Conservation of fragment binding modes revisited

A common assumption when growing or linking fragments is that the binding mode will remain the same. This is often the case, but exceptions occur frequently enough to keep life interesting. Last year we highlighted a study that tried to answer the question of when ligands changed their binding mode by analyzing the protein data bank (PDB). In a new J. Med. Chem. paper, Esther Kellenberger and collaborators at Université de Strasbourg and Eli Lilly have conducted an even more exhaustive study.

The researchers considered all protein structures deposited in the PDB between 2000 and mid-2016 solved to at least 3 Å resolution. This yielded 1079 different fragments (MW < 300 Da) and 1832 larger (“drug-like”) ligands, as well as 126 crystallization additives such as buffers and detergents. In comparing the same protein with different ligands, care was taken to remove mutant proteins that could cause a change in binding mode.

This dataset was used to address several questions.

First, how often does the same fragment bind to the same pocket in the same manner? Often a crystal structure will have several different copies of the same protein in the asymmetric unit. In nearly three-quarters of cases, the fragments bound in a similar manner to the different copies. The exceptions often involved protein conformational changes, in some cases due to different crystal contacts.

Second, how often does a fragment maintain its binding mode when incorporated into a larger molecule? The data set included 359 pairs of ligands on 51 proteins. Again, about three-quarters of fragments had similar binding modes as their larger counterparts. When binding modes changed, protein flexibility often played a role. Polar contacts such as hydrogen bonds were much more highly conserved than hydrophobic contacts. As the earlier study also found, binding modes of very small fragments (MW < 110) were most likely to change, while fragments with MW > 150 almost always retained their binding modes.

Third, do fragments and larger ligands make similar interactions? The data included 235 proteins in which at least one structure contained a fragment and another structure contained a larger ligand.  (The larger ligand didn’t necessarily contain the fragment.) Obviously larger ligands are able to make more interactions than smaller ligands, but, as Stephen Roughley and Rod Hubbard observed back in 2011, enough fragments should allow you to map out the important interactions. After systematically exploring the data, the current researchers suggest that fully mapping a pocket requires nine or more different fragments, a high bar satisfied by just 11 proteins.

Finally, do crystallization additives behave as fragments? The researchers looked at all additives with MW < 300, and separately considered those bound to otherwise free (apo) proteins and those bound to proteins containing other ligands. In general additives showed more variation in their binding modes, though those binding to apo proteins often made similar contacts as made by fragments and larger molecules. Intriguingly, small polar molecules such as DMSO and glycerol often made hydrophobic interactions with proteins.

There is plenty more in the paper than can be summarized here. Laudably, the researchers have provided all of their data in a convenient web portal that even supports chemical substructure searches. Overall the results reassuringly suggest that the binding mode of a fragment usually remains the same as it is optimized. But of course these types of analyses are subject to survivor bias: fragments that change binding mode unexpectedly may be more difficult to optimize, and thus less likely to lead to larger ligands.

The odds may be ever in your favor, but look out for the exceptions.