Bioprocessing, Bioengineering and Process Chemistry in the Biopharmaceutical Industry: Using Chemistry and Bioengineering to Improve the Performance of Biologics

Cover
Half Title
Bioprocessing, Bioengineering and Process Chemistry in the Biopharmaceutical Industry: Using Chemistry and Bioengineering to Improve the Performance of Biologics
Copyright
Dedication
Foreword
Preface
Acknowledgements
Contents
Contributors
About the Editors
Part I. Overview
	1. Bioprocessing, Bioengineering and Process Chemistry in the Biopharmaceutical Industry: Using Chemistry and Bioengineering to Improve the Performance of Biologics
		1.1 Introduction
			1.1.1 The Synopsis of the Volume
		1.2 Synthetic Biology: A Perspective
			1.2.1 Basic Alphabets and Expanded Alphabets of Genetic Building Blocks
			1.2.2 Mutations, Point Mutations, Chemistry, and Health Disorders
				1.2.2.1 Sickle-Cell Disease (SCD) and Potential Treatment
				1.2.2.2 Cystic Fibrosis
				1.2.2.3 Progeria
		1.3 Synergy Between Biologics and Small Molecules
			1.3.1 Process Chemistry and Bioprocessing
			1.3.2 Antibody Drug Conjugates (ADCs): A Conjugation of Small Molecules and Biomolecules
				1.3.2.1 ADC Drugs
		1.4 Top 25 Best-Selling Drugs
		1.5 Outline of the Contents of the Volume
			1.5.1 An Overview
			1.5.2 Synthetic Biology
				1.5.2.1 Synthetic Biology in Drug Development and Beyond
			1.5.3 Oligonucleotide Synthetic Chemistry to DNA Synthesis, Bioprocessing, and Manufacturing
			1.5.4 Process Engineering, Gene Therapy, and Vaccine
			1.5.5 Special Topics: CAR-T and CRISPR Technologies and Applications
			1.5.6 Fusion Proteins, Antibody Drug Conjugates, and Process Chemistry
			1.5.7 Biopharmaceutical Informatics and Analytics
			1.5.8 Biopharmaceutical Regulatory CMC
			1.5.9 Technology Transfer
			1.5.10 Emerging Trends and Future of Biopharmaceuticals
		1.6 Future of Biologics
		References
Part II. Synthetic Biology
	2. Synthetic Biology in Drug Development and Beyond
		2.1 What Is Synthetic Biology?
		2.2 A Brief Overview of Synthetic Biology Tools
		2.3 Synthetic Biology in Drug Discovery and Development
			2.3.1 Gene Editing for the Identification of Drug Targets
		2.4 Engineering Biosynthetic Gene Clusters for Drug Discovery
		2.5 Unprecedented Antibody Discovery and Development Through Synthetic Biology
			2.5.1 B-Cells and Hybridoma Technology for Antibody Discovery and Development
			2.5.2 Synthetic Libraries and Display Systems
		2.6 CAR-T Cell Therapies
		2.7 Conclusion
		References
Part III. Oligonucleotide Synthetic Chemistry to DNA Synthesis, Bioprocessing and Manufacturing
	3. Increasing the Scalability of DNA Synthesis and Its Key Role in Expanding the Biopharmaceutical Discovery Process
		3.1 Introduction
		3.2 Evolution of Gene Synthesis
			3.2.1 Oligonucleotide Synthesis
				3.2.1.1 Early Synthetic Chemistries
			3.2.2 Solid Supports
			3.2.3 Modern Oligo Synthesis Platforms
		3.3 Gene Synthesis
			3.3.1 Early DNA Assembly Methods
			3.3.2 Array-Based Gene Synthesis
			3.3.3 Error Correction and Sequence Validation
		3.4 New Discovery Bottleneck
			3.4.1 Evolution of Antibody Discovery
				3.4.1.1 Hybridoma Technology
				3.4.1.2 Phage Display Technology
				3.4.1.3 Synthetic Antibody Library Construction
					Semi-Synthetic Libraries
					Fully Synthetic Libraries
		3.5 Perspectives
		References
	4. Advancements in the Manufacture of Monoclonal Antibodies and Other Large Molecule Protein Therapeutics: Recent Innovations in Cell Culture Technology Enabling Process Intensification
		4.1 Introduction
		4.2 Modes of Bioreactor Operation
			4.2.1 Batch
			4.2.2 Fed-Batch
			4.2.3 Perfusion—Or the Solution to Pollution Is Dilution!
			4.2.4 Hybrid Processes
			4.2.5 Concentrated Fed-Batch or Perfusion with Ultrafiltration
			4.2.6 Intensification of Classical Perfusion
			4.2.7 Dynamic Perfusion Processes
		4.3 Pragmatic Control of Cellular Metabolism
			4.3.1 The Development of pH or Temperature Shifts
			4.3.2 Glucose Limitation
			4.3.3 The Development of HiPDOG Control Methodology
			4.3.4 Extension of Controlled Glucose Limitation to Perfusion Cultures
			4.3.5 “Whack a Mole” with Inhibitory By-products
		4.4 Other Methods of Process Intensification
			4.4.1 N-1 Perfusion
			4.4.2 N-1 Intensification
			4.4.3 Linked Bioreactors
			4.4.4 Hydrocyclone Use with Linked Bioreactors
		4.5 Process Analytical Technology
		4.6 Single-Use Bioreactors (SUBs)
		4.7 Conclusions
		References
	5. Process Development and Manufacturing Considerations for Multispecific (Bispecific and Trispecific) Antibodies: Case Study
		5.1 Introduction
		5.2 Strategies for Molecule and Cell Engineering to Produce IgG-Like Multispecifics
			5.2.1 Molecular Format Considerations
				5.2.1.1 The Charge-Based Electrostatic Approach
				5.2.1.2 The Knob into Hole Approach
			5.2.2 Cell Line Generation Considerations for Single Cell Line (SCL) Multispecifics
				5.2.2.1 Stable CHO Host Cell Integration System—Random or Targeted?
				5.2.2.2 Expression Vector Considerations
				5.2.2.3 Cell Line Screening Strategy Considerations
		5.3 Process Development of Multispecifics
			5.3.1 Upstream Process Development
			5.3.2 Downstream Process Development Considerations
				5.3.2.1 Unique Impurity Challenges
				5.3.2.2 Stability Concerns
				5.3.2.3 Reduction and Oxidation (REDOX) Step
		5.4 Manufacturing of Multispecifics
		5.5 Case Study: Challenges in Removal of Bispecific Product Related Impurities
			5.5.1 Vector Orientation and Cell Line
			5.5.2 Downstream Process Design: Removal of Impurities
				5.5.2.1 H/H Removal
				5.5.2.2 HMMS Removal
				5.5.2.3 Balancing H/H and HMMS Removal
		References
Part IV. Process Engineering, Gene Therapy and Vaccines
	6. Metabolic and Process Engineering to Control Glycan Structures for Biopharmaceuticals Produced in Cultured Mammalian Cells
		6.1 Introduction
		6.2 Biology of Glycosylation
			6.2.1 N-Linked Glycosylation
			6.2.2 O-Linked Glycosylation
			6.2.3 Glycosaminoglycan Synthesis
		6.3 Effects of Glycosylation on Biological Activity
			6.3.1 Mannosylation
			6.3.2 Fucosylation
			6.3.3 Galactosylation
			6.3.4 Sialylation
		6.4 Choice of Host Cell Line
		6.5 Glycoengineering
			6.5.1 Manipulating Heterogeneity
			6.5.2 Manipulating Sialylation
				6.5.2.1 Increasing α-2,6 Sialylation
				6.5.2.2 Increasing the Sialic Acid Content
			6.5.3 Manipulating Fucosylation
			6.5.4 Manipulating Branching
		6.6 Effects of Bioprocess Conditions
			6.6.1 Temperature
			6.6.2 pH
			6.6.3 Feeding Strategies and Other Bioprocess Manipulations
				6.6.3.1 Glucose and Other Glycosylation Precursors
				6.6.3.2 Amino Acids
				6.6.3.3 Glycosaminoglycan Production
			6.6.4 Culture Additives
		6.7 Perspectives and Future Directions
		References
	7. Even a Worm Will Turn: Immunity Following AAV Vector Administration
		7.1 Introduction
			7.1.1 AAV Gene Therapy
			7.1.2 Immune Response to AAV Vectors
		7.2 Innate Immune Sensing of AAV Vectors
		7.3 Adaptive Immune Responses to AAV
			7.3.1 Humoral Immunity
			7.3.2 Cell-Mediated Immunity
		7.4 Conclusion
		References
	8. COVID-19 Vaccine Manufacturing Processes: Making the Molecules to Solve the Pandemic
		8.1 Introduction
		8.2 mRNA Vaccines
			8.2.1 Background
			8.2.2 Production Process
				8.2.2.1 Overview of Steps
				8.2.2.2 Production
				8.2.2.3 Purification
		8.3 Viral Vectors
			8.3.1 Background
			8.3.2 Production Process
				8.3.2.1 Overview of Steps
				8.3.2.2 Production
				8.3.2.3 Purification
		8.4 Whole Inactivated Virus Vaccines
			8.4.1 Background
			8.4.2 Production Process
				8.4.2.1 Overview of Steps
				8.4.2.2 Production
				8.4.2.3 Viral Inactivation
				8.4.2.4 Purification
		8.5 Protein-Based Vaccines
			8.5.1 Background
			8.5.2 Production Processes
				8.5.2.1 NVX-CoV2373 (Novavax)
				8.5.2.2 CoVLP (Medicago)
				8.5.2.3 EpiVacCorona (Vector Institute)
		8.6 Comparison of Manufacturing Processes for the Different Modalities
		8.7 Conclusions
		References
Part V. Special Topics: CAR-T and CRISPR Technologies and Applications
	9. CAR-T Bioprocessing
		9.1 Introduction
			9.1.1 Generation and Function
		9.2 Transgene and Vector Bioprocessing
			9.2.1 Introduction
			9.2.2 Lentiviral Vector Design
			9.2.3 Cell Culture Technology for the Production of LVVs
			9.2.4 Mode of Production for LVVs
			9.2.5 Upstream Bioprocessing
			9.2.6 Downstream Bioprocessing
		9.3 Cell Product Bioprocessing
			9.3.1 End-to-End Systems
			9.3.2 Apheresis Collection and Preservation
			9.3.3 T-Cell Thawing and Isolation
			9.3.4 Activation
			9.3.5 Cell Transduction and Transfection
			9.3.6 Cell Expansion
			9.3.7 In-Process and Release Testing
			9.3.8 T-Cell Cryopreservation
			9.3.9 Formulation Considerations for the Drug Product
			9.3.10 Scale-Up Considerations: Toward Automated Formulation
		9.4 Supply Chain and Logistic Model
		9.5 Considerations for the CAR-T Field
		References
	10. CRISPR Technology and Its Application in Therapeutics
		10.1 Introduction to CRISPR Technology
			10.1.1 What Is CRISPR?
			10.1.2 Discovery and Adaptation of CRISPR
			10.1.3 Advantages of CRISPR Over Other Gene Editors
			10.1.4 Mechanism Behind CRISPR Gene Editing
		10.2 CRISPR Gene Editing: Techniques and Methods
			10.2.1 Creating Gene Knockouts
			10.2.2 Creating Gene Knock-Ins
			10.2.3 CRISPR Activation and CRISPR Inhibition
			10.2.4 CRISPR Screens
		10.3 CRISPR Evolution and Derivative Technologies
			10.3.1 Derivative Technologies
		10.4 CRISPR Component Format and Delivery Methods
			10.4.1 Gene Editing Components: Cas Nucleases and Cargo Formats
			10.4.2 Delivery Methods
		10.5 CRISPR Therapeutics: Gene Therapies and Gene-Edited Cell Therapies
			10.5.1 What Are Cell and Gene Therapies?
			10.5.2 Role of CRISPR in Cell and Gene Therapy
		10.6 CRISPR in Cancer Therapy
			10.6.1 Tumor-Infiltrating Lymphocyte Therapy
			10.6.2 TCR Engineered T Cell Therapy
			10.6.3 Chimeric Antigen Receptor T Cell Therapy
			10.6.4 In Vivo CRISPR Editing of Solid Tumors
		10.7 CRISPR Treatments for Genetic Disease
			10.7.1 CRISPR Gene Correction for Monogenic Diseases
			10.7.2 CRISPR Knockout of Repeat Hyperexpansions
			10.7.3 CRISPR In Vivo Gene Therapies
		10.8 CRISPR in Infectious Disease Treatment
			10.8.1 Circumventing Antibiotic Resistance in Bacteria
			10.8.2 CRISPR-Edited Cell Therapies for the Treatment of Viral Pathogens
			10.8.3 In Vivo CRISPR Therapy to Excise Integrated Viruses from the Human Genome
		10.9 The Future of CRISPR Therapeutics
			10.9.1 Industrialization of CRISPR Editing: Increasing Safety and Lowering Costs
			10.9.2 Safety Considerations
			10.9.3 Regulatory Issues and Developing New Clinical Frameworks for CRISPR Therapies
		References
Part VI. Fusion Proteins, Antibody Drug Conjugates and Process Chemistry
	11. Fusion Proteins: Current Status and Future Perspectives
		11.1 Introduction
			11.1.1 Definition
			11.1.2 Categories
		11.2 Current Status
			11.2.1 Approved Products
			11.2.2 Market
		11.3 Design
			11.3.1 Building Blocks
			11.3.2 Linkers
			11.3.3 Oligomerization
				11.3.3.1 Monomer
				11.3.3.2 Dimer
				11.3.3.3 Trimer
				11.3.3.4 Tetramer
				11.3.3.5 Pentamer
				11.3.3.6 Hexamer
				11.3.3.7 Octamer
			11.3.4 Orientation
			11.3.5 Protein Engineering
				11.3.5.1 Modifications of Fc as Building Block
				11.3.5.2 Modifications of Human Serum Albumin as Building Block
				11.3.5.3 Modification of Other Functions
			11.3.6 Immunogenicity
		11.4 Manufacturing
			11.4.1 Upstream
			11.4.2 Downstream
			11.4.3 Glycosylation
			11.4.4 Aggregation
			11.4.5 Analytics
		11.5 Therapeutic Concepts
			11.5.1 Half-Life Extension
				11.5.1.1 Half-Life Extension by Size and Recycling
					Albumin Fusions
					Fc Fusions
					Transferrin Fusions
				11.5.1.2 Half-Life Extension by Increasing the Hydrodynamic Radius
					Repetitive Peptide Fusions
					Glycosylated Peptides
				11.5.1.3 Aggregate Forming Peptides
			11.5.2 Targeting Functions
			11.5.3 Applications in Oncology
				11.5.3.1 Fc Domain Receptor-Mediated Toxicity
				11.5.3.2 Toxins
				11.5.3.3 Immunocytokines
				11.5.3.4 Human Enzymes
				11.5.3.5 Apoptosis Induction
		11.6 Summary
		11.7 Future Perspectives
		References
	12. Development of Antibody-Drug Conjugates
		12.1 Introduction
		12.2 ADC History
		12.3 Target Selection
		12.4 Antibody Selection
		12.5 Selection of Linkers and Payloads
		12.6 ADC Technology
		12.7 ADC Clinical Development
		12.8 ADCs Approved for Cancer
			12.8.1 Mylotarg
			12.8.2 Adcetris
			12.8.3 Kadcyla
			12.8.4 Besponsa
			12.8.5 Polivy
			12.8.6 Padcev
			12.8.7 Enhertu
			12.8.8 Trodelvy
			12.8.9 Blenrep
			12.8.10 Zynlonta
			12.8.11 Tivdak
		12.9 Concluding Remarks
		References
	13. Mylotarg: The Journey to FDA Reapproval and Broad International Approval
		13.1 Introduction
		13.2 Gemtuzumab Ozogamicin
		13.3 Gemtuzumab Antibody
		13.4 Calicheamicin
		13.5 Assessing the Regulatory and Commercial Needs
		13.6 Production of Gemtuzumab Antibody
		13.7 Production of the Calicheamicin Linker Payload
			13.7.1 Isolation of γ-Calicheamicin
			13.7.2 Formation of N-Acetyl Calicheamicin
			13.7.3 Isolation of N-Acetyl Calicheamicin
			13.7.4 Production of Activated Calicheamicin Derivative
			13.7.5 Regulatory Challenges Involving Activated Calicheamicin Derivative
		13.8 Production of Gemtuzumab Ozogamicin Drug Substance
		13.9 Production of Mylotarg Drug Product
		13.10 Conclusions
		References
Part VII. Biopharmaceutical Informatics and Analytics
	14. Biopharmaceutical Informatics: A Strategic Vision for Discovering Developable Biotherapeutic Drug Candidates
		14.1 Introduction
			14.1.1 Growing Demand for Improved Developability of Biotherapeutics
			14.1.2 Developability Issues Arising from Unfavorable Biophysical Properties
			14.1.3 Biopharmaceutical Informatics: An Integrated Approach to Discovery and Development of Biotherapeutics
		14.2 In Silico Assessments of Biologics in Research and Development
			14.2.1 Antibody Generation
			14.2.2 Hit Selection and Lead Identification
			14.2.3 Lead Humanization and Optimization
			14.2.4 Formatting of Conventional and Next-Generation Antibodies
			14.2.5 In Silico Assessments in Development
		14.3 In Silico Tools for Developability Assessments
			14.3.1 Structure Prediction
			14.3.2 Biophysical Properties
			14.3.3 Hydrophobicity
			14.3.4 Solution- and Colloidal-State Properties
			14.3.5 Isoelectric Point (pI)
			14.3.6 Viscosity and Diffusion Interaction Parameter (kD)
			14.3.7 Aggregation and Self-Association
			14.3.8 Prediction of Paratope
			14.3.9 Post-Translational Modifications (PTM)
		14.4 Conclusion and Future Directions
		References
	15. Advanced Data Analytics Application in Biomanufacturing Processes
		15.1 Introduction
		15.2 ADA Program Development
			15.2.1 Building a Cross-Functional Team for ADA Program
			15.2.2 IT Infrastructure and Tools
			15.2.3 Project Approach
			15.2.4 Model Library
		15.3 Case Study
			15.3.1 Case Study Selection for ADA Modeling
			15.3.2 Data Sources Identification
			15.3.3 Hypothesis Generation
			15.3.4 EDA and Feature Engineering
			15.3.5 Feature Engineering Example
			15.3.6 Identify Model Output and Model Selection
			15.3.7 Model Insights
		15.4 Conclusion and Discussion
		References
Part VIII. Biopharmaceutical Regulatory CMC
	16. Overview of Complexities of Global CMC Regulatory Affairs
		16.1 Introduction
			16.1.1 Regulatory Bodies in Major Markets
				16.1.1.1 United States
				16.1.1.2 European Union
			16.1.2 Global Markets
			16.1.3 Examples of Core Differences in Regulatory Requirements Globally
		16.2 Complexities in Navigating Global Market Drug Development and Managing Multiple Market Dossiers
		16.3 The Role of WHO and ICH in Global Drug Development
		16.4 Complexities of Emergency Use in a Pandemic
			16.4.1 United States FDA
			16.4.2 European Medicines Agency (EMA)
			16.4.3 The World Health Organization
			16.4.4 Examples of Global Regulatory Challenges During a Pandemic
		References
	17. CMC Considerations for Continuous Bioprocess Design, Development, and Manufacturing
		17.1 Introduction
		17.2 Regulatory Guidance, Expectations, and Support for CBP
		17.3 Current Industrial Practice for mAb Production
			17.3.1 Cell Line Development: The Foundation of Biologics Development
				17.3.1.1 Antibody DNA Sequence and Gene Construction
				17.3.1.2 Clone Selection
				17.3.1.3 Cell Culture Process Development
				17.3.1.4 Harvest and Clarification
			17.3.2 DSP Development for CBP Implementation
				17.3.2.1 Continuous Capture with Multi-columns
				17.3.2.2 Integral of Low pH Viral Inactivation with Capture Step
				17.3.2.3 Continuous Polishing
				17.3.2.4 Design of Continuous Viral Filtration (VF)
				17.3.2.5 Design of Continuous UF/DF
				17.3.2.6 Control of Process Performance and Product Quality
			17.3.3 Analytical Method Development, Qualification, and Validation for CBP Implementation
		17.4 Adeno-Associated Virus (AAV) Vector Production
			17.4.1 AAV Application for Vaccine and Gene Therapy
			17.4.2 AAV Plasmid Construction, Transfection, and Cell Culture
			17.4.3 Harvest and Clarification
			17.4.4 AAV Purification
				17.4.4.1 AAV Capture
				17.4.4.2 Intermediate and Polishing Steps
			17.4.5 Future AAV Manufacturing
		17.5 Summary
		References
Part IX. Technology Transfer
	18. Three Decades of Advancements in Technical Transfer of Biologics: A Blueprint for Advanced Therapeutics
		18.1 Introduction
		18.2 Facility Fit Modeling and Engineering Considerations
		18.3 IND Enabling Technology Transfer of a Clinical Asset to a Single-Use Facility
		18.4 Tech Transfer of Biologic Drug Substance (DS) Process to External CMO for Commercial Manufacturing
		18.5 Technology Transfer of Clinical Asset to a Large-Scale Commercial Facility
		18.6 Tech Transfer of Drug Product Process to CMO Case Study
		18.7 Conclusion
Part X. Emerging Trends and Future of Biopharmaceuticals
	19. Emerging Biopharmaceutical Technologies and Trends
		19.1 Introduction
		19.2 Novel Gene and Cell Therapies
			19.2.1 Gene Therapy
			19.2.2 CRISPR Technology
			19.2.3 Cell Therapy
		19.3 Novel RNA-Based Therapies and Vaccines
			19.3.1 mRNA Therapies and Modes of Action
			19.3.2 mRNA Vaccines
		19.4 Trends in Biotech Manufacturing Modalities
			19.4.1 The Rise of Continuous Processing
			19.4.2 Rapid Cell Line and Process Development Approaches
			19.4.3 Portable Manufacturing
		19.5 Discussion and Future Trends
		References
Index