Breakthrough in Slowing Cancer with Dual Analysis

Fighting cancer effectively often requires stopping the multiplication of cancer cells by understanding the proteins they depend on for survival. Protein profiling is crucial in this process as it helps researchers identify which proteins and their specific parts should be targeted by future drugs. However, past methods have not been detailed enough, leading to some protein targets being overlooked.

Recently, a team of chemists at Scripps Research has combined two protein analysis methods to map over 300 small molecule-reactive cancer proteins and their binding sites. This combination reveals crucial protein targets that, when disrupted by specific chemical compounds or small molecules, can halt cancer cell growth and potentially lead to the development of more effective and precise cancer treatments. These findings were published in Nature Chemistry.

Benjamin Cravatt, Ph.D., co-senior author and the Norton B. Gilula Chair in Biology and Chemistry at Scripps Research, explains that one method provided a broad overview of which proteins interacted with chemicals, while the second method pinpointed the exact locations of these interactions.

Both methods are forms of activity-based protein profiling (ABPP), a technique pioneered by Cravatt that captures protein activity on a global scale. The researchers used their dual approach to identify both the proteins and the protein sites that interacted with a library of stereoprobes—chemical compounds designed to permanently bind to proteins in a selective manner. Stereoprobes help study protein functions and identify potential drug targets.

Bruno Melillo, Ph.D., co-senior author and an investigator in the Department of Chemistry at Scripps Research, notes that their stereoprobes were designed with chemical features often underrepresented in traditional drug discovery, increasing the chances of making significant discoveries that could benefit human health.

The stereoprobes used were electrophilic, designed to irreversibly bind to proteins, specifically to cysteine, an amino acid prevalent in proteins, including those in cancer cells. When chemicals react with cysteine, they can disrupt important bonds and cause proteins to malfunction, interfering with cell growth. Many cancer drugs work by irreversibly binding to cysteines in proteins.

Evert Njomen, Ph.D., the first author and an HHMI Hanna H. Gray Fellow at Scripps Research, explains that cysteine was chosen due to its high nucleophilicity. To identify which proteins bonded with the stereoprobes, the team used a method called protein-directed ABPP, discovering over 300 individual proteins that reacted with the compounds. To delve deeper, they used cysteine-directed ABPP to locate exactly where the stereoprobes were binding on the proteins, similar to focusing on a single spot on a puzzle board to see if a piece fits.

Each stereoprobe molecule has two main components: the binding part and the electrophilic part. The binding component targets the cancer cell protein pocket, and if it fits, the stereoprobe can enter and block the protein's interaction with others, preventing cell division.

Njomen suggests that targeting specific stages in the cell cycle could slow cancer cell growth, causing the cells to remain in a state where they are recognized as defective and targeted for destruction by the immune system.

The team found that their combined approach provided a more accurate picture of protein-stereoprobe reactivity than using a single method alone. They were surprised to discover that using only one technique led to a significant number of missed protein targets.

The researchers hope their findings will contribute to the development of new cancer therapies targeting cell division. Njomen also aims to create new stereoprobe libraries to study protein pockets implicated in other diseases, including inflammatory disorders, where current tools are lacking.