The discovery of high affinity and metabolically stable allosteric cyclin-dependent kinase 2 (CDK2) inhibitors from screening through lead optimization

18 August 2022, Version 2

Abstract

Despite the status of cyclin-dependent kinase 2 (CDK2) as a validated target for both anticancer and contraceptive indications, a CDK2 inhibitor with exquisite selectivity has been historically challenging, largely due to the structural similarity of the ATP-binding site where most kinase inhibitors bind. We previously discovered an allosteric pocket in CDK2 with potential to bind a compound with desirable selectivity. Using high-throughput and virtual screening methods, we discovered and structurally confirmed an anthranilic acid scaffold that binds this pocket with high affinity. We previously reported that these allosteric CDK2 inhibitors demonstrate a negative cooperative relationship with cyclin binding, are selective for CDK2 over the structurally similar kinase CDK1 and show potential as a non-hormonal contraceptive agent. In this work, we describe our screening and lead optimization efforts that led to the discovery of compounds in this series like EF-4-177 with nanomolar affinity for CDK2. EF-4-177 is metabolically stable with a desirably long ½ life and adequate tissue distribution in mice, demonstrating the potential of this series as a therapeutic. This work details the discovery of the highest affinity allosteric CDK inhibitors reported and shows promise for further development of this series to yield an efficacious and selective allosteric CDK2 inhibitor.

Keywords

cyclin-depended kinase 2
medicinal chemistry
structure-activity relationship
X-ray crystallography
HTS
vHTS

Supplementary materials

Title
Description
Actions
Title
Supplementary materials
Description
Effect of ATP site occupancy on the potency of repurchased HTS hits for inhibition of p-Cl-ANS binding from CDK2; Effect of ATP site occupancy on the potency of the ATP site inhibitor SU9516, the HTS hit NPPB, and the vHTS hit salirasib for inhibition of p-Cl-ANS binding to CDK2; HSQC NMR data for HTS and vHTS compounds; Crystal structures of CDK2 with compounds 12 and 20 ITC of compound 23 and EF-4-177 into CDK2; Displacement of p-Cl-ANS binding by hit compounds in the absence and presence of staurosporine compared to the reference ATP site inhibitor SU9516; Crystallization and in-diffusion conditions, crystallization data and refinement statistics; Molecular formula SMILES strings, NMR Spectra of compounds and absolute qNMR data.
Actions

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.