A new study introduces a framework for designing small molecules that engage two binding sites on the same protein, with potential applications in developing more precise drugs.
Illustration Explanation: Created by co-first author Jack W. Stevenson, the illustration above depicts ABL1 bound by a bitopic inhibitor and highlights the dynamic linker connecting its two component ligands.
A study published in Nature introduces a new framework for designing “bitopic” kinase inhibitors, small molecules that engage two binding sites on the same protein. The study, “A design approach for bitopic kinase inhibitors,” was led by co-first authors Jack W. Stevenson and Kevin Lou, with co-corresponding authors Kevin Lou and Kevan M. Shokat of the University of California, San Francisco (UCSF), bringing together researchers from UCSF and several collaborating institutions.
Kinases represent a large and diverse set of proteins that carry out important functions in the cell, including responding to internal and external signals appropriately. Mutations in kinases can lead to inappropriate signaling and the development of cancers, which is why kinase inhibitors are popular targets for chemotherapies.
Most kinase inhibitors are designed to bind a single site on a protein. Because many of these sites are similar across related kinases, it can be challenging to design molecules that are both potent and selective, effectively targeting one kinase without causing unwanted activity against others.
“The biggest takeaway for me is that this study gives us a general blueprint for designing small molecules that can recognize two binding sites that are naturally positioned near one another,” says Kevin Lou, a QBI Fellow. “Most drugs are designed around a single binding site, but by engaging two sites, we can potentially make molecules that bind more tightly and more selectively to their intended targets.”
Researchers first targeted ABL1—a kinase that when fused with the BCR protein (BCR-ABL1) can cause cancers like chronic myeloid leukemia—to investigate how different factors such as the choice of binding molecules, how they are connected, and the length of the connecting linker, affect the activity of bitopic inhibitors. Based on their results, they developed designed principles and built a framework for improved biotopic inhibitor development.
This work led to PonatiLink-2, a bitopic ABL1 inhibitor that links together two existing clinical ABL1 inhibitors, ponatinib and asciminib. In preclinical studies, PonatiLink-2 maintained or improved activity against several drug-resistant forms of BCR-ABL1 while showing greater selectivity than ponatinib alone. The molecule also demonstrated a wider therapeutic window in cellular and mouse models.
The researchers also tested bitopic inhibitors against EGFR, suggesting that the design principles may extend beyond ABL1. Together, the findings establish a framework for exploring when bitopic inhibitors can provide advantages over conventional single-site inhibitors.
The study builds on earlier work from the Shokat lab developing bitopic inhibitors of mTOR, including RapaLink-1, and on subsequent research into linked small molecules. For Lou, the new work opens a broader avenue for exploring molecular proximity in drug design.
“There are many places in biology where different binding sites are close to one another, and this gives us a framework for asking when recognizing more than one of those sites can give us something that a conventional single-site molecule cannot,” Lou says. “There’s still a lot to learn about where this principle will be most useful, but ultimately we hope these ideas can help us design drugs that are more precise in how they recognize their targets.”