Antibody Libraries with Diversified HC CDR3 Lengths
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Solution Overview
Problem
Existing peptide and protein libraries that mimic antibodies lack diversity in both amino acid sequence and length, leading to inefficient construction, increased immunogenicity, and reduced functionality, as they do not accurately represent natural antibody diversity.
Innovation Solution
Development of libraries that encode human antibody heavy chain CDR3s ranging from 3 to 35 amino acids in length, enriched with Tyr and Ser residues, and comprising diversified D regions and extended JH regions, allowing for focused representation of natural antibody diversity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If libraries are constructed with synthetic diversity at every amino acid residue, then sequence diversity is maximized, but construction time increases and many members are non-functional
Solution Approach 1:
The patent segments antibody diversity into distinct functional components: CDR3 length diversity (3-35 amino acids) and sequence diversity (Tyr/Ser enrichment). By separating these dimensions and focusing on CDR3 specifically, the library achieves functional diversity without exhaustively searching all possible sequences, thereby reducing construction time while maintaining biological relevance.
Solution Approach 2:
The patent applies local quality by concentrating diversity generation in the CDR3 region rather than uniformly across all antibody residues. By focusing mutagenesis and diversity generation specifically on CDR3 with Tyr/Ser enrichment, the library achieves high functional relevance in the critical binding region while keeping framework regions more constrained and easier to construct.
2Adaptability or versatility
If libraries include maximum diversity at every position, then amino acid variation is maximized, but immunogenicity increases
Solution Approach 1:
The patent changes the parameter of amino acid composition by enriching for Tyr and Ser residues in CDR3, which are commonly found in natural human antibodies. This parameter change reduces immunogenicity by making the library members more similar to endogenous human proteins, while still maintaining diversity through length variation (3-35 amino acids) and compositional variation.
3Reliability
If libraries are constructed to represent natural antibody diversity, then functionality improves, but library size increases
Solution Approach 1:
The patent applies partial action by focusing diversity generation on the CDR3 region rather than the entire antibody. By concentrating on the functionally critical CDR3 with Tyr/Ser enrichment and length variation (3-35 amino acids), the library achieves high functionality with a smaller, more manageable size, avoiding the need to construct exhaustive libraries of all possible antibody sequences.
Data Source
AI summary
Provided are compositions and methods for preparing and identifying antibodies having CDR3s that vary in sequence and in length from very short to very long which in certain embodiments may bind to a carbohydrate moiety or the active site of an enzyme. Libraries coding for antibodies with the CDR3s are also provided. The libraries can be provided by modifying a pre-existing nucleic acid library.