Multidimensional Free Energy and Accelerated Quantum Library Methods Provide a Gateway to Glycoenzyme Conformational, Electronic, and Reaction Mechanisms

Enzyme reactions are complex to simulate accurately, and none more so than glycoenzymes (glycosyltransferase and glycosidases). A rigorous sampling of the protein frame and the conformationally plural carbohydrate substrate coupled with an unbiased treatment of the electron dynamics is needed to discover the true reaction landscapes. Here, we demonstrate the effectiveness of two computational methods ported in libraries that we have developed. The first is a flat histogram free energy method called FEARCF capable of multidimensional sampling and rapidly converging to a complete coverage of phase space. The second, the Quantum Supercharger Library (QSL), is a method that accelerates the computation of the ab initio electronic wave function as well as the integral derivatives on graphical processing units (GPUs). These QSL accelerated computations form the core components needed for direct quantum dynamics and QM/MM dynamics when coupled with legacy codes such as GAMESS and NWCHEM, making state of the art hyper-parallel electronic computations in chemistry and chemical biology possible. The combination of QSL (acceleration of ab initio QM computation) and FEARCF (multidimensional hyper-parallel reaction dynamics) makes the simulation of ab initio QM/MM reaction dynamics of enzyme catalysis feasible. Enzymes that process carbohydrates pose an added challenge as their pyranose ring substrates span multidimensional conformational space whose sampling is an intimate function of the catalytic mechanism. Here, we use the pairing of FEARCF and QSL to simulate the catalytic effect of the glycoenzyme β-N-acetylglucosamine transferase (OGT). The reaction mechanism is discovered from a variable three bond reaction surface using SCCDFTB. The role of the OGT in distorting the pyranose ring of β-N-acetylglucosamine (GlcNAc) away from the equilibrium 4C1 chair conformation toward the E3 envelope needed for the transition state is discovered from its pucker free energy hypersurfaces (or free energy volume, FEV). A complete GlcNAc ring pucker HF 6-31g FEV is constructed from ab initio QM dynamics in vacuum and ab initio QM/MM dynamics in the OGT catalytic domain. The OGT is shown to clearly lower the pathway toward the transition state E3 ring conformer as well as stabilize it by 1.63 kcal/mol. Illustrated here is the use of QSL accelerated ab initio QM/MM dynamics that thoroughly explores carbohydrate catalyzed reactions through a FEARCF multidimensional sampling of the interdependence between reaction and conformational space. This demonstrates how experimentally inaccessible molecular and electronic mechanisms that underpin enzyme catalysis can be discovered by directly modeling the dynamics of these complex reactions.

Anomeric effect, hyperconjugation and electrostatics: lessons from complexity in a classic stereoelectronic phenomenon

Understanding the interplay of multiple components (steric, electrostatic, stereoelectronic, dispersive, etc.) that define the overall energy, structure, and reactivity of organic molecules can be a daunting task. The task becomes even more difficult when multiple approaches based on different physical premises disagree in their analysis of a multicomponent molecular system. Herein, we will use a classic conformational "oddity", the anomeric effect, to discuss the value of identifying the key contributors to reactivity that can guide chemical predictions. After providing the background related to the relevant types of hyperconjugation and a brief historic outline of the origins of the anomeric effect, we outline variations of its patterns and provide illustrative examples for the role of the anomeric effect in structure, stability, and spectroscopic properties. We show that the complete hyperconjugative model remains superior in explaining the interplay between structure and reactivity. We will use recent controversies regarding the origin of the anomeric effect to start a deeper discussion relevant to any electronic effect. Why are such questions inherently controversial? How to describe a complex quantum system using a model that is "as simple as possible, but no simpler"? What is a fair test for such a model? Perhaps, instead of asking "who is right and who is wrong?" one should ask "why do we disagree?". Stereoelectronic thinking can reconcile quantum complexity with chemical intuition and build the conceptual bridge between structure and reactivity. Even when many factors contribute to the observed structural and conformational trends, electron delocalization is a dominating force when the electronic demand is high (i.e., bonds are breaking as molecules distort from their equilibrium geometries). In these situations, the role of orbital interactions increases to the extent where they can define reactivity. For example, negative hyperconjugation can unleash the "underutilized" stereoelectronic power of unshared electrons (i.e., the lone pairs) to stabilize a developing positive charge at an anomeric carbon. This analysis paves the way for the broader discussion of the omnipresent importance of negative hyperconjugation in oxygen-containing functional groups. From that point of view, the stereoelectronic component of the anomeric effect plays a unique role in guiding reaction design.

Development of a 1,2-difluorofucoside activity-based probe for profiling GH29 fucosidases

GH29 α-l-fucosidases catalyze hydrolysis of terminal α-l-fucosyl linkages with varying specificity and are expressed by prominent members of the human gut microbiota. Both homeostasis and dysbiosis at the human intestinal microbiota interface have been correlated with altered fucosidase activity. Herein we describe the development of a 2-deoxy-2-fluoro fucosyl fluoride derivative with an azide mini-tag as an activity-based probe (ABP) for selective in vitro labelling of GH29 α-l-fucosidases. Only catalytically active fucosidases are inactivated by this ABP, allowing their functionalization with a biotin reporter group via the CuAAC reaction and subsequent in-gel detection at nanogram levels. The ABP we present here is shown to be active against a GH29 α-l-fucosidase from Bacteroides fragilis and capable of labeling two other GH29 α-l-fucosidases with different linkage specificity, illustrating its broader utility. This novel ABP is a valuable addition to the toolbox of fucosidase probes by allowing identification and functional studies of the wide variety of GH29 fucosidases, including those in the gut microbiota.

Synthesis of isobemisiose, neosartose, and fischerose: three α-1,6-linked trehalose-based oligosaccharides identified from Neosartorya fischeri

Three complex α-1,6-linked trehalose-based oligosaccharides with unique preservation properties, isobemisiose, neosartose, and fischerose, were recently identified from the extreme stress-tolerant ascospores of Neosartorya fischeri. Herein, we report the first concise, scalable, and iterative chemical synthesis of these oligosaccharides from a differentially protected thioglycoside donor and a selectively protected, asymmetric trehalose acceptor. This work constitutes an improved synthesis of isobemisiose, and is also the first reported synthesis of neosartose, a tetrasaccharide, and fischerose, a pentasaccharide, in good yield. Importantly, in-depth studies of biological function are enabled by this synthetic platform.

The Experimental Evidence in Support of Glycosylation Mechanisms at the SN1-SN2 Interface

A critical review of the state-of-the-art evidence in support of the mechanisms of glycosylation reactions is provided. Factors affecting the stability of putative oxocarbenium ions as intermediates at the SN1 end of the mechanistic continuum are first surveyed before the evidence, spectroscopic and indirect, for the existence of such species on the time scale of glycosylation reactions is presented. Current models for diastereoselectivity in nucleophilic attack on oxocarbenium ions are then described. Evidence in support of the intermediacy of activated covalent glycosyl donors is reviewed, before the influences of the structure of the nucleophile, of the solvent, of temperature, and of donor-acceptor hydrogen bonding on the mechanism of glycosylation reactions are surveyed. Studies on the kinetics of glycosylation reactions and the use of kinetic isotope effects for the determination of transition-state structure are presented, before computational models are finally surveyed. The review concludes with a critical appraisal of the state of the art.

Mapping the Relationship between Glycosyl Acceptor Reactivity and Glycosylation Stereoselectivity

The reactivity of both coupling partners-the glycosyl donor and acceptor-is decisive for the outcome of a glycosylation reaction, in terms of both yield and stereoselectivity. Where the reactivity of glycosyl donors is well understood and can be controlled through manipulation of the functional/protecting-group pattern, the reactivity of glycosyl acceptor alcohols is poorly understood. We here present an operationally simple system to gauge glycosyl acceptor reactivity, which employs two conformationally locked donors with stereoselectivity that critically depends on the reactivity of the nucleophile. A wide array of acceptors was screened and their structure-reactivity/stereoselectivity relationships established. By systematically varying the protecting groups, the reactivity of glycosyl acceptors can be adjusted to attain stereoselective cis-glucosylations.

Synthetic utility of endocyclic cleavage reaction

Existence of endocyclic cleavage reaction is now clearly shown from experimental evidence of endocyclic cleavage reaction as well as computational chemistry. Not only stereoelectronic factor, several factors could be main factors for endocyclic cleavage reaction. Endocyclic cleavage reaction is useful for 1,2-cis aminoglycoside formation, which is difficult by conventional glycosylation. By using endocyclic cleavage reaction, several glycosides with 1,2-cis aminoglycoside were prepared.

In silico analysis of interaction pattern switching in ligand⋯receptor binding in Golgi α-mannosidase II induced by the protonated states of inhibitors

Different binding modes for charge-neutral and protonated inhibitor forms in Golgi α-mannosidase II active sites may influence their biological activities.

Catalytic stereospecific O-glycosylation

Glycosylation using Tf₂NH or Tf₂NTMS as the catalysts and a trichloroacetimidate donor gives glycosides with inverted anomeric stereochemistry.

Design of α-Selective Glycopyranosyl Donors Relying on Remote Anchimeric Assistance

Oligosaccharides have a variety of versatile biological effects, but unlike peptides and oligonucleotides, investigation of the roles of oligosaccharides is not easy. Since biosynthesis of oligosaccharides does not comply with direct genetic control, their isolation from natural sources and biotechnological preparation are complicated, due to the heterogeneous composition of raw carbohydrates. Oligosaccharide synthesis is needed for the establishment or confirmation of the structure of natural glycocompounds. Also, synthetically prepared, defined oligosaccharides and their derivatives are becoming increasingly important tools for many biological and immunological research projects. The key step of oligosaccharide synthesis involves glycosylation, a reaction that builds glycosidic bonds. Usually, construction of 1,2-trans-bonds is easy, and therefore, this reaction can even be included into automated syntheses. At this time, installation of the 1,2-cis-bond remains simultaneously frustrating and compelling. In our and other laboratories, a strategy of α-selective (1,2-cis) glycosylation, relying on remote anchimeric assistance with acyl groups, is studied. The state of the art in this work is summarized in this review.

Glycosylation intermediates studied using low temperature1H- and19F-DOSY NMR: new insight into the activation of trichloroacetimidates

Low temperature¹H- and¹⁹F-DOSY have been used for analyzing reactive intermediates in glycosylation reactions, where a glycosyl trichloroacetimidate donor has been activated using different catalysts.

Cation Clock Reactions for the Determination of Relative Reaction Kinetics in Glycosylation Reactions: Applications to Gluco- and Mannopyranosyl Sulfoxide and Trichloroacetimidate Type Donors

The development of a cation clock method based on the intramolecular Sakurai reaction for probing the concentration dependence of the nucleophile in glycosylation reactions is described. The method is developed for the sulfoxide and trichloroacetimidate glycosylation protocols. The method reveals that O-glycosylation reactions have stronger concentration dependencies than C-glycosylation reactions consistent with a more associative, S(N)2-like character. For the 4,6-O-benzylidene-directed mannosylation reaction a significant difference in concentration dependence is found for the formation of the β- and α-anomers, suggesting a difference in mechanism and a rationale for the optimization of selectivity regardless of the type of donor employed. In the mannose series the cyclization reaction employed as clock results in the formation of cis and trans-fused oxabicyclo[4,4,0]decanes as products with the latter being strongly indicative of the involvement of a conformationally mobile transient glycosyl oxocarbenium ion. With identical protecting group arrays cyclization in the glucopyranose series is more rapid than in the mannopyranose manifold. The potential application of related clock reactions in other carbenium ion-based branches of organic synthesis is considered.

1,2-cis Alkyl glycosides: straightforward glycosylation from unprotected 1-thioglycosyl donors

A 1,2-cis-alkyl glycosidation protocol that makes use of unprotected phenyl 1-thioglycosyl donors is reported. Glycosylation of various functionalized alcohols was accomplished in moderate to high yield and selectivity to give the 1,2-cis-glycosides. In order to quickly develop optimum glycosylation conditions, an FIA (flow injection analysis)-ESI-TOF-MS method was developed that enabled rapid and quantitative evaluation of yield on small scale. This methodology, coupled with NMR spectroscopy, allowed for rapid evaluation of the overall reactions.

A propos of glycosyl cations and the mechanism of chemical glycosylation; the current state of the art

An overview of recent advances in glycosylation with particular emphasis on mechanism is presented. The mounting evidence for both the existence of glycosyl oxocarbenium ions as fleeting intermediates in some reactions, and the crucial role of the associated counterion in others is discussed. The extremes of the SN1 and SN2 manifolds for the glycosylation reaction are bridged by a continuum of mechanisms in which it appears likely that most examples are located.

The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases

Unraveling the conformational catalytic itinerary of glycoside hydrolases (GHs) is a growing topic of interest in glycobiology, with major impact in the design of GH inhibitors. β-xylanases are responsible for the hydrolysis of glycosidic bonds in β-xylans, a group of hemicelluloses of high biotechnological interest that are found in plant cell walls. The precise conformations followed by the substrate during catalysis in β-xylanases have not been unambiguously resolved, with three different pathways being proposed from structural analyses. In this work, we compute the conformational free energy landscape (FEL) of β-xylose to predict the most likely catalytic itineraries followed by β-xylanases. The calculations are performed by means of ab initio metadynamics, using the Cremer-Pople puckering coordinates as collective variables. The computed FEL supports only two of the previously proposed itineraries, 2SO → [2,5B]ǂ → 5S1 and 1S3 → [4H3]ǂ → 4C1, which clearly appear in low energy regions of the FEL. Consistently, 2SO and 1S3 are conformations preactivated for catalysis in terms of free energy/anomeric charge and bond distances. The results however exclude the OE → [OS2]ǂ → B2,5 itinerary that has been recently proposed for a family 11 xylanase. Classical and ab initio QM/MM molecular dynamics simulations reveal that, in this case, the observed OE conformation has been enforced by enzyme mutation. These results add a word of caution on using modified enzymes to inform on catalytic conformational itineraries of glycoside hydrolases.

Solvent effects in the nucleophilic substitutions of tetrahydropyran acetals promoted by trimethylsilyl trifluoromethanesulfonate: trichloroethylene as solvent for stereoselective C- and O-glycosylations

The selectivities of nucleophilic substitution reactions of tetrahydropyran acetals promoted by trimethylsilyl trifluoromethanesulfonate depend upon the reaction solvent. Polar solvents favor the formation of S(N)1 products, while nonpolar solvents favor S(N)2 products. Trichloroethylene was identified as the solvent most likely to give S(N)2 products in both C- and O-glycosylation reactions.

Pyranosides with 2,3-trans carbamate groups: exocyclic or endocyclic cleavage reaction?

Pyranosides with 2,3-trans carbamate groups exhibit high 1,2-cis selectivity in glycosylation reactions. Using glycosyl donors with N-benzyl 2,3-trans carbamate groups, an anti-Helicobacter pylori oligosaccharide was synthesized in an efficient manner. Moreover, pyranosides with 2,3-trans carbamate groups readily undergo anomerization from the β to the α configuration under mild acidic conditions via endocyclic cleavage. Acyclic cations generated during the endocyclic cleavage reaction were captured using reduction and intramolecular Friedel-Crafts reaction. By exploiting this anomerization, multiply aligned 1,2-trans glycosyl bonds can be transformed to 1,2-cis glycosyl bonds in a single operation.

In a glycosylation reaction how does a hydroxylic nucleophile find the activated anomeric carbon?

The mechanism by which nucleophilic hydroxyls are attracted to activated glycopyranosyl donors is not known. Besides the intrinsic attraction of oxygen centred negative dipoles towards the developing electron deficiency at the anomeric carbon only a few suggestions have been given in the literature. By studying the effect on Density Functional Theory (DFT) modelled glycosylation reactions on the presence of polar additives as tested with acetonitrile two possible effects have been identified. One was noted in a previous publication (Carbohydr. Res.2012, 356, 180-190) and two further examples discovered here that suggest that a lone pair of a nucleophile approaching a donor with a β-leaving group from the α-face can act as the antiperiplanar lone pair that assists leaving group departure. This interaction starts at just under a nucleophile C-1 separation of 3Å and has an incipient bond angle of O-5-C-1-Nuc(O or N) of very close to 90° which can be at C-1 with the p-type orbital at C-1-O-5 of the incipient oxacarbenium ion, that is, the LUMO of the activated donor. The 2nd interaction is less well studied and is suggested to be a similar bonding interaction which moves β-face nucleophiles to O-Nuc-C-1-leaving groups angles close to 180°.

Probing the influence of protecting groups on the anomeric equilibrium in sialic acid glycosides with the persistent radical effect

A method for the investigation of the influence of protecting groups on the anomeric equilibrium in the sialic acid glycosides has been developed on the basis of the equilibration of O-sialyl hydroxylamines by reversible homolytic scission of the glycosidic bond following the dictates of the Fischer-Ingold persistent radical effect. It is found that a trans-fused 4O,5N-oxazolidinone group stabilizes the equatorial glycoside, i.e., reduces the anomeric effect, when compared to the 4O,5N-diacetyl protected systems. This effect is discussed in terms of the powerful electron-withdrawing nature of the oxazolidinone system, which in turn is a function of its strong dipole moment in the mean plane of the pyranose ring system. The new equilibration method displays a small solvent effect and is most pronounced in less polar media consistent with the anomeric effect in general. The unusual (for anomeric radicals) poor kinetic selectivity of anomeric sialyl radicals is discussed in terms of the planar π-type structure of these radicals and of competing 1,3-diaxial interactions in the diastereomeric transition states for trapping on the α- and β-faces of the radical.

Exploring functional cyclophellitol analogues as human retaining beta-glucosidase inhibitors

Of six cyclophellitol analogues, the N-pentylaziridine is the most effective retaining human beta-glucosidase inhibitor considering potency and compound stability.

Phosphodiesters serve as potentially tunable aglycones for fluoro sugar inactivators of retaining β-glycosidases

2-Deoxy-2-fluoroglycosides were synthesised and tested as covalent glycosidase inactivators. β-d-Gluco-, -manno- and -galacto-configured benzyl-benzylphosphonate derivatives efficiently inactivate β-gluco-, β-manno- and β-galactosidases, while α-gluco- and α-manno-configured phosphate and phosphonate derivatives instead served as slow substrates for their cognate α-glycosidases.

Influence of side chain conformation and configuration on glycosyl donor reactivity and selectivity as illustrated by sialic acid donors epimeric at the 7-position

Two N-acetyl 4O,5N-oxazolidinone-protected sialyl thioglycosides epimeric at the 7-position have been synthesized and their reactivity and stereoselectivity in glycosylation reactions have been compared. It is demonstrated that the natural 7S-donor is both more reactive and more α-selective than the unnatural 7R-isomer. The difference in reactivity is attributed to the side chain conformation and specifically to the proximity of O7 to the anomeric center. In the natural 7S-isomer, O7 is closer to the anomeric center than in its unnatural 7R-epimer and, therefore, better able to support incipient positive charge at the locus of reaction. The difference in selectivity is also attributed to the side conformation, which in the unnatural 7R-series is placed perpendicularly above the α-face of the donor and so shields it to a greater extent than in the 7S-series. These observations are consistent with earlier conclusions on the influence of the side chain conformation on reactivity and selectivity derived from conformationally locked models in the glucose and galactose series and corroborate the suggestion that those effects are predominantly stereoelectronic rather than torsional. The possible relevance of side chain conformation as a factor in the influence of glycosylation stereoselectivity by remote protecting groups and as a control element in enzymic processes for glycosidic bond formation and hydrolysis are discussed. Methods for assignment of the anomeric configuration in the sialic acid glycosides are critically surveyed.