. A critical disconnect currently exists between the science that enables discovery of biologic drivers of disease, with the science that enables therapeutic intervention in disease. This disconnect is largely one of chemistry and biophysics, where many of the biomolecular interactions that are involved in regulating cell signaling have proven to be `undruggable' by conventional small molecules. Chief of among biologic targets that have a striking overlap between their validated role in disease and intractability by conventional approaches are transcription factors (TFs). These proteins regulate gene expression programs through formation of protein complexes and, ultimately, sequence-specific binding of DNA stretches in target genes. Despite their validation as drivers in nearly all areas of disease, no chemical class has emerged to interfere with their function outside of the nuclear hormone transcription factor family. My group has recently developed a new chemical platform enabling the synthesis of fully synthetic DNA-Binding Domains (sDBDs), which recapitulate the secondary and tertiary protein structure of basic helix-loop-helix transcription factors. The first validation of this platform has been to mimic the bHLH structure of the Myc/Max heterodimer, which has been a validated driver of oncogenic gene expression programs in many cancers for decades, yet has remained relatively untouched by ligand discovery. Preliminary data presented here establish that sDBDs derived from Myc/Max potently bind consensus E-box DNA sites with comparable affinities to the full-length protein, and directly compete with Myc/Max complex formation on E-box sites in vitro, and interfere with Myc binding to target genes by ChIP-qPCR in situ. These data establish the proof-of-principle for the first chemical class that combines the attributes of synthetic small molecules with the targeting capacity of biologics ? a ?synthetic biologic? - that directly binds DNA to interfere with transcription factor function. While this presents an exciting starting point, we must develop structure activity relationships for this class of molecules as well as validate their ability to reprogram gene expression in cells and animals. The research proposed herein aims to first optimize the structure and function of the sDBDs targeting Myc/Max E-box binding through simultaneous improvements in the stabilization of secondary and tertiary structure, as well as incorporation of additional DNA-binding elements outside of the canonical bHLH binding sites to target larger stretches of DNA. The biologic effects of optimized sDBDs targeting Myc will be explored in Burkitt's Lymphoma, a disease hallmarked by MYC translocation events. Validated cellular models will be employed to identify the genome- wide DNA binding profile of sDBDs, their effects on gene expression and their potential to abrogate oncogenic phenotypes attributed to Myc function in this and other cancers. Together we posit that support of this high-risk goal of directly interfering with transcription factor function through sDBDs has a disproportionately high-reward in an area of biology and disease that has been resistant to most recent advances in science.

Public Health Relevance

Transcription factors are a class of proteins that have been validated to contribute to disease, and yet there are few therapeutic options to interfere with their function in cells and animals. The proposed research aims to establish a new chemical class that regulates transcription factor function by directly and specifically binding target DNA sequences in cells. Here we propose to develop these molecules, synthetic DNA-Binding Domains (sDBDs), to inhibit the function of a prototypical oncogene, cMYC, however this research will also enable the broad development of molecules that interfere with deregulated gene expression programs in a wide range of biological contexts.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
NIH Director’s New Innovator Awards (DP2)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Fabian, Miles
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Chicago
Schools of Arts and Sciences
United States
Zip Code
Yang, Hao; Swartz, Alan M; Park, Hyun June et al. (2018) Evolving artificial metalloenzymes via random mutagenesis. Nat Chem 10:318-324
Bollong, Michael J; Lee, Gihoon; Coukos, John S et al. (2018) A metabolite-derived protein modification integrates glycolysis with KEAP1-NRF2 signalling. Nature 562:600-604
Chang, Jae Won; Montgomery, Jeffrey E; Lee, Gihoon et al. (2018) Chemoproteomic Profiling of Phosphoaspartate Modifications in Prokaryotes. Angew Chem Int Ed Engl 57:15712-15716
Li, Gang; Montgomery, Jeffrey E; Eckert, Mark A et al. (2017) An activity-dependent proximity ligation platform for spatially resolved quantification of active enzymes in single cells. Nat Commun 8:1775