APBA-Modified Cysteine Phage Display for Protein Surface Recognition
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Solution Overview
Problem
Current methods lack effective strategies for developing small molecules that can specifically recognize protein surfaces without binding pockets, particularly for undruggable proteins, and existing peptide binders exhibit modest affinity and limited cell and tissue penetration.
Innovation Solution
Phage display libraries incorporating APBA modified cysteine residues for dynamic covalent conjugation, enabling high-affinity binding to protein surfaces through iminoboronate formation, and subsequent selection and conjugation of therapeutic peptides with submicromolar potency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Length of moving object
If small molecules are used to target proteins, then cell and tissue penetration is improved, but binding affinity to protein surfaces without pockets is insufficient
Solution Approach 1:
The invention creates hybrid molecules combining peptide sequences (for protein surface recognition) with small molecule warheads (for covalent binding). This composite approach allows the peptide portion to recognize the protein surface while the small molecule portion provides strong covalent attachment, achieving both high affinity and cell penetration capabilities
Solution Approach 2:
The invention applies different functional properties to different parts of the molecule: the peptide region provides surface recognition and specificity through its amino acid sequence, while the attached small molecule warhead provides covalent binding strength. This local differentiation of function allows each part to optimize its specific role
2Reliability
If peptides are used to bind protein surfaces, then binding specificity is improved, but cell and tissue penetration is reduced
Solution Approach 1:
The invention extracts only the essential binding domain from full-length antibodies, using short peptide sequences (5-20 amino acids) that specifically recognize protein surfaces. This extracted peptide is then conjugated to small molecules, creating a miniaturized version that retains specificity while improving penetration
Solution Approach 2:
The invention changes the molecular size parameter by using truncated peptide sequences instead of full-length antibodies or large proteins. This parameter reduction from 150 kDa (antibody) to <1 kDa (peptide-warhead) maintains binding specificity while dramatically improving cell and tissue penetration
3Reliability
If conventional phage display libraries are used, then protein surface recognition is achieved, but binding affinity is modest
Solution Approach 1:
The invention modifies the chemical parameter of the phage display library by incorporating non-natural amino acids with reactive warheads (electrophilic groups) into the peptide sequences. This chemical modification transforms moderate-affinity non-covalent interactions into high-affinity covalent bonds, achieving submicromolar potency
Solution Approach 2:
The invention creates composite phage particles that display peptides containing both natural amino acids (for surface recognition) and non-natural warhead amino acids (for covalent binding). This composite structure enables the library to screen for both specificity and covalent binding capability
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
The approach allows for the development of low molecular weight peptides with high specificity and affinity for protein surfaces, capable of penetrating cells and tissues, and effectively targeting enzymes and non-enzyme proteins with single-digit micromolar potency, even in complex media.
Implementation Method 1
APBA modified cysteine residues for dynamic covalent conjugation, enabling high-affinity binding to protein surfaces through iminoboronate formation
Data Source
AI summary
Low molecular weight molecules able to penetrate cells and tissues and having high specificity and affinity for the surfaces of proteins. Methods of making same, pharmaceutical compositions comprising same, and methods of treating cancers, infectious diseases, and diseases and disorders associated with aberrant protein expression using same. A method for selecting a therapeutic peptide for binding to an isolated and/or purified protein of interest by screening a phage display library containing phage particles with phage display peptides which have at least one APBA modified cysteine residue. The APBA modified cysteine residues bind to surface lysine residues on the isolated and/or purified protein of interest by dynamic covalent conjugation to form iminoboronates.