Rumex dentatus L. phenolics ameliorate hyperglycemia by modulating hepatic key enzymes of carbohydrate metabolism, oxidative stress and PPARγ in diabetic rats

Rumex dentatus L. is a flowering plant with promising therapeutic effects. This study investigated the antioxidant efficacy of phenolic compounds isolated from R. dentatus L. in vitro and by conducting density function theory (DFT) studies to explore the mechanisms of action. The antioxidant, anti-inflammatory and antidiabetic effects of polyphenols-rich R. dentatus extract (RDE) were investigated in type 2 diabetic rats. Phytochemical investigation of the aerial parts of R. dentatus resulted in the isolation of one new and seven known compounds isolated for the first time from this species. All isolated phenolics showed in vitro radical scavenging activity. The antioxidant activity of the compounds could be oriented by the hydrogen atom transfer and sequential proton loss electron transfer mechanisms in gas and water phases, respectively. In diabetic rats, RDE attenuated hyperglycemia, insulin resistance and liver injury and improved carbohydrate metabolism. RDE suppressed oxidative stress and inflammation and upregulated PPARγ. In silico molecular docking analysis revealed the binding affinity of the isolated compounds toward PPARγ. In conclusion, the computational calculations were correlated with the in vitro antioxidant activity of R. dentatus derived phenolics. R. dentatus attenuated hyperglycemia, liver injury, inflammation and oxidative stress, improved carbohydrate metabolism and upregulated PPARγ in diabetic ratsThis work has DGI Project no. CTQ2015-63997-C2, a generous allocation of computing time at the Centro de Computación Científica of the UAM is also acknowledge

A quantum-chemical study of the binding ability of βXaaHisGlyHis towards copper(II) ion

The present study analyzed binding of Cu2+ to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches including electron correlation effects. In order to shed light on the character of interactions between Cu2+ and peptides, which are expected to be mainly electrostatic in nature, decomposition of interaction energy into physically meaningful components was applied

Deciphering the Molecular Mechanisms of Reactive Metabolite Formation in the Mechanism-Based Inactivation of Cytochrome p450 1B1 by 8-Methoxypsoralen and Assessing the Driving Effect of phe268

This study provides a comprehensive computational exploration of the inhibitory activity and metabolic pathways of 8-methoxypsoralen (8-MP), a furocoumarin derivative used for treating various skin disorders, on cytochrome P450 (P450). Employing quantum chemical DFT calculations, molecular docking, and molecular dynamics (MD) simulations analyses, the biotransformation mechanisms and the active site binding profile of 8-MP in CYP1B1 were investigated. Three plausible inactivation mechanisms were minutely scrutinized. Further analysis explored the formation of reactive metabolites in subsequent P450 metabolic processes, including covalent adduct formation through nucleophilic addition to the epoxide, 8-MP epoxide hydrolysis, and non-CYP-catalyzed epoxide ring opening. Special attention was paid to the catalytic effect of residue Phe268 on the mechanism-based inactivation (MBI) of P450 by 8-MP. Energetic profiles and facilitating conditions revealed a slight preference for the C4′=C5′ epoxidation pathway, while recognizing a potential kinetic competition with the 8-OMe demethylation pathway due to comparable energy demands. The formation of covalent adducts via nucleophilic addition, particularly by phenylalanine, and the generation of potentially harmful reactive metabolites through autocatalyzed ring cleavage are likely to contribute significantly to P450 metabolism of 8-MP. Our findings highlight the key role of Phe268 in retaining 8-MP within the active site of CYP1B1, thereby facilitating initial oxygen addition transition states. This research offers crucial molecular-level insights that may guide the early stages of drug discovery and risk assessment related to the use of 8-MP

Computational study of the structure and degradation products of alloxydim herbicide

Density functional theory calculations allowed us to study alloxydim herbicide and to identify the most stable conformers, the factors that governs their stability, and the interconversion mechanisms among the most relevant conformers. The degradation chain involves, as a first step, the cleavage of the N–O bond and the formation of a stable intermediate difficult to characterize experimentally. The study performed also allowed us to identify the properties of this elusive intermediate and to determine that the dominant fragmentation process in the gas phase is the homolytic fragmentation. Stability of alloxydim conformers and homolytic fragments were also assessed in the water phase. Computed IR spectra were consistent with those observed experimentally

Pesticide byproducts formation Theoretical study of the protonation of alloxydim degradation products

Density Functional Theory was used to explore the protonation of the amine/imine byproducts of the alloxydim herbicide. An extensive exploration of the possible protonation sites of anionic and neutral fragments was performed. Doubly charged species were also considered. The structure and relative stabilities of different tautomers were determined. Computed infrared spectra allowed a better understanding of the vibrational modes and were consistent with those observed experimentally. Calculated UV–Vis spectra allow to predict a probable further photodegradation

Modeling interactions between an amino acid and a metal dication: Cysteine-calcium(II) Reactions in the gas phase

The gas‐phase interactions between Ca2+ and cysteine (Cys) have been investigated through the use of electrospray ionization/mass spectrometry techniques and B3LYP/6‐311++G(3df,2p)//B3LYP/6‐311+G(d,p) density functional theory computations. The unimolecular collision‐activated decomposition of [Ca(Cys)]2+ is dominated by the loss of ammonia, a Coulomb explosion yielding NH4+ and [CaC3H3O2S]+, and the loss of H2S. The detection of lighter [C3H3OS]+ monocations indicates that the [CaC3H4O2S]2+ doubly charged species produced by the loss of ammonia undergo a subsequent Coulomb explosion yielding [C3H3OS]++CaOH+. This [C3H3OS]+ cation finally decomposes into [C2H3S]++CO. Alternatively, the aforementioned [CaC3H4O2S]2+ dications may also lead to lighter [CaCO2]2+ and [CaC2H4S]2+ dications by the loss of C2H4S and CO2, respectively. A detailed theoretical exploration of the Ca2+/Cys potential‐energy surface indicates that the salt‐bridge structures, in which the metal dication interacts with the carboxylate group of the zwitterionic form of cysteine, are at the origin of the different reaction pathways leading to the observed product ions, even though they lie higher in energy than the charge‐solvated adduct in which the metal interacts simultaneously with the carbonyl oxygen, the amino, and the SH group of its canonical form. The interaction between the metal cation and the base is essentially electrostatic, with a calculated binding energy of 560 kJ mol−1.This study was supported by the DGI Projects (no. CTQ2012‐35513‐C02), by the Project MADRISOLAR2 (Ref. S2009PPQ/1533) of the Comunidad Autónoma de Madrid, and by Consolider on Molecular Nanoscience (no. CSC2007‐00010).Peer Reviewe

Quantum chemistry in environmental pesticide risk assessment

The scientific community and regulatory bodies worldwide, currently promote the development of non-experimental tests that produce reliable data for pesticide risk assessment. The use of standard quantum chemistry methods could allow the development of tools to perform a first screening of compounds to be considered for the experimental studies, improving the risk assessment. This fact results in a better distribution of resources and in better planning, allowing a more exhaustive study of the pesticides and their metabolic products. The current paper explores the potential of quantum chemistry in modelling toxicity and environmental behaviour of pesticides and their by-products by using electronic descriptors obtained computationally. Quantum chemistry has potential to estimate the physico-chemical properties of pesticides, including certain chemical reaction mechanisms and their degradation pathways, allowing modelling of the environmental behaviour of both pesticides and their by-products. In this sense, theoretical methods can contribute to performing a more focused risk assessment of pesticides used in the market, and may lead to higher quality and safer agricultural products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industr

Unveiling the tyrosinase inhibitory potential of phenolics from Centaurium spicatum: bridging in silico and in vitro perspectives

Phenolics, abundant in plants, constitute a significant portion of phytoconstituents consumed in the human diet. The phytochemical screening of the aerial parts of Centaurium spicatum led to the isolation of five phenolics. The anti-tyrosinase activities of the isolated compounds were assessed through a combination of in vitro experiments and multiple in silico approaches. Docking and molecular dynamics (MD) simulation techniques were utilized to figure out the binding interactions of the isolated phytochemicals with tyrosinase. The findings from molecular docking analysis revealed that the isolated phenolics were able to bind effectively to tyrosinase and potentially inhibit substrate binding, consequently diminishing the catalytic activity of tyrosinase. Among isolated compounds, cichoric acid displayed the lowest binding energy and the highest extent of polar interactions with the target enzyme. Analysis of MD simulation trajectories indicated that equilibrium was reached within 30 ns for all complexes of tyrosinase with the isolated phenolics. Among the five ligands studied, cichoric acid exhibited the lowest interaction energies, rendering its complex with tyrosinase the most stable. Considering these collective findings, cichoric acid emerges as a promising candidate for the design and development of a potential tyrosinase inhibitor. Furthermore, the in vitro anti-tyrosinase activity assay unveiled significant variations among the isolated compounds. Notably, cichoric acid exhibited the most potent inhibitory effect, as evidenced by the lowest IC50 value (7.92 ± 1.32 µg/ml), followed by isorhamnetin and gentiopicrin. In contrast, sinapic acid demonstrated the least inhibitory activity against tyrosinase, with the highest IC50 value. Moreover, cichoric acid exhibited a mixed inhibition mode against the hydrolysis of L-DOPA catalyzed by tyrosinase, with Ki value of 1.64. Remarkably, these experimental findings align well with the outcomes of docking and MD simulations, underscoring the consistency and reliability of our computational predictions with the actual inhibitory potential observed in vitro