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Contribution of shape and charge to the inhibition of a family GH99 endo -α-1,2-mannanase

DOI: 10.1021/jacs.6b10075 DOI Help

Authors: Marija Petricevic (University of Melbourne) , Lukasz F. Sobala (University of York) , Pearl Fernandes (University of Melbourne) , Lluís Raich (Universitat de Barcelona) , Andrew James Thompson (University of York) , Ganeko Bernardo-seisdedos (CIC bioGUNE) , Oscar Millet (CIC bioGUNE) , Sha Zhu (Ikerbasque, Basque Foundation for Science) , Matthieu Sollogoub (Ikerbasque, Basque Foundation for Science) , Jesús Jimenez-barbero (CIC bioGUNE; Ikerbasque, Basque Foundation for Science) , Carme Rovira (Universitat de Barcelona; Institució Catalana de Recerca i Estudis Avançats (ICREA)) , Gideon J. Davies (University of York) , Spencer J. Williams (University of Melbourne)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of The American Chemical Society

State: Published (Approved)
Published: December 2016
Diamond Proposal Number(s): 9948

Abstract: Inhibitor design incorporating features of the reaction coordinate and transition-state structure has emerged as a powerful approach for the development of enzyme inhibitors. Such inhibitors find use as mechanistic probes, chemical biology tools and therapeutics. Endo-α-1,2-mannosidases and endo-α-1,2-mannanases, members of glycoside hydrolase family 99 (GH99), are interesting targets for inhibitor development as they play key roles in N-glycan maturation and microbiotal yeast mannan degradation, respectively. These enzymes are proposed to act via an 1,2-anhydrosugar 'epoxide' mechanism that proceeds through a proposed unusual conformational itinerary. Here, we explore how charge and shape contribute to binding of diverse inhibitors of these enzymes. We report the synthesis of neutral dideoxy, glucal and cyclohexenyl disaccharide inhibitors, their binding to GH99 endo-α-1,2-mannanases, and their structural analysis by X-ray crystallography. Quantum mechanical calculations of the free energy landscapes reveal how the neutral inhibitors provide shape but not charge mimicry of the proposed intermediate and transition state structures. Building upon the knowledge of shape and charge contributions to inhibition of family GH99 enzymes, we design and synthesize α-Man-1,3-noeuromycin, which is revealed to be the most potent (KD 13 nM for Bacteroides xylanisolvens GH99 enzyme) inhibitor of these enzymes yet reported. This work reveals how shape and charge mimicry of transition state features can enable the rational design of potent inhibitors.

Journal Keywords: Glycosidase; enzyme inhibitor; carbohydrate; glycobiology; conformational analysis

Subject Areas: Biology and Bio-materials, Chemistry

Instruments: I02-Macromolecular Crystallography , I04-1-Macromolecular Crystallography (fixed wavelength) , I04-Macromolecular Crystallography , I24-Microfocus Macromolecular Crystallography