Protease-catalyzed synthesis of oligopeptides in heterogenous substrate mixtures

A systematic study of enzymatic peptide synthesis in heterogeneous substrate mixtures was carried out, with the aim of establishing the preparative scope of this methodology. Semiliquid eutectics were obtained with various combinations of neutral, acidic, and basic amino acid derivatives, in the presence or absence of adjuvants. A range of serine cysteine, and metalloproteases readily catalyzed the formation of the required dipeptides under these conditions. The synthetic usefulness of the approach was demonstrated by the sequential and convergent synthesis of derivatives of a number of bioactive di-, tri-, and pentapeptides, including aspartame, sweet lysine peptide, kyotorphin amide, ACE-inhibiting and -immunoactive tripeptides, and Leu-enkephalin amide, with overallyields of 21% to 84% and productivities of 0.13 to 0.75 g/g being obtained. (c) 1994 John Wiley & Sons, Inc.     

Gluco-oligosaccharide synthesis by free and immobilized beta-glucosidase

Gluco-oligosaccharides were synthesized through the enzymatic condensation of D-glucose at high concentration using a commercial almond beta-glucosidase. The synthesis reactions were carried out with both free and immobilized enzyme, with or without sorbitol, an efficient depressor of water activity (a(w)) in the presence of different glucose concentrations. The yield and the composition of the gluco-oligosaccharides produced changed with the reaction mixture and the form of the enzyme used (free or immobilized). The use of 5 M glucose solution permitted only disaccharides to be obtained, whereas with a glucose concentration of 7.5 M glucose, di-, tri-, and tetrasaccharides were produced. A 7.5 M glucose solution used with 4.4 M sorbitol gave three times more disaccharides than the same solution without sorbitol. Moreover, the immobilized enzyme was much more active in synthesis. The synthesis yield (oligomers mg/mL . mg of enzyme) after immobilization was 573% compared to that of the free enzyme, when a 7.5 M glucose solution was tested. The effects of substrate concentration, sorbitol addition and enzyme immobilization were investigated. (c) 1993 John Wiley & Sons, Inc.     

Kinetics of DNA-dependent RNA synthesis: coupled synthesis of di- and trinucleotides in the presence of a minimum complement of substrate

The qualitative and quantitative characteristics of the synthesis of the short oligonucleotides by Escherichia coli RNA polymerase on A1 promoter of the bacteriophage T7 deletion mutant delta D111 DNA in the presence of the incomplete set of nucleoside triphosphates were studied. It was shown, that in conformity with the structure of A1 promoter the oligonucleotides pppApU, pppApUpC were synthesized in the presence of ATP, UTP, CTP; the oligonucleotides pApU, pApUpC-in the presence of AMP, UTP, CTP and oligonucleotides pApU, pApUpC, pApUpCpG-in the presence of AMP, UTP, CTP, GTP. The curves of di- and trinucleotide syntheses as the functions of the substrate concentrations were obtained. The analytical formulas for the rates of the coupled synthesis were derived from these curves. A kinetic scheme that is in conformity with the experimental data was proposed. This scheme includes the stage of the reversible, random and release of di- and trinucleotides from the enzyme-template complex.     

Efficient synthesis of lactosaminylated core-2 O-glycans

A series of lactosaminylated oligosaccharides found in mucin type O-glycans was synthesized using a generalized block strategy. The synthesis involved the addition of a protected lactosamine donor to a partially protected T-disaccharide derivative. The nonreducing galactose residues of the deblocked oligosaccharide products could be removed by beta-galactosidase from jack bean to produce the corresponding GlcNAc terminated compounds. A series of tri- to hexasaccharides was thus efficiently produced.     

Regulation of the synthesis of M protein by sugars, Todd Hewitt broth, and horse serum, in growing cells of Streptococcus pyogenes.

Various sugars were tested for their effect on the differential rate of synthesis of M protein during the growth of Streptococcus pyogenes strain 0055 M12T12. In a semisynthetic medium alone, a high rate of M protein synthesis occurred with glucose as a substrate; decreasing rates of synthesis occurred with sucrose and trehalose, in that order, although the rates of growth were approximately equal with all sugars. A period of derepressed synthesis of M protein occurred in the lag phase of growth and in the stationary period as the substrates were being depleted. Although glucose inhibited the utilization of other sugars, diauxie was not apparent from the growth curves. However, synthesis of M protein followed strong diauxie curves with a reduction in rate of synthesis during the utilization of the second sugar. With glucose as a substrate, 2-deoxyglucose showed a strong permanent repression of M protein synthesis, whereas both glucose and 2-deoxyglucose caused temporary repression when sucrose was the substrate. Horse serum increased the rate of synthesis of M protein in a manner very similar to that caused by adding cyclic AMP, although quantitative analyses suggested that cyclic AMP, per se, was not the effector in horse serum. Addition of Todd Hewitt broth permitted the organisms to grow on phosphorylated sugars. Although the rates of growth on phosphorylated sugars were similar to that obtained with glucose, M protein was not synthesized when a phosphorylated sugar was the sole substrate. The addition of phosphorylated sugars with glucose or sucrose as substrates strongly repressed the synthesis of M protein with glucose-1-phosphate and with fructose 1,6-diphosphate repressing M protein synthesis the most. Clearly, M protein synthesis, which was not required for growth, was preferentially induced by glucose as compared to the other sugars and was dependent upon the metabolic route by which glucose was utilized.     

Light-directed simultaneous synthesis of oligopeptides on microarray substrate using a photogenerated acid

Photogenerated acid (PGA) was used as the acid to remove the protection group from amino acids or peptide oligomers. Comparative study of the deprotection using a PGA, trisarylsulfonium antimonyhexafluoride (SSb), and trifluoroacetic acid (TFA) was performed on glass microscope slides. The results showed that PGA can replace TFA in the deprotection step of oligopeptide synthesis with comparable efficiencies. Acids needed for the deprotection step were generated in situ by light activation of the precursor molecule on the microwell substrate. A mask-less laser light illumination system was used to activate the precursor. The accuracy of the amino acid sequence of the synthesized oligopeptide and the location of the synthesis was illustrated by the specific recognition binding of two different models: lead(II) ion-peptide biosensor for lead(II) and human protein p53 (residue 20-25)-mouse MAb DO1. After parallel synthesis of the target peptide models and their analogues based on the predetermined pattern, specific binding treatment, and fluorescence labeling, the fluorescence emission images of the oligopeptide microarray showed fluorescence intensity as a result of specific binding at the correct locations of the array. The stepwise synthesis efficiencies of pentapeptide synthesis on the microwell substrate range are approximately 96-100% and do not decrease with respect to the chain length of the peptide.     

Combinatorial synthesis, selection, and properties of esterase peptide dendrimers

A 65,536-member combinatorial library of peptide dendrimers was prepared by split-and-mix synthesis and screened on solid support for esterolytic activity in aqueous buffer using 8-butyryloxypyrene-1,3,6-trisulfonate (2) as a fluorogenic substrate. Active sequences were identified by analysis of fluorescent beads. The corresponding dendrimers were resynthesized by solid-phase synthesis, cleaved from the resin, and purified by preparative reverse-phase HPLC. The dendrimers showed the expected catalytic activity in aqueous buffer. Catalysis was studied against a pannel of fluorogenic 8-acyloxypyrene-1,3,6-trisulfonate substrates. The catalytic peptide dendrimers display enzyme-like kinetics in aqueous buffer with substrate binding in the range K(M) approximately 0.1 mM, catalytic rate constants k(cat) approximately 0.1 min(-1), and specific rate accelerations over background up to k(cat)/k(uncat) = 10,000.     

Chemoenzymatic synthesis and lectin recognition of a selectively fluorinated glycoprotein

A chemoenzymatic glycosylation remodeling method for the synthesis of selectively fluorinated glycoproteins is described. The method consists of chemical synthesis of a fluoroglycan oxazoline and its use as donor substrate for endoglycosidase (ENGase)-catalyzed transglycosylation to a GlcNAc-protein to form a homogeneous fluoroglycoprotein. The approach was exemplified by the synthesis of fluorinated glycoforms of ribonuclease B (RNase B). An interesting finding was that fluorination at the C-6 of the 6-branched mannose moiety in the Man3GlcNAc core resulted in significantly enhanced reactivity of the substrate in enzymatic transglycosylation. A structural analysis suggests that the enhancement in reactivity may come from favorable hydrophobic interactions between the fluorine and a tyrosine residue in the catalytic site of the enzyme (Endo-A). SPR analysis of the binding of the fluorinated glycoproteins with lectin concanavalin A (con A) revealed the importance of the 6-hydroxyl group on the α-1,6-branched mannose moiety in con A recognition. The present study establishes a facile method for preparation of selectively fluorinated glycoproteins that can serve as valuable probes for elucidating specific carbohydrate–protein interactions.     

Inhibitors can activate proteases to catalyze the synthesis and hydrolysis of peptides

Competitive inhibitors can activate proteases (papain, trypsin, and cathepsin S) to catalyze the synthesis of peptide bonds and accelerate the hydrolysis of poor substrates (from 1 to 99%). Reaction mixtures contained intermediate molecules that were formed by the coupling of the inhibitor with the poor substrate. This and other findings suggest the following chain of events. Part of the binding energy of formation of the enzyme-inhibitor complex was used to activate the inhibitor, i.e., to form acyl-enzyme species with a high-energy bond (e.g., a thioester bond in the case of papain) required for coupling the inhibitor with the substrate to form the intermediate molecule. The latter was subjected to successive reactions which led to a stepwise degradation of the substrate, as well as to the regeneration of the inhibitor. One mole of the inhibitor could catalyze rapid hydrolysis of at least 53 mol of substrate. The intermediate molecules were the species undergoing rapid hydrolysis. Therefore, 1 mol of inhibitor was involved in the synthesis of 53 mol of intermediate molecules; i.e., the inhibitor functioned as a cofactor that catalyzed the synthesis of peptides. Thus, the binding energy of formation of the enzyme-inhibitor complex can be utilized to catalyze the synthesis of peptide bonds in the absence of an exogenous energy source (e.g., ATP).     

Carbachol stimulation of phosphatidic acid synthesis: competitive inhibition by pirenzepine in synaptosomes from rat cerebral cortex

Carbachol stimulated phosphatidic acid synthesis in cholinergically enriched synaptosomes from rat cerebral cortex. Increasing concentrations of pirenzepine (10-1000 nM) produced parallel concentration-response curves to carbachol which were shifted to the right. A pA2 value for pirenzepine of 8.4 +/- 0.3 was obtained from Schild analysis. We hypothesize that high affinity pirenzepine binding to M1 receptors is coupled to phosphatidic acid synthesis in the rat cerebral cortex.     

Precipitation of galactose-specific lectins by complex-type oligosaccharides and glycopeptides: studies with lectins from Ricinus communis (agglutinin I), Erythrina indica, Erythrina arborescens, Abrus precatorius (agglutinin), and Glycine max (soybean)

We have recently demonstrated that certain oligomannose and bisected hybrid type glycopeptides and bisected complex type oligosaccharides are bivalent for binding to concanavalin A and can precipitate the lectin [Bhattacharyya, L., Ceccarini, C., Lorenzoni, P., & Brewer, C.F. (1987) J. Biol. Chem. 262, 1288-1293; Bhattacharyya, L., Haraldsson, M., & Brewer, C.F. (1987) J. Biol. Chem. 262, 1294-1299]. The present results show that tri- and tetraantennary complex type oligosaccharides containing nonreducing terminal galactose residues, and a related triantennary glycopeptide, precipitate the D-galactose-specific lectins from Ricinus communis (agglutinin I) (RCA-I), Erythrina indica (EIL), Erythrina arborescens (EAL), and Glycine max (soybean) (SBA). Nonbisected and bisected biantennary complex type oligosaccharides can precipitate SBA, which is a tetrameric lectin, but not RCA-I, EIL, or EAL, which are dimeric lectins. The relative affinities of the oligosaccharides and glycopeptide were determined by hemagglutination inhibition measurements and their valencies by quantitative precipitin analyses. The equivalence points of the precipitin curves indicate that the tri- and tetraantennary oligosaccharides are tri- and tetravalent, respectively, for EIL, EAL, and SBA binding. However, the oligosaccharides are all trivalent for RCA-I binding due apparently to the larger size of the monomeric subunit of the lectin. The triantennary glycopeptide was also trivalent for RCA-I and EIL binding. Biantennary oligosaccharides with adequate chain lengths were found to be bivalent for binding to SBA; those with shorter chains did not precipitate the lectin.(ABSTRACT TRUNCATED AT 250 WORDS)     

Oligonucleotide N-alkylphosphoramidates: synthesis and binding to polynucleotides

A few different methods for the preparation of oligonucleotide N-alkylphosphoramidates were compared directly. One of these, involving the use of protected nucleoside phosphites as building blocks, provided the requisite N-alkylphosphoramidates via oxidation of the intermediate dinucleoside methyl phosphites with iodine in the presence of the appropriate alkylamine. This method was found to have several attractive features, including the use of building blocks identical with those employed for the synthesis of DNA and compatibility with procedures and instruments employed for the stepwise synthesis of oligonucleotides by solution and solid-phase methods. This procedure was used to make several di-, tri-, and tetranucleotide N-alkylphosphoramidates derived from deoxyadenosine and thymidine; alkyl substituents included N,N-dimethyl, N-butyl, N-octyl, N-dodecyl, and N-(5-aminopentyl). The aminoalkyl derivative of d(TpT) (24) was used to demonstrate the feasibility of introducing an intercalative agent to the alkylphosphoramidate moiety of such derivatives. The oligonucleotide N-alkylphosphoramidates were separated into their component diastereomers and characterized structurally by a number of techniques including circular dichroism, high-field 1H NMR spectroscopy, FAB mass spectrometry, and enzymatic digestion to authentic nucleosides and nucleotides. Physicochemical characterization of several di- and trinucleotide alkyl-phosphoramidates revealed that the adenine nucleotide analogues formed stable complexes with poly-(thymidylic acid). The stabilities of these complexes were found to increase with increasing chain length of the N-alkylphosphoramidate substituents. The finding that N-alkylphosphoramidate substituents can enhance the binding of certain oligonucleotides to their complementary polynucleotides suggests the existence of a novel source of polynucleotide affinity.     

Kinetics and specificity of serine proteases in peptide synthesis catalyzed in organic solvents

Initial rates of peptide-bond synthesis catalyzed by poly(ethylene glycol)-modified chymotrypsin in benzene were determined using high-performance liquid chromatography. Enzymatic synthesis of N-benzoyl-L-tyrosyl-L-phenylalanine amide from N-benzoyl-L-tyrosine ethyl ester and L-phenylalanine amide was found to obey Michaelis-Menten kinetics an to be consistent with a ping-pong mechanism modified by a hydrolytic branch. The catalytic activity of modified chymotrypsin was dependent on both water concentration and type of organic solvent, the highest synthesis rate being obtained in toluene. Since the chymotrypsin specificity in the organic phase was actually altered, the enzyme's apparent kinetic parameters were determined for different substrates and compared to those obtained with other serine proteases in benzene. Both N-benzoyl-L-tyrosine ethyl ester and N-alpha-benzoyl-L-lysine methyl ester were comparable acyl donors in benzene and the (kcat/Km)app value of modified chymotrypsin was only 10-fold smaller than that obtained with poly(ethylene glycol)-modified trypsin in the synthesis of N-alpha-benzoyl-L-lysyl-L-phenylalanine amide. The change in chymotrypsin specificity was also confirmed through the binding of trypsin inhibitors in benzene. The overall results suggest that hydrophobic bonding between the enzyme and its substrate should not be taken into account during catalysis in the organic phase. In general, if hydrophobic interactions are involved in the binding of substrates to the active site in aqueous media, the replacement of water by hydrophobic solvents will induce some change in enzyme specificity. Moreover, secondary residues of enzyme-binding sites may also exert a significant influence on specificity since, as observed in this study, chymotrypsin exhibited high affinity for cationic substrates and cationic inhibitors as well in apolar solvents.     

Nitropyrenes are inducers of polyoma viral DNA synthesis

The biological activity of a series of nitropyrenes was assayed by measuring their ability to induce the asynchronous replication of viral DNA in rat fibroblasts transformed by a ts-a mutant of polyoma virus. Concentrations of 10-30 micrograms/ml of 1-nitropyrene (1-NP) induced viral replication, and this effect was enhanced by addition of rat-liver S9 microsomal fraction (300 micrograms/ml) to the culture medium. The response was less than that obtained with 0.1 micrograms/ml of the activated metabolite of benzo[a]pyrene (BP), BP trans-7,8-dihydrodiol-9,10 epoxide (anti) (BPDE). A series of di-, tri-, and tetra-nitropyrenes were also found to induce polyoma DNA replication, in the absence of exogenous microsomal activation, displaying strongly positive effects at 0.5-2.0 microgram/ml. Dose-response curves with 1,6-dinitropyrene (1,6-DNP) from 0.01 to 0.5 microgram/ml indicated that this compound was approximately equipotent with BPDE for induction of polyoma DNA synthesis. Studies of drug metabolism, DNA binding and DNA adduct formation indicate that 1,6-DNP is metabolized in this cell line, binds to DNA, and forms stable adducts. The level of DNA modification seen with 1,6-DNP is higher than that observed under comparable conditions with an equivalent dose of BPDE. These findings provide additional evidence that the nitropyrene class of compounds can exert biological effects in mammalian cells, and that the dinitropyrenes are more potent than 1-NP.     

Towards regioselective synthesis of oligosaccharides by use of alpha-glucosidases with different substrate specificity

alpha-Glucosidase from two microbial sources, Bacillus stearothermophilus and Brewer's yeast, has been used to catalyze transglycosylation reactions and a comparative study was carried out to determine the regioselectivity of this reaction. Bacterial alpha-glucosidase exhibited higher transfer activity with maltose and was able to synthesize tri- and tetrasaccharides in high yield (27%). In the case of yeast enzyme, only trisaccharides were synthesized in lower yield. Structure analysis of transglycosylation products by means of GC-MS and NMR spectroscopy revealed a correlation between the hydrolytic substrate specificity and the regioselectivity of transglycosylation reaction. Higher substrate specificity of bacterial enzyme, however, influenced its transglucosylation activity toward other saccharide acceptors.     

Cloning of Bacillus stearothermophilus ctaA and heme A synthesis with the CtaA protein produced in Escherichia coli

The Bacillus stearothermophilus ctaA gene, which is required for heme A synthesis, was found upstream of the ctaBCDEF/caaEABCD gene cluster as in B. subtilis and B. firmus. The deduced protein sequence indicate that CtaA is a 35-kDa intrinsic membrane protein with seven hydrophobic segments. Alignment of CtaA sequences showed conserved residues including histidines that may be involved in heme B binding and substrate binding. Expression of ctaA in E. coli resulted in increased formation of a membrane-bound b-type cytochrome, heme A production, and severe growth inhibition. Furthermore, B. stearothermophilus CtaA produced in E. coli was found to catalyze the conversion of heme O to heme A in vitro.     

Kinetics of the enzymatic synthesis of benzylpenicillin

The kinetics of the enzymatic synthesis of benzylpenicillin catalysed by penicillin amidase (EC 3.5.1.11) from Escherichia coli have been studied. Both free phenylacetic acid (PAA) and its activated derivative, phenylacetylglycine (PAG), were used in the synthesis as acylating agents for 6-aminopenicillanic acid (6-APA). The catalytic rate constants for synthesis carried out at pH 6.0 were 11.2 and 25.2 s⁻¹, respectively, i.e. they are close and have high absolute values. The main feature of the enzymatic synthesis of benzylpenicillin from phenylacetylglycine, compared with the synthesis from phenylacetic acid, is the shape of the progress curve of antibiotic accumulation. In the former case, benzylpenicillin gradually accumulates until equilibrium is reached. Thus, if the reaction is carried out at the thermodynamically optimum pH of synthesis (low pH), penicillin can be obtained in high yield. In the case of phenylacetylglycine, the kinetic curves are more complex and are characterized by a clear-cut maximum. The presence of the maximum, its value and position on the time axis depend on reagent concentration and on the pH used. A kinetic scheme is proposed which describes well the experimental dependencies. The possibility of using activated acid derivatives in synthesis and the advantages of using computer calculations for process optimization are discussed.