Protein-based Therapeutics

Preface
Contents
About the Editors
1: Introduction to Protein Therapeutics
1.1 Introduction
1.1.1 Structural Organization of Proteins
1.2 Functions of Proteins
1.3 Therapeutic Proteins
1.3.1 Classification of Therapeutic Proteins
1.3.1.1 Group I: Therapeutic Proteins with Enzymatic Activity
1.3.1.2 Group II: Therapeutic Proteins with Special Targeting Activity
1.3.1.3 Group III: Therapeutic Protein Vaccines
1.3.1.4 Group IV: Therapeutic Protein Diagnostics
1.3.2 Challenges for Therapeutic Proteins
1.3.2.1 Efficacy
1.3.2.2 Quality
1.3.2.3 Stability
1.3.2.4 Immunogenicity
1.4 Methods for Production of Therapeutic Proteins
1.5 Delivery of Therapeutic Proteins
1.5.1 Invasive Delivery Systems
1.5.2 Noninvasive Delivery Systems
1.6 Biosimilars
1.7 Computational Resources for Therapeutic Proteins
1.7.1 THBdB (Database of FDA-Approved Therapeutic Peptides and Proteins)
1.7.2 TTDB (Therapeutic Target Database)
1.7.3 SATPdb (Database of Structurally Annotated Therapeutic Peptides)
1.7.4 CKTTD (Checkpoint Therapeutic Target Database)
1.7.5 HAPPENN (Novel Tool for Hemolytic Activity Prediction for Therapeutic Peptides)
1.7.6 BioDADPep (Bioinformatics Database for Antidiabetic Peptides)
1.8 Conclusions
References
2: Clinical Applications of Protein-Based Therapeutics
2.1 Introduction
2.2 Enzyme as Biologics
2.2.1 Biological Process: How Enzymes Work?
2.2.2 Therapeutic Enzymes
2.3 Antibodies as Biologics
2.3.1 Monoclonal Antibody Products as Biologics
2.3.1.1 Biological Characteristics of mAbs
2.3.1.2 Applications of mAbs
Fab Fragments
Bifunctional Antibodies
2.3.2 Non-Monoclonal Antibody Products as Biologics
2.4 Precision Medicine
2.4.1 Benefits of Precision Medicine
2.4.2 Applications of Precision Medicine
2.4.3 Future Prospects of Precision Medicine
2.5 Computer-Aided Drug Design
2.5.1 Approaches of CADD in Designing Protein-Based Therapeutics
2.5.1.1 Structure-Based Drug Design Approach
2.5.1.2 Ligand-Based Drug Design Approach
2.5.2 Quantitative Structure-Activity Relationship
2.5.3 Applications of CADD in Protein-Based Therapeutics
2.6 Overview of Recently Approved Protein Therapeutics for Clinical Applications
2.6.1 Diabetes
2.6.2 Interferon-beta
2.6.3 Cancer
2.7 Emerging Issues and Developments in Proteins-Based Therapeutics
2.7.1 Issue of Demand and Supply
2.7.2 Issues Related to Immunogenicity
2.7.3 Issue of Protein Stability
2.7.4 Issues of Metabolism and Elimination
2.8 Conclusion and Future Prospects
References
3: Protein Engineering Methods to Design Protein Therapeutics
3.1 Protein Engineering: A Realm for Biological Therapeutics
3.1.1 Introduction
3.1.2 Protein Structure Modeling and Prediction
3.1.2.1 Protein Structure
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
3.1.2.2 Protein Structure Prediction
Comparative Modeling
Fold Recognition
Prediction Based on First Principles Using Data from Database
Prediction Based on First Principles Without Using Data from Database
3.1.3 Protein and Metabolite Identification
3.1.3.1 Peptide Mapping
3.1.3.2 Tandem Mass Spectrometry
3.1.3.3 Protein Databases
3.1.3.4 Bottom-Up and Top-Down Mass Spectrometry
3.1.3.5 Metabolite Identification
MS Metabolite Identification
NMR Metabolite Identification
3.1.4 Folding of Proteins
3.1.4.1 Structural Classes of Proteins
3.1.4.2 Protein Misfolding
3.1.5 Motif, Domains, and Scaffolds
3.1.5.1 Machine Discovery of Protein Motifs
Sequence and Sequence-Structure Motifs
Structure Motifs
Structure-Sequence Motifs
3.1.6 Current and Future Protein Therapeutics
3.2 Therapeutic Protein Engineering
3.2.1 Protein Engineering Techniques
3.2.1.1 Rational Protein Design
3.2.1.2 Random Mutagenesis
3.2.1.3 Combinatorial Protein Design
Error-Prone PCR
DNA Shuffling
3.2.1.4 Knowledge-Based Protein Design
3.2.1.5 Computational Protein Design
3.2.1.6 Directed Evolution
3.2.2 Source, Targets, and Mechanism of Action of Protein Therapeutics
3.2.3 Developing Effective Protein Therapeutic
3.2.3.1 Improving Pharmacokinetics and Reducing Immunogenicity
3.2.4 Examples of Protein Therapeutics
3.2.4.1 Extracellular Targets of Protein/Enzyme Therapeutics
3.2.4.2 Monoclonal Antibodies as Therapeutics
3.2.4.3 Protein Therapeutics as Replacements for Proteins That Are Defective or Insufficient
3.2.4.4 Protein Therapeutics Using Cytokines and Their Receptors
3.3 De Novo Protein Design for Biotechnological Purposes
3.3.1 Physical Principles of Protein Design
3.3.2 De Novo Protein Design
3.3.3 Design of Proteins and Peptides for Therapeutic Applications
3.3.3.1 Alzheimer´s Disease
3.3.3.2 Cancer
3.3.3.3 HIV
3.3.3.4 Antibody Therapeutics
3.3.4 Designing Repeat Proteins
3.3.5 Designing Recombinant Therapeutics
3.3.6 Advances and Challenges
3.4 Unleashing the Potential of Therapeutic Proteins
3.4.1 Advanced Protein Engineering Reinforcing Next-Generation Therapeutics
3.4.2 Genetic Engineering
3.4.3 Antibody and Therapeutic Protein Engineering
3.4.4 Exon Shuffling as a Method of Protein Evolution
3.4.5 Site Saturation Mutagenesis Methods and Applications in Protein Engineering
3.5 Applications of Protein Engineering in Therapeutics
3.6 Case Study: Protein Engineering for Cardiovascular Therapeutics
3.7 Conclusion
References
4: Recombinant Production of Therapeutic Proteins
4.1 Introduction
4.2 Methods for the Production of Recombinant Therapeutic Proteins
4.2.1 Production of Recombinant Proteins in E. coli
4.2.1.1 Host
4.2.1.2 Vector
4.2.1.3 Media Preparation and Fermentation
4.2.2 Therapeutic Protein Production in Bacterial Cultures
4.2.2.1 Therapeutic Enzymes
4.2.2.2 Therapeutic Hormones
4.2.2.3 Recombinant Cytokine Production
4.2.2.4 Recombinant Toxins
4.3 Production of Recombinant Therapeutic Proteins in Mammalian Cell Cultures
4.3.1 Therapeutic Proteins Expressed in Chinese Hamster Ovary (CHO) Cell Lines
4.3.1.1 Enzyme Production
4.3.1.2 Clotting Factor Production
4.3.1.3 Production of Hormones
4.3.1.4 Cytokine Production
4.3.2 Other Mammalian Cell Lines Used for Therapeutic Protein Production
4.4 Production of Recombinant Therapeutic Proteins Using Plant Cell Cultures
4.5 Production of Recombinant Proteins in Transgenic Animals
4.6 Production of Recombinant Proteins in Yeast
4.7 Conclusions
References
5: Antibodies as Therapeutic Agents
5.1 Structure of Antibodies
5.2 Functions of Antibodies
5.2.1 Effector-Independent Functions
5.2.2 Effector-Dependent Functions
5.3 Formats of Antibodies as Therapeutics
5.3.1 Polyclonal Antibodies (pAbs)
5.3.1.1 Production of pAbs
5.3.1.2 Intravenous Immunoglobulin G (IVIG)
5.3.1.3 Recombinant pAbs
5.3.1.4 Transgenic pAbs
5.3.2 Monoclonal Antibodies (mAbs)
5.3.2.1 Production of mAbs
5.3.3 Modified mAbs
5.3.3.1 Chimeric Antibodies
5.3.3.2 Humanized mAbs
5.3.4 Antibody Fragments
5.3.4.1 Single-Chain Variable Fragments (scVF)
Design and Synthesis of scFV
Applications of scFV
5.3.4.2 Heavy-Chain Antibodies (hcAbs) and Single-Domain Antibodies (sdAbs)
VHH Domain
Designing and Expression of sdAbs (Nanobodies)
Applications of sdAbs
Targeting Tumors and Inflammation
Cell Surface ProteinsCell Surface Proteins
Cytokines and Other Soluble ProteinsCytokines and Other Soluble Proteins
sdAbs Against Infectious Agents and Their ToxinssdAbs Against Infectious Agents and Their Toxins
5.4 Challenges and Prospects of Therapeutic Antibodies
5.5 Conclusions
References
6: Strategies for Formulation and Systemic Delivery of Therapeutic Proteins
6.1 Introduction
6.2 General Challenges in the Delivery of Therapeutic Proteins
6.2.1 Chemical and Physical Instability
6.2.2 Biopharmaceutical Challenges
6.3 Invasive Delivery Systems and Delivery Challenges
6.4 Non-Invasive Delivery Systems and Delivery Challenges
6.5 Processing Strategies to Increase the Stability of Therapeutic Proteins
6.5.1 Lyophilization
6.5.2 Spray Freeze-Drying
6.5.3 Other Common Methods
6.6 Formulation Strategies for Overcoming Protein Drug Delivery Challenges
6.6.1 Strategies for Enhanced Delivery and Stability of Therapeutic Proteins Via Invasive Routes
6.6.1.1 Chemical Modifications
6.6.1.2 Controlled Release Drug Delivery Systems
Microspheres
Implants
Liposomes
Hydrogels
Nanoparticles
Solid Lipid Nanoparticles (SLNs) and Nanostructured Lipid Carriers (NLCs)
Vaccine Adjuvants
Others
6.6.2 Strategies for Enhanced Delivery of Therapeutic Proteins Via Non-invasive Routes
6.6.2.1 Oral Delivery
Modifying the Structure
Absorption Enhancers
Enzyme Inhibitors
Micro/Nanocarrier Systems
Formulations Based on Polysaccharides
Formulations Based on Lipids
Formulations Based on Polymers
Others
6.6.2.2 Transdermal Delivery
Formulations Based on Lipids
Formulations Based on Polymers
Others
6.6.2.3 Intranasal Delivery
Formulations Based on Polymers
Formulations Based on Lipids
6.6.2.4 Pulmonary Delivery
Formulations Based on Lipids
Formulations Based on Polymers
6.6.2.5 Rectal Delivery
Formulations Based on Lipids
Formulations Based on Polymers
6.6.2.6 Ocular Delivery
Formulations Based on Polymers
Formulations Based on Lipids
6.7 Computer-Aided Preparation of Formulations
6.8 Conclusion and Future Prospects
References
7: Approved Protein Therapeutics and Their Biochemical Targets
7.1 Overview of Protein Therapeutics Approval Process
7.2 Classification of Protein Therapeutics
7.3 Protein Therapeutics: An Update
7.4 Approved Protein Therapeutics and Their Biochemical Action
7.4.1 Teprotumumab
7.4.2 Risankizumab
7.4.3 Sacituzumab Govitecan
7.4.4 Belantamab Mafodotin
7.4.5 Blinatumomab
7.4.6 Luspatercept
7.4.7 Efmoroctocog Alfa
7.4.8 Afamelanotide
7.4.9 Macimorelin
7.4.10 Pegcetacoplan
7.4.11 Lonapegsomatropin
7.4.12 Setmelanotide
7.4.13 Galium-68-DOTATOC
7.4.14 Pegvaliase
7.4.15 Avalglucosidase Alfa
7.5 Conclusion and Future Perspectives
References
8: Pharmacogenetic Biomarkers of Protein Therapeutics
8.1 Introduction
8.2 Pharmacogenetics Based on Pharmacodynamics of Protein Therapeutics
8.2.1 Protein Therapeutics and Their Effect on Upstream and Downstream Pathways
8.2.1.1 Interferon-Alpha (IFNα)
8.2.1.2 Rituximab
8.2.1.3 Infliximab
8.2.1.4 Etanercept
8.2.1.5 Anakinra
8.2.1.6 Tissue Plasminogen Activator (tPA)
8.2.1.7 Peptide Immunotherapy with Amyloid Beta
8.2.2 Protein Therapeutics and Their Effect on Genetic Variations in Drug Targets
8.2.2.1 Trastuzumab
8.3 Pharmacokinetics-Based Pharmacogenetics
8.4 Pharmacogenetics-Based Immunogenicity Prediction of Protein Therapeutics
8.5 Conclusions
References
9: Immunogenicity of Therapeutic Proteins
9.1 Introduction
9.2 Immunogenicity
9.2.1 Factors Responsible for Immunogenicity [24]
9.2.1.1 Patient-Related Factors
Age
Genetic Factors
Diseases
Pre-Existing Antibodies
9.2.1.2 Product-Related Factors
Protein Source
Protein Structure
Formulation and Packaging
Treatment Duration and Frequency of Dose
Route of Administration
9.2.2 Aggregation
9.2.2.1 Aggregation and Immunogenicity
9.2.2.2 Interaction of Protein Aggregate with Immunity
9.2.2.3 Innate Immunity Against Antigens
9.2.2.4 Antidrug Antibody Formation
9.3 Therapeutic Proteins
9.3.1 Delivery of Therapeutic Proteins
9.3.2 Immunogenicity and Therapeutic Proteins
9.3.3 Safety and Efficacy
9.3.4 Quality
9.3.5 Biopharmaceutics of Therapeutic Proteins
9.4 Prediction of Immunogenicity of Therapeutic Proteins
9.4.1 Analysis of ADAs
9.4.2 In silico Models for Predicting Immunogenicity
9.5 Exclusion and Avoidance of Immunogenicity of Therapeutic Proteins
9.6 Limitations and Future Perspectives
9.6.1 Physicochemical Instability
9.6.2 Pharmacokinetics of Therapeutic Proteins
9.6.3 Manufacturing System
9.7 Conclusions
References
10: Efficacy and Safety of Therapeutic Proteins
10.1 Introduction
10.2 Classification of Therapeutic Proteins
10.2.1 Classification Based on Pharmacological Activity
10.2.2 Classification Based on Molecular Types
10.2.3 Classification Based on the Molecular Mechanism
10.3 Safety
10.3.1 On-Target Activity
10.3.2 Off-Target Activity
10.4 Efficacy
10.5 Consequences of Clinical Approach
10.6 Pharmacokinetics of Therapeutic Protein
10.6.1 Absorption
10.6.2 Distribution
10.6.3 Metabolism
10.6.4 Excretion
10.7 Examples of Therapeutic Proteins
10.7.1 Therapeutic Proteins for Diabetes
10.7.2 Anticancer Proteins
10.7.3 Therapeutic Proteins for Cardiac Diseases
10.7.4 Therapeutic Protein in COVID-19
10.8 Conclusions and Future Perspectives
References
11: Emerging Trends, Challenges, and Opportunities in Protein Therapeutics
11.1 Introduction
11.2 Emerging Strategies for Protein-Based Therapeutics
11.2.1 Generation of Glycosylated Proteins to Synthesize First- and Second-Generation Drugs
11.2.2 Fc Fusion Proteins
11.2.3 Assisted Design of Antibody and Protein Therapeutics (ADAPT)
11.2.4 Injectable Implants in In Situ
11.3 Role of Protein Therapeutics in the Field of Medicine
11.3.1 Cancer-Related Disorders
11.3.2 Inflammatory Diseases
11.3.3 Genetic Disorders
11.4 Process of Drug Development and Food and Drug Administration (FDA)-Approved Protein Therapeutics
11.4.1 Overall Process of Drug Development
11.4.2 Drug Discovery
11.4.3 Preclinical Research
11.4.4 Clinical Research
11.4.4.1 Interventional Studies (Clinical Trials)
11.4.4.2 Observational Studies
11.4.5 Food and Drug Administration (FDA)
11.4.6 Protein Therapeutics
11.4.6.1 Group 1: Regulatory and Enzyme Proteins
11.4.6.2 Group 2: Proteins with Special Targeting Activity
11.4.6.3 Group 3: Protein Vaccines
11.4.6.4 Group 4: Protein Diagnostics
11.5 Engineered Protein Scaffold as Emerging Therapeutic Proteins
11.5.1 Affibody
11.5.2 Adnectin
11.5.3 Anticalins
11.5.4 DARPins
11.6 Production of Recombinant Protein Therapeutics and their Applications
11.6.1 Cloning and Initial Preparation to Produce Recombinant Proteins
11.6.2 Expression of Recombinant Proteins
11.6.2.1 Mammalian Systems
11.6.2.2 Insect Systems
11.6.2.3 Yeast Systems
11.6.2.4 Bacterial Systems
11.6.2.5 Algal Systems
11.6.2.6 Cell-Free Systems
11.6.3 Applications of Recombinant Proteins
11.6.3.1 Medicine
11.6.3.2 Research
11.6.3.3 Industrial Applications
11.6.4 Recombinant Proteins in Diseases and Vaccines
11.7 Developments in Recombinant Protein-Based Vaccines
11.8 Challenges in Protein Therapeutics
11.8.1 Problems Related to In Vivo Administration
11.8.2 Mechanism Involved in Clearance
11.8.3 Strategies for Increasing the Half-Life
11.8.4 Developmental Challenges
11.8.5 Safety and Immunogenicity Issues
11.9 Strategies to Overcome Challenges in Protein Therapeutics
11.10 Opportunities in Protein Therapeutics
11.11 Conclusions
References
12: Biosimilar, Biobetter, and Biosuperior Therapeutic Proteins
12.1 Introduction
12.2 A Brief History of Therapeutic Proteins
12.3 Classification of Therapeutic Proteins
12.4 Overview of Approved Therapeutic Proteins
12.5 Scope of Therapeutic Proteins
12.6 Biosimilar, Biobetter, and Biosuperior Therapeutic Proteins
12.6.1 Biosimilars
12.6.2 Biobetters
12.6.3 Biosuperiors
12.7 Similarities and Differences Between Biosimilar, Biobetter, and Biosuperior Therapeutic Proteins
12.8 Advantages of Biobetters over Biosimilars
12.9 Technologies to Produce Biobetter and Biosuperior Therapeutic Proteins
12.9.1 Protein Production Technology
12.9.1.1 Transgenic Animals
12.9.1.2 Transgenic Plants
12.9.2 Rational Protein Structure Technologies
12.9.2.1 Glycosylation
12.9.2.2 PEGylation
12.9.3 Modification of Therapeutic Proteins Via Fusion
12.9.3.1 Fusion with the Fc Domain of Immunoglobulins
12.9.3.2 Albumin Fusion
12.9.3.3 Antibody-Drug Conjugates
12.9.4 Humanization
12.9.5 Altering Amino Acid Sequences
12.9.6 Sustained Release
12.9.7 New Routes of Administration
12.10 Delivery System of Therapeutic Proteins
12.11 Challenges in the Production of Therapeutic Proteins
12.12 Next-Generation Biosimilar and Bio-Betters: Success and Difficulties
12.12.1 Safety
12.12.2 Immunogenicity
12.12.3 Quality
12.13 Concluding Remarks
References
13: Therapeutic Protein-Based Vaccines
13.1 Introduction
13.2 Types of Vaccines
13.2.1 Protein-Based Vaccines
13.3 Design and Development of Protein-Based Vaccines
13.3.1 Glycoconjugate Vaccines
13.3.2 Protein Subunit Vaccines and Structure-Based Antigen Design
13.4 Delivery and Mechanism of Action of Protein-Based Vaccines
13.4.1 B-Cell Repertoires, Antibody Discovery, and the Human Immune Response
13.4.2 Nucleic Acid Vector Vaccine Delivery Systems
13.4.3 Synthetic Viral Seeds for Rapid Generation of Influenza Vaccines
13.5 Advantages and Limitations of Protein-Based Vaccines
13.6 Recombinant Production of Protein-Based Vaccines
13.6.1 Bacterial Systems
13.6.2 Yeast System
13.6.3 Mammalian Cells
13.6.4 Insect Cells
13.6.5 Plant-Based System
13.7 Current Status of Protein-Based Vaccines
13.7.1 Influenza Vaccine
13.7.2 Cancer
13.7.3 COVID-19
13.7.4 Other Diseases
13.8 Assistance of Artificial intelligence in Vaccine Development
13.9 Challenges and New Approaches for Protein-Based Therapeutics
13.9.1 Safety
13.9.2 Efficacy
13.9.3 Quality
13.10 Conclusion and Future Perspectives
References