Investigation of cannabidiol's potential targets in limbic seizures. In-silico approach.

Even though the vast armamentarium of FDA-approved antiepileptic drugs is currently available, over one-third of patients do not respond to medication, which arises a need for alternative medicine. In clinical and preclinical studies, various investigations have shown the advantage of specific plant-based cannabidiol (CBD) products in treating certain groups of people with limbic epilepsy who have failed to respond to conventional therapies. This work aims to investigate possible mechanisms by which CBD possesses its anticonvulsant properties. Molecular targets for CBD's treatment of limbic epilepsy, including hyperpolarization-activated cyclic nucleotide-gated channel 1 (HCN1), gamma-aminobutyric acid aminotransferase (GABA-AT), and gamma-aminobutyric acid type A receptor (GABAA), were used to evaluate its binding affinity. Interactions with the CB1 receptor were initially modeled as a benchmark, which further proved the efficiency of proposed here approach. Considering the successful benchmark, we further used the same concept for in silico investigation, targeting proteins of interest. As a result of molecular docking, molecular mechanics, and molecular dynamics simulations models of CBD-receptor complexes were proposed and evaluated. While CBD possessed decently high affinity and stability within the binding pockets of GABA-AT and some binding sites of GABAA, the most effective binding was observed in the CBD complex with HCN1 receptor. 100 ns molecular dynamics simulation revealed that CBD binds the open pore of HCN1 receptor, forming a similar pattern of interactions as potent Lamotrigine. Therefore, we can propose that HCN1 can serve as a most potent target for cannabinoid antiepileptic treatment. Communicated by Ramaswamy H. Sarma.

Homology Modeling and Molecular Dynamics-Driven Search for Natural Inhibitors That Universally Target Receptor-Binding Domain of Spike Glycoprotein in SARS-CoV-2 Variants.

The rapid spread of SARS-CoV-2 required immediate actions to control the transmission of the virus and minimize its impact on humanity. An extensive mutation rate of this viral genome contributes to the virus' ability to quickly adapt to environmental changes, impacts transmissibility and antigenicity, and may facilitate immune escape. Therefore, it is of great interest for researchers working in vaccine development and drug design to consider the impact of mutations on virus-drug interactions. Here, we propose a multitarget drug discovery pipeline for identifying potential drug candidates which can efficiently inhibit the Receptor Binding Domain (RBD) of spike glycoproteins from different variants of SARS-CoV-2. Eight homology models of RBDs for selected variants were created and validated using reference crystal structures. We then investigated interactions between host receptor ACE2 and RBDs from nine variants of SARS-CoV-2. It led us to conclude that efficient multi-variant targeting drugs should be capable of blocking residues Q(R)493 and N487 in RBDs. Using methods of molecular docking, molecular mechanics, and molecular dynamics, we identified three lead compounds (hesperidin, narirutin, and neohesperidin) suitable for multitarget SARS-CoV-2 inhibition. These compounds are flavanone glycosides found in citrus fruits - an active ingredient of Traditional Chinese Medicines. The developed pipeline can be further used to (1) model mutants for which crystal structures are not yet available and (2) scan a more extensive library of compounds against other mutated viral proteins.

Computational studies on binding, solvent, and pH effects on (S)-propranolol and methacrylic acid complex.

Density functional theory methods have been applied to understand binding of (s)-propranolol, a template, to a methacrylic acid molecule acting as a functional monomer using basic 1:1 model. The model has been expanded to study the effect of various pH by adding hydronium and hydroxide ions solvated by water molecules to the template-monomer system, to mimic acidic and basic environments, respectively. This could be considered a model study towards a potential use of molecular imprinting method for the design of a transdermal patch for a topical and direct delivery of (s)-propranolol to hemangiomas. In addition, this study provides detailed binding site analysis of the template and functional monomer verified by the theoretical IR spectra analysis, as well as solvent and pH effects on template-monomer binding energy.

N-arylnaphthylamines as inhibitors of human immunodeficiency virus integrase - lens epithelium-derived growth factor interactions: theoretical studies.

Presented work reports a comprehensive theoretical study on the inhibitory nature of N-arylnaphthylamines in Human Immunodeficiency Virus Integrase (HIV IN) - Lens Epithelium-Derived Growth Factor (LEDGF/p75) complexes. Factors influencing the inhibition efficiency in AlphaScreen% assay are evaluated and explained through the structure- and ligand-based studies; including molecular docking, molecular dynamics calculations, and quantitative structure-activity relationship (QSAR) approach. It has been shown that N-arylnaphthylamines possess a wide variety of binding poses. Three QSAR models have been developed using structural descriptors and descriptors derived from docking calculations. The activity of untested N-arylnaphthylamines have been predicted using the most successful model. Proposed here technique could become a useful tool for ligand selection, accelerating the development of a new generation of anti-HIV medications. [Formula: see text] Communicated by Ramaswamy H. Sarma.

Antioxidant Activity of Selected Phenolic Acids-Ferric Reducing Antioxidant Power Assay and QSAR Analysis of the Structural Features.

Phenolic acids are naturally occurring compounds that are known for their antioxidant and antiradical activity. We present experimental and theoretical studies on the antioxidant potential of the set of 22 phenolic acids with different models of hydroxylation and methoxylation of aromatic rings. Ferric reducing antioxidant power assay was used to evaluate this property. 2,3-dihydroxybenzoic acid was found to be the strongest antioxidant, while mono hydroxylated and methoxylated structures had the lowest activities. A comprehensive structure-activity investigation with density functional theory methods elucidated the influence of compounds topology, resonance stabilization, and intramolecular hydrogen bonding on the exhibited activity. The key factor was found to be a presence of two or more hydroxyl groups being located in ortho or para position to each other. Finally, the quantitative structure-activity relationship approach was used to build a multiple linear regression model describing the dependence of antioxidant activity on structure of compounds, using features exclusively related to their topology. Coefficients of determination for training set and for the test set equaled 0.9918 and 0.9993 respectively, and Q2 value for leave-one-out was 0.9716. In addition, the presented model was used to predict activities of phenolic acids that haven't been tested here experimentally.

Theoretical investigation on monomer and solvent selection for molecular imprinting of nitrocompounds.

The aim of this work is to serve as a guideline for the initial selection of monomer and solvent for the synthesis of the nitrocompound-based molecularly imprinted polymers, MIPs. Reported data include evaluation of six systems with the ability to form noncovalently bonded monomer-template complexes. These systems are represented by the following aliphatic and aromatic molecules: acrolein, acrylonitrile, 2,6-bisacrylamide, 4-ethylenebenzoic acid, methyl methacrylate, and 2-vinylpyridine. Cave models for selected monomers are also presented and supported by binding energy analysis under various conditions. Solvent effects on monomer-template binding energy have been studied for four solvents: acetone, acetonitrile, chloroform, and methanol. Additionally, systems such as 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), pentachlorophenol (PCP), and 3,6-dichloro-2-methoxybenzoic acid (Dicamba) have been used to study selectivity of acrolein-based MIP toward TNT detection. The density functional theory, DFT, method has been used for all structural, vibrational frequency, and solvent calculations.

The evolution of bonding and thermodynamic properties of boron-doped small carbon clusters: an ab initio study.

Theoretical studies on BC(n) (n=1-6) clusters are carried out using density functional theory, Møller-Plesset second-order perturbation theory (MP2), coupled-cluster calculations including up to triple excitations (CCSD(T)), and higher-level approaches. All possible isomers depending on the positions of the boron atom are generated and the lowest-energy isomers are determined for doublet and quartet electronic states. The three potential evolution paths of the clusters are determined as a function of their size. The energetic and electronic consequences for the increased size of structures differ significantly, which leads to representatives of the ground electronic state from different structural groups. The ab initio calculated thermal functions allow enhancements to the available atomization energies and improve the agreement between the calculated and experimental heat content.

Photodegradation of selected PCBs in the presence of Nano-TiO2 as catalyst and H2O2 as an oxidant.

Photodegradation of five strategically selected PCBs was carried out in acetonitrile/water 80:20. Quantum chemical calculations reveal that PCBs without any chlorine on ortho-positions are closer to be planar, while PCBs with at least one chlorine atoms at the ortho-positions causes the two benzene rings to be nearly perpendicular. Light-induced degradation of planar PCBs is much slower than the perpendicular ones. The use of nano-TiO(2) speeds up the degradation of the planar PCBs, but slows down the degradation of the non-planar ones. The use of H(2)O(2) speeds up the degradation of planar PCBs greatly (by >20 times), but has little effect on non-planar ones except 2,3,5,6-TCB. The relative photodegradation rate is: 2,2',4,4'-TCB > 2,3,5,6-TCB > 2,6-DCB ≈ 3,3',4,4'-TCB > 3,4',5-TCB. The use of H(2)O(2) in combination with sunlight irradiation could be an efficient and "green" technology for PCB remediation.

Theoretical studies on the bonding and thermodynamic properties of Ge n Si m (m+n=5) clusters: the precursors of germanium/silicon nanomaterials.

Theoretical studies on the Ge n Si m clusters have been carried out using advanced ab initio approaches. The lowest energy isomers were determined for the clusters with compositions n+m=2-5. All possible isomers arising due to permutations of Ge and Si atoms were investigated. The L-shaped structure for the trimers, tetragonal with diagonal bond for tetramers, and a trigonal bipyramid for pentamers represent the energy optimized ground state geometries. The bonding analyses revealed that the trimers and tetramers are stabilized through multicenter pi bonding. In pentamers, this stabilizing factor is eliminated due to the further cluster growth. The ionization of clusters does not change their geometrical characteristics. The agreement of the calculated ionization and atomization energies with those obtained from the mass spectrometric studies (through estimated appearance potential) validated the reported structures of the clusters. The bonding properties of these species are discussed using their molecular orbital characteristics and analysis of natural bond orbital population data.

Thermodynamic studies of bromine-iodine competition in the formation of NaSnXYZ (X, Y, Z, = Br or I) complexes.

The thermodynamic studies of NaSnXYZ (X, Y, Z = Br or I) are presented. The determined theoretical structures and vibrational properties lead to improved experimental values of dissociation enthalpies and entropies. The ab initio thermodynamic data is also reported. The nature of bonding of binary SnXY-NaZ complexes is discussed with the emphasis on differences between bromine and iodine.

Theoretical thermodynamics and the nature of interactions of the quasi-binary NaCl-SnCl(2) system.

The formation of NaSnX(3) (X = halogen) influences the sodium concentration in metal halide lamps making the thermodynamics of such reactions critical for technological developments. Theoretical predictions of the structure and vibrational properties of the quasi-binary NaCl-SnCl(2) system lead to thermodynamical data determined through the third law evaluation. Ab initio enthalpy and entropy of dissociation of NaSnCl(3) also is reported. Additionally, insight into the nature of chemical bonding is provided by electron population analysis and the interaction energy decomposition scheme.

Mass spectrometric and quantum chemical studies of the thermodynamics and bonding of neutral and ionized LnCl, LnCl2, and LnCl3 species (Ln = Ce, Lu).

The mass spectral patterns of CeCl3(g) and LuCl3(g) and appearance energies for the identified ions were measured using a Nier-type mass spectrometer coupled with a Knudsen cell. The molecular ion CeCl3+ was found to be considerably less stable in comparison to LuCl3+. Partial pressures and sublimation enthalpies of LnCl3(s) to monomeric LnCl3(g) and dimeric Ln2Cl6(g) species were obtained in the ranges of 882-1028 (Ln = Ce) and 850-1004 K (Ln = Lu). The contribution of dimeric Ce2Cl6(g) species to equilibrium vapors of CeCl3(s) is considerably smaller than the Lu2Cl6(g) contribution in LuCl3(s) vapors. The measurements were supplemented by quantum chemical ab initio studies of structures, energetics, and vibrational frequencies of neutral and singly ionized LnCl, LnCl2, and LnCl3 species (Ln = Ce, Lu). The theoretical appearance energies of different ions, calculated from the energies of the gaseous species, are in good agreement with experimental data. The fragmentation energies of LnCl, LnCl2, and LnCl3 were also computed and compared with the mass spectral patterns of respective vapor species. The Mulliken and natural bond orbital electron population methods were applied for the systematic analysis of the bonding scheme in molecules and cations.