As drug discovery moves increasingly toward previously “undruggable” targets such as protein–protein interactions, lead compounds are becoming larger and more lipophilic. Although increasing lipophilicity can improve membrane permeability, it can also incur serious liabilities, including poor water solubility, increased toxicity, and faster metabolic clearance. Here we introduce a new efficiency metric, especially relevant to “beyond rule of 5” molecules, that captures, in a simple, unitless value, these opposing effects of lipophilicity on molecular properties. Lipophilic permeability efficiency (LPE) is defined as log D 7.4 dec/w – m lipocLogP + b scaffold, where log D 7.4 dec/w is the experimental decadiene–water distribution coefficient (pH 7.4), cLogP is the calculated octanol–water partition coefficient, and m lipo and b scaffold are scaling factors to standardize LPE values across different cLogP metrics and scaffolds. Using a variety of peptidic and nonpeptidic macrocycle drugs, we show that LPE provides a functional assessment of the efficiency with which a compound achieves passive membrane permeability at a given lipophilicity.

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.

Synthetic and natural cyclic peptides provide a testing ground for studying membrane permeability in nontraditional drug scaffolds. Cyclic peptomers, which incorporate peptide and N-alkylglycine (peptoid) residues, combine the stereochemical and geometric complexity of peptides with the functional group diversity accessible to peptoids. We synthesized cyclic peptomer libraries by split-pool techniques, separately permuting side chain and backbone geometry, and analyzed their membrane permeabilities using the parallel artificial membrane permeability assay. Nearly half of the side chain permutations had permeability coefficients (P) > 1 × 10 cm/s. Some backbone geometries enhanced permeability due to their ability to form more stable intramolecular hydrogen bond networks compared with other scaffolds. These observations suggest that hexameric cyclic peptomers can have good passive permeability even in the context of extensive side chain and backbone variation, and that high permeability can generally be achieved within a relatively wide lipophilicity range.

Large macrocyclic peptides can achieve surprisingly high membrane permeability,a lthough the properties that govern permeability in this chemical space are only beginning to come into focus.W eg enerated two libraries of cyclic decapeptides with stable cross-b conformations,and found that peptoid substitutions within the b-turns of the macrocycle preserved the rigidity of the parent scaffold, whereas peptoid substitutions in the opposing b-strands led to "chameleonic" species that were rigid in nonpolar media but highly flexible in water.B oth rigid and chameleonic compounds showed high permeability over aw ide lipophilicity range,w ith peak permeabilities differing significantly depending on scaffold rigidity.Our findings indicate that modulating lipophilicity can be used to engineer favorable ADME properties into both rigid and flexible macrocyclic peptides,and that scaffold rigidity can be used to tune optimal lipophilicity.