Inhibition of transcription factor-DNA complexes and gene expression by a microgonotropen

Abstract

Developing minor groove-binding drugs to selectively inhibit transcription factor (TF)͞DNA interactions and accompanying gene expression is a current goal in drug development studies. Equipping minor groove-binding agents with positively charged, major groove-contacting side chains yields microgonotropens (MGTs). Previously, we demonstrated that MGTs were superior inhibitors of TF͞DNA complexes in cell-free assays compared with ''classical'' groove binders, but MGTs showed limited ability to inhibit gene expression. To determine what chemical characteristics contribute to or improve activity, we evaluate five MGTs for their effectiveness in inhibiting TF complex formation and resultant transcription by using the c-fos serum response element (SRE) as a target. MGT L1 binds DNA via a bisbenzimidazole equipped with a tripyrrole moiety. It is compared with analog L2, which has been functionalized with propylamines on each of the three pyrroles. L2, which binds DNA at subpicomolar concentrations, was at least three orders of magnitude more potent than L1 at inhibiting TF binding to the c-fos SRE in cell-free assays. Unlike L1 and previous MGTs, L2 also inhibited endogenous c-fos expression in NIH 3T3 cells at micromolar levels. Structure͞activity relationships suggest that, although the tripyrrole͞polyamine functional group of L2 may be largely responsible for its inhibition of TF complexes in cell-free assays, its bisbenzimidazole moiety appears to impart improved cellular uptake and activity. These findings make L2 a promising lead candidate for future, rational MGT design.

Aminoglycoside–Nucleic Acid Interactions: The Case for Neomycin

“…Another intriguing question in this regard was whether the binding would be driven by Hoechst 33258 (duplex-selective groove binder) or neomycin (triplex-selective groove binder). Such ligands with minor/major groove recognition are promising drug candidates for development of inhibitors of transcription factors [141]. To answer these questions, the synthesis and nucleic acid binding of a novel neomycin-Hoechst 33258 conjugate has been recently reported.…”

Transcription Factors As Targets for DNA-Interacting Drugs

“…(1A)), an agent with a weak G⋅C preference [6,8]. No effect was noted for the minor groove binders distamycin A [36,45,64] and netropsin [44].…”

“…The biological consequences of these interactions have been probed not only using EMSAs, but also in more complex environments such as cell-free transcription assays and specific gene expression in cells [45,50,54,[63][64][65]75]. These studies have shown that there are important differences between cell free assays and activity in cells.…”

“…Such DNA binding studies have further been substantiated in many cases by in vitro transcription reactions, reporter gene studies, endogenous expression studies, and viral replication studies [45,54,[63][64][65]75,76]. The development of molecular techniques such as ImmunoFISH [77], chromatin immunoprecipitation [78,79], biospecific interaction analysis [80,81] and expression array technology [82,83] for studying protein/DNA/drug interactions will undoubtedly increase our understanding of the effects of these compounds in cells.…”

AzaHx, a novel fluorescent, DNA minor groove and G·C recognition element: Synthesis and DNA binding properties of a p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (azaHx-PI) polyamide

“…This should expand the ability of Hx-amides to recognize G/C containing sequences. With its resemblance to Hx, 10 Hoechst 33258, 12 and related benzimidazole structures, 13 the azaHx moiety should be fluorescent upon UV excitation. Interestingly, it has also been recently reported that groups with nitrogen acceptors, such as azabenzimidazole in azaHx and pyridine, when added to classical AT specific cationic heterocyclic compounds can confer GC binding selectivity on those compounds as with the polyamides reported here.…”