I Heinrich Klefenz Industrial Pharmaceutical Biotechnology Industrial Pharmaceutical Biotechnology. Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH ISBNs: 3-527-29995-5 (Hardcover); 3-527-60012-4 (Electronic) III Heinrich Klefenz Industrial Pharmaceutical Biotechnology Industrial Pharmaceutical Biotechnology. Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH ISBNs: 3-527-29995-5 (Hardcover); 3-527-60012-4 (Electronic) IV Dr. Heinrich Klefenz Hauptstr. 35 D-76879 Bornheim Germany This book was carefully produced. Nevertheless, author and publisher do not warrant the informa- tion contained therein to be free of errors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate. Cover illustration: Design by ‘das trio kommunikation und marketing gmbh; Mannheim, München’ Copyright of and reprint permissions granted by American Society for Microbiology (Tables 7.1, 7.2; ref. 502) American Association for the Advancement of Science (Tables: 4.7, ref. 219; 5.1, ref. 224; Figures: 4.1, ref. 154; 4.2, ref. 510; 6.1, ref. 301) Nature Publishing Group (Fig. 1.3, ref. 432; Tables: 1.6, ref. 432; 1.7, ref. 433; 1.8, ref. 436; 1.9, ref. 437; 1.10, ref. 439). Library of Congress Card No.: Applied for. British Library Cataloguing-in-Publication Data: A catalogue record for this book is available from the British Library Die Deutsche Bibliothek Cataloguing-in-Publication Data: A catalogue record for this publication is available from Die Deutsche Bibliothek ISBN 3-527-29995-5 © WILEY-VCH Verlag GmbH, Weinheim (Federal Republic of Germany), 2002 Printed on acid-free paper. All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law. Composition: Manuela Treindl, Regensburg Printing: Strauss Offsetdruck GmbH, Mörlenbach Bookbinding: J. Schäffer GmbH & Co. KG, Grünstadt Printed in the Federal Republic of Germany. Industrial Pharmaceutical Biotechnology. Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH ISBNs: 3-527-29995-5 (Hardcover); 3-527-60012-4 (Electronic) V Preface Biotechnology and its applications in medicine, pharma, and related industries represent one of the most influential developments and pose one of the greatest challenges of the 21 st century, both with respect to its political, societal, and ethical implications and in the search for the fulfillment of its promises for health. Biotechnology is stepping beyond previously insurmountable boundaries in understanding and manipulating life, in the efforts to understand biology, to eradicate disease, to maintain health and vigor, and to endow humans and life forms with desired properties. This book aims to describe a fast-moving subject (or rather a whole interconnected sys- tem of subjects) and, like in optics, some parts of the picture may be blurred and will require further refining. It pulls together topics, which are essential for the realization of the promises of biomedicine – the repertoire of genomics, proteomics, cytomics, bio- informatics, and the interaction of networks – and combines with pertinent methods in nanotechnologies, such as engineering tools to design and construct devices, artificial in- telligence and vision processing for nano-devices, implantates, and for the envisioned swarms of remedial nano-robots. Crucial topics for future therapies are regenerative medicine and the cultivation of tis- sues and organs as well as the underlying genetics and regulatory, developmental, bio- chemical networks. Complex traits, critical in multifactor and degenerative diseases, are being dealt with, with a focus on senescence which forms the background against which numerous degen- erative and acute diseases develop, the elucidation of which will facilitate the strengthening of immune responses, the maintenance of homeostasis and biochemical networks, the pres- ervation of the integrity of genetic and cellular structures. Drug discovery encompasses the identification of molecular structures, the creation of active molecules, and the development of novel comprehensive therapies like immuno- therapy and cellular or organismal therapy with genetically engineered cells. Biotechnology, chemistry, physics provide the tools for target identification, for the cre- ation of new molecular structures, and for the recovery of biologically active molecules provided by the biosphere and efficiency-honed during continuous evolutionary processes. The huge amounts of data and information alone will not be sufficient to lead to new molecular entities and novel therapies, since synthesizing millions of compounds will nei- ther fill the universe of potential molecular structures nor allow the identification of those three-dimensional structures specifically interacting with targets. The knowledge of the biological processes and structures as the templates and targets for the identification of active molecules is indispensable. Biological plus chemical functional information and knowledge of interactions and net- works will be the foundation to which the essential components of creativity and innova- Industrial Pharmaceutical Biotechnology. Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH ISBNs: 3-527-29995-5 (Hardcover); 3-527-60012-4 (Electronic) VI tion (and chance) are to be added as keys for the successful application of the pertinent technologies. The reference list of more than 700 literature citations is meant to underpin the contents and the conclusions of the book’s theme, and to serve as a starting point for delving deeper into individual subjects. Special thanks go to Dr. Hovsep Sarkissian for his support in layout, in the production of figures and tables, in proofreading and the generation of a readable manuscript. Thanks are also due to the staff of Wiley-VCH for their organization, continuous encouragement, and stimulation; and to the ‘Muttersprachler’ who critically read the English manuscript pro- vided and contributed to the professionalism of the writing. Utmost to be thankful for is the patience, understanding, and support of my family and our two children who have tolerated extended periods of negligence. Undoubtedly the rapid development in biotechnology, biomedicine, and supporting tech- nologies, will affect many topics of the book’s field and will necessitate modifying, chang- ing, or complementing the subjects. I have no doubt that in our efforts to fulfill the potential of pharmaceutical biotechnol- ogy, we are on a steep uphill slope and the top of the mountain (control of health, disease, and desired properties) is in the clouds at incalculable but reachable distance. I welcome critical comments or suggestions about the book, proposals for areas to be dealt with in the future, and I am ready to provide further details, information, or references about the various topics upon request. H. Klefenz Bornheim, December 2001 e-mail address: sarkle@t-online.de Preface VII Contents Preface V 1 Introduction to Functional Biotechnology 1 1.1 Scientific and Technological Foundations 1 1.2 Genomics 2 1.3 Proteomics 14 1.4 Cytomics 30 1.5 Micro- and Nanotechnology 32 1.6 Cellular Cloning 42 1.7 Tissue Engineering (Organ Cultivation) 50 1.8 Micro- and Nanotechnologies for Medicine 62 1.9 Structural Genomics 66 2 Organizational Structures 73 2.1 Virtual and Real Enterprises 73 2.2 R & D Networks 74 2.3 Outsourcing 75 2.4 Registrations/Permissions 76 3 Markets and Factors 77 3.1 Products and Services 77 3.2 Economies 77 3.3 Manpower 78 3.4 Resources 78 4 Biotechnology and Medicine 79 4.1 Diagnostics 80 4.2 Therapeutics 80 4.3 Gene Therapy 82 4.4 Implantates 92 4.5 Medical Devices and Technology 93 4.6 Complex Traits 96 Industrial Pharmaceutical Biotechnology. Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH ISBNs: 3-527-29995-5 (Hardcover); 3-527-60012-4 (Electronic) VIII Contents 5 Drug Discovery 117 5.1 Substances Derived from Bacteria, Plants, Insects, and Animals 134 5.2 Sources of Active Principles 135 5.3 Assay Systems and Models (e.g., Knock-out Mice) 140 6 Molecular Pharma-Biotechnology 145 6.1 Bioinformatics 146 6.2 Biological Systems and Models 162 6.3 Assay Systems 167 6.4 High-throughput Screening 170 6.5 Automation 172 6.6 Combinatorial Synthesis: Chemistry, Biology, and Biotechnology 173 6.7 Genotyping: Genetic Pre-Disposition, and Heterogeneity 177 6.8 Sequencing 181 6.9 Pharmaco-Genomics 184 7 Research and Development 195 7.1 Biology, Medicine, and Genetics 195 7.2 Pre-clinical and Clinical Development 195 7.3 Processes 195 7.4 Pilot Plants 196 7.5 Engineering 196 7.6 Fermentation Process Development 196 8 Pharmaceutical Production 201 8.1 GenePharming (Animals and Plants) 203 8.2 Vitamins 208 8.3 Amino Acids 208 8.4 Proteins 209 8.5 Antibiotics 212 8.6 Biocatalysis 219 8.7 Natural Compounds 229 8.8 Recovery/(Bio-) Processing 229 8.9 Chemical–Biotechnological Syntheses 231 8.10 Gene Therapy Vectors/Systems 235 8.11 Production: Safety, Efficacy, Consistency, and Specificity 235 8.12 Registration 238 IXContents 9 Safety 239 9.1 Medical Safety 239 9.2 Biological Safety 239 9.3 Chemical Safety 239 9.4 Equipment Safety 240 10 Environment 241 10.1 Pharmaceuticals and the Environment 241 10.2 Biological Containment 241 10.3 Physical/Chemical Containment 242 10.4 Process-Integrated Environmental Protection 242 10.5 Waste/Effluent Treatment and Recycling 242 11 Ethics 245 12 Companies, Institutes, Networks, and Organizations 247 References 263 Index 303 303Index A AAV vectors 92 active principles 76 aeropyrum pernix 147 ageing 99, 102 Agrobacterium tumefaciens 212 algorithm 138 amplified fragment length polymorphism (AFLP) 4 angiogenesis 45 angiopoietin-1 (Ang-1) 83 animal biotechnology 1 anti-infective therapies 145 anti-infectives 134 antibiotics 212, 213 antibody diversity 142 antibody libraries 19 apoptosis 138, 157 Aspergillus awamori 212 Aspergillus terreus 217 assay systems 167 atherosclerotic vascular disease 53 atomic force microscopy (AFM) 176 autoimmune diseases 142 automation 15 B bait 18 biocatalysis 223, 227 biocavity lasers 93 biochips 1, 20 bioengineering 207 bioinformatics 2, 20, 188 biological systems 19 biomaterials 50 biopharmaceuticals 2 biosensors 20, 138 biosynthesis 137 birth defects 44 bone marrow cell 62 Index C C. elegans 96 Caenorhabditis elegans 96 caloric restriction 97 cancer 2, 102 cancer therapy 70 cardiac hypertrophy 5 cardiovascular diseases 82 caspase 123 catalysis 63 catalysts 2, 64 cDNA libraries 9 cellular cloning 42 cellular signaling pathway 118 channelopathies 167 chemoinformatics 160 chiral 174 chromatin 10, 184 chromosomal architecture 49 chromosomal position 87 clinical studies 91 coagulation factors 93 combinatorial chemistry 172 combinatorial synthesis 172 complex traits 155 complexity 159 computational biology 2 crystal growth 39 crystal structure 49 cystic fibrosis (CF) 89 cytomics 2 D DamID 10 database 3, 160 Deinocaccus radiodurans 149 denaturing gradient gel electrophoresis (DGGE) 178 diabetes 80, 177 diagnostics 1, 80 differential display 186 Industrial Pharmaceutical Biotechnology. Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH ISBNs: 3-527-29995-5 (Hardcover); 3-527-60012-4 (Electronic) 304 Index differential expression profiles 7 differential gene expression 97 differentially expressed genes 101 differentiation 102, 103 digital organisms 158 dimerization 216 diploid 207 direct-write technology 33 discovery genetics 189 discovery genomics 189 disruption phenotypes 7 DNA chips 63 DNA computers 41 DNA detection 65 DNA methylation 10 DNA repair 97 DNA sequences 3 DNA sequencing 88 dopamine 18, 27 droplet micro-dispensing 33 Drosophila 10 Drosophila melanogaster 105 drug design 124 drug discovery 131 Duchenne muscular dystrophy 90 dynamic allele-specific hybridization 13 E e-beam 33 effectors 86 electrokinetic flow 33 embryonic carcinoma (EC) 45 embryonic stem cells (ES) 43, 48 enantioselectivity 208 endoscopes 93 endostatin 85 endothelial growth factor (VEGF) 83 energetic field 40 enhancers 85 enzymes 2, 94 epigenomics 2 Escherichia coli 10 ethics 48, 245 eukaryotic genomes 108 expressed sequence tag (EST) 5 expression profiles 2 expression profiling 6 F Fabry disease 84 factor VII 92 factor VIIa 92 factor VIII 92 factor IX 92 factor Xa 92 factor XIIa 92 fiber optics 32 fibrin 82 field-effect transistors 95 filamentous fungi 211 fluorescence-activated cell sorter (FACS) 7 fluorescence resonance energy transfer 228 fluorescent proteins 167 focused ion beam 33 functional genomics 88 functional interactions 2 G GaAs 93 galactose utilization 202 gene analysis 3 gene arrays 3 gene calling 6 gene clusters 212 gene expression 3, 6 gene expression analysis 15 gene expression profiling 27 gene inactivation 61 gene networks 6 gene profiling 118 gene sequencing 3 gene silencing 124 gene therapy 88 gene transcription 31 gene-based diagnostics 2 genepharming 203 genetic ablation 163 genetic engineering 88 genetic testing 178 genomics 2 genomic imprinting 187 genotyping 146 Girardia tigrina 156 glycoconjugates 127 growth factor 45, 49 H Haematococcus pluvialis 201 Haemophilus influenzae 4 Helicobacter pylori 30 [...]... yeast 85 yeast mutants 7 yeast two-hybrid 15 Z zebra fish 125 Industrial Pharmaceutical Biotechnology Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH 1 ISBNs: 3-5 2 7-2 999 5-5 (Hardcover); 3-5 2 7-6 001 2-4 (Electronic) 1 Introduction to Functional Biotechnology 1.1 Scientific and Technological Foundations Pharmaceutical biotechnology focuses on biotechnology with pharmaceutical relevance as the central... changes effected by biotechnology in combination with pharmaceutical science, cell biology, chemistry, electronics, materials science and technology, plus organizational changes on pharmaceutical research, development and industry as well as pharmaceutical- related animal and plant biotechnology (‘Life Sciences’) Pharmaceutical biotechnology exemplifies the transformation towards a knowledge-based society... domains 18 transmembrane receptors 164 transplantation 43, 162 transplants 44 transposon-tagged proteins 7 transposon-tagging 7 triple-helix-forming oligonucleotides (TFO) 124 trophectoderm (TE) 48 Trypanosoma brucei 126 tumor genotyping 118 tumor growth 136 two-dimensional gel electrophoresis 16 two-hybrid 16 two-hybrid-system 16 tyrosine kinase 118 T tag sequences 7 tagging 21 telomerase 59 telomerase... sources for pharmaceutical development Genomics, the study of the whole genome, requires ever-increasing efficiency in the methods used for gene analysis An automated, high-throughput, systematic cDNA display method called total gene expression analysis (TOGA) was developed TOGA utilizes 8-nucleotide sequences, comprised of a 4-nucleotide restriction endonuclease cleavage site and adjacent 4-nucleotide... wells via N-succinimidyl(4-iodoacetyl)amino benzoate (SIAB) chemistry Primer annealing, extension and termination were performed on at the microliter scale directly in the chip wells in parallel Diagnostic products thus generated were detected in situ by using matrix-assisted laser desorption ionization (MALDI)-MS This miniaturized method has applicability for accurate, high-throughput, low-cost identification... large number of HLA-DR matrices, representing the majority of human HLA-DR peptide-binding specificity These virtual matrices were incorporated in software (TEPITOPE) capable of predicting promiscuous HLA class II ligands This software, in combination with DNA microarray technology, provides for the generation of comprehensive databases of candidate promis- 10 1 Introduction to Functional Biotechnology. .. Although MOF is expressed in both sexes, it only associates with the X chromosome in males Its absence causes male-specific lethality MOF is part of a chromosome-associated complex 12 1 Introduction to Functional Biotechnology comprising male-specific lethal (MSL) proteins and at least one non-coding roX RNA The integration of MOF into the dosage compensation complex is still not understood The association... Once constructed, a high-density SNP map of several hundred thousand markers will be an indispensable tool for genome-wide association studies to identify genes that contribute to disease risk and individual differences in drug response To facilitate large-scale SNP identification, new technologies are being developed to replace gel-based resequencing Highly redundant, sequence-specific oligonucleotide... peptidomimetics 174 Pfiesteria piscicida 183 pharmaceutical companies 170 pharmaco-genomics 2, 185, 186 phenotype-based screens 133 phenotypes 47, 133 phenotypic variation 100 Phormidium laminosum 36 phosphatase 55 photolithography 34 pig cloning 47 plasmon-resonant particles (PRP) 64 pluripotent ES cells 45 pluripotent human stem cells 58 Q quantitative trait loci (QTL) 100 R rapid-prototyping 38 rare diseases 87... Genetic strategies such as the onehybrid assay and phage-display techniques suffer from the inability to detect proteins whose specific binding to a DNA element is dependent upon accessory proteins An approach relying on MALDI time-of-flight (TOF) MS identifies DNA-binding proteins isolated from cell extracts by virtue of their interaction with double-stranded DNA probes immobilized onto small, paramagnetic . I Heinrich Klefenz Industrial Pharmaceutical Biotechnology Industrial Pharmaceutical Biotechnology. Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH ISBNs: 3-5 2 7-2 999 5-5 (Hardcover); 3-5 2 7-6 001 2-4 . 3-5 2 7-6 001 2-4 (Electronic) III Heinrich Klefenz Industrial Pharmaceutical Biotechnology Industrial Pharmaceutical Biotechnology. Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH ISBNs: 3-5 2 7-2 999 5-5 . of Germany. Industrial Pharmaceutical Biotechnology. Heinrich Klefenz Copyright © 2002 Wiley-VCH Verlag GmbH ISBNs: 3-5 2 7-2 999 5-5 (Hardcover); 3-5 2 7-6 001 2-4 (Electronic) V Preface Biotechnology