Emergence of hydrogen bonds from molecular dynamics simulation of substituted N-phenylthiourea-catechol oxidase complex.

A series of N-phenylthiourea derivatives was built starting from the X-ray structure in the molecular mechanics framework and the interaction profile in the complex with the catechol oxidase was traced using molecular dynamics simulation. The results showed that the geometry and interactions between ligand and receptor were highly related to the position of the substituted side chains of phenyl moiety. At the end of molecular dynamics run, a concentrated multicenter hydrogen bond was created between the substituted ligand and receptor. The conformation of the ligand itself were also restricted in the receptor pocket. Furthermore, the simulation time of 50 ns were found to be long enough to explore the relevant conformational space and the stationary behavior of the molecular dynamic could be observed.

Discrimination of cinnamon bark and cinnamon twig samples sourced from various countries using HPLC-based fingerprint analysis.

A simple and efficient HPLC method was developed to evaluate the quality of traditional herbal medicines made from cinnamon bark (CB) and cinnamon twig (CT). Seven major bioactive ingredients in 56 samples (24 CB and 32 CT) collected from China, Vietnam, and Indonesia were separated and quantified. The method was validated following the International Conference on Harmonisation (ICH) guidelines. A fingerprint analysis method to discriminate between CB and CT using major component content levels was developed. The discrimination process included the use of similarity indices and partial least-squares discriminant analysis (PLS-DA). Classification accuracy by the PLS-DA method was about 98%. The pattern analysis method was specific and could be readily used for the comprehensive evaluation of cinnamon samples. Therefore, an HPLC fingerprint in combination with pattern analysis provides a very flexible and reliable method for quality assessment of herbal drugs.

Fluorescence spectroscopic and time-dependent DFT studies for intramolecular excimer formation of Di-9H-fluoren-9-yldimethylsilane: dynamics and energetics for conformational change.

Intramolecular excimer formation of di-9H-fluoren-9-yldimethylsilane in various solvents was studied by means of steady-state and time-resolved fluorescence spectroscopies. Solvent viscosity effect on the kinetics for the monomer-excimer transition was found to be very slight, indicating that the transformation is accompanied by a slight conformational change presumably involving a transition from a near face-to-face conformer to a true sandwich conformer. The excitation energies and the corresponding oscillator strengths were derived with the time-dependent B3LYP/cc-pVTZ method. The simulated absorption spectrum involving the variation of the oscillator strengths in terms of the wavelengths accords with the experimental absorption pattern. The TD DFT calculations also reveal that excitation energy is significantly decreased with decreasing the interchromophore separation and the dihedral angle in a fluorene dimer, as an indication that the excimer state emitting the significantly red-shifted fluorescence corresponds to a sandwich conformer.

Racemization of 6-methoxydihydrosanguinarine in methanol investigated by enantioselective dynamic HPLC.

A biologically active benzophenanthridine alkaloid, 6-methoxydihydrosanguinarine (MS), was isolated from Hylomecon plants. Although enantiomers of MS can be separated by chiral HPLC, its isomers rapidly form a racemic mixture in methanol. The rate constants for the racemization of MS enantiomers were 9.20x10(-4)s(-1) and 9.95x10(-4)s(-1) for (+)-MS and (-)-MS, respectively, as determined by dynamic HPLC and chiral chromatography. This unusually rapid racemization may originate from the formation of a stable iminium ion intermediate, sanguinarine. Therefore, the variety of biological activities exhibited by MS may be attributable to a combination of (+)-MS, (-)-MS, and sanguinarine.

Computational studies of COX-2 inhibitors: 3D-QSAR and docking.

The 3D-QSAR (three-dimensional quantitative structure-activity relationships) studies for 88 selective COX-2 (cyclooxygenase-2) inhibitors belonging to three chemical classes (triaryl rings, diaryl cycloalkanopyrazoles, and diphenyl hydrazides) were conducted using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Partial least squares analysis produced statistically significant models with q(2) values of 0.84 and 0.79 for CoMFA and CoMSIA, respectively. The binding energies calculated from flexible docking were correlated with inhibitory activities by the least-squares fit method. The three chemical classes of inhibitors showed reasonable internal predictability (r(2)=0.51, 0.49, and 0.54), but the sulfonyl-containing inhibitors demonstrated distinctively low binding energy compared to the others. The electrostatic interaction energy between the Arg513 of the COX-2 active site and sulfonyl group of the triaryl rings seemed to have the responsibility for difference in binding energy. Comparative binding energy (COMBINE) analyses gave q(2) values of 0.64, 0.63, and 0.50 for triaryl rings, diaryl cycloalkanopyrazoles, and diphenyl hydrazides, respectively. In this COMBINE model, some protein residues were highlighted as particularly important for inhibitory activity. The combination of ligand-based and structure-based models provided an improved understanding in the interaction between the three chemical classes and the COX-2.

Enantioselective stabilization of inclusion complexes of metoprolol in carboxymethylated beta-cyclodextrin.

The inclusion complexes of metoprolol (MT) and carboxymethyl-beta-cyclodextrin (CMCD) were prepared and the stability constants of the complexes were determined. Binding studies performed using high performance liquid chromatography (HPLC), UV spectrometry and capillary electrophoresis (CE) indicated that a complex with 1:1 stoichiometry is predominant in the solution. The enantiomers of MT possess relatively high affinity towards CMCD with stability constants of 288 and 262 per M for (R)- and (S)-MT, respectively. Through nuclear magnetic resonance (NMR) analysis, MT was predicted to be a bent structure with phenyl ring of MT inserted in the shielding cavity of CMCD during complex formation. The NMR data suggested that the chiral side chain and the methoxyethyl moiety of MT are aligned in the deshielding zone, above and below the CMCD torus ring.