SH3 Domain Mutations for Non-Natural Ligand Binding
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Solution Overview
Problem
Current binding molecules, such as monoclonal antibodies, have limitations in terms of biophysical properties and molecular structure, making them less suitable for therapeutic and diagnostic applications, particularly due to immunogenicity and stability issues, and existing SH3 domains are limited in their ability to target non-natural ligands effectively.
Innovation Solution
Development of recombinant derivatives of the SH3 domain of the Fyn kinase with mutated RT and src loops to enhance specificity and affinity for various targets, while maintaining high sequence identity to the native sequence and avoiding immunogenicity, allowing for the creation of non-immunogenic protein therapeutics and diagnostics.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If monoclonal antibodies are used as binding molecules, then high affinity and specificity to target can be achieved, but immunogenicity and stability issues arise
Solution Approach 1:
The patent creates simplified copies of antibody binding sites by using SH3 domains as alternative scaffolds. Instead of using full monoclonal antibodies, the invention transfers the binding function to a smaller, non-immunogenic protein framework that replicates the essential binding capability without the harmful immunogenic properties of complete antibodies
Solution Approach 2:
The patent employs small, simple protein domains (SH3 domains) as disposable binding units rather than complex, expensive monoclonal antibodies. These small protein scaffolds provide the necessary binding function with reduced complexity, lower cost, and minimal immunogenicity, effectively serving as simplified alternatives to full antibody molecules
2Object-affected harmful factors
If SH3 domains are used as binding proteins, then reduced immunogenicity is achieved, but ability to target non-natural ligands is limited
Solution Approach 1:
The patent applies local quality changes by introducing specific mutations in the RT and n-Src loops of the SH3 domain. These localized modifications alter the binding surface properties to recognize non-natural ligands while preserving the overall SH3 domain structure that provides low immunogenicity. The solution targets specific regions rather than redesigning the entire protein
Solution Approach 2:
The patent utilizes parameter changes by systematically mutating amino acids in the RT and n-Src loops to alter binding characteristics. Through controlled changes in sequence composition and loop flexibility, the SH3 domains are reconfigured to bind non-natural ligands while maintaining the core structural parameters that ensure low immunogenicity
3Measurement precision
If mutations are introduced in RT and n-Src loops of SH3 domain, then specificity and affinity for non-natural ligands are enhanced, but deviation from native sequence increases
Solution Approach 1:
The patent applies local quality changes by introducing specific mutations in the RT and n-Src loops of the SH3 domain. These localized modifications alter the binding surface properties to recognize non-natural ligands while preserving the overall SH3 domain structure that provides low immunogenicity. The solution targets specific regions rather than redesigning the entire protein
Solution Approach 2:
The patent employs partial action by introducing mutations only in specific regions (RT and n-Src loops) rather than throughout the entire SH3 domain. This selective mutagenesis achieves the desired binding enhancement while minimizing overall sequence deviation, maintaining sufficient identity to the native sequence for structural integrity
Data Source
AI summary
A library is provided having a plurality of recombinant derivatives of the SH3 domain of the Fyn kinase of SEQ ID NO: 1, where one or more of the derivatives have a specific binding affinity to a protein or peptide that is not a natural SH3 binding ligand. Substantially each of the derivatives of the SH3 domain of the Fyn kinase of SEQ ID NO: 1 has an amino acid sequence with at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 1, and at least 90% identity to the amino acid of SEQ ID NO: 1 outside the src and RT loops. Additionally, the amino acid sequence has at least one amino acid in or positioned up to two amino acids adjacent to the RT loop or the src loop of SEQ ID NO: 1 which is substituted, deleted or added.