A wide
range of drug targets can be effectively modulated by peptides
and macrocycles. Unfortunately, the size and polarity of these compounds
prevents them from crossing the cell membrane to reach target sites
in the cell cytosol. As such, these compounds do not conform to standard
measures of drug-likeness and exist in beyond the rule-of-five space.
In this work, we investigate whether prodrug moieties that mask hydrogen
bond donors can be applied in the beyond rule-of-five domain to improve
the permeation of macrocyclic compounds. Using a cyclic peptide model,
we show that masking hydrogen bond donors in the natural polar amino
acid residues (His, Ser, Gln, Asn, Glu, Asp, Lys, and Arg) imparts
membrane permeability to the otherwise impermeable parent molecules,
even though the addition of the masking group increases the overall
compound molecular weight and the number of hydrogen bond acceptors.
We demonstrate this strategy in PAMPA and Caco2 membrane permeability
assays and show that masking with groups that reduce the number of
hydrogen-bond donors at the cost of additional mass and hydrogen bond
acceptors, a donor–acceptor swap, is effective.