Proteomics in Drug Research

by Hamacher, Michael; Marcus, Katrin; Stühler, Kai; van Hall, Andre; Warscheid, Bettina; Meyer, Helmut E.; Mannhold, Raimund; Kubinyi, Hugo; Folkers, Gerd

• ISBN13: 9783527312269
• ISBN10: 3527312269
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-03-31
• Publisher: Wiley-VCH

Summary

From skillful handling of the wide range of technologies to successful applications in drug discovery-this handbook has all the information professional proteomics users need.Edited by experts working at one of the hot spots in European proteomic research, the numerous contributions by experts from the pharmaceutical industry and public proteomics consortia to provide the necessary perspective on current trends and developments in this exciting field.Following an introductory chapter, the book moves on to proteomic technologies, such as protein biochips, protein-protein interactions, and proteome analysis in situ. The section on applications includes bioinformatics, Alzheimer's disease, neuroproteomics, plasma and T-cell proteomics, differential phosphoproteome analysis and biomarkers, as well as pharmacogenomics.Invaluable reading for medicinal and pharmaceutical chemists, gene technologists, molecular biologists, and those working in the pharmaceutical industry.

Author Biography

All six editors are Researchers at the Medical Proteom-Center hosted by the University of Bochum (Germany). This international research center was established in 2002 under the leadership of Helmut E. Meyer, a co-founder of the Protagen AG. Professor Meyer is also initiator and coordinator of the Human Brain Proteome Project within the German National Genome Research Net (NGFN) as well as of the Brain Proteome Project within the Human Proteome Organisation (HUPO BPP).

Table of Contents

A Personal Foreword	xiii
Preface	xv
List of Contributors	xvii
I. Introduction	1	(30)
Administrative Optimization of Proteomics Networks for Drug Development	3	(16)
Andre van Hall
Michael Hamacher
Introduction	3	(1)
Tasks and Aims of Administration	4	(2)
Networking	6	(1)
Evaluation of Biomarkers	7	(2)
A Network for Proteomics in Drug Development	9	(1)
Realization of Administrative Networking: the Brain Proteome Projects	10	(9)
National Genome Research Network: the Human Brain Proteome Project	11	(3)
Human Proteome Organisation: the Brain Proteome Project	14	(1)
The Pilot Phase	15	(2)
References	17	(2)
Proteomic Data Standardization, Deposition and Exchange	19	(12)
Sandra Orchard
Henning Hermjakob
Manuela Pruess
Rolf Apweiler
Introduction	19	(2)
Protein Analysis Tools	21	(2)
UniProt	21	(1)
InterPro	22	(1)
Proteome Analysis	22	(1)
International Protein Index (IPI)	23	(1)
Reactome	23	(1)
Data Storage and Retrieval	23	(1)
The Proteome Standards Initiative	24	(1)
General Proteomics Standards (GPS)	24	(1)
Mass Spectrometry	25	(2)
Molecular Interactions	27	(1)
Summary	28	(3)
References	28	(3)
II. Proteomic Technologies	31	(154)
Difference Gel Electrophoresis (DICE): the Next Generation of Two-Dimensional Gel Electrophoresis for Clinical Research	33	(24)
Barbara Sitek
Burghardt Scheibe
Klaus Jung
Alexander Schramm
Kai Stahler
Introduction	34	(2)
Difference Gel Electrophoresis: Next Generation of Protein Detection in 2-DE	36	(21)
Application of CyDye DIGE Minimal Fluors (Minimal Labeling with CyDye DIGE Minimal Fluors)	38	(1)
General Procedure	38	(1)
Example of Use: Identification of Kinetic Proteome Changes upon Ligand Activation of Trk-Receptors	39	(5)
Application of Saturation Labeling with CyDye Dige Saturation Fluors	44	(1)
General Procedure	44	(1)
Example of Use: Analysis of 1000 Microdissected Cells from PanIN Grades for the Identification of a New Molecular Tumor Marker Using CyDye Dige Saturation Fluors	45	(2)
Statistical Aspects of Applying DIGE Proteome Analysis	47	(1)
Calibration and Normalization of Protein Expression Data	48	(2)
Detection of Differentially Expressed Proteins	50	(1)
Sample Size Determination	51	(1)
Further Applications	52	(1)
References	52	(5)
Biological Mass Spectrometry: Basics and Drug Discovery Related Approaches	57	(32)
Bettina Warscheid
Introduction	57	(1)
Ionization Principles	58	(4)
Matrix-Assisted Laser Desorption/Ionization (MALDI)	58	(2)
Electrospray Ionization	60	(2)
Mass Spectrometric Instrumentation	62	(3)
Protein Identification Strategies	65	(2)
Quantitative Mass Spectrometry for Comparative and Functional Proteomics	67	(2)
Metabolic Labeling Approaches	69	(4)
15N Labeling	70	(1)
Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)	71	(2)
Chemical Labeling Approaches	73	(5)
Chemical Isotope Labeling at the Peptide Level	75	(1)
Stable Isotope Labeling at the Peptide Level	75	(3)
Quantitative MS for Deciphering Protein-Protein Interactions	78	(2)
Conclusions	80	(9)
References	81	(8)
Multidimensional Column Liquid Chromatography (LC) in Proteomics--Where Are We Now?	89	(24)
Egidijus Machtejevas
Klaus K. Unger
Reinhard Ditz
Introduction	90	(1)
Why Do We Need MD-LC/MS Methods?	91	(1)
Basic Aspects of Developing a MD-LC/MS Method	92	(8)
General	92	(1)
Issues to be Considered	93	(1)
Sample Clean-up	94	(1)
Choice of Phase Systems in MD-LC	94	(3)
Operational Aspects	97	(1)
State-of-the-Art--Digestion Strategy Included	98	(1)
Multidimensional LC MS Approaches	98	(2)
Applications of MD-LC Separation in Proteomics--a Brief Survey	100	(4)
Sample Clean-Up: Ways to Overcome the ``Bottleneck'' in Proteome Analysis	104	(5)
Summary	109	(4)
References	110	(3)
Peptidomics Technologies and Applications in Drug Research	113	(24)
Michael Schrader
Petra Budde
Horst Rose
Norbert Lamping
Peter Schulz-Knappe
Hans-Dieter Zucht
Introduction	114	(1)
Peptides in Drug Research	114	(6)
History of Peptide Research	114	(2)
Brief Biochemistry of Peptides	116	(1)
Peptides as Drugs	117	(1)
Peptides as Biomarkers	118	(1)
Clinical Peptidomics	118	(2)
Development of Peptidomics Technologies	120	(4)
Evolution of Peptide Analytical Methods	120	(1)
Peptidomic Profiling	121	(2)
Top-Down Identification of Endogenous Peptides	123	(1)
Applications of Differential Display Peptidomics	124	(5)
Peptidomics in Drug Development	124	(3)
Peptidomics Applied to in vivo Models	127	(2)
Outlook	129	(8)
References	130	(7)
Protein Biochips in the Proteomic Field	137	(22)
Angelika Lucking
Dolores J. Cahill
Introduction	137	(2)
Technological Aspects	139	(5)
Protein Immobilization and Surface Chemistry	139	(2)
Transfer and Detection of Proteins	141	(1)
Chip Content	142	(2)
Applications of Protein Biochips	144	(6)
Contribution to Pharmaceutical Research and Development	150	(9)
References	151	(8)
Current Developments for the In Vitro Characterization of Protein Interactions	159	(14)
Daniela Moll
Bastian Zimmermann
Frank Gesellchen
Friedrich W. Herberg
Introduction	160	(1)
The Model System: cAMP-Dependent Protein Kinase	161	(1)
Real-time Monitoring of Interactions Using SPR Biosensors	161	(2)
ITC in Drug Design	163	(2)
Fluorescence Polarization, a Tool for High-Throughput Screening	165	(2)
AlphaScreen as a Pharmaceutical Screening Tool	167	(3)
Conclusions	170	(3)
References	171	(2)
Molecular Networks in Morphologically Intact Cells and Tissue-Challenge for Biology and Drug Development	173	(12)
Walter Schubert
Manuela Friedenberger
Marcus Bode
Introduction	173	(1)
A Metaphor of the Cell	174	(2)
Mapping Molecular Networks as Patterns: Theoretical Considerations	176	(1)
Imaging Cycler Robots	177	(2)
Formalization of Network Motifs as Geometric Objects	179	(3)
Gain of Functional Information: Perspectives for Drug Development	182	(3)
References	182	(3)
III. Applications	185	(134)
From Target to Lead Synthesis	187	(22)
Stefan Mullner
Holger Stark
Paivi Niskanen
Erich Eigenbrodt
Sybille Mazurek
Hugo Fasold
Introduction	187	(3)
Materials and Methods	190	(3)
Cells and Culture Conditions	190	(1)
In Vitro Activity Testing	190	(1)
Affinity Chromatography	190	(1)
Electrophoresis and Protein Identification	191	(1)
BI Acore Analysis	191	(1)
Synthesis of Acyl Cyanides	192	(1)
Methyl 5-cyano-5-oxopentanoate	192	(1)
Methyl 6-cyano-6-oxohexanoate	193	(1)
Methyl-5-cyano-3-methyl-5-oxopentanoate	193	(1)
Results	193	(8)
Discussion	201	(8)
References	203	(6)
Differential Phosphoproteome Analysis in Medical Research	209	(14)
Elke Butt
Katrin Marcus
Introduction	210	(1)
Phosphoproteomics of Human Platelets	211	(5)
Cortactin	213	(1)
Myosin Regulatory Light Chain	213	(1)
Protein Disulfide Isomerase	214	(2)
Identification of cAMP- and cGMP-Dependent Protein Kinase Substrates in Human Platelets	216	(2)
Identification of a New Therapeutic Target for Anti-Inflammatory Therapy by Analyzing Differences in the Phosphoproteome of Wild Type and Knock Out Mice	218	(1)
Concluding Remarks and Outlook	219	(4)
References	220	(3)
Biomarker Discovery in Renal Cell Carcinoma Applying Proteome-Based Studies in Combination with Serology	223	(18)
Barbara Seliger
Roland Kellner
Introduction	224	(1)
Renal Cell Carcinoma	224	(1)
Rational Approaches Used for Biomarker Discovery	225	(1)
Advantages of Different Proteome-Based Technologies for the Identification of Biomarkers	226	(2)
Type of Biomarker	228	(1)
Proteome Analysis of Renal Cell Carcinoma Cell Lines and Biopsies	229	(5)
Validation of Differentially Expressed Proteins	234	(1)
Conclusions	235	(6)
References	235	(6)
Studies of Drug Resistance Using Organelle Proteomics	241	(18)
Catherine Fenselau
Zongming Fu
Introduction	242	(1)
The Clinical Problem and the Proteomics Response	242	(1)
Objectives and Experimental Design	243	(9)
The Cell Lines	243	(1)
Organelle Isolation	244	(1)
Criteria for Isolation	244	(1)
Plasma Membrane Isolation	245	(2)
Protein Fractionation and Identification	247	(2)
Quantitative Comparisons of Protein Abundances	249	(3)
Changes in Plasma Membrane and Nuclear Proteins in MCF-7 Cells Resistant to Mitoxantrone	252	(7)
References	254	(5)
Clinical Neuroproteomics of Human Body Fluids: CSF and Blood Assays for Early and Differential Diagnosis of Dementia	259	(20)
Jens Wiltfang
Piotr Lewczuk
Introduction	259	(1)
Neurochemical Markers of Alzheimer's Disease	260	(11)
β-Amyloid Precursor Protein (β-APP): Metabolism and Impact on AD Diagnosis	261	(2)
Tau Protein and its Phosphorylated Forms	263	(1)
Hyperphosphorylation of Tau as a Pathological Event	264	(1)
Phosphorylated Tau in CSF as a Biomarker of Alzheimer's Disease	265	(1)
Apolipoprotein E (ApoE) Genotype	266	(1)
Other Possible Factors	267	(1)
Combined Analysis of CSF Parameters	267	(3)
Perspectives: Novel Techniques to Search for AD Biomarkers--Mass Spectrometry (MS), Differential Gel Electrophoresis (DIGE), and Multiplexing	270	(1)
Conclusions	271	(8)
References	272	(7)
Proteomics in Alzheimer's Disease	279	(20)
Michael Fountoulakis
Sophia Kossida
Gert Lubec
Introduction	279	(1)
Proteomic Analysis	280	(4)
Sample Preparation	280	(2)
Two-Dimensional Electrophoresis	282	(1)
Protein Quantification	282	(1)
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectroscopy	283	(1)
Proteins with Deranged Levels and Modifications in AD	284	(10)
Synaptosomal Proteins	290	(1)
Guidance Proteins	291	(1)
Signal Transduction Proteins	291	(1)
Oxidized Proteins	292	(1)
Heat Shock Proteins	293	(1)
Proteins Enriched in Amyloid Plaques	293	(1)
Limitations	294	(5)
References	294	(5)
Cardiac Proteomics	299	(20)
Emma McGregor
Michael J. Dunn
Heart Proteomics	300	(7)
Heart 2-D Protein Databases	300	(1)
Dilated Cardiomyopathy	300	(1)
Animal Models of Heart Disease	301	(1)
Subproteomics of the Heart	302	(1)
Mitochondria	302	(2)
PKC Signal Transduction Pathways	304	(1)
Proteomics of Cultured Cardiac Myocytes	305	(1)
Proteomic Characterization of Cardiac Antigens in Heart Disease and Transplantation	306	(1)
Markers of Acute Allograft Rejection	307	(1)
Vessel Proteomics	307	(5)
Proteomics of Intact Vessels	307	(1)
Proteomics of Isolated Vessel Cells	308	(3)
Laser Capture Microdissection	311	(1)
Concluding Remarks	312	(7)
References	312	(7)
IV. To the Market	319	(18)
Innovation Processes	321	(16)
Sven Ruger
Introduction	321	(1)
Innovation Process Criteria	322	(1)
The Concept	322	(1)
Market Attractiveness	323	(1)
Competitive Market Position	323	(1)
Competitive Technology Position	324	(1)
Strengthen the Fit	325	(1)
Reward	325	(1)
Risk	325	(1)
Innovation Process Deliverables for Each Stage	326	(1)
Stage Gate-Like Process	326	(9)
Designation as an Evaluation Project (EvP)	327	(2)
Advancement to Exploratory Project (EP)	329	(2)
For Advancement to Progressed Project (PP)	331	(3)
Advancement to Market Preparation	334	(1)
Conclusion	335	(2)
Subject Index	337