Synthetic tools to illuminate matrix metalloproteinase and proteasome activities
Geurink, P.P.
Citation
Geurink, P. P. (2010, October 6). Synthetic tools to illuminate matrix metalloproteinase and proteasome activities. Retrieved from
https://hdl.handle.net/1887/16014
Version: Corrected Publisher’s Version
License: Licence agreement concerning inclusion of doctoral thesis in the Institutional Repository of the University of Leiden
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Synthetic Tools to Illuminate Matrix Metalloproteinase and
Proteasome Activities
PROEFSCHRIFT
ter verkrijging van
de graad van Doctor aan de Universiteit Leiden,
op gezag van Rector Magnificus prof. mr. P. F. van der Heijden, volgens besluit van het College voor Promoties
te verdedigen op woensdag 6 oktober 2010 klokke 15.00 uur
door
Paulus Petrus Geurink
Geboren te Haarlem in 1983
Promotie commissie
Promotores : Prof. dr. H. S. Overkleeft : Prof. dr. G. A. van der Marel Co-promotor : Dr. B. I. Florea
Overige leden : Prof. dr. J. Brouwer
Prof. dr. J. Lugtenburg
Prof. dr. R. P. H. Bischoff Prof. Dr. A. F. Kisselev
Dr. H. Ovaa
“Feiten, waarnemingen en proefnemingen zijn als de bouwmaterialen voor een groot bouwwerk; maar als men ze bij elkaar zoekt, moet men voorkomen dat ze
een ongeordende en hinderlijke puinhoop in de wetenschap worden. In plaats daarvan moet men ernaar streven ze in categorieën in te delen, zodat elk deel
van het bouwwerk nog te onderscheiden is.”
Antoine Laurent Lavoisier, 1777
Table of Contents
List of Abbreviations 6
1 General Introduction 9
2 A Straightforward Synthesis of Peptide Hydroxamate 37 MMP/ADAM Inhibitors
Synthesis and biological evaluation of an inhibitor library
3 Peptide Hydroxamate-Based Photoreactive Probes of 57 Zinc-Dependent Metalloproteases
Synthesis and biological evaluation
4 Incorporation of Fluorinated Phenylalanine Generates 79 Highly Specific Inhibitor of Proteasome’s
Chymotrypsin-like Sites
5 Selective Inhibitors of Proteasome’s Trypsin-like Sites 99
Synthesis and biological evaluation
6 Probing the 20S Proteasome Cavity with Photoreactive 123
Peptide Vinyl Sulfones 7 A Levulinoyl Ester-Based Cleavable Linker for 135
Activity-Based Protein Profiling 8 Summary and Future Prospects 155
Samenvatting 171
List of Publications 174
Curriculum Vitae 176
Nawoord 177
List of Abbreviations
AA, Aa amino acid
ABP activity-based probe ABPP activity-based protein profiling Ac acetyl
Ac2O acetic anhydride AcOH acetic acid ACN acetonitrile Ada 1-adamantyl acetyl
ADAM a disintegrin and metalloprote(in)ase Ahx aminohexanoic acid
AMC 7-acetoxy-4-methylcoumarin AP alkaline phosphatase APT attached proton test ATP adenosine triphosphate aq. aqueous
BAIB [bis(acetoxy)iodo]benzene Bio biotin
BM biotinylated marker Bn benzyl
Boc tert-butyloxycarbonyl
Boc2O tert-butyloxycarbonic anhydride Bodipy boron-dipyrromethene,
boradiazaindacene bs broad singlet Bpa 4-benzoyl-L-phenylalanine BPB bromophenol blue BSA bovine serum albumin Bu butyl
calcd. calculated cat. catalytic amount Cbz benzyloxycarbonyl CL cleavable linker
chemical shift
heating (reflux) d doublet Da Dalton
DBU diazabicyclo[5.4.0]undec-7-ene DCM dichloromethane
dd double doublet ddd double double doublet DIC N,N’-diisopropyl carbodiimide DiPEA diisopropylethylamine DMAP 4-(dimethylamino)pyridine DMF N,N-dimethylformamide DMSO dimethylsulfoxide
dt double triplet DTT dithiothreitol dq double quartet
EDC 1-ethyl-3-(3-dimethyl-aminopropyl)- carbodiimide
EDTA ethylenediaminetetraacetate EL-4 murine lymphoid cell line eq. molar equivalent ESI electron spray ionization Et ethyl
EtOAc ethyl acetate EtOH ethanol
Fmoc (9H-fluoren-9-yl) methoxycarbonyl h hour(s)
HCTU (2-(6-chloro-1H-benzotriazole-1-yl)- 1,1,3,3-tetramethylaminium hexafluorophosphate
HEK human embryonic kidney cell line HEPES 4-(2-hydroxyethyl)-1-
piperazineethanesulfonic acid HMDS hexamethyldisilazane HOBt N-hydroxybenzotriazole HOSu N-hydroxysuccinimide HPLC high performance liquid
chromatography
HRMS high resolution mass spectrometry HRP horse radish peroxydase
Hz Hertz
IC50 inhibition concentration resulting in 50% inhibition of enzyme activity ICAT isotope-coded affinity tagging IR infrared spectroscopy
J coupling constant
LC-MS liquid chromatography coupled to mass spectrometry
Lev levulinoyl ester m multiplet M molar
MBHA para-methylbenzhydryl amine mCPBA meta-chloroperoxybenzoic acid MHC I major histocompatibility complex
class I Me methyl MeOH methanol
MI McIlvaine’s buffer
min. minute(s)
MMP matrix metalloprote(in)ase Mtt 4-methyltrityl
m/z mass-to-charge ratio nBu n-butyl
NHS N-hydroxysuccinimide NMP N-methyl-2-pyrrolidone NMR nuclear magnetic resonance o/n overnight
p pentet
PAGE polyacrylamide gel electrophoresis PAL photoaffinity labelling PBS phosphate buffered saline PD pull-down (buffer) Pd/C palladium on charcoal PE petroleum ether PEG polyethyleneglycol PFP pentafluorophenyl Ph phenyl
ppm parts per million
PPTS pyridinium para-toluenesulfonate PS pre-stained marker q quartet
quant. quantitative ref. reference RP reverse phase RT room temperature Rt retention time s singlet sat. saturated SB sample buffer SDS sodium dodecyl sulphate SPE solid phase extraction SPPS solid phase peptide synthesis Su succinimidyl
t triplet t, tert tertiary T temperature TACE TNF converting enzyme TBS tert-butyldimethylsilyl TBS tris buffered saline tBu tert-butyl
tBuONO tert-butyl nitrite tBuOH tert-butanol
TBS tert-butyl dimethylsilyl
td triple doublet
TEMPO 2,2,6,6-tetramethyl-1-piperidinyloxy TFA trifluoroacetic acid
THF tetrahydrofuran TIMP tussue inhibitor of
metalloprote(in)ases TIS triisopropylsilane TLC thin layer chromatography Tmd trifluoromethyldiazirine TMS tetramethylsilane TNF tumor necrosis factor Tol toluene Tr trityl
Tris 2-amino-2-(hydroxymethyl)-1,3- propanediol
Ts tosyl UV ultra violet VE vinyl ethyl ester VS vinyl methyl sulfone ZBG zinc binding group
Note: the one and three letter codes for the amino acids follow the recommendations of IUPAC. J. Biol. Chem. 1968, 243, 3557-3559 and J. Biol. Chem. 1972, 247, 977-983.
