Development of allosteric, selective cyclin-dependent kinase 2 (CDK2) inhibitors that are negatively cooperative with cyclin binding and show potential as contraceptive agents

Faber, E. B.; Tang, J.; Roberts, E.; Ganeshkumar, S.; Sun, L.; Wang, N.; Rasmussen, D.; Majumbar, A.; John, K.; Yang, A.; Khalid, H.; Hawkinson, J. E.; Levinson, N. M.; Schonbrunn, E.; Chennathukuzhi, V.; Harki, D. A.; Georg, G. I.

doi:10.1101/2022.06.30.497818

bioRxiv · 10.1101/2022.06.30.497818

Development of allosteric, selective cyclin-dependent kinase 2 (CDK2) inhibitors that are negatively cooperative with cyclin binding and show potential as contraceptive agents

Faber, E. B.·Tang, J.·Roberts, E.·Ganeshkumar, S.·Sun, L.·Wang, N.·Rasmussen, D.·Majumbar, A.·John, K.·Yang, A.·Khalid, H.·Hawkinson, J. E.·Levinson, N. M.·Schonbrunn, E.·Chennathukuzhi, V.·Harki, D. A.·Georg, G. I.

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Abstract

Compared to most ATP-site kinase inhibitors, small molecules that target an allosteric pocket have the potential for improved selectivity due to the often observed lower structural similarity at these distal sites. Despite their promise, relatively few examples of structurally confirmed, high-affinity allosteric kinase inhibitors exist. Cyclin-dependent kinase 2 (CDK2) is a target for many therapeutic indications, including non-hormonal contraception.1 However, an inhibitor against this kinase with exquisite selectivity has not reached the market because of the structural similarity between CDKs.1-2 In this paper, we describe the development and mechanism of action of new type III inhibitors that bind CDK2 with nanomolar affinity, making them the highest affinity, structurally confirmed allosteric CDK inhibitors reported. Notably, these anthranilic acid inhibitors exhibit a strong negative cooperative relationship with cyclin binding, which remains an underexplored mechanism for CDK2 inhibition. Furthermore, the binding profile of these compounds in both biophysical and cellular assays demonstrate the promise of this series for further development into a therapeutic selective for CDK2 over highly similar kinases like CDK1. The potential of these inhibitors as efficacious contraceptive agents is seen by incubation with mouse testicular explants, where they recapitulate Cdk2-/- and Spdya-/- phenotypes.

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Faber, E. B., Tang, J., Roberts, E., Ganeshkumar, S., Sun, L., Wang, N., Rasmussen, D., Majumbar, A., John, K., Yang, A., Khalid, H., Hawkinson, J. E., Levinson, N. M., Schonbrunn, E., Chennathukuzhi, V., Harki, D. A., Georg, G. I.. 2022-07-02. Development of allosteric, selective cyclin-dependent kinase 2 (CDK2) inhibitors that are negatively cooperative with cyclin binding and show potential as contraceptive agents. https://doi.org/10.1101/2022.06.30.497818

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