Phage Display Library Encoding Linear and Circular Peptides
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Solution Overview
Problem
Current random peptide libraries are inadequate in covering both linear and circular peptide variants, leading to inefficient target binding due to their limited complexity and reliance on multiple libraries for cyclized peptides, which is time-consuming and elaborate.
Innovation Solution
A library of replicating entities with recombinant vectors having randomized nucleic acid sequences in specific reading frame structures that encode for both linear and circular peptides, ensuring at least 20% of sequences include cysteine codons for disulfide bond formation, allowing for a single library to cover both conformations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If random peptide libraries are generated using randomly generated nucleic acid sequences, then all possible variants of a peptide of a given length are covered, but the library size exceeds the technical handling capacity
Solution Approach 1:
The patent applies local quality by differentiating the treatment of different positions in the peptide sequence. Cysteine residues are specifically targeted at positions where they can form disulfide bonds (typically near termini), while other positions use standard randomization. This localized approach to cysteine incorporation enables circular peptide formation without requiring exhaustive randomization of all positions, thus reducing overall library size while maintaining coverage of structurally diverse variants.
Solution Approach 2:
The patent changes the parameter of cysteine frequency from the standard random distribution (approximately 5% occurrence) to an elevated frequency (at least 20% of CorAA encode for cysteine). This parameter change increases the probability of disulfide bond formation and circular peptide generation within a manageable library size, resolving the contradiction between comprehensive variant coverage and technical handling capacity.
2Adaptability or versatility
If multiple libraries are used to cover both linear and circular peptides, then both conformations are adequately represented, but the screening process becomes time-consuming and elaborate
Solution Approach 1:
The patent merges the coverage of both linear and circular peptide conformations into a single library by incorporating elevated cysteine frequencies that enable disulfide bond formation. This combining approach eliminates the need for separate libraries for linear and circular peptides, reducing screening complexity and time while maintaining comprehensive conformational coverage.
Solution Approach 2:
The patent creates a universal library that serves multiple functions: it covers linear peptides, circular peptides, and variants with different disulfide bond configurations all within a single collection. This multi-functional library design allows one screening process to identify binders across multiple conformational classes, eliminating the need for sequential screening of separate libraries.
3Shape
If cysteine residues are included at defined positions to form disulfide bonds, then circular peptide structures are generated, but the library complexity becomes too small to cover required sequences
Solution Approach 1:
The patent adds the dimension of cysteine frequency as a new parameter to control circular peptide formation. By adjusting cysteine occurrence from standard random levels to at least 20%, the patent creates a new dimensional space in library design that enables circular structure formation while maintaining sufficient sequence diversity through randomized regions outside the cysteine-constrained positions.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach significantly enhances the reliability and efficiency of peptide screening by covering a broader range of peptide conformations within a single library, reducing the need for multiple libraries and improving target binding affinity.
Implementation Method 1
These cysteine residues can form a disulfide bond generating a loop structure
Data Source
AI summary
A library of replicating entities, each entity comprises a recombinant vector comprising a randomized nucleic acid sequence, having the reading frame structure [NXX].sub.n [CorAA] [NXX].sub.m [NZZ].sub.o, or [NZZ].sub.o [NXX].sub.m [CorAA] [NXX].sub.n. Each NXX is independently a codon encoding for any amino acid except cysteine, CorAA is a codon encoding for cysteine or at least one other amino acid, each NZZ is independently a codon encoding for any amino acid, and n is an integer from 0 to 40, m is an integer from 1 to 20, o is an integer from 1 to 40, and at least 20 percent of CorAA encode for cysteine. The invention further relates to a set of recombinant vectors and to a set of randomized oligonucleotides, each oligonucleotide having said structure, as well as to a method for generating a library of replicating entities and to a method for identifying an amino acid polymer.