De Novo Binding Polypeptides With Proline-Constrained Target Specificity

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Solution Overview

Problem

Existing antibody-based reagents are costly and time-consuming, and alternative affinity reagents with improved specificity and affinity are needed to address off-target effects and enhance therapeutic and diagnostic efficacy.

Innovation Solution

Development of de novo binding domain (DBD) polypeptides with specific amino acid sequences, such as MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAAFEKEIAAFESELQAYKGKGNPEVEX55LRX58X59AAX62IRX65X66LQAYRHN (SEQ ID NO:4), which exhibit high target binding affinity and specificity, reducing immunogenicity through conservative and non-conservative substitutions, and are used in fusion proteins and chimeric antigen receptors (CARs) for targeted cancer therapy.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If disulfide bonds are introduced to constrain peptide structure, then affinity and specificity are improved, but improper pairing occurs leading to lower expression and product quality

Engineering Contradiction:

Improvebinding affinity and specificityVSAvoidexpression level and product quality

Core Design Contradiction:

ReliabilityVSManufacturing precision

Solution Approach 1:

The patent extracts the beneficial structural constraint function from disulfide bonds and implements it through alternative means - specifically using proline residues at strategically positioned locations to provide structural rigidity and conformational constraint without the pairing problems inherent to cysteine-based disulfide bonds

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent changes the chemical parameter of structural constraint from covalent disulfide crosslinks to steric and conformational constraints imposed by proline residues, thereby achieving similar structural stabilization effects without the harmful side effects of improper disulfide pairing

Inventive Principle:

Principle #35Parameter changes

2Ease of manufacture

If alternative affinity reagents are developed to reduce cost, then production cost decreases, but binding affinity and specificity may be compromised

Engineering Contradiction:

Improveproduction costVSAvoidbinding affinity and specificity

Core Design Contradiction:

Ease of manufactureVSReliability

Solution Approach 1:

The patent creates composite structural features by combining proline-induced conformational constraints with specifically engineered binding loops, achieving both cost-effectiveness (through simplified production compared to antibodies) and high binding affinity/specificity (through optimized structural constraints and binding interface design)

Inventive Principle:

Principle #40Composite materials

3Reliability

If standard antibody formats are used for therapeutic targeting, then target binding is achieved, but off-target effects occur reducing therapeutic efficacy

Engineering Contradiction:

Improvetarget bindingVSAvoidoff-target effects

Core Design Contradiction:

ReliabilityVSObject-affected harmful factors

Solution Approach 1:

The patent applies local quality optimization by designing specific binding loops with tailored amino acid sequences that recognize unique epitopes on target antigens, while the proline-constrained framework provides localized structural rigidity that enhances binding precision and reduces off-target interactions

Inventive Principle:

Principle #3Local quality

Data Source

PatentUS20250353920A1De novo binding domain containing polypeptides and uses thereof

Publication Date: 2025.11.20 ARCELLX INC

AI summary

Provided herein are de novo binding domain containing polypeptides (DBDpp) that specifically bind a target of interest. Nucleic acids encoding the DBDpp, and vectors and host cells containing the nucleic acids are also provided. Libraries of DBDpp, methods of producing and screening such libraries and the DBDpp identified from such libraries and screens are also encompassed. Methods of making and using the DBDpp are additionally provided. Such uses include, without limitation, affinity purification, and diagnostic and therapeutic applications.