Ligands interacting with abasic (AP) sites in DNA may generate roadblocks in baseâexcision DNA repair (BER) due to indirect inhibition of DNA repair enzymes (e.g., APE1) and/or formation of toxic byproducts, resulting from ligandâinduced strand cleavage or covalent crossâlinks. Herein, a series of 12 putative APâsite ligands, sharing the common naphthalenophane scaffold, but endowed with a variety of substituents, have been prepared and systematically studied. The results demonstrate that most naphthalenophanes bind to AP sites in DNA and inhibit the APE1âinduced hydrolysis of the latter in vitro. Remarkably, their APE1 inhibitory activity, as characterized by IC50 and KI values, can be directly related to their affinity and selectivity to AP sites, as assessed by means of fluorescence melting experiments. On the other hand, the molecular design of naphthalenophanes has a crucial influence on their intrinsic APâsite cleavage activity (i.e., ligandâcatalyzed ÎČâ and ÎČ,ÎŽâelimination reactions at the AP site), as illustrated by the compounds either having an exceptionally high APâsite cleavage activity (e.g., 2,7âBisNPâS, 125âfold more efficacious than spermine) or being totally devoid of this activity (four compounds). Finally, the unprecedented formation of a stable covalent DNA adduct upon reaction of one ligand (2,7âBisNPâNH) with its own product of the APâsite cleavage is revealed.