Session: Current Topics in Biological Chemistry:

The goal to modulate transcription factor (TF) activity has been of significant interest to medicinal chemists, but due to the lack of small molecule binding sites, targeting TFs has been quite difficult. TFs are, thus, often described as “undruggable”. This is in spite of significant efforts in chemical biology for over a decade to find methods to control cellular TF activity. This work is a new approach that aims to prepare DNA sequence-specific-binding heterocyclic amidine derivatives that can bind to the DNA minor groove and allosterically inhibit DNA major groove binding TFs. One of the ETS family TF, PU.1, provides a model system to test the approach. PU.1 is involved in hemopoietisis but also in the generation of a variety of leukemias when normal function is disrupted. We have investigated the binding inhibition of PU.1 at the GGAA consensus sequence by our designed heterocyclic amidine compounds. The sequence lamdaB, 5’-TAAAAGGAAGTGA-3’, from a native PU.1 enhancer, has been chosen as a high-affinity PU.1 cognate binding site. The designed, initial DNA targeting motifs, bind sequence specifically at the minor groove of the pure AT sequences at the 5’ end of the promoter. New compounds bind at the minor groove of each component of the mixed DNA binding sites of lambdaB, such as AAGGAA, AAGTGA etc. The compounds are also taken up in cells and are able to inhibit PU.1-DNA complexes in biologically relevant systems. In this project, we are focusing on (i) programmable design of a new series of highly selective heterocyclic diamidines for both, pure AT and mixed DNA sequences with cell-permeable pharmacophores, (ii) biophysical analysis for a complete understanding of the interactions of designed heterocyclic diamidines with both cognate and non-cognate DNAs and (iii) the development of biophysical allosteric inhibition assay techniques to monitor the inhibition of TF binding to cognate binding sites. The most important considerations of this work are how the affinity and kinetics change with the DNA sequence and compound structure and properties. These studies define the necessary compound components that provide the ability to inhibit TF-DNA complexes. Our initial biophysical development with PU.1 TF shows quite clearly that our minor groove binding compounds can allosterically inhibit major groove binding TFs.

W David Wilson

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