Comprehensive profiling of clinically approved kinase inhibitors reveals mutation-specific inhibitors and opportunities for drug repurposing

nature biotechnology Resource https://doi.org/10.1038/s41587-026-03090-8 Comprehensive profiling of clinically approved kinase inhibitors reveals mutation-specific inhibitors and opportunities for drug repurposing Received: 30 June 2025 Accepted: 10 March 2026 Mehlam Saifudeen1,4, Songli Zhu1,4, Shuguang Liang2,4, Mia Eason2, Alison Goupil2, Deanna F. Mische 1, Christian M. Loch2, Haiching Ma2, Marina Chan1 & Taranjit S. Gujral 1,3 Published online: xx xx xxxx Check for updates Protein kinases are central to cell signaling and key drug targets in cancer. To inform potential repurposing of kinase inhibitors, we profiled 86 of the ~100 approved kinase inhibitors against 758 kinases, including 409 wild-type and 349 oncogenic variants using a biochemical kinase assay. Our results increase the number of druggable kinases from 89 to 235, revealing that 94% of mutations and 97% of fusions represented in our samples are inhibited by at least one existing drug. The dataset revealed mutation-specific selectivity, especially in tyrosine kinases FGFR and MET, highlighting gaps and repurposing opportunities. We experimentally validated several actionable findings, including tepotinib to target the IRAK1/4–cholesterol pathway in glioblastoma, brigatinib to target the MARK2/3–Hippo pathway in pancreatic cancer and gilteritinib to overcome MET mutation-driven drug resistance and metastasis. To facilitate exploration of our data, we provide KIRHub, a web-based tool that allows identification of existing inhibitors of wild-type and mutated kinases to guide precision oncology. Protein kinases are essential mediators of cellular signaling and regulate a myriad of biological processes, including cell proliferation, differentiation, metabolism, migration and apoptosis1. Their phosphorylation of target proteins ensures precise control over cellular responses, making kinases indispensable for maintaining healthy homeostasis. Consequently, dysregulation of kinase activity either through mutations or aberrant expression can drive the onset and progression of various diseases, such as cancer and autoimmune disorders. In cancer, aberrant kinase signaling contributes to key hallmarks, including uncontrolled proliferation, resistance to apoptosis, invasion, metastasis and immune suppression; thus, kinases are critical players in oncogenesis and an important class of targets for drug development2,3. Over the past two decades, kinase inhibitors have transformed cancer therapy4, with nearly 100 inhibitors applied primarily for cancers and some other diseases. Typically, these drugs have been developed using a target-based drug discovery approach that starts with target identification and validation, typically based on genetic and functional studies, and continues through inhibitor discovery, design and optimization. The inhibitor development phase is often informed by structural studies to map molecular features that drive binding affinity and target selectivity and by medicinal chemistry efforts that optimize on-target potency and minimize off-target activity. Before moving into clinical testing, inhibitors are evaluated by preclinical validation that establishes on-target efficacy and safety5. In this paradigm, the efficacy Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA. 2Reaction Biology, Malvern, PA, USA. 3Department of Pharmacology, University of Washington, Seattle, WA, USA. 4These authors contributed equally: Mehlam Saifudeen, Songli Zhu, Shuguang Liang. e-mail: ; 1 Nature Biotechnology Resource of resulting drugs is primarily attributed to inhibition of the target they were designed and optimized for and they are labeled and marketed accordingly. For example, imatinib was designed, developed and used as a BCR-ABL inhibitor, whereas afatinib, erlotinib and osimertinib were designed, developed and used as EGFR inhibitors. However, many approved and clinically used kinase inhibitors bind and inhibit additional kinases. This inhibitor promiscuity is primarily viewed as a liability because it is often associated with off-target toxicity. Nevertheless, in some instances, inhibiting multiple targets correlates with improved efficacy, suggesting that this type of polypharmacology could be of benefit. This is especially true in complex diseases such as cancer in which inhibiting an entire signaling cascade might be preferable to inhibiting a single kinase in a pathway6,7. Despite the potential benefits, polypharmacology remains underused because it is difficult, if not impossible, to accurately predict and rationalize polypharmacological effects because of the lack of qualitative and quantitative data related to selectivity of kinase inhibitors8. Previous efforts in profiling kinase inhibitors have provided valuable foundational insights but were limited in scale and scope. The first large-scale kinase-compound interaction study was reported by Anastassiadis et al.9, who assessed 18 US Food and Drug Administration (FDA)-approved inhibitors across 300 kinases; however, this study, as well as many others since then8,10,11, focused almost exclusively on wild-type kinases with minimal evaluation of mutant, disease-associated variants. For example, Elkins et al.11 profiled 25 FDA-approved inhibitors across 224 wild-type kinases and, more recently, a kinobead assay was used by Klaeger et al.8 to profile 37 FDA-approved drugs across 253 wild-type kinases and by Reinecke et al.12 to profile 50 FDA-approved inhibitors across 318 kinases. The most comprehensive profiling of mutant kinases to date was conducted by Duong-Ly et al.13, who evaluated 13 FDA-approved drugs against 76 mutated kinases derived from 21 corresponding wild-type kinases. Thus, there remains a large gap in understanding the full therapeutic potential of existing kinase inhibitors by either leveraging polypharmacology or repurposing available kinase inhibitors to target previously unrecognized pathways and molecular mechanisms. In this study, we address the current limitations of kinase inhibitor profiling through a comprehensive analysis of 92 clinical kinase inhibitors across 758 kinases (409 wild-type and 349 mutant kinases or kinase gene fusions). Our analysis revealed that the landscape of kinases targeted by clinically approved inhibitors can be expanded from 89 primary kinase targets to 235 kinases. We experimentally validated the importance of several of these previously unidentified targets, including inhibitors targeting IRAK1/4 in glioblastoma and those targeting the MARK family in pancreatic cancer. We integrated this comprehensive kinase inhibitor profiling with kinase-focused dependency maps to uncover lineage-specific kinase vulnerabilities that can be targeted by existing kinase inhibitors. Furthermore, our analysis of clinical kinase inhibitors against mutant kinases and kinases that are products of gene fusion events revealed widespread mutation-specific selectivity. For example, clinica (...truncated)