Enzyme reaction engineering: design of peptide synthesis by stabilized trypsin.

By using very active and very stable trypsin agarose derivatives, we have optimized the design of the synthesis of a model dipeptide, benzoylarginine leucinamide, by two different strategies: (i) kinetically controlled synthesis (KCS), by using benzoyl arginine ethyl ester and leucinamide as substrates, and (ii) thermodynamically controlled synthesis (TCS), by using benzoyl arginine and leucinamide as substrates. In each strategy, we have studied the integrated effect of a number of variables that define the reaction medium on different parameters of industrial interest, e.g. time course of peptide synthesis, higher synthetic yields, and stability of the catalyst, as well as aminolysis/hydrolysis ratios and rate of peptide hydrolysis in the case of KCS. Both synthetic approaches were carried out in monophasic water or water-organic cosolvent systems. We have mainly tested a number of variables, e.g. temperature, polarity of the reaction medium (presence of cosolvents, presence of ammonium sulfate), and exact structure of the trypsin derivatives. Optimal experimental conditions for these synthetic approaches were established in order to simultaneously obtain good values for all industrial parameters. The use of previously stabilized trypsin derivatives greatly improves the design of these synthetic approaches (e.g. by using drastic experimental conditions: 1 M ammonium sulfate (KCS) or 90% organic cosolvents (TCS]. In these conditions, our derivatives preserve more than 95% of activity after 2 months and we have been able to reach synthetic productivities of 180 (KCS) and 1 (TCS) tons of dipeptide per year per liter of catalyst.     

Protein hydrolysis by immobilized and stabilized trypsin

The preparation of novel immobilized and stabilized derivatives of trypsin is reported here. The new derivatives preserved 80% of the initial catalytic activity toward synthetic substrates [benzoyl-arginine p-nitroanilide (BAPNA)] and were 50,000-fold more thermally stable than the diluted soluble enzyme in the absence of autolysis. Trypsin was immobilized on highly activated glyoxyl-Sepharose following a two-step immobilization strategy: (a) first, a multipoint covalent immobilization at pH 8.5 that only involves low pK(a) amino groups (e.g., those derived from the activation of trypsin from trypsinogen) is performed and (b) next, an additional alkaline incubation at pH 10 is performed to favor an intense, additional multipoint immobilization between the high concentration of proximate aldehyde groups on the support surface and the high pK(a) amino groups at the enzyme surface region that participated in the first immobilization step. Interestingly, the new, highly stable trypsin derivatives were also much more active in the proteolysis of high molecular weight proteins when compared with a nonstabilized derivative prepared on CNBr-activated Sepharose. In fact, all the proteins contained a cheese whey extract had been completely proteolyzed after 6 h at pH 9 and 50°C, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Under these experimental conditions, the immobilized biocatalysts preserve more than 90% of their initial activity after 20 days. Analysis of the three-dimensional (3D) structure of the best immobilized trypsin derivative showed a surface region containing two amino terminal groups and five lysine (Lys) residues that may be responsible for this novel and interesting immobilization and stabilization. Moreover, this region is relatively far from the active site of the enzyme, which could explain the good results obtained for the hydrolysis of high-molecular weight proteins.     

Chemically modified, immobilized trypsin reactor with improved digestion efficiency

Tryptic digestion followed by identification using mass spectrometry is an important step in many proteomic studies. Here, we describe the preparation of immobilized, acetylated trypsin for enhanced digestion efficacy in integrated protein analysis platforms. Complete digestion of cytochrome c was obtained with two types of modified-trypsin beads with a contact time of only 4 s, while corresponding unmodified-trypsin beads gave only incomplete digestion. The digestion rate of myoglobin, a protein known to be rather resistant to proteolysis, was not altered by acetylating trypsin and required a buffer containing 35% acetonitrile to obtain complete digestion. The use of acetylated-trypsin beads led to fewer interfering tryptic autolysis products, indicating an increased stability of this modified enzyme. Importantly, the modification did not affect trypsin's substrate specificity, as the peptide map of myoglobin was not altered upon acetylation of immobilized trypsin. Kinetic digestion experiments in solution with low-molecular-weight substrates and cytochrome c confirmed the increased catalytic efficiency (lower K(M) and higher k(cat)) and increased resistance to autolysis of trypsin upon acetylation. Enhancement of catalytic efficiency was correlated with the number of acetylations per molecule. The favorable properties of the new chemically modified trypsin reactor should make it a valuable tool in automated protein analysis systems.     

Ribozyme-catalyzed dipeptide synthesis in monovalent metal ions alone

Previously we have identified a highly active ribozyme (R180, cis ribozyme) that can catalyze dipeptide synthesis using N-biotinylcaproyl-aminoacyl-adenylate anhydride (Bio-aa-5'-AMP) as its substrate. In this work, we re-engineered the cis R180 ribozyme into a 158-nt trans ribozyme (TR158) and designed a new substrate (5'-Phe-linker-20-mer). First, the metal ion requirements were examined and compared between the two ribozymes. Both R180 and TR158 ribozymes were active in Mg2+ and Ca2+ but inert with Zn2+, Cu2+, Mn2+, and Co2+. It is intriguing that both ribozymes were highly active in Li+, Na+, or K+ alone but showed very low activity with NH4+. The two ribozymes showed similar linear concentration dependence on Li+ and K+, while they displayed different dependency behavior on Mg2+. Moreover, by using the trans system, the detailed kinetic studies and pH dependent experiments were performed in either 10 mM Mg2+ or 1.0 M Li+. Analysis of kcat and Km values obtained at different pHs (6.0 to 9.0) indicated that it is the catalytic activity of the ribozyme but not the substrate binding affinity that changes significantly with pH. The slopes of the linear parts of the pH-rate plots were close to 1.0 in both Mg2+- and Li+-mediated reactions, suggesting that one proton transfer is involved in the rate-limiting step of catalysis. Overall, our results suggest that Mg2+ and Li+ function similarly in the ribozyme-catalyzed dipeptide synthesis.     

Cell-free synthesis of the dipeptide antibiotic bacilysin

Summary Bacilysin, a dipeptide antibiotic produced byBacillus subtilis A 14, was synthesized by a cell-free extract of the producing organism from its constitutent amino acids,l-alanine andl-anticapsin. The synthesis required ATP and Mg²⁺ and was optimal at pH 8.1. The same extract also synthesizedl-alanyl-l-alanine. The synthesis of bacilysin was not inhibited by chloramphenicol, DNase or RNase.     

Dipeptide synthesis using acetylated trypsin derivative

A modified trypsin (AA-trypsin, acetylated with acetic acid N-hydroxysuccinimide ester) gave increased yields of Bzl-Arg-Leu-NH₂ dipeptide (90% versus 59% for native trypsin) when used in 95% acetonitrile. AA-Trypsin had decreased K_m and increased k_cat values for amide and ester substrates. k_cat/K_m also increased for each substrate upon modification. AA-Trypsin showed enhanced esterase activity in hydrophilic solvents compared with native enzyme.     

Effects of trypsin on protein synthesis in macrophages

Treatment of rabbit alveolar macrophages with crystalline trypsin (0.04–2 mg/10⁸ cells) inhibits protein synthesis and results in increased leakage of cell proteins. Trypsinization does not significantly decrease cellular DNA content or viability, and it does not increase protein breakdown.Trypsin treatment results in decreased oxidation of [1-¹⁴C]glucose and [6-¹⁴C]glucose, and also a decrease in ATP content. Trypsinization also causes a depression of net leucine transport and a reduction in the translational activity of polyribosomes.When normal and trypsinized macrophages are preincubated at 37 °C for several hours and then pulse-labelled with radioactive leucine, protein synthesis is stimulated to approximately the same extent in both the control and the enzyme-treated cells. Since the trypsinized cells still exhibit depressed protein synthesis, this suggests that the inhibition cannot be readily reversed.Indirect evidence indicates that the inhibition of protein synthesis is not due to entry of trypsin into the cells and suggests that the inhibition is due to changes in metabolism resulting from the action of the enzyme at the cell surface.     

Trypsin-catalyzed synthesis of the arginyl-arginine dipeptide froml-arginine ethyl ester

Summary Trypsin has been found to catalyze oligomerization ofl-arginine ethyl ester in aqueous reaction media. More than 40% of the substrate has been converted mostly to arginyl-arginine under the optimized reaction conditions (pH 10; [trypsin]10M; [substrate]0.5M).     

Asymmetric synthesis of novel quaternary alpha-hydroxy-delta-lactam dipeptide surrogates.

Application of the Sharpless AD protocol to a series of alpha-(E)-benzylidene-delta-lactam precursors followed by selective deoxygenation provided efficient synthetic routes to the chiral quaternary alpha-hydroxy-gammalactam derivatives 4 and 5. These functionalized intermediates and the diol precursors 3 are regarded as novel types of D-Phe-Pro dipeptide surrogates that are useful as enzyme active site probes.     

Kinetically controlled enzymatic synthesis of dipeptide precursor of L-alanyl-L-glutamine

An important nutritional dipeptide precursor, benzoyloxycarbonyl protected L-alanyl-L-glutamine (Z-Ala-Gln), was successfully prepared through a kinetically controlled enzymatic peptide synthesis method. A commercially available and low-cost protease (papain) was used as biocatalyst with Z-Ala-OMe and Gln as acyl donor and nucleophile, respectively. The dipeptide yield was 35.5% under the optimized reaction conditions: 35°C, pH 9.5, and the ratio of acyl donor/nucleophile is 1:10. Based on the reaction mechanism and experimental data, the kinetic model was established, which was in accordance with the Michaelis-Menten equation, and the apparent Michaelis constant K(m)(app) and the apparent maximum reaction rate r(max)(app) were calculated as 1.71 mol/L and 6.09 mmol/(L Min), respectively.     

Enzymatic synthesis of dipeptide units of the D-D-configuration in aqueous media

The enzymatic synthesis of dipeptide units of the D-D-configuration in aqueous media, catalysed by muramoyl-pentapeptide carboxypeptidase (E.C.3.4.17.8), is described. Ac-L-Lys(Ac)-D-Ala-D-Lac-OH and Ac-D-Ala-OMe were used as acyl-components. Neutral, basic, and hydrophobic amino acids acting as nucleophiles were incorporated. The enzyme is stereospecific in that only the D-enantiomers of amino acids or amino acid derivatives were incorporated. As nucleophiles, the unmodified amino acids resulted in higher product yields compared with using the corresponding amino acid derivatives. Product yields ranged from 40 to 87%.     

Enzymatic dipeptide synthesis by surfactant-coated alpha-chymotrypsin complexes in supercritical carbon dioxide

Enzymatic dipeptide synthesis by surfactant-coated alpha-chymotrypsin complexes was performed in supercritical CO(2) and liquid CO(2) at 308.2 and 333.2 K at pressures of 6.1 and 10.1 MPa. The enzymatic activity of coated alpha-chymotrypsin complexes for dipeptides synthesis at 10.1 MPa in supercritical CO(2) (SC-CO(2)) was higher than that in a liquid CO(2) and ethyl acetate solution at 6.1 MPa. The behavior of alpha-chymotrypsin in SC-CO(2) was similar to that in liquid ethyl acetate. And increasing the pressure and temperature increased the maximum conversion and the enzymatic reaction rate in SC-CO(2). Furthermore, the control of the water content in the reaction media had a dominant effect on the enzymatic activity. The maximum conversion for the dipeptide synthesis by the surfactant-coated alpha-chymotrypsin was obtained at 4% water content. The alpha-chymotrypsin complexes exhibited a higher enzymatic activity than native alpha-chymotrypsin in SC-CO(2). The nonionic surfactants l-glutamic acid dialkyl ester ribitol amide and sorbitan monostearate were more favored than the anionic surfactant sodium bis(2-ethylhexyl)sulfosuccinate.     

Automated solid-phase synthesis of metabolically stabilized triazolo-peptidomimetics

The use of 1,4-disubstituted 1,2,3-triazoles as trans-amide bond surrogates has become an important tool for the synthesis of metabolically stabilized peptidomimetics. These heterocyclic bioisosters are generally incorporated into the peptide backbone by applying a diazo-transfer reaction followed by CuAAC (click chemistry) with an α-amino alkyne. Even though the manual synthesis of backbone-modified triazolo-peptidomimetics has been reported by us and others, no procedure has yet been described for an automated synthesis using peptide synthesizers. In order to efficiently adapt these reactions to an automated setup, different conditions were explored, putting special emphasis on the required long-term stability of both the diazo-transfer reagent and the Cu(I) catalyst in solution. ISA·HCl is the reagent of choice to accomplish the diazo-transfer reaction; however, it was found instable in DMF, the most commonly used solvent for SPPS. Thus, an aqueous solution of ISA·HCl was used to prevent its degradation over time, and the composition in the final diazo-transfer reaction was adjusted to preserve suitable swelling conditions of the resins applied. The CuAAC reaction was performed without difficulties using [Cu (CH₃CN)₄]PF₆ as a catalyst and TBTA as a stabilizer to prevent oxidation to Cu(II). The optimized automated two-step procedure was applied to the synthesis of structurally diverse triazolo-peptidomimetics to demonstrate the versatility of the developed methodology. Under the optimized conditions, five triazolo-peptidomimetics (8–5 amino acid residues) were synthesized efficiently using two different resins. Analysis of the crude products by HPLC-MS revealed moderate to good purities of the desired triazolo-peptidomimetics (70–85%). The synthesis time ranged between 9 and 12.5 h.     

New stabilized FastPrep-CLEAs for sialic acid synthesis

N-acetyl-d-neuraminic acid aldolase, a key enzyme in the biotechnological production of N-acetyl-d-neuraminic acid (sialic acid) from N-acetyl-d-mannosamine and pyruvate, was immobilized as cross-linked enzyme aggregates (CLEAs) by precipitation with 90% ammonium sulfate and crosslinking with 1% glutaraldehyde. Because dispersion in a reciprocating disruptor (FastPrep) was only able to recover 40% of the activity, improved CLEAs were then prepared by co-aggregation of the enzyme with 10 mg/mL bovine serum albumin followed by a sodium borohydride treatment and final disruption by FastPrep (FastPrep-CLEAs). This produced a twofold increase in activity up to 86%, which is a 30% more than that reported for this aldolase in cross-linked inclusion bodies (CLIBs). In addition, these FastPrep-CLEAs presented remarkable biotechnological features for Neu5Ac synthesis, including, good activity and stability at alkaline pHs, a high K_M for ManNAc (lower for pyruvate) and good operational stability. These results reinforce the practicability of using FastPrep-CLEAs in biocatalysis, thus reducing production costs and favoring reusability.     

Kinetic study of nucleophile specificity in dipeptide synthesis catalyzed by clostridiopeptidase B

The kinetic parameters of Clostridiopeptidase B-catalyzed aminolysis of carbobenzoxyarginyl methyl ester leading to the formation of various dipeptides are investigated. The deacylation rates of the acylenzyme were evaluated by direct product analysis using high-performance liquid chromatography on a reversed-phase column. On the basis of the partitioning ratio and the first-order and second-order rate constants for the deacylation step, large differences in the nucleophile reactivities, which appear to be related to a S'1-P'1 interaction, were observed. The order of specificity was established as Leu much greater than Ser greater than Phe greater than Val greater than Ala = Gly much greater than Pro with second-order rate constants ranging from 578,614 M-1 s-1 for leucinamide to 5132 M-1 s-1 in the case of prolinamide. All of the amino acid amides had a nucleophilic strength at least 10 times higher than that of water during the deacylation step. The data reported here represent the first experimental evidence for the existence of a S'1 site engaged in the recognition of the amino acid side chain residue for this enzyme. The recognition site showed an increase in the affinity along with an increase in the hydrophobicity of the amino acid amide side chains.     

Design and synthesis of dipeptide mimetics of the brain-derived neurotrophic factor

Low-molecular-weight mimetics of loops 1 and 4 of the brain-derived neurotrophic factor (BDNF) have been designed and synthesized. The compounds represent monomeric and dimeric amides of N-acyldipeptides. Their dipeptide fragments coincide in sequence with the central regions of beta-turns of the corresponding neurotrophin loops, and acyl groups are the bioesosteres of preceding amino acid residues. Hexa- or heptamethylenediamines were used as spacers to link the C-terminal regions of dipeptides in dimeric mimetics of BDNF. These compounds were synthesized by classical methods of peptide synthesis in solution and received the laboratory codes GSB-104 (HO-Suc-Ser-Lys-NH₂), GSB-106 {[HO-Suc-Ser-Lys-NH-(CH₂)₃?]₂}, GSB-207 (HO-Suc-Met-Ser-NH₂), and GSB-214 ([HO-Suc-Met-Ser-NH-(CH₂)_7/2-]₂). It was shown using immortalized hippocampal cells of the HT22 line under conditions of oxidative stress that the dimeric mimetics of both loops at concentrations of 10^?5?10^?8 M possess a neuroprotective activity. The monomeric loop 1 mimetic GSB-207 in the same concentration range is inactive, and the monomeric loop 4 mimetic GSB-104 at a concentration of 10^?7 impairs the survival of neurons. The finding that only dimeric mimetics possess the neuroprotective activity is consistent with the data indicating that BDNF is active in the homodimeric form. As opposed to the dimeric loop 1 mimetic GSB-214, the dimeric loop 4 mimetic GSB-106 exhibits the antidepressant activity typical for BDNF in the Porsolt test on rats at doses of 0.1 and 1 mg/kg injected intraperitoneally. This suggests that the antidepressant activity of BDNF is related to its 4th loop. We believe that the compounds obtained will be useful in studies of the mechanism of action of BDNF and may form the basis for the design of a novel group of drugs with antidepressant and neuroprotective activities.     

Protease-catalyzed peptide synthesis using inverse substrates: the synthesis of Pro-Xaa-bonds by trypsin

Benzyloxycarbonyl-L-proline p-guanidinophenyl ester is an "inverse substrate" for trypsin; i.e., the cationic center is included in the leaving group instead of being in the acyl moiety. This substrate can be used in trypsin-catalyzed acyl-transfer reactions leading to the synthesis of Pro-Xaa peptide bonds. The reaction proceeds about 20 times slower than reaction with similar alanine-containing substrates, but the ratio between synthesis and hydrolysis is more favorable. The investigation of a series of nucleophiles led to information about the specificity of the process. Nucleophiles differing only in the P(1)'-position show an increasing acyl transfer efficiency in the order Phe < Gly < Ley < Ser < Ala < lle. C terminal elongation of the nucleophiles is of minor influence on their efficiency. The formation of an H bond between the acyl-enzyme and the nucleophile seems to play an important role in the aminolysis of the acyl-enzyme.     

Design and synthesis of acidic dipeptide hydroxamate inhibitors of procollagen C-proteinase.

Procollagen C-proteinase (PCP) is essential for the cleavage of procollagen to collagen in the extracellular matrix of animals and is, therefore, of major relevance to studies of ectopic deposition of collagen during fibrosis. In this study, we describe the design and synthesis of acidic side chain hydroxamate dipeptide inhibitors of PCP having IC50 values in the range 0.1-10 microM that mimic the location of aspartic acid residues in the P1' and P2' positions (i.e. immediately C-terminal) of the PCP cleavage site in procollagen. Assays of PCP using purified human type I procollagen (a natural substrate of PCP) showed that the structure activity relationship of the inhibitors was improved with a glutamic acid mimic at the P1' position. The results also showed that the presence of an acidic side chain at the P2' position was not necessary for PCP inhibition. Marimastat and BB3103, which are highly effective inhibitors of matrix metalloproteinases and ADAMS proteinases, respectively, did not inhibit PCP.