Identification of Peptide Ligands for Target RNA Structures Derived from the HIV‐1 Packaging Signal ψ by Screening Phage‐Displayed Peptide Libraries

Abstract

Tying up the package: The HIV‐1 RNA packaging signal ψ is a complex RNA structure located within the 5′‐end of unspliced HIV‐1 RNAs (see picture). Upon binding of the viral polyprotein Gag to the ψ RNA, a process mediated by the nucleocapsid protein NCp7, two RNA genomes are packaged into the assembling virions. By using phage display technology peptides were selected that bind specifically to different RNA structures derived from the ψ RNA.

Flexible Nature and Specific Functions of the HIV-1 Nucleocapsid Protein

“…The methylated oligoribonucleotides appear particularly promising, since their intracellular delivery using a cell-penetrating peptide was found to completely impede HIV-1 replication in primary human cells at sub-nanomolar concentrations. Finally, small peptides or peptidomimetics [156][157][158][159] able to compete with NCp7 for its NA binding, and chaperoning activities were designed. However, these peptides were found to be active only in the micromolar range.…”

Inhibition of HIV‐1 by a Peptide Ligand of the Genomic RNA Packaging Signal Ψ

“…Sequences derived from the consensus peptide HWWPWW identified previously are underlined. [1] 750 www.chemmedchem.org…”

“…[1,15,16] This method has been widely applied for epitope mapping and the identification of protein-protein interaction sites and to investigate peptide-DNA interactions. [17] To our knowledge, this is the first study adapting this method for peptide-RNA interactions.…”

“…After removal of the lysine side-chain protecting group (4-Methyltitryl) with TFA (1 %), TIS (5 %), DCM (94 %), and attachment of the dye 5(6)-Carboxytetramethyl-rhodamine (Novabiochem, Switzerland) to the free lysine side-chain amino group, this resin was used in automatic peptide synthesis on an ABI433A peptide synthesizer as previously described. [1] Anti-HIV assays with the transduced peptides. P4.R5 MAGI cells were seeded at 1 10 4 cells and infected with HIV-1 LAI (MOI of 0.5).…”

“…We and others selected peptide ligands for Y-RNA from phage displayed peptide libraries to interfere with NCp7 binding. [1,14] Interestingly, the selected peptides were rich in tryptophans and these amino acids were important for binding to Y-RNA, such as W37 in the natural ligand NCp7 (Figure 1). Although the selected peptides interacted with Y-RNA, their binding affinity was in the high micromolar range and thus required optimization in view of therapeutic applications.…”