Non-natural amino acids with aromatic or heteroaromatic side chains were incorporated into tripeptides of the general structure Arg-X-Arg and tested as ligands of the HIV RNA element TAR. Some of these compounds could compete efficiently with the association of TAR and Tat and downregulated a TAR-controlled reporter gene in HeLa cells. Peptide 7, which contains a 2-pyrimidinyl-alkyl chain, also inhibited the spread of HIV-1 in cell cultures. NMR studies of 7 bound to HIV-2-TAR gave evidence for contacts in the bulge region.

During HIV-1 entry, binding of the viral envelope glycoprotein gp120 to the cellular CD4 receptor triggers conformational changes resulting in exposure of new epitopes, the highly conserved CD4-induced (CD4i) epitopes that are essential for subsequent binding to chemokine receptor CCR5 or CXCR4. Due to their functional conservation, CD4i epitopes represent attractive viral targets for HIV-1 entry inhibition. The aim of the present study was to select peptide ligands for CD4i epitopes on native dualtropic (R5X4) HIV-1 envelope (Env) glycoproteins by phage display. Using CD4-activated retroviral particles carrying Env from the R5X4 HIV-1 89.6 strain as the target, we performed screenings of random peptide phage libraries under stringent selection conditions. Selected peptides showed partial identity with amino acids in the extracellular domains of CCR5/CXCR4, including motifs rich in tyrosines and aspartates at the N terminus known to be important for gp120 binding. A synthetic peptide derivative (XD3) corresponding to the most frequently selected phages was optimized for Env binding on peptide arrays. Interestingly, the optimized peptide could bind specifically to gp120 derived from HIV-1 strains with different coreceptor usage, competed with binding of CD4i-specific monoclonal antibody (MAb) 17b, and interfered with entry of both a CCR5 (R5)-tropic and a CXCR4 (X4)-tropic Env pseudotyped virus. This peptide ligand therefore points at unique properties of CD4i epitopes shared by gp120 with different coreceptor usage and could thus serve to provide new insight into the conserved structural details essential for coreceptor binding for further drug development.HIV-1 entry (reviewed in reference 2) is a multistep process initiated by binding of the outer envelope (Env) glycoprotein gp120 to the CD4 receptor. This results in conformational changes leading to exposure of CD4-induced (CD4i) epitopes for the subsequent obligatory interaction with the chemokine receptor CCR5 or CXCR4. Further conformational changes in gp120 activate the fusion peptide at the N terminus of the transmembrane glycoprotein gp41 and lead to the assembly of a six-helix bundle structure that triggers membrane fusion and internalization of the viral particles. This sequential HIV-1 entry process allows the virus to protect the functionally important and highly conserved Env entry epitopes by limiting their exposure to antibodies which may neutralize the infection (35). The complex HIV-1 entry process offers the opportunity for therapeutic intervention at multiple steps. Thus, the first HIV-1 entry inhibitor approved by the FDA (T20, enfuvirtide [Fuzeon]) is a peptide inhibiting the very last step of entry, i.e., membrane fusion, by interfering with the six-helix bundle formation (39). A second entry inhibitor (maraviroc [Selzentry]), targeting CCR5, was approved by the FDA in 2007 (46). This drug, like others whose development had to be discontinued due to liver toxicities, is a CCR5 antagonist, and its use is restricted to drug-experienced HIV-1...

In the context of aminoglycosides as efficient binders to RNA, a 2,6-diaminogalactose scaffold was developed for combinatorial syntheses of potential RNA ligands in the solid phase. A set of selectively removable, orthogonally stable protecting groups in combination with a linker stable throughout the synthesis, but selectively cleavable in the detachment process, allows for selective deprotection and introduction of a side chain in each position of this scaffold. A few of the synthesized compounds exhibit inhibition of HIV-1 infection in HeLa cells that contain a TAR-controlled reporter gene.

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