Anti-bacterial targets are not
common among fragment-based lead discovery efforts. We’ve written previously
about AstraZeneca’s work on DNA gyrase, which led to a clinical candidate. In a
recent paper in Bioorg. Med. Chem. Lett.,
Michael Mesleh and collaborators at Cubist and Evotec describe their efforts on
this protein.
Bacterial DNA gyrase has two
subunits, GyrA and GyrB, and is essential during DNA replication. It is also
well-validated, being the target of decades-old antibiotics such as the
fluoroquinolones. The researchers started by screening a library of 5643
fragments against Staphylococcus aureus
GyrB using STD NMR, yielding 304 hits. These were winnowed down to 46 based on
intensity of the STD signal, novelty, and ease of follow-up chemistry. These
were then tested using chemical shift perturbations and crystallography.
Although several crystal structures of fragments bound to GyrB were obtained, these
did not suggest clear ways to advance the hits.
On the other hand, compound 5, which
showed only weak binding by NMR and did not result in a crystal structure, was
appealing because of its novelty and polarity. The researchers knew that most
ligands that interact with GyrB make a pair of hydrogen-bond donor-acceptor
interactions, and they used that knowledge to surmise a binding model. This
suggested that growing the fragment towards a pair of arginine residues could
improve affinity and led to the synthesis of compound 8, with low micromolar
activity.
A crystal structure of a related
molecule confirmed the model and also suggested that removing the methyl group
would stabilize a more planar conformation better matched to the binding site.
Doing so (compound 9) yielded a ten-fold boost in potency. (This methyl is also
a nice example of Teddy’s “Sauron Atom”). In a separate paper published last
year, the researchers further optimized this molecule to compound 2, with low
nanomolar potency and activity in animal models.
Several things stand out about this paper. First, the researchers were willing to pursue a fragment with an affinity lower than other hits. Second, careful modeling and conformational analyses were critical in advancing the molecules. Finally, crystallography was not used in the initial fragment growing. Of course, it helped that the researchers were working with a well-characterized protein amenable to modeling. Still, it is nice to see another example of advancing fragments in the absence of experimentally-determined structures.
nice
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