A Semiempirical Transition State Structure for the First Step in the Alkaline Hydrolysis of Cocaine. Comparison between the Transition State Structure,the Phosphonate Monoester Transition State Analog,and a Newly Designed Thiophosphonate Transition State Analog

Semiempirical molecular orbital calculations have been performed for the first step in the alkaline hydrolysis of the neutral benzoylester of cocaine. Successes, failures, and limitations of these calculations are reviewed. A PM3 calculated transition state structure is compared with the PM3 calculated structure for the hapten used to induce catalytic antibodies for the hydrolysis of cocaine. Implications of these calculations for the computer–aided design of transition state analogs for the induction of catalytic antibodies are discussed.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s0089460020062     

Characteristics of mass spectrometric analyses coupled to gas chromatography and liquid chromatography for 22-oxacalcitriol, a vitamin D3 analog, and related compounds

The characteristics of the mass spectra of vitamin D₃ related compounds were investigated by GC–MS and LC–MS using 22-oxacalcitriol (OCT), an analog of 1,25-dihydroxyvitamin D₃, and related compounds. Fragmentation during GC–MS (electron impact ionization) of TMS-derivatives of OCT and the postulated metabolites gave useful structural information concerning the vitamin D₃-skeleton and its side-chain, especially with respect to the oxidation positions of metabolites. In contrast, few fragment ions were observed in LC–MS (atmospheric pressure chemical ionization), showing that LC–MS gave poor structural information, except for molecular mass. However, when comparing the signal-to-noise ratio (S/N) observed during GC–MS and LC–MS analysis for OCT in plasma extracts, the S/N in LC–MS was over ten-times greater than in GC–MS, possibly due to the low recovery on derivatization and thermal-isomerization in GC–MS. Furthermore, both the GC–MS and the LC–MS allowed the analysis of many postulated metabolites in a single injection without any prior isolation of target metabolites from biological fluids by LC. These results suggest that GC–MS and LC–MS analysis for vitamin D₃ related compounds such as OCT each have unique and distinct advantages. Therefore, the complementary use of both techniques enables the rapid and detailed characterization of vitamin D₃ related compounds.     

Inhibition of Human Platelet Aggregation by Amides and Ester of Salicylic Acid with Platelet-Activating Factor Analogs

The influence of acetyl salicylic acid (ASA) derivatives with platelet-activating factor (PAF) lipid analogs on PAF-induced human platelet aggregation has been studied. It was found that the ASA amide with an ethanolamine plasmalogen PAF analog (1-0-alk-1"-enyl-2-acetyl-sn-glycero-3-phospho-(N-2"-acetoxybenzoyl)ethanolamine) and the ASA ester with a choline plasmalogen PAF analog (1-0-alk-1"-enyl-2-(2"-acetoxybenzoyl)-sn-glycero-3-phosphocholine) at concentrations of 10^–7-10^–6 M effectively inhibit PAF-induced aggregation of human platelets. In contrast to these compounds, the ASA amide with an alkyl PAF analog (1-0-alkyl-2-acetyl-sn-glycero-3-phospho-(N-2"-acetoxybenzoyl)ethanolamine) did not inhibit PAF-induced platelet aggregation. As possible mechanisms of action of the studied compounds, the blockade of PAF-receptor and cyclooxygenase inhibition are proposed.     

Structure of Pyridoxal Kinase from Sheep Brain and Role of the Tryptophanyl Residues

The primary structure of sheep brain pyridoxal kinase has been determined by direct chemical and physical methods. The enzyme contains 312 amino acid residues with an acetylated methionine at the N-terminus, yielding a molecular mass of 34,861 Da. The functional role played by the two tryptophanyl residues in positions 52 and 244 of the polypeptide chain has been investigated by fluorescence spectroscopy. The tryptophanyl residues are not completely exposed to the rapidly relaxing solvent and they are poorly accessible to collisional quenchers. Chemical modification with NBS abolishes the catalytic activity of the kinase. The amino acid sequence of the sheep brain enzyme shows high similarity (86.2% identity) with the human pyridoxal kinase recently reported [Hanna, Turner, and Kirkness, (1997), J. Biol. Chem. 272, 10756–10760]. Comparison of the mammalian proteins with bacterial and yeast putative pyridoxal kinases retrieved from the Swiss-Prot data bank shows a low degree of overall similarity. In particular, the putative ATP-binding domain is conserved, whereas the region that appears to be crucial in the binding of the pyridoxal substrate is not. Thus, the assignment of the bacterial and yeast cDNA-deduced proteins as pyridoxal kinases should be taken with caution.     

Hydrolysis of settleable substrate in domestic sewage

The hydrolysis of settleable substrate in domestic sewage was evaluated using its O₂ utilization rate profile generated in an aerated batch reactor. The hydrolysis rate coefficient was 1.2 d^–1, significantly lower than 3.8 d^–1 and 1.9 d^–1 characterizing soluble and suspended slowly biodegradable fractions. The settled portion of the sewage incorporated an active biomass fraction of 1560 mg COD l^–1 that needed to be accounted for in the hydrolysis kinetics. The texture of the biomass/settled substrate mixture and the gradual hydrolysis of the particulate substrate within the floc structure were examined by microscopic analysis.     

Localization of pyrodoxal phosphate binding site on the mero-receptor domain of the glucocorticoid receptor

Previous studies have demonstrated that the vitamin pyridoxal phosphate can alter the physicochemical properties of glucocorticoid receptors. We now report the localization of a pyridoxal phosphate binding site within the mero-receptor domain of this glucocorticoid receptor. Mero-glucocorticoid receptors that are generated by trypsin (10 μg/ml) or chymotrypsin (100 μg/ml) digestion of intact receptors sediment as 2.6 S species on 5–20% sucrose gradients in the presence or absence of pyridoxal phosphate. Mero-glucocoritcoid receptors prepared by exogenous proteinases are hydrophobic and show no affinity for DEAE Bio-Gel A. Treating either trypsin-generated or chymotrypsin-generated mero-receptors with pyridoxal phosphate rapidly converts the proteins (60 and 35%, respectively) into forms that bind to DEAE Bio-Gel A. Induction of DEAE binding is specific to pyridoxal phosphate, for treating mero-receptors with pyridoxal, pyridoxamine or pyridoxine phosphate is ineffective. Furthermore, DEAE binding cannot be induced by adding other pyridoxal phosphate-treated cytosols to untreated mero-receptors. High-resolution polyacrylamide gel isoelectric focussing studies indicated that treating mero-receptor generated by either proteinase with pyridoxal phosphate shifted the isoelectric points of lower pH values. The conversion of the mero-receptor to a more acidic form also occurred when the intact glucocorticoid receptor was treated with the vitamin prior to proteolysis. These studies localize at least one pyridoxal phosphate binding site on the mero-receptor domain of the rat thymocyte glucocorticoid receptor.     

Production of vitamin B12 in an upflow anaerobic filter continuous reactor using Acetobacterium sp.

The accumulation of biofilm by Acetobacterium sp. during continuous culture in an upflow anaerobic filter (UAF) growing on methanol-formate was the result of space velocity and inlet concentrations of substrate and Co⁺². To achieve good development of biofilm, a space velocity of 0.38 h^–1, inlet substrate concentrations of 125 mM of both methanol and formate, and Co⁺² at 0.16 mM were required. Cell productivities in the effluent of the UAF-reactor were about 6-fold higher than in chemostat cultures (0.20 g l^–1 h^–1 for UAF and 0.035 g l^–1 h^–1 for chemostat) (previous studies), and the maximum vitamin B₁₂ specific concentration was 5.1 mg g cell^–1.     

Optically Active Compounds Derived from Salicylaldehyde and Pyridoxal: Syntheses and Their Chelate Formation Properties in the Interaction with α-Amino Acid

Synthesis of chiral compounds derived from salicylaldehyde and pyridoxal was carried out. In aqueous media containing copper ion, these compounds were analyzed to form Schiff base copper chelate spontaneously with α-amino acid. This complex formation process was reversed by the addition of EDTA. Applicabilities of the compounds to the resolution of α-amino acids are discussed.     

DNA lesion bypass polymerases and 4’-thio-β-Darabinofuranosylcytosine (T-araC)

The 4’-thio-β-D-arabinofuranosylcytosine (T-araC) is a newly developed nucleoside analog that has shown promising activity against a broad spectrum of human solid tumors in both cellular and xenograft mice models. TaraC shares similar structure with another anticancer deoxycytidine analog, β-D-arabinofuranosylcytosine (araC, cytarabine), which has been used in clinics for the treatment of acute myelogenous leukemia but has a very limited efficacy against solid tumors. T-araC exerts its anticancer activity mainly by inhibiting replicative DNA polymerases from further extension after its incorporation into DNA. DNA lesion bypass polymerases can manage the DNA lesions introduced by therapeutic agents, such as cisplatin and araC, therefore reduce the activity of these compounds. In this study, the potential relationships between the lesion bypass Y-family DNA polymerases η, ι and κ (pol η, pol ι, and pol κ) and T-araC were examined. Biochemical studies indicated that the triphosphate metabolite of T-araC is a less preferred substrate for the Y-family polymerases. In addition, cell viability study indicated that pol η deficient human fibroblast cells were more sensitive to T-araC when compared with the normal human fibroblast cells. Together, these results suggest that bypass polymerases reduced cell sensitivity to T-araC through helping cells to overcome the DNA damages introduced by T-araC.     

Transport of osmoprotective compounds in hybridoma cells exposed to hyperosmotic stress

Addition of osmoprotective compounds has a positive effect on growth and monoclonal antibody production in hyperosmotic hybridoma cell cultures. In order to better understand the processes involved in the osmoprotective response, uptake of the osmoprotective compounds glycine betaine, proline, sarcosine and glycine in mouse hybridoma cell line 6H11 during exposure to hyperosmotic stress was studied. Hyperosmotic stress (510 mOsmol/kg) was introduced through the addition of NaCl (100 mM) to the growth medium, and amino acid transport activity was measured immediately after transfer of the cells to the hyperosmotic medium. The osmoprotective capability of the four osmoprotectants tested was negatively affected if methylaminosobutyric acid (MeAiB), a specific substrate for amino acid transport system A, was simultaneously included in the hyperosmotic medium in equimolar amounts with one of the osmoprotective compounds. This was due to accumulation of MeAiB in the stressed cells, giving a significant reduction in the concentration of the osmoprotective compound inside the cells. Furthermore, addition of excess meAiB gave approx. 905 reduction in the initial rate of uptake of glycine betaine, while 40–50% reduction in the initial rate of uptake of proline, glycine and sarcosine. Similarly, addition of proline, glycine or sarcosine also gave a significant reduction in the initial rate of glycine betaine uptake. These results suggest that the four osmoprotective compounds share, at least in part, a common, MeAiB inhibitable carrier for transport into osmotically stressed hybridoma cells. This carrier is probably equal to amino acid transport system A.     

The Catalytic Transition State in ATP Synthase

The catalytic transition state of ATP synthase has been characterized and modeled by combined use of (1) Mg-ADP–fluoroaluminate, Mg-ADP–fluoroscandium, and corresponding Mg-IDP–fluorometals as transition-state analogs; (2) fluorescence signals of -Trp331 and -Trp148 as optical probes to assess formation of the transition state; (3) mutations of critical catalytic residues to determine side-chain ligands required to stabilize the transition state. Rate acceleration by positive catalytic site cooperativity is explained as due to mobility of -Arg376, acting as an arginine finger residue, which interacts with nucleotide specifically at the transition state step of catalysis, not with Mg-ATP- or Mg-ADP-bound ground states. We speculate that formation and collapse of the transition state may engender catalytic site / subunit-interface conformational movement, which is linked to -subunit rotation.     

Direct ab initio dynamics studies of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical

The kinetics of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical were studied using the direct ab initio dynamics approach. BHandHLYP/cc-pVDZ method was employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points for the two reactions were further refined at the QCISD(T)/cc-pVTZ level of theory. No barrier was found at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory for both reactions. The forward and reverse rate constants were evaluated with both canonical variational transition state theory (CVT) and microcanonical variational transition state theory ( VT) in the temperature range of 300–2,500 K. The fitted three-parameter Arrhenius expression of the calculated CVT rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory are k^CVT (n – C₃H₇)=1.68×10^–14 T^0.84 e^(319.5/T) cm³ molecule^–1 s^–1 and k^CVT (iso-C₃H₇)=4.99×10^–14 T^0.90 e^(159.5/T) cm³ molecule^–1 s^–1 for reactions of n-C₃H₇ + H and iso-C₃H₇ + H, respectively, which are in good agreement with available literature data. The variational effects were analysed.Figure Comparison of the calculated forward rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory and the available experimental and theoretical data of the reaction vs 1,000/T for the two reactions.     

Structural—Functional Relationships between Terminal Deoxynucleotidyltransferase and 5′-Triphosphates of Nucleoside Analogs

Substrate properties of nucleoside 5′-triphosphate (NTP) analogs, namely, 5′-triphosphates of L- and D-arabinonucleosides (D-FIAUTP, D-FMAUTP, and L-FMAUTP), D- and L-enantiomers of ddCTP analogs (D-ddCTP, L-ddCTP, D-FOddCTP, L-OddCTP, and L-SddCTP), and acyclic guanosine analogs (acyclovir and penciclovir) towards terminal deoxynucleotidyltransferase (TdT, EC 2.7.7.31) were studied. TdT can polymerize 5′-triphosphates of arabinonucleoside analogs (D-FIAUTP and D-FMAUTP). In contrast, L-FMAUTP is not recognized by TdT as a substrate. Kinetic parameters of D- and L-enantiomers of ddCTP analogs and 5′-triphosphates of acyclic nucleosides were evaluated. It is shown that stereospecificity of dNTP analogs and structure of the furanose residue play crucial roles in the interaction with TdT: L-enantiomers are much less potent as substrates compared to their D-counterparts. 5′-Triphosphates of acyclovir (ACVTP) and penciclovir (PCVTP) are about two orders of magnitude less effective as substrates than nucleosides bearing furanose residues, with PCVTP being a better substrate than ACVTP. It can be assumed that the hydroxyl group of PCVTP mimics the 3′-hydroxyl group of the ribose residue and plays an important role in the interaction with TdT.__________Translated from Biokhimiya, Vol. 70, No. 8, 2005, pp. 1078–1085.Original Russian Text Copyright © 2005 by Kukhanova, Ivanov, Jasko.     

A critical electrostatic interaction mediates inhibitor recognition by human asparagine synthetase

The first sulfoximine-based inhibitor of human asparagine synthetase (ASNS) with nanomolar potency has been shown to suppress proliferation of asparaginase-resistant MOLT-4 cells in the presence of l-asparaginase. This validates literature hypotheses concerning the viability of human ASNS as a target for new drugs against acute lymphoblastic leukemia and ovarian cancer. Developing structure–function relationships for this class of human ASNS inhibitors has proven difficult, however, primarily because of the absence of rapid synthetic procedures for constructing highly functionalized sulfoximines. We now report conditions for the efficient preparation of these compounds by coupling sulfoxides and sulfamides in the presence of a rhodium catalyst. Access to this methodology has permitted the construction of two new adenylated sulfoximines, which were expected to exhibit similar binding affinity and better bioavailability than the original human ASNS inhibitor. Steady-state kinetic characterization of these compounds, however, has revealed the importance of a localized negative charge on the inhibitor that mimics that of the phosphate group in a key acyl-adenylate reaction intermediate. These experiments place an important constraint on the design of sulfoximine libraries for screening experiments to obtain ASNS inhibitors with increased potency and bioavailability.     

2-(3′-Hydroxypropylidene)-1α-hydroxy-19-norvitamin D compounds with truncated side chains

Our recent studies with 2-(3′-hydroxypropylidene) analogs of 1α,25-dihydroxy-19-norvitamin D₃ showed that this 2-substituent creates compounds with very potent biological activity. In the continuing search for vitamin D compounds with selective activity profiles, we prepared a series of 1α-hydroxy-19-norvitamin D analogs characterized by the presence of a 3′-hydroxypropylidene substituent at C-2 and a truncated side chain. These vitamin D compounds were efficiently prepared using convergent syntheses. The C,D-fragments, namely the Grundmann ketones 19, 20, 27, 36 and 37 were synthesized from the known 8β-benzoyloxy-22-aldehydes 12 and 29. These hydrindanones were subjected to Lythgoe type Wittig–Horner coupling with phosphine oxide 21, prepared by us previously, and after hydroxyl deprotection the set of 19-norvitamins 7–11 was successfully obtained. According to our expectations, all analogs (with an exception of the 20R-compound 7) have pronounced in vitro activity. When compared to the natural hormone 1α,25-(OH)₂D₃ (1), they show the same or only slightly reduced affinity for the vitamin D receptor while being similarly effective as 1 in differentiation of HL-60 cells into monocytes.     

pH dependent stabilization of S2QA − and S2QB − charge pairs studied by thermoluminescence

The pH dependence of emission peak temperature and decay time of thermoluminescence arising from S₂Q_B ^– and S₂Q_A ^– recombinations demonstrates that a stabilization of S₂Q_B ^– occurs at low pH whereas stabilization of S₂Q_A ^– occurs at high pH. Based on comparative analysis of thermoluminescence parameters of the two types of recombination, we suggest that in the pH range between 5.3 and 7.5, E_m(S₂/S₁) and E_m(Q_A/Q_A ^–) are constant, but E_m(Q_B/Q_B ^–) gradually increases with decreasing pH, while in the pH range between 7.5 and 8.5, an unusual change occurs on S₂Q_A ^– charge pair, which is interpreted as either a decrease in E_m(S₂/S₁) or an increase in E_m(Q_A/Q_A ^–).     

Determination of isoprostaglandin F2α type III in human urine by gas chromatography–electronic impact mass spectrometry. Comparison with enzyme immunoassay

F₂-Isoprostanes are stable lipid peroxidation products of arachidonic acid, the quantification of which provides an index of oxidative stress in vivo. We describe a method for analysing isoprostaglandin F_2α type III (15-F_2t-IsoP) in biological fluids. The method involves solid-phase extraction on octadecyl endcapped and aminopropyl cartridges. After conversion to trimethylsilyl ester trimethylsilyl ether derivatives, isoprostaglandin F_2α type III is analysed by mass spectrometry, operated in electronic impact selected ion monitoring mode. We have compared enzyme immunoassay (EIA; Cayman, Ann Arbor, MI, USA) to this method with 30 human urine aliquots following the same extraction procedure in order to determine the agreement between both methods. Isoprostaglandin F_2α type III concentrations determined with gas chromatography–mass spectrometry (GC–MS) did not agree with those determined with EIA. Our results suggest that GC–MS and EIA do not measure the same compounds. As a consequence, comparison of clinical results using GC–MS and EIA should be avoided.     

Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase

Pyridoxal kinase catalyzes the phosphorylation of pyridoxal (PL) to pyridoxal 5′-phosphate (PLP). A D235A variant shows 7-fold and 15-fold decreases in substrate affinity and activity, respectively. A D235N variant shows ∼2-fold decrease in both PL affinity and activity. The crystal structure of D235A (2.5 Å) shows bound ATP, PL and PLP, while D235N (2.3 Å) shows bound ATP and sulfate. These results document the role of Asp235 in PL kinase activity. The observation that the active site of PL kinase can accommodate both ATP and PLP suggests that formation of a ternary Enz·PLP·ATP complex could occur in the wild-type enzyme, consistent with severe MgATP substrate inhibition of PL kinase in the presence of PLP.     

Ammonium uptake by Chondrus crispus Stackhouse (Gigartinales,Rhodophyta) in culture

Cultivated Chondrus crispus was used in N-NH₄ uptake experiments in the laboratory. An elevation of temperature increased the apparent rate of uptake, especially up to 11 °C. Uptake in the dark was found to be 83 % of that in the light. The apparent uptake decreased with increasing internal N pool; rates were 26.5, 22.2 and 20.2 µg N g dry wt^–1 min^–1 for internal N pools of 2.7, 3.5 and 4.6%, respectively. Apparent uptake increased with the substrate N concentration. The resulting curve has two components: an active uptake and a diffusion component at high (> 5000 µg N L^–1) external N levels. Ks and V _max were calculated by deducting the diffusion component from the uptake curve: these were of 497 µg N L ^–1 and 14.4 µg N g dry wt^–1 min^–1. respectively, and reflect a low substrate affinity. This could be the result of 10 years of continuous culture of C. crispus. Uptake was similarly followed in the culture tanks and showed comparable results; nighttime would be the most appropriate time to supply nutrients.     

Aroma compounds produced by Kluyveromyces marxianus in solid state fermentation on a packed bed column bioreactor

Studies were carried out for the production of aroma compounds by Kluyveromyces marxianus grown on cassava bagasse in solid state fermentation using packed bed reactors, testing two different aeration rates. Respirometric analysis was used to follow the growth of the culture. Headspace analysis of the culture by gas chromatography showed the production of 11 compounds, out of which nine were identified. Ethyl acetate, ethanol and acetaldehyde were the major compounds produced. Lower aeration rate (0.06l h^–1 g^–1 of initial dry matter) increased total volatile (TV) production and the rate of production was also increased at this aeration rate. Using an aeration rate of 0.06l h^–1 g^–1 maximum TV concentrations were reached at 24 h and at 40 h with 0.12l h^–1 g^–1.