FN3 Protein Scaffolds With Alternative Binding Surfaces
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Solution Overview
Problem
Existing monoclonal antibodies and conventional FN3 domain libraries face limitations in achieving high affinity and specificity for target molecules due to their structural constraints and limited binding surfaces.
Innovation Solution
The development of FN3 domain scaffolds with randomized concave interaction surfaces formed by alternative beta-strands and loops, allowing for increased diversity and affinity to target molecules through randomization of these surfaces.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional FN3 domain libraries use traditional loop randomization (FG, BC, DE loops), then binding specificity is improved, but binding affinity and diversity of targets are limited
Solution Approach 1:
The patent transitions from randomizing only loops to randomizing an alternative surface comprising both beta-strands and loops together. This dimensional expansion in the design space (from 1D loop sequences to 2D surface structures) enables access to novel binding modes and targets while maintaining specificity, directly resolving the contradiction between specificity and versatility.
Solution Approach 2:
The patent changes the fundamental parameter of what is being randomized - shifting from loop-only randomization to alternative surface randomization that includes beta-strands. This parameter change expands the conformational and sequence space explored, enabling discovery of binders with both high specificity and broad target diversity simultaneously.
2Reliability
If monoclonal antibodies are used for high affinity binding, then binding affinity is improved, but structural stability and ease of expression are reduced
Solution Approach 1:
The patent applies local quality by concentrating randomization efforts specifically on the alternative surface (beta-strands and loops) while keeping the rest of the FN3 domain structure fixed and stable. This localized approach enables high affinity binding through diversified binding surfaces while maintaining the overall structural stability and simplicity of the FN3 scaffold.
3Adaptability or versatility
If extensive randomization is performed to increase diversity, then adaptability is improved, but structural stability may be compromised
Solution Approach 1:
The patent segments the FN3 domain into two functional regions: a stable core (the rest of the domain structure) and a diversified surface (the alternative surface with beta-strands and loops). By segmenting the randomization to only the surface region, the patent achieves high library diversity while preserving the structural stability of the core scaffold.
Data Source
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AI summary
Protein scaffolds and scaffold libraries based on a fibronectin type III (FN3) repeat with an alternative binding surface design, isolated nucleic acids encoding the protein scaffolds, vectors, host cells, and methods of making thereof are useful in the generation of therapeutic molecules and treatment and diagnosis of diseases and disorders.