Quinone methides and related electrophiles represent a common class of intermediates that form
during metabolism of drugs and xenobiotics and may lead to DNA alkylation. The intrinsic reactivity of these
species has now been characterized using a stable model compound, O-(tert-butyldimethylsilyl)-2-bromomethylphenol, designed to generate an o-quinone methide in the presence of fluoride. The resulting
deoxynucleoside adducts were assigned unambiguously through use of two-dimensional NMR and, in particular,
heteronuclear multiple-bond connectivity (HMBC). Both purines, dG and dA, reacted at their exo-amino groups.
In contrast, dC had previously been shown to react at its cyclic N3 position [Rokita, S. E.; Yang, J.; Pande,
P.; Greenberg, W. A. J. Org. Chem.
1997, 62, 3010−3012], and the relatively nonnucleophilic T remained
inert under all conditions examined. Surprisingly, the efficiency of cytosine modification exceeded that of
adenine and guanine by more than 10-fold in competition studies with the deoxymononucleosides. Reaction
of all residues was suppressed in duplex DNA, but none was affected more than cytosine (>3600-fold). Guanine
consequently emerged as the predominant target in duplex DNA in accord with the selectivity of most natural
products forming quinone methide-like species. These general observations may then in part reflect the ability
of the exo-amino group of guanine to maintain its reactivity most effectively from nucleoside to helical DNA.
Although both 4,5- and 4, 6-linked aminoglycosides target the same ribosomal site, they appear to bind and effect antibiotic activity in different manners. The aminoglycosides might recognize different RNA conformations or the interaction might involve different RNA tertiary structures that are not equally sampled in our ribosome-free model. These results imply that models of ribosomal RNA must be carefully designed if the data are expected to accurately reflect biological activity.
The structure and activity of the pseudodisaccharide core found in aminoglycoside antibiotics was
probed with a series of synthetic analogues in which the position of amino groups was varied around the
glucopyranose ring. The naturally occurring structure neamine was the best in the series according to assays
for in vitro RNA binding and antibiotic activity. With this result in hand, neamine was used as a common core
structure for the synthesis of new antibiotics, which were evaluated for binding to models of the Escherichia
coli 16S A-site ribosomal RNA, in vitro protein synthesis inhibition, and antibiotic activity. Analysis of RNA
binding revealed some correlation between the relative affinity and specificity of RNA binding and antibacterial
efficacy. However, the correlation was not linear. This result led us to develop the in vitro translation assay
in an effort to better understand aminoglycoside−RNA interactions. A linear correlation between in vitro
translation inhibition and antibiotic activity was observed. In addition, IC50s in the protein synthesis assay
were typically lower than the K
ds obtained for RNA binding, suggesting that binding of these compounds to
intact ribosomes is tighter in these cases than binding to the model RNA oligonucleotides. This reflects possible
differences in RNA conformation between intact ribosomes and the free RNA of the model system, or possible
high-affinity ribosomal binding sites in addition to the A-site RNA.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.