Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design

Ren, Weiwu; Farren-Dai, Marco; Sannikova, Natalia; Świderek, Katarzyna; Wang, Yan; Akintola, Oluwafemi; Britton, Robert; Moliner, Vicent; Bennet, Andrew J.

doi:10.1039/d0sc04401f

Cited by 14 publications

(20 citation statements)

References 51 publications

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“…One crucial point is how the positive charge of glycosyl cations is stabilized by these enzymes, which often rely on intermolecular polar contacts, forming ion-pairs, typically involving carboxylate side chains or even phosphate modifications . It has also been shown that GHs may stabilize transition states even from remote positions to the anomeric center …”

Section: Interactions Of Glycosyl Cations: From Enzymes To Model Systemsmentioning

confidence: 99%

“…73 It has also been shown that GHs may stabilize transition states even from remote positions to the anomeric center. 74 The Influence of Aromatic Interactions on the Stability of Glycosyl Cations. From Enzymes to Model Systems As described above, chemical modifications of the glycosyl donors that facilitate the development of positive charge at the anomeric center provide enhanced reactivities.…”

Section: Enzymes To Model Systems Glycosyl Cations As Central Entitie...mentioning

confidence: 99%

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Glycosyl Oxocarbenium Ions: Structure, Conformation, Reactivity, and Interactions

et al. 2021

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Metrics & MoreArticle Recommendations CONSPECTUS: Carbohydrates (glycans, saccharides, and sugars) are essential molecules in all domains of life. Research on glycoscience spans from chemistry to biomedicine, including material science and biotechnology. Access to pure and well-defined complex glycans using synthetic methods depends on the success of the employed glycosylation reaction. In most cases, the mechanism of the glycosylation reaction is believed to involve the oxocarbenium ion. Understanding the structure, conformation, reactivity, and interactions of this glycosyl cation is essential to predict the outcome of the reaction. In this Account, building on our contributions on this topic, we discuss the theoretical and experimental approaches that have been employed to decipher the key features of glycosyl cations, from their structures to their interactions and reactivity. We also highlight that, from a chemical perspective, the glycosylation reaction can be described as a continuum, from unimolecular S N 1 with naked oxocarbenium cations as intermediates to bimolecular S N 2-type mechanisms, which involve the key role of counterions and donors. All these factors should be considered and are discussed herein. The importance of dissociative mechanisms (involving contact ion pairs, solvent-separated ion pairs, solvent-equilibrated ion pairs) with bimolecular features in most reactions is also highlighted.The role of theoretical calculations to predict the conformation, dynamics, and reactivity of the oxocarbenium ion is also discussed, highlighting the advances in this field that now allow access to the conformational preferences of a variety of oxocarbenium ions and their reactivities under S N 1-like conditions. Specifically, the ground-breaking use of superacids to generate these cations is emphasized, since it has permitted characterization of the structure and conformation of a variety of glycosyl oxocarbenium ions in superacid solution by NMR spectroscopy.We also pay special attention to the reactivity of these glycosyl ions, which depends on the conditions, including the counterions, the possible intra-or intermolecular participation of functional groups that may stabilize the cation and the chemical nature of the acceptor, either weak or strong nucleophile. We discuss recent investigations from different experimental perspectives, which identified the involved ionic intermediates, estimating their lifetimes and reactivities and studying their interactions with other molecules. In this context, we also emphasize the relationship between the chemical methods that can be employed to modulate the sensitivity of glycosyl cations and the way in which glycosyl modifying enzymes (glycosyl hydrolases and transferases) build and cleave glycosidic linkages in nature. This comparison provides inspiration on the use of molecules that regulate the stability and reactivity of glycosyl cations.

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Section: Interactions Of Glycosyl Cations: From Enzymes To Model Systemsmentioning

confidence: 99%

Section: Enzymes To Model Systems Glycosyl Cations As Central Entitie...mentioning

confidence: 99%

Glycosyl Oxocarbenium Ions: Structure, Conformation, Reactivity, and Interactions

et al. 2021

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“…[12] One of the strategies to inhibit a GH is based on designing TS mimics whose conformation is similar to the oxocarbenium ion-like ring. [13][14][15][16] In parallel, developing chemical derivatives of the natural substrate of GHs has emerged as a procedure to inhibit glycosidases. The most common technique utilizes sulfuration of the glycosidic bond (S-glycoside).…”

Section: Introductionmentioning

confidence: 99%

Unlocking the Hydrolytic Mechanism of GH92 α‐1,2‐Mannosidases: Computation Inspires the use of C‐Glycosides as Michaelis Complex Mimics

Alonso-Gil

Parkan

Kaminský

et al. 2022

Chemistry A European J

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The conformational changes in a sugar moiety along the hydrolytic pathway are key to understand the mechanism of glycoside hydrolases (GHs) and to design new inhibitors. The two predominant itineraries for mannosidases go via O S 2 !B 2,5 ! 1 S 5 and 3 S 1 ! 3 H 4 ! 1 C 4 . For the CAZy family 92, the conformational itinerary was unknown. Published complexes of Bacteroides thetaiotaomicron GH92 catalyst with a S-glycoside and mannoimidazole indicate a 4 C 1 ! 4 H 5 / 1 S 5 ! 1 S 5 mechanism. However, as observed with the GH125 family, S-glycosides may not act always as good mimics of GH's natural substrate. Here we present a cooperative study between computations and experiments where our results predict the E 5 !B 2,5 / 1 S 5 ! 1 S 5 pathway for GH92 enzymes. Furthermore, we demonstrate the Michaelis complex mimicry of a new kind of C-disaccharides, whose biochemical applicability was still a chimera.

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“…Compared to the carbasugar covalent inhibitors, acetals require less catalytic assistance to traverse cationic TSs for the formation and hydrolysis of glycosylated GH intermediates. This marked difference in enzyme efficiency toward the natural substrates versus our carbasugar covalent inhibitors gives the carbasugar class of compounds high potential as Chemical Biology tools. , …”

Section: Results and Discussionmentioning

confidence: 99%

Intrinsic Nucleophilicity of Inverting and Retaining Glycoside Hydrolases Revealed Using Carbasugar Glyco-Tools

et al. 2021

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Hydrolyses of cyclohexenyl-based carbasugars that mimic either α-Dglucose or α-D-galactose were explored with two Bacteroides thetaiotaomicron enzymes from glycoside hydrolase family 97: an inverting α-glucosidase (BtGH97a) and a retaining αgalactosidase (BtGH97b). Both enzymes yield nucleophilic substitutions at the pseudoanomeric center of the carbasugar substrates, giving significantly different linear energy relationships for the catalytic rate constant as a function of the leaving group ability. Specifically, the kinetic data for the inverting α-glucosidase is consistent with the reaction giving a hydrolyzed inverted carbaglucose product by a mechanism that proceeds with little nucleophilic participation by the bound water molecule at the reaction transition state. In contrast, the reaction of carbagalactose substrates with the retaining GH97 enzyme involves a rate-limiting nonchemical step, likely a conformational change, followed by rapid substitution involving a nucleophilic amino acid residue to give a covalently bound intermediate. Considering the structural similarities between these two GH97 enzymes, the kinetic data nonetheless reveal a significant (>10 6 ) difference in the rates of nucleophilic attack between the unique enzymatic nucleophileswith the less nucleophilic species being H 2 O in the inverting α-glucosidase and the better nucleophile being a carboxylate in the retaining αgalactosidase. The enzymatic rate constant ratio for the phenyl carbasugars contrasts with the corresponding kinetic data obtained using natural substrate phenyl glycopyranosides. Last, for the galactocarbasugar with a phenol leaving group, the second-order rate constant for alkylation of the GH97 α-galactosidase is only ∼10-fold lower than that for glycosylation of this enzyme by the parent carbohydrate phenyl α-D-galactopyranoside. This modest difference in rate constants underscores our conclusion that retaining glycoside hydrolases may not have optimized the nucleophilicity of their active site nucleophiles with the result that the transition state free energies for formation and hydrolysis of the covalent enzyme intermediate are matched.

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Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design

Abstract: Positive charge stabilized on remote C5-allylic center with catalysis occurring via a loose SN2 transition state.

Cited by 14 publications

References 51 publications

Glycosyl Oxocarbenium Ions: Structure, Conformation, Reactivity, and Interactions

Glycosyl Oxocarbenium Ions: Structure, Conformation, Reactivity, and Interactions

Unlocking the Hydrolytic Mechanism of GH92 α‐1,2‐Mannosidases: Computation Inspires the use of C‐Glycosides as Michaelis Complex Mimics

Intrinsic Nucleophilicity of Inverting and Retaining Glycoside Hydrolases Revealed Using Carbasugar Glyco-Tools

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