Biotransformations in Organic Chemistry: A Textbook PDF
Preview Biotransformations in Organic Chemistry: A Textbook
Kurt Faber – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – Biotransformati –o – –n – s– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – in Organic Chemistry – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – A Textbook – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 7th Edition – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – 123 Biotransformations in Organic Chemistry Kurt Faber Biotransformations in Organic Chemistry A Textbook Seventh extended and corrected edition KurtFaber DepartmentofChemistry UniversityofGraz Graz,Austria ISBN978-3-319-61589-9 ISBN978-3-319-61590-5 (eBook) DOI10.1007/978-3-319-61590-5 LibraryofCongressControlNumber:2017944362 ©SpringerInternationalPublishingAG1992,1995,1997,2000,2004,2011,2018 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilarmethodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthis book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained hereinor for anyerrors oromissionsthat may havebeenmade. Thepublisher remainsneutralwith regardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface The use of natural catalysts – enzymes – for the transformation of nonnatural man-made organic compounds is not at all new: they have been used for more than100years,employedeitheraswholecellsorisolatedenzymes[1].Whilethe object of the early research was the elucidation of biochemical pathways and enzyme mechanisms, it was the steep rise of asymmetric synthesis during the 1980s that the enormous potential of enzymes for the synthesis of nonnatural organic compounds was recognized. What started as an academic curiosity in the late1970sbecameahottopicinsyntheticorganicchemistryinthe1990s.Driven by breathtaking developments in molecular biosciences, the search for novel enzymes,theirproduction,andadaptationtoindustrialprocessesarecontinuously simplified,whichisdemonstratedbythewavelikeappearanceofnovelbiocatalytic principles. As a result of this extensive research, there have been an estimated 18,000 papers published on the subject to date. To collate these data as a kind of “super-review” would clearly be an impossible task, and, furthermore, such a hypotheticalbookwouldbeunpalatableforthenon-expert[2–5]. This textbook is written from an organic chemist’s viewpoint to provide a con- densed introduction into biocatalysis and to persuade synthetic chemists to think outside the box and to consider biocatalytic methods as an alternative tool for stereoselective synthesis. By this means, the wide repertoire of synthetic methods hasbeensignificantlywidenedandcomplemented,whichisillustratedbythefactthat theproportionofpapersonasymmetricsynthesisemployingbiocatalyticmethodshas constantly risen from zero in 1970 to about 8% at present. Certainly, biochemical methodsarenotsuperiorinageneralsense–theyarenopanacea–buttheyprovide powerfultoolstocomplement“chemical”methodologyforabroadrangeofhighly selectiveorganictransformations.Syntheticchemistscapableofusingthispotential haveaclearadvantageoverthoselimitedtononbiologicalmethodstotacklethenew generation of synthetic problems at the interface between chemistry and biology, particularlyinviewofthenecessitytouserenewablefeedstocks. In this book, reliable biotransformations, which already had significant impact on organic chemistry, are put to the fore, including industrial-scale showcases. v vi Preface Enzymes possessing great potential but still having to show their reliability are mentionedmorebriefly.Theliteraturecoveredextendstospring2017andspecial credit is given to selected “very old” papers to acknowledge the appearance of novelconcepts.Themostusefulreferencesareselectedfromthepack,andspecial emphasis is placed on reviews and books, which are mentioned during the early paragraphs of each chapter to facilitate rapid access to a specific field if desired. Afterall,Itriedtoavoidwritingabookwiththecharmofatelephonedirectory! The first edition of this book appeared in 1992 and was composed as a mono- graph.Itwasnotonly wellreceivedbyresearchersinthefield butalsoservedasa basisforcoursesinbiotransformationsworldwide.Insubsequenteditions,emphasis was laid on didactic aspects in order to provide the first textbook on biocatalytic methodsfororganicsynthesis,whichservedasaguideatseveralacademicinstitu- tionsforupdatingadustyorganicchemistrycurriculumbyincorporatingbiochemical methods.Theneedtoaccountforthecontinuousemergenceofnovelenzymes and newprotocolstousethempromptedthisupdatedandextendededition. Mygrowingexperienceinteachingbiotransformationsfororganicsynthesis at several universities and research institutions around the world has enabled me to modifythetextofthisseventheditionsoastofacilitateadeeperunderstandingof theprinciples,nottomentionthecorrectionoferrors,whichescapedmyattention duringpreviouseditions.Iamgratefultonumerousunnamedstudentsforpointing themoutandforraisingtoughquestions. IwishtoexpressmydeepgratitudetoStanleyM.Roberts(UK)forundergoingthe laborioustaskofcorrectingthefirsteditionofthisbook.SpecialthanksgotoMichael Müller,MartinaPohl,Wolf-Dieter(Woody)Fessner,(Germany),NickTurner(UK), andBerndNidetzky(Graz)fortheirhelpfulhintsanddiscussions.Thisrevisededition would not havebeen possible withoutthe great assistance ofWolfgangKroutil for pointing out erroneous absolute configurations, J€org Schrittwieser for discussing didactics,GeorgSteinkellnerforgreatenzymepictures,andMelanieHallforpatiently answeringmyignorantquestionsregardingmolecularbiology. Ishallcertainlybepleasedtoreceivecomments,suggestions,andcriticismfrom readersforincorporationinfutureeditions. Graz,Austria KurtFaber Spring2017 References 1.Forthehistoryofbiotransformations,see: Neidleman SG (1990) The archeology of enzymology. In: Abramowicz D (ed)Biocatalysis,VanNostrandReinhold,NewYork,pp1–24 Roberts SM, Turner NJ, Willetts AJ, Turner MK (1995) Introduction to Biocatal- ysis Using Enzymes and Micro-organisms, Cambridge University Press, Cam- bridge,pp1–33 Preface vii 2.Formonographs,see: JonesJB,SihCJ,PerlmanD(eds)(1976)ApplicationsofBiochemicalSystemsin OrganicChemistry,partIandII,Wiley,NewYork Davies HG, Green RH, Kelly DR, Roberts SM (1989) Biotransformations in PreparativeOrganicChemistry,AcademicPress,London Halgas J(1992) Biocatalysts inOrganic Synthesis, Studies inOrganicChemistry, vol46,Elsevier,Amsterdam PoppeL,NovakL(1992)SelectiveBiocatalysis,VerlagChemie,Weinheim Roberts SM, Turner NJ, Willetts AJ, Turner MK (1995) Introduction to Biocatal- ysis Using Enzymes and Micro-organisms, Cambridge University Press, Cambridge BornscheuerUT,KazlauskasRJ(2006)HydrolasesforOrganicSynthesis,2nded., Wiley-VCH,Weinheim Bommarius AS, Riebel B (2004) Biocatalysis, Fundamentals and Applications, Wiley-VCH,Weinheim Grunwald P (2009) Biocatalysis, Biochemical Fundamentals and Applications, ImperialCollegePress,London 3.Forreferencebooks,see: DrauzK,Gr€ogerH,MayO(eds)(2012)EnzymeCatalysisinOrganicSynthesis,3rd edn,3vols,Wiley-VCH,Weinheim Liese A, Seelbach K, Wandrey C (eds) (2006) Industrial Biotransformations, 2nd edn,Wiley-VCH,Weinheim HilterhausL,LieseA,KettlingU,AntranikianG(eds)(2016)AppliedBiocatalysis, Wiley-VCH,Weinheim,Germany. Riva S, Fessner W-D (eds) (2014) Cascade Biocatalysis, Wiley-VCH, Weinheim, Germany. PGrunwald(ed)(2015)IndustrialBiocatalysis,Stanford,Singapore. 4.Foracollectionofpreparativeprocedures,see: Whittall J, Sutton PW (eds) (2010) Practical Methods for Biocatalysis and Bio- transformations,Wiley,Chichester JerominGE,BertauM(2005)Bioorganikum,Wiley-VCH,Weinheim FaberK,FessnerW-D,TurnerNJ(eds)(2015)BiocatalysisinOrganicSynthesis, in:ScienceofSynthesis,3volsThieme,Stuttgart. 5.Fortheapplicationofbiotransformationstostereoselectivesynthesis,see: Patel(ed)(2016)GreenBiocatalysis,Wiley,Hoboken,NJ. TaoJ,LinG-Q,LieseA(eds)(2009)BiocatalysisforthePharmaceuticalIndustry, Wiley,Singapore. TaoJ,KazlauskasR(eds)(2011)BiocatalysisforGreenChemistryandChemical ProcessDevelopment,Wiley,Hoboken,NJ. Goswami A, Stewart JD (eds) (2016) Organic Synthesis Using Biocatalysis, Elsevier,Amsterdam. TurnerN(2017)BiocatalysisinOrganicSynthesis:TheRetrosynthesisApproach, RSC,London. Contents 1 IntroductionandBackgroundInformation. .. . . . . . . . . . . . . . . .. . 1 1.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 CommonPrejudicesAgainstEnzymes. . . . . . . . . . . . . . . . . . . . . 2 1.3 AdvantagesandDisadvantagesofBiocatalysts. . . . . .. . . . . . . .. 3 1.3.1 AdvantagesofBiocatalysts. . . . . . . . . . . . . . . . . . . . . . . 3 1.3.2 DisadvantagesofBiocatalysts. . . . . . . . . . . . . . . . . . . . . 7 1.3.3 IsolatedEnzymesVersusWholeCellSystems. . . . . . . . . 8 1.4 EnzymePropertiesandNomenclature. . . . . . . . . . . . . . . . . . . . . 11 1.4.1 StructuralBiologyinaNutshell. . . . . . . . . . . . . . . . . . . . 11 1.4.2 MechanisticAspectsofEnzymeCatalysis. . . . . . . . . . . . 13 1.4.3 ClassificationandNomenclature. . . . . . . . . . . . . . . . . . . 20 1.4.4 Coenzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 1.4.5 EnzymeSources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 2 BiocatalyticApplications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 2.1 HydrolyticReactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 2.1.1 MechanisticandKineticAspects. . . . . . . . . . . . . . . . . . . 31 2.1.2 HydrolysisoftheAmideBond. . . . . . . . . . . . . . . . . . . . . 49 2.1.3 EsterHydrolysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 2.1.4 HydrolysisandFormationofPhosphateEsters. . . . . . . . . 104 2.1.5 HydrolysisofEpoxides. . . . . . . . . . . . . . . . . . . . . . . . . . 115 2.1.6 HydrolysisofNitriles. . . . . . . . . . . . . . . . . . . . . . . . . . . 124 2.2 ReductionReactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 2.2.1 RecyclingofCofactors. . . . . . . . . . . . . . . . . . . . . . . . . . 134 2.2.2 ReductionofAldehydesandKetonesUsingIsolated Enzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140 2.2.3 ReductionofAldehydesandKetonesUsingWhole Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146 ix x Contents 2.2.4 ReductionofC¼NBonds. . . . . . . . . . . . . . . . . . . . . . . . 156 2.2.5 ReductionofC¼C-Bonds. . . . . . . . . . . . . . . . . . . . . . . . 161 2.3 OxidationReactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 2.3.1 OxidationofAlcoholsandAldehydes. . . . . . . . . . . . . . . . 168 2.3.2 OxidationofAmines. . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 2.3.3 OxygenationReactions. . . . . . . . . . . . . . . . . . . . . . . . . . 173 2.3.4 PeroxidationReactions. . . . . . . . . . . . . . . . . . . . . . . . . . 198 2.4 FormationofCarbon–CarbonBonds. . . . . . . . . . . . . . . . . . . . . . 204 2.4.1 AldolReactions. . . . . . . . . .. . . . . . . . . .. . . . . . . . . .. . 204 2.4.2 Thiamine-DependentAcyloinandBenzoinReactions. . . . 218 2.5 AdditionandEliminationReactions. . . . . . . . . . . . . . . . . . . . . . 224 2.5.1 AdditionofWater. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224 2.5.2 AdditionofAmmonia. . . . . . . . . . . . . . . . . . . . . . . . . . . 227 2.5.3 CyanohydrinFormationandHenry-Reaction. . . . . . . . . . 229 2.5.4 Michael-TypeAdditions. . . . . . . . . . . . . . . . . . . . . . . . . 233 2.6 TransferReactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235 2.6.1 GlycosylTransferReactions. . . . . . . . . . . . . . . . . . . . . . 235 2.6.2 AminoTransferReactions. . . . . . . . . . . . . . . . . . . . . . . . 245 2.7 HalogenationandDehalogenationReactions. . . . . . . . . . . . . . . . 250 2.7.1 Halogenation.. . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . 251 2.7.2 Dehalogenation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261 3 SpecialTechniques. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315 3.1 EnzymesinOrganicSolvents. . . . . . . . . . . . . . . . . . . . . . . . . . . 315 3.1.1 EsterSynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325 3.1.2 LactoneandLactameSynthesis. . . . . . . . . . . . . . . . . . . . 343 3.1.3 AmideSynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344 3.1.4 PeptideSynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 347 3.1.5 PeracidSynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353 3.1.6 RedoxReactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 354 3.1.7 MediumEngineering. . . . . . . . . . . . . . . . . . . . . . . . . . . . 356 3.2 Cascade-Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357 3.3 Immobilization. . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . 369 3.4 ArtificialandModifiedEnzymes. . . . . . . . . . . . . . . . . . . . . . . . . 379 3.4.1 Non-ProteinogenicEnzymeMimics. . . . . . . . . . . . . . . . . 379 3.4.2 ModifiedEnzymes. . .. . . . . . . . .. . . . . . . .. . . . . . . .. . 379 3.4.3 CatalyticAntibodiesandComputationalDe-NovoDesign ofEnzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 386 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389 4 StateoftheArtandOutlook. . .. . . . .. . . . . .. . . . .. . . . .. . . . . .. 407 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 414 Contents xi 5 Appendix. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 415 5.1 BasicRulesforHandlingBiocatalysts. . . . . . . . . . . . . . . . . . . . . 415 5.2 MakeYourOwnEnzymes:SomeGuidelinesforthe Non-specialist. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 418 5.3 Abbreviations. . . .. . . . . .. . . . . . .. . . . . . .. . . . . .. . . . . . .. . 419 5.4 SuppliersofEnzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 420 5.5 MajorCultureCollections. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421 5.6 PathogenicBacteriaandFungi. . . . . . . . . . . . . . . . . . . . . . . . . . 422 Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423
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