Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level

Weiwu Ren; Robert Joseph Pengelly; Marco Farren-Dai; Saeideh Shamsi Kazem Abadi; Verena Oehler; Oluwafemi Akintola; Jason Draper; Michael Meanwell; Saswati Chakladar; Katazyna Świderek; Vincent Moliner; Robert Britton; Tracey Gloster; Andrew Bennet

doi:10.1038/s41467-018-05702-7

Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level

Weiwu Ren, Robert Joseph Pengelly, Marco Farren-Dai, Saeideh Shamsi Kazem Abadi, Verena Oehler, Oluwafemi Akintola, Jason Draper, Michael Meanwell, Saswati Chakladar, Katazyna Świderek, Vincent Moliner, Robert Britton, Tracey Gloster, Andrew Bennet

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Abstract

Mechanism-based glycoside hydrolase inhibitors are carbohydrate analogs that mimic the natural substrate’s structure. Their covalent bond formation with the glycoside hydrolase makes these compounds excellent tools for chemical biology and potential drug candidates. Here we report the synthesis of cyclohexene-based α-galactopyranoside mimics and the kinetic and structural characterization of their inhibitory activity toward an α-galactosidase from Thermotoga maritima (TmGalA). By solving the structures of several enzyme-bound species during mechanism-based covalent inhibition of TmGalA, we show that the Michaelis complexes for intact inhibitor and product have half-chair (²H₃) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair (²H₃) conformation. Hybrid QM/MM calculations confirm the structural and electronic properties of the enzyme-bound species and provide insight into key interactions in the enzyme-active site. These insights should stimulate the design of mechanism-based glycoside hydrolase inhibitors with tailored chemical properties.

Original language	English
Article number	3243
Number of pages	12
Journal	Nature Communications
Volume	9
DOIs	https://doi.org/10.1038/s41467-018-05702-7
Publication status	Published - 13 Aug 2018

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Ren, W., Pengelly, R. J., Farren-Dai, M., Abadi, S. S. K., Oehler, V., Akintola, O., Draper, J., Meanwell, M., Chakladar, S., Świderek, K., Moliner, V., Britton, R., Gloster, T., & Bennet, A. (2018). Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level. Nature Communications, 9, Article 3243. https://doi.org/10.1038/s41467-018-05702-7

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title = "Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level",

abstract = "Mechanism-based glycoside hydrolase inhibitors are carbohydrate analogs that mimic the natural substrate{\textquoteright}s structure. Their covalent bond formation with the glycoside hydrolase makes these compounds excellent tools for chemical biology and potential drug candidates. Here we report the synthesis of cyclohexene-based α-galactopyranoside mimics and the kinetic and structural characterization of their inhibitory activity toward an α-galactosidase from Thermotoga maritima (TmGalA). By solving the structures of several enzyme-bound species during mechanism-based covalent inhibition of TmGalA, we show that the Michaelis complexes for intact inhibitor and product have half-chair (2H3) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair (2H3) conformation. Hybrid QM/MM calculations confirm the structural and electronic properties of the enzyme-bound species and provide insight into key interactions in the enzyme-active site. These insights should stimulate the design of mechanism-based glycoside hydrolase inhibitors with tailored chemical properties.",

author = "Weiwu Ren and Pengelly, {Robert Joseph} and Marco Farren-Dai and Abadi, {Saeideh Shamsi Kazem} and Verena Oehler and Oluwafemi Akintola and Jason Draper and Michael Meanwell and Saswati Chakladar and Katazyna {\'S}widerek and Vincent Moliner and Robert Britton and Tracey Gloster and Andrew Bennet",

note = "Financial support from the Natural Sciences and Engineering Research Council (NSERC) of Canada (AJB Discovery Grants: 121348–2012 & 2017–04910) was received. T.M.G. and V.O. are funded by a Wellcome Trust Career Development Fellowship, R.P. by Wellcome Trust ISSF, M.M. by a NSERC CGSD, M.F.-D. by a NSERC CGS-MSFSS and a GlycoNet Research Exchange Program, and R.B. by NSERC Discovery Grant and by a MSFHR Career Investigator Award. V.M. and K.{\'S}. thank the Spanish Ministerio de Econom{\'i}a y Competitividad and FEDER funds (project CTQ2015-66223-C2) and a Juan de la Cierva – Incorporaci{\'o}n (ref. IJCI-2016-27503) contract, respectively, and Universitat Jaume I (project UJI·B2017-31). ",

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doi = "10.1038/s41467-018-05702-7",

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AU - Ren, Weiwu

AU - Pengelly, Robert Joseph

AU - Farren-Dai, Marco

AU - Abadi, Saeideh Shamsi Kazem

AU - Oehler, Verena

AU - Akintola, Oluwafemi

AU - Draper, Jason

AU - Meanwell, Michael

AU - Chakladar, Saswati

AU - Świderek, Katazyna

AU - Moliner, Vincent

AU - Britton, Robert

AU - Gloster, Tracey

AU - Bennet, Andrew

N1 - Financial support from the Natural Sciences and Engineering Research Council (NSERC) of Canada (AJB Discovery Grants: 121348–2012 & 2017–04910) was received. T.M.G. and V.O. are funded by a Wellcome Trust Career Development Fellowship, R.P. by Wellcome Trust ISSF, M.M. by a NSERC CGSD, M.F.-D. by a NSERC CGS-MSFSS and a GlycoNet Research Exchange Program, and R.B. by NSERC Discovery Grant and by a MSFHR Career Investigator Award. V.M. and K.Ś. thank the Spanish Ministerio de Economía y Competitividad and FEDER funds (project CTQ2015-66223-C2) and a Juan de la Cierva – Incorporación (ref. IJCI-2016-27503) contract, respectively, and Universitat Jaume I (project UJI·B2017-31).

PY - 2018/8/13

Y1 - 2018/8/13

N2 - Mechanism-based glycoside hydrolase inhibitors are carbohydrate analogs that mimic the natural substrate’s structure. Their covalent bond formation with the glycoside hydrolase makes these compounds excellent tools for chemical biology and potential drug candidates. Here we report the synthesis of cyclohexene-based α-galactopyranoside mimics and the kinetic and structural characterization of their inhibitory activity toward an α-galactosidase from Thermotoga maritima (TmGalA). By solving the structures of several enzyme-bound species during mechanism-based covalent inhibition of TmGalA, we show that the Michaelis complexes for intact inhibitor and product have half-chair (2H3) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair (2H3) conformation. Hybrid QM/MM calculations confirm the structural and electronic properties of the enzyme-bound species and provide insight into key interactions in the enzyme-active site. These insights should stimulate the design of mechanism-based glycoside hydrolase inhibitors with tailored chemical properties.

AB - Mechanism-based glycoside hydrolase inhibitors are carbohydrate analogs that mimic the natural substrate’s structure. Their covalent bond formation with the glycoside hydrolase makes these compounds excellent tools for chemical biology and potential drug candidates. Here we report the synthesis of cyclohexene-based α-galactopyranoside mimics and the kinetic and structural characterization of their inhibitory activity toward an α-galactosidase from Thermotoga maritima (TmGalA). By solving the structures of several enzyme-bound species during mechanism-based covalent inhibition of TmGalA, we show that the Michaelis complexes for intact inhibitor and product have half-chair (2H3) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair (2H3) conformation. Hybrid QM/MM calculations confirm the structural and electronic properties of the enzyme-bound species and provide insight into key interactions in the enzyme-active site. These insights should stimulate the design of mechanism-based glycoside hydrolase inhibitors with tailored chemical properties.

UR - https://doi.org/10.1038/s41467-018-06264-4

U2 - 10.1038/s41467-018-05702-7

DO - 10.1038/s41467-018-05702-7

M3 - Article

SN - 2041-1723

VL - 9

JO - Nature Communications

JF - Nature Communications

M1 - 3243

ER -

Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level

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