A free energy calculation study of the effect of H-->F substitution on binding affinity in ligand-antibody interactions

Changes in binding affinity to catalytic antibody 6D9 of chloramphenicol phosphonate derivatives (CPDs) containing H or F were investigated by performing free energy calculations based on molecular dynamics simulations. We calculated the binding free energy, enthalpy, and entropy changes (DeltaDeltaG, DeltaDeltaH, and -TDeltaDeltaS) attributable to H-->F substitution by comparing results for CPDs containing a trifluoroacetylamino group (CPD-F) or an acetylamino group (CPD-H). The calculated DeltaDeltaG, DeltaDeltaH, and -TDeltaDeltaS values were -2.9, -6.3, and 3.5 kcal mol(-1) and close to experimental values observed for a series of similar ligands, chloramphenicol phosphonates with F and H (-1.4, -3.5, and 2.1 kcal mol(-1)). Therefore, CPD-F binds more strongly to 6D9 than does CPD-H. To clarify the origin of the large difference in DeltaDeltaG, we apportioned the calculated values of DeltaDeltaG and DeltaG for the associated and dissociated states into contributions from various atomic interactions. We found that the H-->F substitution increased the binding affinity mainly by decreasing the hydration free energy and not by increasing favorable interactions with the antibody. The decreased hydration free energy of the ligand was mainly due to unfavorable coulombic interactions between the trifluoroacetylamino group and solvent waters, which increased the free energy of the dissociated state (by about 3.7 kcal mol(-1)). Also, the trifluoroacetylamino group slightly increased the free energy level of the associated state (about 0.8 kcal mol(-1)) because favorable van der Waals interactions compensated for unfavorable coulombic interactions with antibody atoms. In addition, the enthalpy and entropy changes, DeltaDeltaH and -TDeltaDeltaS (computationally -6.3 and 3.5 kcal mol(-1)), originated mainly from a decrease in hydration free energy in the dissociated state. The CPD-F and CPD-H ligands had substantially different structures in the dissociated and complexed states.     

A new method for the synthesis of some 9-β-D-arabinofuranosylpurines by a combination of chemical and enzymatic reactions

An enzymatic transarabinosylation between 2-chlorohypoxanthine and 1-β-$\text{D}$-arabinofuranosyluracil gave 9-β-$\text{D}$-arabinofuranosyl-2-chlorohypoxanthine which was chemically converted to 9-β-$\text{D}$-arabinofuranosylguanine and its derivatives.     

Designer ribozymes: programming the tRNA specificity into flexizyme

Fx3 is an artificial ribozyme with the ability to aminoacylate various tRNAs with phenylalanine and its nonnatural derivatives. Herein we report a simple strategy to build tRNA specificity into the generic Fx3, by appending to its 3'-end a tRNA-specific sequence (TSS), which is complementary to the acceptor stem of the cognate tRNA. This new designer ribozyme, referred to as Fx10, is able to recognize its cognate tRNA via a 10-base-pair interaction that is formed after the invasion of the tRNA acceptor stem by the TSS. We have demonstrated that Fx10 can aminoacylate its cognate tRNA with a high degree of specificity and also discriminate against the noncognate tRNAs. Because the tRNA specificity can be easily programmed into Fx10, it is a custom-made catalyst to generate nonnatural aminoacyl-tRNAs.     

The crystal structure and absolute configuration of the antitumor platinum complex trans(OH)-Pt(OH)2(malonato)(1R,2R-cyclohexanediamine).

The absolute configuration of the anti-tumor complex trans(OH)-Pt(OH)2(malonato)(1R,2R-cyclohexanediamine) was determined by X-ray anomalous scattering technique. The final unit cell was monoclinic, space group P2(1) with a = 9.142 A, b = 7.788 A, c = 11.946 A, beta = 96.48 degrees, Z = 2. The crystal structure was determined by direct method and difference Fourier synthesis, and refined to R = 0.025 and Rw = 0.033 based on 2768 independent reflections. The platinum atom has roughly octahedral coordination. The cyclohexane ring has the expected chair configuration, with two amino groups in equatorial positions while the malonato ligand, in contrast, shows a boat conformation for six membered Pt O-C-C-C-O ring.     

Effects of poly(ethylene glycol) (PEG) concentration on the permeability of PEG-grafted liposomes

Poly(ethylene glycol)-grafted liposomes (PEG-liposomes) were prepared from dipalmitoylphosphatidylcholine (DPPC) with various amounts of distearoyl-N-monomethoxy poly(ethylene glycol)-succinyl-phosphatidylethanolamines (DSPE-PEG) with PEG molecular weights of 1000, 2000, 3000 and 5000. The effects of DSPE-PEG concentration on the permeability of PEG-liposomes were investigated using carboxyfluorescein (CF). In the gel state, the CF leakage from PEG-liposomes was decreased with increasing mole fractions of DSPE-PEG for all PEG molecular weights. In the liquid-crystalline state, the CF leakage from PEG-liposomes containing DSPE-PEG1000 gradually increased with increasing mole fractions of DSPE-PEG, while that of PEG-liposomes whose molecular weight in PEG units was above 2000 rapidly decreased by the addition of DSPE-PEG. Furthermore, no effect of PEG molecular weight on CF leakage was observed. The relationship between the fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene (DPH) (or 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH)) and the mole fraction of DSPE-PEG for PEG-liposomes was also investigated. No significant changes in fluorescence polarization of DPH for liposomal bilayer membranes was observed in the gel and liquid-crystalline states due to the addition of DSPE-PEG, while that of TMA-DPH was decreased compared with that of liposomes without DSPE-PEG in both states.     

Effect of HF addition on the microwave-assisted acid-digestion for the determination of metals in coal by inductively coupled plasma-atomic emission spectrometry

The microwave-assisted acid-digestion for the determination of metals in coal by ICP-AES was investigated, especially focusing on the necessity of adding HF. By testing five certified reference materials, BCR-180, BCR-040, NIST-1632b, NIST-1632c, and SARM-20, it was found that the two-stage digestion without HF (HNO₃ + H₂O₂ was used) was very effective for the pretreatment of ICP-AES measurement. Both major metals (Al, Ca, Fe, and Mg) and minor or trace metals (Co, Cr, Cu, Mn, Ni, Pb, and Zn) in coal gave good recoveries for their certified or reference values. The possibility of ‘HF-memory effect’ was cancelled by the use of a set of vessels which had been never contacted with HF. Twenty-four Japanese standard coals (SS coals) were analyzed by the present method, and the concentrations of major metals measured by the present method provided very high accordance with those from the authentic JIS (Japanese Industrial Standard) method.     

Effect of surface covering of lactose carrier particles on dry powder inhalation properties of salbutamol sulfate

The effect of the surface covering of lactose carrier particles on the dry powder inhalation properties of salbutamol sulfate was investigated. Lactose carrier surfaces were covered with sucrose tristearate (J-1803F) by a high-speed elliptical-rotor-type powder mixer (Theta-Composer). In the present study, drug/carrier powder mixtures were prepared consisting of micronized salbutamol sulfate and lactose carriers with various particle surface conditions prepared by surface covering. These powder mixtures were aerosolized by a Jethaler), and the in vitro inhalation properties of salbutamol sulfate were evaluated by a twin impinger. Compared with the powder mixed with uncovered lactose carrier, the in vitro inhalation properties of the powder mixture prepared using the surface covering lactose carrier were significantly different, showing that the in vitro inhalation properties of salbutamol sulfate were improved. In vitro inhalation properties increased with the percentage of J-1803F added. Using this surface covering system would thus be valuable for increasing the inhalation properties of dry powder inhalation with lactose carrier particles.     

Influence of storage humidity on the in vitro inhalation properties of salbutamol sulfate dry powder with surface covered lactose carrier

The influence of storage humidity on the in vitro inhalation properties of salbutamol sulfate dry powder with surface covered lactose carrier was investigated. In the present study, drug/carrier powder mixtures were prepared consisting of micronized salbutamol sulfate and lactose carriers with different particle surface conditions prepared by surface covering. Lactose carrier surfaces were covered with vegetable magnesium stearate (Mg-St-V) by a high-speed elliptical-rotor-type powder mixer (Theta-Composer). These powder mixtures were aerosolized by a Jethaler), and the in vitro inhalation properties of salbutamol sulfate were evaluated by a twin impinger. Compared with the powder mixed with uncovered lactose carrier, the in vitro inhalation properties of the powder mixture prepared using the surface covered lactose carrier were little decreased with increased in relative humidity (RH), showing that the in vitro inhalation properties of salbutamol sulfate were improved at high RH. Using this surface covering technique would thus be valuable for storage humidity of dry powder inhalation (DPI) with lactose carrier particles.     

Simultaneous discrimination of diastereotopic groups and faces: the first example in intramolecular [3+2] and [2+2+1] cycloaddition reactions

To explore a novel concept for controlling diastereoselectivity, systematic studies on the sense and degree of diastereotopic groups and face selections in intramolecular [3 + 2] (nitrile oxide and nitrone) and [2 + 2 + 1] (Pauson-Khand) cycloadditions have been conducted. Optically pure methyl (S)-3,4-O-isopropylidene-3,4-dihydroxybutanoate (5) and methyl (S)-2,3-O-isopropylidene-2,3-dihydroxypropanoate (6) were converted to substrate aldehydes (1-4) that bear geminal allyl groups and four types of controllers with the intention of imparting a stereochemical bias to the allylic groups and their faces. The controllers involve 1,2-bis(tert-butyldimethylsiloxy), 1,3-bis(tert-butyldimethylsiloxy), 1,2-acetonide, and 1,3-acetonide groups, which are referred to as 1,2-(TBDMSO)(2), 1,3-(TBDMSO)(2), 1,3-dioxolane, and 1,3-dioxane, respectively. Twelve runs of cycloaddition reactions as combinations between the three types of reactions and the four types of substrates were performed to provide bicyclo[4.3.0] or -[3.3.0] adducts of synthetic importance in which isoxazolidine, isoxazoline, or cyclopentenone segments were fused. For every case, high levels of diastereoselectivity have been achieved: >99% (in eight cases), 82%, and 76% for the discrimination of diastereotopic groups and 68-->99% for the discrimination of diastereotopic faces. On the basis of the absolute structures of the cycloadducts, plausible stereochemical models are proposed.     

Direct coupling of microcolumn liquid chromatography with in-tube solid-phase microextraction for the analysis of antidepressant drugs

The direct coupling of in-tube solid-phase microextraction (in-tube SPME) with microcolumn liquid chromatography (micro-LC) has been investigated for the analysis of antidepressants in human urine. The use of in-tube SPME has been clearly shown to be advantageous for the on-line coupling of the SPME method, as the sample pretreatment technique, with micro-LC as the separation technique. This is because much smaller amounts of the sample solutions, desorption solvents and the mobile phase are required compared with conventional SPME-LC systems. The parameters for preconcentration have been investigated for the extraction capillary with the newly developed 'wire-in-tube' configuration.