A series of synthetic analogues of D-GlcN␣1-6-D-myoinositol-1-HPO 4 -sn-1,2-dipalmitoylglycerol, consisting of 22 variants of the D-GlcN or lipid components, were tested in trypanosomal and human (HeLa) cell-free systems. The assays measured the abilities of the analogues to act as substrates or inhibitors of the enzymes of glycosylphosphatidylinositol biosynthesis downstream of GlcNAc-phosphatidylinositol (GlcNAc-PI) de-N-acetylase. One compound, 4-deoxy-D-GlcN␣1-6-D-myo-inositol-1-HPO 4 -sn-1,2-dipalmitoylglycerol, proved to be an inhibitor of both the trypanosomal and HeLa pathways, whereas 4-O-methyl-D-GlcN␣1-6-D-myo-inositol-1-HPO 4 -sn-1,2-dipalmitoylglycerol and the 4-epimer, D-GalN-␣1-6-D-myo-inositol-1-HPO 4 -sn-1,2-dipalmitoylglycerol, were neither substrates nor inhibitors. The results with other analogues showed that the 6-OH of the ␣-D-GlcN residue is not required for substrate recognition in the trypanosomal and human pathways, whereas the 3-OH group is essential for both. Parasite-specific recognition of the -linked analogue D-GlcN1-6-D-myo-inositol-1-HPO 4 -sn-1,2-dipalmitoylglycerol is striking. This suggests that, like the GlcNAc-PI de-N-acetylase, the trypanosomal glycosylphosphatidylinositol ␣-mannosyltransferases, inositol acyltransferse and ethanolamine phosphate transferase, do not recognize the 2-, 3-, 4-, and 5-OH groups of the D-myo-inositol residue, whereas the human inositol acyltransferase and/or first ␣-mannosyltransferase recognizes one or more of these groups. All of the various lipid analogues tested served as substrates in both the trypanosomal and HeLa cell-free systems, suggesting that a precise lipid structure and stereochemistry are not essential for substrate recognition. However, an analogue containing a single C18:0 alkyl chain in place of sn-1,2-dipalmitoylglycerol proved to be a better substrate in the trypanosomal than in the HeLa cell-free system. These findings should have a bearing on the design of future generations of specific inhibitors of the trypanosomal glycosylphosphatidylinositol biosynthetic pathway.A significant proportion of eukaryotic cell-surface glycoproteins is attached to the plasma membrane by covalent linkage to a glycosylphosphatidylinositol (GPI) 1 anchor. The structure and biosynthesis of GPI membrane anchors and related molecules have been reviewed recently (1-5). The basic GPI core structure attached to protein is composed of NH 2 CH 2 CH 2 PO 4 H-6Man␣1-2Man␣1-6Man␣1-4GlcN␣1-6-D-myo-inositol-1-HPO 4 -lipid (EtN-P-Man 3 GlcN-PI), where the lipid can be diacylglycerol, alkylacylglycerol, or ceramide. This minimal GPI structure may be embellished with additional ethanolamine phosphate groups and/or carbohydrate side chains in a species-and tissue-specific manner (2). Protozoa tend to express significantly higher densities of cell-surface GPI-anchored proteins than do higher eukaryotes. For example, Trypanosoma brucei, the causative agent of African sleeping sickness, expresses a dense cell-surface coat consisting of ϳ5 ϫ 10 6 dimers of a GPI-a...