Dissecting Conformational Contributions to Glycosidase Catalysis and Inhibition

This is a repository copy of Dissecting conformational contributions to glycosidase catalysis and inhibition. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/84289/ Version: Published Version Article: Speciale, Gaetono, Thompson, Andrew James orcid.org/0000-0001-7865-1856, Davies, Gideon John orcid.org/0000-0002-7343-776X et al. (1 more author) (2014) Dissecting conformational contributions to glycosidase catalysis and inhibition. CURRENT OPINION IN STRUCTURAL BIOLOGY. pp. 1-13. ISSN 0959-440X https://doi.org/10.1016/j.sbi.2014.06.003 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Available online at www.sciencedirect.com ScienceDirect Dissecting conformational contributions to glycosidase catalysis and inhibition 1 2 2 Gaetano Speciale , Andrew J Thompson , Gideon J Davies and 1 Spencer J Williams Glycoside hydrolases (GHs) are classified into >100 sequence- as of 2014) [2]. What continues to occupy the attention of based families. These enzymes process a wide variety of mechanistic enzymologists is a complete description of complex carbohydrates with varying stereochemistry at the the fine details of the overall reaction coordinate. The anomeric and other ring positions. The shapes that these sugars free energy profile of catalysis is a composite of terms adopt upon binding to their cognate GHs, and the including: bond-making and breaking; the establishment conformational changes that occur along the catalysis reaction and disbandment of stereoelectronic effects; and confor- coordinate is termed the conformational itinerary. Efforts to mational effects. Conformational interactions include define the conformational itineraries of GHs have focussed upon substrate-based: vicinal (e.g. eclipsing, gauche, D2), the critical points of the reaction: substrate-bound (Michaelis), 1,3-diaxial, and 1,4-bridgehead; and enzyme-based: local transition state, intermediate (if relevant) and product-bound. and global conformational changes of the enzyme that Recent approaches to defining conformational itineraries that occur on the time-scale of catalysis [3]. marry X-ray crystallography of enzymes bound to ligands that mimic the critical points, along with advanced computational Two major areas of inquiry are active in the area of methods and kinetic isotope effects are discussed. conformation and glycoside hydrolases: Addresses 1 School of Chemistry and Bio21 Molecular Science and Biotechnology 1. What are the conformational changes that occur during Institute, University of Melbourne, Parkville, Victoria 3010, Australia catalysis upon substrate binding, at the transition 2 Department of Chemistry, University of York, Heslington, York YO10 state(s), intermediates (if relevant), and product? Aside 5DD, United Kingdom from the elemental interest in this question, there is Corresponding author: Williams, Spencer J ([email protected]) the potential for utilizing this information to develop glycosidase inhibitors that take advantage of the considerable amounts of energy used to selectively – Current Opinion in Structural Biology 2014, 28:1 13 bind the transition state (for a glycosidase with a 17 This review comes from a themed issue on Carbohydrate-protein catalytic rate enhancement of 10 , the calculated interactions and glycosylation À22 transition state affinity is 10 M [4]), with the Edited by Harry J Gilbert and Harry Brumer enticing possibility that differences in transition state For a complete overview see the Issue and the Editorial conformation may allow the development of glycosidase-selective inhibitors. Available online 10th July 2014 2. Once transition-state structural information is acquired http://dx.doi.org/10.1016/j.sbi.2014.06.003 and used to inspire inhibitor development, do the 0959-440X/# 2014 The Authors. Published by Elsevier Ltd. This is an resulting inhibitors actually bind by utilizing the same open access article under the CC BY license (http://creativecommons. org/licenses/by/3.0/). interactions that are used to stabilize the transition state — that is, are they genuine transition state mimics? The answers to this question speak to our Glycoside hydrolases catalyze the hydrolytic cleavage of abilities to realize this unique form of rational inhibitor the glycosidic bond. They are enzymes of enduring in- design. terest owing to the ubiquity of carbohydrates in nature and their importance in human health and disease, the In this review we cover recent developments in the food, detergent, oil & gas and biotechnology industries. understanding of conformational reaction coordinates Glycoside hydrolases generally, but not quite exclusively, and how such information is acquired; and what consti- perform catalysis with a net retention or inversion of tutes good transition state mimicry by inhibitors. This anomeric stereochemistry. The gross mechanisms of gly- work extends two recent comprehensive reviews [5,6 ]. cosidases were postulated by Koshland in 1953 [1 ], and his prescient insights remain largely true to this day. The Contortions along the reaction coordinate glycoside hydrolases are an immensely varied group of Substantial evidence has accrued that retaining and enzymes and are usefully classified on the basis of inverting glycoside hydrolases perform catalysis through sequence according to the CAZy system (www.cazy.org; an oxocarbenium ion-like transition state with significant see also Cazypedia: www.cazypedia.org), which reveals a bond breakage to the departing group and limited bond growing and formidable diversity of proteins (133 families formation to the attacking nucleophile (Figure 1a) [7]. On – www.sciencedirect.com Current Opinion in Structural Biology 2014, 28:1 13 – 2 Carbohydrate protein interactions and glycosylation the basis of the four idealized half-chair and boat con- position of O5 has little mechanistic consequence other formations expected for the transition state (see Side than to allow development of the partial double bond. Panel A), four ‘classical’ conformational itineraries may Interactions at C2 are usually (but not always, see: [8]) be identified (Figure 1b). In these simplified presenta- significant and for the b-glucosidase Abg from Agrobacter- tions, it is apparent that C1 scribes an arc along the ium sp. or for a-glucosidase of Saccharomyces cerevisiae [9] À1 – conformational reaction coordinate as it undergoes an have been shown to contribute 18 22 kJ mol to tran- electrophilic migration from the leaving group to a sition state stabilization [10], highlighting that the repo- nucleophile. However, other ring atoms also change po- sitioning of C2 and its substituent and other electronic sitions, in particular O5 and C2. The subtle change in the changes accompanying formation of the oxocarbenium Side panel A Theoretical considerations of the transition state conformation It is a stereoelectronic requirement that the development of a partial that elementary reactions that involve the least change in atomic position double bond between O5 and C1 results in flattening of the system C2– and electronic configuration will be favoured [12,13]. Accordingly, the C1–O5–C5, with the remaining pyranose C3 and C4 atoms having conformational reaction coordinate will most likely involve ground state freedom to move [11]. The possible idealized transition state structures conformations (corresponding to Michaelis, intermediate and product 3 4 2,5 H H B B that satisfy these requirements are 4, 3, and 2,5 (and the closely complexes) that are close neighbors to the transition state conforma- 4 3 E E E E related but usually higher energy , , 4 and 3). As the oxocarbenium tions. The conformational relationships of pyranose rings [14] may be ion-like transition states of glycosidases are ‘central’ transition states it is conveniently summarized using a Cremer-Pople sphere [15] or its appropriate to invoke the principle of least nuclear motion, which states equivalent Mercator and polar projections (Figure I). Figure I (a) Possible flattened transition state conformations (a) Half-chair transition states (c) Envelope transition states LG LG 3 δ+ 4 LG LG O O 4 δ+ δ+ O O 4 3 δ+ Nu Nu 4 Nu Nu 3 4 H4 H3 4 E E4 (b) Boat transition states LG LG 3 LG LG δ+ δ+ 2 δ+ 5 O O O O 2 δ+ 5 3 Nu Nu Nu Nu 3 E E3 2,5 B2,5 B (b) Main conformations of a pyranose ring on the Cremer-Pople sphere and the Mercator projection Cremer-Poplesphere Mercator projection 4C 4C 1 1 0° OS 3,OB B 2 2,5 45° 1S OE OH E 4H 4E 4H E 2H 2E 2H E OH 5 3 5 5 5 3 3 3 1 1 1 S1 B1,4 90° θ 1,4B 3,OB OS B 1S 1,4B 1S B 2S 2,5B 5S B 3S 5 2 2,5 5 3 3,O O 1 1,4 1 S1 1S 3 B 2,5B 3,O 2S 135° O 3E 3H 1H 1E 1H E 5H 5E 5H E 3H 2 E2 2 O O O 4 4 4 180° 1 C4 φ 360° 330° 300° 270° 240° 210° 180° 150° 120° 90° 60° 30° 0° 1 C4 Current Opinion in Structural Biology – Current Opinion in Structural Biology 2014, 28:1 13 www.sciencedirect.com Glycosidase conformational itineraries

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