Synthesis and Antiviral Activity of Ethidium−Arginine Conjugates Directed Against the TAR RNA of HIV-1

Abstract

The regulatory protein Tat is essential for viral gene expression and replication of the human immunodeficiency virus type 1 (HIV-1). Tat transactivates the HIV-1 long terminal repeat (LTR) via its binding to the transactivation responsive element (TAR) and increases the viral transcription. Studies have shown that the binding of arginine and arginine derivatives induces a conformational change of the TAR RNA at the Tat-binding site. The unpaired A17 residue delimits a small cavity which constitutes a receptor site for small molecules, especially for ethidium bromide. These binding characteristics have prompted us to design a series of ethidium-arginine conjugates capable of interacting with the TAR RNA. Here we report the synthesis of six ethidium derivatives equipped with arginine side chains. These molecules were biologically evaluated, and two compounds (17 and 20) exhibited in vitro anti-HIV-1 activity at micromolar concentration, without toxicity (up to 100 microM concentration). Melting temperature studies indicated that the most active molecule (20) bound strongly to TAR in vitro. RNase protection experiments agreed with the molecular modeling studies which suggested that the ethidium moiety of 20 was inserted next to the A17 residue while the arginine side chain occupied the pyrimidine bulge.

Novel bis-phenanthridine derivatives with easily tunable linkers, study of their interactions with DNA and screening of antiproliferative activity

“…[1][2][3] In addition, it was shown that the chemical modulation of the ethidium substituents is a profitable option to tune the nucleic acid recognition properties of phenanthridine dyes. [4] Very recent reports about numerous applications point toward versatility of the phenanthridine core, [5][6][7][8][9] including even intriguing biological activity. [10] A huge number of bis-phenanthridine derivatives were prepared with the aim of not only enhanced affinity due to the bis-intercalation into DNA/RNA but also with the idea of introducing selectivity.…”

Using Modularly Assembled Ligands To Bind RNA Internal Loops Separated by Different Distances

“…For example, bulges in HIV TAR RNA have been targeted with ethidium–arginine conjugates;2 secondary-structure elements present in HIV TAR and RRE RNA, the iron responsive element, and thymidine synthase mRNA have been targeted with neomycin B–chloramphenicol conjugates;3 duplex RNAs have been targeted with peptide–quinoline conjugates;4 and loops in HIV RRE have been targeted with peptide–aminoglycoside conjugates 5. Modular assembly has been shown in these cases and others6 to improve affinity and selectivity.…”

HIV-1 drug discovery: targeting folded RNA structures with branched peptides

“…23 Without the formation of a Tat-TAR complex, the rate of viral transcription is minimal, leading to the production of fragmented transcripts. 24 Therefore, disrupting the Tat-TAR interaction is a utilized strategy to interrupt viral replication, and has been pursued through the use of a wide variety of ligands such as intercalators, 25 aminoglycosides, 26 small molecules, 27 siRNA, 28 and nucleic acids. 29 …”