New technique lights up where drugs go in the body, cell by cell Scripps Research scientists developed a technique that maps drug binding in individual cells throughout the body, potentially explaining side effects and guiding safer drug development.December 22, 2025
LA JOLLA, CA When you take a drug, where in your body does it actually go? For most medications, scientists can make only educated guesses about the answer to this question. Traditional methods can measure the concentration of a drug in an organ like the liver, but they can't pinpoint exactly which cells the drug binds to or reveal unexpected places where the drug takes action.
Usually we have almost no idea, after a drug enters the body, how it actually interacts with its target, says Professor Li Ye, the N. Paul Whittier Endowed Chair at Scripps Research and a Howard Hughes Medical Institute investigator. It's been a black box until now.
Ye and colleagues have developed a groundbreaking imaging technique that illuminates the individual cells where drugs bind throughout an entire mouse body. In a study published today in Cell, they used their method called vCATCH to map two widely prescribed cancer drugs. The results showed that one drug binds unexpectedly in the heart and blood vessels, potentially explaining its cardiovascular risks. Using the approach to test the binding sites of new drugs, during development, could help minimize such risks.
Clinical trials show if a drug works to treat disease and establish any common side effects, but exactly what the drug is doing in every cell of the body has been inaccessible. Previous drug-tracking methods relied on either grinding up tissues for analysis or using low-resolution techniques like radioactive imaging. In both cases, researchers could only get a rough sense for which organs a drug migrated to, but not exactly which cells.
In 2022, Ye's lab debuted CATCH: a method to light up the precise cells where drugs bind across the surfaces of organs like the brain. In the new work, they scaled that approach up so that it works everywhere, including deep inside larger organs like the brain, heart and lungs.
The CATCH method works with covalent drugs, which are medications that form permanent bonds with their targets. Scientists add a tiny chemical handle to these drugs before injecting them into mice. The drugs go on to bind as they usually would, and after tissues are collected, researchers treat them with a fluorescent tag and a copper molecule that enables a fast chemical reaction adding the tag onto the drug's handle, revealing where each drug molecule ended up. This kind of highly selective click chemistry reaction, which snaps chemicals together like LEGO bricks, was developed at Scripps Research by K. Barry Sharpless, the W.M. Keck Professor of Chemistry, who won the 2022 Nobel Prize in Chemistry for the invention.
To get vCATCH working more broadly across organ systems, Ye and his colleagues had to overcome a major obstacle: proteins in tissues were soaking up the copper needed for the chemical reaction, preventing it from penetrating deep into organs. Only drug binding sites on the organs' surfaces were appearing fluorescent.
The group began pre-treating tissues with excess copper to block these binding sites, and then performing up to eight cycles of bathing the tissues in both the copper and the fluorescent tags. In most imaging methods, this kind of repetitive treatment would create background noise, as imaging agents would begin accumulating in places other than their specific binding sites. In vCATCH, it works because the chemical reactions are so incredibly selective.
Click chemistry is intrinsically highly specific and efficient, explains Ye. That allows us to fully saturate the system without causing off-target effects.
Because the imaging generates multiple terabytes of data for each mouse, the team collaborated with engineers to develop AI-based analysis pipelines that can automatically identify drug-bound cells throughout the brain and body.
To test the new approach, Ye's lab mapped the binding of two targeted cancer drugs: ibrutinib (Imbruvica), used to treat blood cancers, and afatinib (Gilotrif), prescribed for non-small cell lung cancer. The whole-body maps confirmed that afatinib spread widely through lung tissue as expected. Ibrutinib showed a more surprising pattern. This drug, known to cause irregular heartbeat and bleeding problems, binds not only to its intended targets in blood cells, but also to immune cells in the liver, heart tissue and blood vessels offering clues about its side effects.
Now researchers can look more precisely at those cells and understand why ibrutinib is binding to them, says Ye.
The applications extend far beyond these two cancer drugs. Ye's team is now using vCATCH to study whether cancer drugs selectively target tumor cells more strongly than healthy tissues, and to investigate which cell types in the brain are bound by drugs like antidepressants and antipsychotics.
This could be an incredibly valuable tool for testing late-stage drug candidates to make sure they are strongly binding their targets and don't have any unwanted binding in other organs, he says.
In addition to Ye, authors of the study, Mapping cellular targets of covalent cancer drugs in the entire mammalian body, include Zhengyuan Pang, Verina H. Leung, Cailynn C. Wang, Hanbing Shen, Logan H. Sigua, Alexandra Selke, Christopher Glynn, Melaina Yender, Senhan Xu, Peng Wu, and Benjamin F. Cravatt of Scripps; Ahmadreza Attarpour, Anthony Rinaldi, and Maged Goubran of Sunnybrook Research Institute; Maria Dolores Moya-Garzon and Jonathan Z. Long of Stanford University; and Claire Rammel and Javid J. Moslehi of University of California San Francisco.
This work was supported by funding from the National
