Dataset Information

MAPK Pathway Inhibition Reshapes Kinase Chemoproteomic Ligandability Reporting on Cellular Activation States

ABSTRACT: Despite the pivotal role of oncogenic kinases in cancer initiation, progression, and resistance, functional profiling of their conformational states within cells remains challenging. Current methodologies often struggle to capture the dynamic structural features and inhibitor-bound conformations of these kinases, particularly in clinically relevant scenarios such as treatment response and relapse, where genomic characterization alone is insufficient.  Chemoproteomic techniques, including activity-based protein profiling (ABPP), offer a powerful means to assess amino acid reactivity in situ as a proxy for protein structure and function. Here, we report that treatment of BRAF mutation positive melanoma cell lines with the BRAF and MEK1/2 inhibitors, vemurafenib and trametinib respectively, results in a significant decrease in cysteine and lysine residue accessibility, consistent with inhibitor-induced conformational changes. Comparison of two ATP-competitive BRAF inhibitors, vemurafenib and dabrafenib, revealed distinct labelling patterns at the DFG-motif aspartate, demonstrating the ability of ABPP to resolve functional residue accessibility within kinase active sites. In melanoma cell lines with acquired resistance to BRAF or MEK inhibition, ABPP identified altered residue specific probe reactivity consistent with mutation-driven conformational shifts. Mass spectrometry validation further revealed similar accessibility changes in MAPK pathway components, including KSR2, suggesting broader pathway-level remodelling. These findings support the utility of ABPP for probing conformational dynamics, ligandability, and resistance-associated structural adaptations in kinases and related signalling proteins.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Melanocyte

SUBMITTER: George M Burslem

LAB HEAD: George Burslem

PROVIDER: PXD063040 | Pride | 2026-05-13

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 27

Publications

MAPK Pathway Inhibition Reshapes Kinase Chemical Probe Reactivity Reflecting Cellular Activation States.

Jarvis Andrew F AF Bhat Mohd Younis MY Maujean Timothé T Abreu Ahlenne L AL Toy Kaitlyn K Burslem George M GM Brady Donita C DC

ACS bio & med chem Au 20260123 2

Despite the pivotal role of oncogenic kinases in cancer initiation, progression, and therapeutic resistance, functionally profiling their activity and conformational dynamics in live cells remains challenging. Existing methods often fail to capture inhibitor-bound structural states of kinases, particularly in clinically relevant contexts, such as treatment response and acquired resistance, where genomic data alone are insufficient. Here, we use activity-based protein profiling (ABPP) to monitor ...[more]

PMID: 42006249

Similar Datasets

Project description:This submission includes MS data for the paper titled "Suppression of pain transmission and behavior by inhibition of peripheral diacylglycerol metabolism", submitted to Cell Chemical Biology.Summary:Diacylglycerol lipase (DAGL) produce 2-arachidonoylglycerol (2-AG) and other proinflammatory lipids. Inactivation of DAGLs reduces the production of 2-AG, arachidonic acid (AA) and eicosanoids and elicits antinociceptive and anti-(neuro)inflammatory effects in rodents. However, inhibitors that enter the brain can cause significant central nervous system (CNS) side effects. Using activity-based protein profiling (ABPP), we report the discovery of A1480LS, a potent, in vivo active, small molecule dual inhibitor of DAGLα/β that is functionally biased to the periphery. We demonstrate that A1480LS reduces pain in animal models of both inflammatory and neuropathic pain. Moreover, A1480LS accomplishes this by reducing 2-AG and other lipids in peripheral tissues, all without causing adverse CNS effects of seizures. Overall, we show that inhibiting DAG metabolism in the periphery elicits antinociceptive effects that can be functionally dissected from adverse central effects and provide preclinical validation for a non-narcotic strategy to treat pain.Raw files for the selectivity experiment profiling of A1480LS in THP1 cells are listed below. Search and quantification results bearing the same file stem are also provided, as well as the fasta database that was used: uniprot_HumanComplete_121105_cdhit98_plus_Reverse_wContaminants150305.fasta.- RAH-NB1-208_A_03.rawRaw files for the in vivo time course experiment in rat kidneys are listed below. A Skyline export bearing the same name is also provided, as well as the fasta database that was used: uniprot_6organism_constructs_contaminants_20190213_forPRMJOB.fasta.- NN-NB2-213_A1.raw: 0h, Vehicle- NN-NB2-213_A2.raw: 0h, Vehicle- NN-NB2-213_A3.raw: 0h, Vehicle- NN-NB2-213_A4.raw: 0h, Vehicle- NN-NB2-213_B1.raw: 1h, A1480LS- NN-NB2-213_B2.raw: 1h, A1480LS- NN-NB2-213_B3.raw: 1h, A1480LS- NN-NB2-213_B4.raw: 1h, A1480LS- NN-NB2-213_B5.raw: 4h, A1480LS- NN-NB2-213_B6.raw: 4h, A1480LS- NN-NB2-213_B7.raw: 4h, A1480LS- NN-NB2-213_B8.raw: 4h, A1480LS- NN-NB2-213_B9.raw: 8h, A1480LS- NN-NB2-213_B10.raw: 8h, A1480LS- NN-NB2-213_B11.raw: 8h, A1480LS- NN-NB2-213_B12.raw: 12h, A1480LS- NN-NB2-213_C1.raw: 12h, A1480LS- NN-NB2-213_C2.raw: 12h, A1480LS- NN-NB2-213_C3.raw: 12h, A1480LS- NN-NB2-213_C4.raw: 24h, A1480LS- NN-NB2-213_C5.raw: 24h, A1480LS- NN-NB2-213_C6.raw: 24h, A1480LS- NN-NB2-213_C7.raw: 24h, A1480LS- NN-NB2-213_C8.raw: 32h, A1480LS- NN-NB2-213_C9.raw: 32h, A1480LS- NN-NB2-213_C10.raw: 32h, A1480LS- NN-NB2-213_C11.raw: 32h, A1480LS

			Action	DRS
	ArSq_Alkyne.msf	Msf
	ArSq_Alkyne.pdResult	Other
	ArSq_Alkyne_TMT_F1.raw	Raw
	ArSq_Alkyne_TMT_F2.raw	Raw
	ArSq_Alkyne_TMT_F3.raw	Raw