Analysis of transition state mimicry by tight binding aminothiazoline inhibitors provides insight into catalysis by human O-GlcNAcase

Cekic, Nevena; Heinonen, Julia; Stubbs, Keith A.; Roth, Christian; He, Yuan; Bennet, Andrew J.; McEachern, Ernest J.; Davies, G.J.; Vocadlo, David J.

doi:10.1039/c6sc00370b

Cited by 34 publications

(56 citation statements)

References 57 publications

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“…In fact, the p K a of an oxazolinium ion in solution has been estimated to be higher than that of a carboxylate . However, recent studies on GH84 O‐GlcNAcase suggest that the intermediate is an oxazoline, which is already the basis for inhibitor design in this family of enzymes . The reaction intermediate in other glycosidase families acting by substrate‐assisted catalysis has been described as either an oxazolinium ion, an oxazoline, or both, since there is no direct experimental proof that can be used to discriminate between both scenarios.…”

Section: Introductionmentioning

confidence: 99%

Oxazoline or Oxazolinium Ion? The Protonation State and Conformation of the Reaction Intermediate of Chitinase Enzymes Revisited

Coines

Alfonso‐Prieto

Biarnés

et al. 2018

Chemistry A European J

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The enzymatic hydrolysis of chitin, one of the most abundant carbohydrates in nature, is achieved by chitinases, enzymes of increasing importance in biomedicine and industry. Unlike most retaining glycosidases, family GH18 chitinases follow a substrate‐assisted mechanism in which the 2‐acetamido group of one N‐acetylglucosamine monomer, rather than a basic residue of the enzyme, reacts with the sugar anomeric carbon, forming an intermediate that has been described as an oxazolinium ion. Based on QM/MM metadynamics simulations on chitinase B from Serratia marcescens, we show that the reaction intermediate of GH18 chitinases features instead a neutral oxazoline in a 4C1/4H5 conformation, with an oxazolinium ion being formed on the pathway towards the reaction products. The role of a well‐defined hydrogen‐bond network that operates around the N‐acetyl group, orchestrating catalysis by protonation events, is discussed.

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Section: Introductionmentioning

confidence: 99%

Oxazoline or Oxazolinium Ion? The Protonation State and Conformation of the Reaction Intermediate of Chitinase Enzymes Revisited

Coines

Alfonso‐Prieto

Biarnés

et al. 2018

Chemistry A European J

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“…Extensive soaking of diverse chemical inhibitors was performed to displace the C-terminal peptide. Structures of complexes with the mechanism-derived inhibitor Thiamet-G ( K i =0.9 nM), 23 the “PUGNAc-imidazole” hybrid ( K i =3.9 μM) 24 and a potent derivative (VV347) of recently described pyrrolidine inhibitors ( K i =8 nM), 25 were determined ( Fig. 2 , Supplementary Fig.…”

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confidence: 99%

Structural and functional insight into human O-GlcNAcase

et al. 2017

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O-GlcNAc hydrolase, OGA, removes O-linked N-acetylglucosamine (O-GlcNAc) from myriad nucleocytoplasmic proteins. Through co-expression and assembly of OGA fragments we determined the 3-D structure of human OGA, revealing an unusual helix exchanged dimer that lays a structural foundation for an improved understanding of substrate recognition and regulation of OGA. Structures of OGA in complex with a series of inhibitors define a precise blueprint for the design of inhibitors having clinical value.

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“…[14] Indeed, the alkyl chain points into the conserved hydrophobic pocket, but once it exceeds the three-carbon optimum length, as in the n-butyl derivative 9 d, significant decreases in both hOGA inhibitory activity (hOGA K i = 350 nM) and selectivity (K i (HexB)/K i (hOGA) = 13 700) are observed. [14] It is worth mentioning that the authors used a nonlinear Morrison [95] fitting method to calculate the K i values for 9 b,9 c, and thiamet-G. The K i value for thiamet-G using that method was determined to be ten times lower (K i = 2.1 nM) than the K i value obtained using a Michaelis-Menten method.…”

Section: Pugnac and Other Related Derivativesmentioning

confidence: 99%

“…[81] Cartoon plots of a series of 2'-aminothiazole in complex with BtOGA have been prepared to assess the relation between the bulkiness of the 2'-position substituents and its effect on both potency and selectivity towards hOGA. [14] Increasing the size of the 2'-aminoalkyl chain does not necessarily increase the potency or the selectivity of inhibitors. Three-carbon alkyl chain derivatives as in N-propyl 9 b or N-allyl derivative 9 c have been uncovered as some of the most active (hOGA K i = 2 and 3.2 nM, respectively) and selective hOGA inhibitors (K i (HexB)/K i (hOGA) = 1 850 000 and 950 000, respectively).…”

Section: Pugnac and Other Related Derivativesmentioning

confidence: 99%

O‐GlcNAcase: Emerging Mechanism, Substrate Recognition and Small‐Molecule Inhibitors

2020

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O‐GlcNAcylation is the dynamic and ubiquitous post‐translational glycosylation of nucleocytoplasmic proteins on serine/threonine residues; it is implicated in regulation of the cell cycle. This protein modification is mainly governed by a pair of enzymes: O‐GlcNAc transferase (OGT) adds the N‐acetylglucosamine moiety to acceptor proteins, and O‐GlcNAcase (OGA) hydrolyses the sugar moiety from protein acceptors. Irregular O‐GlcNAcylation is linked to several diseases including cancer, diabetes and neurodegeneration. Recently, the discovery of small‐molecule OGA inhibitors has enabled the physiological function of O‐GlcNAcylation to be investigated. However, the design of highly potent and selective inhibitors faces several challenges as no full structural data of human OGA has been discovered to date. Moreover, there are a number of mechanistically similar related enzymes such as β‐hexosaminidases (Hex), and the concomitant inhibition of these enzymes leads to undesirable lysosomal‐storage disorders. This review highlights recent insights into the structure of human O‐GlcNAcase and its isoforms. We focus on the catalytic mechanism and substrate recognition by OGA. In addition, it presents an updated overview of small‐molecule OGA inhibitors, with either carbohydrate or noncarbohydrate scaffolds. We discuss inhibitor structures, binding modes, and selectivity towards the enzyme, and potential outcomes in probing O‐GlcNAcylation at cellular levels.

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Analysis of transition state mimicry by tight binding aminothiazoline inhibitors provides insight into catalysis by human O-GlcNAcase

Abstract: 2′-Aminothiazoline inhibitors of human OGA are tight binding transition state mimics for which binding depends on inhibitor pKa.

Cited by 34 publications

References 57 publications

Oxazoline or Oxazolinium Ion? The Protonation State and Conformation of the Reaction Intermediate of Chitinase Enzymes Revisited

Oxazoline or Oxazolinium Ion? The Protonation State and Conformation of the Reaction Intermediate of Chitinase Enzymes Revisited

Structural and functional insight into human O-GlcNAcase

O‐GlcNAcase: Emerging Mechanism, Substrate Recognition and Small‐Molecule Inhibitors

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