Biological and Medicinal Chemistry

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

Authors

  • Erik B. Faber University of Minnesota College of Pharmacy & University of Minnesota Medical School ,
  • Nan Wang University of Minnesota College of Pharmacy ,
  • Kristen John University of Minnesota College of Pharmacy ,
  • Luxin Sun Moffitt Cancer Center ,
  • David Burban University of Minnesota Medical School ,
  • Henry L. Wong University of Minnesota College of Pharmacy ,
  • Rawle Francis University of Minnesota College of Pharmacy ,
  • Defeng Tian University of Minnesota College of Pharmacy ,
  • Kwon H. Hong University of Minnesota College of Pharmacy ,
  • An Yang University of Minnesota College of Pharmacy ,
  • Liming Wang University of Minnesota College of Pharmacy ,
  • Mazen Elsaid University of Minnesota College of Pharmacy ,
  • Hira Khalid University of Minnesota College of Pharmacy & Department of Chemistry at Forman Christian Collegey ,
  • Nicholas Levinson University of Minnesota Medical School ,
  • Ernst Schönbrunn Moffitt Cancer Center ,
  • Jon E. Hawkinson University of Minnesota College of Pharmacy ,
  • Gunda Georg University of Minnesota College of Pharmacy

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.

Version notes

We added authors and affiliations to the supplementary materials.

Content

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Supplementary material

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Supplementary materials
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.