Researchers from UHN’s Princess Margaret Cancer Centre (PM) have developed a new technique to rapidly identify molecules that bind to human protein targets. The method, called enantioselective affinity selection mass spectrometry (E-ASMS), is a highly sensitive screening tool that can detect even weak interactions between small molecules and proteins during the drug discovery process.
Traditionally, discovering possible drug molecules starts with high-throughput screening (HTS), where scientists use a variety of assays to test large libraries of chemicals against a protein target. This process often produces false positives—in which the assay suggests a chemical binds to the protein when it does not—and misses chemicals that bind weakly. Any compounds that show activity must then be confirmed through time and labour-intensive methods.
To address these challenges, the research team developed E-ASMS—an assay with improved sensitivity that works by using a clever twist: it measures how mirror-image versions of a molecule (called enantiomers) interact with proteins. Small molecules may come in two mirror‑image forms—like left and right hands—that can bind differently to the proteins they target. E-ASMS can detect when one form fits better than the other, called enantioselective binding.
To test E-ASMS, the team screened over 8,000 chemical compounds—50/50 mixtures of both mirror image forms of a chemical—against 31 human proteins, including many thought to be difficult targets.
They discovered 16 promising molecules that bind to 12 proteins, as well as solved the 3D structures of several of the protein-molecule complexes identified. Some of these proteins, such as HAT1, which is linked to cancers and developmental disorders, have long been considered nearly “undruggable.”
By detecting interactions that other methods often miss, this approach accelerates the discovery of new molecules from relatively small chemical libraries. In addition, detecting when only one mirror-image of a molecule binds provides an extra layer of evidence against false positives, reducing the need for extra tests.
The team plans to scale up the use of E-ASMS to screen thousands of proteins and create a massive machine-readable open database to accelerate global drug discovery efforts in the near future.
“This could transform how we find chemical starting points for medicines,” says co-senior author Dr. Levon Halabelian, Affiliate Scientist at PM and researcher at The Structural Genomics Consortium (SGC).
Overall, E-ASMS can help reveal hard-to-find chemical–protein interactions with speed and precision, opening the door to finding drug targets that have remained out of reach until now.
Drs. Jianxian Sun, Xiaoyun Wang, and Shabbir Ahmad are co-first authors of this study. Dr. Sun is a research scientist, and Dr. Wang is a Postdoctoral Researcher in Dr. Peng’s lab. Dr. Ahmad is a Scientific Associate at Princess Margaret Cancer Centre.
Drs. Hui Peng and Levon Halabelian are co-corresponding authors of this study. Dr. Peng is an Affiliate Scientist at the Princess Margaret Cancer Centre (PM), Associate Professor in the Department of Chemistry at the University of Toronto, and a Scientist at the Structural Genomics Consortium – Toronto. Dr. Halabelian is an Affiliate Scientist at PM, an Assistant Professor at the Department of Pharmacology and Toxicology at the University of Toronto, and a Scientist at the Structural Genomics Consortium – Toronto.
This work was supported by the Natural Science and Engineering Research Council of Canada, the National Institute of Health, the Government of Ontario, the Canada Foundation for Innovation, and The Princess Margaret Cancer Foundation.
The Structural Genomics Consortium (SGC) receives direct member funding from Amgen Inc., Janssen Pharmaceutica NV, and Bristol-Myers Squibb Company, as well as grant funding from the Innovative Health Initiative Joint Undertaking, the Gates Foundation and the Michael J. Fox Foundation.
SGC also receives financial and in-kind contributions from Pfizer Inc., AstraZeneca UK Limited, Novo Nordisk A/S, Abcam Limited, Chemspace LLC, Enamine Germany GmbH, IBM Research Israel – Science and Technology Ltd., Nuvisan ICB GmbH, Thermo Fisher Scientific (Bremen) GmbH, The Hospital for Sick Children, and Vernalis (R&D) Limited.
Wang X, Sun J, Ahmad S, Yang D, Li F, Chan UH, Zeng H, Simoben CV, Green SR, Silva M, Houliston S, Dong A, Bolotokova A, Gibson E, Kutera M, Ghiabi P, Kondratov I, Matviyuk T, Chuprina A, Mavridi D, Lenz C, Joerger AC, Brown BD, Heath RB, Yue WW, Robbie LK, Beyett TS, Müller S, Knapp S, Owen DR, Harding R, Schapira M, Brown PJ, Santhakumar V, Ackloo S, Arrowsmith CH, Edwards AM, Peng H, Halabelian L. Enantioselective protein affinity selection mass spectrometry (E-ASMS) .Nat Commun. 2025 Dec 17;17(1):651. doi: 10.1038/s41467-025-67403-2.