Features of selective kinase inhibitors

It was quite recently that I came across this fantastic review of kinase inhibitors from 2005 by Kevan Shokat. The reason why I missed it is because it was published in a journal that is usually not in people's top ten list- Chemistry and Biology. So I am putting it into mine from now onwards.

In any case, I think this review should be read by anyone who is concerned with either the experimental or computational design and testing of selective kinase inhibitors. Even now, the holy grail of kinase inhibitor development is selectivity, and Shokat gives a succint account of what we know about designing such molecules until now. I thought there were a few points especially crucial to keep in mind.

1. IC50 is not equal to Ki...usually:
This is a central if simple fact that should always guide computational as well as experimental scientists in their evaluation. The IC50 and Ki values are generally related by the so-called Cheng Prusoff equation:


Here, Km and [S] are the Km and substrate concentrations for the natural substrate of the protein, ATP in this case, which is usually competitively displaced by inhibitors.
What does this mean on a practical basis? Let me take my own example in which this principle helped a lot. We are trying to design a selective kinase inhibitor, and found out that a compound which we had, showed some selectivity for one kinase versus the other. To investigate the source of this selectivity, we started looking at the interactions of the inhibitor with the two kinase pockets; presumably, better the interaction, more it would contribute to the smaller IC50. Or would it? No! Better the interactions, the more it would contribute to the smaller Ki. The point is, only the Ki has to do with how effectively the inhibitor interacts with the active site. But the IC50 is an experimental number which as the above equation indicates, also has to do with how well the natural substrate, in this case ATP, binds to the protein. So if the Km of the protein for ATP is really small, that means ATP binds very well, and even a compound with a low Ki will have a relatively large IC50 and will be a poor inhibitor. So just looking at the active site interactions does not help to rationalize anything about the IC50; what must be known is how well the competitor ATP binds to the site. The bottom line is, in kinase assays, one can only compare Ki's and IC50's if the ratio [S]/Km is kept constant. Otherwise it's not a controlled experiment.

2. There is a minimum threshold of potency below which an inhibitor cannot be selective, irrespective of the in vitro data:
Another important point. If the inhibitor is extremely lousy in the first place, then the dosage needed to achieve selectivity is going to be much higher. On a practical basis, as Shokat says, "more potent compounds are more selective because they can be used at a lower dose". What I take this to mean is that if your compound is extremely potent, then you can essentially use it at such a low concentration, that it binds to only one protein, and is denied to the others. What could be the 'threshold' for a kinase inhibitor? Well, it depends also on what kind of a clinical target you are targeting, but I would think that anything above maybe a micromolar Ki would be enough to raise serious doubts about selectivity.

3. Common features of kinase inhibitors:
This could be educated observation and guesswork at best, but Shokat says many inhibitors show dramatic SAR relationships. The hydrogen bonds between the adenine ring nitrogens and a crucial backbone residue are duplicated by many inhibitors for example. I can vouch for the ubiquity of this particular interaction, as it has shown up even in docking poses. This is what can be called a 'correlated' pair of hydrogen bonds, one which is strong and conserved. The other point about kinase inhibitors being usually relatively rigid and entropically constrained is also interesting. One thing is for sure; kinase inhibitors seem to promise yet another bounty for heterocyclic chemists (We who criticize 'flatland' should quietly slink away now...)

And of course, this is only for ATP competitive inhibitors. Allosteric inhibition will be quite another unexplored terrain. Overall, a highly informative and practically useful review. It helped me ask our biologists questions which they wouldn't have expected from a modeler. The search for selective inhibitors is surely one of the most vigorously explored areas of med chem. The dozens of publications literally every week on Src, PKC, p38 Map, CDK, and Bcr kinases represent only a fraction of the research that is being currently done in pharma as well as academia.