Structural Snapshots for Mechanism‐Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars

Abstract

Glycoside hydrolases (GHs) have attracted considerable attention as targets for therapeutic agents, and thus mechanism‐based inhibitors are of great interest. We report the first structural analysis of a carbocyclic mechanism‐based GH inactivator, the results of which show that the two Michaelis complexes are in 2H3 conformations. We also report the synthesis and reactivity of a fluorinated analogue and the structure of its covalently linked intermediate (flattened 2H3 half‐chair). We conclude that these inactivator reactions mainly involve motion of the pseudo‐anomeric carbon atom, knowledge that should stimulate the design of new transition‐state analogues for use as chemical biology tools.

Synthesis and application of a highly branched, mechanism-based 2-deoxy-2-fluoro-oligosaccharide inhibitor ofendo-xyloglucanases

“…A wide array of generally reactive, photo-activatable, or mecha-nism-based inhibitors based on bespoke glycan specificity motifs has been deployed, including carbasugar-epoxides (e.g. conduritol-β-epoxide, cyclophellitol), cyclopropylcarbasugars, epoxyalkyl glycosides, N-bromoacetylglycosylamines, bromoketone C-glycosides, glucosylthio-hydroquinones, aziridines, cyclosulfates, glycosylmethyl triazenes, activated phenylmethyl glycosides, various photoaffinity labels, and glycosides fluorinated at the 2-or 5-position (see comprehensive reviews and references therein, [12][13][14] and recent primary literature [15][16][17][18][19] ).…”

The transition to magic bullets – transition state analogue drug design

“…However, in all these cases the TSs had been inferred from what was known about the reaction mechanisms of the enzyme-catalysed reaction. [31][32][33][34] It is obvious in hindsight that development of methods to determine the chemical nature of the actual TS of an enzyme catalysed reaction could provide chemists with a blueprint to synthesize the ideal structure of a TS analogue. Sequential incorporation of individual TS features into candidate molecules could dissect the energetics of each enzyme-TS analogue interaction.…”

Rearrangement and nucleophilic trapping of bicyclo[4.1.0]hept-2-yl derived nonclassical bicyclobutenium ions

“…[7][8][9] These bicyclo[4.1.0]heptyl based mimics of galactopyranosides covalently label an α-galactosidase from a retaining glycoside hydrolase family (GH36) on its catalytic nucleophile (aspartate-327), 7,8 a process that presumably involves formation of a non-classical bicyclobutenium ion 2. 10,11 As a result, we are 12 SCHEME 2.…”