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!
4 comments:
Thanks for highlighting our paper Dan. We are working to make the FragLite library available in plate format to allow others to try this out. It should be available shortly through XimBio.
Regarding halogen bonding, this is indeed important in some cases. Ideally, we wished the halogen to be as innocent as possible in the overall contribution to binding as we were chiefly interested in identifying productive H-bonds. This is how it turns out in CDK2 mostly. It is of course possible that in other cases halogen bonds could be observed and this might be important information.
Just a quick note... The FragLite library is now available through Ximbio.
DMSO, 500 mM:
https://ximbio.com/reagent/154152/fraglites-screen-dmso
Ethylene glycol, 100 mM:
https://ximbio.com/reagent/155084/fraglites-screen-eg
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