Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach

Abstract

The varied yet family-specific conformational pathways used by individual glycoside hydrolases (GHs) offer at antalising prospectf or the design of tightly binding and specific enzyme inhibitors. Ac ardinal example of aG H-family-specific inhibitor, and one that finds widespread practical use, is the natural product kifunensine, which is al ow-nanomolar inhibitor that is selectivef or GH family 47 inverting a-mannosidases. Here we show,t hrough quantum-mechanical approaches, that kifunensine is restrained to a" ring-flipped" 1 C 4 conformation with another accessible, but higher-energy,r egion aroundt he 1,4 B conformation.T he conformationso fk ifunensine in complex with ar ange of GH47 enzymes-including an atomic-levelr esolution (1 )s tructure of kifunensinew ith Caulobacter sp. CkGH47 reportedh erein and with GH family 38 and 92 a-mannosidases-werem apped ontot he kifunensine free-energy landscape. These studies revealed that kifunensine has the ability to mimic the product state of GH47 enzymesb ut cannot mimic any conformational states relevant to the reactionc oordinate of mannosidases from other families.There is compelling evidence that the enzymatic hydrolysis of glycosides, catalysed by glycoside hydrolases (GHs) or glycosidases,o ccurs via transition states with significant oxocarbenium ion character.F or pyranoside-active enzymes,S innott was the first to argue that the allowed canonical conformationso f the transition state sugar ring were two half-chairs ( 4 H 3 and 3

A class of low‐cost alternatives to kifunensine for increasing high mannose N‐linked glycosylation for monoclonal antibody production in Chinese hamster ovary cells

“…The addition of different structures creating analogs of serinol modulated the potency of the inhibitors. The increased potency of tris and bis–tris compared to serinol can be correlated to increased molecular weight and is likely a function of the steric effects impacting mannosidase I function 41,42 . The reduced potency of AMPD compared to serinol is not clear.…”

“…The increased potency of tris and bis-tris compared to serinol can be correlated to increased molecular weight and is likely a function of the steric effects impacting mannosidase I function. 41,42 The reduced potency of AMPD compared to serinol is not clear. It is unlikely that the additional methyl group reduces diffusion across the lipid bilayer of the cell as more hydrophobicity is correlated to increased cell membrane permeability.…”

Cell Surface N-Glycans Influence Electrophysiological Properties and Fate Potential of Neural Stem Cells

“…GlcNAc is utilized in both N- and O-glycosylation, so we tested whether GlcNAc effects were specifically due to incorporation in N-glycan branching by pretreating cells with kifunensine (Kif). Kif is a highly specific inhibitor of mannosidase I and blocks the first steps of N-glycan branching ( Figure 2 A) ( Males et al., 2017 ). E12 NSPCs were pre-treated with Kif and maintained in Kif during GlcNAc treatment to prevent GlcNAc incorporation into N-glycan branches ( Figure 7 A).…”

α-d-Gal-cyclophellitol cyclosulfamidate is a Michaelis complex analog that stabilizes therapeutic lysosomal α-galactosidase A in Fabry disease

“…Michaelis complex or product-like conformational competitive inhibitors have been reported to act on other glycosidases, for instance, thio-oligosaccharides [44][45][46] and kifunensine. 47,48 We believe that transferring the structural characteristics of our cyclosulfamidates to differently congured structural analogues may yield potent and selective competitive inhibitors targeting glycosidases and that these may have biological or biomedical value in their own right, be it as stabilizing agents or as classical enzyme inhibitors.…”