The use of cycloamylose to probe the “charge-relay” system

The effect of the combination of imidazolyl and carboxyl groups on the cleavage of m-t-butylphenyl acetate in the presence of α-cyclodextrin was examined to shed light on the role of the “charge-relay” system in serine esterases. 2-Benzimidazole-acetic acid, which has both the imidazolyl and carboxyl groups in the same molecule, accelerates the cleavage of m-t-butylphenyl acetate in the presence of α-cyclodextrin. On the other hand, neither benzimidazole (which has only an imidazolyl group) nor 2-naphthaleneacetic acid (which has only a carboxyl group) exhibited measurable acceleration. The cleavage of m-t-butylphenyl acetate by the α-cyclodextrin-2-benzimidazolecetic acid system takes place through inclusion complex formation between m-t-butylphenyl acetate and α-cyclodextrin, followed by catalysis associated with the combination of the carboxyl anion, the neutral imidazolyl group, and the alkoxide anion. The most probable explanation for the combination of the three groups in the catalysis involves nucleophilic attack by the imidazolyl group, assisted by the carboxyl and alkoxide anions. The mechanism of the combination of the imidazolyl, carboxyl, and hydroxyl groups is apparently different from those shown by the “charge-relay” system in enzymatic reactions.     

Role of arginine in chemical cross-linking with N-hydroxysuccinimide esters

In order to clarify whether arginine has a promoting effect on the acylation of hydroxyl groups of serine, threonine, or tyrosine by homobifunctional cross-linking agents in aqueous solution, we carried out systematic experiments with model peptides, comparing relative reaction yields with covalently protected and unprotected arginines by MALDI-MS. The guanidinium group could be demonstrated to contribute to the reactivity of hydroxyl groups toward N-hydroxysuccinimide esters and catalyze the nucleophilic substitution, probably via hydrogen bonds.     

Cycloamylose-accelerated cleavage of acylimidazoles

Hydrolyses of N-trans-cinnamoylimidazole (1) and N-acetylimidazole (2) were accelerated by cyclohexaamylose (α-CA) and cycloheptaamylose (β-CA) at 25°C. The cleavage of the amide bond in 1 at pH 9.0 was accelerated by α-CA and β-CA by 28- and 38-fold, respectively, whereas the cleavage of the amide bond in 2 at pH 7.0 was accelerated by α-CA and β-CA by 50- and 28-fold, respectively. The β-CA-accelerated hydrolysis of 1 proceeded via binding, acylation of β-CA, and deacylation of β-CA trans-cinnamate, which is consistent with the pathway used by serine proteases. The deuterium oxide solvent isotope effects for acylation and deacylation steps indicate nucleophilic attack in acylation and general basic attack in deacylation. The present finding of the acceleration by cycloamyloses in the cleavages of amide bonds in 1 and 2 indicates that cycloamyloses are an excellent model for hydrolytic enzymes.     

Conformation of the active site of thiolsubtilisin: reaction with specific chloromethyl ketones and arylacryloylimidazoles.

The conformation of the active site of thiolsubtilisin, prepared from subtilisin by transformation of the active site Ser to Cys, was compared with that of subtilisin by kinetic and spectroscopic methods. Carbobenzyloxy-L-alanylglycyl-L-phenylalanine chloromethyl ketone inhibited thiolsubtilisin approximately 10(2) times faster than subtilisin; alkylation occurred at the sulfhydryl rather than the imidazolyl group of the active site. pH dependence of the inhibition is different from that of the reaction between a simple thiol with haloacetamide. Furthermore, several native chromophoric arylacryloyl-thiolsubtilisins and arylacryloyl-subtilisins showed similar red shifts when compared with their denatured forms. The rate of deacylation of arylacryloyl-thiolsubtilisins was faster than (or of the same order of magnitude as) the deacylation rate of the analogous arylacryloyl-subtilisins in 30% dioxane (v/v), pH 5--10. The deacylation rate--pH profiles of these arylacryloyl-thiolsubtilisins in 30% dioxane all give pK values of 7.7 which is identical with the pK in the deacylation of acyl-subtilisins. These facts strongly suggest that the active-site conformation remains intact on conversion from subtilisin to thiolsubtilisin. The low esterase and peptidase activities of thiolsubtilisin are most likely due to the relatively low basicity of -SH (compared with -OH).     

The effect of substrate structure on the chemoselectivity of Candida antarctica lipase B-catalyzed acylation of amino-alcohols

The selective acylation of multifunctional compounds exhibiting both alcohol and amino groups gives interesting products with many applications in food, cosmetic and pharmaceutical industries, but it is real challenge. The current work describes the different behavior shown by Candida antarctica lipase B (Novozym 435) when catalyzing the O-acylation and N-acylation of bifunctional acyl acceptors. The acylation of three amino-alcohols (alaninol, 4-amino-1-pentanol and 6-amino-1-hexanol) was studied using myristic acid as an acyl donor. To achieve this, a structure-reactivity study was performed in tert-amyl alcohol as a solvent, comparing the three amino-alcohols as acyl acceptors and a series of structurally related amines, namely (R)-sec-butylamine, 1-methoxy-2-propylamine and 1,2-diaminopropane. These substrates were designed to investigate the effect of the group located in β-position of the amino group on the acyl acceptor: the more nucleophilic the group, the more the apparent maximal velocity (V_max,app) of N-acylation increases. Moreover, the crucial role of the carbon chain length between the alcohol and amino groups on the chemoselectivity was also demonstrated. The chemoselectivity for the N-acylation was improved when the carbon chain included two carbons (alaninol) whereas the chemoselectivity for the O-acylation was improved when the carbon chain included four carbons or more (4-amino-1-pentanol and 6-amino-1-hexanol).These results provided new insights for the selective synthesis of amides or esters produced from the acylation of bifunctional substrates.     

Kinetic and mechanistic studies of penicillin-binding protein 2x from Streptococcus pneumoniae.

High molecular weight penicillin-binding proteins (PBPs) are bifunctional enzymes that build bacterial cell walls from the glycopeptide lipid II [GlcNAc-MurNAc(L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-pyrophosphate-undecaprenol] by a process involving disaccharide polymerization and peptide cross-linking. The latter reaction involves acyl-transfer chemistry in which the penultimate (D)Ala first acylates the active-site serine, with release of the terminal (D)Ala, and is then transferred to the epsilon-amine of a Lys on a neighboring pentapeptide chain. These enzymes also catalyze hydrolysis of specific thioester substrates and acylation by beta-lactam antibiotics. In this paper, we explore these latter two reactions and report mechanistic experiments on the reaction of Streptococcus pneumoniae PBP 2x with N-benzoyl-(D)Ala-thioacetic acid [Bz-(D)Ala-(S)Gly] and penicillin G. For these experiments, we used PBP 2x, a soluble form of PBP 2x in which the transmembrane domain was deleted. The following results are significant: (1) pH dependencies for acylation of PBP 2x by penicillin G and Bz-(D)Ala-(S)Gly are identical, suggesting that the same ionizable residues are involved in both reactions and that these residues play the same catalytic role in the two processes. On the basis of these results, we propose a mechanistic model that is also consistent with recently published structural data [Gordon, E., et al. (2000) J. Mol. Biol. 299, 477-485]. (2) Pre-steady-state experiments for the PBP 2x-catalyzed hydrolysis of Bz-(D)Ala-(S)Gly at pH 6.5 indicate that k(c) is principally rate-limited by acylation with some contribution from deacylation. The contribution of these steps to rate limitation is pH-dependent, with acylation entirely rate-limiting at pH values less than 5.5 and deacylation principally rate-limiting above pH 8.5. (3) Results of solvent isotope effect and proton inventory experiments for acylation suggest a complex process that is at least partially rate-limited by chemistry with some involvement of changes in solvation and/or enzyme conformation. (4) Analysis of activation parameters suggests that during the acylation of PBP 2x by penicillin G the inherent chemical stability of penicillin's amide bond, as manifested in the enthalpy of activation, is offset by a favorable entropy term that reflects penicillin's rotationally constrained bicyclic system, which presumably allows a less energetically demanding entry into the transition state for acylation.     

Isoleucyl-tRNA synthetase inactivation and the extent of aminoacylation of tRNAIle from Escherichia coli.

A difference in isoleucine acceptance between normal and sulfur-deficient tRNA from Escherichia coli C6 (rel-, met-, cys-) was eliminated when more isoleucyl-tRNA synthetase was added at the reaction plateau. Enzymatic deacylation was similar for both tRNAs. These results suggest that enzyme inactivation caused a premature reaction plateau which was not predicted by the rates of acylation and deacylation.     

Multifunctional hydrolytic catalysis: VI. Catalytic hydrolysis of p-nitrophenyl acetate by N-(4-imidazolylmethyl)benzohydroxamic acid

A bifunctional catalyst, N-(4-imidazolylmethyl)benzohydroxamic acid, was synthesized from benzohydroxamic acid and chloromethylimidazole, and used for the hydrolysis of p-nitrophenyl acetate. The reaction proceeded via the formation of the acetyl hydroxamate and its subsequent decomposition. The deacylation step was shown to be general base-catalyzed by the intramolecular imidazole group on the basis of the deuterium solvent kinetic isotope effect of 2.0. The efficiency of water attack on the acetyl hydroxamate was enhanced 130-fold by the imidazole group. The catalytic process is compared with the reactions of related monofunctional compounds, and finally its significance as a model of the charge relay system is discussed.     

Reaction pathway and free energy profiles for butyrylcholinesterase-catalyzed hydrolysis of acetylthiocholine

The catalytic mechanism for butyrylcholineserase (BChE)-catalyzed hydrolysis of acetylthiocholine (ATCh) has been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical-free energy (QM/MM-FE) calculations on both acylation and deacylation of BChE. Additional quantum mechanical (QM) calculations have been carried out, along with the QM/MM-FE calculations, to understand the known substrate activation effect on the enzymatic hydrolysis of ATCh. It has been shown that the acylation of BChE with ATCh consists of two reaction steps including the nucleophilic attack on the carbonyl carbon of ATCh and the dissociation of thiocholine ester. The deacylation stage includes nucleophilic attack of a water molecule on the carboxyl carbon of substrate and dissociation between the carboxyl carbon of substrate and hydroxyl oxygen of Ser198 side chain. QM/MM-FE calculation results reveal that the acylation of BChE is rate-determining. It has also been demonstrated that an additional substrate molecule binding to the peripheral anionic site (PAS) of BChE is responsible for the substrate activation effect. In the presence of this additional substrate molecule at PAS, the calculated free energy barrier for the acylation stage (rate-determining step) is decreased by ~1.7 kcal/mol. All of our computational predictions are consistent with available experimental kinetic data. The overall free energy barriers calculated for BChE-catalyzed hydrolysis of ATCh at regular hydrolysis phase and substrate activation phase are ~13.6 and ~11.9 kcal/mol, respectively, which are in reasonable agreement with the corresponding experimentally derived activation free energies of 14.0 kcal/mol (for regular hydrolysis phase) and 13.5 kcal/mol (for substrate activation phase).     

Enzymatic acylation of polar dipeptides: Influence of reaction media and molecular environment of functional groups

The enzymatic acylation of polar dipeptides was investigated. First, the Novozym435^®-catalyzed acylation of Lys-Ser, HCl exhibiting three potential acylable sites was carried out in organic media (2-methyl-2-butanol, oleic acid) and in an ionic liquid ([Bmim]⁺[PF₆]^?). In these reactions, the chemo-selectivity of the acylation was exclusively in favour of the N?-lysine acylation and the efficiency (substrate conversion) was demonstrated to be under control of the peptide solubility. The use of [Bmim]⁺[PF₆]^? permitted to significantly improve the dipeptide solubility, and to enhance both substrates conversion and initial rates of acylation reaction. In the three reaction media used, the O-acylated derivative of the dipeptide was never detected suggesting a weak reactivity of the serine hydroxyl group due to its molecular environment and particularly to the presence of a free carboxylic group known for its electroattractor property.Last, the acylation of a natural dipeptide (carnosine), exhibiting a very low solubility in organic solvents, was also performed. Carnosine was successfully N-acylated in 2-methyl-2-butanol, and a yield of 39% was obtained when improving the substrate solubility: a better dispersibility was obtained by application of a high pressure on the reaction medium just before starting the reaction.     

Inhibition of chymotrypsin and pancreatic elastase by 4H-3,1-benzoxazin-4-ones

Eight 3,1-Benzoxazin-4-ones have been used to inactivate chymotrypsin and pancreatic elastase. Whereas 6,7-dimethoxy substitution only slightly decreased the acylation rate constant, the deacylation reaction was nearly unaffected. Bulky alkoxy groups in position 2 of the heterocyclic moiety were shown to increase enormously the acylation rate of chymotrypsin, but not that of elastase.     

Effect of acyl chain length on selective biocatalytic deacylation on O-aryl glycosides and separation of anomers

It has been demonstrated that Lipozyme® TL IM (Thermomyces lanuginosus lipase immobilised on silica) can selectively deacylate the ester function involving the C-5′ hydroxyl group of α-anomers over the other acyl functions of anomeric mixture of peracylated O-aryl α,β-D-ribofuranoside. The analysis of results of biocatalytic deacylation reaction revealed that the reaction time decreases with the increase in the acyl chain length from C₁ to C₄. The unique selectivity of Lipozyme® TL IM has been harnessed for the separation of anomeric mixture of peracylated O-aryl α,β-D-ribofuranosides, The lipase mediated selective deacylation methodology has been used for the synthesis of O-aryl α-D-ribofuranosides and O-aryl β-D-ribofuranosides in pure forms, which can be used as chromogenic substrate for the detection of pathogenic microbial parasites containing glycosidases.     

Cleavage of beta-lactone ring by serine protease. Mechanistic implications

Both enantiomers of 3-benzyl-2-oxetanone (1) were found to be slowly hydrolyzed substrates of alpha-chymotrypsin having k(cat) values of 0.134+/-0.008 and 0.105+/-0.004 min(-1) for (R)-1 and (S)-1, respectively, revealing that alpha-CT is virtually unable to differentiate the enantiomers in the hydrolysis of 1. The initial step to form the acyl-enzyme intermediate by the attack of Ser-195 hydroxyl on the beta-lactone ring at the 2-position in the hydrolysis reaction may not be enzymatically driven, but the relief of high ring strain energy of beta-lactone may constitute a major driving force. The deacylation step is also attenuated, which is possibly due to the hydrogen bond that would be formed between the imidazole nitrogen of His-57 and the hydroxyl group generated during the acylation in the case of (R)-1, but in the alpha-CT catalyzed hydrolysis of (S)-1 the imidazole nitrogen may form a hydrogen bond with the ester carbonyl oxygen.     

Papain-catalysed hydrolysis of some hippuric esters. A new mechanism for papain-catalysed hydrolyses

1. The Michaelis–Menten parameters for the papain-catalysed hydrolysis of a number of alkyl, aryl and alkyl-thiol esters of hippuric acid have been determined. 2. For all the aryl esters and most of the alkyl esters studied, the catalytic constant, k₀, is 2–3sec.⁻¹ and most probably represents deacylation of the common intermediate, hippuryl-papain. 3. Two alkyl esters and hippurylamide, however, have catalytic rate constants, k₀, less than 2–3sec.⁻¹. It is possible to interpret all the available kinetic data in terms of a three-step mechanism in which an enzyme–substrate complex is first formed, followed by acylation of the enzyme through an essential thiol group, followed by deacylation of the acyl-enzyme. 4. The logarithm of the ratio of the Michaelis–Menten parameters, which reflect the acylation rate constant, for four aryl esters of hippuric acid studied give a linear Hammett plot against the substituent constant, σ. Arguments are presented that indicate acid as well as nucleophilic catalysis in the acylation process and that the most likely proton donor is an imidazolium ion. 5. It is suggested that this imidazolium ion is part of the same histidine residue that has been tentatively implicated in the deacylation process (Lowe & Williams, 1965b). 6. A new mechanism is proposed for the papain-catalysed hydrolysis of N-acyl-α-amino acid derivatives.     

Catalytic activity of α-chymotrypsin in which histidine-57 has been methylated

The properties of a derivative of alpha-chymotrypsin in which histidine-57 has been methylated have been examined. Although the modified enzyme binds substrate with the same affinity as does native alpha-chymotrypsin, acylation and deacylation occur at much decreased rates. As for native alpha-chymotrypsin, a basic group of pK(a) approx. 7 is involved in both acylation and deacylation. The significance of these results is considered in relation to the normal function of histidine-57.     

Multifunctional hydrolytic catalysis: II. Hydrolysis of p-nitrophenyl acetate by a polymer catalyst which contains hydroxamate and imidazole functions

A water-soluble polymer catalyst was prepared by radical polymerization of a protected hydroxamate monomer, 1-methyl-2-vinylimidazole and acrylamide, and by the subsequent NH₂NH₂ treatment of the polymer. The hydrolysis of p-nitrophenyl acetate by the bifunctional copolymer obeyed typical burst kinetics: rapid accumulation of acetyl hydroxamate group and its slow decomposition. The acetylation rate of the hydroxamate group was rather close to that of a polymer which does not contain the imidazole unit. However, the deacylation was markedly accelerated by the presence of the imidazole unit, and the difference in rate constants amounted to 60- to 80-fold at pH 8–9. These results indicate that the overall catalytic efficiency of the bifunctional polymer is enhanced due to the complementary action of the imidazole and hydroxamate functions.     

Characterization of the Prostate-Specific Antigen (PSA) Catalytic Mechanism: A Pre-Steady-State and Steady-State Study

Prostate-specific antigen (PSA), an enzyme of 30 kDa grouped in the kallikrein family is synthesized to high levels by normal and malignant prostate epithelial cells. Therefore, it is the main biomarker currently used for early diagnosis of prostate cancer. Here, presteady-state and steady-state kinetics of the PSA-catalyzed hydrolysis of the fluorogenic substrate Mu-His-Ser-Ser-Lys-Leu-Gln-AMC (spanning from pH 6.5 to pH 9.0, at 37.0°C) are reported. Steady-state kinetics display at every pH value a peculiar feature, represented by an initial “burst” phase of the fluorescence signal before steady-state conditions are taking place. This behavior, which has been already observed in other members of the kallikrein family, suggests the occurrence of a proteolytic mechanism wherefore the acylation step is faster than the deacylation process. This feature allows to detect the acyl intermediate, where the newly formed C-terminal carboxylic acid of the cleaved substrate forms an ester bond with the -OH group of the Ser195 catalytic residue, whereas the AMC product has been already released. Therefore, the pH-dependence of the two enzymatic steps (i.e., acylation and deacylation) has been separately characterized, allowing the determination of pK_a values. On this basis, possible residues are tentatively identified in PSA, which might regulate these two steps by interacting with the two portions of the substrate.     

Characterization of a complete cycle of acetylcholinesterase catalysis by <Emphasis Type="Italic">ab initio</Emphasis> QM/MM modeling

The reaction mechanism of acetylcholine hydrolysis by acetylcholinesterase, including both acylation and deacylation stages from the enzyme-substrate (ES) to the enzyme-product (EP) molecular complexes, is examined by using an ab initio type quantum mechanical – molecular mechanical (QM/MM) approach. The density functional theory PBE0/aug-6–31+G* method for a fairly large quantum part trapped inside the native protein environment, and the AMBER force field parameters in the molecular mechanical part are employed in computations. All reaction steps, including the formation of the first tetrahedral intermediate (TI1), the acylenzyme (EA) complex, the second tetrahedral intermediate (TI2), and the EP complex, are modeled at the same theoretical level. In agreement with the experimental rate constants, the estimated activation energy barrier of the deacylation stage is slightly higher than that for the acylation phase. The critical role of the non-triad Glu202 amino acid residue in orienting lytic water molecule and in stabilizing the second tetrahedral intermediate at the deacylation stage of the enzymatic process is demonstrated. Figure The computed energy diagram for the reaction path from the enzyme – substrate complex (ES) to the enzyme-product complex (EP).     

The deacylation of substituted benzol-alpha-chymotrypsins.

An extensive comparison of deacylation rates of mono- and disubstituted benzoyl-α-chymotrypsins indicates that no steric effects on rate or apparent pK_a of deacylation are detectable within this series. Some anomalous effects on deacylation rate appear to be associated with fluoro- and nitro-substituents in particular positions on the ring and may be attributable to specific interactions at the enzyme active site. The extensive series of structurally similar acyl-enzymes prepared has allowed a thorough analysis of the effect of acyl group pK_a on the apparent pK_a of deacylation. The data indicates that polar effects on the apparent pK_a are probably negligible. Rho for the deacylation reaction is in good agreement with model reactions for an imidazole general base-catalyzed model reaction.