The structure of a novel glucuronoyl esterase from Myceliophthora thermophila gives new insights into its role as a potential biocatalyst

The increasing demand for the development of efficient biocatalysts is a consequence of their broad industrial applications. Typical difficulties that are encountered during their exploitation in a variety of processes are interconnected with factors such as temperature, pH, product inhibitors etc. To eliminate these, research has been directed towards the identification of new enzymes that would comply with the required standards. To this end, the recently discovered glucuronoyl esterases (GEs) are an enigmatic family within the carbohydrate esterase (CE) family. Structures of the thermophilic StGE2 esterase from Myceliophthora thermophila (synonym Sporotrichum thermophile), a member of the CE15 family, and its S213A mutant were determined at 1.55 and 1.9 Å resolution, respectively. The first crystal structure of the S213A mutant in complex with a substrate analogue, methyl 4-O-methyl-β-D-glucopyranuronate, was determined at 2.35 Å resolution. All of the three-dimensional protein structures have an α/β-hydrolase fold with a three-layer αβα-sandwich architecture and a Rossmann topology and comprise one molecule per asymmetric unit. These are the first crystal structures of a thermophilic GE both in an unliganded form and bound to a substrate analogue, thus unravelling the organization of the catalytic triad residues and their neighbours lining the active site. The knowledge derived offers novel insights into the key structural elements that drive the hydrolysis of glucuronic acid esters

Halogen-substituted (C-beta-D-glucopyranosyl)-hydroquinone regioisomers: Synthesis, enzymatic evaluation and their binding to glycogen phosphorylase

Electrophilic halogenation of C-(2,3,4,6-tetra-O-acetyl-b-D-glucopyranosyl) 1,4-dimethoxybenzene (1) afforded regioselectively products halogenated at the para position to the D-glucosyl moiety (8, 9) that were deacetylated to 3 (chloride) and 16 (bromide). For preparing meta regioisomers, 1 was efficiently oxidized with CAN to afford C-(2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl) 1,4-benzoquinone 2 which, in either MeOH or H2O-THF containing few equivalents of AcCl, added hydrochloric acid to produce predominantly meta (with respect to the sugar moiety) chlorinated hydroquinone derivatives 5 and 18, this latter being deacetylated to 4. The deacetylated meta (4, 5) or para (3, 16) halohydroquinones were evaluated as inhibitors of glycogen phosphorylase (GP, a molecular target for inhibition of hepatic glycogenolysis under high glucose concentrations) by kinetics and X-ray crystallography. These compounds are competitive inhibitors of GPb with respect to alpha-D-glucose-1-phosphate. The measured IC50 values (mu M) [169.9 +/- 10.0 (3), 95 (4), 39.8 +/- 0.3 (5) 136.4 +/- 4.9 (16)] showed that the meta halogenated inhibitors (4, 5) are more potent than their para analogs (3, 16). The crystal structures of GPb in complex with these compounds at high resolution (1.97-2.05 angstrom) revealed that the inhibitors are accommodated at the catalytic site and stabilize the T conformation of the enzyme. The differences in their inhibitory potency can be interpreted in terms of variations in the interactions with protein residues of the different substituents on the aromatic part of the inhibitors. (C) 2011 Elsevier Ltd. All rights reserved

Unusual ³¹P Hyperfine Strain Effects in a Conformationally Flexible Cu(II) Complex Revealed by Two-Dimensional Pulse EPR Spectroscopy

Strain effects on g and metal hyperfine coupling tensors, A, are often manifested in Electron Paramagnetic Resonance (EPR) spectra of transition metal complexes, as a result of their intrinsic and/or solvent-mediated structural variations. Although distributions of these tensors are quite common and well understood in continuous-wave (cw) EPR spectroscopy, reported strain effects on ligand hyperfine coupling constants are rather scarce. Here we explore the case of a conformationally flexible Cu(II) complex, [Cu{Ph2P(O)NP(O)Ph2-κ2O,O′}2], bearing P atoms in its second coordination sphere and exhibiting two structurally distinct CuO4 coordination spheres, namely a square planar and a tetrahedrally distorted one, as revealed by X-ray crystallography. The Hyperfine Sublevel Correlation (HYSCORE) spectra of this complex exhibit 31P correlation ridges that have unusual inverse or so-called “boomerang” shapes and features that cannot be reproduced by standard simulation procedures assuming only one set of magnetic parameters. Our work shows that a distribution of isotropic hyperfine coupling constants (hfc) spanning a range between negative and positive values is necessary in order to describe in detail the unusual shapes of HYSCORE spectra. By employing DFT calculations we show that these hfc correspond to molecules showing variable distortions from square planar to tetrahedral geometry, and we demonstrate that line shape analysis of such HYSCORE spectra provides new insight into the conformation-dependent spectroscopic response of the spin system under investigation

Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues

GP catalyzes the phosphorylation of glycogen to Glc-1-P. Because of its fundamental role in the metabolism of glycogen, GP has been the target for a systematic structure-assisted design of inhibitory compounds, which could be of value in the therapeutic treatment of type 2 diabetes mellitus. The most potent catalytic-site inhibitor of GP identified to date is spirohydantoin of glucopyranose (hydan). In this work, we employ MD free energy simulations to calculate the relative binding affinities for GP of hydan and two spirohydantoin analogues, methyl-hydan and n-hydan, in which a hydrogen atom is replaced by a methyl- or amino group, respectively. The results are compared with the experimental relative affinities of these ligands, estimated by kinetic measurements of the ligand inhibition constants. The calculated binding affinity for methyl-hydan (relative to hydan) is 3.75 +/- 1.4 kcal/mol, in excellent agreement with the experimental value (3.6 +/- 0.2 kcal/mol). For n-hydan, the calculated value is 1.0 +/- 1.1 kcal/mol, somewhat smaller than the experimental result (2.3 +/- 0.1 kcal/mol). A free energy decomposition analysis shows that hydan makes optimum interactions with protein residues and specific water molecules in the catalytic site. In the other two ligands, structural perturbations of the active site by the additional methyl- or amino group reduce the corresponding binding affinities. The computed binding free energies are sensitive to the preference of a specific water molecule for two well-defined positions in the catalytic site. The behavior of this water is analyzed in detail, and the free energy profile for the translocation of the water between the two positions is evaluated. The results provide insights into the role of water molecules in modulating ligand binding affinities. A comparison of the interactions between a set of ligands and their surrounding groups in X-ray structures is often used in the interpretation of binding free energy differences and in guiding the design of new ligands. For the systems in this work, such an approach fails to estimate the order of relative binding strengths, in contrast to the rigorous free energy treatment

Unusual 31P Hyperfine Strain Effects in a Conformationally Flexible Cu(II) Complex Revealed by Two-Dimensional Pulse EPR Spectroscopy

Strain effects on g and metal hyperfine coupling tensors, A, are often manifested in Electron Paramagnetic Resonance (EPR) spectra of transition metal complexes, as a result of their intrinsic and/or solvent-mediated structural variations. Although distributions of these tensors are quite common and well understood in continuous-wave (cw) EPR spectroscopy, reported strain effects on ligand hyperfine coupling constants are rather scarce. Here we explore the case of a conformationally flexible Cu(II) complex, [Cu{Ph2P(O)NP(O)Ph2-κ2O,O′}2], bearing P atoms in its second coordination sphere and exhibiting two structurally distinct CuO4 coordination spheres, namely a square planar and a tetrahedrally distorted one, as revealed by X-ray crystallography. The Hyperfine Sublevel Correlation (HYSCORE) spectra of this complex exhibit 31P correlation ridges that have unusual inverse or so-called "boomerang" shapes and features that cannot be reproduced by standard simulation procedures assuming only one set of magnetic parameters. Our work shows that a distribution of isotropic hyperfine coupling constants (hfc) spanning a range between negative and positive values is necessary in order to describe in detail the unusual shapes of HYSCORE spectra. By employing DFT calculations we show that these hfc correspond to molecules showing variable distortions from square planar to tetrahedral geometry, and we demonstrate that line shape analysis of such HYSCORE spectra provides new insight into the conformation-dependent spectroscopic response of the spin system under investigation. © 2020 American Chemical Society

Amide-1,2,3-triazole bioisosterism: the glycogen phosphorylase case

Per-O-acetylatedb-D-glucopyranosyl azide was transformed into an intermediate iminophosphorane byPMe3which was then acylated toN-acyl-b-D-glucopyranosylamines. The same azide and substitutedacetylenes gave 1-(b-D-glucopyranosyl)-4-substituted-1,2,3-triazoles in Cu(I)-catalyzed azide–alkynecycloadditions. Deprotection of these products by the Zemplén method furnishedb-D-Glcp-NHCO-Rderivatives as well as 1-(b-D-Glcp)-4-R-1,2,3-triazoles which were evaluated as inhibitors of rabbit mus-cle glycogen phosphorylase b. Pairs of amides versus triazoles with the same R group displayed similarinhibition constants. X-ray crystallographic studies on the enzyme–inhibitor complexes revealed highsimilarities in the binding of pairs with R = 2-naphthyl and hydroxymethyl, while for the R = Ph and 1-naphthyl compounds a different orientation of the aromatic part and changes in the conformation ofthe 280s loop were observed. By this study new examples of amide-1,2,3-triazole bioisosteric relation-ship have been provide