Applied Biocatalysis: From Fundamental Science to Industrial Applications

This reference book originates from the interdisciplinary research cooperation between academia and industry. In three distinct parts, latest results from basic research on stable enzymes are explained and brought into context with possible industrial applications. Downstream processing technology as well as biocatalytic and biotechnological production processes from global players display the enormous potential of biocatalysts. Application of "extreme" reaction conditions (i.e. unconventional, such as high temperature, pressure, and pH value) - biocatalysts are normally used within a well defined process window - leads to novel synthetic effects. Both novel enzyme systems and the synthetic routes in which they can be applied are made accessible to the reader. In addition, the complementary innovative process technology under unconventional conditions is highlighted by latest examples from biotech industry.

Table of Contents:
List of Contributors XVII Preface XXV Part A Molecular Biology, Enzyme Screening and Bioinformatics 1 1 Engineering Lipases with an Expanded Genetic Code 3 Alessandro De Simone,Michael Georg Hoesl, and Nediljko Budisa 1.1 Introduction 3 1.2 Enzyme Activity of Lipases from Different Sources and Engineering Approaches 4 1.3 Noncanonical Amino Acids in Lipase Design and Engineering 5 1.4 Case Study: Manipulating Proline, Phenylalanine, and Methionine Residues in Lipase 7 1.5 “Unnatural” Lipases Are Able to Catalyze Reactions under Different Hostile Environments 8 1.6 Lipase Engineering via Bioorthogonal Chemistries: Activity and Immobilization 9 1.7 Conclusions and Perspectives 10 References 11 2 Screening of Enzymes: Novel Screening Technologies to Exploit Noncultivated Microbes for Biotechnology 13 Jennifer Chow and Wolfgang R. Streit 2.1 Introduction 13 2.2 Sequence- versus Function-Based Metagenomic Approach to Find Novel Biocatalysts 14 2.3 Alternative Hosts, Metatranscriptomics, and Metaproteomics 25 2.4 Future Perspectives 26 References 27 3 Robust Biocatalysts – Routes to New Diversity 31 Anna Krüger, Skander Elleuche, Kerstin Sahm, and Garabed Antranikian 3.1 Introduction 31 3.2 Metagenomics to Retrieve New Genes from Extremophilic Microorganisms 32 3.3 Microbial Expression Hosts for the Production of Extremozymes 36 3.4 Molecular Biology Approaches for Enzyme Improvement 39 3.5 Conclusions and Future Perspectives 45 References 46 4 Application of High-Throughput Screening in Biocatalysis 53 Xin Ju, Jie Zhang, Kui Chan, Xiaoliang Liang, Junhua Tao, and Jian-He Xu 4.1 Introduction 53 4.2 Discussions 54 4.3 Summary 68 References 68 5 Supporting Biocatalysis Research with Structural Bioinformatics 71 Nadine Schneider, Andrea Volkamer, Eva Nittinger, and Matthias Rarey 5.1 Introduction 71 5.2 Computational Tools to Assist Biocatalysis Research 71 5.3 From Active Site Analysis to Protein Stability Considerations 75 5.4 Applying DoGSiteScorer and HYDE to Biocatalytical Questions 85 5.5 Conclusion and Future Directions 95 Acknowledgments 96 References 97 6 Engineering Proteases for Industrial Applications 101 Ljubica Vojcic, Felix Jakob, Ronny Martinez, Hendrik Hellmuth, Timothy O’Connell, Helge Mühl, Michael G. Lorenz, and Ulrich Schwaneberg 6.1 Proteases in Industry 101 6.2 Serine Proteases and Subtilisins 102 6.3 Proteases as Additives in Laundry Detergents 104 6.4 Engineering B. lentus Alkaline Protease toward Increased Inhibition by Benzylmalonic Acid 105 6.5 Engineering Subtilisin Protease toward Increased Oxidative Resistance 108 6.6 Increasing Protease Tolerance against Chaotropic Agents 111 6.7 Directed Evolution of Subtilisin E toward High Activity in the Presence of Guanidinium Chloride and Sodium Dodecylsulfate 112 6.8 Summary 116 Acknowledgment 116 References 117 Part B Biocatalytic Synthesis 121 7 Biocatalytic Synthesis of Natural Products by O-Methyltransferases 123 Ludger Wessjohann, Anne-Katrin Bauer, Martin Dippe, Jakob Ley, and Torsten Geißler 7.1 Introduction 123 7.2 Classification and Mechanistic Aspects of O-Methyltransferases 124 7.3 Cofactor Dependence and Regeneration 126 7.4 Natural OMT Products in Industrial Applications 129 7.5 OMTs in Biocatalytic Synthesis 132 7.6 Challenges and Perspectives 139 7.7 Conclusions 141 Abbreviations 141 Acknowledgments 142 References 142 8 Biocatalytic Phosphorylation of Metabolites 147 Dominik Gauss, Bernhard Schönenberger, Getachew S. Molla, Birhanu M. Kinfu, Jennifer Chow, Andreas Liese, Wolfgang R. Streit, and Roland Wohlgemuth 8.1 Introduction 147 8.2 Synthetic Aspects of Biocatalytic Phosphorylations 149 8.3 Development of Analytical Methods 152 8.4 Stability of Phosphorylated Metabolites 154 8.5 Phosphate Donors 156 8.6 Emerging Biocatalytic Phosphorylation Reactions 157 8.7 Reaction Engineering for Biocatalytic Phosphorylation Processes 160 8.8 Summary and Outlook 167 References 168 9 Flavonoid Biotechnology – New Ways to High-Added-Value Compounds 179 Ioannis V. Pavlidis, Mechthild Gall, Torsten Geißler, Egon Gross, and Uwe T. Bornscheuer 9.1 Flavonoids 179 9.2 Metabolic Pathways of Flavonoids 182 9.3 Biotechnological Processes for the Production of High-Added-Value Flavonoids 186 9.4 Future Prospects 191 Acknowledgments 192 References 192 10 Transaminases – A Biosynthetic Route for Chiral Amines 199 Henrike Brundiek and Matthias Höhne 10.1 Introduction 199 10.2 Biocatalysts as Attractive Alternatives to Access Enantiopure Chiral Amines 199 10.3 Transaminases as a Biosynthetic Route for Chiral Amines 201 10.4 Amine Transaminases (ATAs) for the Production of Chiral Amines 203 10.5 Kinetic Resolution and Asymmetric Reductive Amination Using ATAs 207 10.6 Outlook 213 Acknowledgment 214 References 214 11 Biocatalytic Processes for the Synthesis of Chiral Alcohols 219 Gao-Wei Zheng, Yan Ni, and Jian-He Xu 11.1 Introduction 219 11.2 Statin Side Chain 220 11.3 o-Chloromandelic Acid and Its Derivatives 226 11.4 Ethyl 2-Hydroxy-4-phenylbutyrate 229 11.5 Ethyl 4-Chloro-3-hydroxybutanoate 230 11.6 3-Quinuclidinol 232 11.7 3-Hydroxy-3-phenylpropanenitrile 235 11.8 Menthol 237 11.9 Halogen-Substituted 1-Phenylethanol 240 11.10 Summary and Outlook 243 References 244 Part C Reaction and Process Engineering 251 12 Inorganic Adsorbents in Enzymatic Processes 253 Ulrich Sohling, Kirstin Suck, Patrick Jonczyk, Friederike Sander, Sascha Beutel, Thomas Scheper, Axel Thiefes, Ute Schuldt, Claudia Aldenhoven, Gabriella Egri, Lars Dähne, Annamaria Fiethen, Hubert Kuhn, Oliver Wenzel, Heike Temme, Bernd Niemeyer, Paul Bubenheim, and Andreas Liese 12.1 Introduction 253 12.2 Porous Inorganic Adsorbents for Enzyme Purification Processes (Alumina, Aluminosilicates, Precipitated Silica) 259 12.3 Immobilization of Phospholipase A1 and A2 for the Degumming of Edible Oils 265 12.4 Immobilization of Alcohol Dehydrogenase ‘A’ and Candida antarctica Lipase B on Precipitated Silica by Layer-by-Layer-Technology 270 12.5 Molecular Modeling Calculations of the ADH-‘A‘ Immobilization onto Polyelectrolyte Surfaces 273 12.6 Application of Clays and Zeolites for Adsorption of Educts and Products of Reactions with Alcohol Dehydrogenase in Aqueous Reaction Media 278 12.7 Product Separation from Complex Mixtures of Biocatalytic Transformations 283 12.8 Continuous Production and Discontinuous Selective Adsorption of Short-Chain Alcohols in a Fixed-Bed Reactor with Alumina Oxides 287 12.9 Summary and Outlook 290 Acknowledgment 291 References 291 13 Industrial Application of Membrane Chromatography for the Purification of Enzymes 297 Sascha Beutel, Louis Villain, and Thomas Scheper 13.1 Introduction 297 13.2 Membrane Adsorber 298 13.3 Case Studies and Used Model Enzymes 301 13.4 Experimental 302 13.5 Case Study 1: Purification of Penicillin G Amidase 302 13.6 Case Study 2: Purification of Cellulase Cel5A 307 13.7 Case Study 3: Purification of Lipase aGTL 310 13.8 Conclusion and Outlook 313 Acknowledgment 313 References 314 14 Fermentation of Lactic Acid Bacteria: State of the Art and New Perspectives 317 Ralf Pörtner, Rebecca Faschian, and Detlef Goelling 14.1 Introduction 317 14.2 Factors Effecting Growth and Productivity of Lactic Acid Bacteria 322 14.3 Fermentation Techniques for Growth and Production 323 14.4 Case Study: Fixed-Bed Reactor with Immobilized Cells 328 14.5 Conclusions 335 Acknowledgment 336 References 337 15 The Bubble Column Reactor: A Novel Reactor Type for Cosmetic Esters 343 Sören Baum, Jakob J. Mueller, Lutz Hilterhaus, Marrit Eckstein, Oliver Thum, and Andreas Liese 15.1 Introduction 343 15.2 Bubble Column Reactor in Comparison to Other Reactor Types 346 15.3 Case Study: Enzymatic Production of Cosmetic Esters 349 15.4 In situ Online Measurements in a Bubble Column Reactor by Means of Fourier Transformed Mid-Infrared Spectroscopy 357 15.5 Summary and Outlook 364 References 365 16 Pharmaceutical Intermediates by Biocatalysis: From Fundamental Science to Industrial Applications 367 Ramesh N. Patel 16.1 Introduction 367 16.2 Boceprevir: Oxidation of 6,6-Dimethyl-3-azabicyclo[3.1.0]hexane by Monoamine Oxidase 367 16.3 Pregabalin: Enzymatic Preparation of (S)-3-Cyano-5-methylhexanoic Acid Ethyl Ester 369 16.4 Glucagon-Like Peptide-1 (GLP-1): Enzymatic Synthesis of (S)-Amino-3-[3-{6-(2-methylphenyl)} pyridyl]-propionic Acid 371 16.5 Rhinovirus Protease Inhibitor: Enzymatic Preparation of (R)-3-(4-Fluorophenyl)-2-hydroxy Propionic Acid 373 16.6 Saxagliptin: Enzymatic Synthesis of (S)-N-boc-3-Hydroxyadamantylglycine 374 16.7 Sitagliptin: Enzymatic Synthesis of Chiral Amine 375 16.8 Montelukast: Enzymatic Reduction for the Synthesis of Leukotriene D (LTD) 4 Antagonists 377 16.9 Clopidogrel: Enzymatic Preparation of (S)-2-Chloromandelic Acid Esters 378 16.10 Calcitonin Gene-Related Peptide Receptors Antagonist: Enzymatic Preparation of (R)-2-Amino-3-(7-methyl-1 H-indazol-5-yl)propanoic Acid 379 16.11 Chemokine Receptor Modulators: Enzymatic Desymmetrization of Dimethyl Ester 381 16.12 Regioselective Enzymatic Acylation of Ribavirin 383 16.13 Atorvastatin: Enzymatic Preparation of (R)-4-Cyano-3-hydroxybutyrate 384 16.14 Atazanavir, Telaprevir, Boceprevir: Enzymatic Synthesis of (S)-Tertiary-leucine 385 16.15 Relenza (Zanamivir): Enzymatic Synthesis of N-Acetylneuraminic Acid 387 16.16 Atorvastatin, Rosuvastatin: Aldolase-Catalyzed Synthesis of Chiral Lactol Intermediates 389 16.17 Anticancer Drugs: Epothilone B and Microbial Hydroxylation of Epothiolone B 390 16.18 Corticotropin-Releasing Factor-1 (CRF-1) Receptor Antagonist: Enzymatic Synthesis of (S)-1-Cyclopropyl-2-methoxyethanamine 392 16.19 Conclusion 393 Acknowledgment 394 References 395 17 Biocatalysis toward New Biobased Building Blocks for Polymeric Materials 405 Katrien Bernaerts, Luuk Mestrom, and Stefaan DeWildeman 17.1 Introduction 405 17.2 Questions and Answers that Lead Us toward Sustainability in Plastic Materials 406 17.3 Criteria and Qualifiers for New Biobased Building Blocks for Plastics Applications 413 17.4 Criteria and Qualifiers for Launching New Biobased Building Blocks for Plastics Applications in New Value Chains 414 17.5 Position of Biobased Building Blocks Innovation in the Plastics Pyramid 414 17.6 Biocatalysis Conversions and Challenges toward newBBBB 415 17.7 Biocatalytic Cascade Reactions to Functional Building Blocks for Materials 423 17.8 Conclusion 424 References 426 Index 429

About the Author :
Dr. Lutz Hilterhaus carried out his studies of chemistry at the University Munster before moving to Hamburg. Having obtained his PhD from the Hamburg University of Technology (TUHH) in the working group of Prof. Liese in 2008, he spent one year with Prof. Bornscheuer at the University Greifswald before taking up the possibility to start as a Junior Group Leader at the Institute of Technical Biocatalysis at the TUHH. Dr. Lutz Hilterhaus finalized his habilitation in 2016 and has authored over 30 scientific publications and has received the "Karl-Heinz-Ditze Preis fur besondere Leistungen in den Ingenieurwissenschaften" in 2008. Dr. Andreas Liese is Professor at the Hamburg University of Technology, where he is head of the Institute of Technical Biocatalysis. He studied chemistry at the University of Bonn, Germany, and carried out his doctoral research at the Research Center Julich, Germany. From 1998 to 2003 he was head of the Enzyme Group within the Institute of Biotechnology II (Prof. Dr. C. Wandrey), Research Center Julich. During a sabbatical in 2000 at Pfizer Global Research & Development, San Diego, USA, he there initiated a R&D group on biocatalysis. From 2003 to 2004 he worked as associate professor at the University of Munster. In 2003 Liese received the Award of Up-and-Coming Teacher in Higher Education in the field of biotechnology (DECHEMA, Germany). Since 2014 he is elected member of the steering committee of the DECHEMA e.V. Dr. Ulrich Kettling is Global Director and Head of Market Segment Industrial Enzymes at Clariant. Before he was Head of Biotechnology R&D and Global Director Biotechnology and Biorefinery at Clariant and Sud-Chemie. Before joining Sud-Chemie, Dr. Kettling was co-founder and Chief Scientific Officer of Direvo Biotech AG. Dr. Kettling graduated in Biotechnology at the Technical University Braunschweig and obtained his PhD at the Max Planck Institute for Biophysical Chemistry in Gottingen. Dr. Garabed Antranikian is Professor at the Hamburg University of Technology, where he is head of the Institute of Technical Microbiology. He studied Biology at the American University in Beirut. At the University of Gottingen he completed his PhD in Microbiology in 1980 in the laboratory of Professor Gerhard Gottschalk and qualified as a post-doctoral lecturer (Habilitation) in 1988. In 1989 he was appointed to a professorship in Microbiology at the Hamburg University of Technology. He was president of the International Society for Extremophiles and is chief editor of the scientific journal Extremophiles. In 2004 he was awarded the most prestigious prize for environment protection by the president of the Federal Republic of Germany. Since 2007 he is the coordinator of the "Biocatalysis2021" Cluster and the "Biorefinery2021" Cluster of the Ministry of Education and Research and he is chairman of IBN Industrial Biotechnology North. Since 2011 he is the president of Hamburg University of Technology.