Synthesis of broad-specificity activity-based probes for exo-β-mannosidases

DOI: 10.1039/D1OB02287C

Authors: Nicholas G. S. Mcgregor (The University of York) , Chi-Lin Kuo (Leiden University) , Thomas Beenakker (Leiden University) , Chun-Sing Wong (Leiden University) , Wendy A. Offen (The University of York) , Zachary Armstrong (The University of York) , Bobby I. Florea (Leiden University) , Jeroen D. Codee (Leiden University) , Herman S. Overkleeft (Leiden University) , Hans Aerts (Leiden University) , Gideon Davies (The University of York)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Organic & Biomolecular Chemistry

State: Published (Approved)
Published: December 2021
Diamond Proposal Number(s): 24948 , 18598

Abstract: Exo-β-mannosidases are a broad class of stereochemically retaining hydrolases that are essential for the breakdown of complex carbohydrate substrates found in all kingdoms of life. Yet the detection of exo-β-mannosidases in complex biological samples remains challenging, necessitating the development of new methodologies. Cyclophellitol and its analogues selectively label the catalytic nucleophiles of retaining glycoside hydrolases, making them valuable tool compounds. Furthermore, cyclophellitol can be readily redesigned to enable the incorporation of a detection tag, generating activity-based probes (ABPs) that can be used to detect and identify specific glycosidases in complex biological samples. Towards the development of ABPs for exo-β-mannosidases, we present a concise synthesis of β-manno-configured cyclophellitol, cyclophellitol aziridine, and N-alkyl cyclophellitol aziridines. We show that these probes covalently label exo-β-mannosidases from GH families 2, 5, and 164. Structural studies of the resulting complexes support a canonical mechanism-based mode of action in which the active site nucleophile attacks the pseudo-anomeric centre to form a stable ester linkage, mimicking the glycosyl enzyme intermediate. Furthermore, we demonstrate activity- based protein profiling using an N-alkyl aziridine derivative by specifically labelling MANBA in mouse kidney tissue. Together, these results show that synthetic manno-configured cyclophellitol analogues hold promise for detecting exo-β-mannosidases in biological and biomedical research.

Diamond Keywords: Enzymes

Subject Areas: Biology and Bio-materials, Chemistry


Instruments: I03-Macromolecular Crystallography

Added On: 04/01/2022 14:05

Documents:
d1ob02287c.pdf

Discipline Tags:

Biochemistry Chemistry Structural biology Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)