Amide-to-Chloroalkene Substitution for Peptide Backbone Modification to Enhance Membrane Permeability

Herein, we report a systematic evaluation of backbone
modification
strategies to enhance peptide membrane permeability, focusing on chloroalkene
dipeptide isosteres (CADIs) as amide bond surrogates. A direct comparison
with classical modificationsincluding N-methylation, esterification,
and thioamidationreveals that CADI substitution consistently
provides the highest improvement in both passive diffusion and cellular
uptake. Mechanistic analyses combining A log P calculations, HPLC profiling, and molecular dynamics simulations
attribute this effect primarily to improved lipophilicity and reduced
hydration, rather than conformational changes. Notably, CADI substitution
is successfully extended to longer polar sequences and cyclic scaffolds,
and it preserves or enhances RNA-binding affinity and selectivity
in G-quadruplex-binding RGG peptides. Overall, this study establishes
CADI substitution as a robust backbone modification strategy that
enables the design of peptidomimetics with enhanced membrane permeability
and improved resistance to hydrolytic stability.