Acute Myeloid Leukemia Treatment Shows Promise

Through a collaborative effort, cancer researchers and chemists have identified a new drug target in acute myeloid leukemia (AML) as well as a drug candidate that attacks the target.

The target is a binding pocket on the protein BRD9 called a bromodomain, a subunit of a protein that reads chromatin. BRD9 is subdivided into domains and each have a specific function, with each of these domains encoded by a portion of the BRD9 gene.

Through several experiments, researchers were able to show that BRD9 is a dependency of AML, and the protein’s action was imperative for the activation of the cancer gene MYC. For a study published in Nature Chemical Biology, researchers created several candidate molecules that can bind at BRD9’s bromodomain, which led to the identification of the compound BI-7273.

When BI-7273 was tested against AML cells, it selectively limited cancer cell proliferation and prevented the activation of the MYC oncogene.

“We were of course pleased with these results,” said lead researcher Christopher Vakoc. “But we set an even higher bar. We wanted to be able to show, unambiguously, how the drug worked — we wanted to prove that its target in AML cells was the bromodomain of the BRD9 protein.”

Researchers hypothesized that bromodomain was the binding site of the drug BI-7273. To test that the binding site’s interaction with a drug is the direct cause of the drug’s effect requires a commonly used and intricate method called structure-guided mutagenesis, which changes the shape of the binding pocket so that the drug can no longer fit.

“We figured out a much easier and equally rigorous way of doing this that exploits the modularity of the proteins,” said first study author Anja Hohmann.

There are 61 known bromodomain motifs in at least 48 different proteins, including BRD9. Researchers chose to use simple copy-and-paste techniques that swapped out the bromodomain of the BRD9 protein, and replaced it with the bromodomain that is part of the protein BRD4.

The results of the study showed that the modified BRD9 protein continued to facilitate the reading of chromatin. It was further found that AML cells continued to grow rapidly, and depend on the protein action to engage signaling pathways activated by MYC.

When the new drug BI-7273 was tested, the AML with the swapped out BRD9 bromodomain were found to have no impact on AML cell proliferation.

“This proved that it was specifically the ‘native’ bromodomain of BRD9 that accounted for the drug’s anti-cancer activity,” Vakoc said. “When we swapped it out, even though the protein continued to function, the drug could no longer attach to it. It’s a very elegant way of showing precisely how the drug had its desired effect, by binding the bromodomain native to BRD9.”

Additional experiments demonstrated that the technique was generalizable in other situations where functionally synonymous domains can be switched in for domains that are native to a protein thought to be key to a drug’s action.

Using AML cells, researchers swapped a domain of the protein EZH2 with the functionally synonymous domain from EZH1. The results of the experiment showed that the technique stopped the candidate drug GSK126 from stopping the growth of the AML cells.

“Drugs and their targets are not really like keys and locks,” Vakoc said. “In many instances, a single key will fit many different locks. In other words, in many cases, a drug will interact with many proteins, and because of this we don’t know its precise target. Off-target binding is frequently a cause of unwanted side effects. As the age of precision medicine begins, this is an important issue, a matter of sink or swim for some candidate drugs. Here we’ve described a simple new approach that can unambiguously assign the therapeutic effect of a drug to a single binding site.”