Ribosomal Macrocyclic Peptide Synthesis via Thioether Bonding
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Solution Overview
Problem
Current methods for generating macrocyclic peptides from ribosomally produced polypeptides are limited by instability of chemical linkages, low cyclization efficiency, and limited structural diversity, particularly in forming macrocyclic structures within cells or in vitro.
Innovation Solution
A method involving artificial nucleic acid molecules encoding polypeptides with specific non-canonical amino acids and cysteine residues, allowing for intramolecular thioether bond formation to produce macrocyclic peptides, either alone or fused with inteins, enabling in vivo and in vitro synthesis of macrocyclic, lariat-shaped, or cyclic peptides.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Shape
If chemical cross-linking agents are used to constrain ribosomally produced peptides, then macrocyclic structures can be formed, but the chemical linkages are unstable and multiple undesired products are produced
Solution Approach 1:
The patent replaces chemical cross-linking agents with a ribosomally encoded thiol-disulfide exchange mechanism. The cysteine residue and unnatural amino acid with disulfide bond are incorporated directly into the polypeptide chain during ribosomal synthesis, eliminating the need for external chemical reagents. This biological mechanism provides stable and specific thioether bond formation without the side reactions and instability associated with chemical cross-linking agents.
2Shape
If chemical cross-linking agents are used to form macrocyclic peptides, then cyclization can occur, but cyclization efficiency is low and multiple undesired products are produced
Solution Approach 1:
The patent replaces inefficient chemical cross-linking with a ribosomally encoded thiol-disulfide exchange mechanism that occurs co-translationally. The cysteine residue and unnatural amino acid with disulfide bond are positioned precisely in the polypeptide chain during ribosomal synthesis, enabling efficient and specific intramolecular cyclization. This biological mechanism avoids the low efficiency and side products associated with chemical cross-linking agents.
Solution Approach 2:
The patent incorporates the cysteine residue and unnatural amino acid with disulfide bond directly into the polypeptide chain during ribosomal synthesis before cyclization occurs. This preliminary positioning of the reactive groups during translation ensures they are correctly oriented and proximal for efficient thioether bond formation, eliminating the need for subsequent chemical cross-linking steps and improving overall cyclization efficiency.
3Shape
If conventional peptide synthesis methods are used, then macrocyclic peptides can be produced, but structural diversity is limited
Solution Approach 1:
The patent employs a universal ribosomal synthesis platform that can incorporate various unnatural amino acids with different side-chain functional groups (carboxyl, amino, hydroxyl, thiol, etc.) at programmable positions within the polypeptide chain. This single ribosomal system can generate diverse macrocyclic structures by simply changing the nucleic acid sequence to encode different unnatural amino acids and positions, providing extensive structural diversity without requiring multiple specialized synthesis methods.
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 provides a versatile and efficient method for producing structurally diverse macrocyclic peptides with enhanced stability and binding affinity, suitable for drug discovery and biological applications, while allowing for intracellular production and high-throughput screening.
Implementation Method 1
allowing the functional group FG1, and whenever present, FG2, to react with the side-chain sulfhydryl group (-SH) of the cysteine (Cys) residue(s), thereby producing the macrocyclic peptide
Data Source
Figure 1A~1B
Figure 2A~2B
Figure 3A~3B
AI summary
Methods and compositions are provided for generating macrocyclic peptides from genetically encoded, ribosomally produced polypeptide precursors. Also provided are nucleic acid molecules, polypeptides, and methods for generating combinatorial libraries of macrocyclic peptides. These methods can be used to produce vast libraries of conformationally constrained peptide ligands as well as facilitate the functional screening of these libraries to identify compound(s) with desired activity properties.