Some proteins in our body are simple to target with drugs, as they have a distinct location in their structure where a drug can fit, similar to how a key goes into a lock. However, there are other proteins that are much harder to target because they lack clear spots for drugs to attach.
To create a drug that can inhibit a protein associated with cancer, researchers from Scripps Research looked at a related protein, known as a paralog or “twin.” Through advanced techniques in chemical biology, they identified a site on this paralog where a drug could bind. They then used this information to explore drugs that could attach to a challenging, yet similar spot on the original protein. In the end, they discovered drugs that specifically bound to the target protein without affecting its close relative.
Some proteins in our body are easy to target with drugs, as they have a distinct location in their structure where a drug can fit, similar to how a key goes into a lock. However, there are other proteins that are much harder to target because they lack clear spots for drugs to attach.
To create a drug that can inhibit a cancer-related protein, scientists from Scripps Research examined the protein’s paralog, or “twin.” By employing innovative chemical biology techniques, they identified a site on the paralog that was suitable for drug binding. They then used this information to find drugs that interacted with a similar, but harder-to-identify, location on its twin. Finally, they successfully identified drugs that were selective for the target protein and did not bind to its closely related counterpart.
This method, referred to as “paralog hopping,” was outlined in an article published in Nature Chemical Biology on September 18, 2024. It has the potential to reveal new drug-binding sites and enhance drug development overall, considering that nearly half of the proteins found in human cells—including several tied to cancer and autoimmune diseases—are paralogs.
Senior author Benjamin Cravatt, PhD, who holds the Norton B. Gilula Chair in Biology and Chemistry at Scripps Research, stated, “This method could be widely beneficial when searching for drugs targeting paralogs, as it’s essential to differentiate between these proteins since they can have distinct functions.”
Throughout evolution, many genes have duplicated, resulting in multiple copies within the human genome. Some copies have changed slightly, leading to proteins known as paralogs. Although they are structurally similar, these paralogous proteins often execute overlapping or redundant functions within cells.
Recently, Cravatt’s team developed a strategy to create drugs that specifically attach to the amino acid cysteine, which is a unique building block of proteins with highly reactive properties. Their strategy exploits cysteines as perfect targets for drugs, allowing them to bind permanently and often leading to the protein’s inactivation. Nevertheless, not all proteins feature accessible cysteines, and in some paralogous pairs, only one protein may have a druggable cysteine.
As a case study, the team focused on the paralog pair CCNE1 and CCNE2, both of which are known to be overactive in cancers such as breast, ovarian, and lung cancer. Researchers believed that these proteins had slightly differing functions, indicating that inhibiting just one could improve cancer treatment outcomes.
However, crafting drugs to selectively target either CCNE1 or CCNE2 proved challenging. The team recognized that CCNE2 had a druggable cysteine, while CCNE1 did not. They hypothesized that identifying drugs binding to the same area of CCNE1, despite the absence of a cysteine, would result in the protein’s inhibition.
Initially, scientists introduced a cysteine into CCNE1 to imitate the drug-binding site found in CCNE2. They used this engineered cysteine to identify drugs that interacted with CCNE1. Subsequently, they screened a collection of chemical compounds to find those that competed with the drug for binding to CCNE1. Their aim was to discover compounds that could occupy the same area through mechanisms not reliant on cysteine.
Surprisingly, the team identified various compounds that could bind to CCNE1’s site even after removing the cysteine again. Certain compounds didn’t interact with CCNE2, and some even had opposing functions, enhancing the molecule’s activity instead of inhibiting it. Structural analysis revealed that these compounds bound to a previously unknown cryptic pocket on CCNE1.
The researchers emphasize the significance of broad and innovative screening methods for discovering new drugs.
“If we had focused solely on finding compounds with a particular function, we wouldn’t have uncovered the range of functional molecules available to us. Additionally, if we had only studied CCNE1’s structure, we would have completely overlooked this binding pocket,” Zhang noted.
Further investigation is necessary to evaluate the new compounds’ effectiveness in treating cancers or other diseases where CCNE1 plays a crucial role. The next step for the scientists is applying their paralog-hopping technique to other protein pairs vital for tumor development.
Other contributors to the study include Zhonglin Liu, Sang Joon Won, Divya Bezwada, and Bruno Melillo from Scripps; as well as Marsha Hirschi, Oleg Brodsky, Eric Johnson, Asako Nagata, Matthew D. Petroski, Jaimeen D. Majmudar, Sherry Niessen, Todd VanArsdale, Adam M. Gilbert, Matthew M. Hayward, Al E. Stewart, and Andrew R. Nager from Pfizer, Inc.
This research was funded by the National Cancer Institute (R35 CA231991) and Pfizer.
