Two new APP substrate-based hydroxyethylene isosteres (AT and VI) were prepared and their dipeptide conjugates shown not to inhibit the gamma-secretase-mediated formation of either Abeta1-40 or Abeta1-42. The FG isostere and a des-hydroxy hydroxyethylene isostere also gave inactive compounds. Conversely, a number of compounds containing the intact substrate-unrelated Phe-Phe (FF) hydroxyethylene isostere were shown to be potent inhibitors (ED50 = 14-732 nM). These results show that the factors governing the substrate-based design of gamma-secretase inhibitors are more complicated than first thought. (C) 2002 Elsevier Science Ltd. All rights reserved.