Since completion of the full human genome sequence over a dozen years ago, scientists have been amassing databases that document or predict how specific stretches of DNA letters in the genome encode specific segments of proteins, called domains. Among the domains of greatest interest to drug developers are those that form pocket-like features on the surface of proteins that other molecules can fit into, as keys fit into locks. Drugs are keys that fit into binding-pocket locks, sometimes for the purpose of blocking access to the lock, and other times to initiate a cascade of signaling inside the cell.
“My lab is focused on finding a small number of these binding pockets – ones whose function cancer cells are addicted to,” Vakoc says. “There are a vast number of pockets encoded in our genome; and many of them are present in the proteins found in leukemia cells. We now have a test that will tell you whether a particular pocket matters to a given cancer cell. Which pockets, if you block or disable them, will really hurt a cancer cell? Which ones does the cell rely on to live and prosper?”
CRISPR is a wonderful tool of discovery, since it can be used to change the DNA letters that “spell out” particular binding pockets. If you want to know if a cancer cell depends upon a particular pocket, you mutate it – change its DNA code, causing the pocket to take on an unnatural shape. You mimic the action of an effective drug targeting that particular pocket.
The technique worked precisely and powerfully in the leukemia cells used for demonstration purposes, reported in the paper published today. “If you change the pocket so the protein is no longer functional and you find the cancer can’t survive, then you have a good shot at a useful drug target. We can’t tell if any particular pocket will lead to a fully effective drug; but this is a way to annotate every critical pocket in cancer cells.”
Vakoc’s lab is starting with the kinds of binding pockets that drug makers like to target – considered “druggable” for various technical reasons. “For entirely pragmatic reasons, our lab is prioritizing our search to the kinds of targets chemists like and are willing to design drugs against,” Vakoc says. “We want to have an impact on cancers in the near-term. We want to provide pharmaceutical companies the kind of targets that they have extensive experience figuring out how to hit. And it all comes back to the question: can we identify specific things that cancer cells need—and then deprive them of those things. CRISPR should bring us to the end-game of finding all of the critical pockets of vulnerability in cancer.”
The research described in this story was supported by the National Institutes of Health; Burroughs-Wellcome Fund Career Award for Medical Scientists, Alex’s Lemonade Stand Foundation ‘A’ Award; National Cancer Center Support Grant Development Funds; Simons Center for Quantitative Biology.
“Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains” appears online May 11, 2015 in Nature Biotechnology. The authors are: Junwei Shi, Eric Wang, Joseph P. Milazzo, Zihua Wang, Justin B. Kinney and Christopher R. Vakoc. The paper can be obtained at: http://www.nature.com/nbt/research/index.html?articles=aop