Inhibition of Trypanosoma cruzi α-Hydroxyacid Dehydrogenase-isozyme II by N-Isopropyl Oxamate and its Effect on Intact Epimastigotes

The effect of N-isopropyl oxamate on the activity of α-hydroxyacid dehydrogenase-isozyme II (HADH-isozyme II) from Trypanosoma cruzi was investigated. The kinetic studies showed that this substance was a competitive inhibitor of this isozyme. The attachment of the nonpolar isopropylic branched chain to the nitrogen of oxamate increased 12-fold the affinity of N-isopropyl oxamate for the active site of T. cruzi HADH-isozyme II. N-isopropyl oxamate was a selective inhibitor of HADH-isozyme II, since other T. cruzi dehydrogenases were not inhibited by this substance. Since HADH-isozyme II participates in the energy metabolism of T. cruzi, a trypanocidal effect can be expected with inhibitors of this isozyme. However, although it was not possible to detect any trypanocidal activity with N-isopropyl oxamate when the ethyl ester was tested as a possible trypanocidal prodrug, the expected trypanocidal effect was obtained, comparable to that obtained with nifurtimox and benznidazole.     

Differences and similarities in binding of pyruvate and l-lactate in the active site of M4 and H4 isoforms of human lactate dehydrogenase

We present QM/MM calculations that show differences in geometries of active sites of M₄ and H₄ isoforms of human LDH ligated with oxamate, pyruvate or l-lactate. As the consequence of these differences, binding isotope effects of the methyl hydrogen atoms of pyruvate and l-lactate may be used to experimentally distinguish these isoforms. Based on the FEP calculations we argue that l-lactate is a better candidate for the experimental studies. Our calculations of energies of interactions of ligands with the active site residues provide explanation for the observed experimentally sensitivity to inhibition of the M₄ isoenzyme isoform and pinpoint the differences to interactions of the ligand with the histidine residue. We conclude that pyruvate interacts much stronger in the active site of H₄ than M₄ isoform and that the latter interactions are weaker than with water molecules in the aqueous solution.     

Differences and similarities in binding of pyruvate and L-lactate in the active site of M4 and H4 isoforms of human lactate dehydrogenase

We present QM/MM calculations that show differences in geometries of active sites of M(4) and H(4) isoforms of human LDH ligated with oxamate, pyruvate or L-lactate. As the consequence of these differences, binding isotope effects of the methyl hydrogen atoms of pyruvate and l-lactate may be used to experimentally distinguish these isoforms. Based on the FEP calculations we argue that L-lactate is a better candidate for the experimental studies. Our calculations of energies of interactions of ligands with the active site residues provide explanation for the observed experimentally sensitivity to inhibition of the M(4) isoenzyme isoform and pinpoint the differences to interactions of the ligand with the histidine residue. We conclude that pyruvate interacts much stronger in the active site of H(4) than M(4) isoform and that the latter interactions are weaker than with water molecules in the aqueous solution.     

Inhibition of Trypanosoma cruzi alpha-hydroxyacid dehydrogenase-isozyme II by N-isopropyl oxamate and its effect on intact epimastigotes

The effect of N-isopropyl oxamate on the activity of alpha-hydroxyacid dehydrogenase-isozyme II (HADH-isozyme II) from Trypanosoma cruzi was investigated. The kinetic studies showed that this substance was a competitive inhibitor of this isozyme. The attachment of the nonpolar isopropylic branched chain to the nitrogen of oxamate increased 12-fold the affinity of N-isopropyl oxamate for the active site of T. cruzi HADH-isozyme II. N-isopropyl oxamate was a selective inhibitor of HADH-isozyme II, since other T. cruzi dehydrogenases were not inhibited by this substance. Since HADH-isozyme II participates in the energy metabolism of T. cruzi, a trypanocidal effect can be expected with inhibitors of this isozyme. However, although it was not possible to detect any trypanocidal activity with N-isopropyl oxamate when the ethyl ester was tested as a possible trypanocidal prodrug, the expected trypanocidal effect was obtained, comparable to that obtained with nifurtimox and benznidazole.     

A strain of desulfovibrio able to use oxamate

Summary Strain Monticello 2, a variant of Desulfovibrio desulfuricans, was isolated from an environment associated with Streptococcus allantoicus, which converts allantoin to oxamate. The strain grew with oxamate or oxalate, as well with more conventional substrates for Des. desulfuricans; yeast extract was essential for growth with oxamate, but not for growth with lactate. A cell-free extract formed oxalate quantitatively from oxamate but not from oxamide; it formed a hydroxamate in the presence of hydroxylamine. Unequivocal amidase or transferase activity towards acetamide was not observed. Frozen and thawed organisms decomposed oxalate but a soluble oxalic decarboxylase was not obtained; such preparations did not require ATP; they formed traces of formate from oxalate. The proposition that oxamate is an incomplete substrate of ecological value to this strain is discussed.     

35-Cl nuclear magnetic resonance studies of anion-binding sites in proteins: lactate dehydrogenase.

³⁵Cl nmr relaxation rate measurements have been used to study anion-binding sites in pig heart lactate dehydrogenase. These studies reveal two types of sites, one is intimately associated with the active site, the other is not. The nonactive site has been ascribed to a subunit site in analogy with crystallographic results from the dogfish M₄ enzyme. The binding of either the reduced or the oxidized form of NAD results in an increase in the ³⁵Cl nmr relaxation rate by a factor of 1.8–2. The enhanced nmr relaxation rate of the binary lactate dehydrogenase-NAD complex is reduced on binding of the substrate inhibitor molecules oxamate or oxalate to a value less than that exhibited by lactate dehydrogenase alone. The enhancement of the nmr relaxation rate is attributed to a decrease in the dissociation constant of Cl for the enzyme. The K_p values for Cl binding to the active center site of lactate dehydrogenase is 0.85 m and for lactate dehydrogenase-NADH is 0.25 m. The ratio of these constants, 3.4, agrees well with the measured enhancement value 3.7. The effect of coenzyme analogs on the ³⁵Cl nmr relaxation rate has been examined. 3-Acetylpyridine NAD produces an enhancement of 4.3, thionicotinamide NAD of 2.3, whereas 3-pyridinealdehyde, adenosinediphosphoribose, and adenosine diphosphate do not affect the nmr relaxation state of Cl bound to lactate dehydrogenase.     

On the pathway of forming enzymatically productive ligand-protein complexes in lactate dehydrogenase

We have carried out a series of studies on the binding of a substrate mimic to the enzyme lactate dehydrogenase (LDH) using advanced kinetic approaches, which begin to provide a molecular picture of the dynamics of ligand binding for this protein. Binding proceeds via a binding-competent subpopulation of the nonligated form of the protein (the LDH/NADH binary complex) to form a protein-ligand encounter complex. The work here describes the collapse of the encounter complex to form the catalytically competent Michaelis complex. Isotope-edited static Fourier transform infrared studies on the bound oxamate protein complex reveal two kinds of oxamate environments: 1), a major populated structure wherein all significant hydrogen-bonding patterns are formed at the active site between protein and bound ligand necessary for the catalytically productive Michaelis complex and 2), a minor structure in a configuration of the active site that is unfavorable to carry out catalyzed chemistry. This latter structure likely simulates a dead-end complex in the reaction mixture. Temperature jump isotope-edited transient infrared studies on the binding of oxamate with LDH/NADH suggest that the evolution of the encounter complex between LDH/NADH and oxamate collapses via a branched reaction pathway to form the major and minor bound species. The production of the catalytically competent protein-substrate complex has strong similarities to kinetic pathways found in two-state protein folding processes. Once the encounter complex is formed between LDH/NADH and substrate, the ternary protein-ligand complex appears to “fold” to form a compact productive complex in an all or nothing like fashion with all the important molecular interactions coming together at the same time.     

Lactate dehydrogenase-catalyzed stereospecific hydrogen atom transfer from reduced nicotinamide adenine dinucleotide to dicarboxylate radicals.

The dicarboxylate radical -OOC--CH--CH(OH)COO- was generated in an N2O-saturated fumarate solution by high energy ionizing radiation. When NADH was present in the solution, product analysis indicated a stoichiometry of 2 molecules of the radical reacted with 1 NADH molecule to form 2 malate and 1 enzymatically active NAD+ molecules. In a similar experiment using tritium label on position A of NADH, due to an isotope effect, only 10% of the label was transferred to malate; most of the remaining tritium was found in the NAD+ formed. When lactate dehydrogenase was added, however, no la bel was detectable in NAD+, and over 80% of the tritium lost from NADH was found in malate. The stereospecific transfer of the hydrogen atom from lactate dehydrogenase-bound NADH to the dicarboxylate radical suggested that the free radical reaction must have taken place at the active site. The hydrogen atom transfer was inhibited by oxamate. Results from flow experiments in which an irradiated fumarate solution was mixed with a solutionof lactate dehydrogenase and NADH are in support of a mechanism in which the hydrogen atom transfer occurs in the first oxidation step.     

Intrapopulation variation in carbon and nitrogen stable isotope ratios in the earthworm Aporrectodea longa

The natural abundance variations in carbon and nitrogen stable isotope ratios in a population of the earthworm Aporrectodea longa, a species known to feed on both soil and plant litter, is reported in this paper. Worms were collected from a small land area of an old white clover field and body tissue and mucus were analyzed separately. The range of isotopic values was small, but patterns of variation were not random. Tissue carbon and nitrogen isotope ratios were significantly higher in adult than in juvenile A. longa and tissue nitrogen isotope ratios tended to increase with increasing biomass of individuals. Further, carbon and nitrogen isotope ratios were positively correlated in both tissue and mucus. Possible causes of the observed patterns, including physiological effects, body composition and assimilation of C and N from different plant, soil and microbial sources are discussed. It is concluded that the causes of natural variability in isotopic composition must be understood and validated experimentally before natural abundance stable isotope methods can be used for the analysis of trophic relations among detritivorous soil invertebrates.     

Substrate binding and activation in the active site of cytochrome <Emphasis Type="Italic">c</Emphasis> nitrite reductase: a density functional study

Cytochrome c nitrite reductase is a homodimeric enzyme, containing five covalently attached c-type hemes per subunit. Four of the heme irons are bishistidine-ligated, whereas the fifth, the active site of the protein, has an unusual lysine coordination and calcium site nearby. A fascinating feature of this enzyme is that the full six-electron reduction of the nitrite is achieved without release of any detectable reaction intermediate. Moreover, the enzyme is known to work over a wide pH range. Both findings suggest a unique flexibility of the active site in the complicated six-electron, seven-proton reduction process. In the present work, we employed density functional theory to study the energetics and kinetics of the initial stages of nitrite reduction. The possible role of second-sphere active-site amino acids as proton donors was investigated by taking different possible protonation states and geometrical conformations into account. It was found that the most probable proton donor is His₂₇₇, whose spatial orientation and fine-tuned acidity lead to energetically feasible, low-barrier protonation reactions. However, substrate protonation may also be accomplished by Arg₁₁₄. The calculated barriers for this pathway are only slightly higher than the experimentally determined value of 15.2 kcal/mol for the rate-limiting step. Hence, having proton-donating side chains of different acidity within the active site may increase the operational pH range of the enzyme. Interestingly, Tyr₂₁₈, which was proposed to play an important role in the overall mechanism, appears not to take part in the reaction during the initial stage.     

An assessment of the reproductive biology of the Marico barb Barbus motebensis from the upper Groot Marico catchment,South Africa

Temporal changes in fatty acid composition and δ¹⁵N, δ¹³C stable isotope values of the phytobenthos growing on artificial clay substrates under natural conditions over a 28-day period at an upstream and a downstream site in the Kowie River near Grahamstown were investigated in 2012. High concentrations of diatom markers 16:1ω7 and 20:5ω3 fatty acids were recorded, especially at the downstream site, reflecting the importance of diatoms in contributing to the phytobenthos communities at that station. After day 7 at the downstream site the average δ¹⁵N value of the phytobenthos was lighter, gradually increasing by ～2‰ and ～5‰ overall to heavier values on day 28. At the upstream site there were no significant changes (<1‰ increase) in δ¹⁵N values of the phytobenthos over time. Stable nitrogen (δ¹⁵N) and carbon (δ¹³C) signatures in the phytobenthos communities were significantly different between sites (one-way ANOVA; p < 0.001). The stable isotope values and fatty acid concentrations of phytobenthos at the downstream site were different to those of the phytobenthos at the upstream site, and they changed concurrently with changes in the phytobenthos community structure. At the downstream site there was a strong correlation of the δ¹⁵N of phytobenthos with nitrates (R = 0.56) and time (weeks; R = 0.81). However, the fatty acids were not specific enough to characterise the composition of phytobenthos communities. Other biomarker methods, such as stable isotopes and microscopic examination of the communities, were found to be useful. The results from this relatively small-scale tile experiment indicate the complexity of changes in fatty acid composition and δ¹⁵N, δ¹³C stable isotope values of a phytobenthos community. Stable isotope and fatty acid composition can be successfully used to map changes in phytobenthos composition and carbon and nitrogen flow patterns along a river continuum.     

The conserved active site tryptophan of thioredoxin has no effect on its redox properties

In Staphylococcus aureus thioredoxin (Trx) it has been shown that mutation of the conserved active site tryptophan residue (Trp28) has a large effect on the protein stability, on the pKa of the nucleophilic cysteine and on the redox potential. Since these effects can either be due to the partially unfolding of the Trp28Ala mutant or to the absence of the indole side chain of Trp28 as possible interaction partner for the active site cysteines, the origin of the experimentally observed effects is not known and is beyond experimental approach. With theoretical pKa and density functional theory reactivity analysis on model systems where Trp28 has been replaced by an alanine within the structural environment of Trx it is shown that Trp28 does not affect the redox parameters of Trx. As such, the experimentally observed redox effects of the Trx W28A mutant might be due to structural changes induced by partial unfolding.     

Decarboxylation of oxalacetate by pyruvate carboxylase

The decarboxylation of oxalacetate by pyruvate carboxylase in the absence of ADP and Pi is stimulated 400-fold by the presence of oxamate, which is an inhibitory analogue of pyruvate. The observation of substrate inhibition when either oxamate or oxalacetate is varied at a fixed concentration of the other indicates that both molecules bind at the same site on the enzyme. The pH profiles for this reaction show no evidence of the involvement of an enzymic acid-base catalyst, suggesting that the proton and CO2 units may be exchanged directly between the reactants (although CO2 sequestered in the active site may be an intermediate in the process). The pH profiles of the full reverse reaction of pyruvate carboxylase in which oxalacetate decarboxylation is coupled to ATP formation and where Pi is the variable substrate do, however, indicate that such an acid-base catalyst is involved in the other partial reaction of the enzyme in proton transfer to and from biotin. The enzyme also displays two oxamate-independent oxalacetate decarboxylating activities, one of which is biotin-dependent and the other is independent of biotin.     

Quantum chemical modeling of the kinetic isotope effect of the carboxylation step in RuBisCO

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most important enzyme for the assimilation of carbon into biomass, features a well-known isotope effect with regards to the CO₂ carbon atom. This kinetic isotope effect α = k ₁₂/k ₁₃ for the carboxylation step of the RuBisCO reaction sequence, and its microscopic origin, was investigated with the help of cluster models and quantum chemical methods [B3LYP/6-31G(d,p)]. We use a recently proposed model for the RuBisCO active site, in which a water molecule remains close to the reaction center during carboxylation of ribulose-1,5-bisphosphate [B. Kannappan, J.E. Gready, J. Am. Chem. Soc. 130 (2008), 15063]. Alternative active-site models and/or computational approaches were also tested. An isotope effect alpha for carboxylation is found, which is reasonably close to the one measured for the overall reaction, and which originates from a simple frequency shift of the bending vibration of ¹²CO₂ compared to ¹³CO₂. The latter is the dominant mode for the product formation at the transition state.     

H-tunneling in the multiple H-transfers of the catalytic cycle of morphinone reductase and in the reductive half-reaction of the homologous pentaerythritol tetranitrate reductase

The mechanism of flavin reduction in morphinone reductase (MR) and pentaerythritol tetranitrate (PETN) reductase, and flavin oxidation in MR, has been studied by stopped-flow and steady-state kinetic methods. The temperature dependence of the primary kinetic isotope effect for flavin reduction in MR and PETN reductase by nicotinamide coenzyme indicates that quantum mechanical tunneling plays a major role in hydride transfer. In PETN reductase, the kinetic isotope effect (KIE) is essentially independent of temperature in the experimentally accessible range, contrasting with strongly temperature-dependent reaction rates, consistent with a tunneling mechanism from the vibrational ground state of the reactive C-H/D bond. In MR, both the reaction rates and the KIE are dependent on temperature, and analysis using the Eyring equation suggests that hydride transfer has a major tunneling component, which, unlike PETN reductase, is gated by thermally induced vibrations in the protein. The oxidative half-reaction of MR is fully rate-limiting in steady-state turnover with the substrate 2-cyclohexenone and NADH at saturating concentrations. The KIE for hydride transfer from reduced flavin to the alpha/beta unsaturated bond of 2-cyclohexenone is independent of temperature, contrasting with strongly temperature-dependent reaction rates, again consistent with ground-state tunneling. A large solvent isotope effect (SIE) accompanies the oxidative half-reaction, which is also independent of temperature in the experimentally accessible range. Double isotope effects indicate that hydride transfer from the flavin N5 atom to 2-cyclohexenone, and the protonation of 2-cyclohexenone, are concerted and both the temperature-independent KIE and SIE suggest that this reaction also proceeds by ground-state quantum tunneling. Our results demonstrate the importance of quantum tunneling in the reduction of flavins by nicotinamide coenzymes. This is the first observation of (i) three H-nuclei in an enzymic reaction being transferred by tunneling and (ii) the utilization of both passive and active dynamics within the same native enzyme.     

FTIR spectroelectrochemical study of the activation and inactivation processes of [NiFe] hydrogenases: effects of solvent isotope replacement and site-directed mutagenesis

The kinetics of the activation and anaerobic inactivation processes of Desulfovibrio gigas hydrogenase have been measured in D₂O by FTIR spectroelectrochemistry. A primary kinetic solvent isotope effect was observed for the inactivation process but not for the activation step. The kinetics of these processes have been also measured after replacement of a glutamic residue placed near the active site of an analogous [NiFe] hydrogenase from Desulfovibrio fructosovorans. Its replacement by a glutamine affected greatly the kinetics of the inactivation process but only slightly the activation process. The interpretation of the experimental results is that the rate-limiting step for anaerobic inactivation is the formation from water of a -OH^– bridge at the hydrogenase active site, and that Glu25 has a role in this step.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0559-7     

Synergistic Anti-Cancer Effect of Phenformin and Oxamate

Phenformin (phenethylbiguanide; an anti-diabetic agent) plus oxamate [lactate dehydrogenase (LDH) inhibitor] was tested as a potential anti-cancer therapeutic combination. In in vitro studies, phenformin was more potent than metformin, another biguanide, recently recognized to have anti-cancer effects, in promoting cancer cell death in the range of 25 times to 15 million times in various cancer cell lines. The anti-cancer effect of phenformin was related to complex I inhibition in the mitochondria and subsequent overproduction of reactive oxygen species (ROS). Addition of oxamate inhibited LDH activity and lactate production by cells, which is a major side effect of biguanides, and induced more rapid cancer cell death by decreasing ATP production and accelerating ROS production. Phenformin plus oxamate was more effective than phenformin combined with LDH knockdown. In a syngeneic mouse model, phenformin with oxamate increased tumor apoptosis, reduced tumor size and ¹⁸F-fluorodeoxyglucose (FDG) uptake on positron emission tomography/computed tomography compared to control. We conclude that phenformin is more cytotoxic towards cancer cells than metformin. Furthermore, phenformin and oxamate have synergistic anti-cancer effects through simultaneous inhibition of complex I in the mitochondria and LDH in the cytosol, respectively.     

H4-isozyme of lactate dehydrogenase in a solution of sodium C chloride--6. The effect of oxalate and oxamate on the molecular weight

Some differences between the effects of oxalate and oxamate were observed. The oxalate formed the stable tetramers and some aggregates, while the oxamate formed the mixture of dimers, tetramers, octamers and aggregates. The ratios between these molecular forms were different as the oxamate concentration was changed. In the coexistence of inhibitors and pyruvate, pyruvate may act to decrease the molecular weight and to increase the amount of aggregates. The lower molecular weight may be caused by the existence of the active complex, Ed N S1. The effect of the exchange between pyruvate and oxamate bound with enzyme complexes may be expected.     

Stable‐hydrogen isotope turnover in red blood cells of two migratory thrushes: application to studies of connectivity and carry‐over effects

ABSTRACT Understanding turnover rates of stable isotopes in metabolically active tissues is critical for making spatial connections for migratory birds because samples provide information about pre‐migratory location only until the tissue turns over to reflect local values. We calculated stable‐hydrogen isotope (δ²H) turnover rate in the red blood cells of two long‐distance migratory songbirds, Bicknell's Thrushes (Catharus bicknelli) and Swainson's Thrushes (Catharus ustulatus), using samples collected at a breeding site in New Brunswick, Canada. Blood from both species captured early in the breeding site was more positive in δ²H than blood sampled later in the summer, but did not match blood values for wintering Bicknell's Thrushes. An asymptotic exponential model was used to estimate turnover of red blood cell δ²H and yielded a half‐life estimate of 21 days and 14 days for Bicknell's and Swainson's thrushes, respectively. Red blood cells of both species approached the local breeding site value one month after the first individuals were detected at the site. For Bicknell's Thrushes, estimated δ²H in blood at arrival (?72‰) was closer to blood collected at wintering sites (mean ?61‰) than to expected breeding site δ²H (?120‰). Discrimination values calculated for red blood cells collected at the breeding site for both species were greater than expected based on studies using keratin. Turnover during migration currently limits the use of blood sampled early in the breeding season for connectivity/carry‐over effect studies. However, direct tracking technology such as geolocators can provide information about migration duration, timing, and stopovers that can be used to improve isotopic turnover equations for metabolically active tissues.