Hydrophobicity is a key property that confers cell permeability on cyclic peptides. N- or C-methylation in natural and synthetic cyclic peptides can increase membrane permeability, but it remains unclear why this happens in some cases but not others.
We have shown that the local connected hydrophobic surface area, but not the total hydrophobic surface area, of a compound determines cell uptake. By comparing three-dimensional structures for cyclic peptides from six families, including isomers differing only in the location of an N- or Ca-methyl substituent, we have found that a single methyl group only increases membrane permeability when it connects or expands the size of a hydrophobic surface patches. Positional isomers, with the same molecular weight, hydrogen bond donors/acceptors, rotatable bonds, calculated LogP, topological polar surface area and total hydrophobic surface area, can have very different membrane permeabilities that correlate with the size of the largest continuous hydrophobic surface patch. Results illuminate a key local molecular determinant of membrane permeability.