Mini-perspective on activity cliffs as a medicinal chemistry tool

Recently in group meeting we discussed activity cliffs and their application to medicinal chemistry. The talk was based largely on the excellent mini-perspective on the subject written by Stumpfe et al.

What is an activity cliff?

Activity cliffs are two compounds that represent a small structural change but a large activity change. They are used commonly in the design of new compounds targeting a particular protein (drugs). They work on the principal that if a given structural change has previously had a large affect on activity it is likely to have a similar affect on a different compound series. In this way they can be used as predictive tools to suggest chemical transformations that are likely to improve activity for a given compound.

To define an activity cliff, one must consider what a small structural change and a large activity change mean.

Small structural change

Structural changes can be measured using a seemingly endless array of methods. A lot of methods will condense the chemical information of the molecule into a bit-vector. Each bit indicates the molecule contains a particular type of chemical functionality, e.g. a methyl group. Molecular similarity is then assessed by comparing the bit-vectors, most commonly by finding the Tanimoto similarity between the them. This then returns a single value between 0 and 1 indicating how similar the two molecules are (the greater the more similar). To define small structural change, one must decide upon a threshold value above which two molecules are sufficiently similar.
An alternative method is to find matched molecular pairs – compounds which are identical apart from one structural change. An example of one is shown below. For matched molecular pairs the only parameter required is the size of the non-matching part of the pair. This is usually measured in non-hydrogen atoms. The threshold to use for this parameter is chosen equally arbitrarily however it has a much more intuitive effect.

An example of a matched molecular pair

Which method to use?

Similarity methods are less rigid and are capable of finding molecules that are very similar, however that differ in two or more subtle ways. They however are also liable to find molecules similar when they would not be perceived as so. In this work Stumpfe et al. show that different similarity methods do not agree greatly on which molecules are “similar”. They compare six different fingerprint methods used to find similar molecules. Each method finds around 30% similar molecules in the datasets used, however the consensus between the methods is only 15%. This indicates that there is no clear definition of “similar” using bit-string similarity. Interestingly a third of the molecules found to be similar by all six fingerprint methods are not considered matched molecular pairs. This demonstrates a downside of the matched molecular pair approach, that it is liable to miss highly similar molecules that differ in a couple of small ways.

Matched molecular pairs are, however, least liable to find false-positives, i.e. compounds that are seen as similar but in fact are not actually similar. The transformations they represent are easily understood and this can be easily applied to novel compounds. For these reasons matched molecular pairs were chosen by Stumpfe et al. for this work to indicate small structural changes.

Large activity change

A large activity change is an equally arbitrary decision to make. The exact value that indicates an activity cliff will depend on the assay used and the protein being tested against. Stumpfe et al. reasonably suggest that approximate measures should not be used and that activity scores found between different assays should not be compared.

Rationales for activity cliffs

If structural data is available for an activity cliff, rationales for their corresponding activity change can be suggested. These can then be used to suggest other alterations that might have a similar impact. Stumpfe et al. consider the five most common rationales for activity cliffs.

• H-bond and or ionic interactions: these interactions will increase the binding energy forming specific interactions with the protein
• Lipophilic and aromatic groups: these groups can form specific protein-ligand interactions, e.g. pi-pi stacking and also form favourable interactions with hydrophobic residues in the protein
• Water molecules: One molecule in the pair displaces water molecules from the active site, altering the binding energy
• Stereochemistry changes: for example altering an enantiomeric form of a compound alters the projection of a group, forming or losing favourable/disfavourable protein-ligand interactions
• Multiple effects: a combination of the above, and thus difficult to establish the dominant feature.

Are they generally useful?

Stumpfe et al. consider whether activity cliffs are more useful for some proteins or protein classes than others. They investigate how many compounds form activity cliffs for many protein targets for which activity data is openly available. For proteins with more than 200 compounds with activity data the number of activity cliff forming compounds is roughly equivalent (around 10%). This is an interesting and unexpected result. The proteins used in this study have different binding sites attracting different opportunities for protein-ligand interactions. It would not, therefore naturally be expected that these would attract similar opportunities for generating activity cliffs. This result shows that the activity cliff concept is generically useful, irrespective of the protein being targeted.

Are they predictive?

Although activity cliffs make intuitive sense, Stumpfe et al. consider whether it has been quantitatively successful in previous drug discovery efforts. They investigate all of the times that activity cliff information was available from openly available data. They then find all the times this information was used in a different compound series and if it was used whether it had a positive or negative effect on activity.

Interestingly available activity cliff information had not been used in 75% of cases. They suggest that this indicates this information is an as yet underused resource. Secondly, in the cases where it was used, 60% of the time it was successful in improving activity and 40% of the time is was unsuccessful. They suggest this indicates the activity cliff method is useful for suggesting novel additions to compounds. Indeed it is true that a method that gives a 60% success rate in predicting more potent compounds would be considered useful by most if not all medicinal chemists. It would be interesting to investigate if there were patterns in protein environment or the nature of the structural changes in the cases where the activity cliff method is not successful.

Have they been successful?

Finally Stumpfe et al. investigate whether using activity cliff information gives a higher probability of synthesising a compound in the 10% most active against the target protein. They show that in 54% of cases using activity cliff information a compound in the 10% most active is formed. Conversely when this information is not used only 28% of pathways produce a compound in the 10% most active. They argue this indicates that using activity cliff information improves the chances of producing active compounds.

Conclusion

The paper discussed here offers an excellent overview of the activity cliff concept and its application. They demonstrate, in this work and others, that activity cliffs are generally useful, predictive and currently underused. The method can therefore be used in new tools to improve the efficiency of drug discovery.