Complexation of fisetin with novel cyclosophoroase dimer to improve solubility and bioavailability.

Rhizobium species produce cyclosophoraose (Cys), which is an unbranched cyclic ß-(1,2)-glucan. We synthesized novel cationic cyclosophoraose dimer (Cys dimer) and its structure was confirmed via NMR spectroscopy and MALDI-TOF mass spectrometry analysis. In this study, we investigated the complexation of hardly soluble drug fisetin (3,3',4',7-tetrahydroxyflavone) with Cys dimer to improve the solubility of fisetin, and its solubility was increased up to 6.5-fold. The solubility of fisetin with Cys dimer showed 2.4-fold better than with ß-cyclodextrin. The fisetin-Cys dimer complex was characterized by using, phase solubility diagram, 2D NMR, FT-IR spectroscopy, SEM, DSC analysis and molecular modeling. Through the molecular docking simulations, complexation ability of fisetin with host molecules were in the following order: Cys dimer>Cys monomer>ß-CD. The fisetin-Cys dimer complex showed also higher cytotoxicity to HeLa cells than free fisetin, indicating that the Cys dimer to improve bioavailability of fisetin.

Structural stabilization of a rigid beta-sheet cluster of fucosylated proteinase inhibitor PMPC (Pars intercerebralis major peptide C) against thermal denaturation: An unfolding molecular dynamics simulation study.

Unfolding behavior of glycosylated- and unglycosylated proteinase inhibitor Pars intercerebralis major peptide C (PMPC) at 350 K were traced with molecular dynamics simulations using the CHARMM program. The fucosylated PMPC (FPMPC) possesses a nearly identical protein structure with PMPC, differing only by the presence of a single fucose residue linked to Thr9 in the PMPC. Attachment of a monomeric fucose residue to the Thr9 in PMPC resulted in a change of the denaturing process of FPMPC. Simulations showed that the unfolding of PMPC involved significant weakening of non-local interactions whereas fucosylation led FPMPC to preserve the non-local interactions, even in its denatured form. Even in simulations over 16 ns at 350 K, FPMPC remained relatively stable in a less denatured conformation. However, the conformation of PMPC transformed to a fully unfolded state within 5 ns in the simulation at 350 K. This difference was due to the formation of fucose-mediated hydrogen bonds and non-local contacts by the attached fucose residue of FPMPC. In the case of FPMPC, fucosyl residue was involved in maintaining a rigid beta-sheet cluster through interaction with the hydrogen bond network. These high-temperature unfolding MD simulations provide a theoretical basis for a previous experimental work in which FPMPC showed stable unfolding thermodynamics compared to unfucosylated PMPC, suggesting that single fucosylation induces conformational stabilization of PMPC by tertiary contacts.

Systematic probing of an atomic charge set of sialic acid disaccharides for the rational molecular modeling of avian influenza virus based on molecular dynamics simulations.

A systematic searching approach for an atomic charge set through molecular dynamics simulations is introduced to calculate a reasonable sialic acid carbohydrate conformation with respect to the experimentally observed structures. The present molecular dynamics simulation study demonstrated that B3LYP/6-31G is the most suitable basis set for the sialic acid disaccharides, attaining good agreement with experimental data.

Retardation of the unfolding process by single N-glycosylation of ribonuclease A based on molecular dynamics simulations.

The conformational characteristics of glycosylated- and unglycosylated bovine pancreatic ribonuclease A (RNaseA) were traced with unfolding molecular dynamics simulations using CHARMM program at 470 K. The glycosylated RNase (Glc_RNase) possesses nearly identical protein structure with RNaseA, differing only by presence of a single acetylglucosamine residue N-linked to Asn34 in the RNaseA. Attaching of monomeric N-acetylglucosamine residue to the Asn34 in RNaseA resulted in a change of denaturing process of Glc_RNase. Simulations showed that the unfolding of RNaseA involved significant weakening of nonlocal interactions whereas the glycosylation led Glc_RNase to preserve the nonlocal interactions even in its denatured form. Even in simulations over 8 ns at 470 K, Glc_RNase remained relatively stable as a less denatured conformation. However, conformation of RNaseA was changed to a fully unfolded state before 3 ns of the simulations at 470 K. This difference was due to fact that formation of hydrogen bond bridges and nonlocal contacts induced by the attached N-acetylglucosamine of Glc_RNase showing in the unfolding simulations. These high-temperature unfolding MD simulations provided a theoretical basis for the previous experimental work in which Glc_RNase showed slower unfolding kinetics compared with unglycosylated RNaseA, suggesting that single N-glycosylation induced retardation of unfolding process of the ribonuclease protein.

Molecular dynamics simulations of trehalose as a 'dynamic reducer' for solvent water molecules in the hydration shell.

Systematic computational work for a series of 13 disaccharides was performed to provide an atomic-level insight of unique biochemical role of the alpha,alpha-(1-->1)-linked glucopyranoside dimer over the other glycosidically linked sugars. Superior osmotic and cryoprotective abilities of trehalose were explained on the basis of conformational and hydration characteristics of the trehalose molecule. Analyses of the hydration number and radial distribution function of solvent water molecules showed that there was very little hydration adjacent to the glycosidic oxygen of trehalose and that the dynamic conformation of trehalose was less flexible than any of the other sugars due to this anisotropic hydration. The remarkable conformational rigidity that allowed trehalose to act as a sugar template was required for stable interactions with hydrogen-bonded water molecules. Trehalose made an average of 2.8 long-lived hydrogen bonds per each MD step, which was much larger than the average of 2.1 for the other sugars. The stable hydrogen-bond network is derived from the formation of long-lived water bridges at the expense of decreasing the dynamics of the water molecules. Evidence for this dynamic reduction of water by trehalose was also established based on each of the lowest translational diffusion coefficients and the lowest intermolecular coulombic energy of the water molecules around trehalose. Overall results indicate that trehalose functions as a 'dynamic reducer' for solvent water molecules based on its anisotropic hydration and conformational rigidity, suggesting that macroscopic solvent properties could be modulated by changes in the type of glycosidic linkages in sugar molecules.

Molecular dynamics simulations of a cyclic-beta-(1-->2) glucan containing an alpha-(1-->6) linkage as a 'molecular alleviator' for the macrocyclic conformational strain.

The conformational preferences of a cyclic osmoregulated periplasmic glucan of Ralstonia solanacearum (OPGR), which is composed of 13 glucose units and linked entirely via beta-(1-->2) linkages excluding one alpha-(1-->6) linkage, were characterized by molecular dynamics simulations. Of the three force fields modified for carbohydrates that were applied to select a suitable one for the cyclic glucan, the carbohydrate solution force field (CSFF) was found to most accurately simulate the cyclic molecule. To determine the conformational characteristics of OPGR, we investigated the glycosidic dihedral angle distribution, fluctuation, and the potential energy of the glucan and constructed hypothetical cyclic (CYS13) and linear (LINEAR) glucans. All beta-(1-->2)-glycosidic linkages of OPGR adopted stable conformations, and the dihedral angles fluctuated in this energy region with some flexibility. However, despite the inherent flexibility of the alpha-(1-->6) linkage, the dihedral angles have no transition and are more rigid than that in a linear glucan. CYS13, which consists of only beta-(1-->2) linkages, is somewhat less flexible than other glycans, and one of its linkages adopts a higher energy conformation. In addition, the root-mean-square fluctuation of this linkage is lower than that of other linkages. Furthermore, the potential energy of glucans increases in the order of LINEAR, OPGR, and CYS13. These results provide evidence of the existence of conformational constraints in the cyclic glucan. The alpha-(1-->6)-glycosidic linkage can relieve this constraint more efficiently than the beta-(1-->2) linkage. The conformation of OPGR can reconcile the tendency for individual glycosidic bonds to adopt energetically favorable conformations with the requirement for closure of the macrocyclic ring by losing the inherent flexibility of the alpha-(1-->6)-glycosidic linkage.

Chiral recognition based on enantioselective interactions of propranolol enantiomers with cyclosophoraoses isolated from Rhizobium meliloti.

Cyclosophoraoses isolated from Rhizobium meliloti, as an NMR chiral shift agent, were used to discriminate propranolol enantiomers. Continuous variation plot made from the complex of cyclosophoraoses with propranolol showed that the diastereomeric complex had predominantly 1:1 stoichiometry through UV spectroscopic analysis. The chiral recognition of propranolol enantiomers by cyclosophoraoses was investigated through the determination of binding constant based on the (13)C NMR chemical shift changes. The averaged K(obs) values from the plots were 55.7 M(-1) for (R)-(+)-propranolol and 36.6 M(-1) for (S)-(-)-propranolol, respectively. Enantioselectivity (alpha = K(R+)/K(S(-)) of 1.52 was then obtained. Computational calculation also revealed that (R)-(+) propranolol was more tightly bound with cyclosophoraose than (S)-(-)-propranolol due to the enhanced van der Waals interaction.

Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A).

The conformational preferences of cyclosophoroheptadecaose (Cys-A), which is a member of a class of cyclic (1 --> 2)-beta-D-glucan, were characterized by molecular dynamics simulations. Simulated annealing and constant temperature molecular dynamics simulations were performed on the Cys-A. The simulations produced various types of compact and asymmetrical conformations of Cys-A. Excellent agreement was found between experimental data and corresponding values predicted by molecular modeling. Most glycosidic linkages were concentrated in the lowest energy region of phi-psi energy map, and the values of radius of gyration (R(G)) and the nuclear Overhauser effect (NOE) distance data derived from our simulations were finely consistent with the reported experimental values. This result will also give novel insights for the molecular complexation mechanism of Cys-A with various guest chemicals.