title: Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-α-1,2-Mannanase.
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 a 1,2-anhydrosugar "epoxide" mechanism that proceeds through an unusual conformational itinerary. Here, we explore how shape and charge 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 inhibitor (KD13 nM for Bacteroides xylanisolvens GH99 enzyme) 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.
authors.affiliation: School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia.
authors.forename: Marija
authors.initials: M
authors.lastname: Petricevic
authors.affiliation: York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom.
authors.forename: Lukasz F
authors.initials: LF
authors.lastname: Sobala
authors.affiliation: School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia.
authors.forename: Pearl Z
authors.initials: PZ
authors.lastname: Fernandes
authors.affiliation: Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona , Martí i Franquès 1, 08028 Barcelona, Spain.
authors.forename: Lluís
authors.initials: L
authors.lastname: Raich
authors.affiliation: York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom.
authors.forename: Andrew J
authors.identifier: 0000-0001-7865-1856
authors.initials: AJ
authors.lastname: Thompson
authors.affiliation: Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Spain.
authors.forename: Ganeko
authors.identifier: 0000-0002-1372-3844
authors.initials: G
authors.lastname: Bernardo-Seisdedos
authors.affiliation: Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Spain.
authors.forename: Oscar
authors.initials: O
authors.lastname: Millet
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), UMR 8232, 4, place Jussieu, 75005 Paris, France.
authors.forename: Sha
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), UMR 8232, 4, place Jussieu, 75005 Paris, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Sollogoub
authors.affiliation: Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Spain.|Ikerbasque, Basque Foundation for Science, Marı́a Dı́az de Haro 3, 48013 Bilbao, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Jiménez-Barbero
authors.affiliation: Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona , Martí i Franquès 1, 08028 Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats (ICREA) , Pg. Lluís Companys 23, 08010 Barcelona, Spain.
authors.forename: Carme
authors.identifier: 0000-0003-1477-5010
authors.initials: C
authors.lastname: Rovira
authors.affiliation: York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom.
authors.forename: Gideon J
authors.initials: GJ
authors.lastname: Davies
authors.affiliation: School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia.
authors.forename: Spencer J
authors.identifier: 0000-0001-6341-4364
authors.initials: SJ
authors.lastname: Williams
mesh_terms: D002236:Carbohydrate Conformation; D018360:Crystallography, X-Ray; D005944:Glucosamine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology; D065089:Glycoside Hydrolase Inhibitors / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D008361:Mannosidases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D008958:Models, Molecular
chemical_list: D065089:Glycoside Hydrolase Inhibitors; C433123:noeuromycin; D008361:Mannosidases; D005944:Glucosamine