Chem-Map Detects Where Small Molecule Drugs Interact with Chromatin

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While many effective small molecule drugs are known to act by interacting with the genome, their underlying mechanism often remains unclear. Gaining insight into where and how small molecule drugs interact with the targeted genome is critical to understanding how they affect cellular functions. Now researchers from Sir Shankar Balasubramanian’s group in the UK have developed a new method, Chem-map, for in situ mapping of small molecules interacting with DNA or chromatin-associated proteins.

This research was published in Nature Biotechnology in the article “Chem-map profiles drug binding to chromatin in cells.”

“Understanding how drugs work in the body is essential to creating better, more effective therapies,” says Zutao Yu, PhD, a research fellow in the Balasubramanian Laboratory in the University of Cambridge’s Department of Chemistry. “But when a therapeutic drug enters a cancer cell with a genome that has three billion bases, it’s like entering a black box.”

Chem-map lifts the veil on this genomic black box by enabling researchers to detect where small molecule drugs interact with their targets on the DNA genome. It enables researchers to accurately map small molecule-genome interactions in situ, using small molecule-targeted transposase Tn5 tagmentation. This detects the binding site in the genome where a small molecule binds to genomic DNA or DNA-associated proteins.

“Many life-saving drugs interact directly with DNA to treat diseases such as cancer,” says Jochen Spiegel, PhD, a visiting researcher in the Balasubramanian lab. “Our new method can map exactly where drugs bind to the genome, which will help us develop better drugs in the future.”

The researchers demonstrate Chem-map for three different drug-binding modalities: molecules that target a chromatin protein, a DNA secondary structure, or that intercalate into DNA.

They used Chem-map to determine the direct binding sites in human leukemia cells of the widely used anti-cancer drug doxorubicin. The technique showed how the combined therapy of using doxorubicin on cells already exposed to the histone deacetylase (HDAC) inhibitor tucidinostat could have a potential clinical benefit.

The technique was also used to map the binding sites of G4s – four-stranded secondary structures involved in gene regulation that could be potential targets for future cancer treatments. More specifically, the researchers “mapped the BET bromodomain protein-binding inhibitor JQ1 and provided interaction maps for DNA G-quadruplex structure-binding molecules PDS and PhenDC3.”

“Chem-map is a powerful new method to detect the place in the genome where a small molecule binds to DNA or DNA-associated proteins,” Balasubramanian noted. “It provides tremendous insights into how some drug therapies interact with the human genome, and makes it easier to develop more effective and safer drug therapies.”

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