Oligocholate macrocycles self-assemble into transmembrane nanopores by the associative interactions of water molecules inside the amphiphilic macrocycles. Macrocycles functionalized with a terephthalic acid “side chain” displayed significantly higher transport activity for glucose across lipid bilayers than the corresponding methyl ester derivative. Changing the 1,4-substitution of the dicarboxylic acid to 1,3-substitution lowered the activity. Combining the hydrophobic interactions and the hydrogen-bond-based carboxylic acid dimerization was an effective strategy to tune the structure and activity of self-assembled nanopores in lipid membranes.