Aromatic bisamidines are active against Leishmania sp. and Pneumocystis carinii. The mode of action is not known, but it has been suggested that they bind to B-DNA minor grooves. Within the drug design based upon the receptor structure, we show the binding energies for some pentamidine analogues with B-DNA and results establish a common base for the synthesis of their rigid counterparts. This is done through the identification of pharmacophore conformation that is isohelical to B-DNA. Results also show the closer pharmacophoric conformation the better binding energies.
B-DNA; pentamidine; Pneumocystis carinii; Leishmania sp
