A Conformational Study of 2-Oxanol: Insight into the Role of Ring Distortion on Enzyme-Catalyzed Glycosidic Bond Cleavage

Sialidase Inhibitors with Different Mechanisms

Sialidases, or neuraminidases, are enzymes that catalyze the hydrolysis of sialic acid (Sia)-containing molecules, mostly removal of the terminal Sia (desialylation). By desialylation, sialidase can modulate the functionality of the target compound and is thus often involved in biological pathways. Inhibition of sialidases with inhibitors is an important approach for understanding sialidase function and the underlying mechanisms and could serve as a therapeutic approach as well. Transition-state analogues, such as anti-influenza drugs oseltamivir and zanamivir, are major sialidase inhibitors. In addition, difluoro-sialic acids were developed as mechanism-based sialidase inhibitors. Further, fluorinated quinone methide-based suicide substrates were reported. Sialidase product analogue inhibitors were also explored. Finally, natural products have shown competitive inhibiton against viral, bacterial, and human sialidases. This Perspective describes sialidase inhibitors with different mechanisms and their activities and future potential, which include transition-state analogue inhibitors, mechanism-based inhibitors, suicide substrate inhibitors, product analogue inhibitors, and natural product inhibitors.

Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure

The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. To clarify the mechanism we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ∼18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme-substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.

Deeper insight into hydrolysis mechanisms of polyester/cotton blended fabrics for separation by explicit solvent models

Aiming to get a deeper and accurate understanding on separation of polyester/cotton blended fabrics in subcritical water, the hydrolysis mechanisms of cellulose and polyester were studied using dispersion-corrected density functional theory (DFT-D) method with and without explicit H₂O under the conductor-like screening model (COSMO) set. The number and locations of explicit H₂O were determined by their likely functions including being dissociation and solvent and catalyst. The calculations disclosed that explicit H₂O provide inductive activation on glycosidic bond of cellulose and ester groups at the center of polyester and the assistance on the transfer of proton as proton-carrier and as catalyst of proton shuttle, affecting the reaction and activation energies in a realistic manner. In addition, the number of explicit H₂O molecules functioning as catalyst of proton shuttle may also has a strong influence on catalytic activity. Based on the improved explicit solvation models, the overall activation energies of proposed hydrolysis mechanisms for cellulose and polyester are 14.81 and 21.46 kcal/mol respectively, which explains the preferential hydrolysis of cellulose from experimental results.

Implications of protein conformations to modifying novel inhibitor Oseltamivir for 2009 H1N1 influenza A virus by simulation and docking studies

Recently three FDA approved existing drugs, namely-Oseltamivir, Peramivir and Zanamivir, used against Neuraminidase (NA) for the inhibitory effect on the process of viral progeny release to inhibit infection. All NA subtypes has been divided into two groups (Group 1 and Group 2) based on phylogenetic study. Oseltamivir and Zanamivir drugs are designed for Group 2 NA but are also used against 2009 H1N1 NA that lies in Group 1. There is no specific drug available for H1N1 and, consequently, there is an urgent requirement for the same. The structure-based drug design and fragment-based drug design methods are used for building more effective and economic drug molecules. In this work, the fragment-based drug development followed by fragment evolution on the basis of protein conformations after every 10 ns of 100 ns simulation. There are two analogs of Oseltamivir acid drug discovered in this study. Only analog 1, along with Oseltamivir acid, were then docked with the native protein. The analog 1 (benzoic acid inhibitor 11) exhibited higher binding affinity value of - 10.70 kcal/mol in comparison to its predecessor. The concept of conformations and protein-ligand interactions can be useful in designing new drugs for H1N1 with high specific binding.

Zwitterionic structures: from physicochemical properties toward computer-aided drug designs

Zwitterions, used widely in chemical, biological and medicinal fields, show distinct physicochemical properties relative to ordinary ampholytes, which largely decide their bioavailability and biological activities. In the present manuscript, these properties are discussed in order to facilitate our understanding of zwitterionic structures, followed by various examples of zwitterionic drugs and the critical role these properties play. We specifically focus our discussions on neuraminidase inhibitors (NAIs), which are used in the treatment and prevention of influenza, covering their computer-assisted design, transformation to zwitterionic isomers and interaction mechanisms of NAIs with proteins. The discovery and development of NAIs provide useful insights that may assist in the exploration of new zwitterionic drugs.

Simulation of Raman optical activity of multi-component monosaccharide samples

Determination of the saccharide structure in solution is a laborious process that can be significantly enhanced by chiral optical spectroscopies.

Carbohydrate-protein interactions: molecular modeling insights

The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.

Quantum chemical study of the equatorial/axial exchange of different substituents in nitrogen and phosphorous-containing 6-membered rings: Role of charge transfer interactions

Understanding the nature of equatorial/axial conversion in six-membered rings is important because of involvement of these motifs in some biological systems. In this work we have studied the equatorial/axial exchange of nitrogen and phosphorous bearing six-membered rings with different representative substituents by using quantum chemistry methods. Three possible routes, i.e. heteroatom inversion and two ring flipping modes were considered. The feasibility of equatorial/axial conversion (based on ΔE#) for the substituted piperidine rings with substituents was in the following order; H > CH 3> Cl ~ OH ~ F , whereas for the phosphorous bearing six-membered rings it was H ~ F > OH > Cl ~ CH 3. In the piperidine system hydrogen and methyl substituents preferred the atom inversion route while the other substituents ( Cl , F , OH ) favored C4 site ring flipping in equatorial/axial conversion. For the phosphorous bearing rings, however, phosphorous retards the atom inversion mechanism and heteroatom site ring flipping is the preferred route for all substituents. We demonstrate that charge transfer effect is one of the key factors that determines the favored route in the presence of various substituents. We show how wave function analysis by natural bond orbital (NBO) method can be used as a straightforward technique to explain the most favored route in the equatorial/axial conversion of substituted 6-membered rings.

The electronic nature of the 1,4-β-glycosidic bond and its chemical environment: DFT insights into cellulose chemistry

The molecular understanding of the chemistry of 1,4-β-glucans is essential for designing new approaches to the conversion of cellulose into platform chemicals and biofuels. In this endeavor, much attention has been paid to the role of hydrogen bonding occurring in the cellulose structure. So far, however, there has been little discussion about the implications of the electronic nature of the 1,4-β-glycosidic bond and its chemical environment for the activation of 1,4-β-glucans toward acid-catalyzed hydrolysis. This report sheds light on these central issues and addresses their influence on the acid hydrolysis of cellobiose and, by analogy, cellulose. The electronic structure of cellobiose was explored by DFT at the BB1 K/6-31++G(d,p) level. Natural bond orbital (NBO) analysis was performed to grasp the key bonding concepts. Conformations, protonation sites, and hydrolysis mechanisms were examined. The results for cellobiose indicate that cellulose is protected against hydrolysis not only by its supramolecular structure, as currently accepted, but also by its electronic structure, in which the anomeric effect plays a key role.

Quantum theoretical study of cleavage of the glycosidic bond of 2'-deoxyadenosine: base excision-repair mechanism of DNA by MutY

The enzyme adenine DNA glycosylase, also called MutY, is known to catalyze base excision repair by removal of adenine from the abnormal 2'-deoxyadenosine:8-oxo-2'-deoxyguanosine pair in DNA. The active site of the enzyme was considered to consist of a glutamic acid residue along with two water molecules. The relevant reaction mechanism involving different barrier energies was studied theoretically. Molecular geometries of the various molecules and complexes involved in the reaction, e.g., the reactant, intermediate, and product complexes as well as transition states, were optimized employing density functional theory at the B3LYP/6-31G(d,p) level in the gas phase. It was followed by single-point energy calculations at the B3LYP/AUG-cc-pVDZ, BHandHLYP/AUG-cc-pVDZ, and MP2/AUG-cc-pVDZ levels in the gas phase. Single-point energy calculations were also carried out at the B3LYP/AUG-cc-pVDZ and BHandHLYP/AUG-cc-pVDZ levels in aqueous media as well as in the solvents chlorobenzene and dichloroethane. For the solvation calculations, the integral equation formalism of the polarizable continuum model (IEF-PCM) was employed. It is found that glutamic acid along with two water molecules would effectively cleave the glycosidic bond of adenosine by a new two-step reaction mechanism proposed here which is different from the three-step mechanism proposed by other authors earlier regarding the working mechanism of MutY.

Docking studies on glycoside hydrolase Family 47 endoplasmic reticulum alpha-(1-->2)-mannosidase I to elucidate the pathway to the substrate transition state

Alpha-(1-->2)-mannosidase I from the endoplasmic reticulum (ERManI), a Family 47 glycoside hydrolase, is a key enzyme in the N-glycan synthesis pathway. Catalytic-domain crystal structures of yeast and human ERMan1s have been determined, the former with a hydrolytic product and the latter without ligands, with the inhibitors 1-deoxymannojirimycin and kifunensine, and with a thiodisaccharide substrate analog. Both inhibitors were bound at the base of the funnel-shaped active site as the unusual 1C4 conformer, while the substrate analog glycon is a 3S1 conformer. In the current study, AutoDock was used to dock alpha-D-mannopyranosyl-(1-->2)-alpha-D-mannopyranose with its glycon in chair (1C4,4C1), half-chair (3H2,3H4,4H3), skew-boat (OS2,3S1,5S1), boat (2,5B,3,OB,B1,4,B2,5), and envelope (3E,4E,E3,E4) conformations into the yeast ERManI active site. Both docked energies and forces on docked ligand atoms were calculated to determine how the ligand distorts to the transition state. From these, we can conclude that (1) both 1C4 and OS2 can be the starting conformers; (2) the most likely binding pathway is 1C4-->3H2-->OS2-->3,OB-->3S1-->3E; (3) the transition state is likely to be close to a 3E conformation.

Aspects of Glycosidic Bond Formation in Aqueous Solution: Chemical Bonding and the Role of Water

A model of the specific acid-catalyzed glycosidic bond formation in liquid water at ambient conditions is studied based on constrained Car-Parrinello ab initio molecular dynamics. Specifically the reaction of alpha-D-glucopyranose and methanol is found to proceed by a D(N)A(N) mechanism. The D(N) step consists of a concerted protonation of the O(1) hydroxyl leaving group; this process results in the breaking of the C(1)-O(1) bond, and oxocarbenium ion formation involving C(1)=O(5). The second step, A(N), is the formation of the C(1)-O(m) glycosidic bond, deprotonation of the methanol hydroxyl group O(m)H(m), and re-formation of the C(1)-O(5) single bond. A focus of this study is the analysis of the electronic structure during this condensed phase reaction relying on both Boys/Wannier localized orbitals and the electron localization function ELF. This analysis allows the clear elucidation of the chemical bonding features of the intermediate bracketed by the D(N) and A(N) steps, which is a non-solvent equilibrated oxocarbenium cation. Most interestingly, it is found that the oxygen in the pyranose ring becomes "desolvated" upon double bond/oxocarbenium formation, whereas it is engaged in the hydrogen-bonded water network before and after this period. This demonstrates that hydrogen bonding and thus the aqueous solvent play an active role in this reaction implying that microsolvation studies in the gas phase, both theoretical and experimental, might lead to qualitatively different reaction mechanisms compared to solution.

Three-dimensional Structure of the Barley β-d-Glucan Glucohydrolase in Complex with a Transition State Mimic

Glucophenylimidazole (PheGlcIm), a tetrahydroimidazopyridine-type inhibitor and 4H3 conformer mimic of a glucoside, binds very tightly to a barley beta-d-glucan glucohydrolase, with a Ki constant of 2 x 10(-9) m and a DeltaG of 51 kJ mol(-1). PheGlcIm binds to the barley beta-d-glucan glucohydrolase approximately 2 x 10(5) times tighter than laminarin, which is the best non-synthetic ground-state substrate found so far for this enzyme, 10(6) times tighter than 4-nitrophenyl beta-d-glucopyranoside, and 2 x 10(7) tighter than glucose. The three-dimensional structure of the beta-d-glucan glucohydrolase with bound PheGlcIm indicates that the complex resembles a hypothetical transition state during the hydrolytic cycle, that the enzyme derives substrate binding energy from the "aglycone" portion of the ligand, and that it also reveals an anti-protonation trajectory for hydrolysis. Continuous electron densities at the 1.6 sigma level form between the three active site residues Asp95, His207, and Asp285, and the C6OH, C7OH, C8OH, and C9OH groups of PheGlcIm. These electron densities correspond to the most favorable interactions in the three-dimensional structure of the beta-d-glucan glucohydrolase-PheGlcIm complex and indicate atomic distances equal to or less than 2.55 A. The crystallographic data were corroborated with ab initio molecular orbital calculations. The data indicate that the 4E conformation of the glucose part of PheGlcIm is critical for tight binding and provide the first evidence for probable substrate distortion during catalysis by this enzyme.

Can thioglycosides imitate the oxonium intermediate in glycosyl hydrolases?

Glycosyl hydrolases catalyse the acid hydrolysis of the glycosidic bond of glycans. The structure of barley beta-D-glucan glucohydrolase in complex with a thiol substrate analogue presents very short contacts between the carboxyl oxygen atoms of the catalytic acid and the sulphur atom of the inhibitor. The geometries of acetic acid and dimethylsulfide in various ionisation states from ab initio molecular orbital calculations predict similar short contacts when an acetate anion forms a complex with a sulphonium cation. The energy of this complex is, however, significantly greater than the energy of the complex where both acetic acid and dimethylsulfide are neutral. Calculations on an active site model of barley beta-D-glucan glucohydrolase indicate that the protein environment is able to significantly reduce this energy. The energy required for mechanical constraint of the short S...O separations, however, is identical to that required for the transfer of the proton from the acid to the sulphur. The identity of the species participating in the short contacts remains unanswered.

Glycosidic bond formation in aqueous solution: on the oxocarbenium intermediate

The mechanism of specific acid-catalyzed glycosidic bond formation between methanol and alpha-d-glucopyranoside in aqueous solution at 300 K was studied using Car-Parrinello molecular dynamics. The reaction was found to proceed through a non-solvent equilibrated oxocarbenium cation intermediate characterized by the loss of a hydrogen-bonding interaction between the ring oxygen and solvating water. The mechanism, which was found to be D(N)A(N) in nature, is discussed in detail.

A computational study of interactions between acetic acid and water molecules

Density functional theory calculations were performed for the title reactions to elucidate the difference between the strong cyclic hydrogen bond of (Me-COOH)(2) and the electrolytic dissociation, MeCOOH <==> Me-COO(-) + H(+), as a weak acid. The association of water clusters with acetic acid dimers strengthens the cyclic hydrogen bond. A nucleophilic attack of the carboxylic carbon by a water cluster leads to a first zwitterionic intermediate, MeCOO(-) + H(3)O(+) + (HO)(3)C-Me. The intermediate is unstable and is isomerized to a neutral interacting system, MeCOOH...(HO)(3)C-Me + H(2)O. The ethanetriol, (HO)(3)-CMe is transformed to an acetic acid monomer. The monomer may be dissociated to give a second zwitterionic intermediate with reasonable proton-relay patterns and energy changes. In proton relay reaction channels, H in MeCOOH is not an acidic proton but is always a hydroxy proton.

Can the stereochemical outcome of glycosylation reactions be controlled by the conformational preferences of the glycosyl donor?

Previous static and dynamical density functional theory studies of the 2,6-di-O-acetyl-3,4-O-isopropylidene-D-galactopyranosyl cations and their methanol adducts has led to an hypothesis that these cations exist in two families of conformers characterized as (2)S(O) and B(2,5), respectively. These families differ by ring inversion, each with its own reactivity. New calculations on the 2,6-di-O-acetyl-3,4-di-O-methyl-D-galactopyranosyl cation confirmed these trends. Removing the isopropylidene group allows more flexibility, but two families of conformers can be discerned with the monocyclic oxocarbenium ions in the E(3) conformation and the bicyclic dioxolenium ions in the (4)H(5) conformation. Attack on the beta-face of these monocyclic cations is favored by hydrogen bonding and the anomeric effect. The experimentally observed high beta-stereoselectivity of mannopyranosyl donors and high alpha-stereoselectivity of glucopyranosyl donors with the 4,6-O-benzylidene protecting groups can be rationalized assuming that the trans-fused 1,3-dioxane ring allows population of only one family of conformers. The combination of hydrogen bonding and conformational changes of the pyranose ring in response to the C-5[bond]O-5[bond]C-1[bond]C-2 torsion angle changes are identified as key factors in stereoselectivity. Based on these observations a strategy to design face discriminated glycosyl donors that exist predominantly in only one family of conformers is proposed.

Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase

BACKGROUND

Barley beta-D-glucan glucohydrolases represent family 3 glycoside hydrolases that catalyze the hydrolytic removal of nonreducing glucosyl residues from beta-D-glucans and beta-D-glucooligosaccharides. After hydrolysis is completed, glucose remains bound in the active site.

RESULTS

When conduritol B epoxide and 2', 4'-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside are diffused into enzyme crystals, they displace the bound glucose and form covalent glycosyl-enzyme complexes through the Odelta1 of D285, which is thereby identified as the catalytic nucleophile. A nonhydrolyzable S-glycosyl analog, 4(I), 4(III), 4(V)-S-trithiocellohexaose, also diffuses into the active site, and a S-cellobioside moiety positions itself at the -1 and +1 subsites. The glycosidic S atom of the S-cellobioside moiety forms a short contact (2.75 A) with the Oepsilon2 of E491, which is likely to be the catalytic acid/base. The glucopyranosyl residues of the S-cellobioside moiety are not distorted from the low-energy 4C(1) conformation, but the glucopyranosyl ring at the +1 subsite is rotated and translated about the linkage.

CONCLUSIONS

X-ray crystallography is used to define the three key intermediates during catalysis by beta-D-glucan glucohydrolase. Before a new hydrolytic event begins, the bound product (glucose) from the previous catalytic reaction is displaced by the incoming substrate, and a new enzyme-substrate complex is formed. The second stage of the hydrolytic pathway involves glycosidic bond cleavage, which proceeds through a double-displacement reaction mechanism. The crystallographic analysis of the S-cellobioside-enzyme complex with quantum mechanical modeling suggests that the complex might mimic the oxonium intermediate rather than the enzyme-substrate complex.

Comparative enzymology, biochemistry and pathophysiology of human exo-alpha-sialidases (neuraminidases)

This review summarizes the current research on human exo-alpha-sialidase (sialidase, neuraminidase). Where appropriate, the properties of viral, bacterial, and human sialidases have been compared. Sialic acids are implicated in diverse physiological processes. Sialidases, as enzymes acting upon sialic acids, assume importance as well. Sialidases hydrolyze the terminal, non-reducing, sialic acid linkage in glycoproteins, glycolipids, gangliosides, polysaccharides, and synthetic molecules. Therefore, a variety of assays are available to measure sialidase activity. Human sialidase is present in several organs and cells. Its cellular distribution could be cytosolic, lysosomal, or in the membrane. Human sialidase occurs in a high molecular-mass complex with several other proteins, including cathepsin A and beta-galactosidase. Multi-protein complexation is important for the in vivo integrity and catalytic activity of the sialidase. However, multi-protein complexation, the occurrence of isoenzymes, diverse subcellular localization, thermal instability, and membrane association have all contributed to difficulties in purifying and characterizing human sialidases. Human sialidase isoenzymes have recently been cloned and sequenced. Even though crystal structures for the human sialidases are not available, the highly conserved regions of the sialidase from various organisms have facilitated molecular modeling of the human enzyme and raise interesting evolutionary questions. While the molecular mechanisms vary, genetic defects leading to human sialidase deficiency are closely associated with at least two well-known human diseases, namely sialidosis and galactosialidosis. No therapy is currently available for either disease. A thorough investigation of human sialidases is therefore crucial to human health.

The role of enzyme distortion in the single displacement mechanism of family 19 chitinases

By using molecular dynamics simulations, we have examined the binding of a hexaNAG substrate and two potential hydrolysis intermediates (an oxazoline ion and an oxocarbenium ion) to a family 19 barley chitinase. We find the hexaNAG substrate binds with all sugars in a chair conformation, unlike the family 18 chitinase which causes substrate distortion. Glu 67 is in a position to protonate the anomeric oxygen linking sugar residues D and E whereas Asn 199 serves to hydrogen bond with the C2' N-acetyl group of sugar D, thus preventing the formation of an oxazoline ion intermediate. In addition, Glu 89 is part of a flexible loop region allowing a conformational change to occur within the active site to bring the oxocarbenium ion intermediate and Glu 89 closer by 4-5 A. A hydrolysis product with inversion of the anomeric configuration occurs because of nucleophilic attack by a water molecule that is coordinated by Glu 89 and Ser 120. Issues important for the design of inhibitors specific to family 19 chitinases over family 18 chitinases also are discussed.

Quantum mechanical calculations on biological systems

Improvements in quantum chemical methods have led to increased applications to biological problems, including the development of potential energy functions for molecular mechanics and modeling of the reactive chemistry in enzyme active sites, with particularly interesting progress being made for metal-containing systems. An important direction is the development and application of hybrid quantum chemical-molecular mechanics methods.