Alphabody Libraries for High-Affinity Binder Selection
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Solution Overview
Problem
Current antibody libraries face limitations in generating high-affinity binders for various target proteins due to their large size, sensitivity, and ethical constraints, and lack methods to manipulate Alphabody scaffolds for producing libraries with a high number of binding partners.
Innovation Solution
Development of single-chain Alphabody libraries with varied amino acid sequences, specifically designed to introduce sequence variation in defined regions like the helix surface, groove, and linker fragments, allowing for the selection of Alphabodies with high affinity and specificity, and the use of nucleic acid and vector libraries for their production.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional antibody libraries are used, then high affinity binding can be achieved for specific antigens, but the library complexity must be very high and each antigen requires a separate immune library
Solution Approach 1:
The patent applies universality by creating a single Alphabody library scaffold that can be used to generate high-affinity binders for multiple different target antigens. The standardized Alphabody structure with variable binding regions allows one library system to serve multiple functions across different antigen targets, eliminating the need for separate immune libraries for each antigen.
Solution Approach 2:
The patent employs parameter changes by modifying the Alphabody scaffold structure through systematic variation of amino acid sequences at specific positions (particularly in the binding regions). This allows the same basic scaffold to generate diverse binding specificities and high affinities for different targets by changing sequence parameters rather than requiring completely different library systems.
2Reliability
If traditional antibody libraries are used, then high affinity antibodies can be obtained, but antibodies are large proteins sensitive to heating, freeze-thawing, proteolytic cleavage and have limited administration modes
Solution Approach 1:
The patent applies parameter changes by fundamentally altering the protein scaffold parameters from traditional immunoglobulin structure to an Alphabody coiled-coil structure. This structural parameter change results in improved stability properties (resistance to heating, freeze-thawing, and proteolytic cleavage) while maintaining the ability to achieve high binding affinity through sequence variation in the binding regions.
Solution Approach 2:
The patent uses composite materials by combining the stable Alphabody coiled-coil scaffold structure with variable binding region sequences. This composite approach creates a chimeric protein structure that inherits the stability of the Alphabody core while acquiring target-specific binding capabilities through the variable regions, overcoming the fragility of traditional antibodies.
3Reliability
If Alphabody scaffolds are used, then compact and stable binders can be produced, but methods to manipulate the scaffolds for obtaining libraries with high number of binding partners have not been disclosed
Solution Approach 1:
The patent applies segmentation by dividing the Alphabody scaffold into distinct functional regions: a stable coiled-coil core structure and variable binding regions. This segmentation allows independent manipulation of the binding regions through systematic amino acid variation while preserving the stability of the core scaffold, enabling library construction without compromising therapeutic stability.
Solution Approach 2:
The patent employs parameter changes by systematically varying amino acid sequences at specific positions within the Alphabody scaffold, particularly in the binding regions. This controlled parameter variation enables the generation of diverse binding partners with high affinity while maintaining the overall structural stability and manufacturability of the library system.
Data Source
AI summary
The invention provides single-chain Alphabody library comprising at least 100 different-sequence single-chain Alphabody polypeptides, wherein said Alphabody polypeptides differ from each other in at least one of a defined set of 5 to 20 variegated amino acid residue positions, and wherein at least 70% but not all of said variegated amino acid residue positions are located either in the loop, helix surface or linker region of the Alphabody. The invention further provides methods for use of the Alphabody libraries and Alphabodies obtainable by the methods of the invention.