Slow binding of D-galactal, a "reversible" inhibitor of bacterial beta-galactosidase

Assembly of Glycopeptides in Living Cells Resembling Viral Infection for Cargo Delivery

Self-assembly in living cells represents one versatile strategy for drug delivery; however, it suffers from the limited precision and efficiency. Inspired by viral traits, we here report a cascade targeting-hydrolysis-transformation (THT) assembly of glycosylated peptides in living cells holistically resembling viral infection for efficient cargo delivery and combined tumor therapy. We design a glycosylated peptide via incorporating a β-galactose-serine residue into bola-amphiphilic sequences. Co-assembling of the glycosylated peptide with two counterparts containing irinotecan (IRI) or ligand TSFAEYWNLLSP (PMI) results in formation of the glycosylated co-assemblies SgVEIP, which target cancer cells via β-galactose-galectin-1 association and undergo galactosidase-induced morphological transformation. While GSH-reduction causes release of IRI from the co-assemblies, the PMI moieties release p53 and facilitate cell death via binding with protein MDM2. Cellular experiments show membrane targeting, endo-/lysosome-mediated internalization and in situ formation of nanofibers in cytoplasm by SgVEIP. This cascade THT process enables efficient delivery of IRI and PMI into cancer cells secreting Gal-1 and overexpressing β-galactosidase. In vivo studies illustrate enhanced tumor accumulation and retention of the glycosylated co-assemblies, thereby suppressing tumor growth. Our findings demonstrate an in situ assembly strategy mimicking viral infection, thus providing a new route for drug delivery and cancer therapy in the future.

A near-infrared fluorescent nanoprobe for senescence-associated β-galactosidase sensing in living cells

A near-infrared fluorescent nanoprobe based on semiconducting polymer nanoparticles (SPNs) for the detection of senescence-associated β-gal (SA-β-gal) is developed. Benefiting from the intrinsic lysosome-locating feature, this probe can be successfully used for the visualization of SA-β-gal in living cells.

A universal fluorometric assay strategy for glycosidases based on functional carbon quantum dots: β-galactosidase activity detection in vitro and in living cells

The development of highly sensitive assays for glycosidases is of critical significance to understand their functions, facilely detect associated diseases and screen potential new drugs. In this work, we develop a universal assay strategy for glycosidase enzymes and inhibitor screening based on functional carbon quantum dots through a combined host-guest recognition and specific static quenching-induced signal transduction mechanism. This detection strategy is established in terms of the following facts: (1) β-cyclodextrin as a perfect host can selectively associate with p-nitrophenol due to its hydrophobic character and right size match of the cavity, which renders specific binding between β-cyclodextrin and p-nitrophenol via a host-guest recognition. (2) The formation of an inclusion complex between β-cyclodextrin modified carbon quantum dots (β-CD-CQDs) and p-nitrophenol results in fluorescence quenching with a high quenching efficiency due to the static quenching mechanism. Glycoconjugates of p-nitrophenol as the substrates could be rapidly hydrolyzed to corresponding glycose and p-nitrophenol in the presence of specific glycosidase, and the resulting p-nitrophenol induces the following host-guest interaction and static quenching leading to a change in the fluorescence signal. The activity of different glycosidase enzymes could be evaluated in the same way as long as the glycosyl unit of glycosylated substrates was changed. Here we take β-galactosidase as an example to demonstrate the applicability of the proposed detection strategy because it can act as a molecular target for primary ovarian cancers. A highly sensitive assay for β-galactosidase activity in terms of linear correlation of the fluorescence change with the β-galactosidase level was established with a low detection limit of 0.6 U L^-1. Its function of inhibitor screening was also assessed by using d-galactal as the inhibitor for β-galactosidase, and the positive results indicated its feasibility to screen potential inhibitors. It is also illustrated that the nanoprobe possesses excellent biocompatibility, and can sensitively monitor the intracellular β-galactosidase level in ovarian cancer cells. This work provides a general detection method for glycosidase activity, demonstrates its applicability of monitoring the enzyme level in living cells, and broadens fluorogenic probes in fluorescence-guided diagnostics.

N-Acetyl glycals are tight-binding and environmentally insensitive inhibitors of hexosaminidases

Mono-, di- and trisaccharide derivatives of 1,2-unsaturated N-acetyl-d-glucal have been synthesized and shown to function as tight-binding inhibitors/slow substrates of representative hexosaminidases.

Elucidating the relationship between substrate and inhibitor binding to the active sites of tetrameric β-galactosidase

The stochastic binding and release of two different inhibitors from a tetrameric enzyme is described at the single molecule level.

Structural snapshots illustrate the catalytic cycle of β-galactocerebrosidase, the defective enzyme in Krabbe disease

Glycosphingolipids are ubiquitous components of mammalian cell membranes, and defects in their catabolism by lysosomal enzymes cause a diverse array of diseases. Deficiencies in the enzyme β-galactocerebrosidase (GALC) cause Krabbe disease, a devastating genetic disorder characterized by widespread demyelination and rapid, fatal neurodegeneration. Here, we present a series of high-resolution crystal structures that illustrate key steps in the catalytic cycle of GALC. We have captured a snapshot of the short-lived enzyme-substrate complex illustrating how wild-type GALC binds a bona fide substrate. We have extensively characterized the enzyme kinetics of GALC with this substrate and shown that the enzyme is active in crystallo by determining the structure of the enzyme-product complex following extended soaking of the crystals with this same substrate. We have also determined the structure of a covalent intermediate that, together with the enzyme-substrate and enzyme-product complexes, reveals conformational changes accompanying the catalytic steps and provides key mechanistic insights, laying the foundation for future design of pharmacological chaperones.

LacZ β-galactosidase: structure and function of an enzyme of historical and molecular biological importance

This review provides an overview of the structure, function, and catalytic mechanism of lacZ β-galactosidase. The protein played a central role in Jacob and Monod's development of the operon model for the regulation of gene expression. Determination of the crystal structure made it possible to understand why deletion of certain residues toward the amino-terminus not only caused the full enzyme tetramer to dissociate into dimers but also abolished activity. It was also possible to rationalize α-complementation, in which addition to the inactive dimers of peptides containing the "missing" N-terminal residues restored catalytic activity. The enzyme is well known to signal its presence by hydrolyzing X-gal to produce a blue product. That this reaction takes place in crystals of the protein confirms that the X-ray structure represents an active conformation. Individual tetramers of β-galactosidase have been measured to catalyze 38,500 ± 900 reactions per minute. Extensive kinetic, biochemical, mutagenic, and crystallographic analyses have made it possible to develop a presumed mechanism of action. Substrate initially binds near the top of the active site but then moves deeper for reaction. The first catalytic step (called galactosylation) is a nucleophilic displacement by Glu537 to form a covalent bond with galactose. This is initiated by proton donation by Glu461. The second displacement (degalactosylation) by water or an acceptor is initiated by proton abstraction by Glu461. Both of these displacements occur via planar oxocarbenium ion-like transition states. The acceptor reaction with glucose is important for the formation of allolactose, the natural inducer of the lac operon.

Simple and real-time colorimetric assay for glycosidases activity using functionalized gold nanoparticles and its application for inhibitor screening

The development of real-time assays for enzymes has been receiving a great deal of attention in biomedical research recently. Self-immolative elimination is the spontaneous and irreversible disassembly of a multicomponent construct into its constituent fragments through a cascade of elimination processes, in response to external stimuli. Here, we report a simple and real-time colorimetric assay for glycosidases (β-galactosidase and β-glucosidase). Self-immolative elimination was utilized to release amines to give rise to aggregation and color change by electrostatic attraction after cleavage of the trigger by enzymes displayed on functionalized gold nanoparticles (Gal-Lip-AuNPs and Glc-Lip-AuNPs, where AuNPs denotes gold nanoparticles). The detection limits for β-galactosidase and β-glucosidase were as low as 9.2 and 22.3 nM at 20 min, and they improved slightly over time. Thus, glycosidase activity was detected successfully in real time, and this technique could be used for glycosidase inhibitor screening, based on real-time colorimetric variation.

Structure-Reactivity Relationships for β-Galactosidase (Escherichia coli, lac Z): A Second Derivative Effect on β(nuc) for Addition of Alkyl Alcohols to an Oxocarbenium Ion Reaction Intermediate

Velocities for the synthesis of trifluoroethyl 2-deoxy-β-D-galactopyranoside by transfer of the 2-deoxygalactosyl group from β-galactosidase to trifluoroethanol were determined from studies of the β-galactosidase-catalyzed cleavage of 4-nitrophenyl-2-deoxy-β-D-galactopyranoside as the difference in rates of appearance of 4-nitrophenoxide anion and 2-D-deoxygalactose. These data were used to calculate a rate constant ratio of k(ROH)/k(s) = 2.3 M(-1) for partitioning of the intermediate between addition of trifluoroethanol and solvent water. Velocities for the synthesis of other alkyl 2-deoxy-β-D-galactopyranosides by transfer of the 2-deoxygalactosyl group from β-galactosidase to alkyl alcohols were determined from the effect of alkyl alcohols on the velocity of β-galactosidase-catalyzed cleavage of 4-nitrophenyl-2-deoxy-β-D-galactopyranoside in a reaction where breakdown of the intermediate is rate determining. These data were used to calculate rate constant ratios k(ROH)/k(s) for the reactions of eight alkyl alcohols. Absolute rate constants k(ROH) (M(-1) s(-1)) were calculated from k(ROH)/k(s) and k(s) = 0.002 s(-1) for the addition of water. A Brønsted coefficient of β(nuc) = -0.07 ± 0.08 was determined as the slope of a logarithmic correlation of k(ROH) against alcohol pK(a). The change from a 2-OH to a 2-H substituent at the β-D-galactopyranosyl intermediate causes a 0.12 ± 0.04 increase in the value of β(nuc) for alcohol addition. This anti-Hammond effect provides evidence that general basecatalyzed addition of alcohols to an enzyme bound β-D-galactopyranosyl oxocarbenium ion intermediate proceeds along a reaction coordinate in which there is strong coupling between carbon-oxygen bond formation and proton transfer from the alcohol to a basic residue at the enzyme.

The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates

Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia, gas gangrene, and occasionally food poisoning. Its genome encodes three sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic acids from a variety of glycoconjugates and that play a role in bacterial nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases have suggested that catalysis in all sialidases may proceed via a covalent intermediate similar to that of other retaining glycosidases. Here we provide further evidence to support this suggestion by reporting the 0.97A resolution atomic structure of the catalytic domain of the C. perfringens NanI sialidase, and complexes with its substrate sialic acid (N-acetylneuramic acid) also to 0.97A resolution, with a transition-state analogue (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A resolution. Together, these structures provide high resolution snapshots along the catalytic pathway. The crystal structures suggested that NanI is able to hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid. This was confirmed by NMR, and a mechanism for this activity is suggested.

Stochastic inhibitor release and binding from single-enzyme molecules

Inhibition kinetics of single-beta-galactosidase molecules with the slow-binding inhibitor d-galactal have been characterized by segregating individual enzyme molecules in an array of 50,000 ultra small reaction containers and observing substrate turnover changes with fluorescence microscopy. Inhibited and active states of beta-galactosidase could be clearly distinguished, and the large array size provided very good statistics. With a pre-steady-state experiment, we demonstrated the stochastic character of inhibitor release, which obeys first-order kinetics. Under steady-state conditions, the quantitative detection of substrate turnover changes over long time periods revealed repeated inhibitor binding and release events, which are accompanied by conformational changes of the enzyme's catalytic site. We proved that the rate constants of inhibitor release and binding derived from stochastic changes in the substrate turnover are consistent with bulk-reaction kinetics.

Using surface plasmon resonance to directly measure slow binding of low-molecular mass inhibitors to a VanX chip

VanX, a d,d-dipeptidase, is one of five gene products responsible for vancomycin resistance in pathogenic bacteria and is an attractive drug target in circumventing clinical drug resistance. Our previous combinatorial search of VanX substrates in a dipeptide library of d-X(1)-d-X(2) (19(2)=361) forms has led to the discovery of three new compounds (d-Ala-d-Phe, d-Ala-d-Tyr, and d-Ala-d-Trp) having higher k(cat)/K(M) values than those of its natural substrate, d-Ala-d-Ala. Based on structures of newly identified substrates, two representative transition state analogs of substrates, d-Ala(P,O)d-Phe (6a) and d-Ala(P,O)d-Ala (6b) dipeptide phosphonates, used as VanX inhibitor were rationally designed and chemically synthesized. In the synthesis, eight synthetic steps in total were employed for preparing each VanX inhibitor, and their overall isolated yields were 21 and 11% for 6a and 6b, respectively. Binding interactions of d-Ala(P,O)d-Phe (6a) and d-Ala(P,O)d-Ala (6b) with VanX were confirmed unambiguously and measured quantitatively by surface plasmon resonance. The result reveals that both dipeptide phosphonates are slow-binding inhibitors of VanX (for 6a, k(on)=1.18 x 10(3)M(-1)s(-1), k(off)=2.31 x 10(-3) s(-1), K(D)=1.96 microM, chi(2)=0.0737; for 6b, k(on)=1.09 x 10(3)M(-1)s(-1), k(off)=1.80 x 10(-2)s(-1), K(D)=16.5 microM, chi(2)=0.0599). This suggests that only a fraction of the conformers of the inhibitors in solution adopts a conformation best suited for binding interaction with VanX and that the VanX-inhibitor complex may concomitantly undergo a conformational isomerization from an initial but fast weak-binding adduct to slowly convert to a tight-binding complex with a more stable bound geometry. Moreover, in comparison with 6b, an additional aromatic interaction of 6a with the Phe79 residue in the active site of the enzyme, through an energetically favorable face-to-face offset stacked orientation, may account for its higher affinity than 6b to VanX.

A structural view of the action of Escherichia coli (lacZ) beta-galactosidase

The structures of a series of complexes designed to mimic intermediates along the reaction coordinate for beta-galactosidase are presented. These complexes clarify and enhance previous proposals regarding the catalytic mechanism. The nucleophile, Glu537, is seen to covalently bind to the galactosyl moiety. Of the two potential acids, Mg(2+) and Glu461, the latter is in better position to directly assist in leaving group departure, suggesting that the metal ion acts in a secondary role. A sodium ion plays a part in substrate binding by directly ligating the galactosyl 6-hydroxyl. The proposed reaction coordinate involves the movement of the galactosyl moiety deep into the active site pocket. For those ligands that do bind deeply there is an associated conformational change in which residues within loop 794-804 move up to 10 A closer to the site of binding. In some cases this can be inhibited by the binding of additional ligands. The resulting restricted access to the intermediate helps to explain why allolactose, the natural inducer for the lac operon, is the preferred product of transglycosylation.

Identification of the catalytic nucleophile of the Family 31 alpha-glucosidase from Aspergillus niger via trapping of a 5-fluoroglycosyl-enzyme intermediate

The mechanism-based reagent 5-fluoro-alpha-d-glucopyranosyl fluoride (5F alpha GlcF) was used to trap a glycosyl-enzyme intermediate and identify the catalytic nucleophile at the active site of Aspergillus niger alpha-glucosidase (Family 31). Incubation of the enzyme with 5F alpha GlcF, followed by peptic proteolysis and comparative liquid chromatography/MS mapping allowed the isolation of a labelled peptide. Fragmentation analysis of this peptide by tandem MS yielded the sequence WYDMSE, with the label located on the aspartic acid residue (D). Comparison with the known protein sequence identified the labelled amino acid as Asp-224 of the P2 subunit.

alpha-Mannosidase activity from antibody raised against a glucal antigen

Sixty cell lines of monoclonal antibody were raised against a glucal hapten 1. Among them, Ab 405.4 showed alpha-mannosidase activity as kcat = 0.19/day (kcat/kuncat = 110,000). The chemical modification study and pH profile study of this antibody indicated that carboxyl group(s) in the antigen binding site involved in catalytic mechanism.

Identification of the active site nucleophile in jack bean alpha-mannosidase using 5-fluoro-beta-L-gulosyl fluoride

Mannosidases play a key role in the processing of glycoproteins and thus are of considerable pharmaceutical interest and indeed have emerged as targets for the development of anti-cancer therapies. Access to useful quantities of the mammalian enzymes has not yet been achieved; therefore, jack bean mannosidase, a readily available enzyme, has become the model system. However, the relevance of this enzyme has not been demonstrated, nor is anything known about the active site structure of this, or any other, mannosidase. Hydrolysis by this enzyme occurs with net retention of sugar anomeric configuration; thus, a double displacement mechanism involving a mannosyl-enzyme intermediate is presumably involved. Two new mechanism-based inhibitors, 5-fluoro-alpha-D-mannosyl fluoride and 5-fluoro-beta-L-gulosyl fluoride, which function by the steady state trapping of such an intermediate, have been synthesized and tested. Both show high affinity for jack bean alpha-mannosidase (Ki' = 71 and 86 microM, respectively), and the latter has been used to label the active site nucleophile. The labeled peptide present in a peptic digest of this trapped glycosyl-enzyme intermediate was identified by neutral loss scans on an electrospray ionization triple quadrupole mass spectrometer. Comparative liquid chromatographic/mass spectrometric analysis of peptic digests of labeled and unlabeled enzyme samples confirmed the unique presence of this peptide of m/z 1180.5 in the labeled sample. The label was cleaved from the peptide by treatment with ammonia, and the resultant unlabeled peptide was purified and sequenced by Edman degradation. The peptide identified contained only one candidate for the catalytic nucleophile, an aspartic acid. This residue was contained within the sequence Gly-Trp-Gln-Ile-Asp-Pro-Phe-Gly-His-Ser, which showed excellent sequence similarity with regions in mammalian lysosomal and Golgi alpha-mannosidase sequences. These mammalian alpha-mannosidases belong to family 38 (or class II alpha-mannosidases) in which the Asp in the above sequence is totally conserved. This finding therefore assigns jack bean alpha-mannosidase to family 38, validating it as a model for other pharmaceutically interesting enzymes and thereby identifying the catalytic nucleophile within this family.

Substituted glycals as probes of glycosidase mechanisms

D-Glucal and a series of substituted derivatives have been tested as substrates, inhibitors and inactivators of the Agrobacterium faecalis beta-glucosidase in order to probe structure/function relationships in this enzyme. D-Glucal is shown to be a substrate (kcat = 2.3 min-1, Km = 0.85 mM) undergoing hydration with stereospecific protonation from the alpha-face to yield 2-deoxy-beta-D-glucose. 1-Methyl-D-glucal surprisingly serves as only a poor substrate (kcat = 0.056 min-1, Km = 57 mM), also undergoing protonation from the alpha-face. 2-Fluoro-D-glucal, however is completely inert, as a result of inductive destabilisation of the oxocarbenium ion-like transition state for protonation, and functions only as a relatively weak (Ki = 24 mM) inhibitor. Similar behaviour was seen with almond beta-glucosidase and yeast alpha-glucosidase and for the interaction of 2-fluoro-D-galactal with Escherichia coli beta-galactosidase. A series of of alpha, beta-unsaturated glucal derivatives was also synthesised and tested as potential substrates, inhibitors or inactivators of A. faecalis beta-glucosidase. Of these only 1-nitro-D-glucal functioned as a time dependent, irreversible inactivator (ki = 0.011 min-1, Ki = 5.5 mM), presumably acting as a Michael acceptor. Electrospray mass spectrometric analysis revealed multiple labeling of the enzyme by this inactivator, lessening its usefulness as an affinity label. Less reactive Michael acceptor glycals which might have been more specific (1-cyano-, 2-cyano-, 1-carboxylic acid, 1-carboxylic acid methyl ester) unfortunately did not function as inactivators or substrates, only as relatively weak reversible inhibitors (Ki = 3-96 mM).

[Sugar analog inhibitors for glycosidases, tools for the elucidation of enzymatic hydrolysis of glycosides]

Sugar derivatives with a basic group on C-1 (glycosylamines, 5-amino-5-deoxypyranoses, and 1,5-iminohexitols) are bound by most glycosidases 10(2)- to 10(5)-fold more tightly than their nonbasic counterparts. This high affinity and an up to 10(5)-fold better inhibition relative to hexoses by hexono-delta-lactones and lactams point to a catalytic mechanism characterized by a transition state with a partial positive charge and planar geometry at the anomeric carbon of the substrate. Protonation of the glycosidic oxygen atom and stabilization of the positive charge by a carboxylate group strongly shielded from the aqueous environment lower the free energy of activation to an extent which causes an up to 10(14)-fold rate acceleration relative to the nonenzymatic hydrolysis of glycosides.

Binding energy and catalysis. Fluorinated and deoxygenated glycosides as mechanistic probes of Escherichia coli (lacZ) beta-galactosidase

Kinetic parameters for the hydrolysis of a series of deoxy and deoxyfluoro analogues of 2',4'-dinitrophenyl beta-D-galactopyranoside by Escherichia coli (lacZ) beta-galactosidase have been determined and rates found to be two to nine orders of magnitude lower than that for the parent compound. These large rate reductions result primarily from the loss of transition-state binding interactions due to the replacement of sugar hydroxy groups, and such interactions are estimated to contribute at least 16.7 kJ (4 kcal).mol-1 to binding at the 3, 4 and 6 positions and more than 33.5 kJ (8 kcal).mol-1 at the 2 position. The existence of a linear free-energy relationship between log(kcat./Km) for these compounds and the logarithm of the first-order rate constant for their spontaneous hydrolysis demonstrates that electronic effects are also important and provides direct evidence for oxocarbonium ion character in the enzymic transition state. A covalent intermediate which turns over only extremely slowly (t1/2 = 45 h) accumulates during hydrolysis of the 2-deoxyfluorogalactoside, and kinetic parameters for its formation have been determined. This intermediate is nonetheless catalytically competent, since it re-activates much more rapidly in the presence of the transglycosylation acceptors methanol or glucose, thereby providing support for the notion of a covalent intermediate during hydrolysis of the parent substrates.

Lyase activity of nucleoside 2-deoxyribosyltransferase: transient generation of ribal and its use in the synthesis of 2'-deoxynucleosides

In the absence of acceptors nucleoside 2-deoxyribosyltransferase catalyzes the slow hydrolysis of 2'-deoxynucleosides. During this hydrolytic reaction, D-ribal (1,4-anhydro-2-deoxy-D-erythro-pent-1-enitol), a glycal of ribose hitherto encountered only as a reagent in organic synthesis, is generated spontaneously, disappearing later as 2'-deoxynucleoside hydrolysis approaches completion. Nucleoside 2-deoxyribosyltransferase is found to catalyze the hydration of D-ribal in the absence of nucleic acid bases and the synthesis of deoxyribonucleosides from ribal in their presence, affording a new method for the preparation of 2'-deoxyribonucleosides. The stereochemistry of nucleoside formation from ribal supports the intervention of deoxyribosyl-enzyme intermediate. The equilibrium constant for the covalent hydration of ribal is found to be approximately 65.

Strong inhibitory effect of furanoses and sugar lactones on beta-galactosidase Escherichia coli

Various sugars and their lactones were tested for their inhibition of beta-galactosidase (Escherichia coli). L-Ribose, which in the furanose form has a hydroxyl configuration similar to that of D-galactose at positions equivalent to the 3- and 4-positions of D-galactose, was a very strong inhibitor, and D-lyxose, which in the furanose form also resembles D-galactose, was a much better inhibitor than expected. Structural comparisons prelude the pyranose forms of these sugars from being significant contributors to the inhibition, and inhibition at different temperatures (at which there are different furanose concentrations) strongly supported the conclusion that the furanose form is inhibitory. Studies with sugar derivatives that can only be in the furanose form also supported the conclusion. This is the first report of the inhibitory effect of furanose on beta-galactosidase. Lactones were also inhibitory. Every lactone tested was much more inhibitory than was its parent sugar. D-Galactonolactone was especially good. Experiments indicated that it was D-galactono-1,5-lactone rather than D-galactono-1,4-lactone which was inhibitory. Inhibition of beta-galactosidases from mammalian sources by lactones has been reported previously, but this is the first report of the effect of beta-galactosidase from E. coli. Since furanoses in the envelope form are analogous (in some ways) to half-chair or sofa conformations and since lactones with six-membered rings probably have half-chair or sofa conformations, the results indicate that beta-galactosidase probably destabilizes its substrate into a planar conformation of some type and that the galactose in the transition state may, therefore, also be quite planar.(ABSTRACT TRUNCATED AT 250 WORDS)

Transition-state stabilization by adenosine deaminase: structural studies of its inhibitory complex with deoxycoformycin

Experiments with radioactive deoxycoformycin indicate that the inhibitor is released from calf intestinal adenosine deaminase after the enzyme-inhibitor complex is disrupted by denaturation. Experiments with 2H2O and H218O indicate that the enzyme does not catalyze elimination-addition reactions that could have led to reversible covalent derivatization of the enzyme. Ultraviolet difference spectra and the influence of pH on inhibitor binding indicate that deoxycoformycin is bound intact as the neutral species, at a binding site that is less polar than solvent water. The enzyme-inhibitor complex appears to be held together by hydrogen bonds of extraordinary stability (ca. 10 kcal/mol). These results suggest that deamination proceeds by direct water attack, the enzyme acting as a general-base catalyst.

Reversion reactions of beta-galactosidase (Escherichia coli)

The reversion reactions of beta-galactosidase (Escherichia coli) produced beta-galactosyl-galactoses and beta-galactosyl-glucoses. About 10 beta-galactosyl-galactose and 10 beta-galactosyl-glucose gas-liquid chromatographic peaks were detected and it is thus very likely that every possible isomer of beta-galactosyl-galactose and beta-galactosyl-glucose was formed by the reversion reactions (taking into account both anomers for each isomer). The presence of lactose and allolactose among the beta-galactosyl-glucoses was confirmed with standards. An important finding relating to the role of allolactose as an inducer of the lac operon was that allolactose (beta-D-galactosyl-(1----6)-D-glucose) was the only disaccharide formed initially, and at equilibrium it was present in the largest amount (50%). Obviously the enzyme is specific in its ability to form allolactose, and allolactose is the most stable beta-galactosyl-glucose, both important inducer properties. The equilibrium constant (concentration of disaccharides divided by the concentration of reactants at equilibrium) of the reaction was about 9.5 mM-1. This is the first report of an equilibrium constant for the beta-galactosidase reaction. Of mechanistic significance is the fact that only three compounds were able to replace D-galactose as a reversion reactant. Two of these (L-arabinose and D-fucose) had alterations at carbon 6. The 6 position, therefore, is not essential for reactivity. The third compound was D-galactal. Any other sugars tested (even with very minor changes relative to D-galactose) did not react. Of special consequence is the 2 position. The results strongly suggest that there has to be either an equatorial hydroxyl at the 2 position of a sugar or a special reactivity (as with D-galactal) in order for the enzyme to catalyze the beta-galactosidase reaction.

Mechanistic implications of the inhibition of peptidases by amino aldehydes and bestatin

alpha-Amino aldehydes and bestatin are found to be effective inhibitors of a cytosolic dipeptidase (rat testicular peptidase C), and a cytosolic tripeptidase (rat kidney peptidase B, EC 3.4.11.4), as well as cytosolic leucine aminopeptidase (pig kidney peptidase S, EC 3.4.11.1). Aldehyde hydrates and bestatin share a resemblance to intermediates that might be formed during direct attack by water on peptide substrates, affording a possible explanation for their tight binding. Alternatively, inhibitors of both kinds might form derivatives of an active site nucleophile, resembling intermediates in a double-displacement mechanism. Exchange experiments with H218O suggest that bestatin is bound intact by leucine aminopeptidase, lending support to the first of these two mechanisms.

Synthesis of 5-amino-5-deoxy-D-mannopyranose and 1,5-dideoxy-1,5-imino-D-mannitol, and inhibition of alpha- and beta-D-mannosidases

The title compounds and the corresponding L-gulo derivatives were synthesised in 6 steps from benzyl 2,3:5,6-di-O-isopropylidene-alpha-D-mannofuranoside. The Ki values, determined from inhibition studies with alpha-D-mannosidases from jack beans, almonds, and calf liver, and beta-D-mannosidase from Aspergillus wentii, ranged from 70 to 400 microM for the mannitol derivative and from 1.2 to 20 microM for 5-amino-5-deoxy-D-mannopyranose, i.e., inhibition is 10(2)-10(4)-fold stronger than with D-mannose. Marked enhancement of inhibition with increasing pH is ascribed to the ionisation of a carboxyl group at the active site, forming an ion pair with the protonated inhibitor. The inhibition equilibrium between the jack-bean enzyme and the mannose derivative was approached slowly with kapp 2.0 X 10(5) M-1 X min-1. The mannose-derived inhibitor was also inhibitory against beta-D-glucosidases from almonds and Asp. wentii, with Ki values only 20-150-times larger than those for the inhibition of these enzymes by 5-amino-5-deoxy-D-glucopyranose. This moderate discrimination in binding of D-gluco and D-manno derivatives is in marked contrast to the high specificity shown by the glucosidase in catalysing the hydrolysis of mannosidases. A similar low specificity with respect to binding, combined with highly specific catalysis, was also seen with the mannosidases acting on inhibitors and substrates with the D-gluco configuration.

Waterlogged molecules

Measurements of vapor pressures over their aqueous solutions indicate that organic compounds show profound differences in hydrophilic character. These differences are of such magnitude as to suggest an important role for changing solvation in determining free energy changes associated with metabolic transformations in water, and in governing structural equilibria of proteins and other large molecules in water. When two or more functional groups are present within the same solute molecule, their combined effects on its free energy of solvation are commonly additive. Striking departures from additivity, observed in certain cases, indicate the existence of special interactions between different parts of a solute molecule and the water that surrounds it. Similar considerations presumably apply to activated intermediates in the interconversion of biological materials.

The interaction of substrate-related ketals with bacterial and viral neuraminidases

Arthrobacter sialophilus neuraminidase catalyzes the hydration of 5-acetamido-2,6-anhydro-3,5-dideoxy-D-glycero-D-galacto-non-2-enonic acid (2,3-dehydro-AcNeu) with Km and kcat values of 8.9 X 10(-4) M and 6.40 X 10(-4) s-1, respectively. The methyl ester of 2,3-dehydro-AcNeu as well as 2,3-dehydro-4-epi-AcNeu are also hydrated by the enzyme. The product resulting from the enzymatic hydration of 2,3-dehydro-AcNeu is N-acetylneuraminic acid. A series of derivatives of 2,3-dehydro-AcNeu (K1, 1.60 X 10(-6) M) including 2,3-dehydro-4-epi-AcNeu (2.10 X 10(-4) M) and 2,3-dehydro-4-keto-AcNeu (K1 = 6.10 X 10(-5) M) were each competitive inhibitors of the enzyme. The methyl esters of these ketal derivatives were also competitive enzyme inhibitors. Dissociation constants for these ketals were determined independently by fluorescence enzyme titrations which gave values similar to those found kinetically. These six relatives of 2,3-dehydro-AcNeu were also competitive inhibitors for the influenza viral neuraminidases. For the viral neuraminidases, the dissociation constant for 2,3-dehydro-AcNeu and its methyl ester were 2.40 X 10(-6) and 1.17 X 10(-3) M, respectively. The interpretation placed upon the K1 values determined for these ketals against the Arthrobacter versus influenza neuraminidases is that the bacterial enzyme has a more flexible glycone binding site.

The use of inhibitors in the study of glycosidases

The use of non-covalent as well as covalent inhibitors can be a useful tool to approach the mechanism of activity of glycosidases. An efficient method to determine the essential amino-acid groups directly or indirectly involved in the catalytic process is the use of active site directed irreversible inhibitors. Epoxide derivatives from conduritol B and conduritol C are the most important inhibitors in this group. The use of active site reversible inhibitors: cationic and basic glycosyl derivatives, glycals, glyconolactones, thioglycosides, is effective to study the different charges at the active site or the transition state during catalysis and also to detect conformational adaptability of an enzyme. Furthermore, inhibitors can be valuable tools to investigate various aspects of the physiological role of glycosidases.

Structural requirements for neuraminidase induction in Arthrobacter sialophilus

The effectiveness of 13 N-acetylneuraminic acid derivatives as potential inducers of Arthrobacter sialophilus neuraminidase were examined. N-Acetylneuraminic acid nitrogen and thioglycosides were not inducers, whereas 2,3-dehydro-N-acetylneuraminic acid, a transition state analog for neuraminidases, was the most effective inductive ligand. The C-4 hydroxyl function of N-acetylneuraminic acid was essential for enzyme derepression.