Reaction mechanism of aspartate transcarbamylase from mouse spleen

Novel Highlight in Malarial Drug Discovery: Aspartate Transcarbamoylase

Malaria remains one of the most prominent and dangerous tropical diseases. While artemisinin and analogs have been used as first-line drugs for the past decades, due to the high mutational rate and rapid adaptation to the environment of the parasite, it remains urgent to develop new antimalarials. The pyrimidine biosynthesis pathway plays an important role in cell growth and proliferation. Unlike human host cells, the malarial parasite lacks a functional pyrimidine salvage pathway, meaning that RNA and DNA synthesis is highly dependent on the de novo synthesis pathway. Thus, direct or indirect blockage of the pyrimidine biosynthesis pathway can be lethal to the parasite. Aspartate transcarbamoylase (ATCase), catalyzes the second step of the pyrimidine biosynthesis pathway, the condensation of L-aspartate and carbamoyl phosphate to form N-carbamoyl aspartate and inorganic phosphate, and has been demonstrated to be a promising target both for anti-malaria and anti-cancer drug development. This is highlighted by the discovery that at least one of the targets of Torin2 – a potent, yet unselective, antimalarial – is the activity of the parasite transcarbamoylase. Additionally, the recent discovery of an allosteric pocket of the human homology raises the intriguing possibility of species selective ATCase inhibitors. We recently exploited the available crystal structures of the malarial aspartate transcarbamoylase to perform a fragment-based screening to identify hits. In this review, we summarize studies on the structure of Plasmodium falciparum ATCase by focusing on an allosteric pocket that supports the catalytic mechanisms.

Inhibitors of de novo nucleotide biosynthesis as drugs

Potent inhibitors of enzymes catalyzing reactions in the de novo pathways for biosynthesis of purine and pyrimidine nucleotides are synthetic or natural-product analogues of pathway intermediates or, more recently, inhibitors rationally designed from a knowledge of the catalytic mechanism. Such inhibitors may be effective drugs against cancer, inflammatory disorders, or various infections. For human cancer, the purine pathway may be a better target for inhibition than the pyrimidine pathway, where toxic side effects are more apparent. Drugs such as methotrexate and 6-mercaptopurine have multiple sites of action, making it difficult to quantitatively predict their effects upon cells. Rational design of inhibitors based upon the X-ray structure of the target enzyme has the prospect of yielding drugs with only one site of action in human cells. Such a drug is VX-497, a potent inhibitor of the purine enzyme, IMP dehydrogenase.

Molecular cloning, recombinant expression and partial characterization of the aspartate transcarbamoylase from Toxoplasma gondii

A cDNA coding for a monofunctional aspartate transcarbamoylase (ATCase) was isolated from a Toxoplasma gondii tachyzoite cDNA library using a complementation method. The calculated molecular mass of the deduced amino acid sequence was 46.8 kDa, with a predicted pI of 7.1. Size exclusion chromatography/laser-light scattering showed a single, monodisperse peak with molecular mass of 144 kDa. Amino acid sequence alignments revealed that active site residues of the Escherichia coli ATCase catalytic chain were conserved in the T. gondii sequence, and the latter shared 26-33% overall sequence identity with other ATCases. A recombinant enzyme was overexpressed in E. coli, and was purified with a yield of approximately 0.8 mg l(-1) culture. The temperature dependence of the recombinant enzyme was similar to that of native ATCase in T. gondii extracts. The K(m)'s for aspartate and carbamoyl phosphate were 7.82 mM, and 67.6 microM, respectively. The V(max) was 23900 micromol h(-1) mg(-1). Pyrimidine nucleotides had no significant effect on the enzyme's activity. N-phosphonoacetyl-L-aspartate (PALA) inhibited the enzyme with K(i)=0.38 microM. The T. gondii ATCases contained two additional sequences of approximately 24 residues each, which are not found in other ATCases. One of these sequences was susceptible to proteolysis by elastase.

The role of low-dose PALA in biochemical modulation

Phosphonacetyl-L-aspartate (PALA) is a rationally-synthesized analog of the transition-state intermediate in the formation of carbamyl aspartate from carbamyl phosphate and aspartic acid by aspartate carbamyl transferase (ACTase). PALA is thus a potent inhibitor of the enzyme (Ki about 10(-8) M for ACTases of various origins), which in whole cells blocks the de novo synthesis of pyrimidines. In vivo, low doses of PALA inhibit whole body pyrimidine synthesis. While this action is cytotoxic in vitro, extensive human testing demonstrates that PALA alone is devoid of selective antitumor activity. Recent interest in the therapeutic action of PALA derives from the demonstration that its action potentiates the cytotoxicity of several cytotoxic drugs, notably 5-fluorouracil (5-FU). Results from clinical trials of PALA and 5-FU in combination in colorectal cancer suggest that biochemical modulation with regimens which follow the principles determined in preclinical studies may enhance the efficacy of current therapy.

Metabolism and action of amino acid analog anti-cancer agents

The preclinical pharmacology, antitumor activity and toxicity of seven of the more important amino acid analogs, with antineoplastic activity, is discussed in this review. Three of these compounds are antagonists of L-glutamine: acivicin, DON and azaserine; and two are analogs of L-aspartic acid: PALA and L-alanosine. All five of these antimetabolites interrupt cellular nucleotide synthesis and thereby halt the formation of DNA and/or RNA in the tumor cell. The remaining two compounds, buthionine sulfoximine and difluoromethylornithine, are inhibitors of glutathione and polyamine synthesis, respectively, with limited intrinsic antitumor activity; however, because of their powerful biochemical actions and their low systemic toxicities, they are being evaluated as chemotherapeutic adjuncts to or modulators of other more toxic antineoplastic agents.

Partial characterisation of aspartate transcarbamylase from the mantle of the mussel Mytilus edulis

The stability and the effect of pH and temperature on the activity of aspartate transcarbamylase from mantle of mussel were studied. The Km values for aspartic acid and carbamylphosphate at 35 degrees C are 1.8 X 10(-2) M and 7 X 10(-3) M respectively, values of Vmax being identical at 17.54 nM carbamylaspartate formed/min/mg protein. Allosteric effectors of ATCase (ATP and CTP) have no effect on the activity of mantle ATCase. PHMB and Cu2+ are strong inhibitors of the ATCase activity, organic solvents (DMF, DMSO) having a strong stimulatory action. ATCase from mantle of mussel has been compared to ATCase from different sources.

Binding of radiolabeled N-(phosphonacetyl)-L-aspartate to aspartate transcarbamylase from Ehrlich ascites tumor cells

Binding of N-(phosphonacetyl)-[3H]L-aspartate (PALA) to aspartate transcarbamylase (ATCase, EC 2.1.3.1) in crude extracts from Ehrlich ascites tumor cells was examined. At pH 7.4, the dissociation constant was 1.39 +/- 0.22 nM; the maximal binding capacity indicated an average intracellular ATCase concentration of 0.13 microM. The presence of phosphate, MgCl2, or CaCl2 increased the apparent dissociation constant for [3H]PALA without altering the maximal binding capacity. Phosphate, a product of the ATCase reaction, probably acts as a competitor for the PALA binding site; Mg2+ and Ca2+ may inhibit [3H]PALA binding by forming a chelate which reduces the effective concentration of the free [3H]PALA. Carbamyl phosphate was a relatively weak inhibitor of [3H]PALA binding in N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES) buffer alone. Addition of NaF, an inhibitor of nonspecific phosphatases, decreased the carbamyl phosphate "Ki" as an inhibitor of [3H]PALA binding to 7 microM, a value close to the Km. NaF appears to act as an inhibitor of carbamyl phosphatase activity present in the cell extract. A first-order dissociation rate constant of 0.050 +/- 0.004 min-1 (T1/2 = 14 min) was determined by following displacement of [3H]PALA with excess unlabeled PALA. The dissociation rate was strongly temperature dependent. A second-order rate constant of 3.6 X 10(7) liters mol-1 min-1 was calculated from this rate constant and the dissociation constant. Using these kinetic constants, a simple computer model predicted that PALA binding to ATCase is 95% complete within 14 min under the conditions of the assay; at intracellular ATCase concentrations, binding is slightly faster. These results are discussed in the context of both the kinetics of inhibition and the reversal of inhibition of pyrimidine synthesis within the intact cell.

Metabolic resistance: the protection of enzymes against drugs which are tight-binding inhibitors by the accumulation of substrate

Blockade of a metabolic pathway by interaction of a drug with a particular 'target enzyme' results in depletion of essential end-products of the pathway and accumulation of intermediates prior to the blockade. Metabolic resistance to a particular drug can arise if the substrate of the inhibited enzyme accumulates to levels sufficiently high to compete effectively with the inhibitor, leading to restoration of full activity of the metabolic pathway after a transitory delay. Such resistance has recently been demonstrated in vitro for the interaction of the tight-binding inhibitor N-phosphonacetyl-L-aspartate (PAcAsp) with the aspartate transcarbamoylase activity of the trifunctional protein which initiates pyrimidine biosynthesis in mammals [Christopherson, R. I. and Jones, M. E. (1980) J. Biol. Chem. 255, 11381-11395]. Carbamoyl phosphate, the product of the carbamoyl phosphate synthetase activity of this trifunctional protein, accumulates to a sufficiently high concentration that the inhibitory effect of PAcAsp is effectively abolished. We have developed a theoretical model for metabolic resistance which quantitatively accounts for these experimental data. This model has been used to simulate the interaction between the following potential or proven anti-cancer drugs and their target enzyme, under conditions similar to those which would occur in vivo: PAcAsp with aspartate transcarbamoylase; various OMP analogues [the 5'-monophosphates of 6-azauridine, pyrazofurin and 1-(beta-D-ribofuranosyl)-barbituric acid] with OMP decarboxylase; 5-fluorodeoxyUMP with thymidylate synthase; methotrexate with dihydrofolate reductase; and deoxycoformycin with adenosine deaminase.

Enzymes of the de novo pyrimidine biosynthetic pathway in Toxoplasma gondii

All six enzymes of the de novo biosynthetic pathway leading to the biosynthesis of UMP have been characterized in Toxoplasma gondii. The first three enzymes of the pathway, carbamyl phosphate synthetase-II (CPS-II), aspartate transcarbamylase (ATCase) and dihydroorotase (DHOase) could be consistently separated by sucrose gradient centrifugation. Their molecular weights were estimated to be approximately 540 000, 140 000 and 70 000, respectively. The last two enzymes, orotate phosphoribosyltransferase (OPRTase) and orotidylate decarboxylase (ODCase), cosedimented at the same position, corresponding also to a molecular weight of approximately 70 000. The fourth enzyme, dihydroorotate dehydrogenase (DHO-DHase), was associated with the particulate fraction. Apparent Km values for the respective enzymes were: CPS-II, MgATP2- (19.7 1.2 mM), L-glutamine (12.0 +/- 1.7 microM), ammonia (15.5 +/- 2.7 mM); ATCase, carbamyl phosphate (26.2 +/- 3.5 microM), L-aspartate (17.6 +/- 8.5 mM); DHOase (reverse direction) dihydroorotate (1.6 +/- 0.08 microM); ODCase, orotidine 5'-monophosphate (0.41 +/- 0.04 microM). MgUTP2- was found to act as an inhibitor of CPS-II, with an apparent Ki of 0.41 mM. However, 5-phospho-alpha-D-ribosyl-1-diphosphate, dimethyl sulphoxide and glycerol had no effect on the Km value for MgATP2-. The effect of some inhibitors, including pyrimidine and purine nucleotides and analogs and respiratory chain inhibitors, was also determined for the enzymes of the pathway.

Enzymes of de novo pyrimidine biosynthesis in Babesia rodhaini

The pathway of de novo pyrimidine biosynthesis in the rodent parasitic protozoa Babesia rodhaini has been investigated. Specific activities of five of the six enzymes of the pathway were determined: aspartate transcarbamylase (ATCase: E.C. 2.1.3.2); dihydroorotase (DHOase: E.C. 3.5.2.3); dihydroorotate dehydrogenase (DHO-DHase: E.C. 1.3.3.1); orotate phosphoribosyltransferase (OPRTase: E.C. 2.4.2.10); and orotidine-5'-phosphate decarboxylase (ODCase: E.C. 4.1.1.23). Michaelis constants for ATCase, DHO-DHase, OPRTase, and ODCase were determined in whole homogenates. Several substrate analogs were also investigated as inhibitors and inhibitor constants determined. N-(phosphonacetyl)-L-aspartate was shown to be an inhibitor of the ATCase with an apparent Ki of 7 microM. Dihydro-5-azaorotate inhibited the DHO-DHase (Ki, 16 microM) and 5-azaorotate (Ki, 21 microM) was an inhibitor of the OPRTase. The UMP analog, 6-aza-UMP (Ki, 0.3 microM) was a potent inhibitor of ODCase, while lower levels of inhibition were found with the product, UMP (Ki, 120 microM) and the purine nucleotide, XMP (Ki, 95 microM). Additionally, menoctone, a ubiquinone analog, was shown to inhibit DHO-DHase.

Aspartate carbamoyltransferase activity, drug concentrations, and pyrimidine nucleotides in tissue from patients treated with N-(phosphonacetyl)-L-aspartate

Biopsy specimens were obtained from patients treated with N-(phosphonacetyl)-L-aspartate (PALA) in a phase I clinical trial. Activities of aspartate carbamoyltransferase (ACTase), the target enzyme, in ten specimens before treatment varied from 0.4 to 1.7 units/mg. PALA was measured in protein-free extracts of thirteen specimens by inhibition of rat ACTase. At 1.5 to 145 hr after doses of 1 to 6 g/m2, PALA concentrations were 0.9 to 89 micrograms/g; at 4 hr or later the tissue concentrations were similar to those in plasma (five samples). The observed inhibition of ACTase (17-87%) correlated with the PALA concentrations. Pyrimidine nucleotides were decreased (relative to purine nucleotides) in nine to ten specimens, by 16-72%. ACTase partially purified from human spleen had a Km for carbamoyl phosphate of 20.6 microM and the Ki for PALA was 0.011 microM. The results suggest that inhibition of ACTase by PALA affects the concentration of pyrimidine nucleotides in human tumors in a dose-dependent manner.

Effects of acivicin and PALA, singly and in combination, on de novo pyrimidine biosynthesis

The inhibitory activities of two oncolytic amino acid analogs, acivicin and N-(phosphonacetyl)-L-aspartate, on pyrimidine biosynthesis have been examined in a murine tumor line, the Lewis lung carcinoma. Acivicin, an antimetabolite elaborated by Streptomyces sviceus, inhibits a spectrum of L-glutamine utilizing enzymes including carbamoyl phosphate synthetase II, the inaugurating enzyme of de novo pyrimidine biosynthesis. Profound inhibition of carbamoyl phosphate synthetase II activity by acivicin is demonstrated in vitro as well as in vivo. N-(Phosphonacetyl)-L-aspartate, a rationally-designed transition-state analog of the reaction catalyzed by L-aspartate transcarbamylase, the second enzyme of the pathway, is a potent and specific inhibitor of L-aspartate transcarbamylase. Both agents, at therapeutic doses, exert marked inhibitions of their respective target enzymes and impede flux through the pathway as monitored by inhibition of pyrazofurin-provoked accumulation of orotate and orotidine. Additionally, synergistic effects are observed when acivicin and N-(phosphonacetyl)-L-aspartate are used in combination, both in terms of biochemical and therapeutic endpoints. The salient features of the actions of these drugs on pyrimidine biosynthesis in the Lewis lung carcinoma are summarized in Table 6. Comparison of the effects of acivicin with those of N-(phosphonacetyl)-L-aspartate suggest divergent actions on nucleotide biosynthesis. In spite of its pronounced sensitivity to acivicin, carbamoyl phosphate synthetase II appears not to be a critical target for the antineoplastic activity of this drug.

Mass spectrometric technique for the determination of N-phosphonoacetyl-L-aspartic acid in serum

N-Phosphonoacetyl-L-aspartic acid (PALA), a potent inhibitor of aspartic acid transcarbamylase, is now undergoing Phase I clinical trials. Initial experiments revealed that PALA is not metabolized to phosphonoacetic acid (PAA) in humans. Thus PALA may be quantified in serum after in vitro conversion to PAA. Serum is deproteinized with perchloric acid, lipid extracted with methylene chloride, hydrolyzed with 8 N hydrochloric acid at 100 degrees for 3 h, and evaporated to dryness with nitrogen. The residue is silylated, and PAA is quantified by monitoring the (M + 1)+ ions of the protonated molecular ions of trimethylsilyl derivatives of PAA and phosphonopropionic acid (internal standard) obtained in chemical ionization with methane. Limit of detection is 0.5 microM (150 ng/ml) PALA using 1 ml serum. PALA was given by continuous infusion to cancer patients at various doses. Maximum levels of PALA (50-500 microM range) were obtained at the end of infusion, followed in most cases by biexponential decay. Persistent residual PALA levels (5 microM for 48 h after infusion) correlated with increased toxicity.

A facile enzymatic technique for the estimation of nanomolar concentrations of N-phosphonacetyl-L-aspartic acid in plasma

A sensitive radiometric enzyme-inhibition assay is described for the determination of N-phosphonacetyl-L aspartic acid (PALA, NSC-224,131) in plasma. The assay is based on the inhibition of PALA, at low concentrations of the competitive co-substrate carbamyl phosphate, of L-aspartate transcarbamylase prepared from mouse spleen. The assay responds with good reproducibility and in a proportional way to concentrations of PALA over the range of 2-20 nM; as such, it represents a 100-fold increase in sensitivity over existing methodologies. The applicability and pertinence of this assay to long-term pharmacokinetic studies with PALA is demonstrated by the one month persistence of nanomolar concentrations of PALA in the plasma of mice treated with a single dose of the drug.

Kinetic consequences of a slow substrate binding step in group transferases. Interpretation of product inhibition experiments

The steady state kinetic properties of a simple model for an enzyme catalyzed group transfer reaction between two substrates have been calculated. One substrate is assumed to bind slowly and the other rapidly to the enzyme. Apparent substrate inhibition or substrate activation by the rapidly binding substrate may result if the slowly binding substrate binds at unequal rates to the free enzyme and to the complex between the enzyme and the rapidly binding substrate. Competitive inhibition by each product with respect to its structurally analogous substrate is to be expected if both substrates are in rapid equilibrium with their enzyme-substrate complexes. This product inhibition pattern, however, may also be observed when one substrate binds slowly. Noncompetitive inhibition with respect to the rapidly binding substrate by its structurally analogous product may result if the slowly binding substrate binds more slowly to the enzyme-product complex than to the free enzyme. Inhibition by substrate analogs which are not products should follow the same rules as inhibition by products. Thus substrate analog inhibition experiments are not particularly informative. The form of inhibition by "transition state analog" inhibitors should reveal which substrate binds slowly. There is no sharp conceptual distinction between ordered and random "kinetic mechanisms". I therefore suggest that the use of these concepts should be abandoned.