Modulation of the de novo purine nucleotide pathway as a therapeutic strategy in mitochondrial myopathy.

Mitochondrial myopathy (MM) is characterised by muscle weakness, exercise intolerance and various histopathological changes. Recently, a subset of MM has also been associated with aberrant activation of mammalian target of rapamycin complex 1 (mTORC1) in skeletal muscle. This aberrant mTORC1 activation promotes increased de novo nucleotide synthesis, which contributes to abnormal expansion and imbalance of skeletal muscle deoxyribonucleoside triphosphates (dNTP) pools. However, the exact mechanism via which mTORC1-stimulated de novo nucleotide biosynthesis ultimately disturbs muscle dNTP pools remains unclear. In this article, it is proposed that mTORC1-stimulated de novo nucleotide synthesis in skeletal muscle cells with respiratory chain dysfunction promotes an asymmetric increase of purine nucleotides, probably due to NAD+ deficiency. This in turn could disrupt purine nucleotide-dependent allosteric feedback regulatory mechanisms, ultimately leading to dNTP pools aberration. Pharmacological down-modulation of aminoimidazole carboxamide ribonucleotide transformylase/inosine monophosphate cyclohydrolase (ATIC) activity is also proposed as a potential therapeutic strategy in MM exhibiting mTORC1-driven abnormal metabolic reprogramming, including aberrant dNTPs pools.

Structural Insights into Mycobacterium tuberculosis Rv2671 Protein as a Dihydrofolate Reductase Functional Analogue Contributing to para-Aminosalicylic Acid Resistance.

Mycobacterium tuberculosis (Mtb) Rv2671 is annotated as a 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate (AROPP) reductase (RibD) in the riboflavin biosynthetic pathway. Recently, a strain of Mtb with a mutation in the 5' untranslated region of Rv2671, which resulted in its overexpression, was found to be resistant to dihydrofolate reductase (DHFR) inhibitors including the anti-Mtb drug para-aminosalicylic acid (PAS). In this study, a biochemical analysis of Rv2671 showed that it was able to catalyze the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF), which explained why the overexpression of Rv2671 was sufficient to confer PAS resistance. We solved the structure of Rv2671 in complex with the NADP(+) and tetrahydrofolate (THF), which revealed the structural basis for the DHFR activity. The structures of Rv2671 complexed with two DHFR inhibitors, trimethoprim and trimetrexate, provided additional details of the substrate binding pocket and elucidated the differences between their inhibitory activities. Finally, Rv2671 was unable to catalyze the reduction of AROPP, which indicated that Rv2671 and its closely related orthologues are not involved in riboflavin biosynthesis.

The enzymatic activity of 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase is enhanced by NPM-ALK: new insights in ALK-mediated pathogenesis and the treatment of ALCL.

Anaplastic large cell lymphoma represents a subset of neoplasms caused by translocations that juxtapose the anaplastic lymphoma kinase (ALK) to dimerization partners. The constitutive activation of ALK fusion proteins leads to cellular transformation through a complex signaling network. To elucidate the ALK pathways sustaining lymphomagenesis and tumor maintenance, we analyzed the tyrosine-kinase protein profiles of ALK-positive cell lines using 2 complementary proteomic-based approaches, taking advantage of a specific ALK RNA interference (RNAi) or cell-permeable inhibitors. A well-defined set of ALK-associated tyrosine phosphopeptides, including metabolic enzymes, kinases, ribosomal and cytoskeletal proteins, was identified. Validation studies confirmed that vasodilator-stimulated phosphoprotein and 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine monophosphate cyclohydrolase (ATIC) associated with nucleophosmin (NPM)-ALK, and their phosphorylation required ALK activity. ATIC phosphorylation was documented in cell lines and primary tumors carrying ALK proteins and other tyrosine kinases, including TPR-Met and wild type c-Met. Functional analyses revealed that ALK-mediated ATIC phosphorylation enhanced its enzymatic activity, dampening the methotrexate-mediated transformylase activity inhibition. These findings demonstrate that proteomic approaches in well-controlled experimental settings allow the definition of informative proteomic profiles and the discovery of novel ALK downstream players that contribute to the maintenance of the neoplastic phenotype. Prediction of tumor responses to methotrexate may justify specific molecular-based chemotherapy.

Identification of ATIC as a Novel Target for Chemoradiosensitization.

PURPOSE: Mutations in the gene encoding 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC), a bifunctional enzyme that catalyzes the final 2 steps of the purine de novo biosynthetic pathway, were identified in a subject referred for radiation sensitivity testing. Functional studies were performed to determine whether ATIC inhibition was radiosensitizing and, if so, to elucidate the mechanism of this effect and determine whether small molecule inhibitors of ATIC could act as effective radiosensitizing agents. METHODS AND MATERIALS: Both small interfering RNA knockdown and small molecule inhibitors were used to inactivate ATIC in cell culture. Clonogenic survival assays, the neutral comet assay, and γH2AX staining were used to assess the effects of ATIC inhibition or depletion on cellular DNA damage responses. RESULTS: Depletion of ATIC or inhibition of its transformylase activity significantly reduced the surviving fraction of cells in clonogenic survival assays in multiple cancer cell lines. In the absence of ionizing radiation exposure, ATIC knockdown or chemical inhibition activated cell cycle checkpoints, shifting cells to the more radiosensitive G2/M phase of the cell cycle, and depleted cellular adenosine triphosphate but did not result in detectable DNA damage. Cells in which ATIC was knocked down or inhibited and then treated with ionizing radiation displayed increased numbers of DNA double-strand breaks and a delay in the repair of those breaks relative to irradiated, but otherwise untreated, controls. Supplementation of culture media with exogenous adenosine triphosphate ameliorated the DNA repair phenotypes. CONCLUSIONS: These findings implicate ATIC as an effective, and previously unrecognized, target for chemoradiosensitization and, more broadly, suggest that purine levels in cells might have an underappreciated role in modulating the efficiency of DNA damage responses that could be exploited in radiosensitizing strategies.

Characterization of a novel AICARFT inhibitor which potently elevates ZMP and has anti-tumor activity in murine models.

AICARFT is a folate dependent catalytic site within the ATIC gene, part of the purine biosynthetic pathway, a pathway frequently upregulated in cancers. LSN3213128 is a potent (16 nM) anti-folate inhibitor of AICARFT and selective relative to TS, SHMT1, MTHFD1, MTHFD2 and MTHFD2L. Increases in ZMP, accompanied by activation of AMPK and cell growth inhibition, were observed with treatment of LY3213128. These effects on ZMP and proliferation were dependent on folate levels. In human breast MDA-MB-231met2 and lung NCI-H460 cell lines, growth inhibition was rescued by hypoxanthine, but not in the A9 murine cell line which is deficient in purine salvage. In athymic nude mice, LSN3213128 robustly elevates ZMP in MDA-MB-231met2, NCI-H460 and A9 tumors in a time and dose dependent manner. Significant tumor growth inhibition in human breast MDA-MB231met2 and lung NCI-H460 xenografts and in the syngeneic A9 tumor model were observed with oral administration of LSN3213128. Strikingly, AMPK appeared activated within the tumors and did not change even at high levels of intratumoral ZMP after weeks of dosing. These results support the evaluation of LSN3213128 as an antineoplastic agent.

Methotrexate enhances the antianabolic and antiproliferative effects of 5-aminoimidazole-4-carboxamide riboside.

Because of its ability to mimic a low energy status of the cell, the cell-permeable nucleoside 5-aminoimidazole-4-carboxamide (AICA) riboside was proposed as an antineoplastic agent switching off major energy-consuming processes associated with the malignant phenotype (lipid production, DNA synthesis, cell proliferation, cell migration, etc.). Key to the antineoplastic action of AICA riboside is its conversion to ZMP, an AMP mimetic that at high concentrations activates the AMP-activated protein kinase (AMPK). Here, in an attempt to increase the efficacy of AICA riboside, we pretreated cancer cells with methotrexate, an antimetabolite blocking the metabolism of ZMP. Methotrexate enhanced the AICA riboside-induced accumulation of ZMP and led to a decrease in the levels of ATP, which functions as an intrasteric inhibitor of AMPK. Consequently, methotrexate markedly sensitized AMPK for activation by AICA riboside and potentiated the inhibitory effects of AICA riboside on tumor-associated processes. As cotreatment elicited antiproliferative effects already at concentrations of compounds that were only marginally effective when used alone, our findings on the cooperation between methotrexate and AICA riboside provide new opportunities both for the application of classic antimetabolic chemotherapeutics, such as methotrexate, and for the exploitation of the energy-sensing machinery as a target for cancer intervention.

A kinetic study of the inhibition of yeast AMP deaminase by polyphosphate.

Inorganic pyrophosphate and polyphosphates have acted as potent inhibitors of purified AMP deaminase (EC 3.5.4.6) from yeast: the activity fell to a definite limit with the increase in the concentration of the inhibitor. The effect of polyphosphate was largely on the maximal velocity of the enzyme with some decrease in affinity. The cooperative effect of AMP, analyzed in terms of a Hill coefficient, remained at 2 in the absence and presence of polyphosphate. Binding of polyphosphate to the enzyme showed no cooperativity. The inhibition of AMP deaminase by polyphosphate can be qualitatively and quantitatively accounted for by the partial mixed-type inhibition mechanism. Both the Ki value for the inhibitor and the breakdown rate of the enzyme-substrate-inhibitor complex are dependent on the chain length of polyphosphate, suggesting that the breakdown rate of the enzyme-substrate-inhibitor complex is regulated by binding of polyphosphate to a specific inhibitory site.

Negative homotropic cooperativity in rat muscle AMP deaminase. A kinetic study on the inhibition of the enzyme by ATP.

1. Rat skeletal muscle AMP deaminase (AMP aminohydrolase, EC 3.5.4.6) at optimal KCl concentrations shows a biphasic response to increasing levels of the allosteric inhibitor ATP. 2. Up to 10 micrometer, ATP appears to convert the enzyme to a form exhibiting sigmoidal kinetics while at higher concentrations its inhibitory effect is manifested by an alteration of AMP binding to AMP deaminase indicative of negative homotropic cooperativity at about 50% saturation. 3. AMP deaminase is inactivated by incubation with the periodate oxidation product of ATP. The (oxidized ATP)--AMP deaminase complex stabilized by NaBH4 reduction shows kinetic properties similar to those of the native enzyme in the presence of high ATP concentrations. 4. A plausible explanation of the observed cooperativity is that ATP induces different conformational state of AMP deaminase subunits, causing the substrate to follow a sequential mechanism of binding to enzyme. 5. Binding of the radioactive oxidized ATP shows that 3.2 mol of this reagent bind per mol AMP deaminase.

Specific modification of the GTP binding sites of rat 5'-adenylic acid aminohydrolase by periodate-oxidized GTP.

1. Rat skeletal muscle AMP deaminase (AMP aminohydrolase, EC3.5.4.6) can be inactivated by incubation with the periodate-oxidized analogue of the enzyme inhibitor GTP. 2. Nucleoside triphosphates and KCl at high concentrations protect against inactivation, while ADP has no effect. 3. The inactivation can be reversed by the addition of GTP and amino acids and made irreversible by reduction with NaBH4. This indicates that, in the binding of the oxidized GTP to the enzyme, a Schiff base is formed between the aldehyde groups of the inhibitor and amino groups of the enzyme. 4. The kinetic properties of the reduced (oxidized GTP)-AMP deaminase derivative indicate that the loss of activity results from an increase in Km while no appreciable change in V is observed; consequently, the enzyme shows positive homotropic cooperativity even in the presence of optimal KCl concentration. 5. Since the treated enzyme shows kinetic properties similar to those of the native enzyme in the presence of GTP, and since the loss of sensitivity to GTP is directly proportional to the degree of inactivation, it is concluded that the oxidized GTP specifically modifies the binding sites for GTP. 6. Binding of the radioactive oxidized GTP shows that two binding sites for this reagent exist in the AMP deaminase molecule.

In vitro and in situ studies on the inhibition of yeast AMP deaminase by fatty acids.

The effect of various fatty acids on the purified and in situ AMP deaminase (AMP aminohydrolase, EC 3.5.4.6) was investigated: both the purified AMP deaminase and the permeabilized system of yeast cells were used as the enzyme sources. (1) All the saturated fatty acids, longer than 10 in the hydrocarbon chain, were inhibitors of the purified enzyme in the absence of ATP, whereas no or little inhibition of the enzyme was observed in the presence of ATP. Unsaturated fatty acids acted as more potent inhibitors of the purified enzyme, although the addition of ATP increased the I0.5 values for these fatty acids. Fatty acids acted as non-competitive inhibitors without alteration of the affinity for the substrate in the absence and presence of ATP. (2) Unsaturated fatty acids showed a powerful inhibition of the in situ AMP deaminase, and the presence of ATP could scarcely affect the inhibition of the in situ enzyme by these fatty acids. On the other hand, no or little inhibition of the in situ enzyme by saturated fatty acids was observed in the absence and presence of ATP. The difference in the kinetics properties between the in situ and the purified enzyme suggests that there is difference in protein interactions for AMP deaminase in situ and in vitro.

Inhibition of chicken erythrocyte AMP deaminase by tetraiodofluorescein compounds.

A kinetic study has been performed on the inhibition of the chicken erythrocyte AMP deaminase (AMP aminohydrolase, EC 3.5.4.6) reaction by tetraiodofluorescein and Rose Bengal. These dyes inhibited the enzyme by decreasing its affinity for the substrate without affecting the maximum velocity. Kinetic analysis has shown the inhibition constants for tetraiodofluorescein and Rose Bengal to be 350 and 55 micrometer, respectively, and the presence of 4 binding sites of the enzyme for the inhibitors per enzyme molecule. These results suggest that the fluorescein dyes mimic the AMP binding at the catalytic center of the enzyme, which can be formed by the "dinucleotide fold".

AMPK Activation via Modulation of De Novo Purine Biosynthesis with an Inhibitor of ATIC Homodimerization.

5-Aminoimidazole-4-carboxamide ribonucleotide (known as ZMP) is a metabolite produced in de novo purine biosynthesis and histidine biosynthesis, but only utilized in the cell by a homodimeric bifunctional enzyme (called ATIC) that catalyzes the last two steps of de novo purine biosynthesis. ZMP is known to act as an allosteric activator of the cellular energy sensor adenosine monophosphate-activated protein kinase (AMPK), when exogenously administered as the corresponding cell-permeable ribonucleoside. Here, we demonstrate that endogenous ZMP, produced by the aforementioned metabolic pathways, is also capable of activating AMPK. Using an inhibitor of ATIC homodimerization to block the ninth step of de novo purine biosynthesis, we demonstrate that the subsequent increase in endogenous ZMP activates AMPK and its downstream signaling pathways. We go on to illustrate the viability of using this approach to AMPK activation as a therapeutic strategy with an in vivo mouse model for metabolic disorders.

Design of substrate-site-directed irreversible inhibitors of adenosine 5'-phosphate aminohydrolase. Effect of substrate substituents on affinity for the substrate site.

Derivatives of adenosine 5'-phosphate (AMP) have been synthesized in which the phosphoester (POCH2) grouping of AMP is replaced by PCH(R)CH2 where R is OC(O)Me, CH2NHCOMe, CH2NHCOEt, and CH2NHCOOR' (R' = Me, Et, and Pr). The 2',3'-O-isopropylidene and 2', 3'-di-O-acetyl derivatives of AMP were also prepared. All compounds were competitive inhibitors of rabbit muscle AMP aminohydrolase with enzyme-inhibitor dissociation constants (Ki values) of 330, 20, 17, 19, 16, 14, 260, and 105 muM, respectively. All compounds were substrates except those in which R was CH2NHCOEt and CH2NHCOOR' (R'=Me, Et, and Pr). The previously described allo and talo epimers of 5'-C-acetylaminomethyl-AMP and the allo epimer of 5'-C-propionylaminomethyl-AMP were substrates and competitive inhibitors with Ki values of 18, 47, and 42 muM, respectively. The talo epimer of 5'-C-propionylaminomethyl-AMP was not a substrate and was a noncompetitive inhibitor, Ki

Modulation of deoxynucleotide metabolism by the deoxycytidylate deaminase inhibitor 3,4,5,6-tetrahydrodeoxyuridine.

Tetrahydrodeoxyuridine (dTHU) inhibits deoxycytidine deaminase and, after intracellular phosphorylation to the active 5'-monophosphate, also inhibits deoxycytidylate deaminase (dCMPD). Because in vitro studies have shown that dCMPD may regulate pyrimidine deoxynucleotide metabolism, the objective of this study was to investigate the effects of dTHU on deoxynucleotide metabolism in whole cells. Nearly complete inhibition of dCMPD, measured in intact CCRF-CEM cells by incorporation of [14C]dCyd into dTTP, occurred after a 45-min incubation with 100 microM dTHU. This was accompanied by an 8-fold dCTP pool expansion, although dATP, dTTP, dGTP, and ribonucleoside triphosphate pools were unaffected. Tetrahydrouridine, which inhibits deoxycytidine deaminase exclusively, had no effect on nucleotide pools. The dCTP pool expansion was directly proportional to the dTHU concentration (3-100 microM) and reached a maximum after 2 hr. Inhibition of ribonucleotide reductase by hydroxyurea completely prevented the dTHU-induced dCTP pool expansion, indicating that the substrate of dCMPD was derived from the ribonucleotide pool and that CDP was the predominant precursor of dCTP. dTHU-mediated inhibition of dCMPD appeared reversible. Exposure of cells to 100 microM dTHU followed by washing into fresh medium resulted in a linear decrease of the dCTP pool and an increase in the dTTP pool. The increased dCTP concentration after preincubation with dTHU was associated with an inhibition of deoxycytidine kinase, as indicated by a reduced capacity of cells to phosphorylate ara-C. dTHU is a useful new tool for investigating the role of dCMPD in the regulation of deoxynucleotide metabolism in whole cells.

Theophylline effect on the cyclic AMP degrading multienzyme sequence.

Membrane-bound 3'.5'-cyclic nucleotide phosphodiesterase (EC 3.1.4.17) is closely associated physically with nucleotidase and deaminase, thus forming an enzyme cluster of unique catalytic behaviour [H. Wombacher, Archs. Biochem. Biophys. 201, 8 (1980)]. This multienzyme cluster, which was found in the microsomal fraction of beef adrenal cortex, catalyses the degradation of cyclic AMP, via AMP and adenosine, to inosine. The present study shows how theophylline, a well-known inhibitor of the phosphodiesterase, acts on the membrane-bound multienzyme sequence. The findings were as follows. Firstly, as expected, theophylline inhibited the phosphodiesterase competitively. In particular, the high-affinity enzyme was inhibited by mM concentrations of theophylline. Phosphodiesterase activity was tentatively ascribed to two enzymes, one with a low Km [0.3 microM], one with a high Km [60 microM]. Secondly, theophylline inhibited the nucleotidase activity to a great extent. A detailed kinetic analysis showed the inhibition to be hyperbolic noncompetitive (alpha = 1, beta = 0.35 and Ki = 0.25 mM). Thirdly, theophylline did not inhibit the deaminase activity of the multienzyme sequence. A model of theophylline inhibition is suggested explaining how an effector could modulate the kinetic behaviour of an enzyme cluster by acting at a single allosteric site. Finally, in view of the existence of the cyclic AMP degrading multienzyme sequence and the effect of theophylline on it, the possibility is discussed that physiologically active adenosine is derived from cyclic AMP.

Probing the infra-structure of thymidylate synthase and deoxycytidylate deaminase.

Methods are described for preparing and structurally analyzing two enzymes involved in the formation of dTMP, deoxycytidylate deaminase and thymidylate synthase. In the latter case, it has been possible through the use of recombinant DNA techniques with an amplification plasmid to obtain sufficient amounts of the E. coli and T4-phage synthases to complete the entire sequence of both enzymes by employing a combination of protein and DNA sequencing methods. A comparative analysis of the L. casei and E. coli synthases has revealed a 62% conservation of sequences but an even greater homology in their hydrophobic active site regions (82%), which are primarily hydrophobic in nature. The homology between these enzymes becomes apparent by deleting a 51 amino acid segment (residues 89-139) from the L. casei synthase, which accounts for the difference in size between these enzymes. Methods for obtaining the binding sites of both substrates are described, one being the activation of the carboxyls of folate with a water soluble carbodiimide and the other, the activation of dUMP by ultraviolet light. The DNA and protein sequence of the T4-phage synthase has recently been clarified by us and is in preparation. Of great interest is the finding by Purohit and Mathews (42), based on our sequence data for the synthase, that the gene segment for the carboxyl terminal end of dihydrofolate reductase overlaps with the amino end of the gene for thymidylate synthase. The complete amino acid sequence of T2-phage deoxycytidylate deaminase has been elucidated by conventional protein sequencing methods. The binding characteristics of this enzyme for its positive allosteric effectors and substrates, as determined by equilibrium dialysis, are consistent with the cooperative nature of its kinetic responses. Consistent with these findings was the demonstration that each of the enzyme's six subunits bound an equivalent amount of substrate or allosteric modifier. Similarly the deaminase showed a marked negative change in ellipticity at 280 nm in response to increasing concentrations of dCTP, changes which could be reversed by dTTP. From the information on the enzyme's primary sequence, it should be possible to define the substrate and allosteric binding regions within the deaminase with the appropriately activated compounds. A start in this direction has been initiated by the finding that dTTP is rapidly and apparently covalently fixed to the amino terminal cyanogen bromide peptide of the enzyme in the presence of ultraviolet light.

Inhibition by alanine of AMP-deaminase from rabbit skeletal muscle.

1. Alanine inhibits rabbit muscle AMP-deaminase while aspartate, histidine and glutamate are ineffective. 2. The degree and type of inhibition of AMP-deaminase by alanine depend on pH; at pH 6.5 alanine behaves like an allosteric effector exerting a negative heterotropic effect. At pH 7.0 the inhibition is non-competitive, Ki being as high as 19 mM. 3. The probable significance of the effect of alanine on AMP-deaminase in muscle metabolism is discussed.