Researchers have identified more than 1,000 functional new druggable cancer drug targets using a combination protocol involving gene base editing and chemical proteomics. The research, published in Nature Chemical Biology, focused on editing thousands of bases on more than 1,750 genes known to be correlated with cancer development.
The work focuses on identifying potentially new druggable cysteines—one of the twenty amino acids that, in various combinations, make up all human proteins. The unique reactive chemistry of cysteines makes them easy and ideal drug targets, but because there are hundreds of thousands of cysteines scattered among human proteins, narrowing down which ones to target with drugs is extremely difficult. Even among the few thousand proteins that have been identified as critical to cancer cell growth, there are still more than 13,000 cysteines.
“The main two questions we wanted to answer in our study are what part of the cancer genes proteins are functional, where to target a particular protein,” explains first author Haoxin Li, a postdoctoral associate at Scripps Research. “The second question is whether that part of the protein can be ligated by some molecule.”
Cysteine-targeted drugs—like ibrutinib, osimertinib, and others—have had great success in the clinic so Li and colleagues wanted to find more functional cysteines in the known cancer dependency proteins.
In this new paper, the team introduced base edits on 13,800 spots on more than 1,750 genes previously linked to cancer cell survival through the Cancer Dependency Map (DepMap) developed by the Broad Institute. In each case, the edit targeted a cysteine on the corresponding protein. They then tested how well cancer cells with the mutation grew. Moreover, they integrated their findings with new data on the “druggability” of these cysteines.
“We were excited to see more than 1,000 cysteines are actually functional base based on this base editing approach from these cancer-dependent genes,” adds Li. In total the team found more than 1,300 functional cysteines, some of which were known to have ligand evidence. “So we can design covalent drugs targeting the cysteines in order to have an impact on the cancer dependencies.”
They ultimately found that about 160 of the druggable cysteines, when edited, impacted cancer cell growth—suggesting that drugs binding to these cysteines could potentially work to treat cancer. “But this is based on the current small molecule ligand ability evidence we have now that shows clear evidence for these 160 cysteines,” adds Li. “In the future, maybe 500 or 600 can actually be drugged in the future as we expand our ligand libraries.”
One of the most significant edits yielding a large impact was seen in a change to cysteine80 of the cancer-dependency protein TOE1. Although TOE1 is known to play an important role in trimming the ends of the cell’s RNA molecules, it had not been studied as a cancer drug target. However, the team showed that small molecules could be harnessed to target this “Achilles’ heel” of cancer cells.
“We have found ligand compounds targeting TOE1 cysteine80 and showed these compounds allosterically inhibit its nuclease activity through a fascinating mechanism that appears to involve the trapping of this cancer dependency protein on the spliceosome,” says Li.
The researchers now plan to follow-up on other novel targets that their experiments revealed.
“We were amazed that by using the base editing we can clearly see which cysteines are functional,” adds Li. “With this approach, we can rediscover many of the druggable sites in the cancer dependency map and hopefully a lot more beyond that.”