Cryo-electron Microscopy Offers Atomic-Level Images of How Drug Binds to Cancer Protein

Researchers have produced atomic-level cryo-electron microscopy (cryo-EM) images detailing how a small molecule allosteric-inhibiting drug binds to p97, a cancer cell protein, they reported in the journal Science.

The images allowed direct observation of the investigational drug’s structural interaction with p97, including the shape and positions of binding sites, and even hydrogen bonds linking inhibitor and protein.

The findings provide “new insights into the protein structures and interactions that are critical for the activity of a cancer cell, and this knowledge will hopefully enable the design of clinically useful drugs,” explained senior study author Sriram Subramaniam, PhD, of the National Cancer Institute (NCI) Center for Cancer Research, in a news release.

Cryo-EM imaging uses electron beam scatter detectors to visualize the structures of proteins that have been flash-frozen with liquid nitrogen.

The p97 protein is a hexameric AAA ATPase “that is an attractive target for cancer drug development,” the authors explained. Cryo-EM imaging allowed the team to visualize the structure of p97 alone and with a bound allosteric inhibitor at resolutions of 2.3 to 3.3 Å [Ångström]-much better resolution than previously achieved using X-ray crystallography.

The team was able to image p97 in different functional states, showing how binding at specific attachment sites changes the structure of p97. These images allowed the researchers to “establish the sequence of nucleotide-driven structural changes in p97 at atomic resolution,” the team reported. “They also enable elucidation of the binding mode of an allosteric small molecule inhibitor to p97 and illustrate how inhibitor binding at the interface between D1 and D2 domains prevents propagation of the conformational changes necessary for p97 function.”

“Cryo-EM is positioned to become an even more useful tool in structural biology and cancer drug development,” commended NCI acting director Douglas Lowy, MD. “This latest finding provides a tantalizing possibility for advancing effective drug development.”