A study by means of lactone inhibition of the role of a “half-chair” glycosyl conformation at the active centre of amylolytic enzymes

Specific empirical free energy function for automated docking of carbohydrates to proteins

We present an automated docking protocol specifically optimized to predict the structure and affinity of a protein-carbohydrate complex. A scoring function was developed based on a training set of 30 protein-carbohydrate complexes of known structure and affinity. Combinations of several models for hydrogen bonding, torsional entropy loss, and solvation were tested for their ability to fit the training set data, and the best model was used with AutoDock. The electrostatic empirical coefficient is larger than in a previously obtained model using a training set comprised of various types of protein-ligand complexes, indicating that electrostatic interactions play a more important role in determining the affinity between a carbohydrate and a protein. The differences in the relative weighting of the empirical coefficients in the model yields predicted free energies for the training set with a standard error of 1.403 kcal/mol. The new scoring function was tested on 17 Aspergillus niger glucoamylase inhibitors for which binding energies had been determined experimentally. Free energies of complex formation were predicted with a residual standard error of 1.101 kcal/mol. The new scoring function therefore provides a robust method for predicting free energies of formation and optimal conformations of carbohydrate-protein complexes.

New enzymatic synthesis of 6(3)-modified maltooligosaccharides and their inhibitory activities for human alpha-amylases

Ten new 6(3)-modified maltopentaoses and tetraoses were synthesized by enzymatic reactions utilizing cyclodextrin glycosyltransferase (EC 2.4.1.19) and subsequent human salivary alpha-amylase (HSA) (EC 3.2.1.1). Among these compounds, alpha-D-glucopyranosyl-(1-->4)- alpha-D-glucopyranosyl-(1-->4)-(6-deoxy-alpha-D-glucopyranosyl)-(1-->4)- alpha-D-glucopyranosyl-(1-->4)-D-glucopyranose (11) and alpha-D-glucopyranosyl-(1-->4)-(6-deoxy-alpha-D-glucopyranosyl)-(1-->4)- alpha-D-glucopyranosyl-(1-->4)-D-glucopyranose (12) showed strong inhibitory activities for human pancreatic alpha-amylase (HPA) and HSA. The IC50 of 6(3)-deoxymaltopentaose 11 (8.0 x 10(-5) M for HPA, 1.0 x 10(-4) M for HSA) and 6(3)-deoxymaltotetraose 12 (2.0 x 10(-3) M for HPA, 2.0 x 10(-3) M for HSA) were lower than that of 6(3)-deoxymaltotriose [(6-deoxy-alpha-D-glucopyranosyl)-(1-->4)-alpha-D- glucopyranosyl-(1-->4)-D-glucopyranose 13; 2.0 x 10(-3) M for HPA, 4.2 x 10(-2) M for HSA].

Automated docking of monosaccharide substrates and analogues and methyl alpha-acarviosinide in the glucoamylase active site

Glucoamylase is an important industrial glucohydrolase with a large specificity range. To investigate its interaction with the monosaccharides D-glucose, D-mannose, and D-galactose and with the substrate analogues 1-deoxynojirimycin, D-glucono-1,5-lactone, and methyl alpha-acarviosinide, MM3(92)-optimized structures were docked into its active site using AutoDock 2.1. The results were compared to structures of glucoamylase complexes obtained by protein crystallography. Charged forms of some substrate analogues were also docked to assess the degree of protonation possessed by glucoamylase inhibitors. Many forms of methyl alpha-acarviosinide were conformationally mapped by using MM3(92), characterizing the conformational pH dependence found for the acarbose family of glucosidase inhibitors. Their significant conformers, representing the most common states of the inhibitor, were used as initial structures for docking. This constitutes a new approach for the exploration of binding modes of carbohydrate chains. Docking results differ slightly from x-ray crystallographic data, the difference being of the order of the crystallographic error. The estimated energetic interactions, even though agreeing in some cases with experimental binding kinetics, are only qualitative due to the large approximations made by AutoDock force field.

Roles of the aromatic side chains in the binding of substrates, inhibitors, and cyclomalto-oligosaccharides to the glucoamylase from Aspergillus niger probed by perturbation difference spectroscopy, chemical modification, and mutagenesis

The roles of the aromatic side chains of the glucoamylase from Aspergillus niger in the binding of ligands, as determined by difference spectroscopy using four types of inhibitors (a) valienamine-derived, (b) 1-deoxynojirimycins, (c) D-glucono-1,5-lactone, and (d) maltitol, two types of disaccharide substrates (a) alpha-(1----4)-linked and (b) alpha-(1----6)-linked, and three cyclomalto-oligosaccharides (cyclodextrins, CDs) are discussed. An unusual change in absorbance from 300 to 310-320 nm, obtained only with the valienamine-derived inhibitors or when D-glucono-1,5-lactone and maltose are combined, is concluded to arise when subsite 2 is occupied in a transition-state-type of complex. The single mutations of two residues thought to be involved in binding, namely, Tyr116----Ala and Trp120----Phe, alter, but do not abolish this perturbation. The perturbations in the spectra also suggest that maltose and isomaltose have different modes of binding. The following Kd values (M) were determined: acarbose, less than 6 x 10(-12); methyl acarviosinide, 1.6 x 10(-6); and the D-gluco and L-ido forms of hydrogenated acarbose, 1.4 x 10(-8) and 5.2 x 10(-6), respectively. Therefore, both the valienamine moiety and the chain length of acarbose are important for tight binding. In contrast to the valienamine-derived inhibitors, none of the 1-deoxynojirimycin type protected glucoamylase against inactivating oxidation of tryptophanyl residues, although each had a Kd value of approximately 4 x 10(-6) M. There are two distinct carbohydrate-binding areas in glucoamylase, namely, the active site in the catalytic domain and a starch-granule-binding site in the C-terminal domain. The alpha-, beta-, and gamma-CDs have high affinity for the starch-binding domain and low affinity for the active site, whereas the reverse was found for acarbose.

On porcine pancreatic alpha-amylase action: kinetic evidence for the binding of two maltooligosaccharide molecules (maltose, maltotriose and o-nitrophenylmaltoside) by inhibition studies. Correlation with the five-subsite energy profile

Hydrolysis of small substrates (maltose, maltotriose and o-nitrophenylmaltoside) catalysed by porcine pancreatic alpha-amylase was studied from a kinetic viewpoint over a wide range of substrate concentrations. Non-linear double-reciprocal plots are obtained at high maltose, maltotriose and o-nitrophenylmaltoside concentrations indicating typical substrate inhibition. These results are consistent with the successive binding of two molecules of substrate per enzyme molecule with dissociation constants Ks1 and Ks2. The Hill plot, log [v/(V-v)] versus log [S], is clearly biphasic and allows the dissociation constants of the ES1 and ES2 complexes to be calculated. Maltose and maltotriose are inhibitors of the amylase-catalysed amylose and o-nitrophenylmaltoside hydrolysis. The inhibition is of the competitive type. The (apparent) inhibition constant Kiapp varies with the inhibitor concentration. These results are also consistent with the successive binding of at least two molecules of maltose or maltotriose per amylase molecule with the dissociation constants Ki1 and Ki2. These inhibition studies show that small substrates and large polymeric ones are hydrolysed at the same catalytic site(s). The values of the dissociation constants Ks1 and Ki1 of the maltose-amylase complexes are identical. According to the five-subsite energy profile previously determined, at low concentration, maltose (as substrate and as inhibitor) binds to the same two sites (4,5) or (3,4), maltotriose (as substrate and as inhibitor) and o-nitrophenyl-maltoside (as substrate) bind to the same three subsites (3,4,5). The dissociation constants Ks2 and Ki2 determined at high substrate and inhibitor concentration are consistent with the binding of the second ligand molecule at a single subsite. The binding mode of the second molecule of maltose (substrate) and o-nitrophenylmaltoside remains uncertain, very likely because of the inaccuracy due to simplifications in the calculations of the subsite binding energies. No binding site(s) outside the catalytic one has been taken into account in this model.

Subsite profile of the active center of porcine pancreatic alpha-amylase. Kinetic studies using maltooligosaccharides as substrates

The hydrolysis of several maltooligosaccharides catalysed by porcine pancreatic alpha-amylase was performed in order to determine their kinetic parameters. Maltose behaves as a substrate. Molecular activity (Ko) increases with chain length up to maltopentaose, remaining practically unchanged from maltopentaose to maltoheptaose. Maltose shows the highest Km value while the one for maltotriose is the lowest. Only maltose and maltotriose were directly cleaved to glucose. From Km and Ko values, the binding energy of the total complexes and of the productive ones respectively were calculated. The binding energy at each subsite was determined assuming that each substrate forms a single productive complex and that maltose and maltotriose differ in their binding mode from higher oligosaccharides. The model was checked by calculating theorical Km and Ko. Theorical values agree reasonably well with experimental ones.

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.

Amylases: enzymatic mechanisms

Many types of amylases are found throughout the animal, vegetable and microbial kingdoms. They have evolved along different pathways to enable the organism to convert insoluble starch (or glycogen) into low molecular weight, water soluble dextrins and sugars. Alpha amylases are dextrinogenic and can attack the interior of starch molecules. The products retain the alpha anomeric configuration. Beta amylases act only at the non-reducing chain ends and liberate only beta maltose. Both alpha and beta amylases exhibit multiple (repetitive) attack, that is, after the initial catalytic cleavage, the enzyme may remain attached to the substrate and lead to several more cleavages before dissociation of the enzyme-substrate complex. Amylases have extended substrate binding sites, in the range 4-9 glucose units. This enables the enzyme to stress the substrate and lower the activation energy for hydrolysis. Similarly the enzyme exerts a torsion on the glucose unit at the catalytic site, inducing a transition state conformation (oxycarbonium ion). Alpha and beta amylases differ in the stereospecific hydration of the oxycarbonium ion, in the sequence of liberation of the right-hand vs the left-hand product, and the direction of motion of the retained substrate to give multiple attack.