SPINK2 Peptide Library for Diverse High-Affinity Target Binding
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Solution Overview
Problem
There is a need for the development of novel non-antibody scaffolds with high binding activity against disease-related molecules, as existing scaffolds like Kunitz domain libraries and anticalins are limited in types and applications.
Innovation Solution
A peptide library is created with a diversity of at least 1 × 10^5 to 1 × 10^8 peptides, each with specific amino acid modifications, and a method to identify peptides that bind to target molecules, including serine proteases like trypsin and acrosin, using phage or ribosome display techniques.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If limited types of non-antibody scaffolds (such as Kunitz domain library and anticalin) are used, then the productivity and immunogenicity characteristics are improved, but the diversity in targeting specific molecules is worsened
Solution Approach 1:
The patent applies parameter changes by systematically varying the amino acid sequence parameters of the SPINK2 scaffold. Specifically, the invention modifies the variable region amino acid sequences while maintaining the conserved disulfide bond structure, creating multiple variants with different binding specificities. This allows the same scaffold type to target diverse molecules including trypsin, acrosin, and other proteases, thereby improving versatility without sacrificing the productive characteristics of the scaffold architecture.
Solution Approach 2:
The patent achieves universality by designing the SPINK2-based peptide library to perform multiple functions. The same scaffold structure can bind to various proteases (trypsin, acrosin, chymotrypsin, etc.) by adjusting the variable region sequences. This multi-functional capability allows a single scaffold type to serve multiple therapeutic purposes, addressing different disease targets while maintaining the beneficial productivity and immunogenicity characteristics.
2Reliability
If SPINK2 is used to target endogenous molecules (trypsin and acrosin), then the binding activity is improved, but the ability to target disease-related molecules beyond endogenous targets is worsened
Solution Approach 1:
The patent applies segmentation by dividing the SPINK2 protein into conserved and variable regions. The conserved regions (including disulfide bonds at positions 3-12, 15-24, and 27-36) maintain reliable binding to endogenous targets, while the variable regions (amino acid positions 1-2 and 13-39) are modified to enable targeting of disease-related molecules. This segmentation allows independent optimization of both reliable endogenous binding and versatile disease targeting capabilities.
Solution Approach 2:
The patent implements local quality by making specific localized modifications to the SPINK2 sequence. The variable regions are tailored with specific amino acid compositions to recognize different protease active sites, while the conserved core regions maintain their original binding characteristics. This localized differentiation enables the peptide to simultaneously preserve reliable endogenous target binding while gaining the ability to target diverse disease-related molecules.
Data Source
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AI summary
A peptide library comprising a plurality of different peptides. The peptides each comprise an amino acid sequence encoded by a nucleotide sequence consisting of the sequence of SEQ ID NO: 14. The nucleotide sequence has been modified by replacing a nucleotide sequence consisting of the 43rd base thymine to the 93rd base thymine with a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 1. The peptide library has a diversity of at least 1 × 105. In SEQ ID NO: 1, each of the 1st Xaa to the 5th Xaa, the 7th Xaa, the 9th Xaa, and the 10th Xaa in each peptide is independently any amino acid other than cysteine and proline. Each of the 6th Xaa and the 8th Xaa in each peptide is independently any amino acid other than cysteine. The 11th Xaa in each peptide is independently selected from tyrosine, serine, phenylalanine, leucine, and threonine. The 12th Xaa in each peptide is independently selected from asparagine, aspartic acid, leucine, lysine, glutamine, alanine, and glutamic acid.