Chemical Proteomics: Methods and Protocols

309 Pages·2012·4.016 MB·English

by  Marcus Bantscheff (auth.), Gerard Drewes, Marcus Bantscheff (eds.)

M M B ™
ethods in olecular iology
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Chemical Proteomics
Methods and Protocols
Edited by
Gerard Drewes and Marcus Bantscheff
Cellzome AG, Heidelberg, Germany
Editors
Dr. habil. Gerard Drewes Dr. Marcus Bantscheff
Cellzome AG Cellzome AG
Heidelberg, Germany Heidelberg, Germany
[email protected] [email protected]
ISSN 1064-3745 e-ISSN 1940-6029
ISBN 978-1-61779-363-9 e-ISBN 978-1-61779-364-6
DOI 10.1007/978-1-61779-364-6
Springer New York Dordrecht Heidelberg London
Library of Congress Control Number: 2011937567
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Preface
An Overview of Chemical Proteomics: Methods and Applications
The multidisciplinary science of chemical proteomics studies how small molecules of
synthetic or natural origin bind to proteins and modulate their function. Scientists in the
field have different backgrounds including molecular and cell biology, biochemistry, phar-
macology, organic chemistry, and physics. Chemical Proteomics: Methods and Applications is
directed at molecular biologists and biochemists with either an interest in small molecules
themselves, e.g., in drug discovery projects, or in using small-molecule probes as research
tools to study protein function. The book may also be useful for organic chemists with an
interest in biology and for specialists in protein mass spectrometry.
In the introductory chapters, we discuss analytical strategies for chemical proteomics
projects, with a focus on the current state-of-the-art in protein mass spectrometry, and
describe several examples how chemical proteomics can impact the field of drug discovery.
The consecutive chapters provide detailed experimental protocols. Most chemical proteom-
ics projects consist of three parts. In the first part, the chemical probe is selected or designed,
and then synthesized. In the second part, the probe compound is exposed to the protein
sample or cell extract. In the final part, proteins binding to the probe compound are identi-
fied and often quantified. In simple applications, this is often achieved by antibody-based
detection, but if the aim is the discovery of targets in an unbiased fashion, mass spectrom-
etry is the method of choice. The following chapters cover all of these aspects.
The first set of chapters describes how probes are generated from commercially available
reagents without elaborate chemical synthesis procedures, and how the proteins binding to
the probes can be analyzed by immunodetection or by mass spectrometry. Rix et al. and
Saxena provide protocols for direct noncovalent affinity capture using protein kinase inhibi-
tors as an example, which serves to profile the targets of these compounds and provides
probes for kinase expression and activity. Ge and Sem have developed a target class-specific
probe for the labeling of dehydrogenase enzymes. Kawamura and Mihai, and Codreanu
et al. describe the use of biotin-conjugated probes which form covalent adducts with defined
subproteomes, here consisting of adenine-binding proteins and targets of lipid electrophiles.
Lenz et al. combine features of noncovalent and covalent capturing strategies in their bifunc-
tional ligands designed to target methyltransferases, an emerging class of drug targets.
The second set of chapters is concerned with techniques for the discovery of small-
molecule targets and the probing of target function. Ong et al. describe the use of stable
isotope labeling of amino acids in cell culture (SILAC) in identifying proteins that bind
small-molecule probes in cell extracts. Hopf et al. perform affinity enrichment of target pro-
teins on a probe matrix in the presence of competing free test compound in solution, thus
enabling determination of binding potencies of the free test compound to affinity-captured
proteins from cell extracts. The method employs quantitative mass spectrometry with iso-
baric mass tags to determine the potencies for a large number of targets in a single analysis.
Ge and Sem have developed a protocol for the detection and purification of dehydrogenase
v
vi Preface
enzymes, which may represent targets, but also unwanted off-targets, for certain types of
drugs. Kovanich et al. describe a combination of cAMP-based affinity chromatography with
quantitative mass spectrometry to investigate protein kinase A complexes in extracts of cells
and tissues. De Jong et al. use activity-based chemical probes to profile the activity of the
proteasome, which has recently emerged as an important cancer target, in cells and tissues.
The next three chapters provide innovative protocols for the study of potential drug targets
by chemical cross-linking and mass spectrometry. Mueller et al. provide a method to study
protein–drug interactions, and Gasilova et al. employ cross-linking and MALDI-mass spec-
trometry to study ligand modulation of protein–protein interactions. Jeon et al. provide a
protocol for in vivo cross-linking via time-controlled transcardiac perfusion, which in prin-
ciple enables the direct analysis of protein targets in animal models.
The final set of chapters is concerned with small-molecule ligand and drug discovery.
Casalena et al. describe the discovery of probe compounds by utilizing compound libraries
immobilized on microarrays. Wolf et al. delineate general guidelines for working with small
molecules, including aspects like storage, the preparation of solutions, and the determina-
tion of solubility. The chapter by de Matos et al. provides guidelines for the use of the
ChEBI database, which should be very helpful for researchers tasked with the selection of
a particular probe or with building a small molecule collection to purpose. They describe
the Chemical Entities of Biological Interest (ChEBI) database which helps to find probe
molecules with the desired structural or biological features. Finally, many researchers will
consider whether their research tool compound might have the potential to be developed
into a drug. Zhang delivers a lucid analysis of the features that distinguish drugs from probe
molecules, and lays out a set of rules for “drug likeness.”
Affinity- and activity-based chemical probes, combined with quantitative immunodetec-
tion and mass spectrometry techniques, are increasingly gaining appreciation as powerful
strategies for the molecular analysis of complex biological systems in homeostasis and dis-
ease. We hope that the methodologies described in this volume will contribute to a wider
application of chemical proteomics methods in biochemical and cell biological laboratories.
Heidelberg, Germany Gerard Drewes
Marcus Bantscheff
Contents
Preface.............................................................. v
Contributors.......................................................... ix
Part I IntroductIon
1 Mass Spectrometry-Based Chemoproteomic Approaches..................... 3
Marcus Bantscheff
2 Chemical Proteomics in Drug Discovery................................. 15
Gerard Drewes
Part II Small moleculeS and Probe deSIgn
3 Compound Immobilization and Drug-Affinity Chromatography............... 25
Uwe Rix, Manuela Gridling, and Giulio Superti-Furga
4 Affinity-Based Chemoproteomics with Small Molecule-Peptide Conjugates....... 39
Chaitanya Saxena
5 A Chemical Proteomic Probe for Detecting Dehydrogenases:
Catechol Rhodanine ................................................ 55
Xia Ge and Daniel S. Sem
6 Probing Proteomes with Benzophenone Photoprobes....................... 65
Akira Kawamura and Doina M. Mihai
7 Biotinylated Probes for the Analysis of Protein Modification
by Electrophiles................................................... 77
Simona G. Codreanu, Hye-Young H. Kim, Ned A. Porter,
and Daniel C. Liebler
8 Profiling of Methyltransferases and Other S-Adenosyl-l-Homocysteine-
Binding Proteins by Capture Compound Mass Spectrometry................. 97
Thomas Lenz, Peter Poot, Elmar Weinhold, and Mathias Dreger
Part III target dIScovery and target valIdatIon
9 Identifying Cellular Targets of Small-Molecule Probes and Drugs
with Biochemical Enrichment and SILAC................................ 129
Shao-En Ong, Xiaoyu Li, Monica Schenone, Stuart L. Schreiber,
and Steven A. Carr
10 Determination of Kinase Inhibitor Potencies in Cell Extracts
by Competition Binding Assays and Isobaric Mass Tags..................... 141
Carsten Hopf, Dirk Eberhard, Markus Boesche, Sonja Bastuck,
Birgit Dümpelfeld, and Marcus Bantscheff
11 Affinity-Based Profiling of Dehydrogenase Subproteomes.................... 157
Xia Ge and Daniel S. Sem
vii
viii Contents
12 Probing the Specificity of Protein–Protein Interactions
by Quantitative Chemical Proteomics................................... 167
Duangnapa Kovanich, Thin Thin Aye, Albert J.R. Heck,
and Arjen Scholten
13 Fluorescence-Based Proteasome Activity Profiling.......................... 183
Annemieke de Jong, Karianne G. Schuurman, Boris Rodenko,
Huib Ovaa, and Celia R. Berkers
14 Chemical Cross-Linking and High-Resolution Mass Spectrometry
to Study Protein–Drug Interactions.................................... 205
Mathias Q. Müller and Andrea Sinz
15 Monitoring Ligand Modulation of Protein–Protein Interactions by Chemical
Cross-Linking and High-Mass MALDI Mass Spectrometry................... 219
Natalia Gasilova and Alexis Nazabal
16 Time-Controlled Transcardiac Perfusion Crosslinking
for In Vivo Interactome Studies....................................... 231
Amy Hye Won Jeon and Gerold Schmitt-Ulms
Part Iv lIgand dIScovery
17 Ligand Discovery Using Small-Molecule Microarrays....................... 249
Dominick E. Casalena, Dina Wassaf, and Angela N. Koehler
18 Working with Small Molecules: Preparing and Storing Stock
Solutions and Determination of Kinetic Solubility.......................... 265
Andrea Wolf, Satoko Shimamura, and Friedrich B.M. Reinhard
19 A Database for Chemical Proteomics: ChEBI............................. 273
Paula de Matos, Nico Adams, Janna Hastings, Pablo Moreno,
and Christoph Steinbeck
20 Working with Small Molecules: Rules-of-Thumb of “Drug Likeness” ........... 297
Ming-Qiang Zhang
Index............................................................... 309
Contributors
nIco adamS • Department of Genetics, University of Cambridge, Cambridge, UK
thIn thIn aye • Biomolecular Mass Spectrometry and Proteomics Group,
Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands
marcuS bantScheff • Cellzome AG, Heidelberg, Germany
Sonja baStuck • Cellzome AG, Heidelberg, Germany
celIa r. berkerS • Division of Cell Biology II, The Netherlands Cancer Institute,
Amsterdam, The Netherlands
markuS boeSche • Cellzome AG, Heidelberg, Germany
domInIck e. caSalena • Chemical Biology Platform, The Broad Institute of MIT
and Harvard, Cambridge, MA, USA
Steven a. carr • Proteomics platform, The Broad Institute of MIT and Harvard,
Cambridge, MA, USA
SImona g. codreanu • Vanderbilt University School of Medicine, Nashville, TN, USA
annemIeke de jong • Division of Cell Biology II, The Netherlands Cancer Institute,
Amsterdam, The Netherlands
Paula de matoS • European Bioinformatics Institute, Hinxton, UK
mathIaS dreger • caprotec bioanalytics GmbH, Berlin, Germany
gerard dreweS • Cellzome AG, Heidelberg, Germany
bIrgIt dümPelfeld • Cellzome AG, Heidelberg, Germany
dIrk eberhard • Cellzome AG, Heidelberg, Germany
natalIa gaSIlova • CovalX AG, Schlieren, Switzerland; Department of Chemistry
and Applied Biosciences, ETH, Zürich, Switzerland
XIa ge • Chemical Proteomics Facility at Marquette, Department of Chemistry,
Marquette University, Milwaukee, WI, USA
manuela grIdlIng • CeMM Research Center for Molecular Medicine of the Austrian
Academy of Sciences, Vienna, Austria
janna haStIngS • European Bioinformatics Institute, Hinxton, UK
albert j.r. heck • Biomolecular Mass Spectrometry and Proteomics Group,
Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands
carSten hoPf • Cellzome AG, Heidelberg, Germany
amy hye won jeon • Tanz Centre for Research in Neurodegenerative Diseases
and Department of Laboratory Medicine and Pathobiology, University of Toronto,
Toronto, ON, Canada
akIra kawamura • Department of Chemistry, Hunter College of CUNY, New York,
NY, USA
hye-young h. kIm • Vanderbilt University School of Medicine, Nashville, TN, USA
angela n. koehler • Chemical Biology Platform, The Broad Institute of MIT
and Harvard, Cambridge, MA, USA
duangnaPa kovanIch • Biomolecular Mass Spectrometry and Proteomics Group,
Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands
ix
x Contributors
thomaS lenz • caprotec bioanalytics GmbH, Berlin, Germany
XIaoyu lI • Chemical Biology platform, The Broad Institute of MIT and Harvard,
Cambridge, MA, USA
danIel c. lIebler • Vanderbilt University School of Medicine, Nashville, TN, USA
doIna m. mIhaI • Department of Chemistry, Hunter College of CUNY, New York,
NY, USA
Pablo moreno • European Bioinformatics Institute, Hinxton, UK
mathIaS Q. müller • Department of Pharmaceutical Chemistry and Bioanalytics,
Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale),
Germany
aleXIS nazabal • CovalX AG, Schlieren, Switzerland
Shao-en ong • Proteomics Platform, The Broad Institute of MIT and Harvard,
Cambridge, MA, USA
huIb ovaa • Division of Cell Biology II, The Netherlands Cancer Institute,
Amsterdam, The Netherlands
Peter Poot • Institute of Organic Chemistry, RWTH University, Aachen, Germany
ned a. Porter • Vanderbilt University School of Medicine, Nashville, TN, USA
frIedrIch b.m. reInhard • Cellzome AG, Heidelberg, Germany
uwe rIX • CeMM Research Center for Molecular Medicine of the Austrian Academy
of Sciences, Vienna, Austria
borIS rodenko • Division of Cell Biology II, The Netherlands Cancer Institute,
Amsterdam, The Netherlands
chaItanya SaXena • Shantani Proteome Analytics Pvt. Ltd., Pune, MH, India
monIca Schenone • Proteomics platform, The Broad Institute of MIT and Harvard,
Cambridge, MA, USA
gerold SchmItt-ulmS • Tanz Centre for Research in Neurodegenerative Diseases
and Department of Laboratory Medicine and Pathobiology, University of Toronto,
Toronto, ON, Canada
arjen Scholten • Biomolecular Mass Spectrometry and Proteomics Group,
Utrecht University andNetherlands Proteomics Centre, Utrecht, The Netherlands
Stuart l. SchreIber • Chemical Biology Platform & Chemical Biology Program,
The Broad Institute of MIT and Harvard, Cambridge, MA, USA
karIanne g. Schuurman • Division of Cell Biology II, The Netherlands Cancer
Institute, Amsterdam, The Netherlands
danIel S. Sem • Department of Pharmaceutical Sciences, Concordia University
Wisconsin, Mequon, WI, USA
Satoko ShImamura • Cellzome AG, Heidelberg, Germany
andrea SInz • Department of Pharmaceutical Chemistry and Bioanalytics,
Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg,
Halle (Saale), Germany
chrIStoPh SteInbeck • European Bioinformatics Institute, Hinxton, UK
gIulIo SuPertI-furga • CeMM Research Center for Molecular Medicine
of the Austrian Academy of Sciences, Vienna, Austria
dIna waSSaf • Chemical Biology Platform, The Broad Institute of MIT and Harvard,
Cambridge, MA, USA