Overexpression of zinc-dependent metalloproteinase, aminopeptidase N (APN/CD13), is considered to be involved in the process of tumor invasion and metastasis. Herein we describe the synthesis and in vitro enzymatic inhibition assay of antineoplaston AS2-5 scaffold peptidomimetic compounds. The results demonstrated that most of these L-iso-glutamine derivatives displayed selective inhibitory activity against APN as compared with MMP-2, with IC(50) values in the micromole range. The structure-activity relationships were also briefly discussed.