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PubMed2003

Stability and kinetics of the acid-promoted decomposition of Cu(II) complexes with hexaazacyclophanes: kinetic studies as a probe to detect changes in the coordination mode of the macrocycles.

The synthesis, protonation and Cu(II) coordination features of the novel azacyclophane type receptors 2,6,10,13,17,21-hexaza[22]-(2,6)-pyridinophane (L2), 2,6,9,12,15,19-hexaza[20]-(2,6)-pyridinophane (L5) and 2,6,9,12,15,19-hexaza[20]metacyclophane (L6) are presented. The protonation and Cu(II) constants are analysed and compared with the previously reported open-chain polyamines 4,8,11,15-tetrazaoctadecane-1,18-diamine (L1) and 4,7,10,13-tetraazahexadecane-1,16-diamine (L4) and of the cyclophane 2,6,10,13,17,21-hexaaza[22]paracyclophane (L3). All the systems form mono- and dinuclear complexes whose stability and pH range of existence depend on the type of hydrocarbon chains and molecular topology. The effects of the cyclic or open-chain nature and of the presence of the pyridine rings on the protonation and formation of mono- and dinuclear complexes are discussed. Stopped-flow kinetic measurements on the acid-promoted decomposition of the Cu(II) complexes have been carried out for the different systems. With respect to the decomposition of the dinuclear complexes, because the size of the macrocycles forces both metal ions to be close to each other, the release of the first ion occurs within the mixing time of the stopped-flow except for the dinuclear complexes of L2. However, the most interesting kinetic result is the observation of different kinetics of decomposition for the different mononuclear complexes formed by a given ligand. This effect is especially evident for L3 and L6 and indicates a change in the coordination mode of the ligand for the different mononuclear species. Therefore the Cu(II) ion performs a slippage motion through the macrocyclic cavity driven by pH changes. The stopped-flow experiments are an excellent tool to detect these slippage processes that may be present for the complexes with other macrocycles.

Journal Article↗

PubMed2005

Kinetic resolution and parallel kinetic resolution of methyl (+/-)-5-alkyl-cyclopentene-1-carboxylates for the asymmetric synthesis of 5-alkyl-cispentacin derivatives.

Conjugate addition of lithium dibenzylamide to methyl 5-isopropyl, 5-phenyl- and 5-tert-butyl-cyclopentene-1-carboxylates occurs with high levels of substrate control (>88% de), with preferential addition to the face of the cyclic alpha,beta-unsaturated acceptor anti- to the stereodirecting 5-alkyl substituent. Treatment of a range of methyl (+/-)-5-alkyl-cyclopentene-1-carboxylates with both lithium (+/-)-N-benzyl-N-alpha-methylbenzylamide and lithium (+/-)-N-3,4-dimethoxybenzyl-N-alpha-methylbenzylamide indicates significant enantiorecognition in their mutual kinetic resolutions, with preferential addition anti- to the 5-alkyl substituent, giving the 1,2-syn-1,5-anti-arrangement (E >16) after enolate protonation anti- to the amino functionality. The kinetic resolution of a range of methyl (+/-)-5-alkyl-cyclopentene-1-carboxylates with lithium (S)-N-benzyl-N-alpha-methylbenzylamide, and their efficient parallel kinetic resolution with a pseudoenantiomeric mixture of lithium (S)-N-benzyl-N-alpha-methylbenzylamide and lithium (R)-N-3,4-dimethoxybenzyl-N-alpha-methylbenzylamide are also demonstrated, giving a range of 5-alkyl-cispentacin derivatives in >98% de and high ee after N-deprotection.

Journal Article↗

PubMed2003

Predicting fetal perchlorate dose and inhibition of iodide kinetics during gestation: a physiologically-based pharmacokinetic analysis of perchlorate and iodide kinetics in the rat.

Perchlorate (ClO4-) disrupts endocrine homeostasis by competitively inhibiting the transport of iodide (I-) into the thyroid. The potential for health effects from human exposure to ClO4- in drinking water is not known, but experimental animal studies are suggestive of developmental effects from ClO4- induced iodide deficiency during gestation. Normal hormone-dependent development relies, in part, on synthesis of hormones in the fetal thyroid from maternally supplied iodide. Although ClO4- crosses the placenta, the extent of inhibition in the fetal thyroid is unknown. A physiologically-based pharmacokinetic (PBPK) model was developed to simulate ClO4- exposure and the resulting effect on iodide kinetics in rat gestation. Similar to concurrent model development for the adult male rat, this model includes compartments for thyroid, stomach, skin, kidney, liver, and plasma in both mother and fetus, with additional compartments for the maternal mammary gland, fat, and placenta. Tissues with active uptake are described with multiple compartments and Michaelis-Menten (M-M) kinetics. Physiological and kinetic parameters were obtained from literature and experiment. Systemic clearance, placental-fetal transport, and M-M uptake parameters were estimated by fitting model simulations to experimental data. The PBPK model is able to reproduce maternal and fetal iodide data over five orders of magnitude (0.36 to 33,000 ng/kg 131I-), ClO4- distribution over three orders of magnitude (0.01 to 10 mg/kg-day ClO4-) and inhibition of maternal thyroid and total fetal I- uptake. The model suggests a significant fetal ClO4- dose in late gestation (up to 82% of maternal dose). A comparison of model-predicted internal dosimetrics in the adult male, pregnant, and fetal rat indicates that the fetal thyroid is more sensitive to inhibition than that of the adult.

Animals↗

PubMed1970

Kinetics of C-14 translocation in soybean: I. Kinetics in the stem.

A kinetic study was made of the translocation of (14)C-photosynthate through soybean stems following pulse labeling and during steady state labeling of the first trifoliolate leaf. The translocation profile proceeded down the stem with little or no change in shape. Following pulse labeling, sucrose accounted for 90 to 95% of the radioactivity in the stem at all times up to 2 hours, at which time less than 3% of the activity was in an insoluble form. Kinetic data on the relative specific activities of sucrose in the leaf and petiole indicated that two-thirds of the petiolar sucrose was in the translocation stream and the remaining one-third was in a stationary pool which slowly accumulated sucrose from the translocation stream. With this assumption, the rate of sucrose efflux from the leaf was calculated to be 22 micrograms per minute, which was equivalent to a sucrose mass flux in the sieve tubes of 20 grams per square centimeter per hour.It is concluded that translocation proceeded without a net radial velocity distribution and with slight loss of translocate, mainly as sucrose, from the translocation stream. The kinetics of (14)C translocation must, therefore, be determined primarily by factors operating within the leaf rather than in the stem. One of these factors may be the presence in the soybean leaf of a specialized paraveinal mesophyll. Since there was no spreading of the profile, the results were inconsistent with an "active diffusion" mechanism of translocation (i.e., a mechanism describable by diffusion equations). The data and conclusions are in substantial agreement with those of Moorby, Ebert, and Evans.

Journal Article↗

PubMed1995

Endotoxin Detection in Pharmaceuticals and Medical Devices with Kinetic-QCL, a Kinetic-Quantitative Chromogenic Limulus Amebocyte Lysate Assay.

The observation that endotoxin caused gelation in extracts of Limulus amebocytes has been expanded to the development of an in vitro kinetic, quantitative chromogenic LAL assay (Kinetic-QCL) for the detection of endotoxin in aqueous fluids. Within the last 15 years, the use of Limulus amebocyte lysate to detect and control the presence of pyrogenic substances in pharmaceuticals and medical devices has gained wide international acceptance. Both the United States and European Pharmacopoeias contain descriptions of and requirements for the LAL Bacterial Endotoxin Test. Both pharmacopoeias have begun to remove the rabbit pyrogen test requirement in a majority of drug monographs and have substituted endotoxin limits to be determined by LAL. The use of LAL has proved invaluable in controlling the level of endotoxin in finished product. The endotoxin contribution of raw materials and packaging material can be monitored as well. In-process testing at critical production steps can identify additional sources of endotoxin contamination, and depyrogenation processes can be validated by quantitating the degradation of endotoxin challenges. The speed, reproducibility, sensitivity, and economics of the Kinetic-QCL assay, in conjunction with the ppropriate equipment and software, over both the in vivo rabbit pyrogen test and the more traditional LAL gel-clot assay allow a more in-depth approach to the control of endotoxin in pharmaceuticals and medical devices.

Journal Article↗

PubMedDate not supplied

Dose-dependent kinetics of quinidine in the perfused rat liver preparation. Kinetics of formation of active metabolites.

The disposition of quinidine and the kinetics of metabolite formation were studied in the once-through perfused rat liver preparation by the stepwise increase in quinidine concentration. Dose-dependent kinetics of quinidine were observed; the steady-state hepatic extraction ratio decreased from 0.97 to 0.37 when input quinidine concentration varied from 1.34 to 33.9 micrograms/ml. Moreover, the formation of 3-hydroxyquinidine (detected only in perfusate as unconjugated 3-hydroxyquinidine) remained relatively linear while the formation of O-desmethylquinidine (present in bile and perfusate mostly as conjugates) apparently approached saturation kinetics within the quinidine concentrations used. The dose-dependent character of quinidine elimination cannot be attributed to changes in drug binding, as the blood/plasma ratio (4.07) and the degree of drug unbound in plasma (66.5%) remained unaltered for the quinidine concentrations used.

Animals↗

PubMed1993

Kinetic analysis of the hydrodynamic transition accompanying protein folding using size exclusion chromatography. 2. Comparison of spectral and chromatographic kinetic analyses.

The kinetics of the hydrodynamic volume change associated with the unfolding and refolding of a globular protein can be observed using high performance size exclusion chromatography. Chromatographic profiles that evidence such dynamics can be simulated using equations in which chromatographic partitioning and the conformational transition are described in terms of a finite difference algorithm incorporating an apparent binding model to generate broad and asymmetric peaks. Application of these equations to the simple two-state unfolding transition of ribonuclease A in guanidine hydrochloride indicates that reliable kinetic parameters can be obtained using these equations.

Chromatography, Gel↗

PubMed1978

Kinetics of plasma coagulation and lysis I: Basic kinetic model for time course of coagulation-lysis systems and its potential application to clinical studies.

The time courses of coagulation and coagulation-lysis were spectrophotometrically monitored after the addition of thrombin or thrombin-streptokinase to plasma, diluted 1:5 with normal saline, obtained from normal and presumably abnormal subjects. The kinetics of clotting, after an initial lag period of 0.5-1.5 min, demonstrated essentially first-order dependence on the amount of fibrinogen available to form the clot, and the asymptotic absorbance was independent of thrombin concentration. The rate of clotting was a function of added thrombin, and the ratios of the rate constants at 2.5 and 1.25 units of thrombin/ml of undiluted plasma were 1.65 +/- 0.03 SEM. At early times, the coagulation-lysis curve with thrombin-streptokinase could be superimposed on the clotting curve with thrombin alone for a given plasma with minor compensation for variable lag times. Subsequently, the curves diverged; lysis was monitored by the decrease in absorbance of the coagulation-lysis system. The rate of fibrinolysis increased with streptokinase concentration and was a function of the extent of lysis, and it permitted the description of the kinetics of lysis by a pseudoautocatalytic mechanism where the bimolecular rate constant appears proportional to streptokinase concentration. Ranges of clotting and lytic parameters for the plasma of normal subjects are given, and their potential use in diagnosing abnormalities is described.

Blood Coagulation↗

PubMed1994

Are the steady state kinetics of glutathione transferase always dependent on the deprotonation of the bound glutathione? New insights in the kinetic mechanism of GST P 1-1.

Steady state kinetics measurements performed on human placenta glutathione transferase (GST P 1-1), utilizing 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) as co-substrate, show that the kcat value (approximately equal to 1.2 s-1) is pH-independent between pH 4.0 and 7.0 and is scarcely affected by the nature of the leaving group. The pH profile of kcat/KmNBD-Cl suggests a pKa > or = 6.0 for GSH bound to the enzyme. Pre-steady state experiments demonstrate the presence of a burst-phase in which the conjugation product (or the sigma-complex intermediate) accumulates in an amount stoichiometric to the GST active site concentration. These results indicate that the steady state kinetics of GST P 1-1 with NBD-Cl are independent of the deprotonation of the bound GSH between pH 4.0 and 7.0 because the rate-limiting step is the product release. The occurrence of a fast enzymatic conjugation of GSH with a number of poor substrates or even electrophilic inhibitors of GST, mainly performed in a single turnover reaction, may reveal a further detoxicating role of GST.

4-Chloro-7-nitrobenzofurazan↗

PubMed2000

The kinetic mechanism of the hairpin ribozyme in vivo: influence of RNA helix stability on intracellular cleavage kinetics.

The relationship between hairpin ribozyme structure, and cleavage and ligation kinetics, and equilibria has been characterized extensively under a variety of reaction conditions in vitro. We developed a quantitative assay of hairpin ribozyme cleavage activity in yeast to learn how structure-function relationships defined for RNA enzymes in vitro relate to RNA-mediated reactions in cells. Here, we report the effects of variation in the stability of an essential secondary structure element, H1, on intracellular cleavage kinetics. H1 is the base-paired helix formed between ribozyme and 3' cleavage product RNAs. H1 sequences with fewer than three base-pairs fail to support full activity in vitro or in vivo, arguing against any significant difference in the stability of short RNA helices under in vitro and intracellular conditions. Under standard conditions in vitro that include 10 mM MgCl(2), the internal equilibrium between cleavage and ligation of ribozyme-bound products favors ligation. Consequently, ribozymes with stable H1 sequences display sharply reduced self-cleavage rates, because cleavage is reversed by rapid re-ligation of bound products. In contrast, ribozymes with as many as 26 base-pairs in H1 continue to self-cleave at maximum rates in vivo. The failure of large products to inhibit cleavage could be explained if intracellular conditions promote rapid product dissociation or shift the internal equilibrium to favor cleavage. Model experiments in vitro suggest that the internal equilibrium between cleavage and ligation of bound products is likely to favor cleavage under intracellular ionic conditions.

Base Pairing↗

PubMed1986

Kinetics of circular DNA molecule digestion by restriction endonuclease. Computation of kinetic constants from time dependence of fragment concentrations.

A model for kinetics of circular substrate cleavage by restriction endonuclease was formulated. The aim of the analysis of the model was to extract kinetic constants for all target sites from time-dependence of fragment concentration in reaction products. That was proved to be possible for molecules with an odd number of fragments only. A symmetry of the molecules with an even number of fragment is the cause. A solution for molecules with an odd number of fragments was found and methods for dealing with the other molecules were suggested.

DNA Restriction Enzymes↗

PubMed1977

Steady-state kinetics of electron transfer through cytochrome chain of uncoupled submitochondrial particles. I. General kinetic analysis.

Steady-state kinetics of electron transfer through the cytochrome chain of uncoupled ultrasonic submitochondrial particles at different pH values has been studied. Rate constants calculated from the Pring equation (ki' = V/PirPi+1ox) increased with the increase of the rate of the process. As in the previous work (Saks, V. A., Kupriyanov, V. V. and Luzikov, V. N. (1972) Biochim. Biophys. Acta 283, 42-53) this dependence was linear, but only at comparatively low rates of electron transfer. To explain the experimental data several kinetic models, based on the assumption that respiratory chains are activated when functioning, have been proposed and analysed. The best agreement with the experimental data was obtained for the model suggesting that the rate of activation of the carriers is directly proportional to the overall rate of electron transfer and to the proportion of non-activated respiratory chains in the system. Hence it appeared that electron transfer through already activated chains entailed activation of adjacent non-activated chains. This model allowed rate constants for non-activated (ki) and activated (ki) states of the carriers, as well as the life-time of the activated carriers (tau) to be determined.

Animals↗

PubMed1982

Kinetics of sulfation and glucuronidation of harmol in the perfused rat liver preparation. Disappearance of aberrances in glucuronidation kinetics by inhibition of sulfation.

Harmol is conjugated by glucuronidation and sulfation when it is given to the rat in vivo. In the once-through perfused rat liver preparation glucuronidation of harmol shows kinetic aberrances [Pang et al., J. Pharmac. exp. Ther. 219, 134 (1981)]. In order to further delineate the mechanism behind this, sulfation was inhibited to about 10% of control by 2,6-dichloro-4-nitrophenol. The loss of sulfation was compensated by an increase in the rate of glucuronidation, keeping the total clearance by the liver virtually constant in spite of the loss of sulfation. The inhibition of sulfation eliminated the previously observed lag-phase in the kinetics of glucuronidation; the rate of glucuronidation was now almost linear with the input concentration of the substrate harmol. The constant clearance of harmol in spite of inhibition of sulfation, the occurrence of the lag-phase in glucuronidation in the presence of sulfation, and the disappearance of this lag-phase in the absence of sulfation can be explained by either diffusion-limited metabolism of harmol or a heterogeneous sub-lobular distribution of the sulfating and glucuronidating systems. Activation of glucuronidation by harmol at high concentration can be excluded.

Alkaloids↗

PubMed1983

Adaptation of acyl-enzyme kinetic theory and an experimental method for evaluating the kinetics of fast-acting, irreversible protease inhibitors.

The theory of acyl-enzyme kinetics (Bender, M.L., Kézdy, F.J. and Wedler, F.C. (1967) J. Chem. Educ. 44, 84-88) has been adapted for use in evaluating the kinetics of inhibition of serine proteases by both natural and synthetic irreversible inhibitors. The new theory is based upon formal analysis of the case of an irreversible, active-site-directed inhibitor competing with an irreversible, active-site-directed substrate for the active site of a serine protease. From this theory, an experimentally simple and accurate method is described to obtain a second-order rate constant that is characteristic of the efficiency with which an irreversible inhibitor reacts. The experimental method is particularly useful for characterizing fast-acting, irreversible inhibitors. The theory and method which are applicable to a wide variety of enzymes are verified by analysis of the inhibition of bovine trypsin by three model inhibitors, p-nitrophenyl p'-guanidinobenzoate, soybean trypsin inhibitor and alpha-1-proteinase inhibitor as well as by human antithrombin III in the presence of heparin and by bovine pancreatic trypsin inhibitor.

Kinetics↗

PubMed1989

Kinetic isotope effect and the presteady-state kinetics of the reaction catalyzed by the bacterial formate dehydrogenase.

The primary kinetic isotope effect of the reaction catalyzed by NAD+-dependent formate dehydrogenase (EC 1.2.1.2.) from the methylotrophic bacterium Pseudomonas sp. 101 has been studied. Analysis of the ratios HVm/DVm and H(Vm/KM)/D(Vm/KM) in the pH range 6.1-7.9 showed that the transfer of hydride ion in ternary enzyme-substrate complex is a limiting step of the reaction, and the formate binding to the binary complex (formate dehydrogenase + NAD+) reached equilibrium when the pH of the medium was increased. An approach has been developed to determine the elementary constants of substrate association (kon) and dissociation (koff) at the stages of the binary--ternary enzyme-substrate complexes for the random equilibrium 2-substrate kinetic mechanism. The kon and koff values obtained for the bacterial formate dehydrogenase by using the proposed approach for NAD+ were (4.8 +/- 0.8)*10(5)M-1s-1 and (90 +/- 10) s-1, and for formate (2.0 +/- 1.0)*10(4) M-1s-1 and (60 +/- 20) s-1, respectively.

Aldehyde Oxidoreductases↗

PubMed2004

The kinetic model and simulation of blood coagulation--the kinetic influence of activated protein C.

The paper described a limited part of the coagulation pathway, and in particular the inhibitory effects of activated protein C in the context of thrombin production. This is a computational modeling study with various assumption made of kinetic rates laws and their summation. The level of complexity and assumed parameters makes conclusions uncertain. However, an interesting outcome is that kinetic reaction rates may show oscillation behavior under particular, high levels of protein C feedback inhibition. The model would defy quantitative practical use, but could have predictive value as a qualitative descriptor of coagulation.

Biological Clocks↗

PubMed1988

Kinetic distinction between rapid-equilibrium random and abortive ordered enzymatic mechanisms using alternative substrates or kinetic isotope effects.

Alternative substrates, such as those isotopically-labeled, which differ in their rate constants of catalysis but not in their rate constants of binding, generate identical values of V/Ka in ordered kinetic mechanisms of bireactant enzymes. This is shown to be true even for the rapid-equilibrium ordered mechanism in which an abortive complex between free enzyme and the second substrate is formed. In contrast, rapid-equilibrium random mechanisms have non-identical values for V/Ka. Consequently, the effect of alternative substrates or isotope effects on V/Ka provides a means to distinguish between these nearly identical kinetic mechanisms.

Enzymes↗

PubMed2001

Kinetics of glucose isomerization to fructose by immobilized glucose isomerase: anomeric reactivity of D-glucose in kinetic model.

The substrate specificity of immobilized D-glucose isomerase (EC 5.3. 1.5) is investigated with an immobilized enzyme-packed reactor. A series of isomerization experiments with alpha-, beta-, and equilibrated D-glucose solutions indicates that beta anomer as well as alpha anomer is a substrate of the glucose isomerase at pH 7.5 and 60 degrees C. For substrate concentration of 0.028 mol l(-1) (1% w/v), the initial conversion rate of alpha-D-glucose was 43% higher than that with equilibrated glucose at the same concentration and 113% higher than beta-D-glucose conversion rate. This anomeric reactivity of glucose isomerase is mathematically described with a set of kinetic equations based on the reaction steps complying with Briggs-Haldane mechanism and the experimentally determined kinetic constants. The proposed reaction mechanism includes the mutarotation and the isomerization reactions of alpha- and beta-D-glucose with different rate constants.

Aldose-Ketose Isomerases↗