Reactivity of intermediates in benzoylformate decarboxylase: avoiding the path to destruction

Competing Protonation and Halide Elimination as a Probe of the Character of Thiamin-Derived Reactive Intermediates

Decarboxylation reactions from comparable thiamin diphosphate- and thiamin-derived adducts of p-(halomethyl)benzoylformic acids in enzymic and non-enzymic reactions, respectively, reveal critical distinctions in otherwise similar Breslow intermediates. The ratio of protonation to chloride elimination from the Breslow intermediate is 10²-fold greater in the enzymic process. This is consistent with a lower intrinsic barrier to proton transfer on the enzyme, implicating formation of a localized tetrahedral (sp³) carbanion that is formed as CO₂ is produced. In contrast, slower protonation in solution of the decarboxylated intermediate is consistent with formation of a delocalized planar carbanionic enol/enamine. The proposed structural and reactive character of the enzymic Breslow intermediate is consistent with Warshel's general theory of enzymic catalysis, structural characterization of related intermediates, and the lower kinetic barrier in reactions that occur without changes in hybridization.

Umpolung Reactivity of Aldehydes toward Carbon Dioxide

Carbon dioxide is an intrinsically stable molecule. Therefore, its activation requires extra energy input in the form of reactive reagents and/or activated catalysts and, often, harsh reaction conditions. Reported here is a direct carboxylation reaction of aromatic aldehydes with carbon dioxide to afford α-keto acids as added-value products. In situ generation of a reactive cyanohydrin was the key to the successful carboxylation reaction under operationally mild reaction conditions (25-40 °C, 1 atm CO₂ ). The resulting α-keto acids served as a platform for α-amino acid synthesis by reductive amination reactions, illustrating the chemical synthesis of essential bioactive molecules from carbon dioxide.

Charge Dispersion and Its Effects on the Reactivity of Thiamin-Derived Breslow Intermediates

The enzymic decarboxylation of 2-ketoacids proceeds via their C2-thiazolium adducts of thiamin diphosphate (ThDP). Loss of CO₂ from these adducts leads to reactive species that are known as Breslow intermediates. The protein-bound adducts of the 2-ketoacids and ThDP are several orders of magnitude more reactive than the synthetic analogues in solution. Studies of enzymes are consistent with formulation of protein-bound Breslow intermediates with localized carbanionic character at the reactive C2α position, reflecting the charge-stabilized transition state that leads to this form. Our study reveals that nonenzymic decarboxylation of the related thiamin adducts proceeds to the alternative charge-dispersed enol form of the Breslow intermediate. These differences suggest that the greatly enhanced rate of decarboxylation of the precursors to Breslow intermediates in enzymes arises from maintenance of the carbanionic character at the position from which the carboxyl group departs, avoiding charge dispersion by stabilizing electrostatic interactions with the protein as formulated by Warshel. Applying Guthrie's "no-barrier" addition to Marcus theory also leads to the conclusion that maintaining the tetrahedral carbanion at C2α of the resulting adduct minimizes associated kinetic barriers by avoiding rehybridization as part of steps to and from the intermediate. Finally, maintenance of the reactive energetic carbanion agrees with the concepts of Albery and Knowles as the outcome of evolved enzymic processes.

Radical [1,3] Rearrangements of Breslow Intermediates

Breslow intermediates that bear radical-stabilizing N substituents, such as benzyl, cinnamyl, and diarylmethyl, undergo facile homolytic C-N bond scission under mild conditions to give products of formal [1,3] rearrangement rather than benzoin condensation. EPR experiments and computational analysis support a radical-based mechanism. Implications for thiamine-based enzymes are discussed.

Decarboxylation, CO2 and the reversion problem

Decarboxylation reactions occur rapidly in enzymes but usually are many orders of magnitude slower in solution, if the reaction occurs at all. Where the reaction produces a carbanion and CO2, we would expect that the high energy of the carbanion causes the transition state for C-C bond cleavage also to be high in energy. Since the energy of the carbanion is a thermodynamic property, an enzyme obviously cannot change that property. Yet, enzymes overcome the barrier to forming the carbanion. In thinking about decarboxylation, we had assumed that CO2 is well behaved and forms without its own barriers. However, we analyzed reactions in solution of compounds that resemble intermediates in enzymic reaction and found some of them to be subject to unexpected forms of catalysis. Those results caused us to discard the usual assumptions about CO2 and carbanions. We learned that CO2 can be a very reactive electrophile. In decarboxylation reactions, where CO2 forms in the same step as a carbanion, separation of the products might be the main problem preventing the forward reaction because the carbanion can add readily to CO2 in competition with their separation and solvation. The basicity of the carbanion also might be overestimated because when we see that the decarboxylation is slow, we assume that it is because the carbanion is high in energy. We found reactions where the carbanion is protonated internally; CO2 appears to be able to depart without reversion more rapidly. We tested these ideas using kinetic analysis of catalytic reactions, carbon kinetic isotope effects, and synthesis of predecarboxylation intermediates. In another case, we observed that the decarboxylation is subject to general base catalysis while producing a significant carbon kinetic isotope effect. This requires both a proton transfer from an intermediate and C-C bond-breaking in the rate-determining step. This would occur if the route involves the surprising initial addition of water to the carboxyl, with the cleavage step producing bicarbonate. Interestingly, some enzyme-catalyzed reactions also appear to produce intermediates formed by the initial addition of water or a nucleophile to the carboxyl or to nascent CO2. We conclude that decarboxylation is not necessarily a problem that results from the energy of the carbanionic products alone but from their formation in the presence of CO2. Catalysts that facilitate the separation of the species on either side of the C-C bond that cleaves could solve the problem using catalytic principles that we find in many enzymes that promote hydrolytic processes, suggesting linkages in catalysis through evolution of activity.

Lithium-stabilized nucleophilic addition of thiamin to a ketone provides an efficient route to mandelylthiamin, a critical pre-decarboxylation intermediate

Mandelylthiamin (MTh) is an accurate model of the covalent intermediate derived from the condensation of thiamin diphosphate and benzoylformate in benzoylformate decarboxylase. The properties and catalytic susceptibilities of mandelylthiamin are the subjects of considerable interest. However, the existing synthesis gives only trace amounts of the precursor to MTh as it is conducted under reversible conditions. An improved approach derives from the unique ability of lithium ions to drive to completion the otherwise unfavorable condensation of the conjugate base of thiamin and methyl benzoylformate. The unique efficiency of the condensation reaction in the presence of lithium ions is established in contrast to the effects of other Lewis acids. Interpretation of the pattern of the results indicates that the condensation of the ketone and thiamin is thermodynamically controlled. It is proposed that the addition of lithium ions displaces the equilibrium toward the product through formation of a stable lithium-alkoxide.

Catalyzing decarboxylation by taming carbon dioxide

Decarboxylation reactions on enzymes are consistently much faster than their nonenzymic counterparts. Examination of the potential for catalysis in the nonenzymic reactions revealed that the reaction is slowed by the failure of CO2 to be launched into solution upon C–C bond cleavage. Catalysts can facilitate the reaction by weakening the C–CO2H bond but this is not sufficient. Converting the precursor of CO2 into a precursor of bicarbonate facilitates the forward reaction as does protonation of the nascent carbanion.

CO2 on a tightrope: stabilization, room-temperature decarboxylation, and sodium-induced carboxylate migration

A sterically shielded 3-substituted zwitterionic N,N-dimethylisotryptammonium carboxylate has been synthesized by consecutive chemoselective double alkylation of indole. The carboxylate undergoes a quantitative and unusually facile decarboxylation in dimethyl sulfoxide (DMSO) or dimethyl formamide (DMF) at room temperature. The breaking of a nearly equidistant hydrogen bond by solvent molecules initiates heterolytic C-C cleavage. The decarboxylation rate decreases with increasing CO(2) partial pressure, proving the competitiveness of protonation and re-carboxylation of the carbanionic intermediate. Corresponding spiro compounds containing silylene and stannylene moieties show high thermal stability. Addition of an excess of methyllithium to the sodium salt triggers a reaction sequence comprising a deprotonation, carboxylate transfer, and nucleophilic trapping of the rearranged carboxylate by another equivalent of methyllithium. Hydrolytic work-up of the geminal diolate leads to an acetyl product. The role of the sodium counterion and the mechanism of the rearrangement have been unraveled by deuteration experiments.

Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases

Carbamoyl phosphate (CP) has a half-life for thermal decomposition of <2 s at 100 degrees C, yet this critical metabolic intermediate is found even in organisms that grow at 95-100 degrees C. We show here that the binding of CP to the enzymes aspartate and ornithine transcarbamoylase reduces the rate of thermal decomposition of CP by a factor of >5,000. Both of these transcarbamoylases use an ordered-binding mechanism in which CP binds first, allowing the formation of an enzyme.CP complex. To understand how the enzyme.CP complex is able to stabilize CP we investigated the mechanism of the thermal decomposition of CP in aqueous solution in the absence and presence of enzyme. By quantum mechanics/molecular mechanics calculations we show that the critical step in the thermal decomposition of CP in aqueous solution, in the absence of enzyme, involves the breaking of the C O bond facilitated by intramolecular proton transfer from the amine to the phosphate. Furthermore, we demonstrate that the binding of CP to the active sites of these enzymes significantly inhibits this process by restricting the accessible conformations of the bound ligand to those disfavoring the reactive geometry. These results not only provide insight into the reaction pathways for the thermal decomposition of free CP in an aqueous solution but also show why these reaction pathways are not accessible when the metabolite is bound to the active sites of these transcarbamoylases.

Protein-enhanced decarboxylation of the covalent intermediate in benzoylformate decarboxylase--Desolvation or acid catalysis?

Benzoylformate decarboxylase (BFD) enhances the rate of decarboxylation of its key intermediate compared to the nonenzymic reaction by a factor of about 10(6). It has been proposed that desolvation into a hydrophobic environment will lower the reaction barrier in TDP-dependent decarboxylases. The competition of thiamin thiazolone diphosphate (TTDP) with the cofactor thiamin diphosphate (TDP) provides a dynamic indication of the relative hydrophobicity of the cofactor binding site. BFD binds the more polar TDP tightly in the presence of excess TTDP. Therefore, desolvation would not be likely to occur during catalysis. Unlike TDP enzymes that have electron acceptors as substrates, decarboxylases require protonation to produce the precursor to the aldehyde product. A mechanism involving an associated acid that traps the carbanion generated upon C-C bond breaking will permit diffusional separation of carbon dioxide and generate the appropriate precursor to the product aldehyde. This would also account for avoidance of a competitive reaction. Hasson's detailed structure of BFD shows a highly polar active site with histidines in the vicinity of the substrate. Reports of a reduction of k(cat) to near the nonenzymic rate without a large effect on Km upon specific replacement of these histidines with alanine fit this alternative. In TDP enzymes involving oxidation or condensation, an electrophilic substrate or second cofactor will be bound (and no proton will be required). This will acquire the electron density of the carbanion itself. In such cases, protonated side chains are not functional while hydrophobic environments would promote the internal transfer.

CIC Medal Award Lecture — Molecular keystones: Lessons from bioorganic reaction mechanisms

The work of the author is reviewed in terms of "keystone molecules" that serve as figurative points of support to understand the interactions of smaller molecules within biological macromolecules. The review emphasizes lessons learned in carboxylation of biotin, reactions of cyclic phosphates, the uses of acyl phosphate monoesters, and the mechanism of decarboxylation of thiamin-derived intermediates.Key words: CIC medal, biotin, ATP, mechanisms, cyclic phosphates, thiamin, acyl phosphates, catalysis.

Deuterium labeling as a test of intramolecular hydride mechanisms in the fragmentation of 2-(1-hydroxybenzyl)-N1′-methylthiamin

2-(1-Hydroxybenzyl)-N1′-methylthiamin (1b) is a model for the addition intermediate in the thiamin catalyzed benzoin condensation. However, N-alkylation alters the reactivity of the compound: instead of undergoing base-catalyzed formation of benzaldehyde and N1′-methylthiamin, it rapidly forms trimethyl amino pyrimidine (2b) and phenylthiazole ketone (3). The base-catalyzed fragmentation process is faster than the analogous enzymic reaction (in benzoylformate decarboxylase) under the same conditions. One possible mechanism for the rapid fragmentation is an internal hydride transfer from α-C2 to the methylene bridge between the heterocycles. To test the hydride mechanism we prepared α-C2-deuterated 1b and conducted the fragmentation reaction in normal water. Spectroscopic analysis revealed that the trimethyl aminopyrimidine product does not contain any deuterium, ruling out a hydride transfer mechanism. This supports a mechanism for fragmentation that proceeds instead via a proton transfer from α-C2. Since protonation (and hence, deprotonation) of that site is part of the normal catalytic cycle of benzoylformate decarboxylase, the enzyme must divert the reaction from the lowest energy pathway since it would share a common intermediate with the fragmentation process.Key words: thiamin, fragmentation, benzoylformate decarboxylase, proton transfer, hydride shift.

The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction

Enzymes provide enormous rate enhancements, unmatched by any other type of catalyst. The stabilization of high-energy states along the reaction coordinate is the crux of the catalytic power of enzymes. We report the atomic-resolution structure of a high-energy reaction intermediate stabilized in the active site of an enzyme. Crystallization of phosphorylated beta-phosphoglucomutase in the presence of the Mg(II) cofactor and either of the substrates glucose 1-phosphate or glucose 6-phosphate produced crystals of the enzyme-Mg(II)-glucose 1,6-(bis)phosphate complex, which diffracted x-rays to 1.2 and 1.4 angstroms, respectively. The structure reveals a stabilized pentacovalent phosphorane formed in the phosphoryl transfer from the C(1)O of glucose 1,6-(bis)phosphate to the nucleophilic Asp8 carboxylate.