Advanced investigation of a putative adsorption process of nine non key food odorants (non-KFOs) on the broadly tuned human olfactory receptor OR2W1: Statistical physics modeling and molecular docking study.

In the present paper, statistical physics formalism was used to understand the olfactory perception via the investigation of dose-olfactory response curves of a putative adsorption process of nine non key food odorants (non-KFOs) on the broadly tuned human olfactory receptor OR2W1, in order to quantitative characterize the interactions between the nine studied non-KFOs, i. e., furfuryl sulfide, furfuryl disulfide, benzyl methyl disulfide, furfuryl methyl disulfide, benzyl methyl sulfide, 1-phenylethanethiol, benzyl mercaptan, furfuryl methyl sulfide and 3-phenylpropanol molecules and OR2W1 binding sites at a molecular level. Two advanced adsorption models have been proposed: the advanced monolayer monoenergy model (monolayer model with identical and independent olfactory receptor binding sites) (Model 1) and the advanced monolayer model with two independent types of olfactory receptor binding sites (Model 2). It was concluded that the monolayer monoenergy model was selected as the most adequate model to fit the experimental dose-olfactory response curves tabulated in literature. Actually, the numerical values of the three fitted physico-chemical parameters (RM1, n and C1) were obtained by a non-linear regression. Indeed, modeling results suggested that the number of docked non-KFOs per OR2W1 binding site n values (1.24 < n < 1.94) was always superior to 1, which indicated the non-parallel orientation of the studied odorants on the olfactory receptor and the multi-molecular adsorption mechanism. The estimated molar adsorption energy ΔEa values (ranged from 6.07 to 12.16 kJ/mol) for the nine olfactory systems confirmed the physical the exothermic characters of the adsorption process since ΔEa values were lower than 40 kJ/mol and positive. Furthermore, these estimated parameters were applied to characterize stereographically and energetically the interaction between the nine non-KFOs and OR2W1 through the determination of the human receptor binding site size distributions (RSDs) and the adsorption energy distributions (AEDs), which were spread out from 0.25 to 6.50 nm and from 0 to 22.50 kJ/mol, respectively. The docking computation between these nine non-KFOs and OR2W1 proved that the estimated binding affinities were belonged to the adsorption energies spectrum in general and the specific adsorption energy band or the molecular vibration modes limited spectrum (between 2.50 kJ/mol and 17 kJ/mol) (approximate olfactory band).

Indirect characterizations of mOR-EG: Modeling analysis of five concentration-olfactory response curves via an advanced monolayer adsorption model.

The investigation of the adsorption process putatively involved in the olfactory perception of apocynin, guaiacylacetone, homovanillyl alcohol, 4-ethylguaiacol and homoguaiacol molecules on the mouse eugenol olfactory receptor mOR-EG was a very useful tool for comprising olfaction process at a molecular level. Indeed, the experimental data were correlated by using an advanced monolayer adsorption model with identical and independent binding sites. Thanks to the grand canonical ensemble in statistical physics formalism, the physico-chemical interpretations of modeling results indicated that the five odorants were adsorbed via a multi-molecular mechanism. Hence, the calculation of adsorption energies, that described the interaction between the odorant molecules and the olfactory receptor binding cavities, indicated that weak bonds were made between apocynin, guaiacylacetone, homovanillyl alcohol, 4-ethylguaiacol and homoguaiacol molecules and mOR-EG binding pockets amino acid residues. In addition, theoretical stereographic and energetic characterizations of mOR-EG were made via the determination of the olfactory receptor site size distributions (RSDs) and the adsorption energy distributions (AEDs) relative to apocynin, guaiacylacetone, homovanillyl alcohol, 4-ethylguaiacol, homoguaiacol molecules. The RSD provided the size of different binding cavities of mOR-EG. Indeed, the five RSDs spectrums situated between 0.5 and 10 nm were spread out around an average size each one. The mean values obtained from the peaks of the distributions were 2.14 nm, 2.20 nm, 2 nm, 2.10 nm and 1.83 nm for apocynin, guaiacylacetone, homovanillyl alcohol, 4-ethylguaiacol and homoguaiacol molecules, respectively. The AED gave a whole spectrum of adsorption energies that was activated by the odorant molecule. Thus, the apocynin, guaiacylacetone, homovanillyl alcohol, 4-ethylguaiacol and homoguaiacol AEDs were spread out from 5 to 27.5 kJ/mol, from 5 to 30 kJ/mol, from 5 to 35 kJ/mol, from 0 to 22.5 kJ/mol, 5 to 25 kJ/mol, respectively. The thermodynamic study, via the establishment of the adsorption entropy, indicated that the peak of the disorder was obtained when half of the binding sites were occupied. In addition, the Gibbs free enthalpy and the internal energy were determined and their negative values indicated that the adsorption phenomenon involved in the olfactory perception was spontaneous and exothermic physisorption phenomenon.

Quantum chemical studies on molecular structure, AIM, ELF, RDG and antiviral activities of hybrid hydroxychloroquine in the treatment of COVID-19: Molecular docking and DFT calculations.

Structure-activity relationships for hydroxychloroquine compound and its derivatives resulted in a potent antiviral activity. Where hydroxychloroquine derivatives showed an apparent efficacy against coronavirus related pneumonia. For this reason, the current study is focused on the structural properties of hydroxychloroquine and hydroxychloroquine sulfate. Optimized structures of these molecules have been reported by using DFT method at B3LYP/6-31G* level of theory. The geometric were determined and compared with the experimental crystal structure. The intra and intermolecular interactions which exist within these compounds are analyzed by different methods namely the topological analysis AIM, ELF and the reduced gradient of the density. These approaches make it possible in particular to study the properties of hydrogen bonds. The highest occupied molecular orbital and the lowest unoccupied molecular orbital energy levels are constructed and the corresponding frontier energy gaps are determined to realize the charge transfer within the molecule. The densities of state diagrams were determined to calculate contributions to the molecular orbitals. The molecular electrostatic potential surfaces are determined to give a visual representation of charge distribution of these ligands and to provide information linked to electrophilic and nucleophilic sites localization. Finally, these derivatives were evaluated for the inhibition of COVID-19 activity by using the molecular docking method.

DFT and molecular docking study of chloroquine derivatives as antiviral to coronavirus COVID-19.

The recently emerged COVID-19 virus caused hundreds of thousands of deaths and instigated a widespread fear, threatening the world's most advanced health security. In 2020, chloroquine derivatives are among the drugs tested against the coronavirus pandemic and showed an apparent efficacy. In the present work, the chloroquine and the chloroquine phosphate molecules have been proposed as potential antiviral for the treatment of COVID-19 diseases combining DFT and molecular docking calculations. Molecular geometries, electronic properties and molecular electrostatic potential were investigated using density functional theory (DFT) at the B3LYP/6-31G* method. As results, we found a good agreement between the theoretical and the experimental geometrical parameters (bond lengths and bond angles). The frontier orbitals analysis has been calculated at the same level of theory to determine the charge transfer within the molecule. In order to perform a better description of the FMOs, the density of states was determined. The molecular electrostatic potential maps were calculated to provide information on the chemical reactivity of molecule and also to describe the intermolecular interactions. All these studies help us a lot in determining the reactivity of the mentioned compounds. Finally, docking calculations were carried out to determine the pharmaceutical activities of the chloroquine derivatives against coronavirus diseases. The choice of these ligands was based on their antiviral activities.

Molecular docking studies, structural and spectroscopic properties of monomeric and dimeric species of benzofuran-carboxylic acids derivatives: DFT calculations and biological activities.

Structural optimization, molecular docking analysis, electronic and vibrational properties have been investigated for the 1-benzofuran-2-carboxylic acid (2BF) and 1-benzofuran-3-carboxylic acid (3BF) using DFT/B3LYP/6-311++G(d,p) level of theory. The theoretical parameters have a very good consistency with the experimental ones. The weak intermolecular interactions were analyzed by different tool such as: Hirshfeld surfaces, topological analysis and natural bond orbital studies. The nonlinear optical properties have been investigated. Molecular electrostatic potential and frontier molecular orbitals (FMOs) analysis have been carried out to understand the reactivity of the molecule. In addition, TD-DFT calculation is initiated to simulate the UV-vis absorption spectrum and to determine several important electronic properties like HOMO-LUMO gap energy and electronic transitions. The complete vibrational assignments and the force constants were reported for monomer and dimers of both acids. The biological activities of the tow acids have been studied via molecular docking analysis. The later calculations prove that the studied acids have an inhibitor effect against cancer and microbial diseases.