Molecular recognition, controlled experiments and discrete chemical space

A recent Curious Wavefunction post (The fundamental philosophical dilemma of chemistry) got me thinking a bit.  Ash notes,

“For me the greatest philosophical dilemma in chemistry is the following: It is the near impossibility of doing controlled experiments on the molecular level. Other fields also suffer from this problem, but I am constantly struck by how directly one encounters it in chemistry”.  

I have a subtly different take on this although I do think that Ash is most definitely pointing the searchlight in the right direction and his post was discussed recently by members of the LinkedIn Computational Chemistry Group.

Ash illustrates the problem from a perspective that will be extremely familiar to anybody with experience in pharmaceutical molecular design,

“Let’s say I am interested in knowing how important a particular hydrogen bond with an amide in the small molecule is. What I could do would be to replace the amide with a non hydrogen-bonding group and then look at the affinity, either computationally or experimentally. Unfortunately this change also impacts other properties of the molecules; its molecular weight, its hydrophobicity, its steric interactions with other molecules. Thus, changing a hydrogen bonding interaction also changes other interactions, so how can we then be sure that any change in the binding affinity came only from the loss of the hydrogen bond? The matter gets worse when we realize that we can’t even do this experimentally”

The “gets worse” acknowledges that the contribution of an interaction to affinity is not an experimental observable.  As we noted in a recent critique of ligand efficiency metrics,

“In general, the contribution of a particular intermolecular contact (or group of contacts) to affinity (or the changes in enthalpy, entropy, heat capacity or volume associated with binding) cannot be measured experimentally”

It’s easy to see why this should be the case for interaction of a drug with its target because this happens in an aqueous environment and the binding event is coupled to changes in solvent structure that are non-local with respect to the protein-ligand interactions.  As former colleagues at AZ observe in their critique of enthalpy optimization,

“Both ΔH° and ΔS° are typically sums over an enormous amount of degrees of freedom, many contributions are opposing each other and comparable in amplitude, and in the end sums up to a comparably smaller number, ΔG°”

Water certainly complicates interpretation of binding thermodynamics in terms of structure but, even in gas phase, the contributions of intermolecular contacts are still no more observable experimentally than atomic charges. 

Let’s think a bit about what would constitute a controlled experiment in the context of generating a more quantitative understanding of the importance of individual interactions.  Suppose that it’s possible to turn a hydrogen bond acceptor into (apolar) hydrocarbon without changing the remainder of the molecule. We could measure the difference in affinity/potency pK_d/pIC₅₀ between the compound of interest and its analog in which the hydrogen bond acceptor has been transformed into hydrocarbon. The Figure below shows how this can be done and the pIC₅₀ values (taken from this article) can be interpreted as evidence that hydrogen bonds to one of the pyridazine nitrogen are more beneficial for potency against cathepsins S and L2 than against cathepsin L.

Although analysis like this can provide useful insight for design, it still doesn’t tell us what absolute contributions these hydrogen bonds make to potency because our perception depends on our choice of reference. Things get more complicated if we are trying to assess the importance of the importance of the hydrogen bond donor and acceptor characteristics of a secondary amide in determining activity. We might replace the carbonyl oxygen atom with a methylene group to assess the importance of hydrogen bond acceptor ability.. er... maybe not.  The amide NH could be replaced with a methylene group but this will reduce the hydrogen bond acceptor strength of the carbonyl oxygen atom as well as changing the torsional preferences of the amidic bond.   This illustrates the difficulty, highlighted by Ash, of performing controlled experiments when trying to dissect the influences of different molecular properties on the behavior of compounds.

The above examples raise another issue that rarely, if ever, gets discussed.  Although chemical space is vast, it is still discrete at the molecular level and that may prove to be an even bigger dilemma than not being able perform controlled experiments at the molecular level.  As former colleagues and I suggested in our FBDD screening library article, fragment-based approaches may enable chemical space to be sampled at a more controllable resolution.  Could it be that fragments may have advantages in dealing with the discrete nature of chemical space?