Multiple in Vitro Inhibition of HIV-1 Proteins by 2,6-Dipeptidyl-anthraquinone Conjugates Targeting the PBS RNA.

Elia Gamba,Irene Saccone,Elisa Magli,Alice Sosic,Barbara Gatto,Francesco Frecentese

doi:10.1021/acsmedchemlett.9b00682

Elia Gamba, Irene Saccone + Show 4 more

Open Access

https://doi.org/10.1021/acsmedchemlett.9b00682

Copy DOI

Abstract

We recently reported a series of 2,6-dipeptidyl-anthraquinone conjugates (AQs) as Trans-Activation Response element (TAR) RNA-binding agents able to inhibit in vitro the HIV-1 nucleocapsid (NC) protein-mediated processes. Because NC is a highly adaptable nucleic acid chaperone assisting several crucial steps along reverse transcription, in this study we investigate the ability of AQs to interact with other virus-derived nucleic acid structures thus potentially inhibiting multiple NC functions. Focusing on the HIV-1 Primer Binding Site (PBS) RNA sequence, we demonstrate that properly substituted dipeptidyl-anthraquinone conjugates efficiently inhibit the NC-mediated primer annealing in the low micromolar range. Similarly, we extended the analysis to the HIV-1 trans-activator of transcription (Tat) peptide, which has been recently shown to mimic the annealer functions of NC upon interacting with the same nucleic acid regulatory sequences. Our results highlight how RNA-targeting agents can act as multimode inhibitors of key viral proteins affecting their chaperone activity in reverse transcription processes.

Highlights

We recently reported a series of 2,6-dipeptidyl-anthraquinone conjugates (AQs) as Trans-Activation Response element (TAR) RNA-binding agents able to inhibit in vitro the HIV-1 nucleocapsid (NC) protein-mediated processes
A ntiretroviral therapy exploits a great variety of drugs that efficiently control HIV-1 infection, but the onset of resistance demands the identification of novel pharmacological targets that are less prone to mutate during chronic treatment.[1]
In the attempt to identify small molecules able to impair NC binding/annealing activities, we recently focused our work on dipeptidyl-anthraquinone conjugates (AQs), nucleic acid binding agents acting as threading intercalators able to recognize and stabilize the dynamic structures of nucleic acids which are substrate of NC, impairing the expected nucleic acid rearrangements catalyzed by the viral protein.[6−8] These AQs are characterized by a common anthraquinone scaffold and two side chains at opposite sides of the polycyclic aromatic nucleus: the peptidylside chains are built combining a first amino acid referred as “linker” (R1) and a second amino acid acting as a cationic terminal residue (R2), whose function is to facilitate the interaction with the nucleic acid phosphate backbone

Summary

Introduction

We recently reported a series of 2,6-dipeptidyl-anthraquinone conjugates (AQs) as Trans-Activation Response element (TAR) RNA-binding agents able to inhibit in vitro the HIV-1 nucleocapsid (NC) protein-mediated processes. This RNA−RNA annealing allows the minus-strand synthesis, a step not occurring in the absence of NC.[12] Annealing involves a stretch of 18 nucleotides in the tRNALys3 3′-acceptor stem, with the same sequence as (−)PBS RNA, forming an RNA-duplex with PBS, (+)PBS RNA, that is selectively used as primer by the HIV-1 RT.[12] The stable secondary structure of (+)PBS RNA, to TAR RNA, is the target of the chaperone activity of NC.[13] In this study, we selected from our chemical library of AQs a cluster of 2,6-dipeptidyl-anthraquinone conjugates (Figure 1B) to explore their putative ability to inhibit NC-mediated (+)/(−)PBS RNA annealing in vitro.

Results

Conclusion