Hormone-sensitive cancers, such as those affecting the breast and prostate, frequently depend on a challenging protein known as Forkhead box protein 1 (FOXA1). Mutations in FOXA1 can promote the growth and spread of these cancers. Currently, targeting FOXA1 with drugs is exceptionally difficult, but this may soon change. Researchers have pinpointed a vital binding site on FOXA1 that could open new avenues for cancer therapies. They have also outlined how small drug-like compounds, referred to as small molecules, engage with this protein.
Hormone-sensitive cancers, such as those affecting the breast and prostate, frequently depend on a challenging protein known as Forkhead box protein 1 (FOXA1). Mutations in FOXA1 can promote the growth and spread of these cancers. Currently, targeting FOXA1 with drugs is exceptionally difficult, but this may soon change.
Researchers from Scripps Research have discovered an essential binding site on FOXA1 that could lead to new cancer therapies. Their findings, published in Molecular Cell on October 15, 2024, examined how small molecules interact with FOXA1.
While investigating protein interactions broadly, the team led by co-corresponding author Benjamin Cravatt, PhD, who holds the Norton B. Gilula Chair in Biology and Chemistry, found that small molecules could indeed engage with FOXA1.
“FOXA1 was previously viewed as an unapproachable target for drugs,” states Cravatt. “It was believed to lack the appropriate surfaces for small molecule drugs to attach, which explains the challenges in targeting this protein.”
After making this discovery, Cravatt’s team collaborated with Michael Erb’s lab to gain deeper insights into how these small molecules could influence FOXA1’s functionality.
Both researchers utilized two variations of activity-based protein profiling (ABPP), a method developed by Cravatt’s lab to analyze protein activities on a large scale. This combined strategy enabled them to ascertain not only if a small molecule could attach to FOXA1 but also to identify the precise binding site.
Erb’s team is particularly focused on how transcription factors, such as FOXA1, toggle specific genes “on” and “off,” contributing to cell states that can lead to cancer. Transcription factors bind to particular DNA regions, regulating whether genes are activated or suppressed. This regulation is crucial for cellular function, especially in hormone-driven cancers where FOXA1 often plays a key role in growth.
“FOXA1 is a key regulator of gene control, which we refer to as a lineage-defining factor,” says Erb, co-corresponding author and associate professor in the Department of Chemistry. “We’ve identified a specific site on FOXA1 where small molecules can bind—a significant finding since transcription factors like FOXA1 are promising targets not only for cancer but for other diseases as well.”
Finding a small molecule binding site on a transcription factor is quite uncommon, making this discovery surprising.
“A common analogy is that drugs fit on proteins like keys in locks, but it’s widely believed that most transcription factors lack binding sites,” adds Erb. “The binding site on FOXA1 is akin to a hidden lock; without today’s ABPP technology, discovering it would have been improbable.”
Another notable discovery was that while FOXA1 typically binds to a specific sequence of DNA bases for gene regulation, attaching small molecules altered its preferred sequences, allowing it to target different genes than usual.
This finding could assist future researchers in understanding the effects of such molecules on gene regulation in cancer. If small molecules can modify FOXA1’s DNA binding preferences, they could influence whether certain genes are activated or repressed, potentially impacting cancer progression.
“We discovered that small molecules could affect FOXA1’s ability to interpret the genetic information in the genome,” states Erb.
Moreover, the team found that specific mutations in FOXA1 impact areas near the sites where small molecules can bind. These mutations altered how FOXA1 interacted with DNA, mimicking the effects of small molecules.
“This indicates that a hotspot for cancer-related mutations doubles as a hotspot for small molecule binding,” points out Erb.
Interestingly, the researchers concluded that small molecules couldn’t attach to FOXA1 independently. They could only bind while FOXA1 was already connected to DNA sequences—suggesting that the effectiveness of small molecules in cancer therapy might depend on FOXA1’s interaction with DNA.
Looking forward, Erb and Cravatt plan to refine FOXA1 ligands into antagonists to inhibit its function and limit cancer growth. They also aim to use ABPP to identify small molecule binding sites on other currently undruggable transcription factors.
“Having created chemical probes to examine FOXA1, we hope our research will prompt the development of drugs targeting this protein,” concludes Cravatt.
