Helpful halogens in fragment libraries

A couple weeks ago we highlighted a small fragment collection (MiniFrags) designed for crystallographic screening. We continue the theme this week with two more papers on the topic, with an emphasis on halogens.

The first, published in J. Med. Chem. by Martin Noble, Michael Waring, and collaborators at Newcastle University, describes a library of “FragLites.” These small (< 14 non-hydrogen atom) fragments are designed to explore “pharmacophore doublets,” such as a hydrogen bond acceptor (HBA) next to a hydrogen bond donor (HBD). For example, the universal fragment 5-bromopyrazole contains an HBA separated by one bond from an HBD. The researchers constructed a set of compounds with either two HBAs or an HBA and an HBD separated by 1 to 5 bonds. Importantly, all compounds also contained either a bromine or iodine atom, the idea being that anomalous dispersion could be used to help identify the fragments using crystallography. A total of 31 FragLites are described, with between 1 to 9 examples for each type of connectivity.

As a test case, these were screened against the kinase CDK2, which has previously been screened crystallographically. FragLites were soaked into crystals at 50 mM, and 9 of the FragLites were found to bind in a total of 6 sites, 4 of which had not been previously observed. The anomalous signal provided by the halogens was important: when the researchers used only normal scattering they identified just 10 of the 16 binding events even when using the powerful PanDDA background correction method. The anomalous signal also helped clarify the binding modes.

The ATP-binding site is where 7 of the 9 FragLites bound, with all but one of them making hydrogen bonding interactions to the hinge region. While not surprising, this does demonstrate that the FragLites can be used experimentally to identify the best binding site. Interestingly, (2-methoxy-4-bromophenyl)acetic acid bound in the active site as well as three other secondary sites; one of these sites hosted three copies of the ligand! It will be interesting to see whether this fragment is generally promiscuous in other proteins too.

As the researchers note, the composition of the FragLite library can be optimized. For example, both of the HBA-HBD fragments with 1-bond separation were identified as hits, while only 3 of the 9 HBA-HBD fragments with 2-bond separation were. Is this due to the choice of fragments, the target tested, or both? The approach is conceptually similar to the Astex minimal pharmacophore concept, so it will be useful to include other types of pharmacophores too (a single HBA or HBD, for example).

A related paper was published in Front. Chem. by Frank Boeckler and colleagues at Eberhard Karls Universität Tübingen. Long-time readers will recall his earlier halogen-containing library designed for identifying halogen bonds: favorable interactions between halogens and Lewis bases such as carbonyl oxygen atoms. Perhaps because they have relatively stringent geometric requirements (2.75 – 3.5 Å, and a bond angle of 155-180°), halogen bonds are often ignored; the FragLite paper doesn’t even mention them.

The new Boeckler paper describes the construction of a library of 198 halogen-containing fragments, all of which are commercially available and relatively inexpensive. Most of these are rule-of-three compliant, though quite a few also contain more than three hydrogen bond acceptors. Also, given that each fragment contains a halogen, the molecular weights are skewed upward. Solubility was experimentally determined for about half of the fragments, but the highest concentration tested was only 5 mM, and even here several were not fully soluble.

Although no screening data are provided, the researchers note that their “library is available for other working groups.” In the spirit of international cooperation, I suggest a collaboration with the FragLite group!