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.     

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.     

Physically adsorbed chiral stationary phase of avidin on monolithic silica column for capillary electrochromatography and capillary liquid chromatography

The physical adsorption method proposed previously has been successfully applied to a monolithic silica column. By virtue of the physical adsorption, a chiral stationary phase of avidin was prepared onto the silica monolith. The phase ratio of resulting stationary phase was evaluated with frontal analysis. The method proved to be comparable in phase ratio to the chemical bonding methods used in high-performance liquid chromatography (HPLC). Enantiomer separations were carried out in capillary electrochromatography (CEC) and capillary liquid chromatography (CLC) modes. Due to its larger phase ratio, the resulting column showed more powerful separation capability as compared to open-tubular CEC (OTCEC). Twelve chiral compounds were baseline-resolved. The resulting column showed high separation efficiency, with average theoretical plate numbers of 66 000/m for CLC and 122 000/m for CEC. Good reproducibility was observed, with RSD value less than 1.3% for retention time, retention factor and separation factor, and less than 6.6% for plate counts and resolution (n = 40). Fast separations were achieved with a short column. The test enantiomers were baseline-resolved within 4 min under CLC and CEC modes. In addition, field-enhanced sample injection (FESI) was coupled to CLC as well as CEC to improve the detection sensitivity.     

Control of calcium carbonate polymorphism and morphology through biomimetic mineralization by means of nanotechnology

In vitro biomimetic mineralization by means of nanotechnology allows the formation of calcium carbonate polymorphs at low temperatures (<25 degrees C) under a CO(2) atmosphere of 500-1500 ppm. A two-dimensional zinc-ion ordered array (zinc array), which acts as an active-site mimic of carbonic anhydrase, has been prepared by immersing the self-organized monolayer of 3-(2-imidazolin-1-y)propyltriethosilane on mica (ImSi substrate) into aqueous zinc solution. The zinc array mounted on the ImSi substrate catalyzed the conversion from CO(2) to HCO(3) (-), and accelerated the formation of calcium carbonate. In situ X-ray diffraction data of the formed calcium carbonate on the poly(L-aspartate)-coated chitin substrate (pAsp substrate), with calcium ion-recognition sites, demonstrated that the interaction between the zinc array and pAsp substrates formed both vaterite and calcite at low temperature (15 degrees C) and mainly vaterite at 25 degrees C; this interaction also controlled the morphology of calcium carbonate formed on pAsp substrate.     

Dithiol-mediated immobilization of CdS nanoparticles from reverse micellar system onto Zn-doped silica particles and their high photocatalytic activity

Cds nanoparticles, prepared in a reverse micellar system, were immobilized directly onto alkanedithiol-modified Zn-doped silica particles, which were themselves prepared via hydrolysis of tetraethylorthosilicate in the presence of Zn(NO(3))(2) followed by contact with dithiol molecules. The resulting CdS-Zn-SiO(2) composite was then used as a photocatalyst for the generation of H(2) from 2-propanol aqueous solution. Under UV irradiation (lambda>300 nm), a high photocatalytic activity was observed for the CdS-Zn-SiO(2) composite material. This is effected by electron transfer from the photoexcited ZnS (dithiol-bonded Zn on SiO(2)) to CdS nanoparticles. The photocatalytic activity is increased with a decrease in the number of methylene groups in the dithiol molecules, according to the rank order 1,10-decanedithiol <1,6-hexanedithiol <1,2-ethanedithiol.     

Amidase and peptidase activities of polyclonal immunoglobulin G present in the sera of patients with rheumatoid arthritis

Polyclonal Immunoglobulin (Ig) G from patients with rheumatoid arthritis (RA) and healthy subjects hydrolyzed carbobenzoxy−Val−Gly−Arg p-nitroanilide and D−Pro−Phe−Arg p-nitroanilide. RA IgG exhibited higher activity against the former substrate, but not the latter. On the other hand, RA IgG showed reduced activity against D−Pro−Phe−Arg methylcoumarinamide, when compared with those of the healthy controls. These results suggest that RA IgGs differ from normal IgGs in the substrate specificity of amidase activity. Preliminary studies have shown that two out of three RA IgG samples cleaved a pentapeptide—Gln−Arg−Arg−Arg−Ala−Ala— which is assumed to be associated with the risk of developing RA (Gregersen, P. K. et al. (1987), Arthritis Rheum. 30, 1205–1213). By contrast, virtually no cleavage of the same peptide was observed with IgG from healthy controls. A peptide analog, Gln−Arg−Arg−Trp−Ala, was not cleaved at all by any IgGs examined either from RA patients or healthy controls.     

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.     

Remarkable reactivities of the xanthone ketyl radical in the excited state compared with that in the ground state

The properties and reactivities of the xanthone (Xn) ketyl radical (XnH*) in the doublet excited state (XnH*(D1)) were examined by using two-color two-laser flash photolysis. The absorption and fluorescence of XnH*(D1) were observed for the first time. Several factors governing the deactivation processes of XnH*(D1) such as interaction and reaction with solvent molecules were discussed. The remarkable change of reactivity of XnH*(D1) compared with that in the ground state (XnH*(D0)) was indicated from the experimental results. The rapid halogen abstraction of XnH*(D1) from some halogen donors such as carbon tetrachloride (CCl4) was found to occur. The halogen abstraction occurred more efficiently in the polar solvents than in the nonpolar solvents. It is suggested that the polar solvents promote the spin distribution of XnH*(D1) of the phenyl ring favorable to the halogen abstraction.     

Synthesis and anti-HIV-1 activity of novel 10-thiaisoalloxazines,a structural analog of C-5 and/or C-6 substituted pyrimidine acyclonucleoside

A series of novel 10-thiaisoalloxazine derivatives bearing an alkoxymethyl or benzyloxymethyl moiety at the N-1 position has been synthesized through the bromination of 1-substituted-5-hydroxyuracils and subsequent condensation with aminobenzenethiol in a one-pot reaction. Contrary to the previous report, the formation of intermediary 5,6-diethoxy-5-hydroxy-5,6-dihydrouracil seems to be not the necessary factor for the formation of the thiaisoalloxazines, since the reaction proceeds in tetrahydrofuran (THF) or acetonitrile far more smoothly than in ethanol. The anti-human immunodeficiency virus (HIV)-1 activity of the resulted thiaisoalloxazine derivatives was evaluated in lymphocyte cells based on the inhibitory activity against the viral-induced cytopathic activity. Among the derivatives, compounds 6, 7, and 8 bearing an alkoxymethyl moiety at the N-1 position exhibited modest inhibitory activity towards the cytotopathic effect of HIV-1.     

Synthesis and reactivities of 10-S-3 trithiadiazapentalene derivatives

1,3-Bis(p-substituted-phenylthiocarbamoyl)-2-imidazolidinethiones 3a-f reacted with bromine to give trithiadiazapentalene derivatives 5a-f , bearing the exocyclic C-N double bonds, in moderate yields. The molecular structure of 5b was elucidated by the X-ray crystallographic analysis. The treatment of 5b-f with hydrochloric acid gave the ring-opening products, 1,3-bis(p-substituted-phenylthiocarbamoyl)-2-imidazo-lidinones 9b-f , accompanied by the production of elemental sulfur. Reduction of 5b , 5d , and 5e with sodium borohydride gave the ring-opening compounds, 1,3-bis(p-substituted-phenylthiocarbamoyl)-2-imidazolidines 13b , 13d , and 13e respectively.