Chapter Four · failure evidence
What Kinase Inhibition Assays got wrong, from 26 dissertations
The records describe diverse methodological failures and technical limitations encountered across kinase assay platforms, target profiling, and computational modeling. Researchers frequently faced issues with assay readout artifacts, loss of physiological context in reconstituted systems, protein purification challenges, and poor replication between screening phases. These records come from PhD theses at 10 institutions, 2021 to 2026. Each links to its thesis. They were extracted by language models reading the full text, so treat each as a lead to read, not a verdict.
Kinase activity and engagement assays suffer from readout artifacts and protocol limitations
Assay formats such as cellular thermal shift or commercial TR-FRET assays displayed irregular thermal stabilization profiles or artifactual dependencies on dimerization tags. Other quantitative platforms like single-dose kinome screens, ELISAs, and immunoblot assays were rejected or failed due to high variance, assay oversaturation, or heavy reagent consumption.
Tried and failed
cellular thermal shift assay applied to kinase-inhibitor target engagement. Outcome: unstable. Reason: concentration-dependent irregular stabilization and destabilization at elevated temperatures
Target identification of novel necroptosis inhibitors · Imperial
Considered and rejected
Considered and rejected: Single-dose (50 µM TTM) kinome profiling was rejected as an endpoint due to potential assay over-saturation and false-positive candidate kinase identification, prompting multi-dose profiling (10, 25, 50 µM)
Copper Metabolism Directly Influences Kinase Functionality To Modulate Signal Transduction In Cancer · ScholarlyCommons at Penn
Considered and rejected
Considered and rejected: Rejected relying exclusively on commercial ULight-H3 TR-FRET kinase activity assay due to its artifactual dependency on tag-mediated VRK1 dimerization.
Targeting VRK1: Selective Inhibitors, Chemical Probes, and Biochemical Insights · Harvard
Considered and rejected
Considered and rejected: Rejected RNA pol II CTD immunoblot kinase assay for CDK8 module inhibition kinetics because it was low throughput, non-quantitative, and consumed large quantities of purified complex.
Identifying CDK8/19 as a Novel Regulator of EWS-FLI1 Function in Ewing Sarcoma · DSpace at UTSWMED
Considered and rejected
Considered and rejected: Abandoned ELISA-based measurement of phosphorylated ATF2 in favor of the ADP-Glo luminescent assay due to persistent lack of kinase dependence and high variance.
Inhibition of Mitogen-Activated Protein Kinase p38α by Rooperol and Analogues · TXST Digital Repository
In vitro kinase assays fail due to missing physiological cofactors or lack of substrate structure
Reconstituted in vitro assays failed to confirm phosphorylation or capture paradoxical activation because monomeric systems lacked essential cellular cofactors and scaffold constraints. Additionally, using isolated peptide fragments or recombinant disordered protein segments prevented phosphorylation due to the absence of required tertiary structure and native context.
Tried and failed
in vitro biochemical phosphorylation and kinase mapping assays applied to specific target protein phosphorylation site. Outcome: no signal. Reason: could not biochemically confirm phosphorylation in vitro or identify the responsible upstream kinase
INVESTIGATION OF MOTOR PROTEINS IN HOMOLOGOUS RECOMBINATION · Cornell
Tried and failed
reconstituted in vitro kinase activity assay applied to small molecule paradox activation modeling. Outcome: no signal. Reason: simplified monomeric kinase system lacked necessary cellular cofactors or full-length scaffold constraints required for paradoxical activation
Tried and failed
in vitro kinase validation using peptide fragments applied to mass spectrometry identified kinase substrates. Outcome: no signal. Reason: isolated peptide fragments lacked required tertiary structure or context for phosphorylation by the kinase
Tried and failed
in vitro kinase phosphorylation assay applied to recombinant disordered protein fragment. Outcome: no signal. Reason: None
Disordered proteins regulate stress- & damage-dependent DNA binding · Harvard
Genetic and phosphoproteomic screens fail to identify substrates due to redundancy and low yield
Systematic kinase deletions and comparative phosphoproteomics across knockout lines failed to uncover candidate substrates because redundant or non-canonical kinases maintained phosphorylation. Furthermore, attempting substrate labeling enrichment in a knockout background resulted in diminished phosphopeptide yields and fewer detected peptides compared to wild-type controls.
Tried and failed
systematic kinase deletion screening applied to identifying substrate phosphorylation site kinase. Outcome: no signal. Reason: redundant or non-canonical kinases likely mediate phosphorylation, preventing complete abolishment in single deletion strains
Functional roles of N-terminal intrinsic disorder and phosphorylation in the yeast heterotrimeric G protein gamma subunit, Ste18 · Georgia Tech
Tried and failed
comparative phosphoproteomics across kinase knockout lines applied to identifying novel kinase substrate peptides. Outcome: no signal. Reason: failed to detect consensus motif-containing candidate substrates beyond known targets
Tried and failed
using knockout background for substrate labeling enrichment applied to kinase substrate identification in tissue lysates. Outcome: worse than baseline. Reason: knockout tissue produced lower phosphopeptide yields and fewer detected peptides than wild-type
Computational docking and scoring methods fail to predict binding or beat simple baselines
Three-dimensional convolutional neural network scoring of molecular docking poses failed when experimental assays could not confirm predicted inhibitor binding to homology-modeled kinase targets. Moreover, complex augmented representation models underperformed compared to simpler unaugmented baselines, and datasets excluded allosteric inhibitors due to domain annotation deficiencies.
Tried and failed
3D CNN scoring of molecular docking poses applied to protein kinase ligand binding prediction. Outcome: did not generalise. Reason: experimental assays failed to confirm predicted inhibitor binding to homology-modeled targets
Leveraging diverse data modalities to study kinase inhibitor polypharmacology · Harvard
Considered and rejected
Considered and rejected: Decided against using allosteric kinase inhibitors and multi-domain kinases in the KinCo docking dataset due to lack of domain-level binding annotations and violation of ATP-site binding assumptions.
Leveraging diverse data modalities to study kinase inhibitor polypharmacology · Harvard
Lost to a baseline
On ChEMBL kinase target 10752, unaugmented OriginalFS achieved PR-AUC of 0.289, beating augmented TransFS (0.272) and RedockedFS (0.270)
Deep neural networks for pose validation, affinity prediction, and input attribution · Oxford
Hits identified in high-throughput kinase screens fail during validation assays
Kinase activity screens conducted using yeast surface display enriched candidates that failed to replicate in secondary biochemical and cellular assays. Similarly, candidate inhibitors identified in multi-kinase drug screening failed to demonstrate increased inhibition during subsequent dose-response validation experiments.
Tried and failed
yeast surface display kinase activity screening applied to drug-resistant kinase mutant identification. Outcome: did not generalise. Reason: enrichment in yeast display screen did not replicate in orthogonal biochemical and cellular validation assays
Tried and failed
multi-kinase inhibitor drug screening validation applied to drug-resistant cancer cell lines. Outcome: no signal. Reason: candidate inhibitors failed to replicate increased inhibition during dose-response validation
Identifying Vulnerabilities and Novel Drug Candidates in Platinum-Resistant Ovarian Cancer. · Harvard
Recombinant kinase preparation fails due to background contamination or protein inactivation
Purification of large protein kinases for in vitro assays was impeded by persistent contaminating background kinase activity that could not be eliminated. In addition, extended multi-step chromatographic purification of kinase cascade enzymes caused protein misfolding and complete loss of catalytic activity.
Tried and failed
recombinant kinase purification for in vitro assays applied to large protein kinase preparation. Reason: could not isolate protein without contaminating background kinase activity
MAPPING AND SPATIAL MONITORING OF THE DNA DAMAGE SIGNALING NETWORK USING MASS SPECTROMETRY · Cornell
Tried and failed
multi-step chromatographic protein purification applied to recombinant kinase cascade enzymes. Reason: extended purification time caused protein misfolding and loss of catalytic activity
Left open by the authors
Problems the authors named and did not get to.
Left open
Determine if SteE interacts with and directs phosphorylation on other host kinase substrates using kinase assays or interactome screening. Blocker: Requires wet-lab biochemical assays, protein expression, and kinase interaction screening.
Structural and Functional characterisation of SteE, a Salmonella type III secretion system effector · Imperial
Left open
Map the kinase landscape across tumor-infiltrating immune populations and evaluate cell-specific responses to kinase inhibitors across cancer types. Blocker: Requires wet-lab experimental phosphoproteomics, FACS sorting, cell co-cultures, and mass spectrometry across multiple cancer types.
Signaling at the Tumor-Immune Interface in Glioblastoma · MIT
Left open
Perform in vitro kinase assays with candidate kinases (Ksp1, Ime2, Vhs1, Ptk2, Rim15) to identify the kinase responsible for Ste18Nt S7 phosphorylation. Blocker: Requires a wet-lab biochemistry facility and purified candidate kinases to perform in vitro kinase assays.
Functional roles and underlying mechanism of site-specific N-terminal phosphorylation in a heterotrimeric G protein gamma subunit · Georgia Tech
Left open
Identify the proline-directed kinase responsible for phosphorylating the 112 ATR/RAD1-dependent S/T-P-X-K motifs in mouse spermatocytes. Blocker: Requires wet-lab biochemical or genetic validation (e.g., in vitro kinase assays, kinase perturbation in spermatocytes)
THE ATR-TOPBP1 SIGNALING AXIS IN MAMMALIAN MEIOSIS AND SOMATIC DNA REPAIR · Cornell
Left open
Perform kinome profiling and evaluate off-target specificity for the lead reversible inhibitor YKL-04-125. Blocker: Requires wet-lab kinase screening assay panels and physical samples of YKL-04-125.
Biochemical characterization of EGFR exon 20 insertion variants and their inhibitor sensitivities · Harvard
Left open
Test SPARK for in vitro kinase activity using recombinant protein and complementation with a kinase-dead allele. Blocker: Requires a molecular biology wet lab, recombinant protein expression, and in vitro kinase assays.
Left open
Perform phosphoproteomic analysis to measure phosphorylation states of interactors downstream of oncogenic kinase-containing fusion proteins. Blocker: Requires wet-lab experimental phosphoproteomics assays and cell culture.
PROTEIN-PROTEIN INTERACTION NETWORK PERTURBATIONS CAUSED BY ONCOGENIC FUSION EVENTS · Cornell
Left open
Identify and screen small molecule inhibitors targeting the CpxA sensor kinase for anti-virulence therapeutics. Blocker: Requires wet lab biochemical screening assays and chemical compound libraries
Interplay Between Tryptophan Metabolites and the Virulence Factors of Enteric Pathogens · DSpace at UTSWMED
Left open
Synthesize and evaluate flavonoid derivatives including flavones, isoflavones, flavanones, and isoflavanones as potential FMS kinase inhibitors. Blocker: Requires wet lab facilities for organic synthesis and kinase inhibition assays
Development of structurally novel FMS (CSF-1R) inhibitors for cancer · Imperial
Left open
Obtain pure recombinant Tel1 kinase and perform in vitro kinase assays to confirm direct phosphorylation of the D/E-S/T motif. Blocker: Requires a wet biology lab for protein purification and in vitro kinase assays.
MAPPING AND SPATIAL MONITORING OF THE DNA DAMAGE SIGNALING NETWORK USING MASS SPECTROMETRY · Cornell
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