Structure-Guided Discovery of Selective Polo-Like Kinase 3 inhibitors
ACS Med. Chem. Lett. 2026
Kinases are key catalysts that facilitate the phosphorylation of substrate proteins involved in chemical signalling cascades for every manner of cellular function, from cell division and genome regulation to metabolism and cell death. Typically, a kinase will first extract phosphate from a molecule of ATP (Adenosine Triphosphate), the substrate protein then binds and is itself phosphorylated, continuing the signalling cascade.
While there is high substrate specificity for a given kinase, most will bind a molecule of ATP in the same way: inside a deep crevice between the terminal lobes of the catalytic domain. Drug hunters have long used this ATP-binding active site as a convenient pocket for discovering kinase inhibitors, to block certain signalling pathways and ultimately treat the disease reliant on the same.
The problem with exploiting this pocket to find kinase inhibitors, is that of inter-kinase selectivity, due to the high degree of sequence conservation between them in order to preserve essential ATP-binding. So, highly potent inhibitors that bind to the ATP-binding site (so-called: Type I or II inhibitors) frequently inhibit numerous kinases of a similar type, unless contacts further afield are made. This “shotgun blast” effect leads to a natural complication in the assessment of the mechanism of the biological effect of certain kinase inhibitors and can lead to undesired side effects for a given inhibitor driven by off-targets.
Thus, selective kinase inhibitors are entities that are highly sought after as both potential drugs and also chemical probes to study the effects of cellular signalling pathways. Kinome specificity screening is now routine in chemical biology projects and discovery programs.The authors of this study were seeking to transform a potent literature inhibitor of multiple members of the Polo-Like Kinase family (PLK, nothing to do with the mints unfortunately) into a PLK-3 selective inhibitor, which is over-expressed in ovarian and breast cancers.
From published crystal structures of PLK, they obtained predictions for 3D pharmacophores for PLK-1, PLK-2 and PLK-3 that have a high chance of complementarity to the protein surface. These were then compared back-to-back, leading to hypotheses for the selective inhibition of PLK-3. While this analysis was being carried out, they also conducted high-throughput screening of relevant analogues and parallel chemistry, leading to an injection of novel chemical matter with promising PLK selectivity profiles.
With these tools in hand, a nice chunk of PLK-1,2,3 inhibition data was generated and analysed. What made the search for selective inhibitors difficult, is that PLK-1, PLK-2 and PLK-3 inhibition activity were broadly correlated, a finding that was completely expected coming from the same kinase family. Nevertheless, they found compounds that lie significantly off the line of correlation, suggesting that some key selectivity-determining interactions were found.
Ultimately, they discovered a family of PLK-3 selective inhibitors with selectivity windows of ≥~100x over PLK-2 and/orPLK-1. This window narrowed to 5-50x when tested in a cellular NanoBRET assay, but still a significant improvement from the PLK-1 selective literature inhibitor. With these in hand, they were able tostart asking key questions about PLK-1 vs PLK-2 and PLK-3 inhibition with respect to bone marrow suppression of PLK-1 inhibitors currently undergoing clinical trials. More data is needed before conclusions are drawn, but we can only generate relevant data when we actually have the selective inhibitors as tool compounds in the first place.
To read the article click here
