COOKIE-Pro: covalent inhibitor binding kinetics profiling on the proteome scale

Hanfeng Lin, Bin Yang, Lang Ding, Yen-Yu Yang, Matthew V. Holt, Sung Yun Jung, Bing Zhang, Meng C. Wang and Jin Wang ()
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Hanfeng Lin: Baylor College of Medicine
Bin Yang: Baylor College of Medicine
Lang Ding: Baylor College of Medicine
Yen-Yu Yang: Thermo Fisher Scientific
Matthew V. Holt: Baylor College of Medicine
Sung Yun Jung: Baylor College of Medicine
Bing Zhang: Baylor College of Medicine
Meng C. Wang: Howard Hughes Medical Institute
Jin Wang: Baylor College of Medicine

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract Covalent inhibitors are an emerging class of therapeutics, but methods to comprehensively profile their binding kinetics and selectivity across the proteome have been limited. Here we introduce COOKIE-Pro (COvalent Occupancy KInetic Enrichment via Proteomics), an unbiased method for quantifying irreversible covalent inhibitor binding kinetics on a proteome-wide scale. COOKIE-Pro uses a two-step incubation process with mass spectrometry-based proteomics to determine kinact and KI values for covalent inhibitors against both on-target and off-target proteins. We validated COOKIE-Pro using BTK inhibitors spebrutinib and ibrutinib, accurately reproducing known kinetic parameters and identifying both expected and unreported off-targets. The method revealed that spebrutinib has over 10-fold higher potency for TEC kinase compared to its intended target BTK. To demonstrate the method’s utility for high-throughput screening, we applied a streamlined two-point strategy to a library of 16 covalent fragments. This approach successfully generated thousands of kinetic profiles, enabling the quantitative decoupling of intrinsic chemical reactivity from binding affinity at scale and validating the method’s broad applicability. By providing a comprehensive view of covalent inhibitor binding across the proteome, COOKIE-Pro represents a powerful tool for optimizing the potency and selectivity of covalent drugs during preclinical development.

Date: 2025
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DOI: 10.1038/s41467-025-63491-2

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