Structural research offers ‘how-to’ guide to designing cancer drugs – ScienceDaily

To design drugs that stop aggressive cancers from growing, it helps to know the structures of the proteins that run the cancers’ engines.

In a series of three articles published Proceedings of the National Academy of Sciences, Scripps Research scientists have elucidated the three-dimensional structure of phosphoinositide 3-kinase alpha (PI3Ka), a protein that is frequently mutated in cancer cells. In addition, the research team sheds light on how this structure changes with cancer-associated mutations, paving the way for drugs that can only target mutated versions.

“We hope these detailed structural findings will lead to the discovery of drugs that affect cancer cells but not healthy cells,” says senior author Peter Vogt, professor in the Department of Molecular Medicine at Scripps Research. “This could potentially eliminate the side effects associated with current PI3Ka drugs.”

PI3Ka plays a central role in cell survival and growth. In healthy cells, the protein turns on and off as needed. But in numerous types of cancer, including breast, colorectal, endometrial, and brain, mutations in PI3Ka always activate it, promoting the uncontrolled growth of tumors. Current drugs aimed at curbing PI3Ka bind to a portion of the protein that rarely changes between healthy and mutated versions; this means that all PI3Ka in the body is turned off. Therefore, these PI3Ka inhibitors carry a long list of side effects and toxicities.

“To solve this problem, you have to make inhibitors that only recognize mutated versions of PI3Ka,” says Vogt. “But to do that, you need structural information about what distinguishes mutated, overactive PI3Ka from normal PI3Ka.”

This is no easy feat: PI3Ka is a particularly flexible, “coiled” protein, so getting a single snapshot of its structure is difficult. But Vogt’s group discovered that PI3Ka became more stable when bound to one of the available inhibitors. Inside PNAS Papers published in November 2021 and September 2022 used a type of imaging technique known as cryogenic electron microscopy (cryo-EM) to resolve the three-dimensional structure of PI3Ka. With this knowledge, they first studied the structure of inhibitor-bound PI3Ka. They then used cross-linking molecules to bind different parts of PI3Ka to itself, stabilizing the most flexible parts of the protein, to visualize the protein without the inhibitor.

More recently, the research team used the same cryo-EM toolbox to piece together the structure of two mutated versions of PI3Ka commonly found in cancer cells. This study, published last month, PNASshowed how parts of the mutated PI3Ka resembled the active form of PI3Ka.

“There are some pretty dramatic structural changes,” Vogt says. “And in the end, the changes essentially mimic the normal active form of the protein, the only difference being that it’s always in this active form.”

The findings point to ways to use drugs to turn off this always-on version of PI3Ka in cancer cells without turning off healthy PI3Ka. The key, according to Vogt, is that drugs need to bind to a different part of the PI3Ka protein from where existing PI3Ka inhibitors bind — a part that differs structurally between healthy and mutated versions of the protein.

The lab group is following up on this research with additional studies revealing how existing drugs alter the structure of PI3Ka.

In addition to the authors of the studies, Vogt, “Cryo-EM structures of PI3Ka reveal conformational changes during inhibition and activation,” “Nanobodies and chemical crosslinks advance the structural and functional analysis of PI3Ka,” and “Cryo-EM Constructs cancer-specific helix and kinase domain mutations of PI3Ka” include Su Yang of Scripps Research, Jonathan R. Hart, Lynn Ueno, and Alexandra Quezada.

The work at Scripps Research was supported by funding from the National Cancer Institute (R35 CA197582 and R50 CA243899).

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