Automated scaffold hopping for fragments

A post last month covered high-throughput virtual screening, but most practitioners of FBLD still start with some sort of (bio)physical screen. These initial hits can’t be expected to be optimal, since the average fragment library contains a few thousand compounds at most. Indeed, as Xavier Barril and collaborators at Universitat de Barcelona and Oxford University write, “fragment hits should be seen as beacons indicating privileged areas of chemical space to be further explored.” They describe one way to expedite exploration in a recent J. Med. Chem. paper.

 

As we noted here, most good fragments make at least one essential interaction (such as a hydrogen bond) to the protein. The approach starts with a structure of a fragment bound to the target of interest, with that essential interaction identified.

 

Next, a virtual library is searched for similar molecules, with the definition of “similar” being rather loose (>50% Tanimoto similarity). Ideally the library is large enough to produce lots of hits; the researchers used ZINC15, which contains >15 million ostensibly commercial compounds. Also, only molecules within two non-hydrogen atoms of the starting fragment are considered. In other words, a fragment with ten “heavy” atoms would yield molecules with 8-12 non-hydrogen atoms. This search is similar though perhaps more permissive than Astex’s Fragment Network (which we wrote about here).

 

All the molecules are then superposed on the initial fragment structure and only those that maintain the key interaction and binding mode are kept. Aboout 500 molecules are then selected to represent the best and most-diverse hits. These are subjected to dynamic undocking (DUck), which weeds out fragments that have weaker interactions. If desired, each of the remaining hits can be subjected to further cycles.

 

To demonstrate the approach, the researchers turned to bromodomains, a popular target class for FBLD. They started with 1XA, a fragment Teddy highlighted back in 2013 that led to a clinical compound against BRD4. The isoxazole moiety makes a hydrogen bond with the side chain nitrogen of an asparagine that normally binds to acetylated lysine residues. After one cycle, 58 molecules were selected, but unfortunately only five were actually available commercially. Compound 3 had similar affinity and ligand efficiency as 1XA, and this scaffold had not been reported as a bromodomain ligand. A crystal structure of compound 3 bound to the first bromodomain of BRD4 confirmed the predicted binding mode.

Three additional successive iterations were conducted to look for more ligands, but experimental confirmation was challenging as overall only 17 of more than 100 ligands selected for purchase were commercially available. (Compound 23 was chosen for custom synthesis as it was related to a family of high-scoring molecules.) Encouragingly, eight molecules were active in a differential scanning fluorimetry (DSF) assay, a technique that works well for BRD4. Crystal structures of two of these were obtained: compound 9 contains an isoxazole moiety like 1XA (and indeed resembles this fragment) but compound 23 is quite distinct.

Overall this looks like a valuable method for scaffold hopping. Not only might the described approach lead to novel molecules, it could provide new growth vectors that may not be accessible from the original fragment. Before jumping immediately into chemistry with your fragment hits, it may be worth trying something like this.