The researchers set out to close a major gap in kinome pharmacology. Protein kinases—the 518 enzymes that phosphorylate most human proteins and orchestrate nearly every cellular process—are not merely catalytic cores. Beyond their conserved kinase domains, they carry additional domains that mediate autoinhibition, subcellular localization, and complex formation. Autoinhibitory domains (AIDs) typically keep kinases dormant by docking onto the kinase domain and masking the ATP-binding site, blocking both enzymatic activity and substrate interactions until an activating signal relieves this restraint. Classical structural methods struggle to characterize these domains because many AIDs are intrinsically disordered or connected to the catalytic core through flexible linkers, and most structural studies rely on truncated, purified recombinant proteins that lack the physiological post-translational modifications and binding partners essential for correct function. Whether ATP-competitive inhibitors, which stabilize the active DFG-in conformation of the kinase domain, also force structural changes at the AID remained a poorly explored dark space.

To address this, the team developed a multimodal proteomics strategy combining three complementary mass spectrometry-based approaches. The first, AP-LiP-MS, applies limited proteolysis coupled to mass spectrometry on affinity-purified samples: kinases are purified from human cells under native conditions, treated with an inhibitor, and then exposed to proteinase K, which preferentially cleaves accessible and flexible regions. Changes in the resulting conformation-specific peptide fragments reveal structural shifts with high sequence coverage while preserving the native cellular context. This structural readout was paired with contextual proteomics—affinity purification mass spectrometry (AP-MS) to measure complex formation and in vivo proximity labeling using the miniTurbo biotin ligase to map the kinase’s biochemical neighborhood in living cells. The approach was first benchmarked on the kinase DCLK1, where known X-ray crystal structures of the autoinhibited and inhibitor-bound states confirmed that AP-LiP-MS faithfully detects the anticipated structural rearrangements.

Applying the workflow to three disease-associated kinases with well-characterized ATP-competitive inhibitors—CAMKK2 targeted by SGC-CAMKK2-1, CHEK1 targeted by rabusertib, and PRKCA targeted by Gö 6983—the researchers found a striking common theme. In every case, inhibitor binding produced structural changes precisely at the autoinhibitory domain, with increased proteinase K susceptibility indicating that the AID becomes more solvent-exposed. This is consistent with the AID dissociating from the kinase domain, driving the inhibited enzyme into an open, active-like conformation that mimics the structural unlocking that occurs during normal kinase activation. Notably, a structurally similar negative control compound that does not bind CAMKK2 induced neither structural nor interaction changes, confirming the specificity of the observations. For PRKCA, structural alterations extended into the membrane-binding C2 domain, specifically at a short regulatory segment associated with autoinhibition, hinting that multiple domain-domain interactions are disrupted by drug binding.

The consequences of these conformational shifts proved to be as diverse as they were unexpected. For CAMKK2, the inhibitor stabilized a complex between CAMKK2 and PRKAA1, the catalytic subunit of the AMPK energy-sensing complex. Catalytically inactive and autonomously active CAMKK2 mutants responded to the drug with the same interaction pattern, demonstrating that the effect depends on the conformational change rather than on catalytic inhibition. Structural modeling with AlphaFold3 suggested that the activation-relevant T183 residue of PRKAA1 becomes buried within the predicted CAMKK2–PRKAA1 interface. Functional experiments confirmed the implication: in glucose-starved cells, SGC-CAMKK2-1 reduced T183 phosphorylation of PRKAA1 by upstream kinases such as LKB1, and this suppression was rescued when CAMKK2 was depleted by siRNA. In other words, the inhibited kinase acts as a physical shield that sequesters AMPK and blocks its activation through an entirely non-catalytic, scaffolding mechanism—potentially shutting down both the calcium-dependent and energy-stress branches of AMPK signaling simultaneously.

Strikingly, a disease-associated CAMKK2 variant, the R311C mutation found in a patient with bipolar disorder, completely abolished the inhibitor-induced interaction with PRKAA1. Because R311 faces the predicted interaction interface while the neighboring catalytic residue D312 lies outside it, the finding offers the first mechanistic clue for how this genetic variant may uncouple the CAMKK2–AMPK signaling axis in patients, and it underscores that drug responses can depend critically on the specific disease variant a patient carries—a consideration for personalized medicine.

The second model kinase, CHEK1, revealed a different flavor of paradox. Rabusertib remodeled CHEK1’s interactions with numerous DNA-damage response proteins, increasing binding to 14-3-3 proteins, the deubiquitylating enzyme USP7, PCNA, and MCM replication licensing factors, and elevating phosphorylation at the ATR-targeted S317 site—changes mirroring those seen during genuine DNA damage-induced activation. The single interactor that dissociated was CLPB, a mitochondrial protein previously identified in multiple studies as a CHEK1 partner. CLPB dissociation occurred in both wild-type and catalytically inactive CHEK1 but not in a constitutively open mutant, again implicating the conformational rather than catalytic consequence of inhibition. Because CLPB loss is known to cause mitochondrial fragmentation, the researchers examined mitochondrial morphology by super-resolution microscopy. Rabusertib treatment significantly increased mitochondrial fragmentation, an effect that persisted even when the canonical CDK1–DRP1 fragmentation pathway was blocked with the CDK1 inhibitor RO-3306, and that could not be reproduced by DNA damage alone. While a direct causal link between CHEK1–CLPB dissociation and fragmentation remains to be established, the data suggest that CHEK1 inhibition may disrupt mitochondrial proteostasis through a mechanism independent of the drug’s intended catalytic target.

The third model, PRKCA, demonstrated how inhibitor-induced structural changes can redirect a kinase within the cell. Upon Gö 6983 binding, proximity labeling revealed a rapid shift of PRKCA toward membrane-associated proteins at cell junctions, including tight junction, adherens junction, and desmosome components, as well as the known interactor integrin beta-1. Calcium imaging ruled out changes in intracellular calcium as the driver, and a dose-response experiment showed that these junctional proximity changes occurred at significantly lower drug concentrations than other effects, consistent with a specific on-target mechanism. Catalytically inactive and constitutively active PRKCA mutants responded identically, confirming the phenotype is independent of catalytic inhibition. Live-cell imaging of EGFP-tagged PRKCA captured the kinase relocating to the cell periphery—particularly cell-cell contact sites—within eight minutes of drug addition. The researchers propose that Gö 6983 binding opens the C2 domain, exposing a lysine cluster that can bind the junctional lipid PIP2, thereby recruiting the inhibited kinase to membranes through a calcium-independent route.

Taken together, the study establishes the ATP-binding site as a major organizing center of kinase conformation and interaction, and suggests that inhibitor-induced non-catalytic gain-of-function is likely far more prevalent among kinases with autoinhibitory domains than currently appreciated. The authors point to existing examples such as the JAK2 inhibitor ruxolitinib, which paradoxically primes JAK2 hyperphosphorylation and contributes to side effects after drug withdrawal, and BRAF inhibitors that allosterically promote RAF dimerization and MAPK activation, as evidence that such mechanisms already matter clinically. Because many AID-mediated effects would be missed by conventional target engagement assays focused on catalytic kinetics, the authors advocate for systematic multimodal proteomic profiling of both wild-type and disease-mutant kinases during early drug development. The combination of structural and contextual proteomics is not restricted to kinases and could extend to targets lacking catalytic activity altogether. By mapping inhibitor-modulated conformational and interactome landscapes early, researchers hope to detect unexpected liabilities before they surface in the clinic, ultimately guiding the design of safer and more effective kinase-targeted therapeutics.

Subject of Research: Inhibitor-induced displacement of kinase autoinhibitory domains driving non-catalytic drug effects

Article Title: Paradoxical non-catalytic kinase functions are driven by inhibitor-induced displacement of autoinhibitory domains

Article References: Reber, V., Keller, S., Loosli, S. A., Arima, Y., Kleele, T., Picotti, P., & Gstaiger, M. (2026). Paradoxical non-catalytic kinase functions are driven by inhibitor-induced displacement of autoinhibitory domains. Molecular Systems Biology, 22(9), 1474-1500. https://doi.org/10.1038/s44320-026-00229-2

Image Credits: AI Generated

DOI: 10.1038/s44320-026-00229-2

Keywords: kinase inhibitors, autoinhibitory domains, proteomics, protein-protein interactions, CAMKK2, CHEK1, PRKCA, AMPK, mitochondrial fragmentation, drug mechanisms, conformational change, Molecular Systems Biology