Cover Page
The following handle holds various files of this Leiden University dissertation:
http://hdl.handle.net/1887/58875
Author: Beenakker, T.J.M.
Title: Design and development of conformational inhibitors and activity-based probes for retaining glycosidases
Issue Date: 2017-10-19
Design and development of conformational inhibitors and
activity-based probes for retaining glycosidases
P ROEFSCHRIFT
ter verkrijging van
de graad van Doctor aan de Universiteit Leiden, op gezag van Rector Magnificus prof. mr. C. J. J. M. Stolker,
volgens besluit van het College voor Promoties te verdedigen op donderdag 19 oktober 2017
klokke 15:00 uur
door
Thomas Johannes Maria Beenakker
geboren te Eindhoven in 1989
Promotiecommissie
Promotores Prof. dr. H. S. Overkleeft
Prof. dr. G. A. van der Marel
Co-promotor Dr. J. D. C. Codée
Overige leden Prof. dr. J. Brouwer Prof. dr. J. M. F. G. Aerts
Prof. dr. F. P. J. T. Rutjes (Radboud Universiteit)
Prof. dr. G. J. Davies (University of York, Verenigd Koninkrijk) Dr. L. I. Willems (Simon Fraser University, Canada)
Printed by Ridderprint B.V.
ISBN: 978-94-6299-705-9
iv
List of abbreviations vi
1 General introduction 1
2 A new generation of fluorescent ABPs to target retaining
α-galactosidases 13
3 Activity-based protein profiling of lysosomal GH35 and
GH59 β-galactosidases 29
4 Cyclophellitol based ABPs for broad-spectrum profiling of
retaining exo-α-mannosidases 47
5 Activity-based protein profiling of lysosomal GH2
exo-β-mannosidase 61
6 Synthesis of carba-cyclophellitols:
a new class of cyclophellitol derivatives 75
v
7 Biological evaluation of carba-cyclophellitols 107
8 Synthesis of potential glycosyltransferase inhibitors based
on carba-cyclophellitol 123
9 Summary and future prospects 143
Nederlandse samenvatting 169
List of publications 172
Curriculum vitae 175
vi
2,4-DNPG 2,4-dinitrophenyl-β-D-glucoside 4-mu 4-methylumbelliferyl ABP activity-based probe ABPP activity-based protein profiling Ac acetyl
acac acetylacetonate ACN acetonitrile αGal A α-galactosidase A
α-NAGAL α-N-acetylgalactosaminidase AMP-DNM N-(5´-adamantane-1´-yl-methoxy)-
pentyl-1-deoxynojirimycin Asn asparagine Asp aspartic acid B boat
BCl3 boron trichloride Bn benzyl Boc tert-butoxycarbonyl Boc2O di-tert-butyldicarbonate Bodipy boron-dipyrromethene BSA bovine serum albumin Bz benzoyl C chair calc. calculated
CAZy Carbohydrate Active Enzyme CBB Coomassie Brilliant Blue CBE conduritol B epoxide
Cq quarternary carbon atom Ctrl control experiment
CuAAC copper(I)-catalyzed azide/alkyne cycloaddition
Cy cyanine dye d doublet δ chemical shift Da Dalton
DBU 1,8-diazabicyclo[5.4.0]undec-7-ene DCE dichloroethane
DCI 4,5-dicyanoimidazole DCM dichloromethane dd double doublet ddd double double doublet DFT density functional theory dGMII drosophila Golgi α–mannosidase II DHP 3,4-dihydro-2H-pyran
DIBAL diisobutylaluminium hydride DIC N,N′-diisopropylcarbodiimide DIPEA N,N-diisopropylethylamine DMAP 4-(N,N-dimethylamino)pyridine DMF N,N-dimethylformamide DMSO dimethylsulfoxide DNJ deoxynojirimycin DTT dithiothreitol EDA ethyl diazoacetate
EEDQ 2-ethoxy-1-ethoxycarbonyl-1,2- dihydroquinoline
Em emission
eq. molar equivalents ESI electro-spray ionization Et ethyl
EtOAc ethyl acetate Ex exitation exp. experimental FEL free energy landscape GAA lysosomal α-glucosidase GALC gene encoding
galactosylceramidase GalT galactosyltransferase
GANAB neutral alpha-glucosidase AB GBA1 glucosylceramidase
GBA2 non-lysosomal glucosylceramidase GBA3 cytosolic β-glucosidase
GCS glucosylceramide synthase GH glycosidase hydrolase
vii
GLA gene encoding αGal A GLB1 gene encoding lysosomal acid β- galactosidase
Gln glutamine Glu glutamic acid GT glycosyltransferase GTA α-1,3-N-
acetylgalactosaminyltransferase GTB α-1,3-galactosyltransferase
h hour(s) H half-chair Helix p. Helix pomatia
HEK293 human embryonic kidney 293 HPLC high-performance liquid chromatography HRMS high resolution mass spectrometry IC50 half maximal inhibitory
concentration
IEDDA inverse-electron-demand Diels Alder
J coupling constant KO Knockout
KHMDS potassium hexamethyldisilazane LC/MS liquid chromatography mass spectrometry LDA lithium diisopropylamide LSD lysosomal storage disorder m multiplet
M marker M molar m/z mass to charge ratio MANBA β-mannosidase
mCPBA meta-chloroperoxybenzoic acid MD molecular dynamics Me methyl
MeOH methanol min minute(s)
MS mass spectrometry n.d. not determined NMR nuclear magnetic resonance NOESY nuclear Overhauser effect spectroscopy
PAGE polyacrylamide gel electrophoresis PBS phosphate-buffered saline Pd/C palladium on carbon PDB protein data bank PEG polyethylene glycol Ph phenyl
Piv pivaloyl p-NPG para-nitrophenyl β-D-
glucopyranoside ppm parts per million pTsOH para-toluenesulfonic acid q quartet
rGLA recombinant α-galactosidase A r.m.s. root mean square
rt room temperature Rt retention time
s singlet S skew-boat SDS sodium dodecyl sulfate sp. species
t triplet
TBA tertbutylammonium TBAF tetrabutylammonium fluoride TBAI tetrabutylammonium iodide TBDMS tert-butyldimethylsilyl
TBTA tris[(1-benzyl-1H-1,2,3-triazol-4- yl)methyl]amine
tBu tert-butyl
TFA trifluoroacetic acid THF tetrahydrofuran THP tetrahydropyran TLC thin layer chromatography Tm Thermotoga maritima Tr trityl
Tris tris(hydroxymethyl)aminomethane Trp tryptophan
Ts para-toluenesulfonyl UDP uridine diphosphate UV ultraviolet Val valine WT wild-type
