Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C‑Methylations Fine-Tune Conformation and Properties

Incorporating small
modifications to peptidic macrocycles can have
a major influence on their properties. For instance, N-methylation
has been shown to impact permeability. A better understanding of the
relationship between permeability and structure is of key importance
as peptidic drugs are often associated with unfavorable pharmacokinetic
profiles. Starting from a semipeptidic macrocycle backbone composed
of a tripeptide tethered head-to-tail with an alkyl linker, we investigated
two small changes: peptide-to-peptoid substitution and various methyl
placements on the nonpeptidic linker. Implementing these changes in
parallel, we created a collection of 36 compounds. Their permeability
was then assessed in parallel artificial membrane permeability assay
(PAMPA) and Caco-2 assays. Our results show a systematic improvement
in permeability associated with one peptoid position in the cycle,
while the influence of methyl substitution varies on a case-by-case
basis. Using a combination of molecular dynamics simulations and NMR
measurements, we offer hypotheses to explain such behavior.