Edited by

Oliver Kayser and

Heribert Warzecha

Pharmaceutical Biotechnology

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Handbook of Pharmaceutical Biotechnology

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ISBN: 978-0-471-21386-4

Edited by Oliver Kayser and Heribert Warzecha

Pharmaceutical Biotechnology

Drug Discovery and Clinical Applications

Second, Completely Revised, and Greatly Enlarged Edition

The Editors

Prof. Dr. Oliver KayserTechnical University DortmundLaboratory of Technical BiochemistryEmil-Figge-Straße 6844227 DortmundGermany

Prof. Dr. Heribert WarzechaTU DarmstadtBiological ScienceSchnittspahnstraße 364287 DarmstadtGermany

Cover250 L Setup, © Rentschler Biotechnologie GmbH

DNA molecule© mauritius images/Science Photos Library

Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty can be created or extended by sales representatives or written sales materials. The Advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.

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Print ISBN: 978-3-527-32994-6ePDF ISBN: 978-3-527-65126-9ePub ISBN: 978-3-527-65125-2mobi ISBN: 978-3-527-65124-5oBook ISBN: 978-3-527-63290-9

Composition Toppan Best-set Premedia Limited, Hong KongPrinting and Binding betz-druck GmbH, DarmstadtCover Design Adam-Design, Weinheim

Printed in the Federal Republic of GermanyPrinted on acid-free paper

V

Contents

Preface XXI ListofContributors XXIII

PartOne ConceptsandMethodsforRecombinantDrugProduction 1

1 PharmaceuticalBiotechnologyandIndustrialApplications–LearningLessonsfromMolecularBiology 3

OliverKayserandHeribertWarzecha1.1 Introduction 31.2 ResearchDevelopments 51.2.1 ProteinEngineering 51.2.2 Muteins 61.2.3 Post-translationalEngineering 71.2.4 SyntheticBiology 91.3 ProductionHostsandUpstream/DownstreamProcessing 101.4 FutureOutlook 11 References 12 Weblinks 13

2 ProkaryoticCellsinBiotechProduction 15 AndriyLuzhetskyy,GabrieleWeitnauer,andAndreasBechthold2.1 Introduction 152.2 ProductionofNaturalProductsbyMicroorganisms 152.2.1 ProductionofLibrariesofNaturalProducts 162.2.2 ProductionofNaturalProductsbyCloningandExpressionof

BiosyntheticGeneClusters 182.2.3 CultureManipulationtoWakeUpSilentGeneClusters 192.2.4 GenomicDrivenApproachestoWakeUpSilentGeneClusters 192.2.5 E. coli,anInterestingHostAlsoforNaturalProductSynthesis 192.2.5.1 ProductionofPolyketidesinE. coli 192.2.5.2 MetabolicEngineeringofE. coliforIsoprenoidBiosynthesis 20

VI Contents

2.2.6 Global-ScaleStrategiesforStrainsImprovement 212.2.6.1 SystemBiology,SystemBiotechnology,and“Omic”

Approaches 212.2.6.2 SyntheticBiologyTools 222.2.6.3 WholeGenomeEngineeringApproaches 242.3 ProkaryotesasProducersofRecombinantTherapeuticProteins 262.3.1 ProkaryoticExpressionSystems 272.3.1.1 HostStrains 272.3.1.2 ExpressionVectors 312.3.2 ProductionSteps 342.3.3 Products 342.3.3.1 Somatropin(Somatotropin,STH,HumanGrowthHormone,

hGH) 342.3.3.2 HumanInsulin 36 References 37

3 MammalianCellsinBiotechProduction 43 MariaJ.DeJesusandFlorianM.Wurm3.1 Introduction 433.2 ProcessConceptsandCells 443.3 CHO-DerivedProductionCellLines 463.4 RapidGenerationofHigh-ProducingCellLines 473.5 Silencing–StabilityofExpression 493.6 High-ThroughputBioprocessDevelopment 503.7 DisposableBioreactors 513.8 TransientGeneExpression(TGE) 523.9 Conclusions 53 References 54

4 BiopharmaceuticalsfromPlants 59 HeribertWarzecha4.1 Introduction 594.2 BasicsinPlantBiotechnology 604.3 PlantCellCulturesasProductionSystemforHuman

Glucocerebrosidase 634.4 InsulinfromSafflower–AUniquePurificationScheme 644.5 FastandScalableTransientTobacco-BasedExpressionSystems 654.6 Conclusion 67 References 68

5 ProductionofBiopharmaceuticalsinTransgenicAnimals 71 HeinerNiemann,AlexanderKind,andAngelikaSchnieke5.1 Introduction 715.2 SitesofProduction 735.2.1 Milk 73

Contents VII

5.2.2 Urine 765.2.3 SeminalFluid 775.2.4 Blood 775.2.5 BirdEggs 785.3 TransgenicConstructs 785.3.1 OrganSpecificExpressionVectors 805.3.2 InducibleExpression 815.3.3 Non-integratingVectors 815.4 MethodsfortheProductionofTransgenicAnimals 825.4.1 PronuclearDNAMicroinjection 835.4.1.1 CollectionofFertilizedEggs 835.4.1.2 PreparationofDNA 835.4.1.3 InjectionofDNA 835.4.1.4 TransferandGestationinRecipients 845.4.1.5 IdentificationofFoundersandSubsequentBreeding 855.4.2 ViralMediatedGeneTransfer 865.4.3 Sperm-MediatedGeneTransfer 885.4.4 Transposon-MediatedGeneTransfer 895.4.5 PluripotentStemCells 905.4.5.1 EmbryonicStemCells 905.4.5.2 EmbryonicGermCells 915.4.5.3 InducedPluripotentStemCells(iPSCells) 925.4.6 SpermatogonialStemCells 935.4.7 SomaticCellNuclearTransfer 945.4.8 HighlySpecificDNAEndonucleases 995.5 AnalysisofTransgenicAnimals 995.5.1 AnalysisofIntegratedTransgenes 1005.5.2 Transgene-ExpressionProfile 1015.5.3 Collection,Processing,andProteinPurification 1015.6 QualityandSafetyoftheProduct 1025.7 ConclusionsandOutlook 104 References 105

6 TranslationofNewTechnologiesinBiomedicines:ShapingtheRoadfromBasicResearchtoDrugDevelopmentandClinicalApplication–andBackAgain 113

MichaelBalls,AndrewBennett,andDavidKendall6.1 DrugDiscoveryandDevelopment 1136.2 TheNatureofModelsandtheNeedforThem 1146.3 NewTechnologiesToolbox 1166.3.1 UseofExistingKnowledge 1176.3.2 In ChemicoandOtherPhysicochemicalApproaches 1186.3.3 In SilicoMethods 1196.3.3.1 In SilicoMethodsandDrugDiscovery 1206.3.3.2 In SilicoMethodsandToxicology 121

VIII Contents

6.3.4 In VitroSystems 1226.3.4.1 CellFractions 1226.3.4.2 CellMonolayerorSupensionCultures 1236.3.4.3 Co-cultures,OrganotypicCultures,andReconstitutedTissue

Constructs 1246.3.4.4 TissueEngineering 1256.3.4.5 StemCells 1256.3.4.6 ExamplesofSomeSpecificIn VitroSystems 1276.3.4.7 DynamicBioreactors 1276.3.4.8 Multi-organSystems 1286.3.4.9 ChallengeofCells,Organs,andOrganismsonaChip 1296.3.4.10 In VitroAssays 1296.3.4.11 CoordinatedApproachwithIn VitroModels:theVitrocellomics

Project 1306.3.5 High-ThroughputScreening 1316.3.6 High-ContentScreening 1316.3.7 OmicsApproaches 1316.3.7.1 VarietyofOmics 1326.3.7.2 ApplicationoftheOmics 1326.3.7.3 HandlingInformationProducedbytheOmics 1336.3.8 SystemsModelingandSimulation 1346.3.8.1 PharmacokineticModeling 1346.3.8.2 VirtualTissueModeling 1356.3.8.3 VirtualPatientPopulations 1366.3.9 Biomarkers 1366.3.10 ClinicalImaging 1386.3.11 Bioinformatics 1406.4 StrategicUseoftheNewTechnologyTools 1416.4.1 TheTools 1426.4.2 TheStrategies 1426.4.3 SystemsBiology 1436.4.4 InvolvingthePatient 1446.5 TranslationasaTwo-WayProcess 1456.6 ConcludingComment 146 References 147

PartTwo BringingtheDrugintoAction–FromDownstreamingtoApproval 153

7 OverviewandClassificationofApprovedRecombinantDrugs 155 TheoDingermannandIlseZündorf7.1 Introduction 1557.2 ClassificationofRecombinantDrugsfromaTechnicalPoint

ofView 166

Contents IX

7.3 ExpressionSystems 1677.4 ProteinsDerivedfromModifiedGenes 1707.5 ArtificialProteins 1717.6 Post-expressionModificationsofRecombinantProteins 1737.7 Biosimilars 174 References 177

8 DownstreamProcessing 179 UweGottschalk8.1 Introduction 1798.2 GeneralPrinciplesofDSP 1808.3 Clarification 1818.3.1 Centrifugation 1818.3.2 Filtration 1828.3.3 IncreasingtheEfficiencyofClarification 1858.4 Chromatography 1878.4.1 ColumnChromatography 1878.4.2 MembraneChromatography 1888.4.3 CaptureChromatography 1898.4.4 PolishingChromatography 1918.4.5 ContinuousChromatography 1938.5 Ultrafiltration/Diafiltration,andVirusFiltration 1948.5.1 Ultrafiltration/Diafiltration 1948.5.2 VirusFiltration 1958.6 Crystallization 1968.7 RecentDevelopmentsinDownstreamProcessing 196 References 197

9 CharacterizationofRecombinantProteins 201 ChristophGiese,HenningvonHorsten,andStefanZietze9.1 Introduction 2019.2 PhysicalChemicalCharacterization 2019.2.1 SpectroscopicMethods 2019.2.1.1 UltravioletAbsorptionSpectroscopy 2019.2.1.2 FluorescenceSpectroscopy 2029.2.1.3 FourierTransformInfraredSpectroscopy 2039.2.2 ChromatographicMethods 2059.2.2.1 Size-ExclusionChromatography 2059.2.2.2 Reversed-PhaseChromatography 2069.2.2.3 HydrophilicInteractionChromatography 2079.2.2.4 Ion-ExchangeChromatography 2079.2.3 ElectrophoreticMethods 2089.2.3.1 GelElectrophoresis 2089.2.3.2 CapillaryElectrophoresis 2099.2.4 OtherPhysicalChemicalMethods 210

X Contents

9.2.5 MassSpectrometricAnalysisofBiopharmaceuticalProteins 2119.2.5.1 OperatingPrincipleofMassSpectrometers 2119.2.5.2 CommonMethodsforMSAnalysisofBiopharmaceuticals 2159.3 BiologicalCharacterizationofBiopharmaceuticalsIn Vitro 2199.3.1 Bioassays 2199.3.1.1 Introduction 2199.3.1.2 DefiningBioactivity 2219.3.1.3 BindingAssays 2229.3.1.4 BeadArrayTechnology 2249.3.1.5 ImmunogenicityTesting 2249.3.1.6 Cell-BasedAssays(CBA) 2259.3.1.7 AssayQualificationandValidation 2309.3.1.8 Outlook 231 Acknowledgments 232 Legals 232 References 232

10 FormulationStrategiesforRecombinantProteinandRelatedBiotechDrugs 235

GerhardWinterandJuliaMyschik10.1 Introduction 23510.2 FormulationandStabilityofProteinSolutions 23510.2.1 DryFormulations 23810.2.2 ModernFormulationScreeningStrategies 23910.2.3 Analytics 24010.2.4 FormulationDevelopmentfortheMarket 24110.2.5 InterfacebetweenDownstreamingand“FillandFinish” 24210.2.6 HighlyConcentratedProteinFormulations 24310.2.7 NewProteinsandRelatedFormulationAspects 24410.2.8 Summary 24410.3 FormulationofVaccines 24510.3.1 Analytics 247 References 248

11 DrugApprovalintheEuropeanUnionandUnitedStates 257 GaryWalsh11.1 Introduction 25711.2 RegulationwithintheEuropeanUnion 25711.2.1 EURegulatoryFramework 25711.2.2 EMA 25911.2.3 NewDrugApprovalRoutes 26011.2.3.1 CentralizedProcedure 26011.3 RegulationintheUnitedStatesofAmerica 26211.3.1 CDERandCBER 26311.3.2 ApprovalsProcedure 263

Contents XI

11.4 InternationalRegulatoryHarmonization 26511.5 RegulationofBiosimilars 266

12 PatentsinthePharmaceuticalBiotechnologyIndustry:LegalandEthicalIssues 269

DavidB.Resnik12.1 Introduction 26912.2 PatentLaw 26912.2.1 WhatIsaPatent? 26912.2.2 HowDoesOneObtainaPatent? 27112.2.3 WhatIstheProperSubjectMatterforaPatent? 27212.2.4 TypesofPatentsinPharmaceuticalBiotechnology 27312.2.5 PatentInfringement 27312.2.6 InternationalPatentLaw 27412.3 EthicalandPolicyIssuesinBiotechnologyPatents 27412.3.1 NoPatentsonNature 27512.3.2 ThreatstoHumanDignity 27612.3.3 AccesstoTechnology 27712.3.4 BenefitSharing 28012.4 Conclusion 281 References 282

13 BiosimilarDrugs 285 WalterHinderer13.1 Introduction 28513.2 RecombinantTherapeuticProteins 28613.3 DefinitionofBiosimilars 28713.4 RegulatorySituation 29013.4.1 BasicPrinciples 29013.4.2 EuropeanGuidelines 29113.4.3 RegulatorySituationintheUnitedStates 29413.4.4 RegulationinOtherTerritories 29613.4.5 FinalRemarks 29713.5 PatentSituation 29713.6 FirstWaveofBiosimilarsintheEU 30513.6.1 GeneralRemarks 30513.6.2 HumanGrowthHormone(hGH) 30613.6.3 Erythropoietin(EPO) 30713.6.4 Granulocyte-ColonyStimulatingFactor(G-CSF) 31013.6.5 RejectedorWithdrawnApplications:InterferonsandInsulin 31213.6.6 ConclusionsontheFirst-WaveBiosimilars 31313.7 BiosimilarTargets:SecondWaveofFutureBiosimilars 31313.7.1 PEGylatedProteinDrugs 31313.7.2 RecombinantAntibodiesandFc-FusionProteins 31613.8 BiosimilarDevelopmentsandRequirements 325

XII Contents

13.8.1 ProcessDevelopment 32713.8.2 DevelopmentofAnalyticalMethods 32813.8.3 Non-clinicalandClinicalDevelopment 33013.9 Conclusions 332 References 333

14 PharmacokineticsandPharmacodynamicsofTherapeuticPeptidesandProteins 337

YiZhangandBerndMeibohm14.1 Introduction 33714.2 PharmacokineticsofPeptidesandProteins 33914.2.1 ProteinAbsorption 33914.2.1.1 ParenteralAdministration 34014.2.1.2 InhalationAdministration 34114.2.1.3 IntranasalAdministration 34214.2.1.4 TransdermalAdministration 34214.2.1.5 OralAdministration 34314.2.2 ProteinDistribution 34314.2.3 ProteinBinding 34514.2.4 ProteinElimination 34614.2.4.1 Proteolysis 34614.2.4.2 GastrointestinalProteinMetabolism 34714.2.4.3 RenalProteinMetabolism 34714.2.4.4 HepaticProteinMetabolism 34914.2.4.5 Receptor-MediatedProteinMetabolism 34914.2.5 RoleoftheNeonatalFc-ReceptorintheDispositionofProteins 35014.3 ImmunogenicityandProteinPharmacokinetics 35214.4 Exposure–ResponseCorrelationsforProteinTherapeutics 35314.4.1 DirectLinkPK/PDModels 35414.4.2 IndirectLinkPK/PDModels 35514.4.3 IndirectResponsePK/PDModels 35514.4.4 CellLifeSpanModels 35614.5 SummaryandConclusions 361 References 361

PartThree Vaccines 369

15 Scientific,Technical,andEconomicAspectsofVaccineResearchandDevelopment 371

Jens-PeterGregersen15.1 Introduction 37115.2 FromtheResearchConcepttoaDevelopmentCandidate 37215.3 VaccineResearchProjects 37315.4 ScientificChallengesofVaccineR&D 375

Contents XIII

15.5 TechnicalAspectsofVaccineDevelopment 37915.5.1 PreclinicalDevelopment 38015.5.2 ManufacturingFacilities 38115.5.3 ClinicalDevelopment 38215.5.4 LicensingandRegistrationofVaccineProducts 38315.6 EconomicAspectsofVaccineDevelopment 38415.6.1 VaccineDevelopmentCost 38415.6.2 RisksandOpportunities 38615.7 Conclusions 387 References 388

16 NewNanobiotechnologicalStrategiesfortheDevelopmentofVectorsforCancerVaccines 391

SeanM.Geary,CaitlinD.Lemke,YogitaKrishnamachari,andAliasgerK.Salem

16.1 Introduction 39116.2 BiodegradableNanoparticles 39616.2.1 Poly(D,L-lactic-co-glycolicAcid)(PLGA)andPolylactic

Acid(PLA) 39616.2.2 Acid-DegradableHydrogel-BasedParticles 39816.3 LiposomalNanovectors 39916.3.1 ConventionalLiposomes 40016.3.2 Long-CirculatingLiposomes 40016.3.3 PositivelyChargedLiposomes 40116.3.4 Archaeosomes 40216.3.5 FusogenicLiposomes 40316.4 GelatinNanoparticles 40416.5 Sub-micronEmulsions 40416.6 AmphiphilicBlock-GraftCopolymers 40516.7 IronOxideNanoparticles 40716.8 Viruses–Virus-LikeParticles–Virosomes 40816.8.1 Viruses 40816.8.2 Virus-LikeParticles(VLPs) 41016.8.3 Virosomes 41016.9 Conclusion 412 Acknowledgments 412 References 412

17 RecombinantVaccines:Development,Production,andApplication 423 LukeR.LeGrand,MichaelaWhite,EvanB.Siegel,andRossT.Barnard17.1 Introduction 42317.2 RangeofRecombinantVaccinesontheMarketandinDevelopment

Today 42417.3 VaccineDialectic 42617.4 ComparingVaccineEfficacy 427

XIV Contents

17.5 Vaccines:ABriefOverview 42817.5.1 ConventionalVaccines 42817.5.1.1 WholeOrganism 42817.5.1.2 Toxoid 42817.5.2 RecombinantVaccines 42817.5.2.1 SubunitVaccines 42817.5.2.2 ConjugateVaccines 42917.5.2.3 DNAVaccines 42917.5.2.4 T-CellReceptorPeptideVaccinesandT-CellEpitopeConjugate

Vaccines 43017.5.2.5 Virus-LikeParticles 43017.5.2.6 ViralVectors 43117.5.2.7 RecombinantAttenuatedBacterialVaccines 43317.6 RecombinantVaccineDevelopment 43317.6.1 Manufacturability 43317.6.2 Scalability 43417.6.3 DeliverabilityandAccessibility 43417.7 DeliverySystems 43517.8 AttheVanguard 43617.8.1 AntigenTargeting 43717.8.1.1 ResidentDCsCrucialtoHumoralImmuneResponses 43717.8.2 Prime–BoostStaging 43817.8.2.1 ACaseStudy–RTS,S 43817.8.2.2 TargetingtheConserved/InvariantRegionandMultimerizingthe

Construct 43917.8.3 MultivalentAntigenPresentation 43917.8.3.1 Self-AssemblingPeptideNanoparticlesforMultivalentAntigen

Presentation 44017.8.3.2 Self-AdjuvantingAgents 44117.8.4 AdjuvantsinRecombinantVaccines 44117.9 Novel,RecombinantDNAApproachtoIdentifyingAttenuatedVaccine

Strains 44217.9.1 CombiningtheBiologicalwiththeMolecular 44217.10 ClinicalTrials 44317.11 Conclusion 443 References 444

PartFour RecentApplicationsinPharmaceuticalBiotechnology 451

18 In SilicoandUltrahigh-ThroughputScreenings(uHTS)inDrugDiscovery:anOverview 453

DebmalyaBarh,ShoaibAhmad,andAtanuBhattacharjee18.1 Introduction 45318.1.1 High-ThroughputScreening 453

Contents XV

18.1.2 EnsuringQuality,Quantity,andCostEffectivenessUsingIntegratedApproaches 454

18.1.3 TraditionalversusNovelTargetsinLeadDiscovery 45518.2 In SilicoPharmacologyandVirtualLigandScreeningforDrug

Discovery 45618.2.1 QuantitativeStructure–ActivityRelationship(QSAR) 45818.2.2 VirtualLigandScreening 45918.2.3 VirtualAffinityProfiling 45918.2.4 DataVisualization 46018.2.5 ApplicationsofIn SilicoPharmacology 46118.3 LeadDiscoveryUsingIntegrativeVirtualScreening 46118.3.1 Target-BasedVirtualScreening 46218.3.2 Ligand-BasedVirtualScreening 46218.3.3 ApplicationofIntegrativeVirtualScreening 46318.3.3.1 CaseofCisplatininTumorTherapy 46318.4 ApplicationofMicroarrayTechnologyinHTSandDrug

Discovery 46318.4.1 DNAMicroarray 46318.4.1.1 DNAMicroarrayFabrication 46418.4.1.2 ApplicationofDNAMicroarraysinHTSandDrug

Discovery 46518.4.2 ChemicalMicroarrayforDrugScreeningandDiscovery 46718.4.2.1 ChemicalMicroarraywithImmobilizedTechnology 46718.4.2.2 SmallMoleculeMicroarray(SMM) 46718.4.2.3 DryChemicalMicroarray 46818.4.2.4 SolutionPhaseChemicalMicroarray 46818.4.3 CellMicroarraysinScreeningandDrugDiscovery 46918.4.3.1 TypesofCellMicroarrays 46918.4.3.2 CellMicroarrayFormats 47018.4.3.3 ApplicationsofCellMicroarrays 47018.5 ChemicalProteomicsforDrugDiscoveryandDevelopment 47118.5.1 StructureofaProbe 47118.5.2 StrategiesinChemicalProteomicsinDrugDiscovery 47318.5.2.1 Activity-BasedProbeProfiling 47318.5.2.2 Fragment-BasedApproach 47418.5.2.3 ApplicationsofChemicalProteomics 47518.6 TargetandDrugDiscoveryUsingLipomicProfiling 47518.6.1 ApplicationsofLipomicProfiling 47618.6.1.1 CaseofRosiglitazoneinDiabetesMellitusTreatment 47618.7 DrugDiscoveryUsingIntegrativeGenomics 47618.7.1 ApplicationsofIntegrativeGenomics 47618.7.1.1 InfectomicsandAntimicrobialDrugResistance 47718.7.1.2 YeastasToolforAntifungalDrugDiscovery 47718.7.1.3 GenomicsandProteomicsinAntidiabeticDrugDiscovery 47718.7.1.4 HumanGenomeProjectandAnticancerDrugDiscovery 477

XVI Contents

18.7.1.5 ToxicogenomicsforHepatotoxicity 47818.8 ToxicogenomicsinDrugDiscoveryandDevelopment 47818.8.1 Toxicogenomics 47818.8.2 ToxicogenomicsinDrugDiscovery 47918.8.3 ToxicogenomicStudiesUsingIn VitroModels 48018.8.4 ToxicogenomicStudiesUsingAnimalModels 48018.8.5 ToxicogenomicsandGenePolymorphisms 48018.8.6 ApplicationofToxicogenomics 48118.9 HTPRNAiScreeningforTargetedDrugDiscovery 48218.9.1 HTSUsingRNAiLibraries 48218.9.2 ApplicationsofRNAiinHTS 48318.10 High-ThroughputScreeningwithStemCells 48318.10.1 StemCell 48318.10.2 AdvantagesofStemCells 48418.10.3 ApplicationsofStemCellsinScreeningandDrugDiscovery 48418.11 SystemsBiologyinDrugDiscovery 48518.11.1 IndustryApproachestoSystemsBiology 48518.11.2 SimulationModels 48618.11.3 ApplicationsofSystemsBiology 48618.12 Conclusion 488 References 489

19 MetabolicEngineeringofMedicinalPlantsandMicroorganismsfortheProductionofNaturalProducts 491

OktaviaHendrawati,HermanJ.Woerdenbag,JacquesHille,andOliverKayser

19.1 Introduction 49119.2 ThePlantasaSourceofNaturalProducts 49519.2.1 PlantCellCultures 49519.2.2 TransgenicPlants 49619.3 OptimizingBiochemicalPathways 49819.3.1 StrategiesandGoalsofMetabolicEngineering 49819.3.2 MetabolicPathwaysofInterest 49919.3.3 SyntheticBiology 50119.4 MetabolicEngineeringStrategiesandTechniquesinMedicinalPlant

Biotechnology 50219.4.1 UpregulatingofPathways(Overexpression) 50419.4.2 RedirectingCommonPrecursors 50519.4.3 TargetingMetabolitestoSpecificPlantCellCompartments 50519.4.4 CreationofStorageofOverproducedSecondary

Metabolites 50619.4.5 DownregulatingofPathways(Silencing) 50619.5 ChallengesinPlantMetabolicEngineering 50619.5.1 UnexploredRegulationofSecondaryMetabolism 50619.5.2 PathwaysAreOftenSpeciesSpecific 507

Contents XVII

19.5.3 CellCompartmentalizationandTissueDifferentiation 50719.5.4 UnpredictedorUnexpectedOutcome 50819.6 MetabolicEngineeringApplicationsinMedicinalPlant

Biotechnology 50819.6.1 CaseStudy:PodophyllotoxinProductioninAnthriscus sylvestris 50819.6.2 CaseStudy:ScopolamineBiosynthesisinNicotiana tabacum 50919.6.3 CaseStudy:GenisteinProductioninTransgenicArabidopsis,Tobacco,

Lettuce,Corn,Petunia,andTomato 51019.6.4 CaseStudy:ExpressionofSpearmintLimoneSynthasein

Lavender 51119.6.5 CaseStudy:ArtemisininBiosynthesisinArtemisia annua 51119.6.6 CaseStudy:MorphineBiosynthesisinPapaver somniferum 51219.6.7 CaseStudy:GossypolReductioninCottonseedsbyBlocking

δ-CadineneSynthase 51319.7 CrossingBorders–HeterologousProductionofPlantCompoundsin

Microorganisms 51419.7.1 ArtemisinicAcid 51419.7.2 Stilbenes 51419.7.3 Curcuminoids 51519.7.4 Flavonoids 51519.7.5 Vanillin 51619.8 ConclusionandFutureProspects 516 References 518

20 MetabolomicsasaBioanalyticalToolforCharacterizationofMedicinalPlantsandTheirPhytomedicalPreparations 527

NizarHappyana,RemcoMuntendam,andOliverKayser20.1 Introduction 52720.2 BioanalyticalTools 52820.2.1 SamplePreparation 53020.2.2 NuclearMagneticResonance 53120.2.3 MassSpectrometry 53220.2.3.1 DirectInjectionMassSpectrometry 53320.2.3.2 GasChromatography–MassSpectrometry 53420.2.3.3 LiquidChromatography–MassSpectrometry 53420.2.4 DataProcessing 53520.3 MetabolomicsApplicationsinMedicinalPlants 53820.3.1 DiscriminationforClassificationofMedicinalPlants 53820.3.2 CharacterizationofMetabolitesinPlantCulturesandTransgenic

MedicinalPlants 54020.3.3 QualityControlofMedicinalPlants 54120.3.4 IdentificationofMedicinalPlantBioactivity 54320.3.5 StudyEfficacyofMedicinalPlants 54420.3.6 InvestigationofMedicinalPlantToxicity 54520.4 Conclusions 546

XVIII Contents

Acknowledgment 547 References 547

21 IntegrationofBiotechnologiesfortheDevelopmentofPersonalizedMedicine 553

KewalK.Jain21.1 Introduction 55321.2 GeneticVariationsintheHumanGenome 55421.2.1 SingleNucleotidePolymorphisms 55521.2.2 ComplexChromosomalRearrangements 55621.2.3 InsertionsandDeletionsintheHumanGenome 55621.2.4 Large-ScaleVariationintheHumanGenome 55721.2.5 VariationinCopyNumberintheHumanGenome 55721.2.6 StructuralVariationsintheHumanGenome 55821.3 RoleofBiomarkersintheDevelopmentofPersonalized

Medicine 55921.4 TechnologiesUsedfortheDevelopmentofPersonalized

Medicine 56021.5 MolecularDiagnosisasaBasisforPersonalizedMedicine 56021.5.1 Real-TimePCRandPersonalizedMedicine 56121.5.2 AnalysisofSingleBiologicalMoleculesforPersonalized

Medicine 56321.5.3 MolecularImagingandPersonalizedMedicine 56321.5.4 Point-of-CareDiagnosticsandPersonalizedMedicine 56421.6 SequencingandPersonalizedMedicine 56421.6.1 SequencingofVariationsinHumanGenomes 56521.6.2 StudyofRareVariantsinPinpointingDisease-CausingGenes 56521.7 RoleofBiochips/MicroarraysintheDevelopmentofPersonalized

Medicine 56621.8 RoleofCytogeneticsintheDevelopmentofPersonalized

Medicine 56721.9 Roleof“Omics”inPersonalizedMedicine 56821.9.1 RoleofPharmacogenetics 56821.9.2 RoleofPharmacogenomics 56921.9.3 RoleofPharmacoproteomics 57021.9.4 RoleofPharmacometabolomics 57021.10 RoleofNanobiotechnologyfortheDevelopmentofPersonalized

Medicine 57221.11 SystemsBiologyandPersonalizedMedicine 57321.12 PersonalizedBiologicalTherapies 57421.12.1 RecombinantHumanProteins 57521.12.2 TherapeuticMonoclonalAntibodies 57521.12.3 CellTherapy 57521.12.4 GeneTherapy 57621.12.5 RNAInterference 576

Contents XIX

21.13 PersonalizedVaccines 57721.13.1 PersonalizedVaccinesforViralDiseases 57721.13.2 PersonalizedCancerVaccines 57721.14 ConcludingRemarksandFutureProspectsofPersonalized

Medicine 578 References 579

22 XenotransplantationinPharmaceuticalBiotechnology 581 GregoryJ.BrunnandJeffreyL.Platt22.1 Introduction 58122.1.1 AlternativeSourcesofTransplantableTissues 58122.1.2 ThePigasaSourceofTissuesandOrgansforClinical

Xenotransplantation 58222.2 BiologicalBarrierstoXenotransplantation 58322.2.1 GraftVascularization 58322.2.2 HyperacuteRejection 58422.2.3 ComplementActivation 58522.2.4 AcuteVascularRejection 58622.2.5 Accommodation 58822.2.6 CellularMediatedImmuneResponses 58822.3 PhysiologicalandInfectiousHurdlestoXenotransplantation 59022.3.1 InterspeciesChallenges 59022.3.2 Zoonosis 59122.4 ScenariofortheClinicalApplicationofXenotransplantation 592 References 593

23 Nutraceuticals–FunctionalFoodsforImprovingHealthandPreventingDisease 599

JianZhao23.1 Introduction 59923.2 PlantFood,Pharmaceuticals,Nutraceuticals,andHuman

Health 60023.3 ConceptsofFunctionalFoods,Nutraceuticals,andOtherRelated

Terms 60123.3.1 FunctionalFoods 60223.3.2 Nutraceutical 60223.3.3 MedicalFoods 60323.3.4 NovelFoods 60323.3.5 Food(Dietary)Supplement 60423.3.6 FoodAdditives 60423.3.7 Phytonutrients 60423.3.8 Herbs,HerbalNutraceuticals,orBotanicals 60523.3.9 AlternativeTherapies 60523.4 FFNPrinciplesandTheirPotentialHealthBenefits 60623.4.1 DietaryFibers 606

XX Contents

23.4.2 PhenolicProducts 60723.4.3 Terpenoids 60823.4.4 Phytosterols 60923.4.5 FattyAcidsandLipids 60923.4.6 EssentialAminoAcids 61023.4.7 PrebioticsandProbiotics 61123.4.8 Phytoestrogen 61223.5 HerbalNutraceuticalsandMultipleHerbalComponent

Formulations 61323.6 FFNsandMetabolicSyndrome,FacialAging,andCosmetic

Surgery 61423.7 AbsorptionandMetabolismofFFNsandInteractionwithDrugs 61623.8 EpidermiologicalStudyandClinicalTrialsonFFNs 61823.9 BiotechnologyforImprovedNutritionalValueandCreationof

MedicalFoods 61923.10 FutureDevelopments 621 References 622

Index 629

XXI

Pharmaceutical biotechnology has emerged as one of the major disciplines for drug discovery and development. In the past, the pharmaceutical branch of biotechnology – the former red biotechnology – was limited to fermentation and production of recombinant therapeutic proteins. Today, the shape and vision of pharmaceutical aspects and challenges have completely changed, and the prefix “pharma” can also be accepted as a synonym for integrated life science approaches, ranging from genetics to molecular biology to diagnostics, with the common goal of delivering the best drug to the patient by biotechnological techniques.

If we take a look at the first edition of Pharmaceutical Biotechnology, we see that the focus was more on molecules as potential drugs and less on the production strategies and the molecular concepts behind. The completely updated and rewritten second edition reflects the emerging trend in the pharmaceutical industry where molecular biology techniques and genetics play an increasingly important role. Today, many new biological entities can be characterized as muteins or significantly backbone-modified proteins, an exception in 2004 when we published the first edition (see insulin muteins). We are glad that we were able to attract the majority of the authors from the previous edition as experts. They reviewed the latest trends in their subjects of expertise and shared their experience and open opinion about the developments from the recent years to the near future. Pharmaceutical biotechnology and the pharmaceutical industry is a fast moving business and we all know that the future is hard to predict, but we are glad that with the selected contributors being in touch with industrial needs and challenges, we made the right choice to give answers to the readers’ questions not only about new developments in protein production, host organism selection, and future platform organisms for biosynthesis and vaccine production, but also on biological generics, drug formulation, and legal aspects of biotechnology. In this textbook you will find updated facts and figures about the pharmaceutical industry and the latest drug approvals. In the first part a detailed discussion is provided about production systems for the biosynthesis of both low molecular weight drugs and proteins in prokaryotic and eukaryotic cell cultures and organisms. In the second part the drug formulation and manufacturing process is in focus, but we also want to highlight quality control and bioanalytical aspects, which have been largely neglected before. Therefore, this second part is now updated and dedicated to the

Prefacetothe2ndEdition

XXII Prefacetothe2ndEdition

recombinant therapeutic proteins and vaccines that are already in clinical use, as well as requirements for quality control. In contrast to the first edition we recognized that drug regulation and quality assurance are becoming more important, while the legal aspects of drug patenting, and the drug approval process are again emphasized. In the third part we had a hard task of sorting and structuring the emerging diversity of research and development in this field and bring it under one single chapter. This is nearly impossible, but our aim is to guide the reader through the new upcoming lines of research impacted by genetics, synthetic biology, and nanobiotechnology. Finally we selected chapters showing exemplarily ongoing research trends that, hopefully, will find their way into clinical applications in the future or as approved drugs into the second edition of this textbook. Well-updated by authors from the previous edition, we learn about personalized medicine and xenotransplantation, and we are proud to introduce new contributors telling us about nanocarriers as future drug delivery systems, ultrahigh-throughput screening for accelerated drug discovery, and transgenic plants as future green factories.

The editors want to thank all the authors for their valuable contributions and the time they have invested in this work. We know very well that time was and is a scarce resource and that the chapters were written alongside the authors’ regular duties. Special thanks also to the families behind for their patience and understanding why time was spent in this project. Special thanks to Anne Chassin du Guerny and Gregor Cichetti of Wiley-Blackwell for their professional support in the layout, proofreading, and production of this textbook.

We know that this book is far from being complete and we are aware that by the day of publishing it could be updated again. But our intention is to provide a “primer” for the interested reader to start working and to show how exciting research is in this fast moving field of life science.

Dortmund and Darmstadt, January 2012 Oliver KayserHeribert Warzecha

XXIII

Shoaib AhmadRayat and Bahra Institute of PharmacyDepartment of PharmacologySahauran, Punjab 140104India

Michael BallsFund for the Replacement of Animals in Medical Experiments (FRAME)Russell & Burch House96–98 North Sherwood StreetNottingham NG1 4EEUK

Debmalya BarhInstitute of Integrative Omics and Applied Biotechnology (IIOAB)PB Barh Centre for Bioprocess, Biotechnology, and Renewable EnergyNonakuri, Purba MedinipurWest Bengal 721172India

Ross T. BarnardThe University of Queensland, St LuciaAustralian Infectious Diseases Research CentreSchool of Chemistry and Molecular BiosciencesBrisbane, Queensland 4072Australia

ListofContributors

Andreas BechtholdAlbert Ludwigs University of FreiburgDepartment of Pharmaceutical Biology and BiotechnologyInstitute for Pharmaceutical Sciences79104 FreiburgGermany

Andrew BennettUniversity of Nottingham Medical SchoolSchool of Biomedical SciencesFRAME Alternatives LaboratoryQueen’s Medical CentreNottingham NG7 2UHUK

Atanu BhattacharjeeNorth Eastern Hill UniversityDepartment of Biotechnology and BioinformaticsShillong 22India

Gregory J. BrunnMayo ClinicDepartment of Molecular Pharmacology and Experimental TherapeuticsRochester, MN 55905USA

XXIV ListofContributors

Maria J. De JesusExcellGene SARoute de l′ile-au-bois 1A1870 MontheySwitzerland

Theo DingermannGoethe University FrankfurtInstitute of Pharmaceutical BiologyMax-von-Laue-Straße 960438 Frankfurt/MainGermany

Sean M. GearyUniversity of IowaDepartment of Pharmaceutical Sciences and Experimental TherapeuticsCollege of PharmacyM5S. Grand AvenueIowa City, IA 52242USA

Christoph GieseProBioGen AGGoethestraße 5413086 BerlinGermany

Uwe GottschalkSartorius-Stedim BiotechPurification TechnologiesAugust-Spindler-Straße 1137079 GöttingenGermany

Jens-Peter GregersenNovartis Vaccines and Diagnostics GmbHEmil-von-Behring Straße 7635041 MarburgGermany

Nizar HappyanaTechnical University of DortmundLaboratory of Technical BiochemistryEmil-Figge Straße 6644227 DortmundGermanyandBandung Institute of TechnologyDepartment of ChemistryJl. Ganesha 10Bandung 40132Indonesia

Oktavia HendrawatiUniversity of GroningenPharmaceutical Biology DepartmentAntonius Deusinglaan 19713 AV GroningenThe Netherlands

Jacques HilleUniversity of GroningenMolecular Biology of Plants DepartmentKerklaan 309751 NN HarenThe Netherlands

Walter HindererGedeon Richter Pharma GmbHRobert-Bosch-Straße 11B63225 LangenGermany

Henning von HorstenProBioGen AGGoethestraße 5413086 BerlinGermany

Kewal K. JainJain PharmaBiotechBlaesiring 74057 BaselSwitzerland

ListofContributors XXV

Oliver KayserTechnical University DortmundLaboratory of Technical BiochemistryEmil-Figge Straße 6644227 DortmundGermany

David KendallUniversity of Nottingham Medical SchoolSchool of Biomedical SciencesFRAME Alternatives LaboratoryQueen’s Medical CentreNottingham NG7 2UHUK

Alexander KindTechnical University MunichDepartment of Livestock BiotechnologyLiesel-Beckmann Straße 185354 Freising-WeihenstephanGermany

Yogita KrishnamachariUniversity of IowaDepartment of Pharmaceutical Sciences and Experimental TherapeuticsCollege of PharmacyM5S. Grand AvenueIowa City, IA 52242USA

Luke R. Le GrandThe University of Queensland, St. LuciaSchool of Chemistry and Molecular BiosciencesBrisbane, Queensland 4072Australia

Caitlin D. LemkeUniversity of IowaDepartment of Pharmaceutical Sciences and Experimental TherapeuticsCollege of PharmacyM5S. Grand AvenueIowa City, IA 52242USA

Andriy LuzhetskyyAlbert Ludwigs University of FreiburgDepartment of Pharmaceutical Biology and BiotechnologyInstitute for Pharmaceutical Sciences79104 FreiburgGermany

Bernd MeibohmUniversity of Tennessee Health Science CenterCollege of PharmacyDepartment of Pharmaceutical SciencesMemphis, TN 38163USA

Remco MuntendamUniversity of GroningenDepartment of Pharmaceutical BiologyAntonius Deusinglaan 19713 AV GroningenThe Netherlands

Julia MyschikLudwig-Maximilians-University MunichDepartment of PharmacyPharmaceutical Technology and BiopharmaceuticsButenandtstraße 581377 MunichGermany

XXVI ListofContributors

Heiner NiemannFriedrich Loeffler Institute (FLI)Institute of Farm Animal GeneticsMariensee31535 NeustadtGermany

Jeffrey L. PlattUniversity of MichiganDepartments of Surgery and Microbiology & ImmunologyAnn Arbor, MI 48109USA

David B. ResnikEast Carolina UniversityThe Brody School of MedicineGreenville, NC 27858USA

Aliasger K. SalemUniversity of IowaDepartment of Pharmaceutical Sciences and Experimental TherapeuticsCollege of PharmacyM5S. Grand AvenueIowa City, IA 52242USA

Angelika SchniekeTechnical University MunichDepartment of Livestock BiotechnologyLiesel-Beckmann Straße 185354 Freising-WeihenstephanGermany

Evan B. SiegelGround Zero Pharmaceuticals2600 Michelson DriveIrvine, CA 92612USA

Gary WalshUniversity of LimerickIndustrial Biochemistry Program and the Materials and Surface Science InstituteLimerick CityIreland

Heribert WarzechaTechnische Universität DarmstadtBiologySchnittspahnstraße 3-564267 DarmstadtGermany

Gabriele WeitnauerAlbert Ludwigs University of FreiburgDepartment of Pharmaceutical Biology and BiotechnologyInstitute for Pharmaceutical Sciences79104 FreiburgGermany

Michaela WhiteThomson ReutersLife SciencesAsia PacificMelbourne, Victoria 3001Australia

Gerhard WinterLudwig-Maximilians-University MunichDepartment of PharmacyPharmaceutical Technology and BiopharmaceuticsButenandtstraße 581377 MunichGermany

Herman J. WoerdenbagUniversity of GroningenPharmaceutical Technology and Biopharmacy DepartmentAntonius Deusinglaan 19713 AV GroningenThe Netherlands

ListofContributors XXVII

Florian M. WurmEcole Polytechnique Fédérale de Lausanne (EPFL)Laboratory of Cellular Biotechnology1015 LausanneSwitzerlandandExcellGene SARoute de l′ile-au-bois 1A1870 MontheySwitzerland

Yi ZhangUniversity of Tennessee Health Science CenterCollege of PharmacyDepartment of Pharmaceutical SciencesMemphis, TN 38163USA

Jian ZhaoThe Samuel Roberts Noble Foundation2510 Sam Noble ParkwayArdmore, OK 73401USA

Stefan ZietzeProBioGen AGGoethestraße 5413086 BerlinGermany

Ilse ZündorfGoethe University FrankfurtInstitute of Pharmaceutical BiologyMax-von-Laue-Straße 960438 Frankfurt/MainGermany