Antibody CDR Diversification via Restricted Codon Sets
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Solution Overview
Problem
Current methods for generating libraries of antibodies with diverse CDRs face challenges in achieving sufficient diversity while maintaining high yield and target antigen binding capability, often requiring broad amino acid substitutions and inefficient production due to improper folding and stop codons.
Innovation Solution
The method involves diversifying a minimal number of amino acid positions using a restricted codon set to generate highly diverse libraries of polypeptides with high-quality target binding characteristics, allowing for further diversification and high-yield production by identifying solvent-accessible and diverse amino acid positions in CDRs.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If broad amino acid substitutions are used to generate diverse antibody libraries, then sequence diversity is improved, but production yield deteriorates due to improper folding and stop codons
Solution Approach 1:
The patent applies local quality by restricting amino acid substitutions to only those positions in the CDR regions that are solvent-accessible and contribute to antigen binding. This selective approach maintains sequence diversity where needed while preserving proper protein folding and expression yield in non-critical regions.
Solution Approach 2:
The invention changes the parameter of amino acid substitution from broad (all 20 amino acids) to restricted (only specific amino acids at specific positions). This parameter change resolves the contradiction by maintaining sufficient diversity for binding while eliminating substitutions that cause improper folding or stop codons.
2Adaptability or versatility
If all 20 amino acids are used for CDR diversification, then binding diversity is improved, but library quality deteriorates due to stop codons and improper folding
Solution Approach 1:
The patent applies local quality by restricting amino acid substitutions to only those positions in the CDR regions that are solvent-accessible and contribute to antigen binding. This selective approach maintains sequence diversity where needed while preserving proper protein folding and expression yield in non-critical regions.
Solution Approach 2:
The invention converts the potential harm of broad amino acid substitution (which causes stop codons and improper folding) into a benefit by systematically identifying and restricting substitutions to only those that are beneficial for binding while eliminating harmful ones. This transforms a problematic approach into a refined, high-quality method.
3Adaptability or versatility
If large libraries are generated to ensure finding high-affinity binders, then probability of success is improved, but practical limitations are exceeded due to size and complexity
Solution Approach 1:
The invention changes the parameter of library generation from exhaustive (all possible amino acid combinations) to targeted (only substitutions at solvent-accessible, binding-contributing positions). This parameter change achieves sufficient diversity for finding high-affinity binders while keeping library size and complexity within practical limits.
Data Source
AI summary
The invention provides antibodies or antigen binding fragments thereof to DR5 and HER-2. The antibodies and/or antigen binding fragments thereof comprise variant CDRs comprising highly restricted amino acid sequence diversity. The invention also provides these polypeptides as fusion polypeptides to heterologous polypeptides such as at least a portion of phage or viral coat proteins, tags and linkers. In addition, compositions and methods of use for treatment of cancer and immune related conditions are provided.