17 November 2018

From noncovalent to covalent fragment for BTK

The approved anti-cancer drug ibrutinib is a poster child for covalent modifiers, with projected 2018 sales of more than $1.2 billion. The molecule reacts with a cysteine residue in the kinase BTK as well as several other kinases, forming an irreversible bond. However, it is also a potent noncovalent inhibitor of multiple kinases, leading to various side effects. This is because the so-called “hinge-binding” moiety is quite promiscuous. To find a more selective and potentially safer molecule, researchers at EMD Serono, Constellation Pharmaceuticals, and Hoffmann-La Roche turned to fragments, and describe their results in two recent Bioorg. Med. Chem. Lett. papers.

In the first, Richard Caldwell and collaborators disclose Fragment A. Although no details are provided as to how this was discovered, the researchers were able to determine a crystal structure of the fragment bound to BTK, revealing that the carboxamide forms interactions with the hinge region. The binding mode also suggested how an acrylamide warhead could be positioned to react with the nearby cysteine residue, and indeed compound A7 turned out to be a nanomolar inhibitor. Further fragment growing ultimately led to compound A17, with subnanomolar biochemical activity and nanomolar cell activity. Unfortunately, this compound had poor oral bioavailability in mice.

The second paper, by Hui Qiu and collaborators, picks up the story. Hypothesizing that the number of nitrogen atoms in compound A17 could be deleterious, the researchers swapped the added portion of the molecule with the phenoxyphenyl moiety present in ibrutinib. Compound B7 did indeed show good permeability, albeit at a cost in potency. However, a crystal structure of this molecule bound to BTK revealed the potential for improving hydrophobic interactions.

The best molecule reported, B16, has picomolar activity in a biochemical assay and nanomolar activity in cells. Moreover, it is orally bioavailable in rats. While ibrutinib inhibits 35/270 kinases at 1 ┬ÁM, compound B16 only inhibits 4. However, the compound does inhibit hERG, which can cause cardiac complications, so more work needs to be done. A crystal structure reveals that B16 (gray) binds in a similar manner to the initial Fragment A (cyan).

We have previously described examples of covalent fragments being used to target kinases, but these new papers are a useful reminder that it is also possible to start with ordinary non-covalent fragments and introduce a warhead later. Or not – as we highlighted in 2015 regarding a noncovalent BTK inhibitor from Takeda. The possibilities are limited only by your creativity.


Joe Patel said...

Hi Dan, Slight typo, the gray structure is B7 not B16...

"A crystal structure reveals that B16 (gray) binds in a similar manner to the initial Fragment A (cyan)."

Dan Erlanson said...

Hi Joe,
Thanks for the comment. The gray structure is actually compound 16 in the paper (pdb 6DI5), though as depicted it does indeed look deceptively like compound 7 - sorry about that!