Analysis of the antioxidant activity of 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid derivatives using quantum-chemistry descriptors and molecular docking

Strategic design, theoretical insights, synthesis, and unveiling antioxidant potential in a novel ascorbic acid analog

CONTEXT

In this study, we investigated the antioxidant potential of a novel ascorbic acid analog, DsD, assessing its interactions with the methylperoxyl (CH3OO·) radical in aqueous and lipid environments. Our focus was on understanding the acid-base equilibrium and how pH affects DsD's primary reaction mechanisms. Our findings indicate a marked preference for hydrogen atom transfer in lipid media, contrasting with sequential proton loss electron transfer (SPLET) in aqueous solutions. Remarkably, DsD's radical scavenging activity significantly outperforms ascorbic acid, being 4.05 and 9469.70 times more potent in polar and lipid contexts, respectively. This suggests DsD's superior efficacy as an antioxidant, potentially offering enhanced protection in biological systems. Additionally, we have demonstrated DsD's synthetic feasibility through a straightforward condensation reaction between ascorbic acid and 1,2-diaminoethane, followed by comprehensive physicochemical and spectroscopic characterization.

METHODS

All computational analyses in this study were conducted using the Gaussian 09 software suite, employing the M05-2X functional and the 6-31 + G(d) basis set. Enthalpy calculations were executed under standard conditions (298.15 K and 1 atm), incorporating appropriate thermodynamic corrections. Rate constants were evaluated using transition state theory (TST), and the overall assessment of radical scavenging activity was guided by the Quantum Mechanics-based Test for Overall Radical Scavenging Activity (QMORSA) protocol.

Investigation and Comparison of Antioxidant Potential of Catechins Present in Green Tea: DFT Study

DFT calculations were applied to compare the antioxidant potential of four major catechins present in green tea. The thermodynamic parameters related to three key mechanisms of primary antioxidant action were investigated in detail. Molecular orbital energies, absolute hardness, electronegativity, and electrophilicity index, which contributed to the radical scavenging were also investigated. The radical scavenging potential of each hydroxyl group of these polyphenolic antioxidants were investigated independently.

Shape Theory Applied to Molecular Docking and Automatic Localization of Ligand Binding Pockets in Large Proteins

Automatic search of cavities and binding mode analysis between a ligand and a 3D protein receptor are challenging problems in drug design or repositioning. We propose a solution based on a shape theory theorem for an invariant coupled system of ligand-protein. The theorem provides a matrix representation with the exact formulas to be implemented in an algorithm. The method involves the following results: (1) exact formulae for the shape coordinates of a located-rotated invariant coupled system; (2) a parameterized search based on a suitable domain of van der Waals radii; (3) a scoring function for the discrimination of sites by measuring the distance between two invariant coupled systems including the atomic mass; (4) a matrix representation of the Lennard-Jones potential type 6-12 and 6-10 as the punctuation function of the algorithm for a molecular docking; and (5) the optimal molecular docking as a solution of an optimization problem based on the exploration of an exhaustive set of rotations. We apply the method in the xanthine oxidase protein with the following ligands: hypoxanthine, febuxostat, and chlorogenic acid. The results show automatic cavity detection and molecular docking not assisted by experts with meaningful amino acid interactions. The method finds better affinities than the expert software for known published cavities.

Mechanism of Antioxidant Activity of Betanin, Betanidin and Respective C15-Epimers via Shape Theory, Molecular Dynamics, Density Functional Theory and Infrared Spectroscopy

Betanin and betanidin are compounds with extensive interest; they are effectively free radical scavengers. The present work aims to elucidate the differences between the mechanism of the antioxidant activity of betanin, betanidin, and their respective C15-epimers. Shape Theory establishes comparisons between the molecules’ geometries and determines parallelisms with the descriptors BDE, PA, ETE IP, PDE, and infrared spectra (IR) obtained from the molecule simulations. Furthermore, the molecules were optimized using the B3LYP/6-31+G(d,p) protocol. Finally, the molecular docking technique analyzes the antioxidant activity of the compounds in the complex with the therapeutic target xanthine oxidase (XO), based on a new proposal for the geometrical arrangement of the ligand atoms in the framework of Shape Theory. The results obtained indicate that the SPLET mechanism is the most favorable in all the molecules studied and that the first group that loses the hydrogen atom in the four molecules is the C17COOH, presenting less PA the isobetanidin. Furthermore, regarding the molecular docking, the interactions of these compounds with the target were favorable, standing out to a greater extent the interactions of isobetanidin with XO, which were analyzed after applying molecular dynamics.

Synthesis, antioxidant activity and bioinformatics studies of L-3-hydroxytyrosine templated N-alkyl/aryl substituted urea/thioureas

A new series of urea/thiourea derivatives have been efficiently synthesized from the reaction of L-3-hydroxytyrosine with selective isocyanates/isothiocyanates and characterized by Infra-red, proton & carbon-13 nuclear magnetic resonance spectral and mass spectrometry studies. All the synthesized compounds have been screened for their antioxidant activity by 1,1-diphenyl1-2-picrylhydrazyl radical assay, ferric reducing antioxidant power assay and also studied their molecular docking interaction profiles against 1N8Q and 3NRZ enzymatic proteins. The in vitro antioxidant activity has further supported by quantitative structure activity relationship, absorption, distribution, metabolism, and excretion & toxicity studies, bioactivity studies & enzyme inhibition assay and identified that they were potentially bound to ASP490 & ASP361 aminoacid residue in chain A of 1N8Q protein and GLN1194 aminoacid residue in chain L of 3NRZ protein and are responsible for potential antioxidant activity. It is proved that urea derivatives linked with 4-fluoro & 4-nitro and thiourea derivatives linked with 3-chloro & 4-fluoro have exhibited promising antioxidant activity. In eventual synthesized compounds have been identified as potential blood-brain barrier penetrable compounds and proficient central nervous system active neuro-protective antioxidant agents as they have envisaged as easily penetrable to blood-brain barrier thresholds, a neuroprotective property.

Multiple molecular targets mediated antioxidant activity, molecular docking, ADMET, QSAR and bioactivity studies of halo substituted urea derivatives of α-Methyl-l-DOPA

A series of novel α-methyl-l-DOPA urea derivatives viz., 3-(3,4-dihydroxyphenyl)-2-methyl-2-(3-halo/trifluoromethyl substituted phenyl ureido)propanoic acids (6a-e) have been synthesized from the reaction of α-methyl-l-DOPA (3) with various aryl isocyanates (4a-e) by using triethylamine (5, TEA) as a base catalyst in THF at reflux conditions. The synthesized compounds are structurally characterized by spectral (IR, ¹H &¹³C NMR and MASS) and elemental analysis studies and screened for their in-vitro antioxidant activity against DPPH, NO and H₂O₂ free radical scavenging assays and identified compounds 6c &6d as potential antioxidants. The acquired in vitro results were correlated with the results of molecular docking, ADMET, QSAR and bioactivity studies performed for them and predicted that the recorded in silico binding affinities are in good correlation with the in vitro antioxidant activity results. The molecular docking analysis has comprehended the strong hydrogen bonding interactions of 6a-e with 1CB4, 1N8Q, 3MNG, 1OG5, 1DNU, 3NRZ, 2CDU, 1HD2 and 2HCK proteins of their respective SOD, LO, PRXS5, CP450, MP, XO, NO, PRY5 and HCK enzymes. This has sustained the effective binding of 6a-e and resulted in functional inhibition of selective aminoacid residues to be pronounced as multiple molecular targets mediated antioxidant potent compounds. In addition, the evaluated toxicology risks of 6a-e are identified with in the potential limits of drug candidates. The conformational analysis of 6c & 6d prominently infers that urea moiety uniting α-methyl-l-DOPA with halo substituted aryl units into a distinctive orientation to comply good structure-activity to inhibit the proliferation of reactive oxygen species in vivo.

Investigation of Reaction Mechanisms and Kinetics of the Radical Scavenging Ability of 5-Tert-Butylbenzene-1,2,3-Triol and 3,5-di-Tert-Butylbenzene-1,2-Diol Compounds Towards OOH Radical

The antioxidant properties of the synthesised 5- tert-butylbenzene-1,2,3-triol (system A) and the designed 3,5-di -tert-butylbenzene-1,2-diol (system B) have been explored through density functional theory at the M05-2X/6-31+G(d,p) level of theory. The quantum mechanics-based test for overall free radical scavenging activity (QM- ORSA) protocol has been employed to account for their radical-scavenging capacity against the hydroperoxyl radical (HOO•) in the gas phase and in toluene solvent as a mimic lipid medium. The different mechanisms of the chemical reactions of the studied systems with HOO• have been considered, namely (i) the hydrogen atom transfer (HAT), (ii) the single electron transfer followed by proton transfer and (iii) the radical adduct formation. Our calculations provide evidence that HAT is the most favoured reaction mechanism in both the gas phase and in lipid media and the calculated thermodynamic and kinetic parameters indicate that the designed compound is more efficient than the synthesised system A and the reference system (α-tocopherol).

Theoretical insight into the substituent effects on the antioxidant properties of 8-hydroxyquinoline derivatives in gas phase and in polar solvents

The objective of this work is to perform a theoretical analysis of the antioxidant properties of a series of 8-hydroxyquinolines (8-HQs) to rationalize the available experimental results and to design new potent 8-HQ derivatives. The study was carried out in gas phase and in methanol at the DFT/B3LYP/ 6-311++G(d,p) computational level. The formation of stable ArO• radicals is discussed on the basis of different mechanisms, namely, hydrogen atom transfer (HAT), single electron transfer followed by proton transfer (SET-PT), and single proton loss electron transfer (SPLET). The obtained results show that the HAT mechanism is, thermodynamically, more favoured in gas phase, whereas the SPLET pathway is more favoured in polar solvents. The calculated thermochemical descriptors allow classification of the antioxidant power of the studied compounds.