DFT studies on global parameters, antioxidant mechanism and molecular docking of amlodipine besylate

In silico study on antidiabetic and antioxidant activity of bioactive compounds in Ficus carica L

Hyperglycemia is one of the diagnostic issues in diabetes mellitus and is considered as a complex metabolic condition. It has been one of the most prevalent illnesses of the twenty-first century and still rising at an alarming rate across the globe and expected to impact 693 million individuals by 2045. Therefore, it is mandatory to develop more effective and safer treatments to manage diabetes. One of the ways to manage hyperglycemia is through inhibiting carbohydrate digestion and thereby lowering the glucose formation in the human body. The enzyme salivary amylase and pancreatic amylase is responsible for cleaving α-1,4-glucoside bond. Amylase inhibitors can lower blood glucose in diabetics by slowing digestion. Ficus carica is commonly known for its medicinal properties due to its various phytochemicals. In the present study, 10 phytochemicals present in F. carica compounds named, β-carotene, lutein, cyanidin-3-glucoside, gallic acid, luteolin, catechin, kaempferol, vanillic acid, peonidin-3-glucoside, and quercetin hydrate were taken to study their inhibition potential against pancreatic amylase and salivary amylase through molecular docking and molecular dynamics simulations. Further, density functional theory calculations are used to investigate the delocalization of electron density on the molecule as well as study ADME properties of the molecules take. A QSAR model has been developed using the binding energy obtained using molecular docking and thermodynamic parameters from DFT calculations.Communicated by Ramaswamy H. Sarma.

Potential antioxidant and antiradical agents from Allium ascalonicum: Superoxide dismutase and density functional theory in silico studies

Antioxidants are compounds that can inhibit excessive free radical reactions in the body. Excessive free radicals can cause system imbalances in the body which can trigger oxidative stress and cause serious illness. The limitations of antioxidants in the body can be overcome by consuming safe natural additional antioxidants that can be obtained from natural products. Isolating compounds of Allium ascalonicum leaves as antioxidant and antiradical agents in inhibiting excessive free radicals by in vitro and in silico. The extracted compounds were purified by column chromatography. The compounds obtained were then characterized using ultraviolet, infrared, NMR, and mass spectrometry. Determination of antioxidant activity was carried out by in vitro using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and the non-enzymatic superoxide dismutase (SOD) methods. The in silico study used the density functional theory (DFT) calculation method with global descriptive parameters (GDP), donor acceptor map (DAM), and frontier molecular orbitals (FMO) analysis. Three compounds have been isolated, of which compound 1 is a new compound. In the DPPH method, compound 1 has more strong antioxidant activity than others, as well as in the non-enzymatic SOD method. Whereas, in the DFT calculation shows that compound 1 has the best reactivity and stability between other compounds and was categorized as the best antiradical. Compound 1 has the highest antioxidant activity compared to the other compounds by in vitro both the DPPH and non-enzymatic SOD methods. In silico, compound 1 has the potential as the best antiradical.

A theoretical study on radical scavenging activity of phenolic derivatives naturally found within Alternaria alternata extract

The increasing oxidative stress demands potential chemical compounds derived from natural resources with good antioxidant activity to overcome adverse health issues. In this context, we investigated the antioxidant properties of four dibenzopyrone phenolic compounds obtained from the endophytic fungus Alternaria alternata: altenusin, altenusin B, alterlactone, and dehydroaltenusin using DFT calculations. Our investigation focused on understanding the structure-antioxidant property relationship. It delved into probing the activity by modelling the antioxidant mechanisms. The computed transition states and thermochemical parameters, along with the structural attributes, indicate that altenusin B has good antioxidant efficacy among the four compounds, and it follows the HAT mechanism in an aqueous phase. Remarkably, our findings indicate that altenusin B exhibits potent HOO˙ radical scavenging properties, characterized by the computed high rate constant. The molecular docking studies of these compounds with the pro-oxidant enzyme xanthine oxidase (XO) gave insights into the binding modes of the compounds in the protein environment. Furthermore, molecular dynamics (MD) simulations were employed to study the interaction and stability of the compounds inside the XO enzyme. Our exploration sheds light on the radical scavenging potential of the -OH sites and the underlying antioxidant mechanisms that underpin the compounds' effective antioxidant potential.

Synthesis, DFT Study, and In Vitro Evaluation of Antioxidant Properties and Cytotoxic and Cytoprotective Effects of New Hydrazones on SH-SY5Y Neuroblastoma Cell Lines

A series of ten new hydrazide-hydrazone derivatives bearing a pyrrole ring were synthesized and structurally elucidated through appropriate spectral characteristics. The target hydrazones were assessed for radical scavenging activity through 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) tests, with ethyl 5-(4-bromophenyl)-1-(2-(2-(4-hydroxy-3,5-dimethoxybenzylidene)hydrazine-yl)-2-oxoethyl)-2-methyl-1H-pyrrole-3-carboxylate (7d) and ethyl 5-(4-bromophenyl)-1-(3-(2-(4-hydroxy-3,5-dimethoxybenzylidene) hydra zine-yl)-3-oxopropyl)-2-methyl-1H-pyrrole-3-carboxylate (8d) highlighted as the best radical scavengers from the series. Additional density functional theory (DFT) studies have indicated that the best radical scavenging ligands in the newly synthesized molecules are stable, do not decompose into elements, are less polarizable, and with a hard nature. The energy of the highest occupied molecular orbital (HOMO) revealed that both compounds possess good electron donation capacities. Overall, 7d and 8d can readily scavenge free radicals in biological systems via the donation of hydrogen atoms and single electron transfer. The performed in vitro assessment of the compound's protective activity on the H2O2-induced oxidative stress model on human neuroblastoma cell line SH-SY5Y determined 7d as the most perspective representative with the lowest cellular toxicity and the highest protection.

Investigations of Electronic, Structural, and In Silico Anticancer Potential of Persuasive Phytoestrogenic Isoflavene-Based Mannich Bases

Isoflavenes have received the greatest research attention among the many groups of phytoestrogens. In this study, various isoflavene-based Mannich bases were selected for their theoretical studies. The purpose of this research was to discover the binding potential of all the designated Mannich bases acting as inhibitors against cancerous proteins EGFR, cMet, hTrkA, and HER2 (PDB codes: 5GTY, 3RHK, 6PL2, and 7JXH, respectively). For their virtual screening, DFT calculations and molecular docking studies were undertaken using in silico software. Docking studies predicted that ligands 5 and 15 exhibited the highest docking score by forming hydrogen bonds within the active pocket of protein 6PL2, ligands 1 and 15 both with protein 3RHK, and 7JXH, 12, and 17 with protein 5GTY. Rendering to the trends in polarizability and dipole moment, the energy gap values (0.2175 eV, 0.2106 eV) for the firm conformers of Mannich bases (1 and 4) replicate the increase in bioactivity and chemical reactivity. The energy gap values (0.2214 eV and 0.2172 eV) of benzoxazine-substituted isoflavene-based Mannich bases (9 and 10) reflect the increase in chemical potential due to the most stable conformational arrangements. The energy gap values (0.2188 eV and 0.2181 eV) of isoflavenes with tertiary amine-based Mannich bases (14 and 17) reflect the increase in chemical reactivity and bioactivity due to the most stable conformational arrangements. ADME was also employed to explore the pharmacokinetic properties of targeted moieties. This study revealed that these ligands have a strong potential to be used as drugs for cancer treatment.

In silico approach for enhancing innate lipid content of Yarrowia lipolytica, by blocking the acyl-CoA oxidase-1 enzyme, using various analogous compounds of lipids

Yarrowia lipolytica is used as a model in this study to screen the potential candidates for inflating the innate lipid content of the cell. This study focuses on reducing the lipid degradation that occurs by the β-oxidation process and discursively increasing the innate lipid content. Acyl-CoA oxidase-1, the primary and initial enzyme involved in the lipid degradation pathway, was selected as a target and blocked using various lipid analogous compounds. The blocking study was carried out using molecular docking and dynamic studies using computation tools. The largest active site pocket located around the Phe-394 amino acid of the target protein is taken as a site for docking. The molecular docking was performed for the selected compounds (citric acid, Finsolv, lactic acid, oxalic acid, Tween-80 and Triton X-100) and the docking results were compared with the outcome of the standard molecule (octadecatrienoic acid). Citric acid, Finsolv, Tween-80 and Triton X-100 were found to be the potential candidates for blocking the target molecule in the static condition using docking studies, revealing a minimum binding energy requirement than the standard molecule. They were further taken for a dynamics study using GROMACS software. The RMSD, RMSF, number of hydrogen bond interactions and radius of gyration of the complex molecules were studied in a dynamic approach for 100 ns. Citric acid has been found to be the potential hit compound to block acyl-CoA oxidase-1 enzyme with its maximum hydrogen interaction and minimum fluctuations. It also revealed out the minimum total energy requirement for the complex formation.

Inversion Theory Leveling as a New Methodological Approach to Antioxidant Thermodynamics: A Case Study on Phenol

Antioxidants are various types of compounds that represent a link between biology and chemistry. With the development of theoretical and computational methods, antioxidants are now being studied theoretically. Here, a novel method is presented that aims to reduce the estimated wall times for DFT calculations that result in the same or higher degree of accuracy in the second derivatives over energy than is the case with the regular computational route (i.e., optimizing the reaction system at a lower model and then recalculating the energies at a higher level of theory) by applying the inversion of theory level to the universal chemical scavenger model, i.e., phenol. The resulting accuracy and wall time obtained with such a methodological setup strongly suggest that this methodology could be generally applied to antioxidant thermodynamics for some costly DFT methods with relative absolute deviation.

Network analysis and ligand-based pharmacophore modeling for discovery of small molecule against glioblastoma multiforme

Aim: This study uses network pharmacology to design a c-Src inhibitor followed by pharmacophore modeling to combat glioblastoma multiforme. These in silico approaches are suitable for designing and developing new molecules of interest. Materials & methods: The authors performed virtual screening, pharmacophore analysis and validation of results using various in silico tools and reliable data from different types of literature and databases. Results: The in silico pipeline the authors followed produced reliable chemical information to combat glioblastoma. The authors identified a chemical template against the c-Src protein, which was validated statistically and computationally. Conclusion: The authors have successfully identified a chemical template against c-Src, which will be developed into a promising inhibitor in future studies.

Antioxidant activity of erlotinib and gefitinib: theoretical and experimental insights

Erlotinib and gefitinib are quinazoline derivatives with antineoplastic properties. Usually, intake of antineoplastic agents results in much a greater degree of oxidative stress, i.e. the production of free radicals, than induced by cancer itself. Hence, anticancerous drugs must also exhibit antioxidant activity but this has not been studied thus far. In this study, the antioxidant activity of erlotinib and gefitinib was examined by experimental and computational studies. It was found that erlotinib and gefitinib exhibit good 2,2-dipheny l-1-picrylhydrazyl (DPPH) radical and hydroxyl radical scavenging (HRS) activities. In DPPH assay, the IC₅₀ for erlotinib and gefitinib were 0.584 and 0.696 mM, respectively, while IC₅₀ for HRS assay were 0.843 and 1.03 mM for erlotinib and gefitinib, respectively. Structural characteristics such as frontier molecular orbitals (FMOs), molecular electrostatic potential maps (MESPs), and global descriptive parameters were calculated at DFT/B3LYP/6-311++G (d,p) on the optimized geometries of erlotinib and gefitinib. UV-visible spectroscopy revealed the possible electronic transitions between the FMOs and their associated excitation energies of both drugs and found that erlotinib has π to π* transitions while gefitinib has π to π* and σ to π* transitions. To elucidate the antioxidant activity of erlotinib and gefitinib, three mechanisms namely hydrogen atom transfer (HAT), single electron transfer proton transfer (SETPT), and sequential proton-loss electron-transfer (SPLET) were employed and articulated the results in arithmetic parameters like bond dissociation energy (BDE), proton affinity (PA), ionization potential (IP), electron transfer enthalpy (ETE), and proton dissociation enthalpy (PDE). Further, molecular docking studies have been carried out to have a better understanding of binding sites and modes of interaction with a well-known antioxidant target protein monoamine oxidase-B (MAO-B) employing docking scores and types of interactions. All the calculated parameters point out that though gefitinib and erlotinib were interchangeable, erlotinib requires a lesser amount of energy for proton transfer and electron transfer, moreover it scavenges radicals easily.

Theoretical Insights into the Radical Scavenging Activity of Glipizide: DFT and Molecular Docking Studies

Glipizide is a N-sulfonylurea compound used in the treatment of hyperglycemia in patients with Type 2 diabetes mellitus. In the present study, DFT-based computational methods and molecular docking studies have been performed to systematically evaluate the radical scavenger behavior of the title molecule. Structural characteristics such as molecular descriptors, frontier molecular orbitals, molecular potential mapping, and Mulliken charge population have been investigated. Thermodynamic parameters like proton affinity (PA), ionization potential (IP), bond dissociation energy (BDE), electron transfer enthalpy (ETE), and proton dissociation enthalpy (PDE) related to three antiradical mechanisms namely hydrogen atom transfer (HAT), sequential electron transfer proton transfer (SETPT) and sequential proton loss electron transfer (SPLET) have been studied. Also, molecular docking studies have been carried out to have a theoretical understanding of the molecular mechanism and for the elucidation of binding mode/modes of a compound targeted through non-covalent interactions. The obtained results are of great significance in better understanding the reaction mechanism of the title molecule and open new perspectives for the design of new potent antioxidant agents.

Improving the antioxidant activity of natural antioxidant honokiol by introducing the amino group

Exploring and synthesizing the compounds with stronger antioxidant activity have always been the goal of researchers. Herein, the substitution effects of the amino (NH₂-) group with the excellent electron-donating ability in different positions on the antioxidant activity of Honokiol (Hon) were systematically explored by using the quantum chemistry calculation based on the density functional theory method. The three possible antioxidant mechanisms of Hon and its four NH₂-substituted derivatives (Hon1-Hon4), containing the hydrogen atom transfer (HAT), single electron transfer followed by proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET), were explored in depth considering the gas and solvent phases. In addition, the frontier molecular orbital energies, natural bond orbital (NBO) charge population, and global descriptive parameters were used to study their antioxidant activity. The results indicate that compared with the original molecule Hon, the NH₂ substituents would have the stronger antioxidant activity. Moreover, the radical scavenging process of Hon and its derivatives has a disposition to the HAT and SPLET mechanisms in the gas and solvent phases, respectively. Meaningfully, owing to the lowest bond dissociation enthalpy and proton affinity values, Hon4 would show the most prominent antioxidant activity by comparison with the other compounds. In conclusion, this work will provide the purposeful reference for designing and synthesizing the antioxidants with more outstanding performance.

Density functional theory studies of the antioxidants-a review

The following review article attempts to compare the antioxidant activity of the compounds. For this purpose, density functional theory/Becke three-parameter Lee-Yang-Parr (DFT/B3LYP) methodology was carried out instead of using pharmacological methodologies because of economic benefits and high accuracy. This methodology filtrates the compounds with the lowest antioxidant activity. At first, the Koopmans' theorem was carried out to calculate some descriptors to compare antioxidants. The energy of the highest occupied molecular orbitals (HOMO) was accepted as the best indicator, and then some studies confirmed that the highest occupied molecular orbital/lowest unoccupied molecular orbital (HOMO-LUMO) energy gap is the more precise descriptor. Although it would be better to compare spin density distribution (SDD) on the oxygen of the corresponding radical in the polarizable continuum model (PCM) to evaluate their capability to chain reaction inhibition. Next, it was mentioned that in the multi-target directed ligands (MTDLs), the antioxidant is connected to other moieties in para positions to create better antioxidants or novel hybrid compounds. Indeed, SDD was introduced as a descriptor for MTDL antioxidant effectiveness. Then, the relation between antioxidants and aromaticity was investigated. The more the aromaticity of an antioxidant, the more stable the corresponding radical is. Subsequently, in preferred antioxidant activity, it was defined that the hydrogen atom transfer (HAT) mechanism is more favored in metabolism phase I. It has been seen that the solvent model can change the antioxidant mechanism. Therefore, the solvent model is more important than the chemical structure of antioxidants, and an ideal antioxidant should be evaluated in PCM for pharmacological evaluations.