Redox Biocatalysis: Fundamentals and Applications

546 Pages·2012·4.007 MB·English

by  Daniela Gamenara, Gustavo A. Seoane, Patricia Saenz?Mendez, Pablo Dominguez de Maria(auth.)

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REDOX BIOCATALYSIS
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REDOX BIOCATALYSIS
FUNDAMENTALS AND APPLICATIONS
Daniela Gamenara
Gustavo A. Seoane
Patricia Saenz-Me´ndez
Pablo Dom´ınguez de Mar´ıa
AJOHNWILEY&SONS,INC.,PUBLICATION
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LibraryofCongressCataloging-in-PublicationData:
Redoxbiocatalysis:fundamentalsandapplications/DanielaGamenara ... [etal.].
p.cm.
Includesbibliographicalreferencesandindex.
ISBN978-0-470-87420-2(cloth)
1.Environmentalchemistry. 2.Environmentalchemistry–Industrialapplications.
3.Oxidation-reductionreaction. 4.Enzymes. I.Gamenara,Daniela,1964–
TD193.R432012
660.6(cid:2)34–dc23
2012025734
PrintedintheUnitedStatesofAmerica.
ISBN:9780470874202
10 9 8 7 6 5 4 3 2 1
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CONTENTS
PREFACE ix
1. EnzymesInvolvedinRedoxReactions:NaturalSourcesand
MechanisticOverview 1
1.1 Motivation:GreenChemistryandBiocatalysis 1
1.2 SourcesofBiocatalysts 2
1.2.1 PlantsandAnimalsasSourcesofRedoxBiocatalysts 3
1.2.2 Wild-TypeMicroorganisms 7
1.2.2.1 Yeasts 7
1.2.2.2 Fungi 8
1.2.2.3 Bacteria 8
1.2.3 MetagenomicAssessments 9
1.3 OverviewofRedoxEnzymes 10
1.3.1 Dehydrogenases 13
1.3.1.1 Zn-DependentDehydrogenases 14
1.3.1.2 Flavin-DependentDehydrogenases 15
1.3.1.3 Pterin-DependentDehydrogenases 16
1.3.1.4 QuinoproteinDehydrogenases 17
1.3.1.5 DehydrogenaseswithoutProstheticGroup 18
1.3.2 Oxygenases 19
1.3.2.1 Monooxygenases 20
1.3.2.2 Dioxygenases 38
1.3.3 Oxidases 50
1.3.3.1 Iron-ContainingOxidases 50
1.3.3.2 Copper-ContainingOxidases 51
1.3.3.3 Flavin-DependentOxidases 56
1.3.4 Peroxidases 61
1.4 ConcludingRemarks 64
References 64
2. NaturalCofactorsandTheirRegenerationStrategies 86
2.1 TypesofNaturalCofactors—Mechanisms 86
2.2 CofactorRegeneration 88
2.2.1 EnzymaticRegenerationofReducedCofactors 88
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vi CONTENTS
2.2.1.1 Substrate-AssistedMethod 88
2.2.1.2 Enzyme-AssistedMethod 89
2.2.2 EnzymaticRegenerationofOxidizedCofactors 92
2.2.3 ChemicalRegenerationofCofactors 94
2.2.4 ElectrochemicalRegenerationofCofactors 95
2.2.5 PhotochemicalRegenerationofCofactors 96
2.3 ConcludingRemarks 97
References 98
3. ReactionsInvolvingDehydrogenases 101
3.1 GeneralConsiderations 101
3.2 ReductionofCarbonylGroups 105
3.2.1 ReductionofAliphaticandAromaticKetones 106
3.2.2 Reductionofα-andβ-ketoEstersandDerivatives 119
3.2.3 ReductionofDiketones 126
3.2.4 ReductionofAldehydes 128
3.3 RacemizationandDeracemizationReactions 130
3.4 PreparationofAmines 135
3.5 ReductionofC–CDoubleBonds 142
3.6 OxidationReactions 152
3.7 Dehydrogenase-CatalyzedRedoxReactionsin
NaturalProducts 159
3.8 ConcludingRemarks 164
References 165
4. ReactionsInvolvingOxygenases 180
4.1 Monooxygenase-CatalyzedReactions 180
4.1.1 HydroxylationofAliphaticCompounds 181
4.1.2 HydroxylationofAromaticCompounds 187
4.1.3 Baeyer–VilligerReactions 189
4.1.3.1 ClassificationandMetabolicRoleofBVMOs 192
4.1.3.2 IsolatedEnzymesversusWhole-CellSystems
(Wild-TypeandRecombinantMicroorganisms) 194
4.1.3.3 SubstrateProfileofAvailableBaeyer–Villiger
Monooxygenases 195
4.1.3.4 SyntheticApplicationsofBVMOs 201
4.1.4 EpoxidationofAlkenes 240
4.2 Dioxygenase-CatalyzedReactions 251
4.2.1 AromaticDioxygenases 251
4.2.1.1 DihydroxylationofAromaticCompounds 251
4.2.1.2 OtherOxidationReactionsPerformedby
AromaticDioxygenases 274
4.2.2 MiscellaneousDioxygenases 279
4.2.2.1 Lipoxygenase 279
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CONTENTS vii
4.3 ConcludingRemarks 285
References 286
5. ReactionsInvolvingOxidasesandPeroxidases 303
5.1 Oxidase-CatalyzedReactions 304
5.1.1 OxidasesActingonC–OBonds 304
5.1.1.1 GalactoseOxidase 304
5.1.1.2 PyranoseOxidase 308
5.1.1.3 AlcoholOxidase 311
5.1.1.4 GlucoseOxidase 313
5.1.1.5 GlycolateOxidase 313
5.1.2 LaccasesandTyrosinases(PhenolOxidases) 315
5.1.2.1 Laccase 315
5.1.2.2 TyrosinaseandOtherPolyphenolOxidases 352
5.1.3 OxidasesActingonC–NBonds 361
5.1.3.1 d-AminoAcidOxidase 361
5.1.3.2 l-AminoAcidOxidase 368
5.1.3.3 MonoamineOxidase 368
5.1.3.4 CopperAmineOxidases 371
5.1.4 Miscellaneous 371
5.1.4.1 CholesterolOxidase 372
5.1.4.2 VanillylAlcoholOxidase 373
5.1.4.3 AlditolOxidase 373
5.2 Peroxidase-CatalyzedReactions 375
5.2.1 PeroxidaseMediatedTransformations 379
5.2.1.1 OxidativeDehydrogenation(2RH + H O →
2 2
2R• + 2H O→R-R) 379
2
5.2.1.2 OxidativeHalogenation(RH + H O +X− +
2 2
H+→RX + 2H O) 385
2
5.2.1.3 Oxygen-TransferReactions(RH + H O →
2 2
ROH + H O) 390
2
5.3 ConcludingRemarks 403
References 404
6. Hydrolase-MediatedOxidations 433
6.1 HydrolasePromiscuityandinsituPeracidFormation.
Perhydrolasesvs.Hydrolases.OtherPromiscuous
Hydrolase-MediatedOxidations 433
6.2 Hydrolase-MediatedBulkOxidationsinAqueousMedia(e.g.,
Bleaching,Disinfection,etc.) 436
6.3 Lipase-MediatedOxidations:PrileshajevEpoxidationsand
Baeyer–VilligerReactions 439
6.4 Hydrolase-MediatedOxidationandProcessingofLignocellulosic
Materials 445
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viii CONTENTS
6.5 ConcludingRemarks 448
References 448
7. BridgingGaps:FromEnzymeDiscoverytoBioprocesses 453
7.1 Context 453
7.2 EnzymeDirectedEvolutionandHigh-Throughput-Screeningof
Biocatalysts 454
7.3 SuccessfulCase:Baker’sYeastRedoxEnzymes,TheirCloning,
andSeparateOverexpression 467
7.4 Whole-Cellsvs.IsolatedEnzymes:MediumEngineering 473
7.5 Beyond:MultistepDominoBiocatalyticProcesses 477
7.6 ConcludingRemarks 482
References 483
8. IndustrialApplicationsofBiocatalyticRedoxReactions:From
AcademicCuriositiestoRobustProcesses 487
8.1 Motivation:DriversforIndustrialBiocatalyticProcesses 487
8.2 KeyAspectsinIndustrialBiocatalyticProcesses 488
8.3 IndustrialBiocatalyticRedoxProcesses:FreeEnzymes 492
8.4 IndustrialBiocatalyticRedoxProcesses—Whole-Cells:The
“DesignerBug”ConceptandBeyond(MetabolicEngineering) 500
8.5 ConcludingRemarksandFuturePerspectives 511
References 516
INDEX 521
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PREFACE
Theuseofenzymesforredoxprocesseshasgainedanincreasinginterestinthelast
decades,becominginmanycases“thefirstchoice”forscoutingnovelindustrialsyn-
theticroutes.Thishasbeenrealizedbysolvingissuesrelatedtocofactorregeneration,
oftenneededfortheseenzymes,togetherwiththedevelopmentsinmolecularbiology
areasthathaveenabledtheprovisionofenzymesinlargeandreproduciblescalein
afermentativesustainablemanner.Thedevelopmentofenvironmentallysoundsyn-
theticprotocolsismandatoryinthiscenturyand,inthisregard,oxidoreductasesare
ideally suited to the task, providing efficient and green alternatives to conventional
synthetic procedures. This is particularly remarkable in oxidative processes, where
oxidases and oxygenases perform clean and selective oxidations by activation of
molecularoxygenwithnoneedofheavymetalsorexpensivechemocatalysts.Onthe
reductive side, these enzymes find ample application in the industry and academia
forthegenerationofenantioenrichedcompounds.
This book provides a comprehensive and updated overview on the use of redox
enzymes and enzyme-mediated oxidative processes. Chapters 1 and 2 provide an
introductiononbiochemicalfeaturesofredoxenzymes,togetherwithaspectsrelated
to cofactors, and cofactor regeneration methods. Chapters 3–5 describe in detail
the biocatalytic applications of different redox enzymes, namely, dehydrogenases
(Chapter 3), oxygenases (Chapter 4), and oxidases and peroxidases (Chapter 5).
Enzyme-mediated oxidative processes based on biocatalytic promiscuity (e.g., of
hydrolases)arecoveredinChapter6.Chapter7focusesonthenecessarystepsstarting
fromthediscoveryofacertainenzymewithacatalyticactivitytoarobustindustrial
process (e.g., directed evolution, high-throughput-screening methods, and medium
engineering).Lastbutnotleast,Chapter8providesanoverviewonindustrialcases
using oxidoreductases, already commercialized or close to, showing that academic
researchisendingupwithsuccessfulcasesattheindustrialarena.Overall,webelieve
that our contribution may well serve as a complete and first approach to academic
and industrial research groups in the field of redox biocatalysis. It is our hope that
readerswillfindthisbookanattractiveandusefultool.
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x PREFACE
Finally,wewouldliketoacknowledgeMs.AnitaLekhwani,SeniorAcquisitions
EditoratJohnWiley&Sons,aswellasthewholeeditorialteamforthetrust,hard
work,interest,andpatiencethattheyhaveputintothisproject.
DanielaGamenara
GustavoSeoane
PatriciaSaenz-Me´ndez
PabloDom´ınguezdeMar´ıa
Montevideo,Uruguay,andAachen,Germany,
December2011
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CHAPTER 1
Enzymes Involved in Redox Reactions:
Natural Sources and Mechanistic
Overview
1.1 MOTIVATION:GREENCHEMISTRYANDBIOCATALYSIS
CurrentenvironmentalconcernsarepressuringChemicalandPharmaceuticalindus-
tries to develop novel synthetic approaches that may operate under more benign
conditions. This trend has paramounted the appearance of the “Green Chemistry”
as a core discipline, with an increasing importance both in academia and industry.
Inanutshell,GreenChemistry—aswellasGreenEngineering—hasbeencompiled
underseveralprinciples,asstatedbyAnastasandZimmerman,andTangandcowork-
ers [1,2]. From the Green Chemistry approach, these principles are gathered in the
acronym“PRODUCTIVELY”:
(cid:2)
Preventwastes
(cid:2)
Renewablematerials
(cid:2)
Omitderivatizationsteps
(cid:2)
Degradablechemicalproducts
(cid:2)
Usesafesyntheticmethods
(cid:2)
Catalyticreagents
(cid:2)
Temperature,ambientpressure
(cid:2)
In-processmonitoring
(cid:2)
Veryfewauxiliarysubstances
(cid:2)
E-factor,maximizefeedinproduct
(cid:2)
Lowtoxicityofchemicalproducts
(cid:2)
Yet,it’ssafe
RedoxBiocatalysis:FundamentalsandApplications,FirstEdition.
DanielaGamenara,GustavoA.Seoane,PatriciaSaenz-Me´ndez,andPabloDom´ınguezdeMar´ıa.
(cid:2)c 2013JohnWiley&Sons,Inc.Published2013byJohnWiley&Sons,Inc.
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