Nonclassical Size Dependence of Permeation Defines Bounds for Passive Adsorption of Large Drug Molecules

Macrocyclic peptides are considered
large enough to inhibit “undruggable” targets, but the
design of passively cell-permeable molecules in this space remains
a challenge due to the poorly understood role of molecular size on
passive membrane permeability. Using split-pool combinatorial synthesis,
we constructed a library of cyclic, per-N-methlyated peptides spanning
a wide range of calculated lipohilicities (0 < AlogP < 8) and molecular weights (∼800
Da < MW < ∼1200 Da). Analysis by the parallel artificial
membrane permeability assay revealed a steep drop-off in apparent
passive permeability with increasing size in stark disagreement with
current permeation models. This observation, corroborated by a set
of natural products, helps define criteria for achieving permeability
in larger molecular size regimes and suggests an operational cutoff,
beyond which passive permeability is constrained by a sharply increasing
penalty on membrane permeation.