Small molecule inhibitors of the HIV-1 virulence factor, Nef

Abstract

Although antiretroviral therapy has revolutionized the clinical management of AIDS, life-long treatment is required because these drugs do not eradicate HIV- infected cells. Chronic antiretroviral therapy may not protect AIDS patients from cognitive impairment, raising important quality of life issues. Because of the rise of HIV strains resistant to current drugs and uncertain vaccine prospects, an urgent need exists for the discovery and development of new therapeutic approaches. This review is focused on one such approach, which involves targeting HIV-1 Nef, a viral accessory protein essential for AIDS pathogenesis.

Figure 1. The Nef antagonists DLC27 and 2C bind opposite faces of the Nef protein

Left: The X-ray crystal structure of HIV-1 Nef (blue) in complex with a Src-family kinase SH3 domain (red) is shown on the left. Key structural elements of this interaction surface include the Nef PPII helix which involves conserved residues P72 and P75, an ionic interaction between Nef R77 and SH3 D100, and a hydrophobic pocket formed in part by Nef residues F90, W113, and Y120. This pocket interacts with I96 from the RT-loop of the SH3 domain. Nef residues undergoing major NMR chemical shift changes following binding of the Nef antagonists DLC27 (center) and 2C (right) are highlighted on the structure of the Nef:SH3 complex as spheres (cyan). Note that the DLC27 binding site involves residues that interact directly with the SH3 domain RT-loop, including W113 and F90. In contrast, the 2C compound binds at a distance from the SH3 docking site, and is believed to inhibit SH3 binding and Src-family kinase activation through an allosteric mechanism. Models were rendered using the Nef:SH3 X-ray crystal structure of Lee et al. [17]. The NMR chemical shift data used to create the figure are from Betzi et al. for DLC27 [19] and Dikeakos et al. for 2C [21].

Figure 2. The diphenylpyrazolo Nef antagonist B9 is predicted to bind to the Nef dimerization interface

Possible binding sites for B9 were explored using AutoDock Vina [43] and the X-ray crystal structure of the HIV-1 Nef dimer (PDB: 1EFN) [17]. Two energetically favorable binding sites were predicted, with the most favorable site located at the Nef-dimerization interface (Site 1) and a less favorable site on the surface of each monomer (Site 2; only a single B9 molecule is shown in this site for clarity). Two views of the overall structure of the Nef dimer are shown on the left, with the individual Nef subunits colored blue and green. A close-up view of Site 1 is shown on the lower right, where B9 is predicted to make polar contacts with conserved Nef residues Q104, Q107, and N126. A role for N126 in B9 binding to Nef has been demonstrated experimentally, and B9 has been shown to disrupt Nef dimers in a cell-based assay [36]. The structure of B9 is shown at the top right.