The development of highly active antiviral therapy has resulted in greater expected life spans and slower progression to AIDS for patient infected with human immunodeficiency virus (HIV) (25, 26). However, the emergence of drug-resistant viruses during treatment and extensive subsequent intraclass cross-resistance has been a limiting factor in the success of treatment (5, 6). Due to this limitation, antiretrovirals with a novel mechanism of action have been the focus of extensive drug discovery research. Enfuvirtide is one novel HIV-1 inhibitor already in clinical use; it blocks fusion of viral and cellular membranes by binding to heptad repeat region 1 (HR1) of virus gp41 (10, 15). Enfuvirtide is homologous to a segment of the HR2 region of gp41 corresponding to amino acids 127 to 162 and binds to the HR1 region of gp41 (39, 40). Enfuvirtide interferes with the formation of the six-helix bundle, composed of an inner coiled-coil trimer of the HR1 and HR2 regions aligned in an antiparallel manner, thereby blocking the final step of virus entry, the fusion of the viral membrane with the target cell membrane (28). A slightly longer, 39-amino-acid peptide, T-1249, binds to a region of HR1 that overlaps the binding site of enfuvirtide and is active against HIV-1, HIV-2, and simian immunodeficiency virus (11). In addition, several other fusion inhibitors have been studied, for example, T-649 (corresponding to amino acids 117 to 152 of gp41) and C34 (corresponding to amino acid 117 to 150 of gp41). Both block the formation of the hairpin structure in a way similar to enfuvirtide (4, 34, 40). A wide range of susceptibility to enfuvirtide has been described in virus isolates from naive patients (13, 16, 18). Early in vitro studies using enfuvirtide showed the development of resistance is associated with changes in a conserved amino acid triad (GIV) at positions 36 to 38 in the HR1 region of gp41 (34). These findings were confirmed by site-directed mutagenesis experiments and in vivo studies which expanded the core region of functional importance to amino acids 36 to 45 (16, 30, 35, 38). Single amino acid substitutions in this region are the most common and cause various degrees of susceptibility loss. Double amino acid substitutions have also been observed and these are associated with the highest levels of resistance, some combinations (G36S/V38M) exhibiting an approximately 100-fold reduction in enfuvirtide susceptibility (30, 34, 38). In addition, changes in HR2 may equally be involved in enfuvirtide resistance as well (20, 36). Most variants that are resistant to enfuvirtide maintain susceptibility to T-1249 and T-649 (12, 34). The rapid emergence of enfuvirtide-resistant viruses and the lack of oral bioavailability are major obstacles that hinder widespread application of enfuvirtide as part of an extended therapy option (5). To overcome these problems, the enfuvirtide peptide was engineered for expression on the cell membrane, leading to a high local concentration of peptide at the site of action (14). Surface expression was achieved by fusing an N-terminal signal peptide and a C-terminal scaffold consisting of a hinge and a membrane anchor to the antiviral peptide M87. This membrane-anchored peptide was expressed from a retroviral vector (pM87) and had good antiviral activity in cell lines. Recently, we developed a retroviral vector expressing a membrane-anchored antiviral peptide that was also highly effective in primary cells and had minimal potential immunogenicity and no detectable toxicity (8). This membrane-anchored peptide was expressed from an optimized retroviral vector (pM87o) and encodes a larger antiviral peptide 46 amino acids in length (M87o). This extended membrane-anchored antiviral peptide can be viewed as a combination of the previously described antiviral peptides T-20 and T-649 (or C34) and is almost similar to DP207, a soluble peptide 45 amino acids in length shown to be a potent fusion inhibitor (40). In an effort to characterize the mechanism of action of this membrane-anchored peptide in comparison to the soluble peptide T-20, we selected resistant variants of HIV-1NL4-3 and HIV-1BaL by serial virus passage using PM1 cells stably expressing peptide M87. Sequence analysis of the resistant isolates showed different patterns of selected point mutations in heptad repeat regions 1 and 2 for the two viruses analyzed. Site-directed mutagenesis studies confirmed the importance of the characterized point mutations (L33S, I48V, and N126K) to confer resistance to M87 as well as to soluble T-20 and to T-649. In addition, replication capacity and dual-color competition assays revealed that the double mutation I48V/N126K in HIV-1BaL results in a strong reduction of viral fitness, whereas the L33S mutation in HIV-1NL4-3 did enhance viral fitness compared to the parental viruses.