About the Editors .............................................. XI
List of Contributors ......................................... XIII
1 Catalysis with Cytochrome P450 Monooxygenases ................ 1
Vlada B. Urlacher
1.1 Properties of Cytochrome P450 Monooxygenases ............ 1
1.1.1 General Aspects .................................. 1
1.1.2 Chemistry of Substrate Oxidation by P450
Monooxygenases ................................... 2
1.1.3 Redox Partners of P450 Monooxygenases ............ 4
1.1.4 Major Reactions Catalyzed by P450
Monooxygenases ................................... 5
1.2 Biotechnological Applications of P450 Monooxygenases .... 7
1.2.1 Human P450s in Drug Development .................. 7
1.2.2 Microbial Oxidation for Synthesis of
Pharmaceutical Intermediates ..................... 8
1.2.3 Plant P450s and Transgenic Plants ................10
1.3 Optimization of P450 Monooxygenase-Based Catalytic
Systems ................................................ 12
1.3.1 Replacement or Regeneration of the Cofactor
NAD(P)H ......................................... 12
1.3.2 Engineering of New Substrate Specificities of
P450s ........................................... 14
1.3.2.1 Engineering of Bacterial P450s ......... 14
1.3.2.2 Engineering of Mammalian P450s ......... 16
1.3.3 Stability of P450s .............................. 17
1.3.3.1 Thermostability of P450s ............... 17
1.3.3.2 Process Stability of P450s ............. 17
1.4 Outlook ................................................ 18
References ............................................. 19
2 Biocatalytic Hydrolysis of Nitrites ......................... 27
Dean Brady
2.1 The Problem with Nitrile Hydrolysis .................... 27
2.2 Biocatalysis as a Green Solution ....................... 28
2.3 Nitrile Biocatalysts ................................... 29
2.3.1 Nitrilase ....................................... 29
2.3.2 Nitrile Hydratase ............................... 30
2.3.3 Amidase ......................................... 32
2.4 Synthetic Utility ...................................... 32
2.4.1 Chemoselectivity ................................ 32
2.4.2 Regioselectivity ................................ 33
2.4.3 Enantioselectivity .............................. 33
2.5 Commercial Examples .................................... 35
2.5.1 Chemical Synthesis .............................. 35
2.5.1.1 Acrylamide ............................. 35
2.5.1.2 Nicotinamide and Nicotinic Acid ........ 35
2.5.1.3 Atorvastatin ........................... 36
2.5.1.4 5-Cyanovaleramide ...................... 37
2.5.1.5 Mandelic Acid .......................... 37
2.5.1.6 Pyrazinecarboxylic Acid ................ 38
2.5.1.7 (E)-2-Methyl-2-Butenoic Acid ........... 38
2.5.1.8 l,5-Dimethyl-2-Piperidone, a Lactam .... 38
2.5.1.9 3-Hydroxyvaleric Acid .................. 39
2.5.2 Surface Modification of Polymers ................ 40
2.5.3 Bioremediation .................................. 41
2.6 Challenges ............................................. 41
2.6.1 Biocatalyst Stability ........................... 41
2.6.2 Availability .................................... 43
2.7 Conclusion ............................................. 44
References ............................................. 45
3 Biocatalytic Processes Using Ionic Liquids and
Supercritical Carbon Dioxide ................................ 51
Pedro Lozano, Teresa De Diego, and José L Iborra
3.1 Introduction ........................................... 51
3.2 Biocatalytic Processes in Ionic Liquids ................ 52
3.2.1 Solvent Properties of ILs for Biocatalysis ...... 52
3.2.2 Enzymes in ILs .................................. 54
3.3 Biocatalytic Processes in Supercritical Carbon
Dioxide ................................................ 59
3.3.1 Basic Properties of scCO2 ....................... 59
3.3.2 Enzymes in scCO2 ................................ 61
3.4 Biocatalysis in IL-scCO2 Biphasic Systems .............. 63
3.4.1 Phase Behavior of IL-scCO2 Systems .............. 64
3.4.2 Biocatalytic Processes in IL-scCO2 Biphasic
Systems ......................................... 66
3.5 Future Trends .......................................... 69
References .................................................. 70
4 Thiamine-Based Enzymes for Biotransformations ............... 75
Martina Pohl, Dorte Gocke, and Michael Muller
4.1 Introduction ........................................... 75
4.1.1 Thiamine Diphosphate ............................ 76
4.1.2 Enzyme Structures ............................... 79
4.1.3 Reaction Mechanism .............................. 79
4.1.3.1 Lyase and Carboligase Activity Occur
at the Same Active Site ................ 79
4.2 Carboligation: Chemo- and Stereoselectivity ........... 81
4.2.1 Carboligations with Two Different Aldehydes ..... 81
4.2.1.1 Chemoselectivity ....................... 81
4.2.1.2 Stereoselectivity ...................... 83
4.3 Selected Enzymes ....................................... 84
4.3.1 2-Keto Acid Decarboxylases ...................... 84
4.3.1.1 Pyruvate Decarboxylases ................ 84
4.3.1.2 Branched-Chain Keto Acid
Decarboxylases ......................... 90
4.3.1.3 Benzoylformate Decarboxylases .......... 90
4.3.1.4 Phenylpyruvate Decarboxylases/
Indole-3-pyruvate Decarboxylases ....... 91
4.3.2 Benzaldehyde Lyases ............................. 92
4.3.3 Acetohydroxy Acid Synthases ..................... 94
4.4 Enzymes for Special Products ........................... 94
4.4.1 Mixed Carboligation of Benzaldehyde and
Acetaldehyde .................................... 94
4.4.2 Mixed Carboligation of Larger Aliphatic and
Substituted Aromatic Aldehydes .................. 97
4.4.3 Self-Ligation of Aromatic Aldehydes ............. 97
4.4.4 Self-Ligation of Aliphatic Aldehydes ............ 97
4.4.5 Carboligation of Unstable Aldehydes ............. 98
4.4.5.1 LlKdcA Catalyzes the Mixed
Carboligation of CH-Acidic Aldehydes
and Acetaldehyde ....................... 98
4.4.6 Accessing (S)-2-Hydroxy Ketones ................. 98
4.5 Investigation of Structure-Function Relationships ..... 100
4.5.1 Deducing General Principles for Chemo- and
Enantioselectivity ............................. 100
4.5.2 Substrate Channel .............................. 103
4.5.3 Proton Relay System ............................ 103
4.5.4 Donor Binding Site ............................. 103
4.5.5 Acceptor Binding Site .......................... 104
4.5.5.1 The S-Pocket Approach ................. 105
4.5.5.2 S-Pockets are Widespread Among ThDP-
dependent Enzymes but Not Always
Accessible ............................ 105
4.5.5.3 Carboligation of Two Similar
Aldehydes ............................. 107
References ................................................. 108
5 Baeyer-Villiger Monooxygenases in Organic Synthesis ........ 115
Anett Kirschner and Uwe T. Bornscheuer
5.1 Introduction .......................................... 115
5.2 General Aspects of the Baeyer-Villiger Oxidation ...... 116
5.2.1 Mechanistic Aspects ............................ 116
5.2.2 Chemical Versus Enzymatic Baeyer-Villiger
Oxidation ...................................... 116
5.3 Biochemistry of Baeyer-Villiger Monooxygenases ........ 119
5.3.1 Catalytic Mechanism ............................ 119
5.3.2 Structural Features ............................ 120
5.4 Application of Baeyer-Villiger Monooxygenases in
Organic Chemistry ..................................... 121
5.4.1 Isolated Enzymes Versus Whole Cells ............ 121
5.4.2 Baeyer-Villiger Monooxygenases Relevant for
Synthetic Applications ......................... 124
5.4.3 Representative Synthetic Applications .......... 126
5.4.3.1 Kinetic Resolutions of Racemic
Ketones ............................... 126
5.4.3.2 Desymmetrization of Prochiral
Ketones ............................... 130
5.4.3.3 Regiodivergent Transformations ........ 135
5.4.3.4 Large-Scale Application ............... 138
5.4.3.5 Heteroatom Oxidation .................. 138
5.5 Protein Engineering .............................. 140
5.6 Conclusions and Perspectives ..................... 143
References ................................................. 143
6 Bioreduction by Microorganisms ............................. 151
Leandro Helgueira Andrade and Kaoru Nakamura
6.1 Introduction .......................................... 151
6.2 Enzymes and Coenzymes ................................. 152
6.2.1 Classification ................................. 152
6.2.2 Hydrogen Source ................................ 153
6.2.2.1 Alcohols as a Hydrogen Source for
Reduction ............................. 153
6.2.2.2 Sugars as a Hydrogen Source for
Reduction ............................. 153
6.2.2.3 Formate as a Hydrogen Source for
Reduction ............................. 154
6.2.2.4 Molecular Hydrogen as a Hydrogen
Source for Reduction .................. 154
6.2.2.5 Light Energy as a Hydrogen Source
for Reduction ......................... 155
6.2.2.6 Electric Power as a Hydrogen Source
for Reduction ......................... 155
6.3 Methodologies ......................................... 156
6.3.1 Search for the Ideal Biocatalysts .............. 156
6.3.1.1 Biocatalysts from Screening
Techniques ............................ 157
6.3.1.2 Biocatalysts from Recombinant
Microorganisms ........................ 158
6.3.2 Reaction Systems for Bioreduction .............. 159
6.3.2.1 Bioreduction Using Whole-Cell
Biocatalysts in an Aqueous Solvent .... 160
6.3.2.2 Bioreduction Using Whole-Cell
Biocatalysts in a Conventional
Organic Solvent and an Aqueous-
Organic Solvent ....................... 161
6.3.2.3 Bioreduction Using Whole-Cell
Biocatalysts in Supercritical Carbon
Dioxide, Ionic Liquids and Fluorous
Solvents .............................. 164
6.3.2.4 Bioreduction Using Isolated Enzymes ... 165
6.4 Conclusion ....................................... 167
References ............................................ 167
7 Biotransformations and the Pharma Industry ................. 171
Hans-Peter Meyer, Oreste Ghisalba, and James E.
Leresche
7.1 Introduction .......................................... 171
7.2 Small-Molecule Pharmaceuticals ........................ 172
7.3 The Concept of Green Chemistry ........................ 174
7.4 The Organic Chemistry Toolbox ......................... 176
7.4.1 Small-Molecule Synthesis ....................... 177
7.4.2 Peptide Synthesis .............................. 177
7.4.3 What Should Chemists Consider? ................. 189
7.5 The Enzyme Toolbox (a Selective Analysis) ............. 190
7.5.1 EC 1 Oxidoreductases ........................... 191
7.5.1.1 EC 1.2.1 Dehydrogenases ............... 192
7.5.1.2 EC 1.14.14 P450 Monooxygenases ........ 194
7.5.1.3 EC 1.14.13 Baeyer-Villiger
Monooxygenases ........................ 195
7.5.1.4 EC 1.4.3 Oxidases ..................... 196
7.5.2 EC 2 Transferases .............................. 196
7.5.2.1 EC 2.3 Acyltransferases ............... 196
7.5.2.2 EC 2.4 Glycosyltransferases ........... 196
7.5.2.3 EC 2.6 Transfer of N-Containing
Groups ................................ 197
7.5.2.4 EC 2.7 Phosphotransferases ............ 197
7.5.3 EC 3 Hydrolases ................................ 198
7.5.3.1 EC 3.1.1.1 Esterases and EC
3.1.1.3 Lipases ....................... 199
7.5.3.2 EC 3.2 Glycosidases ................... 200
7.5.3.3 EC 3.3 Reaction with Ether Bonds ...... 201
7.5.3.4 EC 3.4 Peptidases ..................... 201
7.5.3.5 EC 3.5 Reactions with C-N Bonds
Except Peptide Bonds .................. 201
7.5.3.6 EC 3.7 Reactions with C-C Bonds ....... 202
7.5.3.7 EC 3.8 Reactions with Halogen Bonds ... 202
7.5.4 EC 4 Lyases .................................... 202
7.5.4.1 EC 4.2.1 Nitrile Hydratases ........... 202
7.5.4.2 EC 4.3.1.5 Phenylalanine Ammonia
Lyase (PAL) ........................... 202
7.5.4.3 EC 4.1.2 Aldolases .................... 203
7.5.4.4 EC 4.1.2 Hydroxynitrile Lyases
(Oxynitrilases) ....................... 205
7.5.4.5 EC 4.1.1 Decarboxylases ............... 206
7.5.5 EC 5 Isomerases ................................ 206
7.5.6 EC 6 Ligases ................................... 207
7.6 Outlook and Conclusions ............................... 207
References ............................................ 209
8 Hydrogenases and Alternative Energy Strategies ............. 213
Olaf Rüdiger, António L. De Lacey, Victor M. Fernández,
and Richard Cammack
8.1 Introduction: The Future Hydrogen Economy ............. 213
8.1.1 Biological Hydrogen Energy Metabolism .......... 215
8.2 Chemistry of Hydrogenase Catalytic Sites .............. 216
8.2.1 NiFe ........................................... 217
8.2.2 NiFeSe ......................................... 219
8.2.3 FeFe ........................................... 219
8.2.4 Fe (non-Fe-S) Hydrogenase (Hmd) ................ 220
8.2.5 Biosynthesis of the Active Sites ............... 221
8.3 Experimental Approaches ............................... 221
8.3.1 EPR and Related Methods ........................ 222
8.3.2 FTIR Spectroscopy .............................. 222
8.3.3 Protein Film Voltammetry (PFV) ................. 223
8.4 Catalytic Mechanisms of Hydrogenases .................. 224
8.5 Progress So Far with Biological Hydrogen Production
Systems ............................................... 225
8.5.1 Fermentation ................................... 225
8.5.2 Oxygenic Photosynthesis ........................ 226
8.5.3 Anaerobic Photosynthesis ....................... 227
8.5.4 Emulation: Hydrogenase Model Compounds ......... 228
8.5.5 Hydrogenases on Electrodes ..................... 230
8.5.5.1 Sensitivity and Resistance of
Hydrogenases to O2, CO and Other
Inhibitory Gases ...................... 233
8.6 Conclusion and Future Directions ...................... 235
References ............................................ 236
9 PAH Bioremediation by Microbial Communities and
Enzymatic Activities ....................................... 243
Vincenza Andreoni and Liliana Gianfreda
9.1 Introduction .......................................... 243
9.2 Fate of PAHs in the Environment ....................... 244
9.3 Population of РАН-Polluted Environments ............... 246
9.4 Microbial Degradation of PAHs ......................... 248
9.5 Dioxygenases as Key Enzymes in the Aerobic
Degradation of PAHs and Markers of Bacterial
Degradation ........................................... 251
9.6 PAH Transformation by Extracellular Fungal Enzymes .... 254
9.7 In Situ Strategies to Remediate Polluted Soils ........ 257
9.7.1 Intrinsic or Natural Attenuation ............... 257
9.7.2 Biostimulation and Bioaugmentation ............. 258
9.7.3 Phytoremediation ............................... 261
9.7.4 Feasibility of Bioremediation Technologies ..... 264
References ................................................. 265
Index ......................................................... 269
|
