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

This research is 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,” said Zutao Yu, PhD, research associate in the Balasubramanian lab in the department of chemistry at the University of Cambridge. “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 of this genomic black box by enabling researchers to detect where small molecule drugs interact with their targets on the DNA genome. It allows researchers to conduct in situ mapping of small molecule-genome interactions with precision, using small-molecule-directed transposase Tn5 tagmentation. This detects the binding site in the genome where a small molecule binds to genomic DNA or DNA-associated proteins.

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

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

They used Chem-map to determine the direct binding sites in human leukemia cells of the widely used anticancer 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 advantage.

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

“Chem-map is a powerful new method to detect the site in the genome where a small molecule binds to DNA or DNA-associated proteins,” noted Balasubramanian. “It provides enormous insights on 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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