Non-covalent DNA groove-binding by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine

Abstract

The cooked meat mutagen 2-amino-1-methyl-6-phenyl-imidazo[4,5-b]pyridine (PhIP) is metabolized in vivo to electrophilic intermediates that covalently bind to DNA guanines. Here we address the mechanism of PhIP's non-covalent interaction with DNA by using spectroscopic and computational methodologies. NMR methodologies indicated that upon addition of DNA, PhIP aromatic protons underwent a small, 0.11-0.12 p.p.m. upfield shift. DNA phosphorus resonances of non-covalent PhIP-DNA complexes broadened and slightly shifted upfield, while DNA base imino proton resonances shifted slightly downfield relative to DNA alone. UV and fluorescence spectra of PhIP titrated with DNA showed no detectable shifting and hypochromism of absorbance or fluorescence bands. In the presence of DNA, PhIP fluorescence was efficiently quenched by acrylamide, but not by silver ion. Further, the NMR spectra suggest that PhIP is in fast exchange with the DNA, and is slightly specific for adenine-thymine (A-T) sequences. Finally, structural arguments based on quantum chemistry calculations suggested that PhIP and its metabolites are unlikely to intercalate into DNA. These data collectively indicate that PhIP non-covalently binds in a groove of DNA.

Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses

“…Various benzimidazole analogues have been demonstrated to intercalate into dsRNA and/or dsDNA structures [38–40], and may modify their properties as substrates for NTPase/helicases, as is the case with some imidazo[4,5‐d]pyridazine derivatives [41]. Moreover, the interaction of these compounds with RNA and/or DNA appears to be dependent on the base sequence of the polynucleotide [42].…”

Characterization of Imidazo[4,5- d ]Pyridazine Nucleosides as Modulators of Unwinding Reaction Mediated by West Nile Virus Nucleoside Triphosphatase/Helicase: Evidence for Activity on the Level of Substrate and/or Enzyme

“…To the best of our knowledge, little is known to date on how imidazo [4,5-d]pyridazine nucleosides interact with DNA. Chemically related compounds like 2-amino-1-methyl-6-phenylimidazo [4,5-b]pyridine and its derivatives are reported to be noncovalent DNA groove-binding agents with slight specificity for adenine-thymidine (AT) sequences (26). Whether this kind of interaction between the imidazo [4,5-d]-pyridazine nucleosides and DNA may lead to decreased stability of the DNA duplex and therefore to an enhanced level of unwinding remains to be verified.…”

Synthesis and Biological Activity of 1H-benzotriazole and 1H-benzimidazole Analogues — Inhibitors of the NTPase/Helicase of HCV and of Some Related Flaviviridae

“…The construct used in this work contained W501, hence the reason of differences in biological activity lays rather in different interactions of the above mentioned compounds with DNA and RNA substrates. Moreover, the interaction of the above mentioned inhibitors may be dependent on the base sequence of the oligonucleotide (Marsch et al, 1994). To explain the mechanism of inhibition of the HCV helicase further NMR and crystallographic studies have been undertaken.…”