**1. Introduction**

38 Biochemistry

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Protein-protein interactions play important roles in many critical processes in the life sciences, such as signal transduction, lipid membrane fusion, receptor recognition, *etc.*, and many of them are important targets for drug development and design (Wilson 2009; Tavassoli 2011). Unlike an enzyme-substrate interaction which usually has a deep binding pocket in the protein for substrate binding, protein-protein interactions usually involve a large interacting interface; as a result, it is a big challenge for small molecule drugs to efficiently competitively occupy the interface and disrupt protein-protein interactions that modulate these life processes. Proteins are natural ligands that can modulate protein-protein interactions; however, they are not ideal therapeutic agents because of their expensive production costs and the fact that they are not able to be administered orally. In proteinprotein interactions, energy is not always equally distributed throughout the binding interface; a couple of focused areas may account for the main protein-protein interaction energy, called a hot spot, which can be the target for a small molecule protein-protein interaction inhibitor (PPII).

Peptides, with suitable molecular size, provide a bridge between protein and small molecule drugs. Similar to proteins, many peptides are natural ligands that modulate protein-protein interactions in important life processes; they are used as drug leads and/or modified to increase potency and selectivity. Compared with small molecules, peptides are more efficient PPIIs due to their relatively large size, and can be useful tools to probe proteinprotein interactions for PPII design.

HIV-1 gp41 mediated virus-cell membrane fusion is critical for HIV-1 infection and *in vivo* propagation (Eckert & Kim 2001; Caffrey 2011), and the mechanism is shared by many other viruses using a class 1 fusion protein as membrane fusion machinery, including some life threatening pathogens such as influenza virus, respiratory syncytial virus (RSV), Ebola virus, and severe acute respiratory syndrome (SARS) virus (Harrison 2008). A critical step in HIV-1 infection is a protein-protein interaction between the gp41 N- and C-terminal heptad repeats (NHR and CHR), that form a coiled-coil six-helical bundle (6-HB), providing energy for virus-cell membrane fusion (Fig. 1). Peptides derived from CHR or NHR can interact with their counterparts in gp41 to prevent fusogenic 6-HB formation and inhibit HIV-1-cell membrane fusion, thus preventing HIV-1 infection and replication. T20 (Fuzeon, enfuvirtide), a 36-mer peptide from HIV-1 gp41 CHR, was approved by the USA FDA in 2003 as the first fusion inhibitor for salvage therapy in HIV/AIDS patients unresponsive to common antiretroviral therapy. Its application has been limited by i) the high cost of peptide synthesis, ii) rapid *in vivo* proteolysis, and iii) poor efficacy against emerging T20-resistant strains. These drawbacks have called for a new generation of fusion inhibitors with improved antiviral and pharmacokinetic profiles.

In this chapter, we will focus on the development of HIV-1 fusion inhibitors, concentrating on C-peptide fusion inhibitors and their peptidomimetics, which have been used as probes and tools to elucidate gp41 NHR-CHR interactions for future fusion inhibitor design and improve, and in the long run, the development of small molecule inhibitors that can disrupt this important protein-protein interaction.

Fig. 1. HIV-1 gp41 mediated virus-cell membrane fusion.
