A DFT study of the chemical reactivity properties, spectroscopy and bioactivity scores of bioactive flavonols

Identification of potent inhibitors of HDAC2 from herbal products for the treatment of colon cancer: Molecular docking, molecular dynamics simulation, MM/GBSA calculations, DFT studies, and pharmacokinetic analysis

The histone deacetylase 2 (HDAC2), an enzyme involved in gene regulation, is a potent drug target for the treatment of colon cancer. Phytocompounds having anticancer properties show the ability to interact with HDAC2 enzyme. Among the compounds, docking scores of caffeic acid (CA) and p-coumaric acid (pCA) with HDAC2 showed good binding efficacy of -5.46 kcal/mol and -5.16 kcal/mol, respectively, with small inhibition constants. The higher binding efficacy of CA compared to pCA can be credited to the presence of an extra oxygen atom in the CA molecule, which forms an additional hydrogen bond with Tyr297. The HDAC2 in complex with these molecules was found to be stable by analyzing RMSD, RMSF, Rg, and SASA values obtained through MD simulations. Furthermore, CA and pCA exhibited low MM/GBSA free energies of -16.32 ± 2.62 kcal/mol and -17.01 ± 2.87 kcal/mol, respectively. The HOMO and LUMO energy gaps, dipole moments, global reactivity descriptor values, and MEP surfaces showed the reactivity of the molecules. The favourable physicochemical and pharmacokinetic properties, along with absence of toxicity of the molecules determined using ADMET analysis, suggested both the acids to be regarded as effective drugs in the treatment of colon cancer.

Investigating the effects of solvent polarity and temperature on the molecular, photophysical, and thermodynamic properties of sinapic acid using DFT and TDDFT

Sinapic acid (SA) is widely used in cosmetics, foods, and pharmaceuticals due to its antioxidant, anti-inflammatory, neuroprotective, antimicrobial, antifungal, anticancer, and cardioprotective properties. However, environmental factors such as solvent polarity and temperature can influence its biological activity. This work determined how solvent polarity and temperature affected the molecular, photophysical, and thermodynamic properties of SA in gas and various solvents using semi-empirical (MP6), Hartree-Fock (HF) with the B3LYP method and a 6-311++G(d,p) basis set, and density functional theory (DFT) with various basis sets, such as 3TO-3G*, 3-21G+, 6-31G++G(d,p), 6-311++G(d,p), aug-CC-PVDZ, LanL2DZ, SDD, and DGD2VP. The results indicated that solvent polarity influences molecular and spectroscopic properties, such as bond angles, dihedral angles, bond lengths, FTIR spectra, solvation energy, dipole moments, HOMO-LUMO band gaps, chemical reactivity, and thermodynamic properties, resulting from interactions between the drug and solvent molecules. The findings suggested that increasing the temperature within the range of 100 to 1000 Kelvin leads to an increase in heat capacity, enthalpy, and entropy due to molecular vibrations, ultimately causing degradation and instability in SA. Furthermore, the results showed that SA underwent a redshift in the absorption peak (from 320.18 to 356.26 nm) and a shift in the fluorescence peak (from 381 to 429 nm) in the solvent phase compared to those in the gas phase. Overall, this study provides background knowledge on how solvent polarity and temperature affect the properties of SA molecules.

Exploring the inhibitory action of betulinic acid on key digestive enzymes linked to diabetes via in vitro and computational models: approaches to anti-diabetic mechanisms

Phytochemicals are now increasingly exploited as remedial agents for the management of diabetes due to side effects attributable to commercial antidiabetic agents. This study investigated the structural and molecular mechanisms by which betulinic acid exhibits its antidiabetic effect via in vitro and computational techniques. In vitro antidiabetic potential was analysed via on α-amylase, α-glucosidase, pancreatic lipase and α-chymotrypsin inhibitory assays. Its structural and molecular inhibitory mechanisms were investigated using Density Functional Theory (DFT) analysis, molecular docking and molecular dynamics (MD) simulation. Betulinic acid significantly (p < 0.05) inhibited α-amylase, α-glucosidase, pancreatic lipase and α-chymotrypsin enzymes with IC50 of 70.02 μg/mL, 0.27 μg/mL, 1.70 μg/mL and 8.44 μg/mL, respectively. According to DFT studies, betulinic acid possesses similar reaction in gaseous phase and water due to close values observed for highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) and the chemical descriptors. The dipole moment indicates that betulinic acid has high polarity. Molecular electrostatic potential surface revealed the electrophilic and nucleophilic attack-prone atoms of the molecule. Molecular dynamic studies revealed a stable complex between betulinic acid and α-amylase, α-glucosidase, pancreatic lipase and α-chymotrypsin. The study elucidated the potent antidiabetic properties of betulinic acid by revealing its conformational inhibitory mode of action on enzymes involved in the onset of diabetes.

Significant Increase in the Dipole Moment of Graphene on Functionalization: DFT Calculations and Molecular Dynamics Simulations

The limited solubility of graphene in water can be attributed to the existence of π-π bonds connecting its layers. Functionalized graphene or graphene oxide (GO) is frequently produced in order to overcome the shortcomings of graphene. Using density functional theory (DFT) calculation, functionalized graphene with various combinations of hydroxyl, epoxy, and carboxylic functional groups were investigated computationally. The study focused on the effects of functional group combinations on the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies, giving information about the chemical reactivity and stability of the molecules under investigation. Global chemical reactivity descriptors, including chemical hardness, softness, electronegativity, chemical potential, and electrophilicity index, were calculated to further elucidate the overall stability and reactivity of the molecules. The results demonstrated that the introduction of oxygen-containing functional groups on graphene significantly influenced its electronic properties, leading to variations in the chemical reactivity and stability. Molecular electrostatic potential (MEP) maps highlighted the susceptibility of specific regions to electrophilic and nucleophilic attacks. The flexibility and stability of functionalized graphene through root mean square fluctuation (RMSF) and root mean square deviation (RMSD) analyses indicate the stability of functionalized graphene in water. This comprehensive computational investigation provides valuable insights into the design and understanding of functionalized graphene for potential applications in drug delivery.

Waste to Medicine: Evidence from Computational Studies on the Modulatory Role of Corn Silk on the Therapeutic Targets Implicated in Type 2 Diabetes Mellitus

Type 2 diabetes mellitus (T2DM) is characterized by insulin resistance and/or defective insulin production in the human body. Although the antidiabetic action of corn silk (CS) is well-established, the understanding of the mechanism of action (MoA) behind this potential is lacking. Hence, this study aimed to elucidate the MoA in different samples (raw and three extracts: aqueous, hydro-ethanolic, and ethanolic) as a therapeutic agent for the management of T2DM using metabolomic profiling and computational techniques. Ultra-performance liquid chromatography-mass spectrometry (UP-LCMS), in silico techniques, and density functional theory were used for compound identification and to predict the MoA. A total of 110 out of the 128 identified secondary metabolites passed the Lipinski's rule of five. The Kyoto Encyclopaedia of Genes and Genomes pathway enrichment analysis revealed the cAMP pathway as the hub signaling pathway, in which ADORA1, HCAR2, and GABBR1 were identified as the key target genes implicated in the pathway. Since gallicynoic acid (-48.74 kcal/mol), dodecanedioc acid (-34.53 kcal/mol), and tetradecanedioc acid (-36.80 kcal/mol) interacted well with ADORA1, HCAR2, and GABBR1, respectively, and are thermodynamically stable in their formed compatible complexes, according to the post-molecular dynamics simulation results, they are suggested as potential drug candidates for T2DM therapy via the maintenance of normal glucose homeostasis and pancreatic β-cell function.

BeO nanotube as a promising material for anticancer drugs delivery system

In this research, the application of BeO nanotube (BeONT) as a nanocarrier for Fluorouracil (5-FU) anticancer drug has been studied by density functional theory (DFT) approach. The method ωB97XD with 6-31 G** basis set were employed. A precise surface study, shows that there are two directions for 5-FU adsorption that did not deliver any of the imaginary frequency vibrational spectra, identifying that all relaxation structures are at the lowest energy level. Based on our calculations, the energy of adsorption for 5FU@BeONT structures are range -120 to -168 kJ/mol, in the gas phase and -395 to 4-00 kJ/mol in the aqueous phase. The highest and the lowest values of adsorption energy are both in strong physical adsorption. Due to receiving an electronic charge from 5-FU, BeONT exhibited a p-type semiconducting feature for all positions. In addition, based on natural bond orbital (NBO) analysis, the direction of charge transfer was from fluorine's σ orbitals of the drug to n* orbitals (O and Be atoms) of BeONT with a considerable amount of transferred energy. BeONT can be employed as a potential strong carrier for 5-FU drugs for practical purposes based on our findings.

Cheminformatics bioprospection of selected medicinal plants metabolites against trypsin cleaved VP4 (spike protein) of rotavirus A

Rotaviruses have continued to be the primary cause of acute dehydrating diarrhoea in children under five years of age despite the global introduction of four World Health Organization (WHO) prequalified oral vaccines in over 106 countries. Currently, no medication is approved by the Food and Drug Administration (FDA) specifically for treating rotavirus A-induced diarrhoea. Consequently, it is important to focus on developing prophylactic and curative therapeutics to combat rotaviral infections. For the first time, this study computationally screened and identified metabolites from Spondias mombin, Macaranga barteri and Dicerocaryum eriocarpum as potential novel inhibitors with broad-spectrum activity against VP5* and VP8* (spike protein) of rotavirus A (RVA). The initial top 20 metabolites identified through molecular docking were further filtered using drug-likeness and pharmacokinetics parameters. The molecular properties of the resulting top-ranked compounds were predicted by conducting density functional theory (DFT) calculations, while molecular dynamics (MD) simulation revealed their thermodynamic compatibility with a significant affinity towards VP8* than VP5*. Except for ellagic acid (-11.78 kcal/mol), the lead compounds had higher binding free energy than the reference standard (VP5* (-11.81 kcal/mol), VP8* (-14.12 kcal/mol)) with 2SG (-20.98 kcal/mol) and apigenin-4'-glucoside (-23.56 kcal/mol) having the highest affinity towards VP5* and VP8*, respectively. Of all the top-ranked compounds, better broad-spectrum affinities for both VP5* and VP8* than tizoxanide were observed in 2SG (VP5* (-20.98 kcal/mol), VP8* (-20.13 kcal/mol)) and sericetin (VP5* (-20.46 kcal/mol), VP8* (-18.31 kcal/mol)). While the identified leads could be regarded as potential modulators of the investigated therapeutic targets for effective management of rotaviral infection, additional in vitro and in vivo evaluation is strongly recommended, and efforts are on-going in this regard.Communicated by Ramaswamy H. Sarma.

First and second order hyperpolarizabilities of flavonol derivatives: A density functional theory study

In this study, seventeen flavonol derivatives (1-17) were evaluated with regard to their first- and second-order hyperpolarizability parameters. For this purpose, the molecular geometries of 1-17 were optimized by using B3LYP/6-311++G(d,p) level. Spectroscopic characterizations for 1-17 were executed through the calculations of IR, UV-vis, ¹H NMR and ¹³C NMR spectra. The quantum chemical parameters such as electronegativity, chemical hardness, chemical potential and electrophilicity indexes were obtained by using the frontier molecular orbital (FMO) energies. The potential energy distribution (PED) analysis was used to provide a detailed assignment of vibrational bands. Important contributions to electronic absorption bands from FMOs were also evaluated. The distribution of FMOs to the whole molecule was investigated to determine the nature of electronic charge transfers in 1-17. The static and dynamic first- and second-order hyperpolarizability parameters for 1-17 were calculated by using B3LYP/6-311++G(d,p) level. The static β and γ were calculated at the ranges of 9.8279-0.0303 × 10^-29 esu and 80.200-268.40 × 10^-36 esu. The dynamic β and γ (ω = 532 nm) were also obtained in the field of 1.0440-71.786 × 10^-29 esu and 306.20-3607.00 × 10^-36 esu. This wide range of β and γ values indicate that flavonol derivatives with rational substitution may be promising candidates for first- and second-order NLO applications.

The effect of structural configuration on the DNA binding and in vitro antioxidant properties of new copper(ii) N2O2 Schiff base complexes

DNA interaction with cis and trans-copper NO complexes favours the cis configuration due to low energies observed in the cis configuration.