OB-Fold Protein Binders That Block Multimeric Protein Assembly
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Solution Overview
Problem
Existing technologies fail to provide molecules that can specifically bind to the subunit of multimeric proteins to inhibit their formation, particularly for biologically active proteins like TNF-alpha, RANKL, and TRAIL, which are part of the TNF superfamily, and are not effective in preventing their multimerization.
Innovation Solution
Development of variants of the OB-fold Sac7d family proteins with specific mutations in the binding site that bind to the subunit of multimeric proteins, such as TNF-alpha, RANKL, and TRAIL, preventing the formation of biologically active multimers.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If existing molecules are used to bind multimeric proteins, then they can interact with the target protein, but they cannot specifically inhibit the formation of biologically active multimers
Solution Approach 1:
The patent applies local quality by designing OB-fold domain variants with specific mutations in the binding site that confer selective affinity for monomeric subunits. The mutations are localized to the binding interface, allowing the molecule to distinguish between monomeric and multimeric forms based on local structural differences at the binding site, while maintaining overall binding capability.
Solution Approach 2:
The patent employs parameter changes by introducing specific amino acid mutations in the OB-fold domain binding site that alter the binding characteristics. These mutations change the affinity parameters to preferentially bind monomeric subunits over multimeric forms, thereby shifting the binding equilibrium and inhibiting multimer formation without losing overall binding capability.
2Reliability
If molecules bind to multimeric proteins to reduce biological activity, then they can inhibit activity, but they cannot prevent multimerization of the protein
Solution Approach 1:
The patent applies preliminary action by having the OB-fold domain variants bind to monomeric subunits before they can assemble into multimeric complexes. This preemptive binding to the monomeric form prevents the assembly process from occurring, thereby both reducing biological activity (which requires multimeric form) and preventing multimerization simultaneously.
Solution Approach 2:
The patent extracts the monomeric subunit from the multimerization process by selectively binding to it. The OB-fold variants specifically recognize and sequester monomeric subunits, removing them from the equilibrium between monomers and multimers, thereby preventing multimer formation while reducing biological activity.
3Ease of operation
If traditional binding molecules are used, then they can interact with target proteins, but they require injection or infusion administration and cause immune response
Solution Approach 1:
The patent employs small protein variants (OB-fold domains of approximately 7 kDa) that are smaller and less immunogenic than traditional antibody-based therapies. These smaller molecules have shorter half-lives and can be administered orally or topically, avoiding the immune response and administration constraints associated with large protein therapeutics.
Solution Approach 2:
The patent changes the physical and immunological parameters of the binding molecule by using small OB-fold domain variants instead of large antibodies. This size reduction alters pharmacokinetic parameters (enabling oral absorption), immunogenicity parameters (reducing immune response), and administration parameters (allowing topical application).
Data Source
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AI summary
The invention relates to variants of OB-fold proteins, in particular of the Sac7d family that are able to bind a subunit of a multimeric protein and inhibit the formation of the multimer.