James M Macdonald

University of British Columbia - Vancouver, Vancouver, British Columbia, Canada

Are you James M Macdonald?

Claim your profile

Publications (10)49.55 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: "Chemical Equation Presented" A good imitation: Di- and trisaccharide analogues of the oxazoline intermediate formed during enzymatic hydrolysis of chitin were found to be potent inhibitors of chitinaseA. The high affinity and enzymatic stability of a readily synthesized thioamide trisaccharide (two molecules of which are shown in the enzyme active site), and the mechanism-based mode of inhibition, make this analogue a promising candidate for broad-spectrum chitinase inhibition.
    No preview · Article · Mar 2010 · Angewandte Chemie International Edition
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The genomes of various Mycobacterium tuberculosis strains encode proteins that do not appear to play a role in the growth or survival of the bacterium in its mammalian host, including some implicated in plant cell wall breakdown. Here we show that M. tuberculosis H37Rv does indeed possess a functional cellulase. The x-ray crystal structure of this enzyme, in ligand complex forms, from 1.9 to 1.1A resolution, reveals a highly conserved substrate-binding cleft, which affords similar, and unusual, distortion of the substrate at the catalytic center. The endoglucanase activity, together with the existence of a putative membrane-associated crystalline polysaccharide-binding protein, may reflect the ancestral soil origin of the Mycobacterium or hint at a previously unconsidered environmental niche.
    Preview · Article · Jun 2005 · Journal of Biological Chemistry
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The understanding of transition state mimicry in glycoside hydrolysis is increasingly important both in the quest for novel specific therapeutic agents and for the deduction of enzyme function and mechanism. To aid comprehension, inhibitors can be characterized through kinetic, thermodynamic, and structural dissection to build an "inhibition profile." Here we dissect the binding of a tetrahydrooxazine inhibitor and its derivatives, which display Ki values around 500 nm. X-ray structures with both a beta-glucosidase, at 2 A resolution, and an endoglucanase at atomic (approximately 1 A) resolution reveal similar interactions between the tetrahydrooxazine inhibitor and both enzymes. Kinetic analyses reveal the pH dependence of kcat/Km and 1/Ki with both enzyme systems, and isothermal titration calorimetry unveils the enthalpic and entropic contributions to beta-glucosidase inhibition. The pH dependence of enzyme activity mirrored that of 1/Ki in both enzymes, unlike the cases of isofagomine and 1-deoxynojirimycin that have been characterized previously. Calorimetric dissection reveals a large favorable enthalpy that is partially offset by an unfavorable entropy upon binding. In terms of the similar profile for the pH dependence of 1/Ki and the pH dependence of kcat/Km, the significant enthalpy of binding when compared with other glycosidase inhibitors, and the tight binding at the optimal pH of the enzymes tested, tetrahydrooxazine and its derivatives are a significantly better class of glycosidase inhibitor than previously assumed.
    Preview · Article · Dec 2004 · Journal of Biological Chemistry
  • James M. Macdonald · Maria Hrmova · Geoffrey B. Fincher · Robert V. Stick
    [Show abstract] [Hide abstract]
    ABSTRACT: The glycosylation of 4,6-O-benzylidene-N-benzyloxycarbonylisofagomine with a D-glucosyl and a laminari-biosyl trichloroacetimidate has given, after removal of protecting groups, 3-O-(β-D-glucopyranosyl)- and 3-O-(β-laminaribiosyl)-isofagomines. Also included are similar glycosylations of a related tetrahydrooxazine. 3-O-(β-D-Glucopyranosyl)- and 3-O-(β-laminaribiosyl)-isofagomines acted as potent inhibitors of a barley 1,3-β-D-glucan endo-hydrolase, with ID50 values of 7.8 and 3.1 μM, respectively.
    No preview · Article · Jun 2004 · ChemInform
  • James M. Macdonald · Robert V. Stick
    [Show abstract] [Hide abstract]
    ABSTRACT: Benzyl 4-cyano-4-deoxy-α-D-arabinoside was converted into both its2,3-di-O-acetyl and 2,3-di-O-(tert-butyldimethylsilyl)derivatives. The latter, by a process of hydrogenolysis, oxidation, and methanolysis, gave methyl2,3-di-O-(tert-butyldimethylsilyl)-4-cyano-4-deoxy-D-arabinonate. Reductionof this methyl ester with borane dimethyl sulfide gave, after deprotection, isofagomine lactam.
    No preview · Article · Jan 2004 · Australian Journal of Chemistry
  • [Show abstract] [Hide abstract]
    ABSTRACT: The design and synthesis of transition-state mimics reflects the growing need both to understand enzymatic catalysis and to influence strategies for therapeutic intervention. Iminosugars are among the most potent inhibitors of glycosidases. Here, the binding of 1-deoxynojirimycin and (+)-isofagomine to the "family GH-1" beta-glucosidase of Thermotoga maritima is investigated by kinetic analysis, isothermal titration calorimetry, and X-ray crystallography. The binding of both of these iminosugar inhibitors is driven by a large and favorable enthalpy. The greater inhibitory power of isofagomine, relative to 1-deoxynojirimycin, however, resides in its significantly more favorable entropy; indeed the differing thermodynamic signatures of these inhibitors are further highlighted by the markedly different heat capacity values for binding. The pH dependence of catalysis and of inhibition suggests that the inhibitory species are protonated inhibitors bound to enzymes whose acid/base and nucleophile are ionized, while calorimetry indicates that one proton is released from the enzyme upon binding at the pH optimum of catalysis (pH 5.8). Given that these results contradict earlier proposals that the binding of racemic isofagomine to sweet almond beta-glucosidase was entropically driven (Bülow, A. et al. J. Am. Chem. Soc. 2000, 122, 8567-8568), we reinvestigated the binding of 1-deoxynojirimycin and isofagomine to the sweet almond enzyme. Calorimetry confirms that the binding of isofagomine to sweet almond beta-glucosidases is, as observed for the T. maritima enzyme, driven by a large favorable enthalpy. The crystallographic structures of the native T. maritima beta-glucosidase, and its complexes with isofagomine and 1-deoxynojirimycin, all at approximately 2.1 A resolution, reveal that additional ordering of bound solvent may present an entropic penalty to 1-deoxynojirimycin binding that does not penalize isofagomine.
    No preview · Article · Dec 2003 · Journal of the American Chemical Society
  • [Show abstract] [Hide abstract]
    ABSTRACT: Glycosidases are some of the most ubiquitous enzyme in nature. Their biological significance, coupled to their enormous catalytic prowess derived from tight binding of the transition state, is reflected in their importance as therapeutic targets. Many glycosidase inhibitors are known. Imino sugars are often potent inhibitors, yet many facets of their mode of action, such as their degree, if any, of transition-state "mimicry" and their protonation state when bound to the target glycosidase remain unclear. Atomic resolution analysis of the endoglucanase, Cel5A, in complex with a cellobio-derived isofagomine in conjunction with the pH dependence of Ki and kcat/KM reveals that this compound binds as a protonated sugar. Surprisingly, both the enzymatic nucleophile and the acid/base are unprotonated in the complex.
    No preview · Article · Jul 2003 · Journal of the American Chemical Society
  • [Show abstract] [Hide abstract]
    ABSTRACT: The treatment of benzyl 2,3-O-isopropylidene-β-L-xylopyranoside with N-hydroxyphthalimide under Mitsunobu conditions, followed by protecting-group interchange, gave benzyl 4-O-[(tert-butoxycarbonyl)amino]-2,3- O-isopropylidene-α-D-arabinoside. Mild acid hydrolysis and catalytic hydrogenolysis afforded 4-O-[(tert-butoxycarbonyl)amino]-D-arabinose that, upon heating in water, gave the dihydrooxazine [(4R,5S,6R)-5,6-dihydro-4,5-dihydroxy-6-hydroxymethyl-4H-1,2-oxazine] as a crystalline solid. A single-crystal structure determination of this solid showed it to exist in the 5H6 conformation. Reduction of the dihydrooxazine gave the tetrahydrooxazine [(4R,5S,6R)-4,5-dihydroxy-6-hydroxymethyl-3,4,5,6-tetrahydro-2H-1,2-oxazine]. The dihydrooxazine was an effective inhibitor of two β-glucosidases (Ki = 27 and 35 µM). Benzyl 2,3-O-isopropylidene-β-L-xylopyranoside, via the derived imidazylate, was converted into a nitrile that, upon reduction and protecting-group manipulations, gave benzyl 4-C-aminomethyl-4-deoxy-α-D-arabinoside. Treatment of this amine with hydrogen and palladium-on-carbon gave isofagomine.Key words: dihydrooxazine, tetrahydrooxazine, isofagomine, iminosugars, glycosidase inhibitors.
    No preview · Article · Jun 2002 · Canadian Journal of Chemistry

  • No preview · Conference Paper · Apr 2002
  • [Show abstract] [Hide abstract]
    ABSTRACT: Isofagomine and a carbohydrate-like tetrahydrooxazine, as their N-benzyloxycarbonyl derivatives, have been subjected to a glycosynthase in the presence of α-D-glucopyranosyl fluoride as a glucosyl donor. In each case, after protecting group removal, a mixture of 1,4-β-linked di-, tri-, and tetra-'saccharides' was obtained. These novel oligosaccharide derivatives were tested as inhibitors of the endo-glycanase Cex from Cellulomonasfimi. Affinities increased progressively as additional D-glucosyl residues were incorporated, which is consistent with the known substrate specificity of this enzyme.
    No preview · Article · Jan 2002 · Australian Journal of Chemistry

Publication Stats

325 Citations
49.55 Total Impact Points


  • 2010
    • University of British Columbia - Vancouver
      • Department of Chemistry
      Vancouver, British Columbia, Canada
  • 2005
    • Aix-Marseille Université
      Marsiglia, Provence-Alpes-Côte d'Azur, France
  • 2003-2004
    • University of Western Australia
      Perth City, Western Australia, Australia
    • University of Zurich
      Zürich, Zurich, Switzerland