Formation and stability of peptide enolates in aqueous solution

Disulfides form persulfides at alkaline pH leading to potential overestimations in the cold cyanolysis method

It is well established that proteins and peptides can release sulfur under alkaline treatment, mainly through the β-elimination of disulfides with the concomitant formation of persulfides and dehydroalanine derivatives. In this study, we evaluated the formation of glutathione persulfide (GSSH/GSS-) by exposure of glutathione disulfide (GSSG) to alkaline conditions. The kinetics of the reaction between GSSG and HO- was investigated by UV-Vis absorbance, reaction with 5,5'-dithio-bis-(2-nitrobenzoic acid) (DTNB), and cold cyanolysis, obtaining an apparent second-order rate constant of ∼10-3 M-1 s-1 at 25 °C. The formation of GSSH and the dehydroalanine derivative was confirmed by HPLC and/or mass spectrometry. However, the mixtures did not equilibrate in a timescale of hours, and additional species, including thiol and diverse sulfane sulfur compounds were also formed, probably through further reactions of the persulfide. Cold cyanolysis is frequently used to quantify persulfides, since it measures sulfane sulfur. This method involves a step in which the sample to be analyzed is incubated with cyanide at alkaline pH. When cold cyanolysis was applied to samples containing GSSG, sulfane sulfur products that were not present in the original sample were measured. Thus, our results reveal the risk of overestimating the amount of sulfane sulfur compounds in samples that contain disulfides due to their decay to persulfides and other sulfane sulfur compounds at alkaline pH. Overall, our study highlights that the β-elimination of disulfides is a potential source of persulfides, although we do not recommend the preparation of GSSH from incubation of GSSG in alkali. Our study also highlights the importance of being cautious when doing and interpreting cold cyanolysis experiments.

Preparation of Deuterium-Labeled Armodafinil by Hydrogen–Deuterium Exchange and Its Application in Quantitative Analysis by LC-MS

Armodafinil, the R enantiomer of modafinil, was approved in 2007 by the US Food and Drug Administration as a wake-promoting agent for excessive sleepiness treatment. Due to its abuse by students and athletes, there is a need of its quantification. Quantitative analysis by liquid chromatography-mass spectrometry, however, though very common and sensitive, frequently cannot be performed without isotopically labeled standards which usually have to be specially synthesized. Here we reported our investigation on the preparation of deuterated standard of armodafinil based on the simple and inexpensive hydrogen–deuterium exchange reaction at the carbon centers. The obtained results clearly indicate the possibility of introduction of three deuterons into the armodafinil molecule. The introduced deuterons do not undergo back exchange under neutral and acidic conditions. Moreover, the deuterated and non-deuterated armodafinil isotopologues revealed co-elution during the chromatographic analysis. The ability to control the degree of deuteration using different reaction conditions was determined. The proposed method of deuterated armodafinil standard preparation is rapid, cost-efficient and may be successfully used in its quantitative analysis by LC-MS.

Enzymatic Cβ-H Functionalization of l-Arg and l-Leu in Nonribosomally Derived Peptidyl Natural Products: A Tale of Two Oxidoreductases

Muraymycins are peptidyl nucleoside antibiotics that contain two C_β-modified amino acids, (2S,3S)-capreomycidine and (2S,3S)-β-OH-Leu. The former is also a component of chymostatins, which are aldehyde-containing peptidic protease inhibitors that─like muraymycin─are derived from nonribosomal peptide synthetases (NRPSs). Using feeding experiments and in vitro characterization of 12 recombinant proteins, the biosynthetic mechanism for both nonproteinogenic amino acids is now defined. The formation of (2S,3S)-capreomycidine is shown to involve an FAD-dependent dehydrogenase:cyclase that requires an NRPS-bound pathway intermediate as a substrate. This cryptic dehydrogenation strategy is both temporally and mechanistically distinct in comparison to the biosynthesis of other capreomycidine diastereomers, which has previously been shown to proceed by C_β-hydroxylation of free l-Arg catalyzed by a member of the nonheme Fe²⁺- and α-ketoglutarate (αKG)-dependent dioxygenase family and (eventually) a dehydration-mediated cyclization process catalyzed by a distinct enzyme(s). Contrary to our initial expectation, the sole nonheme Fe²⁺- and αKG-dependent dioxygenase candidate Mur15 encoded within the muraymycin gene cluster is instead demonstrated to catalyze specific C_β hydroxylation of the Leu residue to generate (2S,3S)-β-OH-Leu that is found in most muraymycin congeners. Importantly, and in contrast to known l-Arg-C_β-hydroxylases, the Mur15-catalyzed reaction occurs after the NRPS-mediated assembly of the peptide scaffold. This late-stage functionalization affords the opportunity to exploit Mur15 as a biocatalyst, proof of concept of which is provided.

Trends in the Hydrogen-Deuterium Exchange at the Carbon Centers. Preparation of Internal Standards for Quantitative Analysis by LC-MS

The application of internal standards in quantitative and qualitative bioanalysis is a commonly used procedure. They are usually isotopically labeled analogs of the analyte, used in quantitative LC-MS analysis. Usually, ²H, ¹³C, ¹⁵N and ¹⁸O isotopes are used. The synthesis of deuterated isotopologues is relatively inexpensive, however, due to the isotopic effect of deuterium and the lack of isotopologue co-elution, usually they are not considered as good internal standards for LC-MS quantification. On the other hand, the preparation of ¹³C, ¹⁵N and ¹⁸O containing standards of drugs and their metabolites requires a complicated multistep de novo synthesis, starting from the isotopically labeled substrates, which are usually expensive. Therefore, there is a strong need for the development of low-cost methods for isotope-labeled standard preparations for quantitative analysis by LC-MS. The presented review concentrates on the preparation of deuterium-labeled standards by hydrogen−deuterium exchange reactions at the carbon centers. Recent advances in the development of the methods of isotopologues preparation and their application in quantitative analysis by LC-MS are evaluated.

Racemisation in Chemistry and Biology

The two enantiomers of a compound often have profoundly different biological properties and thus their liability to racemisation in aqueous solutions is an important piece of information. The authors reviewed the available data concerning the process of racemisation in vivo, in the presence of biological molecules (e.g., racemase enzymes, serum albumin, cofactors and derivatives) and under purely chemical but aqueous conditions (acid, base and other aqueous systems). Mechanistic studies are described critically in light of reported kinetic data. The types of experimental measurement that can be used to effectively determine rate constants of racemisation in various conditions are discussed and the data they provide is summarised. The proposed origins of enzymatic racemisation are presented and suggest ways to promote the process that are different from processes taking place in bulk water. Experimental and computational studies that provide understanding and quantitative predictions of racemisation risk are also presented.

Unusually high α-proton acidity of prolyl residues in cyclic peptides

The acidity of the α-proton in peptides has an essential role in numerous biochemical reactions and underpins their stereochemical integrity, which is critical to their biological function. We report a detailed kinetic and computational study of the acidity of the α-proton in two cyclic peptide systems: diketopiperazine (DKP) and triketopiperazine (TKP). The kinetic acidity (protofugality) of the α-protons were determined though hydrogen deuterium exchange studies in aqueous solutions. The acidities of the α-proton in prolyl residues were increased by 3–89 fold relative to other amino acid residues (prolyl > glycyl ≫ alanyl > tyrosyl). Experimental and computational evidence for the stereoelectronic origins of this enhanced prolyl reactivity is presented. TKPs were 10⁶-fold more reactive than their DKP analogues towards deprotonation, which we attribute to the advanced development of aromaticity in the earlier transition state for proton transfer in these cases. A Brønsted linear free energy analysis of the reaction data was conducted to provide estimates of α-proton pK_as.

Kinetic and computational studies reveal that prolyl residues in cyclic peptides are substantially more acidic than other residues due to a stereoelectronic effect.

Photochromic Behaviour of N-Arylsulfonyl Peptides

Deep, persistent, but structurally sensitive photoyellowing observed in photochemical studies of a wide range of arylsulfonyl derivatives of amines, amino acids and peptides can be attributed to a novel kind of photochromism in which intramolecular photoinduced electron transfer promotes the formation of a metastable cyanine-type chromophore involving sulfur d-orbitals.

Substituent Effects on Carbon Acidity in Aqueous Solution and at Enzyme Active Sites

Methods are described for the determination of pK_as for weak carbon acids in water. The application of these methods to the determination of the pK_as for a variety of carbon acids including nitriles, imidazolium cations, amino acids, peptides and their derivatives and, α-iminium cations is presented. The substituent effects on the acidity of these different classes of carbon acids are discussed; and, the relevance of these results to catalysis of the deprotonation of amino acids by enzymes and by pyridoxal 5'-phosphate is reviewed. The procedure for estimating the pK_a of uridine 5'-phosphate for C-6 deprotonation at the active site of orotidine 5'-phosphate decarboxylase is described, and the effect of a 5-F substituent on carbon acidity of the enzyme-bound substrate is discussed.

Predicting pKa in Implicit Solvents: Current Status and Future Directions

Computational prediction of condensed phase acidity is a topic of much interest in the field today. We introduce the methods available for predicting gas phase acidity and pKas in aqueous and non-aqueous solvents including high-level electronic structure methods, empirical linear free energy relationships (LFERs), implicit solvent methods, explicit solvent statistical free energy methods, and hybrid implicit–explicit approaches. The focus of this paper is on implicit solvent methods, and we review recent developments including new electronic structure methods, cluster-continuum schemes for calculating ionic solvation free energies, as well as address issues relating to the choice of proton solvation free energy to use with implicit solvation models, and whether thermodynamic cycles are necessary for the computation of pKas. A comparison of the scope and accuracy of implicit solvent methods with ab initio molecular dynamics free energy methods is also presented. The present status of the theory and future directions are outlined.

The unusual hydrogen-deuterium exchange of α-carbon protons in N-substituted glycine-containing peptides

Hydrogens connected to α-carbon (α-C) of amino acid residues are usually resistant to hydrogen-deuterium exchange (HDX) unless reaction conditions promote racemization. Although N-methylglycine (sarcosine) residue has been found in biologically active peptide such as cyclosporine, to the best of our knowledge, the HDX of α-C protons of this residue was not explored yet. Here, we presented a new and efficient methodology of α-C deuteration in sarcosine residues under basic aqueous conditions. The deuterons, introduced at α-C atom, do not undergo back-exchange in acidic aqueous solution. The electrospray ionization-MS and MS/MS experiments on proposed model peptides confirmed the HDX at α-C and revealed the unexpected hydrogen scrambling in sarcosine-containing peptides. Although the observed HDX of α-C protons is only successful in N-acylglycine when the amide possesses a certain degree of alkylation, it offers a new approach to the analysis of sarcosine-containing peptides such as cyclosporine.

Stabilities of Uracil and Pyridone-Based Carbanions: A Systematic Study in the Gas Phase and Solution and Implications for the Mechanism of Orotidine-5'-Monophosphate Decarboxylase

The stabilities of the C6-centered carbanions derived from 1,3-dimethyluracil, N-methyl-2-pyridone, and N-methyl-4-pyridone were systematically investigated in the gas phase and in DMSO and water solutions. The stabilities of the carbanions in the gas phase and DMSO were directly measured through their reactions with carbon acids with known proton affinity or pK_a values. The stabilities of the carbanions in DMSO were also probed through their kinetic isotope effects of protonation over deuteriation using acids with different acidity. The stabilities of the carbanions in water were determined through the rates of hydrogen-deuterium exchange reactions of the corresponding conjugate acids. The carbanions derived from the two pyridones were found to have the same stability, whereas the carbanion derived from 1,3-dimethyluracil was more stable. The order of the stability of the carbanions showed no correlation with the decarboxylation rates of their corresponding carboxylic acids. The implications of the results for the mechanism of orotidine-5'-monophosphate decarboxylase (ODCase) are discussed.

Isopentenyl diphosphate isomerase catalyzed reactions in D2O: product release limits the rate of this sluggish enzyme-catalyzed reaction

The E. coli isopentenyl diphosphate isomerase (IDI) catalyzed reaction of isopentenyl diphosphate (IPP) in D(2)O gives a 66% yield of dimethylallyl diphosphate labeled with deuterium at the (E)-methyl group (d-DMAPP) and a 34% yield of IPP labeled with 1 mol of deuterium at C-2 (d-IPP). This shows that the release to D(2)O of the initial product of the IDI-catalyzed reaction (d-DMAPP) is slower than its conversion to d-IPP. Product dissociation is therefore rate determining for isomerization of IPP with a rate constant k(dis) ≈ k(cat) = 0.08 s(-1). The data provide an estimated rate constant of k(as) = 6 × 10(3) M(-1) s(-1) for binding of DMAPP to E. coli IDI that is similar to rate constants determined for the binding of N-protonated 2-amino ethyl diphosphate intermediate analogs to IDI from yeast [Reardon, J. E.; Abeles, R. H. Biochemistry1986, 25, 5609-5616]. We propose that ligand binding to IDI is relatively slow because there is a significant kinetic barrier to reorganization of the initial encounter complex between enzyme, substrate, and an essential Mg(2+) to form the Michaelis complex where the metal cation bridges the protein and the substrate diphosphate group.

Enzymatic Catalysis of Proton Transfer and Decarboxylation Reactions

Deprotonation of carbon and decarboxylation at enzyme active sites proceed through the same carbanion intermediates as for the uncatalyzed reactions in water. The mechanism for the enzymatic reactions can be studied at the same level of detail as for nonenzymatic reactions, using the mechanistic tools developed by physical organic chemists. Triosephosphate isomerase (TIM) catalyzed interconversion of D-glyceraldehyde 3-phosphate and dihydroxyacetone phosphate is being studied as a prototype for enzyme catalyzed proton transfer, and orotidine monophosphate decarboxylase (OMPDC) catalyzed decarboxylation of orotidine 5'-monophosphate is being studied as a prototype for enzyme-catalyzed decarboxylation. ¹H NMR spectroscopy is an excellent analytical method to monitor proton transfer to and from carbon catalyzed by these enzymes in D₂O. Studies of these partial enzyme-catalyzed exchange reactions provide novel insight into the stability of carbanion reaction intermediates, that is not accessible in studies of the full enzymatic reaction. The importance of flexible enzyme loops and the contribution of interactions between these loops and the substrate phosphodianion to the enzymatic rate acceleration are discussed. The similarity in the interactions of OMPDC and TIM with the phosphodianion of bound substrate is emphasized.

Validation of the distal effect of electron-withdrawing groups on the stability of peptide enolates and its exploitation in the controlled stereochemical inversion of amino acid derivatives

Theoretical studies had predicted that N-electron-withdrawing substituents, hydrogen bonding, and protonation at amide nitrogen selectively increase the acidity of a distal proton adjacent to the amide carbonyl to the extent that the α-carbonyl acidity of some N-substituted amides exceeds that of typical ketones. Now, in the present work, competitive, base-catalyzed hydrogen-deuterium exchange experiments, with diisopropyl ketone and a series of N-substituted acetamides and diketopiperazines, have established that there is a strong correlation between the calculated acidities and the experimental rates of deprotonation in these systems. The results show that the rates of exchange of the distal protons of N-acylated and N-sulfonylated amides are more than 4 orders of magnitude faster than those of the N-methylated analogues and that the acylated and sulfonylated amides are much more reactive in this regard than diisopropyl ketone. The magnitude and regioselectivity of the distal effect is sufficient for practical applications and has been exploited in the manipulation of N-acetyl α,α'-disubstituted diketopiperazines for the controlled α-deuteration and stereochemical inversion of N-methylamino acids, and in the production of α-deuterated (2R,3S)-N-methylalloisoleucine from the nondeuterated (2S,3S)-isoleucine diastereomer.

Wildtype and engineered monomeric triosephosphate isomerase from Trypanosoma brucei: partitioning of reaction intermediates in D2O and activation by phosphite dianion

Product yields for the reactions of (R)-glyceraldehyde 3-phosphate (GAP) in D2O at pD 7.9 catalyzed by wildtype triosephosphate isomerase from Trypanosoma brucei brucei (Tbb TIM) and a monomeric variant (monoTIM) of this wildtype enzyme were determined by (1)H NMR spectroscopy and were compared with the yields determined in earlier work for the reactions catalyzed by TIM from rabbit and chicken muscle [O'Donoghue, A. C., Amyes, T. L., and Richard, J. P. (2005), Biochemistry 44, 2610 - 2621]. Three products were observed from the reactions catalyzed by TIM: dihydroxyacetone phosphate (DHAP) from isomerization with intramolecular transfer of hydrogen, d-DHAP from isomerization with incorporation of deuterium from D2O into C-1 of DHAP, and d-GAP from incorporation of deuterium from D2O into C-2 of GAP. The yield of DHAP formed by intramolecular transfer of hydrogen decreases from 49% for the muscle enzymes to 40% for wildtype Tbb TIM to 34% for monoTIM. There is no significant difference in the ratio of the yields of d-DHAP and d-GAP for wildtype TIM from muscle sources and Trypanosoma brucei brucei, but partitioning of the enediolate intermediate of the monoTIM reaction to form d-DHAP is less favorable ((k(C1))(D)/(k(C2))(D) = 1.1) than for the wildtype enzyme ((k(C1))(D)/(k(C2))(D) = 1.7). Product yields for the wildtype Tbb TIM and monoTIM-catalyzed reactions of glycolaldehyde labeled with carbon-13 at the carbonyl carbon ([1-(13)C]-GA) at pD 7.0 in the presence of phosphite dianion and in its absence were determined by (1)H NMR spectroscopy [Go, M. K., Amyes, T. L., and Richard, J. P. (2009) Biochemistry 48, 5769-5778]. There is no detectable difference in the yields of the products of wildtype muscle and Tbb TIM-catalyzed reactions of [1-(13)C]-GA in D2O. The kinetic parameters for phosphite dianion activation of the reactions of [1-(13)C]-GA catalyzed by wildtype Tbb TIM are similar to those reported for the enzyme from rabbit muscle [Amyes, T. L. and Richard, J. P. (2007) Biochemistry 46, 5841-5854], but there is no detectable dianion activation of the reaction catalyzed by monoTIM. The engineered disruption of subunit contacts at monoTIM causes movement of the essential side chains of Lys-13 and His-95 away from the catalytic active positions. We suggest that this places an increased demand that the intrinsic binding energy of phosphite dianion be utilized to drive the change in the conformation of monoTIM back to the active structure for wildtype TIM.

Substituent effects on electrophilic catalysis by the carbonyl group: anatomy of the rate acceleration for PLP-catalyzed deprotonation of glycine

First-order rate constants, determined by (1)H NMR, are reported for deuterium exchange between solvent D(2)O and the α-amino carbon of glycine in the presence of increasing concentrations of carbonyl compounds (acetone, benzaldehyde, and salicylaldehyde) and at different pD and buffer concentrations. These rate data were combined with (1)H NMR data that define the position of the equilibrium for formation of imines/iminium ions from addition of glycine to the respective carbonyl compounds, to give second-order rate constants k(DO) for deprotonation of α-imino carbon by DO(-). The assumption that these second-order rate constants lie on linear structure-reactivity correlations between log k(OL) and pK(a) was made in estimating the following pK(a)'s for deprotonation of α-imino carbon: pK(a) = 22, glycine-acetone iminium ion; pK(a) = 27, glycine-benzaldehyde imine; pK(a) ≈ 23, glycine-benzaldehyde iminium ion; and, pK(a) = 25, glycine-salicylaldehyde iminium ion. The much lower pK(a) of 17 [Toth, K.; Richard, J. P. J. Am. Chem. Soc. 2007, 129, 3013-3021] for carbon deprotonation of the adduct between 5'-deoxypyridoxal (DPL) and glycine shows that the strongly electron-withdrawing pyridinium ion is unique in driving the extended delocalization of negative charge from the α-iminium to the α-pyridinium carbon. This favors carbanion protonation at the α-pyridinium carbon, and catalysis of the 1,3-aza-allylic isomerization reaction that is a step in enzyme-catalyzed transamination reactions. An analysis of the effect of incremental changes in structure on the activity of benzaldehyde in catalysis of deprotonation of glycine shows the carbonyl group electrophile, the 2-O(-) ring substituent and the cation pyridinium nitrogen of DPL each make a significant contribution to the catalytic activity of this cofactor analogue. The extraordinary activity of DPL in catalysis of deprotonation of α-amino carbon results from the summation of these three smaller effects.

The Distal Effect of N-Electron-withdrawing Groups on the Stability of Peptide Carbon Radicals

The effect of electron-withdrawing substituents, hydrogen bonding and protonation at amide nitrogen on the stability of radicals formed by loss of either a distal C–H adjacent to the amide carbonyl or one proximal to the amide nitrogen for a series of acetamides and diketopiperazines has been studied via high-level ab initio methods. These studies show that the effect is to destabilize the radicals formed by abstraction of the proximal hydrogens, typically by 10–20 kJ mol–1, and stabilize the distal radicals typically by 5–10 kJ mol–1, but only if the distal radicals are polarized by another dative substituent. The different radical stabilities are not directly mirrored in calculated activation energies or experimental rates of radical formation in bromination reactions, because there is significant charge development in these reaction transition states.

The PLP cofactor: lessons from studies on model reactions

Experimental probes of the acidity of weak carbon acids have been developed and used to determine the carbon acid pK(a)s of glycine, glycine derivatives and iminium ion adducts of glycine to the carbonyl group, including 5'-deoxypyridoxal (DPL). The high reactivity of the DPL-stabilized glycyl carbanion towards nucleophilic addition to both DPL and the glycine-DPL iminium ion favors the formation of Claisen condensation products at enzyme active sites. The formation of the iminium ion between glycine and DPL is accompanied by a 12-unit decrease in the pK(a) of 29 for glycine. The complicated effects of formation of glycine iminium ions to DPL and other aromatic and aliphatic aldehydes and ketones on carbon acid pK(a) are discussed. These data provide insight into the contribution of the individual pyridine ring substituents to the catalytic efficiency of DPL. It is suggested that the 5'-phosphodianion group of PLP may play an important role in enzymatic catalysis of carbon deprotonation by providing up to 12 kcal/mol of binding energy that is utilized to stabilize the transition state for the enzymatic reaction. This article is part of a Special Issue entitled: Pyridoxal Phospate Enzymology.

The distal effect of electron-withdrawing groups and hydrogen bonding on the stability of peptide enolates

Relative gas-phase carbon acidities have been computed for a series of acetamides, diketopiperazines, and linear dipeptides. The results show that N-electron-withdrawing substituents, protonation, and hydrogen bonding at amide nitrogen in these systems increase the acidity of both a C-H proton adjacent to the amide carbonyl and that of one proximal to the amide nitrogen. There is a good correlation between the magnitudes of the increases at the two positions, but the extent of the increase for the distal C-H adjacent to the carbonyl is greater than that for the proximal C-H, in most cases by a factor of about two. The effects on the stability of the distal enolate are shown to result from predominantly inductive affects. The size of these effects is such that protonation and hydrogen bonding at nitrogen increase the acidity of the distal C-H to almost the same extent as seen for the analogous interactions at the carbonyl oxygen. The effect is also seen in solution, where the computed aqueous pK(a) values are greater for the C-H adjacent to the amide carbonyl, by up to 13 units, and where preliminary experimental studies have shown that N-acetylation of an amide increases the rate of hydrogen-deuterium exchange via formation of the corresponding distal enolate by more than 3 orders of magnitude above the rates of exchange via the proximal enolate, of the nonacetylated amide and of diisopropylketone. The results also indicate that hydrogen bonding to amide nitrogen could be as important as bonding to oxygen in enzyme-catalyzed cleavage of alpha-C-H bonds.

An experimental investigation of the evolution of chirality in a potential dynamic peptide system: N-terminal epimerization and degradation into diketopiperazine

The APED model (activation-polymerization-epimerization-depolymerization) is a unique example of a chemical system that allows symmetry breaking through a dynamic process involving indirect network autocatalysis. In its simplest version, the autocatalytic behavior of this model partly relies on the reproduction of local chiral centers in dipeptides through an epimerization process, with a thermodynamic preference for homochiral chains. We studied the reactivity of di- and tripeptides, containing a N-terminal phenylglycine (Phg) residue, as model compounds for the experimental determination of the kinetic and thermodynamic parameters related to the N-terminal epimerization process. Although the N-terminal residue is prone to spontaneous epimerization, catalysis was required for the epimerization to reach the equilibrium state in reasonable time. Unexpectedly, the observed equilibrium diastereoisomeric excesses have shown a general tendency for more stable heterochiral peptides, especially strong in the case of dipeptides. In parallel to this process, a stereoselective peptide cleavage through diketopiperazine formation was observed. Contrary to the N-terminal epimerization of peptides, the diketopiperazine formation did not need any catalyst, and heterochiral peptides were shown to be dynamically unstabilized, as they were cleaved faster than homochiral peptides. The validity of the extrapolation of these results to other residues and longer peptide chains is discussed, and some directions for future developments of the theoretical model are given.

Substituent effects on the thermodynamic stability of imines formed from glycine and aromatic aldehydes: implications for the catalytic activity of pyridoxal-5'-phosphate

Equilibrium constants for addition of glycine to substituted benzaldehydes to form the corresponding imines and pK(a)'s for ionization of the iminium ions were determined by (1)H NMR analysis in D(2)O. The introduction of a phenoxide anion substituent into the aromatic ring of benzaldehyde leads to a substantial increase in the pK(a) of the iminium ion from 6.3 to 10.2 for p-hydroxybenzaldehyde and to 12.1 for salicylaldehyde. An analysis of the differential effect of ortho- versus para-substitution shows that the iminium ion to salicylaldehyde is stabilized by an intramolecular hydrogen bond in aqueous solution, with an estimated energy ca. 3 kcal/mol larger than can be accounted for by a simple electrostatic interaction. A comparison of the o-O(-) substituent effect on the acidity of the iminium ions of glycine to benzaldehyde and 4-pyridine-carboxaldehyde provides evidence for the existence of an internal hydrogen bond of similar strength in pyridoxal 5'-phosphate (PLP) iminium ions in water. The effects of other ring substituents on the stability of PLP iminium ions are discussed.

Structure-reactivity effects on primary deuterium isotope effects on protonation of ring-substituted alpha-methoxystyrenes

Primary product isotope effects (PIEs) on L(+) and carboxylic acid catalyzed protonation of ring-substituted alpha-methoxystyrenes (X-1) to form oxocarbenium ions X-2(+) in 50/50 (v/v) HOH/DOD were calculated from the yields of the alpha-CH(3) and alpha-CH(2)D labeled ketone products, determined by (1)H NMR. A plot of PIE against reaction driving force shows a maximum PIE of 8.7 for protonation of 4-MeO-1 by Cl(2)CHCOOH (DeltaG(o) = 1.0 kcal/mol). The PIE decreases to 8.1 for protonation of 4-MeO-1 by L(3)O(+) (DeltaG(o) = -2.8 kcal/mol) and to 5.1 for protonation of 3,5-di-NO(2)-1 by MeOCH(2)COOH (DeltaG(o) = 13.1 kcal/mol). The PIE maximum is around DeltaG(o) = 0. Arrhenius-type plots of PIEs on protonation of 4-MeO-1 and 3,5-di-NO(2)-1 by L(3)O(+) and on protonation of X-1 by MeOCH(2)COOH in 50/50 (v/v) HOH/DOD give similar slopes and intercepts. These were used to calculate values of [(E(a))(H) - (E(a))(D)] = -1.2 kcal/mol and (A(H)/A(D)) = 1.0 for the difference in activation energy for reactions of A-H and A-D and for the limiting PIE at infinite temperature, respectively. These parameters are consistent with reaction of the hydron over an energy barrier. There is no evidence for quantum mechanical tunneling of the hydron through the barrier. These PIEs suggest that the transferred hydron at the transition state lies roughly equidistant between the acid donor and base acceptor and contrast with the recently published Brønsted parameters [Richard, J. P.; Williams, K. B. J. Am. Chem. Soc. 2007, 129, 6952-6961], which are consistent with a product-like transition state. An explanation for these seemingly contradictory results is discussed.

Pyridoxal 5'-phosphate: electrophilic catalyst extraordinaire

Studies of nonenzymatic electrophilic catalysis of carbon deprotonation of glycine show that pyridoxal 5'-phosphate (PLP) strongly enhances the carbon acidity of alpha-amino acids, but that this is not the overriding mechanistic imperative for cofactor catalysis. Although the fully protonated PLP-glycine iminium ion adduct exhibits an extraordinary low alpha-imino carbon acidity (pK(a)=6), the more weakly acidic zwitterionic iminium ion adduct (pK(a)=17) is selected for use in enzymatic reactions. The similar alpha-imino carbon acidities of the iminium ion adducts of glycine with 5'-deoxypyridoxal and with phenylglyoxylate show that the cofactor pyridine nitrogen plays a relatively minor role in carbanion stabilization. The 5'-phosphodianion group of PLP likely plays an important role in catalysis by providing up to 12 kcal/mol of binding energy that may be utilized for transition state stabilization.

Glutamate racemase as a target for drug discovery

The bacterial cell wall is a highly cross-linked polymeric structure consisting of repeating peptidoglycan units, each of which contains a novel pentapeptide substitution which is cross-linked through transpeptidation. The incorporation of D-glutamate as the second residue is strictly conserved across the bacterial kingdom. Glutamate racemase, a member of the cofactor-independent, two-thiol-based family of amino acid racemases, has been implicated in the production and maintenance of sufficient d-glutamate pool levels required for growth. The subject of over four decades of research, it is now evident that the enzyme is conserved and essential for growth across the bacterial kingdom and has a conserved overall topology and active site architecture; however, several different mechanisms of regulation have been observed. These traits have recently been targeted in the discovery of both narrow and broad spectrum inhibitors. This review outlines the biological history of this enzyme, the recent biochemical and structural characterization of isozymes from a wide range of species and developments in the identification of inhibitors that target the enzyme as possible therapeutic agents.

Glycine enolates: the effect of formation of iminium ions to simple ketones on alpha-amino carbon acidity and a comparison with pyridoxal iminium ions

Equilibrium constants in D2O were determined by 1H NMR analyses for formation of imines/iminium ions from addition of glycine methyl ester to acetone and from addition of glycine to phenylglyoxylate. First-order rate constants, also determined by 1H NMR, are reported for deuterium exchange between solvent D2O and the alpha-amino carbon of glycine methyl ester and glycine in the presence of increasing concentrations of ketone and Brønsted bases. These rate and equilibrium data were used to calculate second-order rate constants for deprotonation by DO- and by Brønsted bases of the alpha-imino carbon of the ketone adducts. Formation of the iminium ion between acetone and glycine methyl ester and between phenylglyoxylate and glycine is estimated to cause 7 unit and 15 unit decreases, respectively, in the pKa's of 21 and 29 for deprotonation of the parent carbon acids. The effect of formation of iminium ions to phenylglyoxylate and to 5'-deoxypyridoxal (DPL) [Toth, K.; Richard, J. P. J. Am. Chem. Soc. 2007, 129, 3013-3021] on the carbon acidity of glycine is similar. However, DPL is a much better catalyst than phenylglyoxylate of deprotonation of glycine, because of the exceptionally large thermodynamic driving force for conversion of the amino acid and DPL to the reactive iminium ion.

Stability of the 6-carbanion of uracil analogues: mechanistic implications for model reactions of orotidine-5'-monophosphate decarboxylase

[Structure: see text] The pKa's of the 6-CH groups of N-methyl-2-pyridone and N-methyl-4-pyridone in aqueous solution were determined. No correlation between the stability of the carbanions and the rate of decarboxylation of the corresponding carboxylic acids was found.

Covalent catalysis by pyridoxal: evaluation of the effect of the cofactor on the carbon acidity of glycine

First-order rate constants for deprotonation of the alpha-imino carbon of the adduct between 5'-deoxypyridoxal (1) and glycine were determined as the rate constants for Claisen-type addition of glycine to 1 where deprotonation is rate determining for product formation. There is no significant deprotonation at pH 7.1 of the form of the 1-glycine iminium ion with the pyridine nitrogen in the basic form. The value of kHO for hydroxide ion-catalyzed deprotonation of the alpha-imino carbon increases from 7.5 x 10(2) to 3.8 x 10(5) to 3.0 x 10(7) M(-1) s(-1), respectively, with protonation of the pyridine nitrogen, the phenoxide oxyanion, and the carboxylate anion of the 1-glycine iminium ion. There is a corresponding decrease in the pKas for deprotonation of the alpha-imino carbon from 17 to 11 to 6. It is proposed that enzymes selectively bind and catalyze the reaction of the iminium ion with pKa = 17. A comparison of kB = 1.7 x 10(-3) s(-1) for deprotonation of the alpha-imino carbon of this cofactor-glycine adduct (pKa = 17 by HPO4(2-) with k(cat)/K(m) = 4 x 10(5) M(-1) s(-1) for catalysis of amino-acid racemization by alanine racemase shows that the enzyme causes a ca 2 x 10(8)-fold acceleration of the rate of deprotonation the alpha-imino carbon. This corresponds to about one-half of the burden borne by alanine racemase in catalysis of deprotonation of alanine.

Formation and stability of organic zwitterions — The carbon acid pKas of the trimethylsulfonium and tetramethylphosphonium cations in water

We report second-order rate constants of kDO = 7.5 × 10–4 and 9.9 × 10–5 (mol/L)–1 s–1 for exchange for deuterium of the first methyl proton of the trimethylsulfonium and tetramethylphosphonium cations, respectively, in D2O at 25 °C and I = 1.0 (KCl). The data were analyzed to give the following carbon acidities for these cationic carbon acids in water: (CH3)3S+, pKa = 28.5; (CH3)4P+, pKa = 29.4. These acidities are close to those of the neutral carbon acids acetonitrile and dimethylacetamide. This provides evidence that a portion of the stabilization of the cyanomethyl carbanion is due to resonance delocalization of negative charge from carbon to cyano nitrogen.Key words: carbon acids, carbanions, ylides, proton transfer.

On the importance of being zwitterionic: enzymatic catalysis of decarboxylation and deprotonation of cationic carbon

Carbanion ylides are strongly stabilized by electrostatic interactions between opposing charges at neighboring atoms and this stabilizing electrostatic interaction increases with decreasing dielectric constant of the medium through which the charges interact. Consequently, there is a large increase in the thermodynamic driving force, with decreasing dielectric constant of the reaction medium, for deprotonation of cationic carbon acids and decarboxylation to form related ylides. This favors catalysis of the formation of unstable ylides at enzyme active sites of low dielectric constant. A brief survey of enzymes that catalyze deprotonation of cationic carbon acids and related decarboxylation reactions shows catalysis generally occurs for substrates that are bound in a deep pocket on the protein, with an apparent dielectric constant that is much lower than for the solvent water. In several cases, proton transfer is to a catalytic residue that is relatively weakly solvated in water. We suggest that there is a strong advantage for evolution of protein catalysts that utilize weakly solvated basic side chains which are relatively easily buried in nonpolar active sites that are favorable for zwitterion formation.

Carbon acidity of the α-pyridinium carbon of a pyridoxamine analog

We report second-order rate constants of kDO = 120 dm(3) mol(-1) s(-1) and kB = 6.4 x 10(-4) dm(3) mol(-1) s(-1) for exchange for deuterium of the first alpha-methylene proton of the 4-(aminomethyl)pyridine dication in D2O at 25 degree C and I= 1.0 (KCl). These data are consistent with a carbon acid pKa between 17 and 19 for ionization of this simple carbon acid and they show that the effect of an alpha-pyridinium substituent on carbon acidity is similar to that of an alpha-ester substituent.

Direct synthesis of unprotected 4-aryl phenylalanines via the Suzuki reaction under microwave irradiation

[formula: see text] 4-Aryl phenylalanines were prepared as free amino acids from the Suzuki coupling of 4-borono phenylalanine with aryl halides in high yields within 5-10 min under microwave irradiation.