Acetyl Coenzyme†A Analogues as Rationally Designed Inhibitors of Citrate Synthase.

In this study, we probed the inhibition of pig heart citrate synthase (E.C. 4.1.3.7) by synthesising seven analogues either designed to mimic the proposed enolate intermediate in this enzyme reaction or developed from historical inhibitors. The most potent inhibitor was fluorovinyl thioether 9 (Ki =4.3 µm), in which a fluorine replaces the oxygen atom of the enolate. A comparison of the potency of 9 with that of its non-fluorinated vinyl thioether analogue 10 (Ki =68.3 µm) revealed a clear "fluorine effect" favouring 9 by an order of magnitude. The dethia analogues of 9 and 10 proved to be poor inhibitors. A methyl sulfoxide analogue was a moderate inhibitor (Ki =11.1 µm), thus suggesting hydrogen bonding interactions in the enolate site. Finally, E and Z propenoate thioether isomers were explored as conformationally constrained carboxylates, but these were not inhibitors. All compounds were prepared by the synthesis of the appropriate pantetheinyl diol and then assembly of the coenzyme A structure according to a three-enzyme biotransformation protocol. A quantum mechanical study, modelling both inhibitors 9 and 10 into the active site indicated short CF⋅⋅⋅H contacts of ≈2.0 Å, consistent with fluorine making two stabilising hydrogen bonds, and mimicking an enolate rather than an enol intermediate. Computation also indicated that binding of 9 to citrate synthase increases the basicity of a key aspartic acid carboxylate, which becomes protonated.

Acetyl-CoA production by encapsulated pyruvate ferredoxin oxidoreductase in alginate hydrogels.

Pyruvate ferredoxin oxidoreductase from Citrobacter sp. S-77 (PFORS77) was purified in order to develop a method for acetyl-CoA production. Although the purified PFORS77 showed high O2-sensitivity, the activity could be remarkably stabilized in anaerobic conditions. PFORS77 was effectively immobilized on ceramic hydroxyapatite (PFORS77-HA) with an efficiency of more than 96%, however, after encapsulation of PFORS77-HA in alginate, the rate of catalytic acetyl-CoA production was highly reduced to 36% when compared to that of the free enzyme. However, the operational stability of the PFORS77-HA in alginate hydrogels was remarkable, retaining over 68% initial activity even after ten repeated cycles. The results suggested that the PFORS77-HA hydrogels have a high potential for biotechnological application.

Bisubstrate inhibition: Theory and application to N-acetyltransferases.

Bisubstrate inhibitors represent a potentially powerful group of compounds that have found significant therapeutic utility. Although these compounds have been synthesized and tested against a number of enzymes that catalyze sequential bireactant reactions, the detailed theory for predicting the expected patterns of inhibition against the two substrates for various bireactant kinetic mechanisms has, heretofore, not been presented. We have derived the rate equations for all likely sequential bireactant mechanisms and provide two examples in which bisubstrate inhibitors allow the kinetic mechanism to be determined. Bisubstrate inhibitor kinetics is a powerful diagnostic for the determination of kinetic mechanisms.

The importance of the amide bond nearest the thiol group in enzymatic reactions of coenzyme A.

Analogues of coenzyme A (CoA) and of CoA thioesters have been prepared in which the amide bond nearest the thiol group has been modified. An analogue of acetyl-CoA in which this amide bond is replaced with an ester linkage was a good substrate for the enzymes carnitine acetyltransferase, chloramphenicol acetyltransferase, and citrate synthase, with K(m) values 2- to 8-fold higher than those of acetyl-CoA and V(max) values from 14 to >80% those of the natural substrate. An analogue in which an extra methylene group was inserted between the amide bond and the thiol group showed less than 4-fold diminished binding to the three enzymes but exhibited less than 1% activity relative to acetyl-CoA with carnitine acetyltransferase and no measurable activity with the other two enzymes. Analogues of several CoA thioesters in which the amide bond was replaced with a hemithioacetal linkage exhibited no measurable activity with the appropriate enzymes. The results indicate that some aspects of the amide bond and proper distance between this amide and the thiol/thioester moiety are critical for activity of CoA ester-utilizing enzymes.

Effect of Zn on acetyl coenzyme a synthase: evidence for a conformational change in the alpha subunit during catalysis.

Acetyl coenzyme A synthase (ACS) is an alpha2beta2 tetramer in which the active-site A-cluster, located in the alpha subunits, consists of an Fe4S4 cubane bridged to a {Nip Nid} binuclear site. The alpha subunits exist in two conformations. In the open conformation, Nip is surface-exposed, while the proximal metal is buried in the closed conformation. Nip is labile and can be replaced by Cu. In this study, the effects of Zn are reported. ACS in which Zn replaced Nip was inactive and did not exhibit the so-called NiFeC EPR signal nor the ability to accept a methyl group from the corrinoid-iron-sulfur protein (CoFeSP). Once Zn-bound, it could not be replaced by subsequently adding Ni. The Zn-bound A-cluster cannot be reduced and bound with CO or become methylated, probably because Zn (like Cu) is insufficiently nucleophilic for these functions. Unexpectedly, Zn replaced Nip only while ACS was engaged in catalysis. Under these conditions, replacement occurred with kapp approximately 0.6 min-1. Replacement was blocked by including EDTA in the assay mix. Zn appears to replace Nip when ACS is in an intermediate state (or states) of catalysis but this(these) state(s) must not be present when ACS is reduced in CO alone, or in the presence of CoA, CoFeSP, or reduced methyl viologen. Nip appears susceptible to Zn-attack when the alpha subunit is in the open conformation and protected from attack when it is in the closed conformation. This is the first evidence that the structurally-characterized conformations of the alpha subunit change during catalysis, indicating a mechanistic role for this conformational change.

3-hydroxy-3-methylglutaryl-coenzyme A synthase reaction intermediates: detection of a covalent tetrahedral adduct by differential isotope shift 13C nuclear magnetic resonance spectroscopy.

Binding of [1,2-(13)C]acetyl-CoA to wild-type 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) synthase is characterized by large upfield shifts for C1 (184 ppm, Deltadelta = 20 ppm) and C2 (26 ppm, Deltadelta = 7 ppm) resonances that are attributable to formation of the covalent [1,2 -(13)C]acetyl-S-enzyme reaction intermediate. NMR spectra of [1, 2-(13)C]acetyl-S-enzyme prepared in H(2)(16)O versus H(2)(18)O indicate a 0.055 ppm upfield shift of the C1 resonance in the presence of the heavier isotope. The magnitude of this (18)O-induced (13)C shift suggests that the 184 ppm resonance is attributable to a reaction intermediate in which C1 exhibits substantial carbonyl character. No significant shift of the C2 resonance occurs. These observations suggest that, in the absence of second substrate (acetoacetyl-CoA), enzymatic addition of H(2)(18)O to the C1 carbonyl of acetyl-S-enzyme occurs to transiently produce a tetrahedral species. This tetrahedral adduct exchanges oxygen upon backward collapse to re-form the sp(2)-hybridized thioester carbonyl. In contrast with HMG-CoA synthase, C378G Zoogloea ramigera beta-ketothiolase, which also forms a (13)C NMR-observable covalent acetyl-enzyme species, exhibits no (18)O-induced shift. Formation of the [(13)C]acetyl-S-enzyme reaction intermediate of HMG-CoA synthase in D(2)O versus H(2)O is characterized by a time-dependent isotope-induced upfield shift of the C1 resonance (maximal shift = 0. 185 ppm) in the presence of the heavier isotope. A more modest upfield shift (0.080 ppm) is observed for C378G Z. ramigera beta-ketothiolase in similar experiments. The slow kinetics for the development of the deuterium-induced (13)C shift in the HMG-CoA synthase experiments suggest a specific interaction (hydrogen bond) with a slowly exchangeable proton (deuteron) of a side chain/backbone of an amino acid residue at the active site.

Synthesis of O-[11C]Acetyl CoA, O-[11C]Acetyl-L-carnitine, and L-[11C]carnitine labelled in specific positions, applied in PET studies on rhesus monkey.

The syntheses of L-carnitine, O-acetyl CoA, and O-acetyl-L-carnitine labelled with 11C at the 1- or 2-position of the acetyl group or the N-methyl position of carnitine, using the enzymes acetyl CoA synthetase and carnitine acetyltransferase, are described. With a total synthesis time of 45 min, O-[1-11C]acetyl CoA and O-[2[11C]acetyl CoA was obtained in 60-70% decay-corrected radiochemical yield, and O-[1-11C]acetyl-L-carnitine and O-[2-11C] acetyl-L-carnitine in 70-80% yield, based on [1-11C]acetate or [2-11C]acetate, respectively. By an N-methylation reaction with [11C]methyl iodide, L-[methyl-11C]carnitine was obtained within 30 min, and O-acetyl-L-[methyl-11C]carnitine within 40 min, giving a decay-corrected radiochemical yield of 60% and 40-50%, respectively, based on [11C]methyl iodide. Initial data of the kinetics of the different 11C-labelled L-carnitine and acetyl-L-carnitines in renal cortex of anaesthetized monkey (Macaca mulatta) are presented.

alpha-Fluoro acid and alpha-fluoro amide analogs of acetyl-CoA as inhibitors of citrate synthase: effect of pKa matching on binding affinity and hydrogen bond length.

An alpha-fluoro acid analog and an alpha-fluoro amide analog of acetyl-CoA have been synthesized. The ternary complexes of these inhibitors with oxaloacetate and citrate synthase have been crystallized and their structures analyzed at 1.7 A resolution. The structures are similar to those reported for the corresponding non-fluorinated analogs (Usher et al., 1994), with all forming unusually short hydrogen bonds to Asp 375. The alpha-fluoro amide analog binds with an affinity 1.5-fold lower than that of a previously described amide analog lacking the alpha-fluoro group. The alpha-fluoro acid analog binds with a 50-fold decreased affinity relative to the corresponding unfluorinated analog. The binding affinities are consistent with increased strengths of hydrogen bonds to Asp 375 with closer matching of pKa values between hydrogen bond donors and acceptors. The results do not support any direct correlation between hydrogen bond strength and hydrogen bond length in enzyme-inhibitor complexes.

Efficient synthesis of radiolabeled propionyl-coenzyme A and acetyl-coenzyme A.

The efficient microscale synthesis of [1-14C]propionyl-CoA from commercially available sodium [1-14C]-propionate using 1,1'-carbonyldiimidazole in yields of nearly 70% is reported for the first time. A substantial improvement in the process for making [1-14C]acetyl-CoA from sodium [1-14C]acetate was also achieved. Yields of greater than 90% were consistently obtained for the latter synthesis. The salt-free CoA-thioesters were obtained in homogenous form by reverse-phase HPLC. The products were judged to be pure by 1H NMR analysis: neither iso-CoA analogs nor contaminants frequently found in commercial samples could be detected. The samples of acetyl- and propionyl-CoA were shown to be radiochemically pure by HPLC and by analysis of the products of incubations with acetyl- and propionyl-CoA carboxylase. This highly efficient synthesis is a cost-effective method for the preparation of radiolabeled CoA thioesters and can easily be adapted to the production of other acyl-CoA analogs.

Synthesis of radiolabeled acetyl-coenzyme A from sodium acetate.

The synthesis of high specific radioactivity [14C]-acetyl-Coenzyme A from [14C]sodium acetate, 2,6-dichlorobenzoic acid, 1,1'-carbonyldiimidazole, and CoA is reported. Starting with 1 mumol of [14C]sodium acetate, this method yields pure [14C]acetyl-CoA in yields approaching 40%. Chromatography on a reversed-phase ODS column was used to separate acetyl-CoA from Coenzyme A and side products. The acetylating agent is apparently a reaction intermediate, acetylimidazole.

Differential inhibition of histone and polyamine acetylases by multisubstrate analogues.

Mammalian cells contain a number of enzymes catalyzing the acetylation of polyamines and histones including an inducible spermidine/spermine N1-acetyltransferase which may play a key role in regulating the interconversion of polyamines [Matsui, I., Wiegand, L., & Pegg, A. E. (1981) J. Biol. Chem. 256, 2454-2459]. The present experiments were carried out in order to provide a method to distinguish this enzyme from other polyamine/histone acetylases and to test whether specific inhibitors of its activity could be obtained. Rabbit antiserum to homogeneous rat liver spermidine/spermine N1-acetyltransferase had no effect on the activity of a crude nuclear extract from rat liver, indicating that its spermidine acetylating capability is not related to the cytosolic spermidine/spermine N1-acetyltransferase induced by hepatotoxins. Potential multisubstrate analogues were prepared by attaching various polyamines to coenzyme A via an acetic acid linkage and tested as potential inhibitors of the acetylation of spermidine and histones. There was little difference in the potency of these polyamine derivatives as inhibitors of histone or spermidine acetylation by the crude nuclear extracts which appeared to contain at least two such activities, one inhibited completely by 20-30 microM and the other amounting to 50% of the total being unaffected by 100 microM. Spermidine/spermine N1-acetyltransferase was also inhibited by all the derivatives, but the potency toward this enzyme differed widely. The derivative from sym-norspermidine was a very strong inhibitor, giving 50% inhibition at 0.3 microM, and was more than 1 order of magnitude more active than the others.(ABSTRACT TRUNCATED AT 250 WORDS)

Preparation of bromo[1-14C]acetyl-coenzyme A as an affinity label for acetyl-coenzyme A binding sites.

Bromo[1-14C]acetyl-CoA has been prepared from CoASH and the N-hydroxysuccinimide ester of bromo[1-14C]acetic acid, and unlabeled bromoacetyl-CoA by reaction of CoASH with bromoacetyl bromide. The products were purified by high-pressure liquid chromatography. Purified bromoacetyl-CoA was characterized, and found to be a potent alkylating agent with a substantial stability in aqueous solution: it decomposed at 30 degrees C and pH 6.6 and 8.0 with halftimes of 3.3 and 2.5 h, respectively. The major breakdown products were CoASH and CoAS X CO X CH2 X SCoA. Bromo[1-14C]acetyl-CoA has been used to affinity label the acetyl-CoA binding site of 3-hydroxy-3-methylglutaryl-CoA synthase from ox liver. It was found to irreversibly inhibit the enzyme activity and bind covalently with a stoichiometry for complete inhibition of about 0.8 mol/mol enzyme dimer.