Nucleophilic acceleration of the cleavage of β-cyclodextrin trans-cinnamate by amines

The cleavage of β-cyclodextrin trans-cinnamate (1) was accelerated by amines such as quinuclidine and piperidine by 27- and 13-fold, respectively. The reaction involves complex formation of 1 with the amines, and proceeds via nucleophilic attack by the neutral amine, which was shown by the production of amide in the reaction of 1 with piperidine. Quinuclidine exhibited real catalysis of hydrolysis without production of amide. The present finding indicates that the rates of the rate-determining deacylation step in the cyclodextrin-accelerated hydrolyses of phenyl esters can be made larger than the rates of uncatalyzed hydrolyses by an amine such as quinuclidine, resulting in the use of cyclodextrin as a true catalyst and as a better enzyme model.     

The role of N-terminal heterocycles in hydrogen bonding to α-chymotrypsin

A series of dipeptide aldehydes containing different N-terminal heterocycles was prepared and assayed in vitro against α-chymotrypsin to ascertain the importance of the heterocycle in maintaining a β-strand geometry while also providing a hydrogen bond donor equivalent to the backbone amide nitrogen of the surrogate amino acid. The dipeptide containing a pyrrole constraint (10) was the most potent inhibitor, with >30-fold improved activity over dipeptides which lacked a nitrogen hydrogen bond donor (namely thiophene 11, furan 12 and pyridine 13). Molecular docking studies of 10 bound to α-chymotrypsin demonstrates a hydrogen bond between the pyrrole nitrogen donor and the backbone carbonyl of Gly₂₁₆ located in the S₃ pocket which is proposed to be critical for overall binding.     

Syntheses and spectroscopic properties of α- and β-phosphatidylcholines and phosphatidylethanolamines

The widely used partial synthesis of phospholipids via deacylation of naturally occurring phospholipids, followed by reacylation with fatty acid anhydrides, is accompanied by phosphoryl migration. The resulting mixture of α- and β-phospholipids was separated by short-column chromatography. Milder acylation procedures in which no phosphoryl migration occurs, were developed. 1,2-Dilinoleoyl-sn-glycero-3-phosphocholine was prepared in 50% yield by acylation of sn-glycero-3-phosphocholine (GPC) with N-linoleoylimidazole. Detailed NMR and infrared spectra of α- and β-phosphatidylcholines (PCs) and -ethanolamines (PEs) are reported and the differences between isomers discussed.     

A rate-limiting step of enteropeptidase hydrolysis

It has been shown for the first time that deacylation is the rate-limiting step in the enteropeptidase-catalyzed hydrolysis of highly effective oligopeptide substrates containing four Asp residues in positions P2–P5. On the other hand, the rate-limiting step in the hydrolysis of low-efficiency peptide substrates containing less than four Asp or Glu residues in positions P2–P5 is acylation, as it has previously been suggested for all amide and peptide substrates of serine proteases on the basis of classical works of Bender et al. The method of introduction of an additional nucleophile or another effector that selectively affects the deacylation step was used to determine the rate-limiting step in the enteropeptidase hydrolysis of N ^α-benzyloxycarbonyl-L-lysine thiobenzyl ester, the highly efficient amide substrate GlyAsp₄-Lys β-naphthyl amide, and the low-efficiency peptide substrate VLSAADK-GNVKAAWG (where a hyphen denotes the hydrolysis site).     

Mechanism of heparin acceleration of tissue inhibitor of metalloproteases-1 (TIMP-1) degradation by the human neutrophil elastase

Heparin has been shown to regulate human neutrophil elastase (HNE) activity. We have assessed the regulatory effect of heparin on Tissue Inhibitor of Metalloproteases-1 [TIMP-1] hydrolysis by HNE employing the recombinant form of TIMP-1 and correlated FRET-peptides comprising the TIMP-1 cleavage site. Heparin accelerates 2.5-fold TIMP-1 hydrolysis by HNE. The kinetic parameters of this reaction were monitored with the aid of a FRET-peptide substrate that mimics the TIMP-1 cleavage site in pre-steady-state conditionsby using a stopped-flow fluorescence system. The hydrolysis of the FRET-peptide substrate by HNE exhibits a pre-steady-state burst phase followed by a linear, steady-state pseudo-first-order reaction. The HNE acylation step (k ₂ = 21±1 s⁻¹) was much higher than the HNE deacylation step (k ₃ = 0.57±0.05 s⁻¹). The presence of heparin induces a dramatic effect in the pre-steady-state behavior of HNE. Heparin induces transient lag phase kinetics in HNE cleavage of the FRET-peptide substrate. The pre-steady-state analysis revealed that heparin affects all steps of the reaction through enhancing the ES complex concentration, increasing k ₁ 2.4-fold and reducing k ₋₁ 3.1-fold. Heparin also promotes a 7.8-fold decrease in the k ₂ value, whereas the k ₃ value in the presence of heparin was increased 58-fold. These results clearly show that heparin binding accelerates deacylation and slows down acylation. Heparin shifts the HNE pH activity profile to the right, allowing HNE to be active at alkaline pH. Molecular docking and kinetic analysis suggest that heparin induces conformational changes in HNE structure. Here, we are showing for the first time that heparin is able to accelerate the hydrolysis of TIMP-1 by HNE. The degradation of TIMP-1is associated to important physiopathological states involving excessive activation of MMPs.     

Chemical synthesis of β-d-psicofuranosyl disaccharides

Disaccharides composed of a β-d-psicofuranosyl unit were prepared by the glycosylation reaction of monosaccharide acceptors including three 2,3,4,6-tetra-O-protected hexopyranoses with a d-psicofuranosyl benzyl phthalate derivative (4). A β-d-psicofuranosidic bond was formed by the TMSOTf-promoted reaction with high selectivity. Removal of the O-protecting groups from the resulting α-d-hexopyranosyl β-d-psicofuranosides furnished the first chemical synthesis of α-d-gluco-, α-d-galacto-, and α-d-mannopyranosyl β-d-psicofuranosides. The common β-d-psicofuranosyl donor 4 was derived efficiently from d-psicose in five steps.     

Kinetics and mechanism of large rate enhancement in an acidic aqueous cleavage of the tertiary amide bond of N-(2-methoxyphenyl)-N'-morpholinophthalamide (1)

The rate of conversion of 1 to N-(2-methoxyphenyl)phthalimide (2) within [HCl] range 5.0 × 10⁻³-1.0 M at 1.0 M ionic strength (by NaCl) reveals the presence of both uncatalyzed and specific acid-catalyzed kinetic terms in the rate law. Intramolecular carboxamide group-assisted cleavage of amide bond of 1 reveals rate enhancement of much larger than 10⁶-fold compared to the expected rate of analogous intermolecular reaction.     

Methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis: substrate specificity and coenzyme A binding

Methylmalonate-semialdehyde dehydrogenase (MSDH) belongs to the CoA-dependent aldehyde dehydrogenase subfamily. It catalyzes the NAD-dependent oxidation of methylmalonate semialdehyde (MMSA) to propionyl-CoA via the acylation and deacylation steps. MSDH is the only member of the aldehyde dehydrogenase superfamily that catalyzes a β-decarboxylation process in the deacylation step. Recently, we demonstrated that the β-decarboxylation is rate-limiting and occurs before CoA attack on the thiopropionyl enzyme intermediate. Thus, this prevented determination of the transthioesterification kinetic parameters. Here, we have addressed two key aspects of the mechanism as follows: 1) the molecular basis for recognition of the carboxylate of MMSA; and 2) how CoA binding modulates its reactivity. We substituted two invariant arginines, Arg-124 and Arg-301, by Leu. The second-order rate constant for the acylation step for both mutants was decreased by at least 50-fold, indicating that both arginines are essential for efficient MMSA binding through interactions with the carboxylate group. To gain insight into the transthioesterification, we substituted MMSA with propionaldehyde, as both substrates lead to the same thiopropionyl enzyme intermediate. This allowed us to show the following: 1) the pK(app) of CoA decreases by ～3 units upon binding to MSDH in the deacylation step; and 2) the catalytic efficiency of the transthioesterification is increased by at least 10(4)-fold relative to a chemical model. Moreover, we observed binding of CoA to the acylation complex, supporting a CoA-binding site distinct from that of NAD(H).     

Synthesis of some glycodipeptides containing hydroxyamino acids, and their stabilities to acids and bases

The following new compounds were prepared and characterized: N-benzyl-oxycarbonyl-O-(tetra-O-acetyl-β-D-glucopyranosyl)-N-glycyl-L-serine methyl ester (1) and L-threonine methyl ester (2), N-benzyloxycarbonyl-O-(β-D-glucopyranosyl)-N-glycyl-L-serine amide (3), N-benzyloxycarbonyl-O-(β-D-glucopyranosyl)-N-glycyl-L-threonine methyl ester (4) and L-threonine amide (5), N-benzyloxycarbonyl-O-(tri-O-acetyl-2-deoxy-2-trifluoroacetamido-β-D-glucopyranosyl)-N-glycyl-L-serine methyl ester (6), and N-benzyloxycarbonyl-O-(2-deoxy-2-trifluoroacetamido-β-D-glucopyranosyl)-N-glycyl-L-serine amide (7). Although various modifications of the Koenigs-Knorr synthesis were used, the best, over-all yields of the deacetylated dipeptide derivatives were only 5–10%. Although the products are alkali-labile, deacetylation was accomplished with methanolic ammonia. Of the deacetylated products, the threonine derivatives (4 and 5) were more rapidly hydrolyzed by acids than phenyl β-D-glucopyranoside, which in turn was more rapidly cleaved than the serine derivatives (3 and 7). The stabilities of 3, 4, 5, and 7 to sodium hydroxide and sodium borohydride were similar, and essentially complete β-elimination of the glycosyl residue occurred for the amide derivatives (3, 5, and 7). For the ester derivative 4, pH 9 was optimal; above this pH, ester hydrolysis was more rapid than β-elimination, and the resulting carboxyl derivatives did not undergo β-elimination. Under optimal conditions with sodium borohydride, the β-elimination reaction was complete, but the corresponding alanine and α-aminobutyric acid residues were not formed; presumably reductions to the amino alcohols occurred. A mechanism for the β-elimination is proposed.     

A new GLP-1 analogue with prolonged glucose-lowering activity in vivo via backbone-based modification at the N-terminus

Glucagon-like peptide-1 (GLP-1) is an endogenous insulinotropic hormone with wonderful glucose-lowering activity. However, its clinical use in type II diabetes is limited due to its rapid degradation at the N-terminus by dipeptidyl peptidase IV (DPP-IV). Among the N-terminal modifications of GLP-1, backbone-based modification was rarely reported. Herein, we employed two backbone-based strategies to modify the N-terminus of tGLP-1. Firstly, the amide N-methylated analogues 2–6 were designed and synthesized to make a full screening of the N-terminal amide bonds, and the loss of GLP-1 receptor (GLP-1R) activation indicated the importance of amide H-bonds. Secondly, with retaining the N-terminal amide H-bonds, the β-peptide replacement strategy was used and analogues 7–13 were synthesized. By two rounds of screening, analogue 10 was identified. Analogue 10 greatly improved the DPP-IV resistance with maintaining good GLP-1R activation in vitro, and showed approximately a 4-fold prolonged blood glucose-lowering activity in vivo in comparison with tGLP-1. This modification strategy will benefit the development of GLP-1-based anti-diabetic drugs.     

Further purification of epidermal growth factor by high-performance liquid chromatography

Epidermal growth factor (EGF) purified by the method of Savage and Cohen (J. Biol. Chem.247, 7601–7611 (1972) using DEAE-cellulose chromatography as the final purification step was further resolved into two major uv-absorbing components by reverse-phase high-performance liquid chromatography (HPLC). Both components, referred to as α-EGF and β-EGF, competed with ¹²⁵I-labeled EGF for the EGF receptor, induced premature eye opening in neonatal mice, and had an amino acid composition similar to that published by Savage et al. (J. Biol. Chem.247, 7612–7621 (1972). β-EGF migrated slightly faster than α-EGF during sodium dodecyl sulfate-urea-polyacrylamide gel electrophoresis. α-EGF was fourfold more potent than β-EGF and was 10-fold more potent than DEAE-purified EGF in stimulating DNA synthesis in quiescent Rat-1 cells. HPLC purification of EGF can replace the DEAE-cellulose chromatography step currently used and produces a more potent and less heterogeneous EGF species.     

2,5-Dideoxy-2,5-imino-d-altritol as a new class of pharmacological chaperone for Fabry disease

Chromatographic separation of the extract from roots of Adenophora triphylla resulted in the isolation of two pyrrolidines, six piperidines, and two piperidine glycosides. The structures of new iminosugars were elucidated by spectroscopic methods as 2,5-dideoxy-2,5-imino-d-altritol (DIA) (2), β-1-C-butenyl-1-deoxygalactonojirimycin (8), 2,3-dideoxy-β-1-C-ethyl-1-deoxygalactonojirimycin (9), and 6-O-β-d-glucopyranosyl-2,3-dideoxy-β-1-C-ethyl-1-deoxygalactonojirimycin (10). β-1-C-Butyl-1-deoxygalactonojirimycin (7) and compound 8 were found to be better inhibitors of α-galactosidase than N-butyl-1-deoxygalactonojirimycin. The present work elucidated that DIA was a powerful competitive inhibitor of human lysosome α-galactosidase A (α-Gal A) with a K_i value of 0.5 μM. Furthermore, DIA improved the thermostability of α-Gal A in vitro and increased intracellular α-Gal A activity by 9.6-fold in Fabry R301Q lymphoblasts after incubation for 3 days. These experimental results suggested that DIA would act as a specific pharmacological chaperone to promote the smooth escape from the endoplasmic reticulum (ER) quality control system and to accelerate transport and maturation of the mutant enzyme.     

Torsional strain considerations in the mechanism of the proteolytic enzymes,with particular application to carboxypeptidase A

Torsional deformation of the peptide linkage by anti distortion of cis substituents (i.e., forcing groups attached to one side of an amide partial π bond out of plane in opposite directions) leads to rehybridization of the constituent atoms (nitrogen and carbonyl carbon) toward tetrahedral geometry. In consequence the partial π bond is uniquely activated toward trans (antarafacial) addition with defined steric orientation of addends. Application of these considerations to the known structure of an enzyme-substrate complex of carboxypeptidase A leads to a unique mechanistic hypothesis for proteolytic cleavage by this enzyme. Extant evidence concerning the mode of catalysis is considered in light of a mechanism involving electrostatically induced torsional activation of the scissile peptide bond, Lewis acid coordination of zinc to amide carbonyl, proton donation from Glu 270 to the amide nitrogen of the scissile bond, with concerted attack upon the amide carbonyl by solvent water.     

The thylakoid carbonic anhydrase associated with photosystem II is the component of inorganic carbon accumulating system in cells of halo- and alkaliphilic cyanobacterium Rhabdoderma lineare

The organization of carbonic anhydrase (CA) system in halo- and alkaliphilic cyanobacterium Rhabdoderma lineare was studied by Western blot analysis and immunocytochemical electron microscopy. The presence of putative extracellular α-CA of 60 kDa in the glycocalyx, forming a tight sheath around the cell, and of two intracellular β-CA is reported. We show for the first time that the β-CA of 60 kDa is expressed constitutively and associated with polypeptides of photosystem II (β-CA-PS II). Another soluble β-CA of 25 kDa was induced in low-bicarbonate medium. Induction of synthesis of the latter β-CA was accompanied by an increase in the intracellular pool of inorganic carbon, which suggests an important role of this enzyme in the functioning of a CO₂-concentrating mechanism.     

Chromophoric peptide substrates for activity determination of animal aspartic proteinases in the presence of their zymogens: A novel assay

Solid-phase synthesis was used for the preparation of pyroglutamyl-histidyl-p-nitrophenylalanyl-phenylalanyl-alanyl-leucine amide (I) and glycyl-glycyl-histidyl-p-nitrophenylalanyl-phenylalanyl-alanyl-leucine amide (II), two water-soluble and sensitive chromophoric substrates of chicken pepsin, hog pepsin A, and bovine spleen cathepsin D. The kinetic constants of hydrolysis of the p-nitrophenylalanyl-phenylalanyl bond of the substrates were measured by difference spectrophotometry at 308 nm (Δ? = 860 m^?1 cm^?1) and by ninhydrin colorimetry (substrate I, ?₅₇₀ = 2.31 × 10⁴m^?1 cm^?1). The pH optimum of cleavage is 5 for the pepsins and 3.7 for cathepsin D. Since all three proteinases still have a significant activity at pH 5.5–6 a new, simple assay was designed for submicrogram quantities of pepsins in the presence of pepsinogens without interference of the latter. The method is particularly suitable for the analyses of the zymogen activation mixtures.     

Catalytic action of comicelles containing imidazolyl and hydroxyl groups in the hydrolysis of enantiomeric esters

The rate constants for hydrolysis of the enantiomers of amino acid p-nitrophenyl esters catalyzed by bifunctional comicellar catalysts containing the imidazolyl and hydroxyl groups have been determined at pH 7.30, 0.02 m phosphate buffer, and 25°C. The kinetic analysis suggests a reaction scheme which involves acylation followed by deacylation at the imidazolyl group. Although no appreciable cooperative catalytic efficiencies are observed between the bifunctional groups in the acylation step, it is found that the deacylation rates are thus accelerated by surfactant hydroxyl groups, and some of the stereoselective acyl transfer reaction occurs from the imidazolyl to the hydroxyl group in optically active comicellar systems.     

Stereochemistry involved in the mechanism of action of dextransucrase in the synthesis of dextran and the formation of acceptor products

A proposed sequence of events in the synthesis of dextran and in the formation of acceptor products by dextransucrase from Leuconostoc mesenteroides B-512F has been developed with molecular models. The following mechanism is postulated: (1) two nucleophiles at the active site displace fructose from two sucrose molecules, giving two β-glucosyl intermediates; (2) these two β-glucosyl units rotate together so that the C₆-hydroxyl of each is apposed to the α-side of C₁ of the other; (3) one glucosyl unit assumes a boat conformation in which the bond to the enzyme is axial; (4) the C₆-hydroxyl oxygen of the other glucosyl unit makes a nucleophilic attack on C₁ of the first, displacing the enzyme nucleophile and making an α-1,6 bond; (5) rotations about the new α-1,6 linkage remove the transferred glucose from the active site. The free enzyme nucleophile attacks another sucrose as in step (1), and then steps (2)–(5) are repeated as the reducing-end glucosyl unit of the growing chain assumes the boat conformation and is attacked by the C₆-hydroxyl of the new glucosyl unit, which displaces the enzyme nucleophile and forms another α-1,6 linkage, about which rotations occur to remove the growing dextran chain from the active site. An additional feature of the mechanism presented here is a pair of enzymic proton-exchange groups, which protonate the glycosidic oxygen of sucrose to facilitate cleavage, and then remove a proton from the attacking C₆ hydroxyl during the polymerization reaction.Acceptors are polyhydroxy compounds which are capable of nucleophilic attack on enzyme-bound β-glucosyl or dextranosyl units to give α-glucosides or dextranosides. Noting the broad acceptor specificity of the enzyme and the unusual structure of some of the acceptor products, we have proposed that acceptor specificity is determined not by an enzymic binding site per se, but by the formation of hydrogen-bonded complexes between the acceptors and the glucosyl or dextranosyl enzyme intermediates. The acceptor attack on C₁ of the β-glucosyl enzyme is mediated by the same proton-exchange group as that proposed for catalysis of polymerization. It is shown that specific multiple hydrogen bonding to the glucosyl-enzyme intermediate can account for the formation of the observed acceptor products from α-methyl-d-glucoside, d-fructopyranose, isomaltose, maltose, β-d-mannopyranose, β-d-galactofuranose, cellobiose, lactose, β,β-trehalose, α,β-trehalose, and raffinose.     

Reaction of acetyl hypofluorite with pyranoid and furanoid glycals

The regiospecific syn-addition of acetyl hypofluorite to glycals derived from pentopyranoses led to mixtures of stereoisomers. Stereospecific reactions occurred with furanoid glycals, the direction of addition being governed by the nature of the substituent at C-3. Whereas a benzyloxy group caused attack from the opposite, less-hindered face of the double bond, a hydroxyl group induced addition from the same side. From these reactions, 2-deoxy-2-fluoro derivatives of β-d-arabino-, α-d-ribo-, β-d-lyxo-, and α-d-xylo-pyranose as well as β-d-manno-, α-d-gluco-, α-d-ribo-, and β-d-arabino-furanose were obtainedl their ¹H-, ¹³C-, and ¹⁹F-n.m.r. data are given.     

Differential utilization of enzyme-substrate interactions for acylation but not deacylation during the catalytic cycle of Kex2 protease

Kex2 protease from Saccharomyces cerevisiae is the prototype for a family of eukaryotic proprotein processing proteases belonging to the subtilase superfamily of serine proteases. Kex2 can be distinguished from degradative subtilisins on the basis of stringent substrate specificity and distinct pre-steady-state behavior. To better understand these mechanistic differences, we have examined the effects of substrate residues at P(1) and P(4) on individual steps in the Kex2 catalytic cycle with a systematic series of isosteric peptidyl amide and ester substrates. The results demonstrate that substrates based on known, physiological cleavage sites exhibit high acylation rates (> or =550 s(-1)) with Kex2. Substitution of Lys for the physiologically correct Arg at P(1) resulted in a > or =200-fold drop in acylation rate with almost no apparent effect on binding or deacylation. In contrast, substitution of the physiologically incorrect Ala for Nle at P(4) resulted in a much smaller defect in acylation and a modest but significant effect on binding with Lys at P(1). This substitution also had no effect on deacylation. These results demonstrate that Kex2 utilizes enzyme-substrate interactions in different ways at different steps in the catalytic cycle, with the S(1)-P(1) contact providing a key specificity determinant at the acylation step.