The emergence and spread of drug resistance challenges our ability to control many life-threatening diseases and new classes of drugs with mechanisms of action that differ from current small molecule drugs are urgently needed. To address this need, we are developing peptide-based drugs using PDIP, a helix-loop-helix peptide macrocycle that encompasses the active domain from a human defence protein. We have developed PDIP analogues with a superior selectivity for diseased over healthy cells compared to other antimicrobial peptides, that can rapidly cross cell membranes to access intracellular targets without becoming trapped in endosomes. Capitalizing on these selective cell-penetrating properties, we employed late-stage conjugation strategies to produce peptide-drug conjugates that have cargo-driven potencies toward intracellular targets. As part of the conjugate design, we evaluated the role of the carrier peptide by comparing PDIP to other cell-penetrating peptides; linker properties by varying length, hydrophobicity, and ability to liberate free drug cargo; and the effect of conjugation on the activity of a range of small molecule drug cargoes.