On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds.

Backbone N-methylation is common among peptide natural products and has a substantial impact on both the physical properties and the conformational states of cyclic peptides. However, the specific impact of N-methylation on passive membrane diffusion in cyclic peptides has not been investigated systematically. Here we report a method for the selective, on-resin N-methylation of cyclic peptides to generate compounds with drug-like membrane permeability and oral bioavailability. The selectivity and degree of N-methylation of the cyclic peptide was dependent on backbone stereochemistry, suggesting that conformation dictates the regiochemistry of the N-methylation reaction. The permeabilities of the N-methyl variants were corroborated by computational studies on a 1,024-member virtual library of N-methyl cyclic peptides. One of the most permeable compounds, a cyclic hexapeptide (molecular mass = 755 Da) with three N-methyl groups, showed an oral bioavailability of 28% in rat

Utilizing advanced techniques in NMR spectroscopy to study the conformational aspects of membrane permeability for N-methylated cyclic peptides

The conformational hypothesis of membrane permeability hypothesizes that certain macrocyclic scaffolds can exhibit an abnormally high degree of permeability producing a larger logP value than expected due to intramolecular hydrogen bonding which locks the macrocycle into a specific conformation where the hydrophilic functional groups are buried within the molecule causing it to become lipophilic enough to cross the membrane. Exploring this concept in previous work resulted in the synthesis of a 32 membered library of cyclic peptides with the same sequence varying in stereochemistry and N-methylation pattern. From this library two cyclic peptides, compounds 1 and 2 were found to exhibit an abnormally large logP value when assayed using the PAMPA permeability assay. This result lead us to synthesize more of these compounds and subject them to a series of NMR and other analytical experiments to computationally determine these two molecules 3D structure as they exist in chloroform solution, used to mimic the environment of the inside of membrane bilayer. These NMR structures were produced using NOESY derived distance restraints and the molecular modeling program CYANA. These structures provide valuable information about what types of conformational motifs can be used when designing novel therapeutic compounds

On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds

Backbone N-methylation is common among peptide natural products and has a significant impact on both the physical properties and the conformational states of cyclic peptides. However, the specific impact of N-methylation on passive membrane diffusion in cyclic peptides has not been investigated systematically. Here we report a method for the selective, on-resin N-methylation of cyclic peptides to generate compounds with drug-like membrane permeability and oral bioavailability. The selectivity and degree of N-methylation of the cyclic peptide was determined by backbone stereochemistry, suggesting that conformation dictates the regiochemistry of the N-methylation reaction. The permeabilities of the N-methyl variants were corroborated by computational studies on a 1024-member virtual library of N-methyl cyclic peptides. One of the most permeable compounds, a cyclic hexapeptide (MW = 755) with three N-methyl groups, showed an oral bioavailability of 28% in rat