Scientists Discover Surprising Protein Binding Mechanism That Could Lead to New Therapies
November 22, 2024 | by Dave Defusco
Understanding how proteins recognize and bind to specific molecules has long been a critical component of drug design and therapeutic development. A team of researchers in the Department of Chemistry has published a study in the Journal of the American Chemical Society that presents new insights into these mechanisms, specifically challenging conventional understanding of cation−π interactions—a key noncovalent force that has been central to our understanding of protein binding for the last 40 years. Moreover, these findings have the potential to lead to new therapeutic approaches.
For a long time, scientists believed that cation−π interactions are a key way proteins bind to a class of charged molecules called tetraalkylammonium ligands, which are found in proteins, metabolites and disease biomarkers. This type of interaction happens between a positively charged ion, or cation, and a part of the protein that has many electrons, usually found in ring-shaped structures called aromatic rings.
“A common example of this is when proteins bind to a specific marker on histone proteins called trimethyllysine (Kme3), which is a type of tetraalkylammonium ion. This binding is important for controlling gene expression, which is how cells use genes to create proteins,” said Dr. Marcey Waters, senior author of the study and Glen H. Elder, Jr., Distinguished Professor. “Overall, cation−π interactions were believed to be required for binding between Kme3 and its ‘reader’ protein.”
However, the study, “Trimethyllysine Reader Proteins Exhibit Widespread Charge-Agnostic Binding via Different Mechanisms to Cationic and Neutral Ligands,” has revealed that these protein-ligand interactions are more complex than previously thought. The researchers compared how ~200 Kme3 reader proteins bind to two types of molecules: the native ligand, Kme3, which has a positive charge, and tBuNle, a similar molecule that is the same size and shape but lacks the positive charge.
The study uncovered surprising results: while most Kme3 reader proteins preferred the native Kme3 ligand, about 5% to 6% of these proteins were found to interact with the neutral molecule tBuNle as strongly or even stronger than to the charged molecule Kme3, which is unprecedented.
“This is the first time we have seen Kme3 reader proteins that prefer neutral molecules over charged ones, which goes against the long-standing belief that cation-π interactions were the most important in these cases,” said Dr. Christopher Travis, lead researcher on the paper and an NSF graduate research fellow at UNC. “This is exciting because tBuNle may provide an unexplored approach to developing inhibitors for the 5% to 6% of proteins that bind to it.”
Delving deeper into the molecular mechanisms of these interactions, the researchers discovered that Kme3 and tBuNle interact with the same reader protein by different mechanisms. Protein binding to Kme3 was found to occur via the established mechanism using cation−π interactions. In contrast, binding of the neutral tBuNle is driven by the hydrophobic effect, in which nonpolar substances do not interact well with water and instead preferentially interact with each other in an aqueous environment. Although both types of molecules fit into the same part of the protein, these results show that there isn’t just one mechanism that can make the interaction favorable.
“This discovery helps explain some puzzling results from earlier research, where certain proteins showed unusual ways of binding that the traditional understanding of cation−π interactions couldn’t clarify,” said Dr. Waters. “This finding suggests new strategies for designing drugs, especially for creating targeted treatments that focus on proteins based on whether they prefer charged or neutral molecules.”
These findings are particularly important for developing new treatments that target Kme reader proteins. Dysfunction of these proteins often leads to diseases, including cancer. Since many Kme3 readers bind to the same specific site on histone proteins, it’s been difficult to design drugs that can precisely target just one protein without affecting others. This has made it challenging to create treatments that are both effective and specific.
This study suggests a novel approach: by exploiting the differences in how proteins bind neutral versus charged ligands, researchers can potentially develop inhibitors that selectively target specific proteins, thereby overcoming one of the key challenges in therapeutic development for these proteins.
This research is a big step forward in understanding how proteins recognize and bind to other molecules, and it shows that certain parts of proteins, called aromatic cages, can bind to neutral molecules in ways that don’t rely on the usual cation−π interactions.
“This challenges what scientists have believed for a long time and offers a new way to think about designing drugs,” said Dr. Waters. “These findings could help create more targeted and effective treatments, especially for diseases related to gene regulation and epigenetics.”