Establishment of gene expression patterns defines cellular function and the first critical step in this process is transcription. Exogenous agents that can alter transcription hold tremendous utility as chemical genetic probes and as therapeutics. In my dissertation research I have pursued strategies for controlling the transcription of genes with small drug-like molecules.

The transcriptional status of genes is defined by coregulatory complexes recruited to gene promoters. To achieve control of this recruitment, small molecules that bind to these proteins must be discovered. By use of a high-throughput biochemical screen, sekikaic acid was discovered as a potent ligand of the transcriptional coactivator protein CBP. Sekikaic acid binds to the KIX domain of CBP and its binding precludes the in vitro interaction of transcriptional activation domains from the human transcription factors MLL and CREB to two distinct sites on KIX.

In order for a small molecule to recruit target proteins to individual genes, it must have the ability to localize to DNA. Nuclear receptors were identified as potential targets that could tether bifunctional molecules to their target genes. Conjugates of glucocorticoid receptor (GR) ligands and a ligand of the FK506 binding protein (FKBP) were prepared, and it was demonstrated that the conjugates bind the receptor and recruit an FKBP fusion protein that influence the transcriptional control of target genes in concert with intrinsic GR activity. The ability to recruit nuclear receptor extrinsic functionality to target genes with receptor targeting bifunctional molecules has potential to greatly increase our level of control over the therapeutically relevant genes that can be targeted via nuclear receptors.

The traditional paradigm of artificial transcription factor design is an attempt to mimic natural transcription factors by binding their direct interaction partners. The arsenal of ligands that bind these proteins is limiting, and instead untraditional recruitment targets have been identified: the enzymatic subunits of chromatin modifying complexes. High affinity ligands of these subunits have been discovered and it is demonstrated in this work that a histone deacetylase inhibitor can be incorporated into NR targeting bifunctional recruiters that retain the ability of each conjugate partner to bind its respective protein target.