Hybrid Peptidic Non-Peptidic Macrocycles for Diverse Ligand Libraries
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Solution Overview
Problem
Current methods for generating peptide libraries face limitations in structural and functional diversity due to reliance on natural amino acids, and challenges in deconvoluting cyclic peptide libraries, including instability and complexity in identifying active compounds.
Innovation Solution
The development of methods for creating macrocyclic peptide-containing molecules with a hybrid peptidic/non-peptidic backbone using genetically encoded polypeptides and synthetic molecules, allowing for variation in amino acid sequences and chemical linkages to form covalent bonds, facilitating the production of conformationally constrained ligands.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If biosynthetic methods are used to prepare peptide libraries, then very large collections of peptide ligands can be generated, but the structural and functional diversity is limited by reliance on natural amino acids
Solution Approach 1:
The patent creates hybrid peptide-small molecule compounds that combine the advantages of both peptides and small molecules. The hybrid structures incorporate natural amino acids from biosynthetic methods along with unnatural amino acids and synthetic moieties, achieving both large library sizes and enhanced structural diversity. This composite approach allows the peptide portion to maintain biological recognition while the synthetic portion adds novel chemical properties and functional groups.
Solution Approach 2:
The invention systematically varies multiple parameters including amino acid sequence, unnatural amino acid incorporation, macrocycle size, and chemical linkage types to generate diverse hybrid compounds. By changing these parameters in a controlled manner during library preparation, the method achieves broad structural and functional diversity while maintaining reproducibility and systematic exploration of chemical space.
2Ease of manufacture
If linear peptides are used as pharmacological agents, then they can be synthesized easily, but they are prone to proteolytic degradation and poor membrane crossing
Solution Approach 1:
The patent divides the linear peptide into segments and connects them through macrocyclization to form cyclic structures. This segmentation and reconnection approach protects the peptide backbone from proteolytic degradation while maintaining the ability to synthesize the components separately. The cyclic structure reduces conformational flexibility and increases metabolic stability while preserving binding affinity.
Solution Approach 2:
The hybrid peptide-small molecule compounds combine the stability of small molecules with the biological activity of peptides. The synthetic moiety provides enhanced chemical stability and membrane permeability, while the peptide portion maintains target recognition. This composite structure overcomes the limitations of linear peptides by integrating complementary properties from both peptide and small molecule domains.
3Reliability
If conformationally constrained peptides are created to improve stability and binding, then affinity increases, but the complexity of library preparation and screening increases
Solution Approach 1:
The patent incorporates conformational constraints and macrocyclic structures during the library preparation phase rather than attempting to identify and constrain active compounds after screening. By pre-organizing the peptide backbone into constrained conformations that favor the active state, the method reduces the conformational entropy penalty upon binding and enhances affinity from the outset, while maintaining systematic library preparation procedures.
4Reliability
If cyclic peptide libraries are prepared to improve pharmacological properties, then stability and membrane crossing improve, but deconvolution and identification of active compounds becomes challenging
Solution Approach 1:
The patent employs affinity tags and handle sequences as intermediaries that facilitate the handling, purification, and identification of cyclic peptide compounds. These auxiliary sequences allow for easy tracking and deconvolution of library members without interfering with the pharmacological properties of the core cyclic peptide structure. The intermediaries enable systematic screening and identification of active compounds despite the cyclic conformation.
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 enhances the structural diversity of peptide libraries, improves the stability and binding affinity of peptides, and simplifies the identification of active compounds, enabling high-throughput screening and potential drug development.
Implementation Method 1
contacting the polypeptide with the chemical species for a time and under conditions to allow a covalent bond-forming reaction between FG1 and cFG1
Implementation Method 2
allowing the polypeptide self-processing biosynthetic precursor to undergo cyclization, thereby producing the macrocyclic peptide-containing molecule
Implementation Method 3
facilitating the production of conformationally constrained ligands
Data Source
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AI summary
Methods and compositions are provided that utilize synthetic molecules and genetically encoded polypeptides to generate macrocyclic peptide-containing molecules with a hybrid peptidic/non-peptidic backbone. Also provided are nucleic acid molecules, polypeptides, and methods for generating libraries of macrocyclic peptide-containing molecules with a hybrid peptidic/non-peptidic backbone. These methods can be used to increase the structural diversity of ligand libraries as well as facilitate the functional screening of these libraries to identify compound(s) with desired activity properties.