Density-functional study of mechanisms for the cofactor-free decarboxylation performed by uroporphyrinogen III decarboxylase

Uroporphyrinogen III decarboxylase catalyzes the fifth step in heme biosynthesis: the elimination of carboxyl groups from the four acetate side chains of uroporphyrinogen III to yield coproporphyrinogen III. The enzyme acts by successively protonating each of the four pyrrole rings present in the substrate, thereby allowing decarboxylation of their side chains, but the identity of the proton donors has not been established yet. Tyr164 has been suggested as a proton donor, and Asp86 has been proposed to act either as a proton donor or as an intermediate-stabilizing residue. We have performed density-functional calculations to study this reaction mechanism, and found that the rate-limiting step is substrate protonation, rather than decarboxylation. Surprisingly, whereas Tyr164 is unable to protonate the substrate, this protonation can be effected by a nearby arginine residue (Arg37), with a free energy barrier of 21.4 kcal.mol(-1), in remarkable agreement with the experimental value of 19.5 kcal.mol(-1). The central positioning of this residue in close proximity to all four pyrrole rings in the substrate may play a key role in the sequential activation of each of these moieties.     

Synthesis and Cytotoxicity Evaluation of Metal‐Chelator‐Bearing Flavone,Carbazole, Dibenzofuran,Xanthone, and Anthraquinone

2‐(Aryloxymethyl)‐5‐benzyloxy‐1‐methyl‐1H‐pyridin‐4‐ones 8a – 8g , 2‐(aryloxymethyl)‐5‐hydroxy‐4H‐pyran‐4‐ones 9a – 9g , and 2‐(aryloxymethyl)‐5‐hydroxy‐1‐methyl‐1H‐pyridin‐4‐ones 10a – 10g were prepared from the known 5‐benzyloxy‐2‐(hydroxymethyl)pyran‐4‐one ( 3 ) in a good overall yield. These compounds were evaluated in vitro against a three‐cell lines panel consisting of MCF7 (breast), NCI‐H460 (lung), and SF‐268 (CNS), and the active compounds passed on for evaluation in the full panel of 60 human tumor cell lines derived from nine cancer cell types. The results indicated that 5‐hydroxy derivatives are more favorable than their corresponding 5‐benzyloxy precursors ( 10a – 10g vs. 8a – 8g ), and 1‐methyl‐1H‐pyridin‐4‐ones are more favorable than their corresponding pyran‐4(1H)‐ones ( 10a – 10g vs. 9a – 9g ). Among these three types of compounds, 2‐(aryloxymethyl)‐5‐hydroxy‐1‐methyl‐1H‐pyridin‐4‐ones 10a – 10g were the most cytotoxic; they inhibited the growth of almost all the cancer cells tested. On the contrary, compound 8a (a mean GI₅₀=27.8 μM ), 8b (38.5), 8d (11.0), and 8e (30.5) are especially active against the growth of SK‐MEL‐5 (a melanoma cancer cell) with a GI₅₀ of <0.01, 5.65, 0.55, and 0.03 μM , respectively (cf. Table 2).     

Effects of Self—coiling of Organic Molecules on Intramolecular Exciplex Formation and Fluoresscence Quenching in DX—H2O Solvent System

Effects of self-coiling of organic molecules on intramolecular exciplex formation of compound I,in which the carbazole chromophore and terephthalic acid methylester acceptor group are linked by one (CH2)10 chain,and the decrease of the fluorescence intensities of compounds Ⅱ，Ⅲ，and Ⅳ,in which the carbazole chromophore and 3,5-dinitrobenzoate are connected by one aliphatic chain of (CH2)10 (Ⅱ），（CH2）12（Ⅲ）,or (CH2)4(Ⅳ）,have been studied in the dioxane (DX)-H2O binary system.The results show that self-coiling of organic molecules in DX-H2O facilitates intramolecular exciplex formation of I and induces the decrease of fluorescence intensities of Ⅱ,bacause of the proximity effect brought about by selfcoiling of organic molecules under hydrophobic-lipophilic interaction(HLI) between the excited carbazole chromophore and the acceptor.Since the similar effects are observed even when the concentration of the probes are less than their CAgCs(critical aggregate concentrations )in the DX-H2O mixture with the same φ values,formation of the intermolecular exciplex has been excluded.The effects are found to be strongly depended on φ values,indication that they are mainly driven by HLI.The properties of the acceptors can also affect the intramolecular exciplex formation.With terephthalic acid methylester moiety as the acceptor,the carbazole chromophore exhibits the fluorescence spectra of the exciplex,while with 3,5-dinitrobenzoate moiety as the acceptor,only the fluorescence spectra of excited carbazolyl chromophore are observed.     

Fluorine-NMR competition binding experiments for high-throughput screening of large compound mixtures

High-throughput ligand-based NMR screening with competition binding experiments is extended to (19)F detection. Fluorine is a favorable nucleus for these experiments because of the significant contribution of the Chemical Shift Anisotropy (CSA) to the (19)F transverse relaxation of the ligand signal when bound to a macromolecular target. A low to moderate affinity ligand containing a fluorine atom is used as a reference molecule for the detection and characterization of new ligands. Titration NMR experiments with the selected reference compound are performed for finding the optimal set-up conditions for HTS and for deriving the binding constants of the identified NMR hits. Rapid HTS of large chemical mixtures and plant or fungi extracts against the receptor of interest is possible due to the high sensitivity of the (19)F nucleus and the absence of overlap with the signals of the mixtures to be screened. Finally, a novel approach for HTS using a reference molecule in combination with a control molecule is presented.     

Atom transfer radical homo‐ and block copolymerization of methyl 1‐bicyclobutanecarboxylate

A non‐olefinic monomer, methyl 1‐bicyclobutanecarboxylate (MBC), was successfully polymerized by the controlled/“living” atom transfer radical polymerization (ATRP) technique, resulting in a well‐defined homopolymer, PMBC, with only cyclobutane ring units in the polymer chain. An AB block copolymer poly(methyl 1‐bicyclobutanecarboxylate)‐b‐polystyrene (PMBC‐b‐PS), having an all‐ring unit segment, was also synthesized with narrow polydispersity and designed number‐average molecular weight in addition to precise end groups. The ¹H NMR spectra, glass‐transition temperature, and thermal stability of PMBC, PMBC‐b‐PS, and PS‐b‐PMBC were investigated. The experimental results showed that the cyclobutane rings in the two block polymers improved their thermal stability. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1929–1936, 2002     

3′-Methylsulfinyl-3,4′-diquinolinyl sulfides

Reactions of 4-methoxy- or 1,4-dihydro-4-oxo-3′-methylthio-3,4′-diquinolinyl sulfides 1 and 7 with a nitrating mixture ran as the 3′-methylthio group 5-mono-oxidation followed by C₆- and C₈-nitration and led to the mixture composed of products 3, 4, 5 and 6 (in the case of substrate 1 ) or compounds 5 and 6 (for substrate 7 ). In the reaction with hydrochloric acid 4-methoxy-3′-methylsulfinyl-3,4′-diquinolinyl sulfides 3 and 4 could be hydrolysed to 3′-methylsulfinyl-4(1H)-quinolinones 5 or 6 respectively, the methylsulfinyl group remaining unaffected.     

Electro-optic characteristics of aqueous beta-FeOOH particles

This paper presents a detailed analysis of the electro-optic behavior of suspensions of noninteracting monodisperse beta-FeOOH particles. The electro-optic parameters are determined for aqueous suspensions of the oxide particles and the influences of surface charge and Debye layer thickness are verified. Since the conventional method of frequency analysis is inconsistent in the low-frequency range, new electro-optic parameters are introduced to define the frequency variation of the effects. Electric polarizability is determined with precision to a constant, and its relative variations are followed. As reported for other oxides, electric polarizability correlates with charge variations in the diffuse part of the particle surface electric layer, and its relaxation frequency increases with surface charge density, indicating a Maxwell-Wagner type of surface polarization. The alternating component of the responses yields particle relaxation frequency and the phase shift of the responses at this frequency. For all studied samples the phase shift at particle relaxation frequency is 45 degrees. The relative changes in the steady component of the responses in the low-frequency range are followed by field intensity curves at characteristic frequencies of the samples. Electrophoretic rotation is the process consistent with our data for the low-frequency effect. The results show that it is enhanced by the combined actions of low or slowly relaxing polarizability and significant electrophoretic mobility.     

Synthesis and Crystal Structure of Two One—dimensional Chain Copper Complexes [Cu（TTA）2（4,4‘’—azpy）] and [Cu（TTA）2（3,3‘’—azpy）

Two copper complexes [Cu(TTA)₂(4,4′‐azpy)] (1) and [Cu‐(TTA)₂(3,3′‐azpy)] (2) (HTTA = 1,1,1‐trifluoro‐3‐(2‐thenoyl)‐acetone, 4,4′‐azpy = 4,4′‐azobispyridine, 3,3′‐azpy = 3,3′‐azobispyridine) were synthesized and characterized. The crystal structures were determined by X‐ray diffraction analysis. The crystal 1 belongs to triclinic with space group P1 , a = 0.8515(2) nm, b = 0.9259(2) nm, c = 0.9468(2) nm, a = 66.126(9)°, β = 79.667(9)°, γ = 90.13(1)°, Z = 1, V = 0.6692(2) nm³, D_c = 3.425 g/cm³, γ = 2.113 mm^?1, F(000) = 694, R₁ = 0.0594, wR₂ = 0.1499. The crystal 2 belongs to monoclinic with space group P2₁/c, a = 1.0661(2) nm, b = 1.4296(3) ran, c = 1.0041(3) nm, β = 114.50(3)°, V = 1.3926(5) nm³, Z = 2, D_c = 1.646 g/ cm³, μ = 1.015 mm^?1, F(000) = 694, R₁, = 0.0535, wR₂ = 0.1113. In the crystals of complexes 1 and 2, the copper atoms have distorted octahedral symmetry. The two compounds possess very similar one‐dimensional linear chains linked through the rodlike 4,4′‐azpy ligands or 3,3′‐azpy ligands.     

Affinity capillary electrophoresis study of the linkage existing between proton and zinc ion binding to bacitracin A1

Measurements by capillary electrophoresis (CE) of bacitracin A(1) effective mobility at different pH values permitted to estimate the five acidic dissociation constants and the Stokes radii at different protonation stages of the macrocyclic dodecapeptide. The pK(a) values were 3.6 and 4.4 for the two carboxylic groups of the lateral chains of D-Asp-11 and D-Glu-4, respectively, 6.4 for the aza-atom of the imidazole ring of His-10, 7.6 for the amino group of N-terminal Ile-1 and 9.7 for the delta-amino group of D-Orn-7, very close to the values obtained by other researchers by titration experiments. In agreement with a rigid macrocyclic structure the Stokes radii of different protonated forms ranged only between 14.3 and 14.8 A. Best fitting procedures performed on experimental mobility measured at two different pH values (5.50 and 6.72) in the presence of increasing Zn(+2) concentration allowed confirming the model that assumes the binding of Zn(+2) to P(0) peptide form with a 1.5 x 10(3) M(-1) intrinsic association constant. Following to Zn(+2) binding, the pK(a) of the amino group of N-terminal Ile-1 is shifted from 7.6 to 5.9 and the Stokes radius is reduced of about 3 A. The mean charge of the bacitracin A(1)-Zn(+2) complex resulted +1.67 and +1.12 at pH 5.50 and 6.72, respectively. These results suggest that the amino group of N-terminal Ile-1 is not essential for Zn(+2) binding.     

Metallomacrocycle (MacM) complex with cyanide as bridged ligand: Electronic structures of [MacMCN]n

The electronic structures of complexes and one‐dimensional metallomacrocycles with cyanide as bridged ligand, such as [MacM(CN)₂]^? and [MacM(CN)]_n [Mac=phthalocyanine, tetrabenzoporphyrine; M=Co(III), Rh(III)] have been investigated using density functional theory. The results of this study show that the intrinsic semiconductivity properties depend on the frontier bands. The valence band is composed by the π‐macrocycle orbital. The conduction band for the cobalt polymers is a mixture of orbitals between this metal and the cyanide ligand along of the stacking direction. However, in the rhodium polymers such a band is exclusively composed of the π* system of the macrocycles. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002