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Green Biocatalysis

Ramesh N. Patel (Editor)
ISBN: 978-1-118-82229-6
792 pages
June 2016
Green Biocatalysis (1118822293) cover image

Description

Green Biocatalysis presents an exciting green technology that uses mild and safe processes with high regioselectivity and enantioselectivity. Bioprocesses are carried out under ambient temperature and atmospheric pressure in aqueous conditions that do not require any protection and deprotection steps to shorten the synthetic process, offering waste prevention and using renewable resources.

Drawing on the knowledge of over 70 internationally renowned experts in the field of biotechnology, Green Biocatalysis discusses a variety of case studies with emphases on process R&D and scale-up of enzymatic processes to catalyze different types of reactions. Random and directed evolution under process conditions to generate novel highly stable and active enzymes is described at length. This book features:

  • A comprehensive review of green bioprocesses and application of enzymes in preparation of key compounds for pharmaceutical, fine chemical, agrochemical, cosmetic, flavor, and fragrance industries using diverse enzymatic reactions
  • Discussion of the development of efficient and stable novel biocatalysts under process conditions by random and directed evolution and their applications for the development of environmentally friendly, efficient, economical, and sustainable green processes to get desired products in high yields and enantiopurity
  • The most recent technological advances in enzymatic and microbial transformations and cuttingedge topics such as directed evolution by gene shuffling and enzyme engineering to improve biocatalysts

 With over 3000 references and 800 figures, tables, equations, and drawings, Green Biocatalysis is an excellent resource for biochemists, organic chemists, medicinal chemists, chemical engineers, microbiologists, pharmaceutical chemists, and undergraduate and graduate students in the aforementioned disciplines.

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Table of Contents

Preface xix

About the Editor xxiii

Contributors xxv

Chapter 1 Biocatalysis and Green Chemistry 1
Roger A. Sheldon

1.1 Introduction to Sustainable Development and Green Chemistry 1

1.2 Green Chemistry Metrics 2

1.3 Environmental Impact and Sustainability Metrics 4

1.4 Solvents 5

1.5 The Role of Catalysis 6

1.6 Biocatalysis and Green Chemistry 6

1.7 Examples of Green Biocatalytic Processes 8

1.8 Conclusions and Future Prospects 13

Chapter 2 Enzymatic Synthesis of Chiral Amines using ω-Transaminases, Amine Oxidases, and the Berberine Bridge Enzyme 17
Eduardo Busto, Robert C. Simon, Nina Richter, and Wolfgang Kroutil

2.1 Introduction 17

2.2 Synthesis of Chiral Amines using ω ]Transaminases 18

2.3 Amine Oxidases 34

2.4 Berberine Bridge Enzymes 50

2.5 Conclusions 52

Chapter 3 Decarboxylation and Racemization of Unnatural Compounds using Artificial Enzymes Derived from Arylmalonate Decarboxylase 59
Kenji Miyamoto

3.1 Introduction 59

3.2 Discovery of a Bacterial α ]Aryl ]α ]Methylmalonate Decarboxylase 61

3.3 Purification and Characterization of the Decarboxylase (Amdase) 61

3.4 Cloning of the Amdase Gene 62

3.5 Stereochemical Course of Amdase ]Catalyzed Decarboxylation 62

3.6 Directed Evolution of Amdase to an Artificial Profen Racemase 63

3.7 Inversion of Enantioselectivity Dramatically Improves Catalytic Activity 65

3.8 Future Prospects 68

Chapter 4 Green Processes for the Synthesis of Chiral Intermediates for the Development of Drugs 71
Ramesh N. Patel

4.1 Introduction 71

4.2 Saxagliptin: Enzymatic Synthesis of (S) ]N ]Boc ]3 ]Hydroxyadamantylglycine 71

4.3 Sitagliptin: Enzymatic Synthesis of Chiral Amine 72

4.4 Vanlev: Enzymatic Synthesis of (S) ]6 ]Hydroxynorleucine 73

4.5 Vanlev: Enzymatic Synthesis of Allysine Ethylene Acetal 74

4.6 Vanlev: Enzymatic Synthesis of Thiazepine 74

4.7 Tigemonam: Enzymatic Synthesis of (S) ]β ]Hydroxyvaline 76

4.8 Autoimmune Diseases: Enzymatic Synthesis of (S) ]Neopentylglycine 76

4.9 Atazanavir: Enzymatic Synthesis of (S) ]Tertiary Leucine 77

4.10 Thrombin Inhibitor (Inogatran): Synthesis of (R) ]Cyclohexylalanine 78

4.11 Gamma Secretase Inhibitor: Enzymatic Synthesis of (R) ]5,5,5 ]Trifluoronorvaline 79

4.12 NK1/NK2 Dual Antagonists: Enzymatic Desymmetrization of Diethyl 3 ][3′,4′ ]Dichlorophenyl] Glutarate 80

4.13 Pregabalin: Enzymatic Synthesis of Ethyl (S) ]3 ]Cyano ]5 ]Methylhexanoate 81

4.14 Chemokine Receptor Modulator: Enzymatic Synthesis of (1S,2R) ]2 ](Methoxycarbonyl)-Cyclohex ]4 ]ene ]1 ]Carboxylic Acid 82

4.15 Enzymatic Synthesis of (3S,5R) ]3 ](Aminomethyl) ]5 ]Methyloctanoic Acid 82

4.16 Atorvastatin (Lipitor): Enzymatic Desymmetrization of 3 ]Hydroxyglutaronitrile 83

4.17 Anticancer Drugs: Enzymatic Synthesis of Taxane Side Chain 84

4.18 Antidiabetic and CNS Drugs: Enzymatic Hydrolysis of Dimethyl Bicyclo[2.2.1] Heptane ]1,4 ]Dicarboxylate 85

4.19 Clopidogrel (Plavix): Enzymatic Preparation of 2 ]Chloromandelic Acid Esters 85

4.20 Antiviral Drug: Regioselective Enzymatic Acylation of Ribavirin 86

4.21 Anticholesterol Drug: Enzymatic Acylation of Alcohol 87

4.22 Saxagliptin: Enzymatic Synthesis of (5S) ]4,5 ]Dihydro ]1H ]Pyrrole ]1,5 Dicarboxylic Acid, 1 ](1,1 ]Dimethylethyl) ]5 ]Ethyl Ester 88

4.23 Montelukast: Synthesis of Intermediate for LTD4 Antagonists 89

4.24 Atazanavir: Enzymatic Synthesis of (1S,2R) ][3 ]Chloro ]2 ]Hydroxy ]1 (Phenylmethyl) Propyl] ]Carbamic Acid,1,1 ]Dimethyl ]Ethyl Ester 90

4.25 Atorvastatin: Enzymatic Synthesis of (R) ]4 ]Cyano ]3 ]Hydroxybutyrate 91

4.26 Antianxiety Drug: Enzymatic Synthesis of 6 ]Hydroxybuspirone 92

4.27 Protease Inhibitor: Enzymatic Synthesis of (R) ]3 ](4 ]Fluorophenyl) ]2 ]Hydroxy Propionic Acid 93

4.28 Dermatological and Anticancer Drugs: Enzymatic Synthesis of 2 ](R) ]Hydroxy ]2 ](1′,2′,3′, 4′ ]Tetrahydro ]1′,1′,4′,4′ ]Tetramethyl ]6′ ]Naphthalenyl) Acetate 94

4.29 Antipsychotic Drug: Enzymatic Reduction of 1 ](4 ]Fluorophenyl)4 ][4 ](5 ]Fluoro ]2 ]Pyrimidinyl)1 ]Piperazinyl] ]1 ]Butanone 95

4.30 Cholesterol ]Lowering Agents: Enzymatic Synthesis of (3S,5R) ]Dihydroxy ]6 ](Benzyloxy) Hexanoic Acid, Ethyl Ester 95

4.31 Antimigraine Drugs: Enzymatic Synthesis of (R) ]2 ]Amino ]3 ](7 ]Methyl ]1H ]Indazol ]5 ]yl) Propanoic Acid 96

4.32 Antidiabetic Drug (GLP ]1 Mimics): Enzymatic Synthesis of (S) ]Amino ]3 ][3 ]{6 ](2 ]Methylphenyl)} Pyridyl] ]Propionic Acid 97

4.33 Ephedrine: Synthesis of (R) ]Phenylacetylcarbinol 98

4.34 Zanamivir: Enzymatic Synthesis of N ]Acetylneuraminic Acid 99

4.35 Epivir: Enzymatic Deamination Process for the Synthesis of (2′R ]cis) ]2′ ]Deoxy ]3 ]Thiacytidine 100

4.36 HMG ]CoA Reductase Inhibitors: Aldolase ]Catalyzed Synthesis of Chiral Lactol 101

4.37 Boceprevir: Oxidation of 6,6 ]Dimethyl ]3 ]Azabicyclo[3.1.0]Hexane by Monoamine Oxidase 102

4.38 Crixivan: Enzymatic Synthesis of Indandiols 103

4.39 Potassium Channel Opener: Preparation of Chiral Epoxide and trans ]Diol 104

4.40 Epothilones (Anticancer Drugs): Epothilone B and Epothilone F 105

4.41 β ]Adrenergic Blocking Agents: Synthesis of Intermediates for Propranolol and Denopamine 106

4.42 Conclusion 106

Chapter 5 Dynamic Kinetic Resolution of Alcohols, Amines, and Amino Acids 115
Jusuk Lee, Yoon Kyung Choi, Jaiwook Park, and Mahn ]Joo Kim

5.1 Introduction 115

5.2 Dynamic Kinetic Resolution of Secondary Alcohols 119

5.3 Dynamic Kinetic Resolution of Amines and Amino Acids 133

5.4 Applications of Dynamic Kinetic Resolution 139

5.5 Summary 145

Appendix: List of Abbreviations 145

Chapter 6 Recent Developments in Flavin-Based Catalysis: Enzymatic Sulfoxidation 149
Patricia B. Brondani, Marco W. Fraaije, and Gonzalo de Gonzalo

6.1 Introduction 149

6.2 Enzymatic Sulfoxidation Catalyzed by Flavoprotein Oxidases 150

6.3 Use of Flavoprotein Monooxygenases for the Synthesis of Chiral Sulfoxides 151

6.4 Asymmetric Sulfoxidation using Flavins as Catalysts 160

6.5 Summary and Outlook 162

Chapter 7 Development of Chemoenzymatic Processes: An Industrial Perspective 165
Rajesh Kumar, Carlos Martinez, Van Martin, and John Wong

7.1 Introduction 165

7.2 Synthetic Route Design and Integration of Biocatalysis 166

7.3 Screening and Biocatalyst Selection 169

7.4 Chemoenzymatic Process Development 169

7.5 Conclusions 176

Chapter 8 Epoxide Hydrolases and their Application in Organic Synthesis 179
Alain Archelas, Gilles Iacazio, and Michael Kotik

8.1 Introduction 179

8.2 Sources and Reaction Mechanism of EHs 181

8.3 Directed Evolution and Genetic Engineering of EHs 183

8.4 Immobilized EHs and Reactions in Nonaqueous Media 186

8.5 Monofunctional Epoxides as Chiral Building Blocks for the Synthesis of Biologically Active Compounds 188

8.6 Preparation of Valuable Chiral Building Blocks for the Synthesis of Biologically Active Compounds Starting from Bifunctional Epoxides 204

8.7 Application to Natural Product Synthesis 210

8.8 Bienzymatic Process Implying One Epoxide Hydrolase 216

8.9 Conclusions 219

Chapter 9 Enantioselective Acylation of Alcohol and Amine Reactions in Organic Synthesis 231
Vicente Gotor ]Fernández and Vicente Gotor

9.1 Introduction 231

9.2 Enantioselective Acylation of Alcohols 234

9.3 Acylation of Amines 248

9.4 Conclusions 260

Chapter 10 Recent Advances in Enzyme-Catalyzed Aldol Addition Reactions 267
Pere Clapés

10.1 Introduction 267

10.2 Pyruvate-Dependent Aldolases 269

10.3 Dihydroxyacetone Phosphate (DHAP)-Dependent Aldolases, d-Fructose-6-Phosphate Aldolase (FSA) and Transaldolases 276

10.4 Threonine Aldolases 287

10.5 Aldol Type Reactions Catalyzed by Non ]Aldolases 293

10.6 Computational De Novo Enzyme Design 294

10.7 Conclusions and Perspectives 295

Chapter 11 Enzymatic Asymmetric Reduction of Carbonyl Compounds 307
Tomoko Matsuda, Rio Yamanaka, and Kaoru Nakamura

11.1 Introduction 307

11.2 Mechanisms 307

11.3 Preparation of Biocatalysts 309

11.4 Solvent Engineering 316

11.5 Examples for Biocatalytic Asymmetric Reductions 317

11.6 Conclusions 325

Chapter 12 Nitrile ]Converting Enzymes and their Synthetic Applications 331
Ludmila Martínková

12.1 Introduction 331

12.2 Screening Methodology 332

12.3 Nitrilases 333

12.4 Nitrile Hydratases 340

12.5 Conclusions 343

Acknowledgements 343

Chapter 13 Biocatalytic Epoxidation for Green Synthesis 351
Hui Lin, Meng ]Yu Xu, Yan Liu, and Zhong ]Liu Wu

13.1 Introduction 351

13.2 Enzymes for Asymmetric Epoxidation 352

13.3 Application of Bioepoxidation in Organic Synthesis 354

13.4 Protein Engineering for Biocatalytic Epoxidation Reaction 362

13.5 Conclusions and Outlook 367

Acknowledgments 368

Chapter 14 Dynamic Kinetic Resolution via Hydrolase–Metal Combo Catalysis 373
Pilar Hoyos, Vittorio Pace, María J. Hernáiz, and Andrés R. Alcántara

14.1 Introduction 373

14.2 DKR of Secondary Alcohols 374

14.3 DKR of Amines 386

14.4 Conclusion 391

Chapter 15 Discovery and Engineering of Enzymes for Peptide Synthesis and Activation 397
Ana Toplak, Muhammad I. Arif, Bian Wu, and Dick B. Janssen

15.1 Introduction 397

15.2 Classification of Enzymes for Peptide Coupling 399

15.3 Serine and Cysteine Proteases for Peptide Synthesis 402

15.4 Protease Discovery 409

15.5 Proteases Engineered for Improved Synthesis 410

15.6 Enzymes for Peptide Terminal Modification 412

15.7 Conclusions 415

Chapter 16 Biocatalysis for Drug Discovery and Development 421
Youyun Liang, Mingzi M. Zhang, Ee Lui Ang, and Huimin Zhao

16.1 Introduction 421

16.2 Single Enzymatic Reactions 423

16.3 Multienzyme Biocatalytic Reactions 437

16.4 Future Perspective: Biocatalysts for the Pharmaceutical Industry 445

16.5 Conclusion 448

Chapter 17 Application of Aromatic Hydrocarbon Dioxygenases 457
Watumesa A. Tan and Rebecca E. Parales

17.1 Introduction 457

17.2 Challenges in Aromatic Hydrocarbon Dioxygenase Applications 457

17.3 Protein Engineering to Improve Enzymatic Activity and Alter Substrate Specificity 459

17.4 Protein Engineering for the Production of Specific Chemicals 464

17.5 Strain Modification for the Development of New Biodegradation Pathways 467

17.6 Phytoremediation: The Expression of Bacterial Dioxygenases in Plant Systems for Bioremediation Purposes 468

17.7 Concluding Remarks 469

Acknowledgments 469

Chapter 18 Ene ]reductases and their Applications 473
Tanja Knaus, Helen S. Toogood, and Nigel S. Scrutton

18.1 Introduction 473

18.2 Substrate Classes and Industrial Applications 474

18.3 Multienzyme Reactions 478

18.4 Alternative Hydride Sources 479

18.5 Improvements of Productivity, Stereoselectivity, and/or Conversion 482

Chapter 19 Recent Developments in Aminopeptidases, Racemases, and Oxidases 489
Yasuhisa Asano, Seiji Okazaki, and Kazuyuki Yasukawa

19.1 Aminopeptidase 489

19.2 Racemase 492

19.3 Amino Acid Oxidase 495

Chapter 20 Biocatalytic Cascades for API Synthesis 503
John M. Woodley

20.1 Introduction 503

20.2 Multienzymatic Biocatalysis 504

20.3 Process Aspects for Multistep Biocatalysis 506

20.4 Process Development 511

20.5 Biocatalytic Cascade Examples 512

20.6 Future Outlook 515

Chapter 21 Yeast-Mediated Stereoselective Synthesis 519
René Csuk

21.1 Introduction 519

21.2 Reductions of Aldehydes and Ketones 521

21.3 Reduction of Thiocarbonyls or Sulfur ]Containing Compounds 524

21.4 Reduction of Functionalized Carbonyl and Dicarbonyl Compounds 524

21.5 Reduction of Keto Esters 527

21.6 Hydrolysis of Esters 529

21.7 Immobilized Baker’s Yeast 530

21.8 Whole ]Cell Biocatalysis in Ionic Liquids and Deep Eutectic Solvents 531

21.9 C„ŸC Bond ]Forming and Breaking Reactions 532

21.10 Miscellaneous Reactions 533

21.11 Conclusions 534

Chapter 22 Biocatalytic Introduction of Chiral Hydroxy Groups using Oxygenases and Hydratases 545
Jun Ogawa, Makoto Hibi, and Shigenobu Kishino

22.1 Introduction 545

22.2 Regio ] and Stereoselective Hydroxylation of Propylbenzene and 3 ]Chlorostyrene by Cytochrome P450 BM ]3 and its Mutant 546

22.3 Regio ] and Stereoselective Hydroxylation of Aliphatic Amino Acids by Fe(Ii)/α ]Ketoglutarate ]Dependent Dioxygenases 547

22.4 Regio ] and Stereoselective Hydration of Unsaturated Fatty Acids by a Novel Fatty Acid Hydratase 551

22.5 Conclusion 553

Acknowledgment 553

Chapter 23 Asymmetric Synthesis with Recombinant Whole ]Cell Catalyst 557
Harald Gröger, Werner Hummel, and Severin Wedde

23.1 Introduction 557

23.2 The Design/Construction of Whole ]Cell Catalysts 558

23.3 Biotransformations with Whole ]Cell Catalysts 561

23.4 Conclusion 581

Chapter 24 Lipases and Esterases as User-Friendly Biocatalysts in Natural Product Synthesis 587
Kenji Mori

24.1 Introduction 587

24.2 Desymmetrization of Prochiral or meso ]Diols and Diacetates 587

24.3 Kinetic Resolution of Racemic Alcohols 592

24.4 Preparation of Enantiopure Intermediate(s) from a Mixture of Stereoisomers 599

24.5 Conclusion 601

Acknowledgments 601

Chapter 25 Hydroxynitrile Lyases for Biocatalytic Synthesis of Chiral Cyanohydrins 603
Romana Wiedner, Helmut Schwab, and Kerstin Steiner

25.1 Introduction 603

25.2 Discovery of Hydroxynitrile Lyases: Bioprospecting 604

25.3 Applications of Hydroxynitrile Lyases 609

25.4 Structural and Mechanistic Aspects 611

25.5 Engineering of Hydroxynitrile Lyases 612

25.6 Reaction Engineering and Reaction Systems 620

25.7 Conclusion 623

Acknowledgment 623

Chapter 26 Biocatalysis: Nitrilases in Organic Synthesis 629
Jin ]Song Gong, Jin ]Song Shi, and Zheng ]Hong Xu

26.1 Introduction 629

26.2 Nitrilase Discovery 630

26.3 Nitrilase Improvement 631

26.4 Applications in Organic Synthesis 635

26.5 Conclusions and Future Prospects 638

Acknowledgments 639

Chapter 27 Biotechnology for the Production of Chemicals, Intermediates, and Pharmaceutical Ingredients 643
Hans ]Peter Meyer

27.1 Introduction 643

27.2 Value Chains and Markets 645

27.3 The Toolbox 661

27.4 Sustainability, Green Premium Pricing, and Subsidies 665

27.5 Regulatory Aspects and Public Perception 667

27.6 Innovation (Not Only in the Laboratory!) 669

27.7 Conclusions 670

Acknowledgments 671

Chapter 28 Microbial Transformations of Pentacyclic Triterpenes 675
Robert Azerad

28.1 Introduction 675

28.2 Typical Biotransformations in the Lupane Family 677

28.3 Typical Biotransformations in the Oleane Family 680

28.4 Typical Biotransformations in the Ursane Family 692

28.5 Microbial Transformations of Other Pts 704

28.6 Glycosylations and Deglycosylations 704

28.7 Conclusion and Perspectives 710

Chapter 29 Transaminases and their Applications 715
Sarah-Marie Dold, Christoph Syldatk, and Jens Rudat

29.1 Introduction 715

29.2 General Properties of Transaminases 715

29.3 Synthesis Strategies with Transaminases 719

29.4 Approaches to Optimize the Transaminase ]Catalyzed Reactions 735

29.5 Conclusion 743

Index 747

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Author Information

Ramesh N. Patel, Ph.D., has 44 years of experience in pharmaceutical and chemical industries. He obtained his Ph.D. in Biochemistry from the University of Texas, Austin, and completed an NIH and ACS Postdoctoral Research Fellowship in Biology from Yale University, New Haven. His professional experience includes working in Bristol-Myers Squibb and ExxonMobil Research and Engineering, where he has a record of achievements including over 175 original publications, 79 process patents, and over 113 invited/external presentations. Dr. Patel is the recipient of the 2004 Biotechnology Lifetime Achievement Award from the American Oil Chemists’ Society, the 2008 Biocat Industrial Research Award from the International Congress on Biocatalysis, and the 2012 Distinction of Academic Award from the International Society of World Academy of Biocatalysis and Agricultural Biotechnology. Currently he is working as a consultant in Biocatalysis and Biotechnology.
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