Design of Thioether Cyclic Peptide Scaffolds with Passive Permeability and Oral Exposure

J Med Chem. 2021 Mar 11;64(5):2622-2633. doi: 10.1021/acs.jmedchem.0c01505. Epub 2021 Feb 25.

Abstract

Advances in the design of permeable peptides and in the synthesis of large arrays of macrocyclic peptides with diverse amino acids have evolved on parallel but independent tracks. Less precedent combines their respective attributes, thereby limiting the potential to identify permeable peptide ligands for key targets. Herein, we present novel 6-, 7-, and 8-mer cyclic peptides (MW 774-1076 g·mol-1) with passive permeability and oral exposure that feature the amino acids and thioether ring-closing common to large array formats, including DNA- and RNA-templated synthesis. Each oral peptide herein, selected from virtual libraries of partially N-methylated peptides using in silico methods, reflects the subset consistent with low energy conformations, low desolvation penalties, and passive permeability. We envision that, by retaining the backbone N-methylation pattern and consequent bias toward permeability, one can generate large peptide arrays with sufficient side chain diversity to identify permeability-biased ligands to a variety of protein targets.

MeSH terms

  • Administration, Oral
  • Animals
  • Caco-2 Cells
  • Cell Membrane Permeability
  • Dogs
  • Humans
  • Madin Darby Canine Kidney Cells
  • Male
  • Methylation
  • Molecular Structure
  • Peptides, Cyclic / administration & dosage
  • Peptides, Cyclic / chemical synthesis
  • Peptides, Cyclic / pharmacokinetics
  • Peptides, Cyclic / pharmacology*
  • Protein Conformation
  • Rats
  • Rats, Sprague-Dawley
  • Small Molecule Libraries / administration & dosage
  • Small Molecule Libraries / chemical synthesis
  • Small Molecule Libraries / pharmacokinetics
  • Small Molecule Libraries / pharmacology
  • Sulfides / administration & dosage
  • Sulfides / chemical synthesis
  • Sulfides / pharmacokinetics
  • Sulfides / pharmacology*
  • Thermodynamics

Substances

  • Peptides, Cyclic
  • Small Molecule Libraries
  • Sulfides