Structural and biochemical evidence for a boat-liketransition state in b-mannosidasesLouise E Tailford1,7, Wendy A Offen2,7, Nicola L Smith1,7, Claire Dumon1, Carl Morland1, Julie Gratien3,Marie-Pierre Heck3, Robert V Stick4, Yves Bleriot5, Andrea Vasella6, Harry J Gilbert1 & Gideon J Davies2

Enzyme inhibition through mimicry of the transition state is a major area for the design of new therapeutic agents. Emergingevidence suggests that many retaining glycosidases that are active on a- or b-mannosides harness unusual B2,5 (boat) transitionstates. Here we present the analysis of 25 putative b-mannosidase inhibitors, whose Ki values range from nanomolar to millimolar,on the Bacteroides thetaiotaomicron b-mannosidase BtMan2A. B2,5 or closely related conformations were observed for all tightlybinding compounds. Subsequent linear free energy relationships that correlate log Ki with log Km/kcat for a series of active centervariants highlight aryl-substituted mannoimidazoles as powerful transition state mimics in which the binding energy of the arylgroup enhances both binding and the degree of transition state mimicry. Support for a B2,5 transition state during enzymaticb-mannosidase hydrolysis should also facilitate the design and exploitation of transition state mimics for the inhibition ofretaining a-mannosidases—an area that is emerging for anticancer therapeutics.

One of the emerging themes in glycosidase research is thatdifferent enzyme classes use distinct substrate conformational itiner-aries for catalysis1. Stereoelectronic considerations dictate that thepyranose ring should be distorted, at or near the transition state, toone of four conformations: one of two classical boats (B2,5 and 2,5B) orone of two half-chairs (4H3 and 3H4, and/or their closely relatedenvelope forms 4E and 3E) (Fig. 1)2. Such conformations are theonly ring forms that can accommodate the developing doublebond character between the anomeric carbon and the endocyclicoxygen, which must occur at or close to the transition state in orderto accommodate the developing positive charge. The revelationthat different enzymes harness different pathways and transitionstates offers a powerful route into specific enzyme inhibitors forcellular use. Knowledge of the conformational pathways andtransition state structures harnessed by different enzyme classes isthus central to the design and application of transitionstate mimics both as mechanistic and cellular probes and astherapeutic agents3.

In solution, mannoside chemistry is intrinsically recalcitrant,reflecting the potential 1,2 steric clashes that occur during nucleophilicdisplacement at the anomeric carbon (for example, see refs. 4,5),which has led to great interest in how these reactions are accomplished‘‘on-enzyme.’’ Enzymatic mannoside hydrolysis is also of burgeoningimportance in cellular biology, not least because Golgi a-mannosidase

II activity is a prerequisite for b-1,6-N-acetylglucosaminyltransferase V(MGAT5) action, which is associated with malignancy and metastaticprogression6. Inhibition of Golgi mannosidase II is thus considered apotential anticancer target—one that could be targeted by specifictransition state mimics7–9.

In 2002, it was first proposed that enzymatic mannoside hydrolysisuses an unusual conformational pathway10. Studies of the endo-b-mannanase CjMan26A, which acts with retention of anomericconfiguration, at different stages along its reaction coordinate revealedan unusual 1S5 conformation for the Michaelis complex of unhydro-lyzed substrate (Fig. 1a). This observation implied that the B2,5

conformation, adjacent to 1S5 on the skew-boat interconversionitinerary11 (Fig. 1b), would be the one adopted by the reactiontransition state. Subsequently, the covalent intermediate of thisenzyme was indeed trapped, and the pyranose ring was observed inthe OS2 conformation. Catalysis was thus considered as following a 1S5

to B2,5 to OS2 agenda (Fig. 1), which is consistent with electrophilicmigration of C1 through a B2,5 transition state. Such a conformationalpathway, which places O2 pseudo-equatorial, explains how nature hasevaded the unfavorable 1,2 coplanar interaction upon nucleophilicsubstitution at the anomeric carbon of mannosides. Partial supportfor the proposal came from historical observations that some manno-configured compounds, sp2 hybridized at the anomeric position, alsofavor this unusual boat conformation in a variety of solvents12,13.

Received 31 August 2007; accepted 15 February 2008; published online 13 April 2008; doi:10.1038/nchembio.81

1Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK. 2Structural BiologyLaboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK. 3Commissariat a l’Energie Atomique Centre de Saclay, Direction des Sciencesdu Vivant, Institut de Biologie et de Technologies de Saclay, Service de Chimie Bioorganique et de Marquage, Batiment 547, 91191 Gif Sur Yvette cedex, France.4Chemistry M313, School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia.5Universite Pierre et Marie Curie (Paris 6), Institut de Chimie Moleculaıre (Federation of Research 2769), Laboratoire de Chimie Organique (Unıte Mixte de RechercheCentre National de la Recherche Scientifique 7611), 4 place Jussieu, C. 181, 75005 Paris, France. 6Laboratorium fur Organische Chemie, HCI H317, ETH Zurich,Wolfgang Paulistrasse 10, CH-8093 Zurich, Switzerland. 7These authors contributed equally to this work. Correspondence should be addressed to H.J.G.(h.j.gilbert@ncl.ac.uk) or G.J.D. (davies@ysbl.york.ac.uk).

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However, direct observation of the binding of b-mannosidase inhibi-tors on-enzyme has proven difficult.

The 1S5 to B2,5 to OS2 pathway for retaining GH26 b-mannanasesinferred that retaining a-mannosidases might use a similar pathway,again through the B2,5 transition state conformation, but in reverse.There is now strong support for this pathway for Golgi a-mannosidaseII, notably following the observation of the 1S5 conformation for itstrapped covalent glycosyl-enzyme intermediate14. Given the role ofthis enzyme in cancer metastasis, support for or against a B2,5

conformation is important in the context of inhibitor design. Indeed,though it appears that mannose-specific (retaining) glycoside hydro-lases use a B2,5 transition state, this hypothesis is based on theinterrogation of a limited number of enzyme families and complexes.Furthermore, the structural features of inhibitors that mimic thetransition state are poorly understood.

Here we have explored the capacity of 25 putative mannosidaseinhibitors to bind to the GH2 retaining b-mannosidase BtMan2A(ref. 15), with kinetic analysis revealing Ki values ranging from 57 nMto 4400 mM. X-ray structure determination for the tightest bindingcompounds reveals that they all adopt conformations close to B2,5,lending considerable support to the view that this conformation isadopted by the transition state during the hydrolysis of mannosidesby this class of enzyme. Transition state mimicry has been probed foreight of these compounds using linear free energy relationships(correlating log Ki and log Km/kcat for a series of enzyme variants).Substituted mannoimidazoles, which are observed in the B2,5 con-formation and are able to harness aglycon interactions, are quantifi-ably the ‘‘best’’ transition state mimics.

RESULTSb-mannosidase inhibition by a panel of 25 compoundsA panel of different putative mannosidase inhibitors (Fig. 2; synthesesdescribed in refs. 13,16–22) was assessed for inhibition at the pHoptimum for catalysis (pH 5.6) of BtMan2A using 2,4-dinitrophenylb-D-mannopyranoside (17) as substrate. Ki values ranged from 57 nMfor the phenethylmannoimidazole 1b to 4400 mM for compound 16.The spread of Ki values reveals good inhibition by many classes ofcompound previously reported as glycosidase inhibitors, and, as inearly studies23, no slow-onset inhibition was observed for any ofthe compounds.

As with many systems (recent examples include refs. 3,24–26),sugar-derived imidazoles are among the most powerful inhibitors,

with aryl substitutions increasing their potency to the low nanomolarrange. All the glycoamidines tested consistently had Ki values aroundthe 1–2 mM range. What is most noteworthy about the panel ofinhibitors is how the generic signature of inhibition often contrastswith that reported for b-glucosidase inhibition with chemically similarcompounds24. For example, isofagomine 8, a 2-deoxy aza sugar, isamong the most powerful b-glucosidase inhibitors known, withKi values in the low nanomolar range23,27. Yet 8, whose lack of a2-hydroxy substituent renders the compound as ‘‘similar’’ to mannoseas to glucose, is an extremely poor b-mannosidase inhibitor, with aKi 410 mM (Fig. 2). Similarly, oxazine 9, which is also a 2-deoxysugar, is a 400 nM inhibitor of b-glucosidases but displays a Ki value inexcess of 20 mM with BtMan2A. In marked contrast to 8 and 9, theaza sugar noeuromycin 5, which has a 2-hydroxy substituent, displaysa Ki of approximately 1 mM. The reduction in binding for the 2-deoxyspecies may have many causes, but the tight binding of 5 certainlyindicates a role for the interactions between O2 and BtMan2A,thus strongly implying an important role for the O2 interactionsduring catalysis.

In order to formally quantify the contributions of the O2 interac-tions, the rate of hydrolysis of 4-nitrophenyl 2-deoxy-b-D-mannoside(18; formally 4-nitrophenyl 2-deoxy-b-D-arabinohexopyranoside) wascompared with that of 4-nitrophenyl b-D-mannopyranoside (19).Second-order rate constants are 26,000 min–1 mM–1 for the hydrolysisof 20 but only 0.2 min–1 mM–1 for the 2-deoxy substrate, whichindicates a substantial (130,000-fold) reduction in kcat/Km correspond-ing to a DDGz of 29 kJ mol–1. A similar reduction (DDGz of 21 kJmol–1) was observed previously on the related Cellulomonas fimi GH2b-mannosidase28, which confirms the importance of interactions ofthe O2 group in b-mannosidase catalysis. Furthermore, these valuesplace a lower limit on the contribution of the O2 group to catalysisgiven that the electron-withdrawing effect of OH renders 19 approxi-mately 2,000 times intrinsically less reactive than the equivalent2-deoxy molecule29.

Although the difference in potencies of isofagomine and oxazinemay reflect the contribution of the 2 position to binding, such amechanism does not readily explain the poor mannosidase inhibitionby mannotetrazole 7 and deoxymannojirimycin 11. Glucose-derivedtetrazoles are reasonably strong b-glucosidase inhibitors (glucotetra-zole inhibits the Thermatoga maritima GH1 b-glucosidase with a Ki of170 nM; ref. 24), whereas the binding of mannotetrazole 8 toBtMan2A is almost 10,000 times weaker, with a Ki of 1 mM. In

O

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Figure 1 The conformational agenda of glycosidases. (a) Schematic diagram of the proposed

conformational itinerary for the glycosylation step of retaining b-mannosidases. OR is the leaving

group, and X could be either hydrogen (where the substrate is a mannoside) or another sugar moiety

in the case of an oligosaccharide substrate. (b) The conformational itinerary of pyranosides, as

proposed previously11. Three of the four potential transition state conformations, 4H3, B2,5 and 2,5B, are shown boxed. There is strong evidence suggesting

that retaining a-mannosidases also use a B2,5 transition state, as discussed in the text in the context of retaining b-mannosidases.

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contrast, gluco-imidazoles and manno-imidazoles bind similarly totheir respective targets, and it is thus not immediately apparent whythe tetrazoles are significantly poorer mannosidase inhibitors. Onepossibility is that proton transfer is more advanced at the transitionstate for mannoside hydrolysis (consistent with previous studies28)and that the imidazoles better resemble (geometrically and electro-nically) the (putative) oxocarbenium ion–like transition state, whereasthe low basicity of the tetrazole does not allow more than a partialproton transfer. In a similar manner, deoxynojirimycin 10 inhibitsb-glucosidases with Ki values around 10 mM (for example, ref. 24),whereas the manno-configured version 11 has a Ki greater than30 mM for BtMan2A and is no better an inhibitor than the gluco-configured version itself (10; Ki of 14 mM), which may reflect theobservation that the favored chair conformation of protonated deoxy-mannojirimycin is equally as poor as that of gluco-configureddeoxynojirimycin. In order to probe in more detail the binding ofthe better inhibitors, three-dimensional structures of BtMan2A weredetermined at resolutions between 2.3 and 1.8 A for the tightestbinding compounds representative of each class.

Structures of mannosidase–inhibitor complexesThe crystal structures of wild-type BtMan2A were determined, atresolutions between 2.3 and 1.8 A (Supplementary Table 1 online;

Figs. 3 and 4), in complex with a panel of representative compounds:mannoimidazole 1a, substituted mannoimidazole 1c, mannoamidines2a and 2c, isoquinuclidine 4 and noeuromycin 5. The noeuromycin 5complex was also determined with the W645A mutant in order tohelp explain unusual Ki effects with this mutant (discussed furtherbelow). The structure with isofagomine lactam 6 was alsodetermined in order to allow comparison with similar complexeson b-glucosidases24,30.

Consistent with the proposals that retaining b-mannanases andhence b-mannosidases use a B2,5 transition state conformation10,30,31,the complexes with all of the above compounds were observed in orclose to the B2,5 conformation where an sp2 center was appropriatelyplaced (1a, substituted mannoimidazole 1c and mannoamidines 2aand 2c). It is notable that both mannoimidazoles and mannoamidinesare observed in the B2,5 conformation, for whereas mannoamidines insolution are known to favor this conformation13, mannoimidazolesfavor 3H4 and E4 forms21. Even those compounds without a doublebond mimicking that between the anomeric carbon and endocyclicoxygen show conformations close to B2,5; both isoquinuclidine 4 andnoeuromycin 5 are observed in an approximately 1S5 (skew-boat)conformation that is reminiscent of those observed previously fortrapped Michaelis complexes of retaining mannanases10. Noeuro-mycin 5 is observed in what equates to its manno hemiaminalconfiguration; it is also observed distorted to a conformation closeto 1S5 and B2,5. Isofagomine lactam 6 is chemically constrained by itsamide functionality, but it too is also distorted away from its favored4H5 toward an E5 (envelope) conformation, as observed previously ona retaining exo-b-mannanase30. All complexes thus provide strongsupport for the B2,5 transition state, which is important not just onthis enzyme but in the realm of anticancer strategies via a-mannosi-dase inhibition. Not surprisingly, compound 16, which is likely lockedinto a B2,5 conformation by a propyl three-carbon link betweenC2 and C5 (ref. 18), is a very poor binder; this reflects steric clasheswith the catalytic center more than a lack of appropriate conforma-tion. This is evidenced by the fact that 16 binds 200-fold more tightlyto the less congested active center of the catalytically compromisedW645A mutant.

All complexes confirm the importance of the 2-OH interactions,with the oxygen atom receiving hydrogen bonds from both Asn461and Trp395 and presumably donating a hydrogen bond to thecarbonyl oxygen of the nucleophile. This latter O2-nucleophile inter-action has historically been discussed in the context of glucosidaseaction but is clearly as (if not more) important in mannosidase actiongiven that the pseudo-equatorial orientation for O2 in the B2,5

conformation permits interactions with the catalytic machinery simi-lar to those seen for gluco-configured substrates with glucosidases.The structures clearly give a powerful rationale for both the exceed-ingly weak binding of ‘‘2-deoxy’’ inhibitors and the substantialcontribution of O2 interactions to catalysis, discussed previously.

Linear free energy relationshipsThe observations here that all tight-binding compounds bind in orclose to B2,5 conformations provide support for a B2,5 transition state.But it is important to probe whether these compounds inhibitthrough mimicry of the reaction transition state, mimicry of thesubstrate or simply via adventitious interactions. The question of whatmakes an inhibitor a transition state mimic is one that has long vexedthe enzyme field, where ‘‘transition state mimic’’ is a term often(mis)used to describe tight-binding compounds. Although crystalstructure analyses can provide insight into protein-ligand interactions,they cannot ascertain how the interactions that drive binding of the

1a, R = H (1,400 nM) 1b, R = CH2CH2Ph (57 nM)1c, R = CH2NHPh (72 nM) 1d, R = CH2OPh (401 nM) 1e, R = C CPh (2,400 nM)

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2d, R = CH2CH2CH2OH (2.2 µM)2e, R = CH2CH2CH3 (1.9 µM)

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Figure 2 Putative mannosidase inhibitors used in this study. Also shown in

parentheses are their Ki values for wild-type protein, at the pH optimum for

catalysis (pH 5.6).

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inhibitor compare to those forces governing catalysis. Arguably, themost rigorous method for defining whether a potent inhibitor is a truetransition state mimic comes from linear (Gibbs) free energy relation-ships (LFERs), in which the free energy of inhibitor binding (reflectedin log Ki) is correlated with the free energy of transition statestabilization (reflected in log Km/kcat)

32. Where possible, this may beachieved through systematic modification of both substrate andinhibitor in the same manner (for example, ref. 33). With classicalglycosidases, such an approach is rarely feasible, and more often thecorrelation is made between log Ki and log Km/kcat for a series ofenzyme variants (examples include refs. 26,34–36). In the case that theforces governing catalysis and binding of the inhibitor are similar(which would seem a reasonable definition of a transition statemimic37), one expects both a strong correlation between log Ki andlog Km/kcat, and a slope of 1.0. Conversely, if the forces drivinginhibitor binding are not those governing binding of the transitionstate, there is substantially less (or no) correlation between log Ki

and log Km/kcat.LFERs were determined for compounds generally representative of

different chemical classes: mannoimidazole1a, substituted mannoimidazoles 1b, 1c and1d, mannoamidines 2a and 2e, N-benzyliso-quinuclidine 4 and noeuromycin 5. kcat/Km

and Ki were thus determined for wild-typeBtMan2A and six additional active centervariants (details in Supplementary Tables 2and 3 online). Inspection of the three-dimen-sional structure of BtMan2A (Fig. 3)informed construction of Q646A, Y537A,N461A, W198A, W395A and W645A as resi-dues directly involved either in hydrogenbonding to the ligands or in the maintenanceof the hydrophobic sheath around the ligand.We also devised a methylumbelliferyl b-D-mannopyranoside (20) plate-based screenusing degenerate primers from which weadditionally selected the W198G mutant forfurther study. It is immediately apparent(Fig. 5; Table 1) that the arylmannoimidazolederivatives 1b–1d are the most persuasive

transition state mimics, with near-unity cor-relations between log Ki and log Km/kcat.Furthermore, for these compounds the slopesare also B1.0 (using all data), in contrast tomany reports of putative transition statemimicry in similarly unsaturated com-pounds26,34,36. The unsubstituted mannoimi-dazole 1a yields an r2 of 0.78 with slope 1.06,while other compounds that display a reason-able degree of quantifiable transition statemimicry include N-benzylisoquinuclidine 4a(slope 0.65 with correlation 0.88) and man-noamidines 2a and 2e, which have lessercorrelations (0.61 and 0.67) but have slopesof 0.91 and 0.57, respectively. Amidines 2aand 2e also show different slopes relative toeach other, which suggests that the forcesgoverning binding of these two compoundsare different. Given the importance ofcharged interactions in amidine binding (dis-cussed more fully below), the hydrogen bond

between the primary amino group of 2a and the catalytic acid-baseGlu462 may help explain these puzzling effects. For the majority ofcompounds, correlations of log Ki with log Km (which approximatesKs) are considerably less (Table 1)—typically around 0.3 to 0.5 lowerthan the correlations with log Km/kcat—which shows that the com-pounds do not bind through mimicry of the substrate.

Among the compounds that we have analyzed, two stand out aspeculiarities worthy of special consideration. The first, noeuromycin 5,yields a correlation of just 0.03, which is dominated by theW645A mutant, whose catalysis is greatly impaired but which binds5 approximately five times more tightly than the wild-type enzyme. Ifthe W645A data point is excluded, the correlation increases to0.56 with a slope of 0.6 ± 0.26, which is more consistent with thevalues displayed for aza and imino sugar glycosidase inhibitorsstudied previously26,35. Noeuromycin 5 is not a single compound; aand b hemiaminal and pyranose forms interconvert through open-chain species38. The three-dimensional structure of the W645Amutant in complex with noeuromycin 5 reveals that, in contrastto the wild-type protein, 5 binds in the opposite hemiaminal

Figure 3 Active center of wild-type BtMan2A, in complex with substituted mannoimidazole 1c.

Residues selected for site-directed mutants (Q646A, Y537A, N461A, W198G, W395A and W645A)

and the catalytic acid/base and nucleophile (Glu462 and Glu555, respectively) are shown. Also shown

are the interactions of the +1 subsite, notably Trp217, Trp533 and Tyr537, which enrobe the

hydrophobic groups of 1c. The figure is in divergent stereo with the 2Fo – Fc map shown at 1s.

Glu462

Glu555

5 (W645A) 5 and 5 (W645A)

1c

65

1a 2a 4a2c

Figure 4 Observed electron density for compounds 1a, 1c, 2a, 2c, 4a, 5 and 6 bound to BtMan2A in

‘‘side-on’’ and ‘‘end-on’’ views. The 2Fo – Fc map is shown at 1s. Also shown is the complex of 5 with

the W645A mutant and the overlap of the wild-type (gray) and W645A (yellow) complexes with 5.

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form, equating to a gluco-configured compound in 4C1 chairconformation (Fig. 4).

DISCUSSIONThe putative B2,5 transition state for both retaining a- andb-mannosidases/mannanases not only provides an elegant andconvincing solution to the steric problems of substitution at theanomeric carbon of mannose but also is of burgeoning importancefor cellular a-mannosidase inhibition in cancer therapy. Structural andlinear free energy relationships, here on a retaining b-mannosidase,provide very strong support for this transition state, with all tight-binding compounds binding in or close to the B2,5 conformation.

Although protein crystallography is able toreveal structurally similar modes of inter-action with the enzyme, it is unable to probethermodynamics and gives no insight intowhether the forces governing binding of theinhibitors are the same as those responsiblefor catalysis. In contrast, LFER studies directlyreveal the extent of transition state mimicryand show that this varies greatly for thecompounds studied. Though all the data sup-port the B2,5 transition state, conformational(B2,5) mimicry alone is insufficient to define acompound as a good transition state mimic.With the exception of the substitutedmannoimidazoles, many other compounds(although adopting a B2,5 conformation inthe active site) display poorer correlations,which shows the power of the LFER techniqueto reveal the significance of binding inter-actions and probe the degree of transitionstate mimicry. Notable in this context arethe amidines that, despite sp2 anomeric cen-ters and solution B2,5 conformations, are (atthe pH optimum for catalysis) both weakerbinders than the imidazoles and less quantifi-ably transition state mimics. The reason forthis most likely stems from the high (8–10)pKa values39–41 of the amidines, which cannotaccept a favorable hydrogen bond from thecatalytic acid at pH 5.6. The interaction ofcatalytic acid with the glycosidic oxygen in

catalysis is known to be highly significant, and the exploitation of thishydrogen bond directed the design of the imidazole inhibitors, inwhich the lone pair on the imidazole nitrogen is poised to make ahighly productive interaction with the enzyme. At pH 5.6, theprotonated state of the amidinium ion is likely to hinder binding,which is consistent with the observation that the Ki for amidine 2adecreases from B1 mM at pH 5.6 to 49 nM at pH 7.5 (similar to thatobserved previously for snail b-mannosidase inhibition13).

There is a substantial improvement—both in binding (1.4 mM toB60 nM) and LFER correlation and slope for mannoimidazoles upontheir modification with aryl substituents—that likely reflects theharnessing of the additional binding energy of the +1 aglycon subsitein a manner similar to that used by the natural substrates. Impor-tantly, the phenyl ring nestles into the hydrophobic cavity provided inpart by Trp470, Trp533 and Tyr537 (Fig. 3) and sits ‘‘above’’ themodified sugar, as would also be expected for the substrate aglycon.Furthermore, the aryl moiety sits approximately where the equivalentaglycone moiety is in the Michaelis complex of the endomannanaseCjMan26A (ref. 10). Also, given that the B2,5 is not the favoredsolution conformation for mannoimidazoles, harnessing of the agly-con site interactions may provide additional binding energy tocompensate for the required distortion.

Though compounds having sp2 centers, especially substituted man-noimidazoles, are persuasive transition state mimics, poorer correla-tions are generally seen with charged inhibitors—for example, bothnoeuromycin 5 (reported here) and a variety of compounds studiedelsewhere26,35 and in this work. To some extent this implies that theforces governing the binding of aza and imino sugars are not correlatedwith those binding the transition state; however, this is potentiallymisleading. LFER work of this kind, in which interactions are

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Figure 5 Linear free energy relationships. LFERs are shown for correlations for the relationship between

log Ki (Ki expressed in mM) and log Km/kcat (derived from Km/kcat in units of mM min) for nine inhibitors

with a panel of seven Man2A constructs (data in Supplementary Table 3), including the wild-type

enzyme. For compound 5, the fit shown excludes the W645A data point (shown as a filled triangle), as

5 is known to bind as a different anomer to this mutant (see text and Fig. 4).

Table 1 Linear free energy correlations

Compound

Correlation (r2) log

Km/kcat

Slope log

Km/kcat

Correlation

(r 2) log Km

Mannoimidazole 1a 0.78 1.06 ± 0.25 0.41

Mannoimidazole 1b 0.94 1.09 ± 0.12 0.58

Mannoimidazole 1c 0.95 0.97 ± 0.10 0.65

Mannoimidazole 1d 0.92 1.03 ± 0.10 0.60

Mannoamidine 2a 0.61 0.91 ± 0.32 0.52

Mannoamidine 2e 0.67 0.57 ± 0.26 0.78

Isoquinuclidine 4a 0.88 0.65 ± 0.11 0.44

Noeuromycin 5 0.03 0.15 ± 0.38 0.04

Noeuromycin 5 without W645A 0.56 0.60 ± 0.26 0.28

Correlations are shown for the relationship between log Ki and log Km/kcat for nineinhibitors with a panel of seven Man2A constructs. Wild-type data are included (data inSupplementary Table 3). The analysis for noeuromycin 5 is given both for all data andfor data with the W645A point omitted (see text for details).

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perturbed through site-directed enzyme variants, is necessarily a crudeapproach. It is widely believed that a major contributor to the bindingof charged aza and imino sugars is via charge-charge interactions withthe enzymatic nucleophile and acid/base. These two interactions,whose importance is revealed, for example, in pH profiles for binding,cannot be interrogated through LFER analyses without rendering theenzyme inactive. Thus the key interactions that govern binding of thisclass of compound are the ones the technique cannot interrogate.

The work presented here strongly supports the idea of a B2,5

transition state for (retaining) b-mannoside hydrolysis, with all tight-binding inhibitors observed in this (or similar) conformation. Linearfree energy relationships reveal that substituted mannoimidazoles areamong the best transition state mimics tested26,34–36. More crucially,the work highlights the essential synergy of structural analyses intandem with linear free energy studies. While structure alone supportsthe B2,5 transition state, only LFER can reveal that there is more tomimicking the transition state than simply adopting the correctconformation. Although LFER cannot provide insight about the actualconformation adopted by a compound, it does reveal how theinteractions of that compound are related to the forces governingcatalysis; that is, whether binding does mimic the transition state andto what extent. In the work reported here, either structure or LFERalone, in the absence of the complementary technique, would haveyielded very ambiguous results. The goal of studying enzyme inhibitionthrough transition state mimicry is two-fold. The first is to probe theputative transition state and question proposals about its conforma-tion. The second is to build on appropriate transition state mimicry forthe development of therapeutic agents. The work presented herestrongly supports mechanistic proposals that retaining mannosidasesuse a B2,5 transition state; the future may see such insight aiding thedevelopment of clinically relevant inhibitors of Golgi a-mannosidase.

METHODSEnzyme inhibition studies. BtMan2A wild type and variants were expressed in

Escherichia coli strain BL21 (DE3) and purified essentially as described

previously15 (primer details in Supplementary Table 2). A panel of 25 putative

mannosidase inhibitors (Fig. 2) were screened against wild-type BtMan2A. The

activity of BtMan2A was determined at 37 1C, in 43.5 mM sodium phosphate

plus 10 mM citric acid (PC) buffer, pH 5.6, containing 1 mg ml–1 bovine serum

albumin and 20 mM substrate (B5-fold lower than the Km) in a final volume of

500 ml. Reactions were initiated by addition of BtMan2A to a final concentra-

tion of 0.625 nM. The release of 2,4-dinitrophenolate (DNP; e ¼ 14,368 M–1

cm–1 at pH 5.6) from 2,4-dinitrophenyl-b-D-mannopyranoside (DNP-Man)

was monitored continuously at 400 nm, and the rate was used to determine

kcat/Km. The reactions were carried out with a range of inhibitor concentrations

that spanned the Ki, which was calculated using the following equation:

vo

vi¼ 1

Ki�½I�+ 1

where v0 and vi are the rates of the reaction in the absence and presence of

inhibitor, respectively. Under conditions where [S] oo Km, the fractional

decrease in rate thus yields the Ki for a competitive inhibitor42. For poorer

inhibitors (Ki 4 5 mM) it was not possible to use inhibitor concentrations

spanning the range 0.5 to 2 Ki due to the solubility/availability of the inhibitor.

In these cases a single concentration of inhibitor (the highest possible) was used

in triplicate, and the Ki was calculated from the equation.

In LFER studies the kinetic parameters of wild-type BtMan2A and six active

center variants were determined and plotted against the Ki for selected

inhibitors. Wild-type inhibition was determined using three substrates

(DNP-Man (17), PNP-Man (19) and methylumbelliferyl b-D-mannopyrano-

side (20)) to ensure similar effects of the mutants on different substrates. The

data showed that the D199A mutant, unlike the other variants, displayed

profound differences in kcat/Km for these different substrates (with a consider-

ably lesser effect on the DNP mannopyranoside, likely indicating an effect

through a reduction on the pKa of the acid/base Glu462, which is thus unable

to protonate the leaving group). This mutant was therefore not considered

appropriate for further study. The variants were generated by QuickChange Kit

(Stratagene) using the primers listed in Supplementary Table 2. Assays

contained the same components as described above, except the substrate,

methylumbelliferyl b-D-mannopyranoside, was used at a final concentration

of 66 nM. The fluorescent product, 4-methylumbelliferone (MU), released

from MU-Man, has an e ¼ 3.2 � 108 M–1 cm–1 at pH 5.6 and was measured

continuously in a CARY (Varian, Inc.) Eclipse fluorescence spectrophotometer

at 325 nm (excitation) and 450 nm (emission). The correlation between log Ki

and log Km/kcat was calculated using Prism 4 (GraphPad Software, Inc.) or

GRAFIT (Erithacus Software).

Plate screening assay. Site-directed mutagenesis using a QuickChange Kit

(Stratagene) was carried out with degenerate primers (Supplementary Table 1)

that would randomize the codons for Asn461 and Trp198. E. coli strain C41

(DE3) was transformed with plasmids encoding potential variants of BtMan2A,

plated out onto LB agar containing 10 mg ml–1 kanamycin and incubated at

37 1C for 18 h. The colonies were overlaid with 4 ml of 0.7% (w/v) agarose

containing 1 mM isopropyl b-D-thiogalactopyranoside and 1 mM 19. The

fluorescent haloes of MU released from the cleavage of MU-Man around the

E. coli colonies were visualized after 30 min with UV light. Controls with E555A

(inactive mutant) and wild-type BtMan2A were carried out in parallel.

Structure solution and refinement. BtMan2A was crystallized by the hanging

drop method, with protein at 7.5 mg ml–1 in 4 mM Tris (2-carboxyethyl)pho-

sphine HCl, 8 mM HEPES pH 8.0, diluted 1:1 with well solution comprising

0.1 M 2-(N-morpholino)ethanesulfonic acid (MES) buffer pH 6.4, 0.2 M NaBr,

12–18% polyethylene glycol 3350. Crystals took 2–3 weeks to grow at 18 1C and

were fished into fresh drops of mother liquor, to which one of the inhibitors

had been added at the following concentrations: 1 mM 6, 1 mM 2a, 1 mM 2e,

0.33 mM 1a, 1 mM 5, 2 mM 1c, 10 mM 4a. After soaking for 40 min to 1 h,

crystals were harvested into nylon fiber loops and transferred to a cryoprotec-

tant solution consisting of the mother liquor supplemented with the appro-

priate inhibitor at the same concentration and ethylene glycol (to 25% v/v),

before freezing in liquid nitrogen.

X-ray data were collected on beamline ID29 at the European Synchrotron

Radiation Facility (Grenoble) as shown in Supplementary Table 1. The

structures are in the same cell and space group as the original BtMan2A

(Protein Data Bank code 2JE8), and so that was used as the starting model for

refinement with REFMAC43, with other programs from the CCP4 suite44 used

throughout. Identical reflections were maintained for cross-validation as used

previously. Model building was performed with COOT45. Ligand structures

were built into REFMAC-weighted 2Fo – Fc and Fo – Fc electron density maps.

Water inclusion and manual corrections were performed with COOT. Struc-

tural figures were prepared with BOBSCRIPT46.

Accession codes. Protein Data Bank: The structures of BtMan2A complexes

have been deposited under accession codes 2VJX, 2VL4, 2VMF, 2VOT, 2VO5,

2VQT, 2VGU and 2VR4.

Note: Supplementary information and chemical compound information is available onthe Nature Chemical Biology website.

ACKNOWLEDGMENTSThe Biotechnology and Biological Sciences Research Council (BBSRC) is thankedfor funding. G.J.D. is the recipient of a Royal Society-Wolfson Research MeritAward. S. Withers (University of British Columbia) is thanked for provisionof 4-nitrophenyl 2-deoxy-b-D-arabino-hexopyranoside. A.V. thanks the SwissNational Science Foundation, Hoffmann-La Roche (Basle) and Syngenta (Basle)for generous support. This work is dedicated by M.-P.H., A.V. and J.G. to thememory of C. Mioskowski (deceased on June 2, 2007).

Published online at http://www.nature.com/naturechemicalbiology

Reprints and permissions information is available online at http://npg.nature.com/

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