Each year, the Chemistry of Life Processes Institute’s Executive Advisory Board selects a few exceptional high-risk, high-reward research projects to receive $50,000 to kickstart their research. The funding is part of the Institute’s Cornew Innovation Awards, a board-supported program. This year’s recipients, Shana Kelley (Chemistry, Biomedical Engineering, Biochemistry, and Molecular Genetics), Joshua Leonard (Chemical and Biological Engineering) Gabriel Rocklin (Pharmacology), and Xiaoyu Zhang (Chemistry) are pushing the boundaries of biology and paving the way for more effective and targeted therapies for cancer and other diseases.

A transdisciplinary approach to bring protein drugs to new targets

All antibody-based drugs on the market today have one thing in common—they interact with extra-cellular targets, such as receptors that sit on the surface of cells or cytokines that are secreted outside cells. This is because these drugs lack the critical ability to penetrate cells. Cornew Award recipients Kelley, Leonard and Rocklin are joining forces to pioneer a new way to screen and characterize elusive proteins with cell-penetrating capabilities, an approach that can open the door to more powerful and effective drug development and optimization.

“There’s this huge area of missing targets: things we know are biologically really important, but they can’t be targeted with small molecules or antibodies,” says Rocklin. “A major class of these missing targets are intracellular protein-protein interactions that are important in cancer, autoimmunity, and other diseases, but targeting these interactions is exceedingly difficult.”

The collaborators are studying miniproteins, natural escape artists that are very efficient at penetrating cells, and yet little is known about them.

“Only a very small number have ever been characterized and there’s no efficient way for screening them,” says Rocklin.  “In all drug discovery, high throughput screening is really important. How do you find a small molecule inhibitor of an enzyme? You screen a million things and then you see what works.  How do you find an antibody that binds to a target? You screen a million antibody sequences and see what binds. But there’s just no system that can do that for figuring out if a protein is being internalized into a cell.”

Each droplet contains a yeast cell making a different miniprotein (red, green, violet, or yellow), along with an engineered reporter cell that fluoresces if the miniprotein makes it inside.

The team aims to create a high throughput screening process for miniproteins by employing specialized techniques. The Kelley lab will use microfluidics to compartmentalize each experiment into a microfluidic droplet so that each compartment tests only one mini-protein. The Leonard lab will engineer reporter cells that will fluoresce when penetrated by a miniprotein, making it possible to detect which droplets have contain active miniproteins. The Rocklin lab will use DNA sequencing to analyze the results to determine the properties of the cell-penetrating proteins and identify “design rules” for creating miniproteins that enter into cells more efficiently.

The researchers believe their findings will inform the design of miniproteins that can enter cells and function as intracellular therapeutics.

Elucidating the essentiality and druggability of cancer-acquired cysteines for developing cancer-specific therapy

One of the biggest challenges in cancer drug development is stopping cancer growth without killing normal healthy tissue or triggering severe side effects. Cornew awardee Xiaoyu Zhang (Chemistry) believes there is huge potential in targeting cysteines, one of 20 amino acids found in the human body.

Amino acids form the building blocks of proteins and play an important role in health and disease. Approximately seventeen percent of all cancer mutations lead to the formation of acquired cysteines.

“Among the estimated 49,000 acquired cysteines in cancer, only one of them, a KRAS G12C mutation (that causes a fraction of lung cancer) is being targeted with an approved small molecule drug,” says Zhang.

Zhang’s project has three key aims: to determine which of the acquired cysteines have an essential function in cancer survival, how many are druggable, and which small molecules are effective against them. To determine which of the many thousands of acquired cysteines are essential and druggable, Zhang will integrate functional genomics and chemical proteomics to search the mutant proteins in human cancer.

“If the acquired cysteines are located in hydrophobic pockets, we can make small molecules to target them,” says Zhang.

Development of cancer-specific treatment targeting cancer-acquired cysteines

Zhang will use his in-house small molecule compound library as a starting point for drug discovery.

If successful in screening compounds that can target the essential and druggable acquired cysteines, Zhang believes he can develop small molecules that can specifically target cancer without affecting normal healthy tissues.

“The mechanism of this award is to support people who have big ideas to get initial data,” says Zhang. “Later, I will use those data to not only apply for bigger grants but to translate those discoveries into potential new therapies. This is a very important initial step.”

by Lisa La Vallee