Conformational modulation of DNA by polyamide binding: structural effects of f‐Im‐Py‐Im based derivatives on 5′‐ACGCGT‐3′

Abstract

The DNA sequence 5’-ACGCGT-3’ is in the core site of the Mlu1 cell-cycle box, a transcriptional element in the promoter region of human Dbf4 gene which is highly correlated with a large number of aggressive solid cancers. The polyamide formamido-Imidazole-Pyrrole-Imidazole-Amine+ (f-Im-Py-Im-Am+) can target the minor groove of 5’-ACGCGT-3’ as an antiparallel stacked dimer and has shown good activity in inhibiting transcription factor (TF) binding. Recently, f-Im-Py-Im-Am+ derivatives that involve different orthogonally positioned substituents were synthesized to target the same binding site, and some of them have displayed improved binding and pharmacological properties. In this study, the gel electrophoresis-ligation ladders assay was used to evaluate the conformational effects of f-Im-Py-Im-Am+ and derivatives on the target DNA, an essential factor for establishing the molecular basis of polyamide-DNA complexes and their TF inhibition. The results show that the ACGCGT site in DNA has a relatively wide minor groove and a B-form like overall structure. After binding with f-Im-Py-Im-Am+ derivatives, the DNA conformation is changed as indicated by the different mobilities in the gel. These conformational effects on DNA will at least help to point to the mechanism for the observed Mlu 1 inhibition activity of these polyamides. Therefore, modulating DNA transcription by locking the DNA shape or altering the minor groove geometry to affect the binding affinity of certain TFs is an attractive possible therapeutic mechanism for polyamides. Some of the substituents are charged with electrostatic interactions with DNA phosphate groups and their charge effects on DNA gel mobility have been observed.

Dynamic hydrogen bonding and DNA flexibility in minor groove binders: molecular dynamics simulation of the polyamide f‐ImPyIm bound to the Mlu1 (MCB) sequence 5′‐ACGCGT‐3′ in 2:1 motif

“…Examining how this sequence changes in the presence of a minor‐groove binder allows for guided drug design to target the MCB box with the goal of depleting Cdc7 kinase and forcing apoptosis of cancer cells. Recent experimental work has shown that when f‐ImPyIm and its derivatives bind in the minor groove, they reduce the flexibility of the DNA sequence to which they are bound (Wang et al ., ), potentially contributing to their ability to deplete Cd7 kinase (Ito et al ., ).…”

“…and forcing apoptosis of cancer cells. Recent experimental work has shown that when f-ImPyIm and its derivatives bind in the minor groove, they reduce the flexibility of the DNA sequence to which they are bound (Wang et al, 2013), potentially contributing to their ability to deplete Cd7 kinase (Ito et al, 2012).…”