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Structural Mass Spectrometry Probes the Inhibitor-Induced Allosteric Activation of CDK12/CDK13-Cyclin K Dissociation

The rational design and development of effective inhibitors for cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) are largely dependent on the understanding of the dynamic inhibition conformations but are difficult to be achieved by conventional characterization tools. Herein, we integrate the structural mass spectrometry (MS) methods of lysine reactivity profiling (LRP) and native MS (nMS) to systematically interrogate both the dynamic molecular interactions and overall protein assembly of CDK12/CDK13-cyclin K (CycK) complexes under the modulation of small molecule inhibitors. The essential structure insights, including inhibitor binding pocket, binding strength, interfacial molecular details, and dynamic conformation changes, can be derived from the complementary results of LRP and nMS. We find the inhibitor SR-4835 binding can greatly destabilize the CDK12/CDK13-CycK interactions in an unusual allosteric activation way, thereby providing a novel alternative for the kinase activity inhibition. Our results underscore the great potential of LRP combination with nMS for the evaluation and rational design of effective kinase inhibitors at the molecular level.

 

Comments:

The passage describes a study that employs structural mass spectrometry methods, specifically lysine reactivity profiling (LRP) and native MS (nMS), to investigate the dynamic molecular interactions and overall protein assembly of cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) in complex with cyclin K (CycK) under the influence of small molecule inhibitors. These methods provide valuable insights into the structural details, binding properties, and conformational changes induced by the inhibitors.

By integrating LRP and nMS, the researchers aim to achieve a better understanding of the dynamic inhibition conformations of CDK12/CDK13. Conventional characterization tools often fall short in capturing these dynamic interactions accurately. LRP allows the researchers to profile the reactivity of lysine residues, which can serve as probes to identify specific regions involved in inhibitor binding or conformational changes. On the other hand, nMS provides information about the overall protein assembly and complex stability.

The study highlights the findings regarding the inhibitor SR-4835, which was observed to bind to CDK12/CDK13-CycK complexes and destabilize their interactions. Interestingly, this destabilization leads to an allosteric activation, offering a unique alternative for inhibiting the kinase activity. This discovery emphasizes the potential of LRP in combination with nMS for evaluating and designing effective kinase inhibitors at the molecular level.

Overall, the study demonstrates the utility of integrating LRP and nMS to gain essential structural insights into kinase complexes and their interactions with small molecule inhibitors. This information can be crucial for the rational design and development of effective CDK12/CDK13 inhibitors.

Related Products

Cat.No. Product Name Information
S8894 SR-4835 SR-4835 is a highly selective dual inhibitor of CDK12 and CDK13 with IC50 of 99 nM and Kd of 98 nM for CDK12 and IC50 of 4.9 nM for CDK13. SR-4835 disables triple-negative breast cancer (TNBC) cells. SR-4835 promotes synergy with DNA-damaging chemotherapy and PARP inhibitors.

Related Targets

CDK