Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation.

Area of Science:

• Medicinal Chemistry
• Drug Discovery
• Chemical Biology

Background:

• Developing ligands beyond small molecules is crucial for modulating challenging protein targets.
• Macrocyclic peptides from mRNA display show high affinity but suffer from poor membrane permeability, limiting their use to extracellular targets.

Purpose of the Study:

• To investigate passive membrane permeability of macrocyclic peptides.
• To improve the design of macrocyclic peptide libraries for intracellular targets.

Main Methods:

• Screened over 200 macrocyclic 10-mers utilizing a thioether cyclization motif.
• Identified optimal lipophilicity for permeability in cyclic peptide-peptoid hybrid scaffolds.
• Analyzed conformational changes impacting permeability.

Main Results:

• Determined the optimal lipophilicity range for enhanced permeability in thioether-cyclized 10-mer scaffolds.
• Demonstrated that backbone permutations maintain permeability.
• Observed a novel saddle-shaped fold in a highly permeable scaffold due to a single amino acid change, sequestering backbone NH groups.

Conclusions:

• Physicochemical knowledge can guide the design of permeable macrocyclic peptide mRNA display libraries.
• This approach enables biasing libraries toward permeability by design.
• Geometrically diverse, permeable scaffolds exist outside conventional drug-like chemical space.