imines were evaluated for their antioxidant and cytotoxic potentials. Several of them exerted potent scavenging capacity towards ABTS radical and hydrogen peroxide. The insight into the preferable antioxidative mechanism was reached employing density functional theory. In the absence of free radicals, the SPLET mechanism is dominant in polar surroundings, while HAT is prevailing in a non-polar environment. The results obtained for the reactions of the most active compounds with some medically relevant radicals pointed out competition between HAT and SPLET mechanisms. The assessment of their cytotoxic properties revealed inhibition of ER-a human breast adenocarcinoma cells or estrogen-independent prostate cancer cells. Molecular docking study with the cyclooxygenase (COX) 2 enzyme was performed to examine the most probable bioactive conformations and possible interactions between the tested derivatives and COX-2 binding pocket.

A Novel Insight into Screening for Antioxidant Peptides from Hazelnut Protein: Based on the Properties of Amino Acid Residues

This study used the properties of amino acid residues to screen antioxidant peptides from hazelnut protein. It was confirmed that the type and position of amino acid residues, grand average of hydropathy, and molecular weight of a peptide could be comprehensively applied to obtain desirable antioxidants after analyzing the information of synthesized dipeptides and BIOPEP database. As a result, six peptides, FSEY, QIESW, SEGFEW, IDLGTTY, GEGFFEM, and NLNQCQRYM were identified from hazelnut protein hydrolysates with higher antioxidant capacity than reduced Glutathione (GSH) against linoleic acid oxidation. The peptides having Tyr residue at C-terminal were found to prohibit the oxidation of linoleic acid better than others. Among them, peptide FSEY inhibited the rancidity of hazelnut oil very well in an oil-in-water emulsion. Additionally, quantum chemical parameters proved Tyr-residue to act as the active site of FSEY are responsible for its antioxidation. This is the first presentation of a novel approach to excavating desired antioxidant peptides against lipid oxidation from hazelnut protein via the properties of amino acid residues.

Exploration of electronic properties, radical scavenging activity and QSAR of oxadiazole derivatives by molecular docking and first-principles approaches

Eight new oxadiazole derivatives were designed then geometries for ground state were optimized through Density Functional Theory (DFT) at B3LYP/6-31G** level. Single electron transfer mechanism has been studied to understand the antioxidant ability of the oxadiazole derivatives. Then molecular electrostatic potential and quantitative structure–activity relationship (QSAR) was probed. Additionally, we shed light on different molecular descriptors, e.g., electrophilicity(ω), electronegativity(χ), electrophilicity indices(ωi), hardness(η), softness(S) and chemical potential(μ).The smaller value of ionization potential for 5a is showing that it might be efficient antioxidant candidate. The electrophilic reactive sites in 2a, 3a, 4a, 5a and 7a derivatives might be a good choice for reactivity that would be advantageous to improve the biological activity. The polar surface area of 3a, 4a and 5a derivatives was found < 60 A² which is enlightening that these drugs might be suitable as orally active and for brain penetration. First-principles calculations and molecular docking results revealed that 5a would lead to superior antioxidant activity.

Experimental and theoretical study on structure-tautomerism among edaravone, isoxazolone, and their heterocycles derivatives as antioxidants

Edaravone is a heterocyclic pyrazolone compound. It has pronounced effect against free radicals, however renal and hepatic disorders have been reported. Isoxazolones are considered bioisosteric analogues of pyrazolones and may have comparable properties. Thus, we investigated the structural and electronic influences for edaravone, isoxazolone, and their tautomers on antioxidant process. Structure and tautomerism study among edaravone, isoxazolone and their heterocycles derivatives were related to antioxidant mechanisms by using the hybrid DFT method B3LYP with the basis sets 6-31++G(2d,2p). The C—H tautomer was the most stable and energetically favored among them. Intramolecular N—H—N hydrogen bonds and polar medium were responsible for the low energy differences among all possible tautomers. N—H tautomers in both systems proved to be better antioxidant by SET (single electron transfer), while O—H tautomers were better antioxidant on HAT (homolytic hydrogen atom transfer) mechanism. Theoretical calculation showed that edaravone is more potent than phenylisoxazolone, however, both has similar antioxidant scavenging on experimental DPPH. The carbonyliminic system played a very important role in the antioxidant activity for both studied classes.

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.

Kinetics and Mechanism of the Antioxidant Activities of C. olitorius and V. amygdalina by Spectrophotometric and DFT Methods

The kinetics and mechanism of the antioxidant activities of the methanolic extract of the leaves of two vegetables [Corchorus olitorius (C. olitorius) and Vernonia amygdalina (V. amygdalina)] have been studied using experimental and theoretical approaches. The kinetics (second order and pseudo-first order) of the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities of the leaf extracts at varying times (30-90 min) were determined using the UV-visible spectrophotometry method at λ_max = 517 nm, whereas the mechanism was studied by density functional theory at two levels of functionals (B3LYP and LC-ωPBE) using bond dissociation enthalpy and adiabatic ionization potential values. Molecular properties such as the highest occupied molecular orbital, lowest unoccupied molecular orbital, electronegativity (χ), electrophilicity (ω), hardness (η), and softness (S) of the predominant phenolic antioxidants were also compared. The second-order kinetics is favored by both plants rather than pseudo-first order; however, V. amygdalina with a second-order rate constant k ₂ of 0.0152 (mM)^-1 min^-1 is faster in scavenging DPPH radicals than C. olitorius with a k ₂ value of 0.0093 (mM)^-1min^-1. Chlorogenic acid and luteolin-7-O-β-glucuronide, which are the most abundant phenolic acid antioxidant in C. olitorius and V. amygdalina, both preferably scavenge the DPPH radical via a hydrogen atom transfer mechanism. This is evident from their lower bond dissociation enthalpy values than the adiabatic ionization potential values. Successful molecular docking of these phenolic compounds indicates that both compounds form favorable interactions with the therapeutic target, xanthine oxidase.

Toward of Safer Phenylbutazone Derivatives by Exploration of Toxicity Mechanism

A drug design for safer phenylbutazone was been explored by reactivity and docking studies involving single electron transfer mechanism, as well as toxicological predictions. Several approaches about its structural properties were performed through quantum chemistry calculations at the B3LYP level of theory, together with the 6-31+G(d,p) basis sets. Molecular orbital and ionization potential were associated to electron donation capacity. The spin densities contribution showed a preferential hydroxylation at the para-positions of phenyl ring when compared to other positions. In addition, on electron abstractions the aromatic hydroxylation has more impact than alkyl hydroxylation. Docking studies indicate that six structures 1, 7, 8 and 13–15 have potential for inhibiting human as well as murine COX-2, due to regions showing similar intermolecular interactions to the observed for the control compounds (indomethacin and refecoxib). Toxicity can be related to aromatic hydroxylation. In accordance to our calculations, the derivatives here proposed are potentially more active as well safer than phenylbutazone and only structures 8 and 13–15 were the most promising. Such results can explain the biological properties of phenylbutazone and support the design of potentially safer candidates.

Synthesis, structural characterization, QSAR and docking studies of a new binuclear nickel (II) complex based on the flexible tetradentate N-donor ligand as a potent antibacterial and anticancer agent

A new nickel (II)complex namely [Ni₂(Lt)Cl₄] derived from the NiCl₂.6H₂O and 1,1,3,3-tetrakis(3,5-dimethyl-1-pyrazolyl)propane (Lt) has been synthesized and fully characterized by the single crystal X-ray diffraction, elemental analysis, FT-IR, UV-vis, density functional theory (DFT) calculations, antibacterial and anticancer activities. In the title complex, each of the Ni(II) atoms is tetrahedrally coordinated by two N atoms from one of the chelating bidentate bis(3,5-dimethylpyrazolyl)methane units of the Lt ligand and two Cl as terminal ligands. The neighboring [Ni₂(Lt)Cl₄] molecules are linked together by the intermolecular CH⋯Cl hydrogen bonds to generate a 1D chain structure. The chains are further stabilized by the intermolecular CH⋯π interactions to form a two-dimensional non-covalent bonded structure. The antibacterial activity of the free Lt ligand and its Ni (II) complex shows that the ability of these compounds to inhibit growth of the tested bacteria increase from the Lt to binuclear nickel (II) complex. Scanning probe microscopy (SPM) study of the treated B. subtilis and E. coli bacteria was implemented to understand the structural changes caused by the interactions between the nickel (II) complex and the target bacteria. The cytotoxicity test of the Lt ligand and its complex was evaluated against the human carcinoma cell line (Caco-2) using the MTT assay. The results indicate that the Lt ligand and its complex display cytotoxicity against Caco-2 with the IC50 values of 36.29μM and 12.97μM, respectively. Therefore, the complex can be nominated as a potential anticancer agent. Molecular docking investigations on the five standard antibiotic, five standard anticancer drugs, free Lt ligand, title complex and twelve receptors were performed by Autodock vina function. The results of docking and DFT calculations are in line with the in vitro data obtained via the antibacterial and anticancer activity of Lt ligand and its made-complex.

Z-Isomers of (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=OH. Conformational properties, electronic structure and aqueous solvent effects

Procyanidins are highly hydroxylated polymers known as antioxidant compounds, thereby exhibiting beneficial effects. These compounds are protective agents against oxidative stress and the damage induced by free radicals in membranes and nucleic acids. This paper describes a study of the conformational space of (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=OH as part of a larger study of similar structures with different substitutions. The relationships between aqueous solution-vacuum variations of some properties were studied, as well as the stabilization and reactivity of (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=H, R'=H, R=OH, R'=R=OH, and (+)-catechin. The variations in geometric parameters and electronic properties due to conformational changes, as well as the effects of substituents and polar solvents, were evaluated and analyzed. Bader's theory of atoms in molecules was applied to characterize intramolecular interactions, along with a natural bond orbital analysis for each conformer described. The molecular electrostatic potential was rationalized by charge delocalization mechanisms and interatomic intramolecular interactions, relating them to the structural changes and topological properties of the electron charge density. Molecular polarizability and permanent electric dipole moment values were estimated. The results show the importance of a knowledge of the conformational space, and values for each conformer. Based on our previous results, we showed the existence of electron charge delocalization mechanisms acting cooperatively as "delocalization routes", showing interactions between different rings not even sharing the same plane. These "delocalization routes" were more effective for (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=OH than for (+)-catechin, and are proposed as adding insight into the structure-antioxidant activity relationship of flavans.

Experimental and theoretical study of antioxidative properties of some salicylaldehyde and vanillic Schiff bases

A set of ten phenolic Schiff bases was evaluated for their antioxidative properties. Two of them, one salicylaldehyde and one vanillic, showed high activity. Parameters obtained by DFT supported the experimental findings.

DPPH radical scavenging activity of tricin and its conjugates isolated from "Njavara" rice bran: a density functional theory study

Structural, electronic, and energetic characteristics of tricin, tricin-4'-O-(erythro-β-guaiacylglyceryl)ether (TEGE), and tricin-4'-O-(threo-β-guaiacylglyceryl)ether (TTGE), isolated from "Njavara" rice bran have been studied using DFT to explain their experimentally determined radical scavenging activity (EC(50) values) in comparison with known standards such as quercetin, myricetin, and catechin. Among the three mechanisms proposed for explaining the antioxidant activity, proton coupled-electron transfer (PC-ET), sequential proton loss electron transfer (SPLET), and electron transfer-proton transfer (ET-PT), our results support the second one. The O-H bond dissociation enthalpy (BDE) and the spin density on the oxygen with the radical character are excellent descriptors of radical scavenging activity. BDE (in kcal/mol) increased in the order myricetin (74.6) < quercetin (78.1) < catechin (78.3) < tricin (81.5) < TTGE (90.6) < TEGE (91.1), while the EC(50) increased exponentially with increase in BDE, 20.51, 42.98, 45.07, 90.39, 208.01, and 352.04 μg/mL for myricetin, quercetin, catechin, tricin, TTGE, and TEGE, respectively.

A systematic computational study on flavonoids

17 selected flavones derivatives, flavonoids, were analyzed through a systematic B3LYP/6-311++G** computational study with the aim of understanding the molecular factors that determine their structural and energetic properties in gas phase. Flavonoids were selected in a systematic way to infer the effect of the number and relative positions of hydroxyl groups on molecular properties. Different conformers for each flavonoid were analyzed and the strength and topology of the intramolecular hydrogen bonds studied through the computation of the corresponding torsional profiles. Atoms in a Molecule, and Natural Bond Orbital methodology was applied to the analysis of charge distribution along the studied molecules, and the intramolecular hydrogen bonds. Molecular shapes were studied through full geometry optimization, and the position of the catechol ring analyzed through dihedral scans.

Theoretical study of the mechanism of inhibition of xanthine oxidase by flavonoids and gallic acid derivatives

Xanthine oxidase is a flavoprotein enzyme which catalyzes the oxidative hydroxylation of purine substrates. Because of its availability, it has become a model for structural molybdoenzymes in general. The enzyme is a well-established target of drugs against gout and hyperuricemia and exists in two forms: oxidase and deshydrogenase. In some pathologies, its level increases in oxidase form, being the source of free radicals which can cause damage to surrounding tissues. It is important to understand the mechanisms of the enzyme inhibition to help in the search of new inhibitors. The main active center is a molybdopterin buried in a cavity. Theoretical calculations can be of some help for distinguishing the important aspects in the inhibition: attraction inside the cavity and anchorage. In this paper, the molybdopterin molecule geometry has been optimized by ab initio with the DFT method and the results have been shown to be very similar to the X-ray coordinates. In order to evaluate the attraction inside the cavity, the electrostatic potential between the charged molybdopterin molecule and two series of inhibitors, some flavonoids, and some gallic acid derivatives have been calculated using the multipolar development supplied by the Gaussian package. The good concordance between the electrostatic force and IC(50) indicates that the attraction is an important factor in the inhibition and must be taken into account in the designing of new drugs.

Antioxidant mechanisms of Quercetin and Myricetin in the gas phase and in solution--a comparison and validation of semi-empirical methods

Flavonoids have long been recognized for their general health-promoting properties, of which their antioxidant activity may play an important role. In this work we have studied the properties of two flavonols, quercetin and myricetin, using semi-empirical methods in order to validate the application of the recent Parametric Model 6 and to understand the fundamental difference between the two molecules. Their geometries have been optimized and important molecular properties have been calculated. The energetic of the possible antioxidant mechanisms have also been analyzed. The two studied flavonols do not differ significantly in their molecular properties, but the antioxidant mechanisms by which they may act in solution can be rather different. Moreover, we also show that the Parametric Model 6 can produce reliable information for this type of compounds.