Executive Summary
Engineering next generation protein drugs
Strategies and technologies for protein engineering
Engineering improved monoclonal antibodies
Engineering alternatives to antibodies
Engineering other protein and peptide drugs
Engineering protein therapeutics for delivery
Trends and opportunities
Chapter 1 Engineering next generation
protein drugs
Summary
Introduction
Background on proteins
Patenting of proteins
Regulatory requirements
Commercial imperatives in protein engineering
Introduction
Application markets
Manufacturer markets
Product markets
Geographical markets
Patenting considerations
Usefulness of patent metrics
The protein engineering patent data set
Analysis by assignee patent count
Analysis by forward citation count
Commercial outlook for engineered proteins
Chapter 2 Strategies and technologies for
protein engineering
Summary
Introduction
Recombinant protein production
Site-directed mutagenesis
Post-translational modifications (PTMs)
Glycosylation of natural proteins
Manufacture of glycoproteins
Glyco-remodeling
Other PTMs
Protein characterization
Directed evolution
Display technologies
Use of protein scaffolds
Peptide and protein synthesis
Chemoselective ligation
In silico protein design
Technology-related patents
Monoclonal antibodies
Other proteins and peptides
Chapter 3 Engineering improved
monoclonal antibodies
Summary
Natural antibodies
Human IgG
Generation of antibody diversity
Monoclonal antibodies
Evolution of mAbs
Drivers for innovation
The mAb business landscape
Products on the US market
Products in development
Improving mAb production systems
Cell lines
Automation
Manipulating mAb glycosylation profiles
Enhancing mAb serum stability
Engineering fully human mAbs
Human mAbs from recombinant antibody libraries
Immune and nonimmune antibody libraries
Optimization
Phage display libraries
Ribosome and mRNA display antibodies
Yeast-display antibodies
Human mAbs from transgenic mice and chickens
Human mAbs on the market and in development
Engineering novel antibody fragments
Monovalent fragments
Multivalent fragments
Fragments on the market and in development
Engineering for specific therapeutic applications
Cancer
Unconjugated mAbs
Conjugated mAbs and fusion proteins
Immune and inflammatory disorders
Other areas
Chapter 4 Engineering alternatives to
antibodies
Summary
Introduction
Comparison with monoclonal antibodies
Combinatorial scaffold libraries
Scaffolds used in library construction
Beta-sheet frameworks
Mixed/irregular secondary structures
Alpha-helical frameworks
Repeat proteins
Scaffold optimization and diversification
Selection technologies
Recognition proteins as therapeutics
Products in commercial development
Adnexus Therapeutics
Evogenix
Bristol Myers-Squibb
Pieris Proteolab
Avidex
Affibody
Molecular Partners
Aptanomics
Selecore
Avidia
BioRexis
Isogenica
Bracco Research
Chapter 5 Engineering other protein and
peptide drugs
Summary
Introduction to protein/peptide drugs
Drivers for innovation
The business landscape
Products on the market and in development
Improving production systems
Recombinant methods
Transgenic methods
Chemical methods
Tackling immunogenicity
Manipulating PTMs
Glycoprotein profiling
Glyco-engineering
Amgen
Genzyme
Neose Technologies
University of Maryland
Other PTMs
Altering plasma half-lives
Amino acid modifications
Variations in glycosylation
PEGylation
Chemical modification
Other novel approaches
Case study: Erythropoiesis-stimulating agents
Expediting peptide drug discovery
Phage and other display technologies
Dyax
California Institute of Technology
Rational design
Peptide mimetics
Case study: Antimicrobial peptide discovery
Exploring the role of pharmacogenomics
Chapter 6 Engineering protein therapies for
delivery
Summary
Introduction
Injectable protein delivery
Half-life extension technologies
PolyTherics’ TheraPEG PEGylation technology
Affymaxs’ PEGitecture technology
Neose Technologies' GlycoPEGylation technology
Approved PEGylated biopharmaceuticals
Other approaches
Depot systems
Biodegradable drug carrier systems
Microsphere-based delivery systems
Nanoparticle dispersions
Drug release mechanisms
Pulmonary delivery
Exubera (inhalable recombinant insulin)
Alkermes' AIR dry powder
Aradigm's AERx system
Baxter Healthcare's Promaxx technology
Syntonix Pharmaceuticals' Fc Fusion Proteins
Nasal delivery
Oral and other forms of delivery
Cell penetrating peptides and polymeric nanoparticles
Emisphere's Eligen technology
Merrion Pharmaceuticals' GIPET
Nobex's drug delivery technology
Mucoadhesive polymer technologies
Nautilus Biotech
Other approaches
Affinergy
Raptor Pharmaceutical
Chapter 7 Trends and opportunities
Summary
Creating non-immunogenic monoclonal antibodies
The next wave of monoclonal antibody-based agents
Beyond monoclonal antibodies
The challenge of follow-on biologics
The promise of synthetic peptides and proteins
New frontier: de novo protein design
Chapter 8 Appendix
Index
List of Figures
Figure 1.1: US protein engineering patents and published applications by filing and publication
years, 1992-2006
Figure 2.2: Protein scaffold used to create designer protein drugs
Figure 2.3: Protein engineering patents: technologies and applications
Figure 5.4: Innovators in therapeutic protein production
List of Tables
Table 1.1: World pharma market by indication, 2006 - 2011
Table 1.2: Protein engineering markets by application, 2006 - 2011
Table 1.3: mAb protein engineering markets by company, 2006 - 2011
Table 1.4: Non-mAb protein engineering markets by company, 2006 - 2011
Table 1.5: Total protein engineering markets by company, 2006 - 2011
Table 1.6: Protein Engineering Markets by Product, 2006
Table 1.7: Protein engineering markets by product, 2011
Table 1.8: World Pharma Market by Region, 2006 - 2011
Table 1.9: Protein Engineering Market by Region, 2006 - 2011
Table 1.10: US patent codes dealing with antibody related subject matter
Table 1.11: Protein engineering US patents and published applications by leading assignees
Table 1.12: Top 50 protein engineering patent assignees by forward citation count
Table 2.13: Fully human engineered immunoglobulin patents: US filings, 1992-2006
Table 3.14: Launched mAb products, 2006
Table 3.15: Phase 3 mAb products, 2006
Table 3.16: Phase 2 mAb products, 2006
Table 3.17: Phase 1 mAb products, 2006
Table 3.18: Pre-clinical mAb products by name, 2006
Table 4.19: Non-immunoglobulin binding proteins in development
Table 5.20: Examples of launched engineered human recombinant therapeutic proteins
Table 5.21: Examples of launched engineered human recombinant therapeutic proteins continued.
Table 5.22: Therapeutic human proteins produced in animal bioreactors: products in development
Table 5.23: Engineered small peptide and peptidomimetic drugs: examples from antimicrobial
R&D
Table 6.24: Injectable protein delivery: half-life extension technologies
Table 6.25: Injectable protein delivery: depot technologies
Table 8.26: Top 50 Cited Protein Engineering Patents (US Filings, 1992-2006)
