Inhibitor Selectivity for Cyclin-Dependent Kinase 7: A Structural, Thermodynamic, and Modelling Study
Pascale Hazel1, Sebastian H B Kroll2, Alexander Bondke2
1Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
Abstract:
Deregulation of the cell cycle by mechanisms that lead to elevated activities of cyclin-dependent kinases (CDK) is a feature of many human diseases, cancer in particular. We identified small-molecule inhibitors that selectively inhibit CDK7, the kinase that phosphorylates cell-cycle CDKs to promote their activities. To investigate the selectivity of these inhibitors we used a combination of structural, biophysical, and modelling approaches. We determined the crystal structures of the CDK7-selective compounds ICEC0942 and ICEC0943 bound to CDK2, and used these to build models of inhibitor binding to CDK7. Molecular dynamics (MD) simulations of inhibitors bound to CDK2 and CDK7 generated possible models of inhibitor binding. To experimentally validate these models, we gathered isothermal titration calorimetry (ITC) binding data for recombinant wild-type and binding site mutants of CDK7 and CDK2. We identified specific residues of CDK7, notably Asp155, that are involved in determining inhibitor selectivity. Our MD simulations also show that the flexibility of the G-rich and activation loops of CDK7 is likely an important determinant of inhibitor specificity similar to CDK2.
Insights
Researchers identified small molecules that selectively inhibit CDK7, a key regulator in cell cycle control crucial for cancer. This discovery offers potential new therapeutic strategies for cancer by targeting cell cycle deregulation.
Area of Science:
- Biochemistry
- Molecular Biology
- Drug Discovery
Background:
- Cell cycle deregulation, particularly elevated cyclin-dependent kinase (CDK) activity, is a hallmark of human diseases, especially cancer.
- CDK7 plays a critical role by phosphorylating cell-cycle CDKs, thereby promoting their activity.
Purpose of the Study:
- To identify and characterize small-molecule inhibitors that selectively target CDK7.
- To elucidate the molecular mechanisms underlying the selectivity of these inhibitors for CDK7 over other CDKs.
Main Methods:
- X-ray crystallography to determine the structures of inhibitors bound to CDK2.
- Molecular dynamics (MD) simulations to model inhibitor binding to CDK2 and CDK7.
- Isothermal titration calorimetry (ITC) to experimentally validate binding interactions with wild-type and mutant CDK7 and CDK2.
Main Results:
- Crystal structures revealed inhibitor binding modes to CDK2, facilitating modeling of CDK7 interactions.
- MD simulations provided insights into inhibitor binding and the role of protein flexibility.
- ITC data identified specific residues, such as Asp155 in CDK7, critical for inhibitor selectivity.
- Flexibility in CDK7's G-rich and activation loops was identified as a key factor in inhibitor specificity, mirroring observations in CDK2.
Conclusions:
- Small-molecule inhibitors targeting CDK7 have been identified with potential for selective inhibition.
- Structural, biophysical, and computational methods elucidated key molecular determinants of CDK7 inhibitor selectivity.
- Understanding these interactions, including the role of specific residues and loop flexibility, is crucial for developing targeted cancer therapies.
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