Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Temperature dependence of methanol and ethanol vapor sorption in polyhedral oligomeric silsesquioxane (POSS) containing methacrylate membranes

This study aimed to determine the solubility and temperature dependence of methanol and ethanol vapor caused by the difference in the substituents of polyhedral oligomeric silsesquioxane (POSS)-containing polymethacrylate membranes and the spacer length between the backbone and POSS backbone. Vapor sorption of methanol and ethanol was measured at 25°C, 35°C, and 45°C for three kinds of POSS-containing polymer membranes, namely, poly(methacryl isobutyl POSS), poly(methacrylate isobutyl POSS), and poly(methacryl phenyl POSS). The primary structures of the three POSS-containing polymer chains were columnar. The solubility of alcohol vapor on the POSS-containing polymer membranes followed the mechanism of solid adsorption and not the general dissolution diffusion. The sorption amount at all three temperatures was related to the surface area of the cylindrical primary structure and the solid adsorption property of the alcohol molecule of the POSS substituent. The sorption amount increased because of the large surface area and adsorption property of alcohol molecules. Although a typical glassy polymer shows exothermic mixing and a rubbery polymer displays endothermic mixing, the sample with the POSS substituent of isobutyl group exhibited an unusual behavior of endothermic mixing despite being a glassy polymer.     

Acidic‐pH‐Activatable Fluorescence Probes for Visualizing Exocytosis Dynamics

Live imaging of exocytosis dynamics is crucial for a precise spatiotemporal understanding of secretion phenomena, but current approaches have serious limitations. We designed and synthesized small‐molecular fluorescent probes that were chemically optimized for sensing acidic intravesicular pH values, and established that they can be used to sensitively and reliably visualize vesicular dynamics following stimulation. This straightforward technique for the visualization of exocytosis as well as endocytosis/reacidification processes with high spatiotemporal precision is expected to be a powerful tool for investigating dynamic cellular phenomena involving changes in the pH value.     

Incorporation of Pseudo‐complementary Bases 2,6‐Diaminopurine and 2‐Thiouracil into Serinol Nucleic Acid (SNA) to Promote SNA/RNA Hybridization

Serinol nucleic acid (SNA) is a promising candidate for nucleic acid‐based molecular probes and drugs due to its high affinity for RNA. Our previous work revealed that incorporation of 2,6‐diaminpurine (D), which can form three hydrogen bonds with uracil, into SNA increases the melting temperature of SNA‐RNA duplexes. However, D incorporation into short self‐complementary regions of SNA promoted self‐dimerization and hindered hybridization with RNA. Here we synthesized a SNA monomer of 2‐thiouracil (sU), which was expected to inhibit base pairing with D by steric hindrance between sulfur and the amino group. To prepare the SNA containing D and sU in high yield, we customized the protecting groups on D and sU monomers that can be readily deprotected under acidic conditions. Incorporation of D and sU into SNA facilitated stable duplex formation with target RNA by suppressing the self‐hybridization of SNA and increasing the stability of the heteroduplex of SNA and its complementary RNA. Our results have important implications for the development of SNA‐based probes and nucleic acid drugs.     

Development of a New Benzylating Reagent Spontaneously Releasing Benzyl Cation Equivalents at Room Temperature

A new O‐benzylating reagent, that is, 4‐(4,6‐diphenoxy‐1,3,5‐triazin‐2‐yl)‐4‐benzylmorpholinium trifluoromethanesulfonate (DPT‐BM), has been developed. Benzyl cation equivalents are generated from DPT‐BM by dissolving the compound in a solvent at room temperature under non‐acidic conditions. The benzylation of various alcohols by using a combination of DPT‐BM and magnesium oxide provided the benzyl ethers in good yields.     

Determination of kynurenic acid levels in rat brain microdialysis samples and changes in kynurenic acid levels induced by N‐acetylaspartic acid

The levels of kynurenic acid, an endogenous antagonist of α₇ nicotinic acetylcholine and N‐methyl‐D ‐aspartate receptors, were measured in microdialysis samples obtained from the prefrontal cortices of rats using column‐switching high‐performance liquid chromatography with fluorescence detection. When the perfusate was constantly infused at a rate of 1.0 μ/min, the in vitro recovery of kynurenic acid through the dialysis membrane was approximately 20.4%, and the precision was within 1.31%. Endogenous kynurenic acid in the microdialysis sample was clearly detected using column‐switching high‐performance liquid chromatography. As an application study, N‐acetyl‐L ‐aspartic acid, an endogenous metabolite and precursor of N‐acetyl‐L ‐aspartyl‐L ‐glutamic acid, which is an agonist of metabotropic glutamate receptors, was infused for 120 min through the microdialysis probe. The kynurenic acid level significantly increased during the infusion of N‐acetyl‐L ‐aspartic acid, suggesting that kynurenic acid might have some association with N‐acetyl‐L ‐aspartic acid in vivo. Copyright © 2009 John Wiley & Sons, Ltd.