We’ve previously discussed the proliferation of metrics used to evaluate fragments. Ligand efficiency is by far the most popular, and what it and most other measurements have in common is that they represent binding affinity (or inhibition, or some other surrogate). Binding affinity is associated with thermodynamics – how well a molecule binds to a target – but this measure says nothing about how rapidly a molecule associates and dissociates from the target (kinetics). In the November issue of Drug Discovery Today Geoffrey Holdgate and Adrian Gill at AstraZeneca propose a new metric, kinetic efficiency (KE), to address this issue:
KE = τ / (# of heavy atoms) = t1/2 / (0.693 * (# of heavy atoms))
where τ is the residence time or relaxation constant and is, in the simplest case, 1/koff
koff is the dissociation rate constant
and t1/2 is the half-life for dissociation
Why are the kinetics of dissociation important? Holdgate and Gill list a series of drugs for hypertension and note that compounds that remain bound to the receptor longer avoid rapid clearance and thus have superior clinical activity. On the other hand, drugs for schizophrenia that bind the D2 dopamine receptor can cause side effects if they remain bound too long. Thus, optimal kinetic efficiency is case-dependent .
Though kinetics of ligand binding can be assessed with techniques like SPR, this parameter is often ignored. However, as Holdgate and Gill point out, slow-binders are likely to be lead-sized or drug-sized molecules. Indeed, none of the roughly two-dozen examples they present would satisfy the rule of 3.
This raises an interesting question: how often do fragments dissociate slowly? Slowly-dissociating fragments are often flagged as pathological in SPR studies. Intuitively it seems that smaller molecules would have faster kinetics; a small fragment is likely to be able to dart in and out of a protein-binding site more rapidly than a larger molecule that requires some movement on the part of the protein to accommodate its binding. Still, there must be some cases of fragments with slow dissociation rate constants. If you know of any please mention them in the comments section.
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5 comments:
I have seen two very similar Kd fragments have very different off-rates (from NMR experiments). I think there are probably a jillion instances of this out there, but who ever looks for kinetic effects? I don't think we need a metric for comparing rate constants to the heavy atom count. It might end up being the least used metric ever.
Something to remember about binding kinetics is that slow binding is that, for a given Kd, a slower off-rate means a slower on-rate. In a pharmacokinetic context (concentration is a function of time and location) this means drug has not engaged target to the full (i.e. what you would expect on the basis of concentration and Kd) extent before the concentration starts to fall. Generally, the binding kinetics need to be slower than the distribution kinetics in order to be relevant.
The other issue with using off-rates is that they will get slower as Kd gets smaller and they contain both thermodynamic and kinetic information. I think of fast kinetics as diffusion-controlled association with an off-rate determined by Kd. Expressing the on-rate as a fraction of the diffusion-controlled rate would give a cleaner measure of the slowness of binding kinetics.
I was curious about why Geoff and Adrian didn’t use a logarithmic transformation of off-rate in the efficiency definition. To the best of my knowledge, all the efficiency metrics based on binding either take the negative log of IC50 or Kd or transform these quantities to free energies.
Similarly to Pete, I was also wondering why they haven't used logarithmic transformation - all in all, a great post!
Yes, there are some cases of fragments with slow dissociation rate constants. I can't write down everything here, all I can give you now is a good source about such information. I hope his helps. http://dissociationconstant.com/
I just found this post from 10 years ago, looking for what to do with my slow binding fragments. Not sure if anyone ever going to read this, but who knows!
I work on a Malaria drug target, and during my screening I found some fragments with slow kon and koff. One of them is especially slow, with a koff in the 10^-6 range!
In our case, a longer residence time would definitely be an advantage, so I was thinking to trying to maintain this slow kinetics along the drug design process, just like one would keep an eye on the LE or the logP.
But I am new to the field, and I am not sure if this can actually be done!
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