A scientific paper on a member of the RAS family of oncogenes published last summer so intrigued Frederick National Laboratory computational scientist Trent Balius that he and his and colleagues performed a follow-up study, shedding more light on the topic.
Balius and FNL colleagues in the National Cancer Institute’s RAS Initiative shared their findings as a letter to the editor in the Proceedings of the National Academy of Sciences USA, the journal where the original article was published. In that original paper, Kessler et al. from drug maker Boehringer Ingelheim and Vanderbilt University identified a molecule that could bind to a small pocket on the surface of KRAS and inhibit its activity.
The search for a direct RAS inhibitor has been one of the primary goals of RAS research in recent years. This particular molecule, BI-2852, had never been published before and was among the most potent small molecules discovered to bind to KRAS.
Upon reading Kessler, Balius delved into the data and used molecular visualization software to view the experimentally determined structure of BI-2852 bound to KRAS. Something caught his eye.
“It looked odd, like it was folded on itself in a strange way,” Balius said.
He noted that the molecule was binding at a protein-protein interface, that is, interacting with two KRAS molecules. This interaction was not discussed in the original Kessler paper. It was present in their structure, but not a first glance.
Summer Intern Muyan Zhou of Georgetown University, mentored by Balius, performed a series of molecular docking and computational studies that ultimately convinced Balius and colleagues to pursue experiments to verify his theory. Although these computational studies were not included, her analysis and contributions were acknowledged in the paper.
Using a sample of BI-2852 provided by Boehringer Ingelheim, Tim Tran, Patrick Alexander and others in the RAS Initiative got to work. Analysis of data gleaned using chromatography (separating, or sorting a solution of molecules by size), mass spectrometry (the detection of the weight of the molecules in an elution) and other technologies confirmed what Balius initially saw: BI-2852 induces the formation of a dimer – four molecules come together, two BI-2852 and two RAS molecules – to form a complex that enhances BI-2852’s ability to bind to KRAS. This is significant, as it could represent a novel method of targeting KRAS.
“Our findings open up a novel strategy in drugging KRAS by honing in on small molecules that can artificially ‘dimerize’ KRAS and thus make it nonfunctional,” Tran said.
The FNL investigators shared the discovery with the scientific community in a letter to the editor. It was the ideal format because they were noting something directly observed from the original paper’s data, adding their own insight to the research.
“We did not contradict any of their data, but we were providing an alternative explanation for how BI-2852 works—the dimer formation—and adding to Kessler’s findings. We were pointing out something we observed,” Balius added.
The authors have since responded to the letter, noting they were encouraged by the potential therapeutic approach in general.
“We all are discovering things together. That’s why publication is so valuable,” Balius said. “The point of publishing a paper is to let the scientific community know what you have found so they can then build on it. Every scientist hopes that their papers are read and help the field move forward.”
Photo: Trent Balius
By Chris Worthington and Mary Ellen Hackett