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Biocatalysis

Biocatalysis

Gonzalo de Gonzalo | Pablo Domínguez de María

(2017)

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Book Details

Abstract

Implementing biocatalytic strategies in an industrial setting at a commercial scale is a challenging task, necessitating a balance between industrial need against economic viability. With invited contributions from small and large-scale chemical and pharmaceutical companies, this book bridges the gap between academia and industry. Contributors discuss current processes, types of biocatalysts and improvements, industrial motivation and key aspects to economically succeed. With its focus on industry related issues, this book will be a useful tool for future research by both practitioners and academics.

Table of Contents

Section Title Page Action Price
Cover Cover
Biocatalysis: An Industrial Perspective i
Preface vii
Contents ix
Part I - Context and Challenges for Industrial Biocatalysis 1
Chapter 1 - An Appreciation of Biocatalysis in the Swiss Manufacturing Environment 3
1.1 Introduction 3
1.1.1 Biocatalysis in the Swiss Manufacturing Environment 7
1.1.2 Current Status 7
1.1.3 Patent Analysis 14
1.2 Selected Enzyme Classes Used in the Swiss Manufacturing Environment 16
1.2.1 Oxidoreductases EC1 17
1.2.2 Transferases EC2 22
1.3 Challenges 25
1.3.1 Regulation 25
1.3.1.1 Technical Enzymes 26
1.3.1.2 Food Processing Enzymes 26
1.3.1.3 Feed Enzymes 28
1.3.1.4 Enzymes in Cosmetics 28
1.3.1.5 Enzymes for the Manufacture of APIs 29
1.3.2 Development Time 30
1.3.3 Technological Lock-in 32
1.3.4 Public Perception 32
1.3.5 Education 33
1.4 Opportunities 35
1.4.1 Starting Materials 35
1.4.2 Sustainability and Greenness 36
1.4.3 Swiss Industrial Biocatalysis Consortium 36
1.4.4 New Business Ideas 37
1.5 Future Directions 37
Acknowledgements 39
References 39
Chapter 2 - Biocatalysis – A Greener Alternative in Synthetic Chemistry 44
2.1 Introduction 44
2.2 Motivation for Industry to Use/Research on Biocatalysis 47
2.3 Challenges Faced by Biocatalysis in Industry2 49
2.4 Prospects2,79 52
2.5 Overview of Current Enzyme-based Processes Implemented/In-progress at Industrial, Commercial Scale 52
2.6 Our Experience in Some Chemoenzymatic Projects 56
2.6.1 Protease-mediated Synthesis of Valganciclovir Intermediate135 58
2.6.2 Chemoenzymatic Synthesis of Optically Pure Rivastigmine Intermediate Using ADH from Baker’s Yeast and KRED142,143 58
2.6.3 Preparation of Deoxynojirimycin, Key Intermediate of an Anti-diabetic Drug 60
2.7 Potential Safety Aspects 66
2.8 Conclusions 67
Abbreviations 68
Glossary 68
References 70
Chapter 3 - Biocatalytic Synthesis of Small Molecules – Past, Present and Future 77
3.1 Introduction 77
3.2 Biocatalytic Conversions of Racemates 78
3.2.1 Biocatalytic Resolution of Racemates 79
3.2.2 Biocatalytic Deracemizations 79
3.3 Biocatalytic Desymmetrizations 80
3.4 Biocatalytic Asymmetric Oxidations and Reductions 81
3.4.1 Biocatalytic Asymmetric Oxidations 81
3.4.2 Biocatalytic Asymmetric Reductions 83
3.5 Biocatalytic Asymmetric Hydrolysis and Acylation Reactions 84
3.5.1 Biocatalytic Asymmetric Hydrolysis Reactions 85
3.5.2 Biocatalytic Asymmetric Acylation Reactions 86
3.6 Biocatalytic Asymmetric Transfer Reactions 86
3.7 Biocatalytic Asymmetric Addition and Elimination Reactions 88
3.8 Summary and Outlook 89
References 90
Chapter 4 - EntreChem: Building a Sustainable Business Case in Biotechnology: From Biocatalysis to Synthetic Biology 98
4.1 Introduction 98
4.2 Biocatalysis 99
4.2.1 Enantiopure Chiral Building Blocks 99
4.2.2 Cascade Processes Taking Advantage of Biocatalysis 100
4.3 Drug Development 105
4.3.1 Natural Products in Drug Discovery 105
4.3.2 EntreChem’s Approach to Natural Products Drug Discovery 107
4.3.3 Aureolic Acids: The Quest for Clinically Viable “Mithralogs” 109
4.3.4 Collismycin Analogs as Immunosuppressive and Neuroprotective Drugs 112
4.3.5 Glycosylated Indolocarbazoles as Potent and Selective Kinase Inhibitors 115
4.4 Business Models in Biocatalysis and Natural Products Drug Discovery 117
References 121
Part II - Biocatalysis: from Pharmaceuticals to Bulk Chemistry 125
Chapter 5 - Bristol-Myers Squibb: Preparation of Chiral Intermediates for the Development of Drugs and APIs 127
5.1 Introduction 127
5.2 Anti-Alzheimer's Drug. Enzymatic Preparation of (R)-5,5,5-Trifluoronorvaline 128
5.3 Cholesterol Lowering Agents 130
5.3.1 Enantioselective Enzymatic Acylation of Racemic Alcohol 130
5.3.2 Enzymatic Synthesis of (3S,5R)-Dihydroxy-6-(benzyloxy)hexanoic Acid, Ethyl Ester 131
5.4 Calcitonin Gene-related Peptide Receptors Antagonists (Migraine Treatment): Enzymatic Preparation of (R)-2-Amino-3-(7-methyl-... 132
5.5 Antidiabetic Drugs 134
5.5.1 Saxagliptin: Enzymatic Synthesis of (S)-N-Boc-3-hydroxyadamantylglycine 134
5.5.2 Saxagliptin: Enzymatic Synthesis of N-Cbz-4,5-dehydro-L-prolineamide and N-Boc-4,5-dehydro-L-prolineamide 136
5.5.3 Saxagliptin: Enzymatic Ammonolysis of (5S)-4,5-Dihydro-1H-pyrrole-1,5-dicarboxylic Acid, 1-(1,1-Dimethylethyl)-5-ethyl Este... 137
5.5.4 GLP-1 Receptor Agonists: Enzymatic Preparation of (S)-Amino-3-[3-{6-(2-methylphenyl)}pyridyl]-propionic Acid 138
5.6 Antihypertensive Drugs 140
5.6.1 Enzymatic Synthesis of (S)-6-Hydroxynorleucine 140
5.6.2 Vanlev: Enzymatic Synthesis of Allysine Ethylene Acetal 141
5.6.3 Vanlev: Enzymatic Synthesis of Thiazepine 142
5.6.4 Captopril: Enzymatic Preparation of (S)-3-Benzoylthio-2-methylpropanoic Acid 143
5.7 Antiviral Drugs. Case Study: Atazanavir 144
5.7.1 Atazanavir: Enzymatic Synthesis of (S)-Tertiary-leucine 144
5.7.2 Atazanavir: Enzymatic Preparation of (1S,2R)-[3-Chloro-2-hydroxy-1-(phenylmethyl)propyl]carbamic Acid, 1,1-Dimethyl-ethyl E... 146
5.8 Antianxiety Drug. Buspirones: Enzymatic Preparation of 6-Hydroxybuspirone 147
5.9 Antiviral Drugs. Hepatitis B Viral (HBV) Inhibitor: Enzymatic Asymmetric Hydrolysis and Acetylation 149
5.10 Chemokine Receptor Modulators: Enzymatic Desymmetrization of Dimethyl Ester 150
5.11 Anticancer Drugs 151
5.11.1 Paclitaxel Semisynthetic Process 151
5.11.2 Water-soluble Taxane Derivatives 154
5.11.3 Epothilones: Epothilone B and Epothilone F 155
5.11.4 IGF-1 Receptor Inhibitor: Enzymatic Preparation of (S)-2-Chloro-1-(3-chlorophenyl)ethanol 157
5.11.5 Retinoic Acid Receptor Agonist: Enzymatic Preparation of 2-(R)-Hydroxy-2-(1′,2′,3′,4′-tetrahydro-1′,1′,4′,4′-tetramethyl-6... 158
5.12 Microbial Hydroxylation of Mutilin and Pleuromutilin 158
5.13 Conclusions 160
Acknowledgements 161
References 161
Chapter 6 - Johnson Matthey: A Technology Provider Perspective to Biocatalysis in the Fine Chemicals Industry 168
6.1 Introduction 168
6.2 Commercial Considerations 170
6.2.1 Technology Value 170
6.2.2 Manufacturing 172
6.2.3 Market Analysis 172
6.2.4 Catalyst Portfolio 173
6.3 Technical Considerations 174
6.3.1 Enzyme Recruitment 175
6.3.2 Enzyme Engineering 179
6.3.3 Process Improvement 182
6.4 Conclusions 186
Acknowledgements 188
References 188
Chapter 7 - EnzymeWorks: Recent Advances in Enzyme Engineering for Chemical Synthesis 190
7.1 Introduction to EnzymeWorks 190
7.1.1 Current Status of Biocatalyst Development 191
7.2 Biocatalysis in the Food and Beverage Industry 192
7.2.1 Introduction of Stevia Development 193
7.2.2 Plant Family 1 UDP-glycosyltransferase Applications 194
7.2.3 Chemoenzymatic Synthesis of Rebaudioside M 199
7.2.4 Enzyme Immobilization and Whole Cell Biosynthesis Development 201
7.2.5 Future Perspectives on Biocatalysis in the Food and Beverage Industry 202
7.3 Ketoreductase (KRED) Applications 202
7.3.1 Ibrutinib Development 205
7.3.2 Future Perspectives on Ketoreductase (KRED) Biocatalysis 208
7.4 Biocatalysis in the Antibiotic Industry 208
7.4.1 Introduction to Cephalosporin C Acylase (CCA) 210
7.4.2 Gene Expression, Structure and Catalytic Mechanism of Acylases 212
7.4.3 Recent Advances in Cephalosporin C Acylase (CCA) Development 216
7.4.4 Future Perspectives on Acylase Biocatalysis 217
7.4.5 Introduction to Deacetoxycephalosporin C Synthase 217
7.4.6 Deacetoxycephalosporin C Synthase Structure and Mechanism 219
7.4.7 Recent Advances in Deacetoxycephalosporin C Synthase Development 220
7.4.8 Future Perspectives of Antibiotic Biocatalysis 222
7.5 Future Perspectives of Biocatalyst Development 222
References 223
Chapter 8 - Almac: An Industrial Perspective of Ene Reductase (ERED) Biocatalysis 229
8.1 Introduction 229
8.1.1 Almac Group 229
8.1.2 Biocatalysis at Almac 230
8.1.3 The Rise of Biocatalysis 230
8.2 Introduction to Alkene Reduction 231
8.3 An Introduction to Ene Reductases and How They Work 232
8.4 Examples of Ene Reductase Reactions Reported in the Literature 233
8.4.1 Ene Reductases as Part of a Reaction Sequence 234
8.4.2 Ene Reductases and Solvents 239
8.4.3 Challenges of Co-factor Recycle 240
8.4.4 Avoiding the Use of Nicotinamide Co-factors 241
8.4.5 Impact of Synthetic Biology 245
8.4.6 Ene Reductases in Reverse: Oxidation 247
8.4.7 Thermophilic Ene-reductases 248
8.4.8 Alternative Screening Methods 248
8.5 Example of Utilisation of an ERED at Industrial Scale 249
8.6 Transition of Ene Reductases to Mainstream Biocatalytic Use 251
8.7 Conclusions 252
Acknowledgements 253
References 253
Chapter 9 - GSK: Biocatalyst Discovery and Optimisation 257
9.1 Introduction 257
9.2 Biocatalyst Discovery 260
9.2.1 Design of Enzyme Panels 260
9.2.2 Imine Reductase Panel – Importance and Applicability 260
9.2.2.1 In silico Identification of Novel IREDs 262
9.2.2.2 Panel Composition and Enzyme Production 263
9.2.2.3 Activity Screening for Functional IREDs 265
9.3 Biocatalyst Optimisation 268
9.3.1 Nelarabine Case Study 269
9.3.1.1 Library Design 270
9.3.1.2 Activity Assay 270
9.3.1.3 Results from Mutant Libraries 272
9.4 Conclusions 272
Acknowledgements 273
References 273
Chapter 10 - PETROBRAS: Efforts on Biocatalysis for Fuels and Chemicals Production 276
10.1 PETROBRAS Overview 276
10.2 Hydrolysis of Lignocellulosic and Starchy Biomass 277
10.3 Synthesis of Solvents 280
10.3.1 Glycerol Carbonate 280
10.3.2 Butyl Acetate 281
10.4 Synthesis and Degradation of Polymers 282
10.4.1 Synthesis of Polyesters 282
10.4.2 Depolymerization of Poly(ethylene terephthalate) 284
10.5 Synthesis of Biolubricants 285
10.6 Synthesis of Biodiesel 289
10.7 Concluding Remarks 292
References 292
Chapter 11 - MetGen: Value from Wood – Enzymatic Solutions 298
11.1 Introduction 298
11.1.1 METGEN – Masters of Enzyme Technology and Genetic Engineering 298
11.1.2 Biocatalysis of Wood – Motivation and Challenges 300
11.2 Enzymes in Pulp and Paper 301
11.2.1 Enzymes in Pulp & Paper Industry Sector – Business Aspect 301
11.2.2 Major Enzyme Components for Wood Applications 302
11.2.3 Enzyme Development – from Laboratory to Industry 304
11.2.4 MetZyme® LIGNO™ 305
11.2.5 MetZyme® BRILA™ 309
11.2.6 Concluding Remarks on Enzymes in Pulp and Paper 313
11.3 Biorefinery Enzymes 313
11.3.1 Renewable Chemical Industry Segment – Business Aspect 313
11.3.2 Wood Biorefinery Concept 314
11.3.3 Biomass Hydrolysis – Chemicals and Enzymes 315
11.3.4 Biomass Is Not Oil; It Is More Like Soup of the Day 316
11.3.5 Beyond Sugars 317
11.3.6 Biorefinery Enzymes – Concluding Remarks 320
11.3.7 Wood in Pulp and Paper and Biorefinery – Common Problems or Window for Opportunity 320
Abbreviations 320
References 320
Part III - Biocatalyst Optimization with Industrial Perspectives 323
Chapter 12 - LentiKat’s: Industrial Biotechnology, Experiences and Visions 325
12.1 Introduction 325
12.2 Lentikats Biotechnology 326
12.2.1 Potential of Lentikats Biotechnology 327
12.2.2 Properties of Lentikats Biotechnology 329
12.2.2.1 Advantages of Lentikats Biocatalyst & Lentikats Biotechnology 329
12.2.2.2 Specific Advantages of Lentikats Biocatalysts with Immobilized Whole-cells 330
12.2.2.3 Disadvantages of Lentikats Biocatalyst & Lentikats Biotechnology 330
12.2.3 Production of Lentikats Biocatalyst 330
12.3 Experiences in Wastewater Treatment 331
12.3.1 Municipal Wastewater Treatment 331
12.3.2 Industrial Wastewater Treatment 332
12.3.3 Special Applications 332
12.3.4 Advantages of Lentikats Biotechnology in Wastewater Treatment 332
12.3.5 Product Lines 333
12.3.5.1 Nitrification 333
12.3.5.2 Nitritation 333
12.3.5.3 Denitrification 333
12.3.5.4 Deammonification 334
12.3.5.5 Biological Oxygen Demand (BOD) Removal 334
12.3.5.6 Selective Biodegradations 334
12.3.6 Wastewater Treatment Applications 334
12.3.6.1 Pilot-scale Applications 334
12.3.6.2 Industrial Applications 336
12.4 Experiences in the Pharmaceutical & Food Industry 338
12.4.1 Food Technology Industry 338
12.4.2 Pharmaceutical Industry 338
12.4.3 Bio-based Chemicals Industry 339
12.4.4 Advantages of Lentikats Biotechnology in the Pharmaceutical & Food Industry 339
12.4.5 Application Examples in the Pharmaceutical & Food Industry 339
12.4.5.1 Penicillin G Acylase 339
12.4.5.2 Whole-cell Catalysts 340
12.4.5.3 Monoamine Oxidase 340
12.4.5.4 Baeyer–Villiger Monooxygenase (BVMO) 340
12.4.5.5 Spores 340
12.4.5.6 Oxynitrilase 341
12.4.5.7 β-Galactosidase 341
12.4.5.8 ω-Transaminase 341
12.4.6 Pharmaceutical & Food Applications 342
12.4.6.1 Main Laboratory and Pilot-scale Applications 343
12.4.6.2 Ongoing Projects and Projects in Preparation 343
12.5 Vision 343
References 344
Chapter 13 - EziG: A Universal Platform for Enzyme Immobilisation 345
13.1 Introduction 345
13.2 A General Methodology for Enzyme Reuse 348
13.2.1 The Potential of Biocatalysis by Far Exceeds Its Current Exploitation 348
13.2.2 Unlocking the Potential of Enzymes 349
13.2.3 Immobilised Enzymes for the Pharmaceutical Industry 350
13.2.4 The Reusable Enzyme Utopia – Enzymes Anchored in Space 350
13.2.5 The EziG Technology 351
13.2.6 Standardised Procedure for Immobilisation 354
13.2.7 Lower Cost Materials versus High Performance 354
13.3 Case Studies27 355
13.3.1 In-reactor Enzyme Immobilisation 355
13.3.2 Two-phase System in Flow for in situ Product Removal 356
13.3.3 Candida antarctica Lipase B (CalB) 357
13.3.4 Co-immobilisation for Cascade Reactions 358
13.4 Prospects 359
13.4.1 Stability versus Activity – Replacing Low Cost Catalysts 359
13.4.2 Biocatalysis in Flow – Towards Manufacturing Processes in Continuous Mode 360
13.5 Conclusions 360
Acknowledgements 361
References 361
Chapter 14 - Cross-linked Enzyme Aggregates (CLEAs): From Concept to Industrial Biocatalyst 363
14.1 Introduction: Biocatalysis is Green and Sustainable 363
14.2 Immobilisation of Enzymes 364
14.3 The CLEA Technology 365
14.3.1 The Concept 365
14.3.2 Preparation of CLEAs 366
14.3.2.1 Aggregation 367
14.3.2.2 Cross-linking 367
14.3.2.3 Effect of Additives 368
14.3.2.4 Key Factors Influencing the Cost-effectiveness of CLEAs 368
14.3.2.5 CLEA-polymer Composites 369
14.3.3 Physical Properties of CLEAs 369
14.3.4 Advantages and Limitations of CLEAs 370
14.3.5 Reactor Design 371
14.4 Scope of the CLEA Technology 373
14.4.1 Hydrolase CLEAs 373
14.4.2 Oxidoreductase and Lyase CLEAs 376
14.5 Multi- and Combi-CLEAs 378
14.6 Magnetic CLEAs: The New Frontier 381
14.7 Applications of CLEAs, Combi-CLEAs and mCLEAs 384
14.7.1 1G and 2G Biofuels Production 385
14.7.2 Food and Beverages Processing 387
14.7.3 Synthesis of Semi-synthetic Penicillin and Cephalosporin Antibiotics 388
14.7.4 Removal of Dyes, Pharma Residues and Endocrine Disruptors from Waste Water 389
14.7.5 Other Potential Applications 389
14.8 Conclusions and Future Prospects 390
References 390
Chapter 15 - SynBiocat: Protein Purification, Immobilization and Continuous-flow Processes 397
15.1 Introduction 397
15.2 SynBiocat – From Protein Purification to Continuous-flow Processes 398
15.2.1 Enzyme Production and Purification 400
15.2.1.1 Enzymes at SynBiocat and Fermentia 400
15.2.1.2 Hydrophobic Adsorption-based Protein Separation 400
15.2.1.3 Metal Ion Affinity Based Protein Purification 402
15.2.2 Enzyme Immobilization 405
15.2.2.1 Enzyme Entrapment in Nanostructured Systems 406
15.2.2.1.1\rEnzyme Entrapment in Sol–Gel Matrices.Sol–gel encapsulation of enzymes, which involves the formation of a silica matrix with the... 406
15.2.2.1.2\rEnzyme Entrapment Within Electrospun Nanofibers.Recent developments in nanotechnology have provided a wealth of diverse nano-sca... 408
15.2.2.2 Carrier-free Enzyme Immobilization by Enzyme–Enzyme Cross-linking 410
15.2.2.3 Enzyme Immobilization onto Solid Nano- or Micro-sized Supports 413
15.2.2.3.1\rEnzyme Immobilization on Surface-grafted Silica Supports by Adsorption.Among the many available carrier-based immobilization met... 414
15.2.2.3.2\rEnzyme Immobilization onto Solid Supports by Covalent Bonds.As stated before, when applied under aqueous conditions, enzymes imm... 414
15.2.2.4 Hybrid Immobilization 417
15.2.3 Desktop Bioreactor Applications 418
15.2.3.1 Biotransformations in Packed-bed Minireactors 419
15.2.3.2 Biotransformations in Magnetic Chip Reactors 421
15.3 Conclusion 423
List of Abbreviations 424
Acknowledgements 425
References 425
Part IV - Emerging Industrial Biocatalysis 431
Chapter 16 - Microvi: MicroNiche Engineering™ for Biocatalysis in the Water and Chemical Industries 433
16.1 Introduction to Microvi 433
16.2 Microvi’s MicroNiche Engineering™ Platform 436
16.3 Case Study: MicroNiche Biocatalysts for Water Purification 443
16.4 Producing Case Study: MicroNiche Biocatalysts for Biobased Chemicals 449
16.5 Conclusions 454
References 455
Chapter 17 - Nofima: Peptide Recovery and Commercialization by Enzymatic Hydrolysis of Marine Biomass 459
17.1 Nofima: The Company 459
17.2 Hydrolysis of Marine Biomass 461
17.2.1 Chemical Hydrolysis of Marine Biomass 461
17.2.2 Enzymatic Hydrolysis of Marine Biomass 462
17.3 Enzymes Used for Bioconversion 464
17.4 Quality and Classification of Marine Biomass 465
17.5 Functional Properties and Bioactivities of Hydrolyzed Marine Biomass 466
17.6 Commercialization of Products from Marine Biomass 471
17.7 Conclusions 472
17.8 Case Examples 472
17.8.1 Marealis – Producing a Nutraceutical from Shrimp Peels 472
17.8.2 Polybait AS – Producing Fishing Bait from Fisheries By-products 473
References 473
Chapter 18 - CO2 Solutions: A Biomimetic Approach to Mitigate CO2 Emissions – The Use of Carbonic Anhydrase in an “Industrial Lung” 477
18.1 Introduction 477
18.2 Conventional Post-combustion CO2 Capture Technologies 478
18.3 CSI’ Technology: An Industrial Lung 481
18.4 Selection and Development of a Robust CA 484
18.4.1 Elevated Ionic Strength 485
18.4.2 High pH 486
18.4.3 Temperatures Above 60 °C 486
18.4.4 Effect of High Surface Volume Ratio 486
18.4.5 Effect of High Shear Stress 487
18.4.6 Effect of Contaminants 487
18.4.7 Effect of Solid–Liquid Interface 488
18.4.8 Carbonic Anhydrase Development 488
18.5 Technology Validation/Demonstration at Pilot Scale 491
18.6 Conclusions 494
Acknowledgements 494
References 495
Subject Index 497