Structure-Guided Peptidomimetic Design Leads to Nanomolar β-Hairpin Inhibitors of the Tat−TAR Interaction of Bovine Immunodeficiency Virus^,

Abstract

The Tat protein of immunodeficiency viruses is the main activator of viral gene expression. By binding specifically to its cognate site, the transactivator response element (TAR), Tat mediates a strong induction of the production of all viral transcripts. In seeking a new chemical solution to inhibiting viral protein-RNA interactions, we recently identified inhibitors of the viral Tat protein from the bovine immunodeficiency virus (BIV) using conformationally constrained beta-hairpin peptidomimetics. We identified a micromolar ligand, called BIV2, and the structure of its complex with BIV TAR was determined by NMR. In this work, we demonstrate that this chemistry can rapidly yield highly potent and selective ligands. On the basis of the structure, we synthesized and assayed libraries of mutant peptidomimetics. Remarkably, we were able in just a few rounds of design and synthesis to discover nanomolar inhibitors of the Tat-TAR interaction in BIV that selectively bind the BIV TAR RNA compared to RNA structures as closely related as the HIV-1 TAR or RRE elements. The molecular recognition principles developed in this study have been exploited in discovering related peptidomimetic inhibitors of the Tat-TAR interaction in HIV-1.

RETRACTED: Selection of cyclic peptide aptamers to HCV IRES RNA using mRNA display

“…Although high-affinity cationic linear peptides are easily obtained, they are often not very specific for the particular target RNA sequence, because the electrostatic interaction of the cationic side chains with the anionic RNA backbone typically dominates the binding (26). Recent work on cyclic peptides suggests that rigid structures may yield selective binding not dominated by electrostatics (e.g., 29,30). We have attempted to address the specificity problem by selection from a very large library of cyclic peptide-mRNA fusions under conditions that stringently select against nonspecific binding.…”

Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein

“…We used structure-based methods to discover low nM inhibitors of the Tat-TAR interaction in BIV (15,16). This was achieved by mimicking (14) the ␤-hairpin formed by the RNA-binding domain of BIV Tat protein upon binding its cognate TAR (12,13) with cyclic peptides stabilized by the heterochiral D-Pro-LPro template (17).…”

“…The synthesis of the cyclic peptides was conducted as described (15,16). The ADP-1 peptide (10) was prepared on MBHA-Rink amide resin by using Fmoc chemistry on an Applied Biosystems 433A peptide synthesizer.…”

“…HIV-1 TAR RNA preparation, 3Ј-end labeling of TAR, and EMSA assays were done as described (15,16). Inhibition assays were performed in the same way but by preforming the complex of HIV TAR with the ADP-1 peptide (150 nM) before peptide addition and fractionation by electrophoresis.…”

“…We based the design of these compounds on the structure of the bovine immunodeficiency virus (BIV) complex whose high-resolution structure is available (12)(13)(14). BIV Tat protein and TAR RNA are highly homologous to HIV-1 Tat and TAR, and we recently demonstrated that it is possible to mimic BIV Tat protein by using cyclic peptides that bind to BIV TAR with nM affinity (15,16).…”