This early-stage drug discovery project aimed to establish test-tube screening materials and methods, followed by library screening and hit expansion, to produce inhibitors of our targets that could be used in later stage drug discovery efforts. Our target enzymes are Flap EndoNucleases (FENs) which process the branched DNA structures (5′ flaps) arising during DNA replication. FENs are found as independent globular proteins in eukaryotes including parasites, the subject of this study. Knockouts of genes encoding FEN enzymes have proved lethal in all organisms tested to date. Thus, identifying specific inhibitors of parasite FEN proteins with good pharmacological properties, i.e. not toxic to humans, cheap to produce and with good bioavailability in vivo, could  potentially lead to the development of a new class of anti-parasite drugs.