Human cathepsin D is a lysosomal aspartic protease that has been implicated in breast cancer metastasis and Alzheimer's disease. Based on a crystal structure of a human cathepsin D-pepstatin A complex, a series of statine-containing inhibitors was designed, synthesized, and tested for inhibitory activity toward the enzyme in vitro. The compounds were modified systematically at individual positions (P4, P3, Pz, PI, and Pi) with the aim of mapping the cathepsin D subsite preferences. The experimentally obtained SAR data were correlated on the basis of molecular modeling. Side-chain preferences for the peptidomimetic inhibitors differed from those found previously using peptide substrates , Protein Sci 2:264-276). In addition, the effects of single side-chain modifications were often nonadditive. Structure-activity relationships, modeling, and thermodynamic analysis indicated that entropy plays a major stabilizing role in inhibitor binding to cathepsin D.Keywords: human cathepsin D; inhibitors; statine; structure-based design Cathepsin D is an intracellular aspartic protease normally found in lysosomes. The main physiological role of cathepsin D is not well established, but it is thought to function in protein catabolism through the degradation of cellular and phagocytosed proteins (Barrett, 1977). Several studies suggest that cathepsin D plays a primary role in processing of proteins for the MHC II antigen presenting pathway (van Lierop et al., 1994). Cathepsin D has also been implicated in a number of diseases. Elevated levels of procathepsin D have been correlated with poor prognosis in breast cancer and with metastasis (Westley & May, 1996). Recent studies have suggested that cathepsin D cleaves the P-amyloid precursor protein to produce the AP peptide responsible for pathogenic plaque formation (Dreyer et al., 1994; Ladror et al., 1994). Abnormally high extracellular cathepsin D levels have also been associated with senile plaque formation and with degenerative brain changes found in the progression of Alzheimer's disease (Kenessey et al., 1989;Castaldo & Nixon, 1990;Yanker et al., 1990). Recently, mice with a deletion of the cathepsin D gene were shown to exhibit developmental abnormalities in intestinal and lymphoid tissue (Saftig et al., 1995). These studies all point to important physiological roles for this enzyme, and suggest that human cathepsin D may be a target of therapeutic significance.Aganval and Rich (1 986 cathepsin D was included in studies on inhibition of human aspartic proteases using human renin inhibitors (Greenlee, 1990;Jupp et al., 1990;Rao et al., 1993). The subsite specificity of human cathepsin D was mapped using a series of synthetic peptide substrates combined with a model of the enzyme .We set out to rationally design a series of inhibitors for cathepsin D starting from the 2.5-A resolution crystal structure of the human cathepsin D-pepstatin A complex solved in our laboratory (Baldwin et al., 1993), with the goal of systematically mapping subsite specificity and ultimately...