The Future of Pharmaceuticals: A Nonlinear Analysis

Cover
Half Title
Title Page
Copyright Page
Dedication
Table of Contents
Preface
Acknowledgments
Author
List of Important Terminology
Chapter 1 Understanding Nonlinearity
	1.1 Background
	1.2 Predictions
		1.2.1 Examples
	1.3 Modeling Systems
		1.3.1 Bayes’ Theorem
			1.3.1.1 Phases of Paradigm Shift
		1.3.2 Future Shifts
	1.4 Conclusion
	Additional Reading
Chapter 2 The Evolution of Pharmaceuticals
	2.1 Background
	2.2 The Pre-Historical Era
	2.3 The New World Era
	2.4 The Regulatory Era
	2.5 The Legal Era
	2.6 The Gene Era
		2.6.1 The Biological Medicine Era
		2.6.2 Nobel Prizes
	2.7 The Future Era
	2.8 New Entities
		2.8.1 A Special Case
	2.9 Conclusion
	2.10 Appendix: New Molecular Entities Approved by the FDA 2011–2020
	Additional Reading
Chapter 3 Artificial Intelligence
	3.1 Background
	3.2 Bioinformatics
	3.3 Artificial Intelligence
	3.4 Deep Learning Architecture
		3.4.1 Graph Representation Learning
	3.5 Repurposing
	3.6 Data and Model Harmonization
	3.7 Drug Discovery and Development
		3.7.1 Stepwise Approach
		3.7.2 Application Types
		3.7.3 An Example of AI Application
	3.8 AI Tools
	3.9 Conclusion
	Additional Reading
Chapter 4 Drug Discovery Trends
	4.1 Background
	4.2 High-Throughput Screening (HTS)
		4.2.1 Phenotypic Screening
		4.2.2 Modeling
		4.2.3 Screening Using Fragments (FBS)
		4.2.4 Ligandomics
		4.2.5 Gene-Based Testing
		4.2.6 Target Identification
			4.2.6.1 Hit Identification
			4.2.6.2 Hit to Lead
			4.2.6.3 Target Validation and Efficacy
			4.2.6.4 Cell-Based Models
			4.2.6.5 In Vivo Testing
	4.3 Structural Biology
	4.4 Hit Optimization
		4.4.1 PK–PD Relationship
	4.5 Chemistry and Formulation
		4.5.1 Lipinski’s Rule of Five (RO5)
	4.6 Safety Testing
		4.6.1 Animal Models
		4.6.2 Replacing Animal Testing
	4.7 Synthetic Biology
	4.8 Libraries
		4.8.1 DNA Libraries
	4.9 Microphysiometry
		4.9.1 Microfluidics
		4.9.2 Organs-on-a-Chip (OOC)
		4.9.3 Brain-on-a-Chip
		4.9.4 Lung-on-a-Chip
		4.9.5 Heart-on-a-Chip
		4.9.6 Kidney-on-a-Chip
		4.9.7 Nephron-on-a-Chip
		4.9.8 Vessel-on-a-Chip
		4.9.9 Skin-on-a-Chip
		4.9.10 Human-on-a-Chip
	4.10 Clinical Trials
		4.10.1 Biomarkers
			4.10.1.1 BEST
	4.11 Exploratory IND
	4.12 Repurposing
	4.13 Orphan Drugs
	4.14 Conclusion
	Additional Reading
Chapter 5 Drug Development Assays
	5.1 Background
		5.1.1 Assay Optimization
	5.2 Assay Development and Validation
		5.2.1 Pre-Study Validation
		5.2.2 In-Study Validation
		5.2.3 Cross-Validation
		5.2.4 Critical Path
	5.3 Receptor Binding Assays in HTS
		5.3.1 Scintillation Proximity Assays (SPA)
		5.3.2 Filtration Assays
	5.4 In Vitro Biochemical Assays
		5.4.1 Definitions
		5.4.2 Signs of Enzymatic Contamination
		5.4.3 Solutions for Enzymatic Contamination
		5.4.4 Batch Testing
			5.4.4.1 Identity and Mass Purity
			5.4.4.2 Methods for Confirming Identity and Mass Purity
			5.4.4.3 Protein Stain of SDS-PAGE
			5.4.4.4 Western Blot with the Specific Antibody
			5.4.4.5 Analytical Gel Filtration
			5.4.4.6 Reversed-Phase HPLC
			5.4.4.7 Mass Spectrometry
			5.4.4.8 Whole Mass for Protein
			5.4.4.9 Peptide Mass Finger Printing
			5.4.4.10 Edman Sequencing
			5.4.4.11 Crude Enzyme Preparations
			5.4.4.12 Commercial Enzymes
			5.4.4.13 Co-Purification of Contaminating Enzymes
			5.4.4.14 Mock Parallel Purification
			5.4.4.15 Reversal of Enzyme Activity
		5.4.5 Detecting Enzyme Impurities
			5.4.5.1 Consequences of Substrate Selectivity
			5.4.5.2 Substrate Km
			5.4.5.3 Enzyme Concentration
			5.4.5.4 Format Selection
		5.4.6 Validating Enzymatic Purity
			5.4.6.1 Inhibitor-Based Studies
			5.4.6.2 IC50 Value
			5.4.6.3 Hill slope
		5.4.7 Substrate-Based Studies
			5.4.7.1 Substrate Km Determination
			5.4.7.2 Substrate Selectivity Studies
			5.4.7.3 Comparison Studies
			5.4.7.4 Enzyme Source
			5.4.7.5 Format Comparison
	5.5 Enzymatic Assays for HTS
		5.5.1 Basic Concept
			5.5.1.1 Initial Velocity
		5.5.2 Reagents and Method Development
			5.5.2.1 Detection System Linearity
			5.5.2.2 Enzyme Reaction Progress Curve
			5.5.2.3 Measuring the Initial Velocity of an Enzyme Reaction
			5.5.2.4 Measurement of Km and Vmax
			5.5.2.5 What Does the Km Mean?
			5.5.2.6 How to Measure Km
			5.5.2.7 Determination of IC50 for Inhibitors
			5.5.2.8 Optimization Experiments
	5.6 ELISA-Type Assays
		5.6.1 Basic Concept
		5.6.2 General Considerations
			5.6.2.1 Assay Design and Development
		5.6.3 Fluorescence Polarization/Anisotropy
			5.6.3.1 Assay Design
		5.6.4 Fluorescent/Förster Resonance Energy Transfer and Time-Resolved (TR) FRET
		5.6.5 AlphaScreen Format
			5.6.5.1 Optical Biosensors
			5.6.5.2 Nuclear Magnetic Resonance (NMR)
			5.6.5.3 Isothermal Calorimetry (ITC)
			5.6.5.4 Sedimentation Analysis (SA; Analytical Ultracentrifugation)
			5.6.5.5 X-Ray Crystallography
	5.7 In Vitro Toxicity and Drug Efficacy Testing
	5.8 In Vivo Assay Validation
		5.8.1 General Concepts
			5.8.1.1 Pre-Study Validation
			5.8.1.2 In-Study Validation
			5.8.1.3 Cross-Validation
			5.8.1.4 Resources
		5.8.2 Assay Validation Procedures
			5.8.2.1 Pre-Study Validation
	5.9 Pharmacokinetics and Drug Metabolism
		5.9.1 In Vitro Analysis
			5.9.1.1 Lipophilicity
			5.9.1.2 Solubility
			5.9.1.3 Hepatic Microsome Stability
			5.9.1.4 Plasma Stability
			5.9.1.5 Plasma Protein Binding
			5.9.1.6 Screening Cytotoxicity and Hepatotoxicity Test
			5.9.1.7 CYP450 Inhibition Profiling
			5.9.1.8 Permeability
	5.10 Conclusion
	Additional Reading
Chapter 6 Nanomedicine
	6.1 Background
	6.2 Delivery Routes
	6.3 Liposomes
	6.4 Dendrimers
	6.5 Polymers
	6.6 Metal Particles
	6.7 Quantum Dots
	6.8 Fullerenes
	6.9 Theranostics
	6.10 Diagnostics
	6.11 Specific Diseases
		6.11.1 IBD
		6.11.2 Diabetes
		6.11.3 Cancer
	6.12 Regulatory
	Additional Reading
Chapter 7 Antimicrobials
	7.1 Background
	7.2 Eradicable Diseases
		7.2.1 Polio
		7.2.2 Guinea Worm Disease (Dracunculiasis)
		7.2.3 Lymphatic Filariasis
		7.2.4 Measles, Mumps, and Rubella
		7.2.5 Cysticercosis
		7.2.6 Yaws
		7.2.7 Trachoma
		7.2.8 Onchocerciasis
		7.2.9 Malaria
	7.3 Vaccines
		7.3.1 Live-Attenuated Vaccines
		7.3.2 Inactivated Vaccines
		7.3.3 Subunit, Recombinant, Polysaccharide, and Conjugate Vaccines
		7.3.4 Toxoid Vaccines
		7.3.5 Nucleic Acid Vaccines
	7.4 Antibiotics
		7.4.1 Antibiotic Discovery
			7.4.1.1 Semi-Synthetic
			7.4.1.2 Synthetic
			7.4.1.3 Genomic Approaches
		7.4.2 Reverse Genomics: Revival of Cell-Based Screening
		7.4.3 Post-Genomics
			7.4.3.1 Transcriptomics, Proteomics, and Lipidomics
			7.4.3.2 Metabolomics to Meta-Omics
	7.5 Phage Therapy
	7.6 Microbiome
		7.6.1 Impact on Health
		7.6.2 Drug Metabolism
		7.6.3 Drug Toxicity
		7.6.4 Biomarkers
	7.7 Conclusion
	Additional Reading
Chapter 8 Therapeutic Proteins
	8.1 Background
	8.2 Protein Structure and Properties
		8.2.1 Primary Structure
		8.2.2 Secondary Structure
			8.2.2.1 Alpha Helix
			8.2.2.2 Beta-Sheet
		8.2.3 Tertiary Structure
		8.2.4 Quaternary Structure
		8.2.5 Post-Translational Modification (PTM)
		8.2.6 Association and Aggregation
	8.3 Non-Antibody Therapeutic Proteins
		8.3.1 Hormone Peptide Drugs
		8.3.2 Human Hematopoietic Factor
		8.3.3 Human Cytokines
		8.3.4 Human Plasma Protein Factor
		8.3.5 Human Bone Formation Protein
		8.3.6 Enzymes
	8.4 Antibody Therapeutic Proteins
		8.4.1 Mode of Action
		8.4.2 Types of Antibodies
			8.4.2.1 Recombinant Antibodies
			8.4.2.2 Synthetic Antibodies
			8.4.2.3 Affimer Proteins
			8.4.2.4 Structural Protein Scaffolds
			8.4.2.5 Bispecific Antibodies (BsAbs)
			8.4.2.6 Multi-Specific Antibodies (MsAbs)
			8.4.2.7 Fab Fragments and Single-Chain Antibodies
			8.4.2.8 Humanized and Chimeric mAbs
			8.4.2.9 Affinity Maturation
			8.4.2.10 Antigenized Antibodies
			8.4.2.11 IgG1 Fusion Proteins
			8.4.2.12 Drug or Toxin Conjugation
			8.4.2.13 Future Antibodies
		8.4.3 Development of Antibodies
		8.4.4 Exogenous Methods
			8.4.4.1 Mouse Hybridoma
			8.4.4.2 Transgenic Mice
		8.4.5 Surface Display Libraries
			8.4.5.1 Phage Display
			8.4.5.2 Yeast Display
			8.4.5.3 Ribosome Display
			8.4.5.4 mRNA Display
		8.4.6 Recombinant Expression
	8.5 Immunogenicity
		8.5.1 Protein Immunogenicity
		8.5.2 Immunogenicity Testing
		8.5.3 Innate System
		8.5.4 Adaptive System
	8.6 Pharmacokinetics of Therapeutic Proteins
		8.6.1 Absorption
		8.6.2 Distribution
		8.6.3 Elimination
		8.6.4 Pharmacokinetic Manipulations
			8.6.4.1 Protein Modification to Increase Duration of Action
			8.6.4.2 Protein Pegylation
			8.6.4.3 Unnatural Construction
	8.7 Conclusion
	Additional Reading
Chapter 9 Manufacturing Trends
	9.1 Background
	9.2 Process Optimizations
		9.2.1 Cell Line Development
		9.2.2 Media
		9.2.3 High Cell Density Cryopreservation
		9.2.4 Cell Culture Operations
		9.2.5 Bioreactor Cycle
	9.3 Single-Use Technology (SUT)
		9.3.1 Containers and Mixing Systems
		9.3.2 Drums, Containers, and Tank Liners
			9.3.2.1 2D Bags
			9.3.2.2 3D Bags
		9.3.3 Advantages
		9.3.4 Single-Use Bioreactors (SUBS)
		9.3.5 Other Components
			9.3.5.1 Optical Sensors
			9.3.5.2 Biomass Sensors
			9.3.5.3 Electrochemical Sensors
			9.3.5.4 Pressure Sensors
			9.3.5.5 Sampling Systems
			9.3.5.6 Connectors
			9.3.5.7 Tubing
			9.3.5.8 Pumps
			9.3.5.9 Tube Welder and Sealers
		9.3.6 Sampling
		9.3.7 Downstream Processing
			9.3.7.1 Cell Harvest
			9.3.7.2 Purification
			9.3.7.3 Virus Removal
			9.3.7.4 Filtration—UF/DF and TFF
			9.3.7.5 General Filtration Applications
		9.3.8 Fill Finish Operations
		9.3.9 Safety
			9.3.9.1 Polymers and Additives
			9.3.9.2 Material Selection
			9.3.9.3 Testing
			9.3.9.4 Regulatory
	9.4 Online Monitoring
	9.5 Continuous Manufacturing
		9.5.1 Continuous Chromatography Operations
			9.5.1.1 Straight Through Processing (STP)
			9.5.1.2 Periodic Countercurrent Chromatography (PCC)
			9.5.1.3 Simulated Moving Bed (SMB) Chromatography
	9.6 Conclusion
	Appendix: Databases Relevant to Antibodies
	Additional Reading
Chapter 10 Therapeutic Protein Delivery Systems
	10.1 Background
	10.2 Route Selection
		10.2.1 Selection
		10.2.2 Excipients and Properties
			10.2.2.1 pH
			10.2.2.2 Surface Tension
			10.2.2.3 Tonicity
			10.2.2.4 Protectants
			10.2.2.5 Stabilizers
		10.2.3 Liquid Formulations
		10.2.4 Lyophilized Formulations
	10.3 Delivery Routes
		10.3.1 Intravenous
		10.3.2 Subcutaneous
		10.3.3 Oral
		10.3.4 Nasal
		10.3.5 Transdermal
		10.3.6 Pulmonary
		10.3.7 Ocular
		10.3.8 Rectal
	10.4 Formulation Technologies
		10.4.1 Hydrogels and In Situ Forming Gels
		10.4.2 Nanoparticles
		10.4.3 Liposome
		10.4.4 Higher Concentration Formulations
	10.5 Examples of Formulation
		10.5.1 Oprelvekin Injection (Interleukin IL-11)
		10.5.2 Interleukin Injection (IL-2)
		10.5.3 Interferon Alfa-2a Injection
		10.5.4 Interferon Beta-1b
		10.5.5 Interferon Beta-1a Injection
		10.5.6 Interferon Alfa-n3 Injection
		10.5.7 Interferon Alfacon-1 Injection
		10.5.8 Interferon Gamma-1b Injection
		10.5.9 Infliximab for Injection
		10.5.10 Daclizumab for Injection
		10.5.11 Coagulation Factor VIIa (Recombinant) Injection
		10.5.12 Reteplase Recombinant for Injection
		10.5.13 Alteplase Recombinant Injection
	10.6 Conclusion
	Appendix 10.1 Physicochemical Properties of Proteins and Peptides Approved by the FDA
Chapter 11 Gene and Cell Therapy
	11.1 Background
	11.2 Gene Therapy
		11.2.1 Viral Vector Manufacturing
		11.2.2 Downstream Manufacturing
		11.2.3 Risks of Gene Therapy
		11.2.4 Gene Editing
		11.2.5 Techniques
		11.2.6 Gene Editing Technologies
		11.2.7 CRISPR
		11.2.8 DNA-Based Therapeutics
		11.2.9 Gene Transfer Technologies
			11.2.9.1 Mechanical and Electrical Techniques
			11.2.9.2 Vector-Assisted Delivery Systems
		11.2.10 Approved Products
	11.3 Cell Therapy
		11.3.1 Types of Cell Therapies
		11.3.2 CAR-T Therapy
		11.3.3 Allogenic Cell Therapy
	11.4 Regulatory Considerations
		11.4.1 Development and Characterization of Cell Populations for Administration (https://www​.fda​.gov​/media​/72402​/download)
			11.4.1.1 Collection of Cells
			11.4.1.2 Tissue Typing
			11.4.1.3 Procedures
		11.4.2 Characterization and Release Testing of Cellular Gene Therapy Products
			11.4.2.1 Cell Identity
			11.4.2.2 Potency
			11.4.2.3 Viability
			11.4.2.4 Adventitious Agent Testing
			11.4.2.5 Purity
			11.4.2.6 General Safety Test
			11.4.2.7 Frozen Cell Banks
		11.4.3 Additional Applications: Addition of Radioisotopes or Toxins to Cell Preparations
		11.4.4 Production, Characterization, and Release Testing of Vectors for Gene Therapy
			11.4.4.1 Vector Construction and Characterization
			11.4.4.2 Vector Production System
			11.4.4.3 Master Viral Banks
			11.4.4.4 Lot-to-Lot Release Testing and Specifications for Vectors
			11.4.4.5 Adventitious Agents
		11.4.5 Issues Related to Particular Classes of Vectors for Gene Therapy
			11.4.5.1 Additional Considerations for the Use of Plasmid Vector Products
			11.4.5.2 Additional Considerations for the Use of Retroviral Vector Products
			11.4.5.3 Additional Considerations for the Use of Adenoviral Vectors
		11.4.6 Modifications in Vector Preparations
		11.4.7 Preclinical Evaluation of Cellular and Gene Therapies
			11.4.7.1 General Principles
			11.4.7.2 Animal Species Selection and Use of Alternative Animal Models
			11.4.7.3 Somatic Cell and Gene-Modified Cellular Therapies
			11.4.7.4 Direct Administration of Vectors In Vivo
			11.4.7.5 Expression of Gene Product and Induction of Immune Responses
			11.4.7.6 Vector Localization to Reproductive Organs
	11.5 Conclusion
	Additional Reading
Chapter 12 Nucleic Acid Vaccines
	12.1 Background
	12.2 mRNA Vaccine
		12.2.1 Development Cycle
		12.2.2 Formulation and Delivery
		12.2.3 COVID-19 Vaccine
	12.3 DNA Vaccine
		12.3.1 Delivery
		12.3.2 Antibody Response
	Additional Reading
Chapter 13 Botanical Products
	13.1 Overview
	13.2 Complimentary Medicines
		13.2.1 History
		13.2.2 Development Innovations
		13.2.3 Technologies
		13.2.4 Genomics and Biomarkers
		13.2.5 Proteomics
		13.2.6 Target Identification of Label-Free Botanical Products
		13.2.7 Metabolomics and Metabonomics
	13.3 Regulatory Plan
		13.3.1 Background
		13.3.2 Chemistry
		13.3.3 Specifications
		13.3.4 Standardization
		13.3.5 Efficacy and Safety
		13.3.6 Prior Human Use
		13.3.7 CMC
			13.3.7.1 Starting Material
			13.3.7.2 Control of Botanical Substances and Preparations
			13.3.7.3 Control of Vitamins and Minerals (If Applicable)
			13.3.7.4 Control of Excipients
			13.3.7.5 Stability Testing
			13.3.7.6 Testing Criteria
			13.3.7.7 Botanical Substances
			13.3.7.8 Botanical Product
	13.4 Conclusion
	Additional Reading
Chapter 14 Regulatory Optimization
	14.1 Background
	14.2 Scope
		14.2.1 Assumptions
		14.2.2 Definitions
	14.3 New Chemical Entities
		14.3.1 Decision Stage #1—Target Identification
		14.3.2 Decision Stage #2—Target Validation
		14.3.3 Decision Stage #3—Identification of Actives
		14.3.4 Decision Stage #4—Confirmation of Hits
		14.3.5 Decision Stage #5—Identification of Chemical Lead
		14.3.6 Decision Stage #6—Selection of Optimized Chemical Lead
		14.3.7 Decision Stage #7—Selection of a Development Candidate
		14.3.8 Decision Stage #8—Pre-IND Meeting with the FDA
		14.3.9 Decision Stage #9—Preparation and Submission of an IND Application
		14.3.10 Decision Stage #10—Human Proof of Concept
		14.3.11 Decision Stage #11—Clinical Proof of Concept
	14.4 Repurposing of Marketed Drugs
		14.4.1 Decision Stage #1: Identification of Actives
		14.4.2 Decision Stage #2: Confirmation of Hits
		14.4.3 Decision Stage #3: Gap Analysis/Development Plan
		14.4.4 Decision Stage #4: Clinical Formulation Development
		14.4.5 Decision Stage #5: Preclinical Safety Data Package
		14.4.6 Decision Stage #6: Clinical Supplies Manufacture
		14.4.7 Decision Stage #7: IND Preparation and Submission
		14.4.8 Decision Stage #8: Human Proof of Concept
	14.5 Drug Delivery Platform Technology
		14.5.1 Decision Stage #1: Clinical Formulation Development
		14.5.2 Decision Stage #2: Development Plan
		14.5.3 Decision Stage #3: Clinical Supplies Manufacture
		14.5.4 Decision Stage #4: Preclinical Safety Package
		14.5.5 Decision Stage #5: IND Preparation and Submission
		14.5.6 Decision Stage #6: Human Proof of Concept
		14.5.7 Decision Stage #7: Clinical Proof of Concept
	14.6 Biological Products
		14.6.1 Batch
		14.6.2 Upstream
		14.6.3 Downstream
		14.6.4 Facility
		14.6.5 Equipment
		14.6.6 Validation
		14.6.7 Testing
		14.6.8 Quality
		14.6.9 Fill
		14.6.10 Water
		14.6.11 Facility Design
		14.6.12 Cleaning
		14.6.13 Filling and Finishing
	14.7 Testing
	14.8 Documentation Process
		14.8.1 Process Analytical Technology (PAT)
		14.8.2 Automation
	14.9 Predictions
	14.10 Conclusion
	Additional Reading
Chapter 15 Intellectual Property
	15.1 Background
	15.2 About Patents
	15.3 Patent Landscape
	15.4 Patent Laws
		15.4.1 Pharmaceutical Patenting Practices
	15.5 Types of Patents
		15.5.1 Utility Model in the EU
		15.5.2 Provisional Application
	15.6 Nonobviousness
	15.7 Patent Management
		15.7.1 Broad Coverage
		15.7.2 Submarine Patents
		15.7.3 System Expression Patents
		15.7.4 Process Patents of Originator
		15.7.5 Third-Party Process Patents
		15.7.6 Formulation Composition
		15.7.7 Lifecycle Formulation Projections
		15.7.8 Alternate Offering
		15.7.9 Delivery Devices
		15.7.10 Unpatentable Inventions
		15.7.11 Software Patents
		15.7.12 Medical Method Patents
	15.8 Patent Classification
		15.8.1 Class 435
		15.8.2 Class 424
		15.8.3 Class 801
	15.9 Biological Patents
		15.9.1 Biological Products
		15.9.2 Monoclonal Antibody Technology
		15.9.3 Antisense Technology
		15.9.4 Transgenic Plants
	15.10 Freedom to Operate
	15.11 Conclusion
	Additional Reading
Index