Guanidinoneomycin B Recognition of an HIV‐1 RNA Helix

Abstract

Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site.

Conjugation of a Ru(II) Arene Complex to Neomycin or to Guanidinoneomycin Leads to Compounds with Differential Cytotoxicities and Accumulation between Cancer and Normal Cells

“…IC 50 The concentration-response curves, plotted in Figure 2, revealed that the cytotoxic activity of conjugates 2-4 was very dependent on the nature of the glycoside moiety in these cell lines. As previously reported, 24 To assess the conjugates' selectivity for tumor cells rather than normal cells, we determined the cell viability of a non-tumorigenic HEK293 cell line, in the presence of conjugates 2-4.…”

“…Their anti-proliferative activity, together with that of cisplatin as positive control and the unconjugated compounds (complex 1, neomycin, neamine and guanidinoneomycin), was first determined in two human tumor cell lines, the breast cancer cell line MCF-7 and the prostate carcinoma cell line DU-145, by using the MTT test that measures mitochondrial dehydrogenase activity as an indication of cell viability ( Table 1). The compounds were screened at a wide range of concentrations (from 0 to 250 µM) to determine the concentration that inhibits cell growth by 50% (IC 50 ). The compounds that did not inhibit cell growth by more than 50% at 250 µM were considered to be inactive.…”

“…[47][48][49] Like naturally occurring aminoglycosides, guanidinoglycosides bind RNA over DNA preferentially, but they have shown higher binding affinity and selectivity against several RNA targets. 46,50 This strategy was first explored by Tor and collaborators by conjugating a platinum(II) complex with neomycin B and guanidinoneomycin B. 51 The fact that these compounds were able to selectively crosslink an RNA structure derived from HIV Rev Response Element demonstrated that therapeutically relevant RNA structures could be targeted with metal complexes by using the appropriate glycoside.…”

Ribosomal Frameshift Signals in Viral Genomes

“…A well defined RNA molecule like the HIV-1 FSS makes a suitable target to screen for compounds able to bind. Indeed, it was found that some compounds are able to bind the upper portion of the HIV stem-loop with high affinity (Palde et al, 2010;Staple et al, 2008). Increasing or decreasing the stability of this stem-loop will likely affect frameshifting.…”

“…Staple et al, (2008) investigated the binding of a modified synthetic aminoglycoside to the HIV FSS. Using NMR they were able to show that Guanidinoneomycin B bound to the major groove of the upper stem-loop and this resulted in the repositioning of the 5'-ACAA-3' tetraloop.…”